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1

Bacterial control of host gene expression through RNA polymerase II  

PubMed Central

The normal flora furnishes the host with ecological barriers that prevent pathogen attack while maintaining tissue homeostasis. Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation in which some patients infected with Escherichia coli develop acute pyelonephritis, while other patients with bacteriuria exhibit an asymptomatic carrier state similar to bacterial commensalism. It remains unclear if the lack of destructive inflammation merely reflects low virulence or if carrier strains actively inhibit disease-associated responses in the host. Here, we identify a new mechanism of bacterial adaptation through broad suppression of RNA polymerase II–dependent (Pol II–dependent) host gene expression. Over 60% of all genes were suppressed 24 hours after human inoculation with the prototype asymptomatic bacteriuria (ABU) strain E. coli 83972, and inhibition was verified by infection of human cells. Specific repressors and activators of Pol II–dependent transcription were modified, Pol II phosphorylation was inhibited, and pathogen-specific signaling was suppressed in cell lines and inoculated patients. An increased frequency of strains inhibiting Pol II was epidemiologically verified in ABU and fecal strains compared with acute pyelonephritis, and a Pol II antagonist suppressed the disease-associated host response. These results suggest that by manipulating host gene expression, ABU strains promote tissue integrity while inhibiting pathology. Such bacterial modulation of host gene expression may be essential to sustain asymptomatic bacterial carriage by ensuring that potentially destructive immune activation will not occur.

Lutay, Nataliya; Ambite, Ines; Hernandez, Jenny Gronberg; Rydstrom, Gustav; Ragnarsdottir, Bryndis; Puthia, Manoj; Nadeem, Aftab; Zhang, Jingyao; Storm, Petter; Dobrindt, Ulrich; Wullt, Bjorn; Svanborg, Catharina

2013-01-01

2

Genes as Early Responders Regulate Quorum-Sensing and Control Bacterial Cooperation in Pseudomonas aeruginosa  

PubMed Central

Quorum-sensing (QS) allows bacterial communication to coordinate the production of extracellular products essential for population fitness at higher cell densities. It has been generally accepted that a significant time duration is required to reach appropriate cell density to activate the relevant quiescent genes encoding these costly but beneficial public goods. Which regulatory genes are involved and how these genes control bacterial communication at the early phases are largely un-explored. By determining time-dependent expression of QS-related genes of the opportunistic pathogen Pseudomonas aerugionsa, we show that the induction of social cooperation could be critically influenced by environmental factors to optimize the density of population. In particular, small regulatory RNAs (RsmY and RsmZ) serving as early responders, can promote the expression of dependent genes (e.g. lasR) to boost the synthesis of intracellular enzymes and coordinate instant cooperative behavior in bacterial cells. These early responders, acting as a rheostat to finely modulate bacterial cooperation, which may be quickly activated under environment threats, but peter off when critical QS dependent genes are fully functional for cooperation. Our findings suggest that RsmY and RsmZ critically control the timing and levels of public goods production, which may have implications in sociomicrobiology and infection control.

Zhao, Kelei; Li, Yi; Yue, Bisong; Wu, Min

2014-01-01

3

Computational design of a Zn2+ receptor that controls bacterial gene expression  

NASA Astrophysics Data System (ADS)

The control of cellular physiology and gene expression in response to extracellular signals is a basic property of living systems. We have constructed a synthetic bacterial signal transduction pathway in which gene expression is controlled by extracellular Zn2+. In this system a computationally designed Zn2+-binding periplasmic receptor senses the extracellular solute and triggers a two-component signal transduction pathway via a chimeric transmembrane protein, resulting in transcriptional up-regulation of a -galactosidase reporter gene. The Zn2+-binding site in the designed receptor is based on a four-coordinate, tetrahedral primary coordination sphere consisting of histidines and glutamates. In addition, mutations were introduced in a secondary coordination sphere to satisfy the residual hydrogen-bonding potential of the histidines coordinated to the metal. The importance of the secondary shell interactions is demonstrated by their effect on metal affinity and selectivity, as well as protein stability. Three designed protein sequences, comprising two distinct metal-binding positions, were all shown to bind Zn2+ and to function in the cell-based assay, indicating the generality of the design methodology. These experiments demonstrate that biological systems can be manipulated with computationally designed proteins that have drastically altered ligand-binding specificities, thereby extending the repertoire of genetic control by extracellular signals.

Dwyer, M. A.; Looger, L. L.; Hellinga, H. W.

2003-09-01

4

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism  

PubMed Central

We have identified a highly conserved RNA motif located upstream of genes encoding molybdate transporters, molybdenum cofactor (Moco) biosynthesis enzymes, and proteins that utilize Moco as a coenzyme. Bioinformatics searches have identified 176 representatives in ?-Proteobacteria, ?-Proteobacteria, Clostridia, Actinobacteria, Deinococcus-Thermus species and DNAs from environmental samples. Using genetic assays, we demonstrate that a Moco RNA in Escherichia coli associated with the Moco biosynthetic operon controls gene expression in response to Moco production. In addition, we provide evidence indicating that this conserved RNA discriminates against closely related analogues of Moco. These results, together with extensive phylogenetic conservation and typical gene control structures near some examples, indicate that representatives of this structured RNA represent a novel class of riboswitches that sense Moco. Furthermore, we identify variants of this RNA that are likely to be triggered by the related tungsten cofactor (Tuco), which carries tungsten in place of molybdenum as the metal constituent.

Regulski, Elizabeth E; Moy, Ryan H; Weinberg, Zasha; Barrick, Jeffrey E; Yao, Zizhen; Ruzzo, Walter L; Breaker, Ronald R

2008-01-01

5

Dynamics of bacterial gene regulation  

NASA Astrophysics Data System (ADS)

The phenomenon of diauxic growth is a classical problem of bacterial gene regulation. The most well studied example of this phenomenon is the glucose-lactose diauxie, which occurs because the expression of the lac operon is strongly repressed in the presence of glucose. This repression is often explained by appealing to molecular mechanisms such as cAMP activation and inducer exclusion. I will begin by analyzing data showing that these molecular mechanisms cannot explain the strong lac repression because they exert a relatively weak effect. I will then present a minimal model accounting only for enzyme induction and dilution, which yields strong repression despite the absence of catabolite repression and inducer exclusion. The model also explains the growth patterns observed in batch and continuous cultures of various bacterial strains and substrate mixtures. The talk will conclude with a discussion of the experimental evidence regarding positive feedback, the key component of the minimal model.

Narang, Atul

2009-03-01

6

Mutations in the Control of Virulence Sensor Gene from Streptococcus pyogenes after Infection in Mice Lead to Clonal Bacterial Variants with Altered Gene Regulatory Activity and Virulence  

PubMed Central

The cluster of virulence sensor (CovS)/responder (CovR) two-component operon (CovRS) regulates ?15% of the genes of the Group A Streptococcal pyogenes (GAS) genome. Bacterial clones containing inactivating mutations in the covS gene have been isolated from patients with virulent invasive diseases. We report herein an assessment of the nature and types of covS mutations that can occur in both virulent and nonvirulent GAS strains, and assess whether a nonvirulent GAS can attain enhanced virulence through this mechanism. A group of mice were infected with a globally-disseminated clonal M1T1 GAS (isolate 5448), containing wild-type (WT) CovRS (5448/CovR+S+), or less virulent engineered GAS strains, AP53/CovR+S+ and Manfredo M5/CovR+S+. SpeB negative GAS clones from wound sites and/or from bacteria disseminated to the spleen were isolated and the covS gene was subjected to DNA sequence analysis. Numerous examples of inactivating mutations were found in CovS in all regions of the gene. The mutations found included frame-shift insertions and deletions, and in-frame small and large deletions in the gene. Many of the mutations found resulted in early translation termination of CovS. Thus, the covS gene is a genomic mutagenic target that gives GAS enhanced virulence. In cases wherein CovS? was discovered, these clonal variants exhibited high lethality, further suggesting that randomly mutated covS genes occur during the course of infection, and lead to the development of a more invasive infection.

Mayfield, Jeffrey A.; Liang, Zhong; Agrahari, Garima; Lee, Shaun W.; Donahue, Deborah L.; Ploplis, Victoria A.; Castellino, Francis J.

2014-01-01

7

Measurement of bacterial gene expression in vivo.  

PubMed Central

The complexities of bacterial gene expression during mammalian infection cannot be addressed by in vitro experiments. We know that the infected host represents a complex and dynamic environment, which is modified during the infection process, presenting a variety of stimuli to which the pathogen must respond if it is to be successful. This response involves hundreds of ivi (in vivo-induced) genes which have recently been identified in animal and cell culture models using a variety of technologies including in vivo expression technology, differential fluorescence induction, subtractive hybridization and differential display. Proteomic analysis is beginning to be used to identify IVI proteins, and has benefited from the availability of genome sequences for increasing numbers of bacterial pathogens. The patterns of bacterial gene expression during infection remain to be investigated. Are ivi genes expressed in an organ-specific or cell-type-specific fashion? New approaches are required to answer these questions. The uses of the immunologically based in vivo antigen technology system, in situ PCR and DNA microarray analysis are considered. This review considers existing methods for examining bacterial gene expression in vivo, and describes emerging approaches that should further our understanding in the future.

Hautefort, I; Hinton, J C

2000-01-01

8

Bacterial ice crystal controlling proteins.  

PubMed

Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions. PMID:24579057

Lorv, Janet S H; Rose, David R; Glick, Bernard R

2014-01-01

9

Bacterial Ice Crystal Controlling Proteins  

PubMed Central

Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions.

Lorv, Janet S. H.; Rose, David R.; Glick, Bernard R.

2014-01-01

10

Essential Bacterial Functions Encoded by Gene Pairs??  

PubMed Central

To address the need for new antibacterials, a number of bacterial genomes have been systematically disrupted to identify essential genes. Such programs have focused on the disruption of single genes and may have missed functions encoded by gene pairs or multiple genes. In this work, we hypothesized that we could predict the identity of pairs of proteins within one organism that have the same function. We identified 135 putative protein pairs in Bacillus subtilis and attempted to disrupt the genes forming these, singly and then in pairs. The single gene disruptions revealed new genes that could not be disrupted individually and other genes required for growth in minimal medium or for sporulation. The pairwise disruptions revealed seven pairs of proteins that are likely to have the same function, as the presence of one protein can compensate for the absence of the other. Six of these pairs are essential for bacterial viability and in four cases show a pattern of species conservation appropriate for potential antibacterial development. This work highlights the importance of combinatorial studies in understanding gene duplication and identifying functional redundancy.

Thomaides, Helena B.; Davison, Ella J.; Burston, Lisa; Johnson, Hazel; Brown, David R.; Hunt, Alison C.; Errington, Jeffery; Czaplewski, Lloyd

2007-01-01

11

Large Variations in Bacterial Ribosomal RNA Genes  

PubMed Central

Ribosomal RNA (rRNA) genes, essential to all forms of life, have been viewed as highly conserved and evolutionarily stable, partly because very little is known about their natural variations. Here, we explored large-scale variations of rRNA genes through bioinformatic analyses of available complete bacterial genomic sequences with an emphasis on formation mechanisms and biological significance. Interestingly, we found bacterial genomes in which no 16S rRNA genes harbor the conserved core of the anti–Shine-Dalgarno sequence (5?-CCTCC-3?). This loss was accompanied by elimination of Shine-Dalgarno–like sequences upstream of their protein-coding genes. Those genomes belong to 1 or 2 of the following categories: primary symbionts, hemotropic Mycoplasma, and Flavobacteria. We also found many rearranged rRNA genes and reconstructed their history. Conjecturing the underlying mechanisms, such as inversion, partial duplication, transposon insertion, deletion, and substitution, we were able to infer their biological significance, such as co-orientation of rRNA transcription and chromosomal replication, lateral transfer of rRNA gene segments, and spread of rRNA genes with an apparent structural defect through gene conversion. These results open the way to understanding dynamic evolutionary changes of rRNA genes and the translational machinery.

Lim, Kyungtaek; Furuta, Yoshikazu; Kobayashi, Ichizo

2012-01-01

12

Large variations in bacterial ribosomal RNA genes.  

PubMed

Ribosomal RNA (rRNA) genes, essential to all forms of life, have been viewed as highly conserved and evolutionarily stable, partly because very little is known about their natural variations. Here, we explored large-scale variations of rRNA genes through bioinformatic analyses of available complete bacterial genomic sequences with an emphasis on formation mechanisms and biological significance. Interestingly, we found bacterial genomes in which no 16S rRNA genes harbor the conserved core of the anti-Shine-Dalgarno sequence (5'-CCTCC-3'). This loss was accompanied by elimination of Shine-Dalgarno-like sequences upstream of their protein-coding genes. Those genomes belong to 1 or 2 of the following categories: primary symbionts, hemotropic Mycoplasma, and Flavobacteria. We also found many rearranged rRNA genes and reconstructed their history. Conjecturing the underlying mechanisms, such as inversion, partial duplication, transposon insertion, deletion, and substitution, we were able to infer their biological significance, such as co-orientation of rRNA transcription and chromosomal replication, lateral transfer of rRNA gene segments, and spread of rRNA genes with an apparent structural defect through gene conversion. These results open the way to understanding dynamic evolutionary changes of rRNA genes and the translational machinery. PMID:22446745

Lim, Kyungtaek; Furuta, Yoshikazu; Kobayashi, Ichizo

2012-10-01

13

Evolutionary relationships of bacterial and archaeal glutamine synthetase genes.  

PubMed

Glutamine synthetase (GS), an essential enzyme in ammonia assimilation and glutamine biosynthesis, has three distinctive types: GSI, GSII and GSIII. Genes for GSI have been found only in bacteria (eubacteria) and archaea (archaebacteria), while GSII genes only occur in eukaryotes and a few soil-dwelling bacteria. GSIII genes have been found in only a few bacterial species. Recently, it has been suggested that several lateral gene transfers of archaeal GSI genes to bacteria may have occurred. In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme thermophile Pyrococcus furiosus and the extreme halophile Haloferax volcanii. Our phylogenetic analysis, which included most available GS sequences, revealed two significant prokaryotic GSI subdivisions: GSI-alpha and GSI-beta. GSI-alpha-genes are found in the thermophilic bacterium, Thermotoga maritima, the low G+C Gram-positive bacteria, and the Euryarchaeota (includes methanogens, halophiles, and some thermophiles). GSI-beta-type genes occur in all other bacteria. GSI-alpha- and GSI-beta-type genes also differ with respect to a specific 25-amino-acid insertion and adenylylation control of GS enzyme activity, both absent in the former but present in the latter. Cyanobacterial genes lack adenylylation regulation of GS and may have secondarily lost it. The GSI gene of Sulfolobus solfataricus, a member of the Crenarchaeota (extreme thermophiles), is exceptional and could not be definitely placed in either subdivision. PMID:7916055

Brown, J R; Masuchi, Y; Robb, F T; Doolittle, W F

1994-06-01

14

Bacterial symbiosis in arthropods and the control of disease transmission.  

PubMed Central

Bacterial symbionts may be used as vehicles for expressing foreign genes in arthropods. Expression of selected genes can render an arthropod incapable of transmitting a second microorganism that is pathogenic for humans and is an alternative approach to the control of arthropod-borne diseases. We discuss the rationale for this alternative approach, its potential applications and limitations, and the regulatory concerns that may arise from its use in interrupting disease transmission in humans and animals.

Beard, C. B.; Durvasula, R. V.; Richards, F. F.

1998-01-01

15

Motion control of artificial bacterial flagella  

Microsoft Academic Search

Miniaturized helical swimmers we call artificial bacterial flagella (ABFs) are promising for biomedical applications, such as targeted drug delivery and cell manipulation. ABFs possess several advantageous characteristics, such as high swimming velocity and precise motion control, indicating their potential for diverse applications. The velocity and the propulsive force of ABFs can be controlled by the input frequency of the rotating

Li Zhang; Kathrin E. Peyer; Tristan Petit; Bradley E. Kratochvil; Bradley J. Nelson

2010-01-01

16

Control of Gene Expression at a Bacterial Leader RNA, the agn43 Gene Encoding Outer Membrane Protein Ag43 of Escherichia coli.  

PubMed

The family of agn alleles in Escherichia coli pathovars encodes autotransporters that have been implicated in biofilm formation, autoaggregation, and attachment to cells. The alleles all have long leader RNAs preceding the Ag43 translation initiation codon. Here we present an analysis of the agn43 leader RNA from E. coli K-12. We demonstrate the presence of a rho-independent transcription terminator just 28 bp upstream of the main translation start codon and show that it is functional in vitro. Our data indicate that an as-yet-unknown mechanism of antitermination of transcription must be operative in earlier phases of growth. However, as bacterial cell cultures mature, progressively fewer transcripts are able to bypass this terminator. In the K-12 leader sequence, two in-frame translation initiation codons have been identified, one upstream and the other downstream of the transcription terminator. For optimal agn43 expression, both codons need to be present. Translation from the upstream start codon leads to increased downstream agn43 expression. Our findings have revealed two novel modes of regulation of agn43 expression in the leader RNA in addition to the previously well-characterized regulation of phase variation at the agn43 promoter. PMID:24837285

Wallecha, Anu; Oreh, Heather; van der Woude, Marjan W; deHaseth, Pieter L

2014-08-01

17

Optimization and control in bacterial Lag phase  

PubMed Central

The lag phase of bacterial growth is important from a medical and food safety perspective, but difficult to study due to the low density and metabolic rate of cells. A new study by Alon and colleagues reveals that the gene expression program during early lag phase prioritizes carbon source utilization enzymes over genes responsible for biomass accumulation. This cellular strategy ultimately maximizes growth, making the best long-term use of the new nutrient-rich environment. See research article: http://www.biomedcentral.com/1752-0509/7/136

2013-01-01

18

Molecular Control of Bacterial Death and Lysis  

PubMed Central

Summary: Although the phenomenon of bacterial cell death and lysis has been studied for over 100 years, the contribution of these important processes to bacterial physiology and development has only recently been recognized. Contemporary study of cell death and lysis in a number of different bacteria has revealed that these processes, once thought of as being passive and unregulated, are actually governed by highly complex regulatory systems. An emerging paradigm in this field suggests that, analogous to programmed cell death in eukaryotes, regulated cell death and lysis in bacteria play an important role in both developmental processes, such as competence and biofilm development, and the elimination of damaged cells, such as those irreversibly injured by environmental or antibiotic stress. Further study in this exciting field of bacterial research may provide new insight into the potential evolutionary link between control of cell death in bacteria and programmed cell death (apoptosis) in eukaryotes.

Rice, Kelly C.; Bayles, Kenneth W.

2008-01-01

19

LATERAL GENE TRANSFER AND THE HISTORY OF BACTERIAL GENOMES  

SciTech Connect

The aims of this research were to elucidate the role and extent of lateral transfer in the differentiation of bacterial strains and species, and to assess the impact of gene transfer on the evolution of bacterial genomes. The ultimate goal of the project is to examine the dynamics of a core set of protein-coding genes (i.e., those that are distributed universally among Bacteria) by developing conserved primers that would allow their amplification and sequencing in any bacterial taxa. In addition, we adopted a bioinformatic approach to elucidate the extent of lateral gene transfer in sequenced genome.

Howard Ochman

2006-02-22

20

Mechanical Control of Bacterial Cell Shape  

PubMed Central

In bacteria, cytoskeletal filament bundles such as MreB control the cell morphology and determine whether the cell takes on a spherical or a rod-like shape. Here we use a theoretical model to describe the interplay of cell wall growth, mechanics, and cytoskeletal filaments in shaping the bacterial cell. We predict that growing cells without MreB exhibit an instability that favors rounded cells. MreB can mechanically reinforce the cell wall and prevent the onset of instability. We propose that the overall bacterial shape is determined by a dynamic turnover of cell wall material that is controlled by mechanical stresses in the wall. The model affirms that morphological transformations with and without MreB are reversible, and quantitatively describes the growth of irregular shapes and cells undergoing division. The theory also suggests a unique coupling between mechanics and chemistry that can control organismal shapes in general.

Jiang, Hongyuan; Si, Fangwei; Margolin, William; Sun, Sean X.

2011-01-01

21

Simultaneous Identification of Bacterial Virulence Genes by Negative Selection  

Microsoft Academic Search

An insertional mutagenesis system that uses transposons carrying unique DNA sequence tags was developed for the isolation of bacterial virulence genes. The tags from a mixed population of bacterial mutants representing the inoculum and bacteria recovered from infected hosts were detected by amplification, radiolabeling, and hybridization analysis. When applied to a murine model of typhoid fever caused by Salmonella typhimurium,

Michael Hensel; Jacqueline E. Shea; Colin Gleeson; Michael D. Jones; Emma Dalton; David W. Holden

1995-01-01

22

Evolutionary relationships of bacterial and archaeal glutamine synthetase genes  

Microsoft Academic Search

Glutamine synthetase (GS), an essential enzyme in ammonia assimilation and glutamine biosynthesis, has three distinctive types: GSI, GSII and GSIII. Genes for GSI have been found only in bacteria (eubacteria) and archaea (archaebacteria), while GSII genes only occur in eukaryotes and a few soil-dwelling bacteria. GSIII genes have been found in only a few bacterial species. Recently, it has been

J. R. Brown; Y. Masuchi; F. T. Robb; W. F. Doolittlel

1994-01-01

23

Reservoir of Bacterial Exotoxin Genes in the Environment  

PubMed Central

Many bacteria produce secreted virulence factors called exotoxins. Exotoxins are often encoded by mobile genetic elements, including bacteriophage (phage). Phage can transfer genetic information to the bacteria they infect. When a phage transfers virulence genes to an avirulent bacterium, the bacterium can acquire the ability to cause disease. It is important to understand the role played by the phage that carry these genes in the evolution of pathogens. This is the first report of an environmental reservoir of a bacterial exotoxin gene in an atypical host. Screening bacterial isolates from the environment via PCR identified an isolate with a DNA sequence >95% identical to the Staphylococcus aureus enterotoxin A gene (sea). 16S DNA sequence comparisons and growth studies identified the environmental isolate as a psychrophilic Pseudomonas spp. The results indicate that the sea gene is present in an alternative bacterial host, providing the first evidence for an environmental pool of exotoxin genes in bacteria.

Casas, Veronica; Magbanua, Joseph; Sobrepena, Gerico; Kelley, Scott T.; Maloy, Stanley R.

2010-01-01

24

Transport of Magnesium by a Bacterial Nramp-Related Gene  

PubMed Central

Magnesium is an essential divalent metal that serves many cellular functions. While most divalent cations are maintained at relatively low intracellular concentrations, magnesium is maintained at a higher level (?0.5–2.0 mM). Three families of transport proteins were previously identified for magnesium import: CorA, MgtE, and MgtA/MgtB P-type ATPases. In the current study, we find that expression of a bacterial protein unrelated to these transporters can fully restore growth to a bacterial mutant that lacks known magnesium transporters, suggesting it is a new importer for magnesium. We demonstrate that this transport activity is likely to be specific rather than resulting from substrate promiscuity because the proteins are incapable of manganese import. This magnesium transport protein is distantly related to the Nramp family of proteins, which have been shown to transport divalent cations but have never been shown to recognize magnesium. We also find gene expression of the new magnesium transporter to be controlled by a magnesium-sensing riboswitch. Importantly, we find additional examples of riboswitch-regulated homologues, suggesting that they are a frequent occurrence in bacteria. Therefore, our aggregate data discover a new and perhaps broadly important path for magnesium import and highlight how identification of riboswitch RNAs can help shed light on new, and sometimes unexpected, functions of their downstream genes.

Rodionov, Dmitry A.; Freedman, Benjamin G.; Senger, Ryan S.; Winkler, Wade C.

2014-01-01

25

Detection of bacterial blight resistance genes in basmati rice landraces.  

PubMed

Aromatic basmati rice is vulnerable to bacterial blight disease. Genes conferring resistance to bacterial blight have been identified in coarse rice; however, their incorporation into basmati varieties compromises the prized basmati aroma. We identified bacterial blight resistance genes Xa4, xa5, Xa7, and xa13 in 52 basmati landraces and five basmati cultivars using PCR markers. The Xa7 gene was found to be the most prevalent among the cultivars and landraces. The cultivars Basmati-385 and Basmati-2000 also contained the Xa4 gene; however, xa5 and xa13 were confined to landraces only. Ten landraces were found to have multiple resistance genes. Landraces Basmati-106, Basmati-189 and Basmati-208 contained Xa4 and Xa7 genes. Whereas, landraces Basmati-122, Basmati-427, Basmati-433 were observed to have xa5 and Xa7 genes. Landraces Basmati-48, Basmati-51A, Basmati-334, and Basmati-370A possessed Xa7 and xa13 genes. The use of landraces containing recessive genes xa5 and xa13 as donor parents in hybridization with cultivars Basmati-385 and Basmati-2000, which contain the genes Xa4 and Xa7, will expedite efforts to develop bacterial blight-resistant basmati rice cultivars through marker assisted selection, based on a pyramiding approach, without compromising aroma and grain quality. PMID:22869552

Ullah, I; Jamil, S; Iqbal, M Z; Shaheen, H L; Hasni, S M; Jabeen, S; Mehmood, A; Akhter, M

2012-01-01

26

Expression of a Bacterial Ice Nucleation Gene in Plants 1  

PubMed Central

We have introduced an ice nucleation gene (inaZ) from Pseudomonas syringae pv. syringae into Nicotiana tabacum, a freezing-sensitive species, and Solanum commersonii, a freezing-tolerant species. Transformants of both species showed increased ice nucleation activity over untransformed controls. The concentration of ice nuclei detected at ?10.5°C in 15 different primary transformants of S. commersonii varied by over 1000-fold, and the most active transformant contained over 100 ice nuclei/mg of tissue. The temperature of the warmest freezing event in plant samples of small mass was increased from approximately ?12°C in the untransformed controls to ?4°C in inaZ-expressing transformants. The threshold nucleation temperature of samples from transformed plants did not increase appreciably with the mass of the sample. The most abundant protein detected in transgenic plants using immunological probes specific to the inaZ protein exhibited a higher mobility on sodium dodecyl sulfate polyacrylamide gels than the inaZ protein from bacterial sources. However, some protein with a similar mobility to the inaZ protein could be detected. Although the warmest ice nucleation temperature detected in transgenic plants is lower than that conferred by this gene in P. syringae (?2°C), our results demonstrate that the ice nucleation gene of P. syringae can be expressed in plant cells to produce functional ice nuclei. Images Figure 2 Figure 3

Baertlein, Dawn A.; Lindow, Steven E.; Panopoulos, Nicholas J.; Lee, Stephen P.; Mindrinos, Michael N.; Chen, Tony H. H.

1992-01-01

27

Bacterial blight of soybean: Regulation of a pathogen gene determining host cultivar specificity  

SciTech Connect

Soybean cultivars resistant to Pseudomonas syringae pathovar glycinea (Psg), the causal agent of bacterial blight, exhibit a hypersensitive (necrosis) reaction (HR) to infection. Psg strains carrying the avrB gene elicit the HR in soybean cultivars carrying the resistance gene Rpg1. Psg expressing avrB at a high level and capable of eliciting the HR in the absence of de novo bacterial RNA synthesis have been obtained in in vitro culture. Nutritional signals and regions within the Psg hrp gene cluster, an approximately 20-kilobase genomic region also necessary for pathogenicity, control avrB transcription.

Huynh, T.V.; Dahlbeck, D.; Staskawicz, B.J. (Univ. of California, Berkeley (USA))

1989-09-22

28

Bacteriophage-encoded shiga toxin gene in atypical bacterial host  

PubMed Central

Background Contamination from fecal bacteria in recreational waters is a major health concern since bacteria capable of causing human disease can be found in animal feces. The Dog Beach area of Ocean Beach in San Diego, California is a beach prone to closures due to high levels of fecal indicator bacteria (FIB). A potential source of these FIB could be the canine feces left behind by owners who do not clean up after their pets. We tested this hypothesis by screening the DNA isolated from canine feces for the bacteriophage-encoded stx gene normally found in the virulent strains of the fecal bacterium Escherichia coli. Results Twenty canine fecal samples were collected, processed for total and bacterial fraction DNA, and screened by PCR for the stx gene. The stx gene was detected in the total and bacterial fraction DNA of one fecal sample. Bacterial isolates were then cultivated from the stx-positive fecal sample. Eighty nine of these canine fecal bacterial isolates were screened by PCR for the stx gene. The stx gene was detected in five of these isolates. Sequencing and phylogenetic analyses of 16S rRNA gene PCR products from the canine fecal bacterial isolates indicated that they were Enterococcus and not E. coli. Conclusions The bacteriophage-encoded stx gene was found in multiple species of bacteria cultivated from canine fecal samples gathered at the shoreline of the Dog Beach area of Ocean Beach in San Diego, California. The canine fecal bacteria carrying the stx gene were not the typical E. coli host and were instead identified through phylogenetic analyses as Enterococcus. This suggests a large degree of horizontal gene transfer of exotoxin genes in recreational waters.

2011-01-01

29

Replication and Control of Circular Bacterial Plasmids  

PubMed Central

An essential feature of bacterial plasmids is their ability to replicate as autonomous genetic elements in a controlled way within the host. Therefore, they can be used to explore the mechanisms involved in DNA replication and to analyze the different strategies that couple DNA replication to other critical events in the cell cycle. In this review, we focus on replication and its control in circular plasmids. Plasmid replication can be conveniently divided into three stages: initiation, elongation, and termination. The inability of DNA polymerases to initiate de novo replication makes necessary the independent generation of a primer. This is solved, in circular plasmids, by two main strategies: (i) opening of the strands followed by RNA priming (theta and strand displacement replication) or (ii) cleavage of one of the DNA strands to generate a 3?-OH end (rolling-circle replication). Initiation is catalyzed most frequently by one or a few plasmid-encoded initiation proteins that recognize plasmid-specific DNA sequences and determine the point from which replication starts (the origin of replication). In some cases, these proteins also participate directly in the generation of the primer. These initiators can also play the role of pilot proteins that guide the assembly of the host replisome at the plasmid origin. Elongation of plasmid replication is carried out basically by DNA polymerase III holoenzyme (and, in some cases, by DNA polymerase I at an early stage), with the participation of other host proteins that form the replisome. Termination of replication has specific requirements and implications for reinitiation, studies of which have started. The initiation stage plays an additional role: it is the stage at which mechanisms controlling replication operate. The objective of this control is to maintain a fixed concentration of plasmid molecules in a growing bacterial population (duplication of the plasmid pool paced with duplication of the bacterial population). The molecules involved directly in this control can be (i) RNA (antisense RNA), (ii) DNA sequences (iterons), or (iii) antisense RNA and proteins acting in concert. The control elements maintain an average frequency of one plasmid replication per plasmid copy per cell cycle and can “sense” and correct deviations from this average. Most of the current knowledge on plasmid replication and its control is based on the results of analyses performed with pure cultures under steady-state growth conditions. This knowledge sets important parameters needed to understand the maintenance of these genetic elements in mixed populations and under environmental conditions.

del Solar, Gloria; Giraldo, Rafael; Ruiz-Echevarria, Maria Jesus; Espinosa, Manuel; Diaz-Orejas, Ramon

1998-01-01

30

Controlling rice bacterial blight in Africa: needs and prospects.  

PubMed

Rice cultivation has drastically increased in Africa over the last decade. During this time, the region has also seen a rise in the incidence of rice bacterial blight caused by the pathogen Xanthomonas oryzae pv. oryzae. The disease is expanding to new rice production areas and threatens food security in the region. Yield losses caused by X. oryzae pv. oryzae range from 20 to 30% and can be as high as 50% in some areas. Employing resistant cultivars is the most economical and effective way to control this disease. To facilitate development and strategic deployment of rice cultivars with resistance to bacterial blight, biotechnology tools and approaches, including marker-assisted breeding, gene combinations for disease control, and multiplex-PCR for pathogen diagnosis, have been developed. Although these technologies are routinely used elsewhere, their application in Africa remains limited, usually due to high cost and advanced technical skills required. To combat this problem, developers of the technologies at research institutions need to work with farmers from an early stage to create and promote the integration of successful, low cost applications of research biotech products. Here, we review the current knowledge and biotechnologies available to improve bacterial blight control. We will also discuss how to facilitate their application in Africa and delivery to the field. PMID:21963588

Verdier, Valérie; Vera Cruz, Casiana; Leach, Jan E

2012-06-30

31

Mechanisms of post-transcriptional gene regulation in bacterial biofilms  

PubMed Central

Biofilms are characterized by a dense multicellular community of microorganisms that can be formed by the attachment of bacteria to an inert surface and to each other. The development of biofilm involves the initial attachment of planktonic bacteria to a surface, followed by replication, cell-to-cell adhesion to form microcolonies, maturation, and detachment. Mature biofilms are embedded in a self-produced extracellular polymeric matrix composed primarily of bacterial-derived exopolysaccharides, specialized proteins, adhesins, and occasionally DNA. Because the synthesis and assembly of biofilm matrix components is an exceptionally complex process, the transition between its different phases requires the coordinate expression and simultaneous regulation of many genes by complex genetic networks involving all levels of gene regulation. The finely controlled intracellular level of the chemical second messenger molecule, cyclic-di-GMP is central to the post-transcriptional mechanisms governing the switch between the motile planktonic lifestyle and the sessile biofilm forming state in many bacteria. Several other post-transcriptional regulatory mechanisms are known to dictate biofilm development and assembly and these include RNA-binding proteins, small non-coding RNAs, toxin-antitoxin systems, riboswitches, and RNases. Post-transcriptional regulation is therefore a powerful molecular mechanism employed by bacteria to rapidly adjust to the changing environment and to fine tune gene expression to the developmental needs of the cell. In this review, we discuss post-transcriptional mechanisms that influence the biofilm developmental cycle in a variety of pathogenic bacteria.

Martinez, Luary C.; Vadyvaloo, Viveka

2014-01-01

32

Mechanisms of post-transcriptional gene regulation in bacterial biofilms.  

PubMed

Biofilms are characterized by a dense multicellular community of microorganisms that can be formed by the attachment of bacteria to an inert surface and to each other. The development of biofilm involves the initial attachment of planktonic bacteria to a surface, followed by replication, cell-to-cell adhesion to form microcolonies, maturation, and detachment. Mature biofilms are embedded in a self-produced extracellular polymeric matrix composed primarily of bacterial-derived exopolysaccharides, specialized proteins, adhesins, and occasionally DNA. Because the synthesis and assembly of biofilm matrix components is an exceptionally complex process, the transition between its different phases requires the coordinate expression and simultaneous regulation of many genes by complex genetic networks involving all levels of gene regulation. The finely controlled intracellular level of the chemical second messenger molecule, cyclic-di-GMP is central to the post-transcriptional mechanisms governing the switch between the motile planktonic lifestyle and the sessile biofilm forming state in many bacteria. Several other post-transcriptional regulatory mechanisms are known to dictate biofilm development and assembly and these include RNA-binding proteins, small non-coding RNAs, toxin-antitoxin systems, riboswitches, and RNases. Post-transcriptional regulation is therefore a powerful molecular mechanism employed by bacteria to rapidly adjust to the changing environment and to fine tune gene expression to the developmental needs of the cell. In this review, we discuss post-transcriptional mechanisms that influence the biofilm developmental cycle in a variety of pathogenic bacteria. PMID:24724055

Martínez, Luary C; Vadyvaloo, Viveka

2014-01-01

33

Variation in dissolved organic matter controls bacterial production and community composition.  

PubMed

An ongoing debate in ecology revolves around how species composition and ecosystem function are related. To address the mechanistic controls of this relationship, we manipulated the composition of dissolved organic matter (DOM) fed to aquatic bacteria to determine effects on both bacterial activity and community composition. Sites along terrestrial to aquatic flow paths were chosen to simulate movement of DOM through catchments, and DOM was fed to downslope and control bacterial communities. Bacterial production was measured, and DOM chemistry and bacterial community composition (using denaturing gradient gel electrophoresis of 16S rRNA genes) were characterized following incubations. Bacterial production, dissolved organic carbon (DOC)-specific bacterial production, and DOC consumption were greatest in mesocosms fed soil water DOM; soil water DOM enhanced lake and stream bacterial production by 320-670% relative to lake and stream controls. Stream DOM added to lake bacteria depressed bacterial production relative to lake controls in the early season (-78%) but not the mid-season experiment. Addition of upslope DOM to stream and lake bacterial communities resulted in significant changes in bacterial community composition relative to controls. In four of five DOM treatments, the bacterial community composition converged to the DOM source community regardless of the initial inoculum. These results demonstrate that shifts in the supply of natural DOM were followed by changes in both bacterial production and community composition, suggesting that changes in function are likely predicated on at least an initial change in the community composition. The results indicate that variation in DOM composition of soil and surface waters influences bacterial community dynamics and controls rates of carbon processing in set patterns across the landscape. PMID:16937646

Judd, Kristin E; Crump, Byron C; Kling, George W

2006-08-01

34

Genomic islands: tools of bacterial horizontal gene transfer and evolution.  

PubMed

Bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. Besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. The horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. A significant part of the horizontal gene transfer is or has been facilitated by genomic islands (GEIs). GEIs are discrete DNA segments, some of which are mobile and others which are not, or are no longer mobile, which differ among closely related strains. A number of GEIs are capable of integration into the chromosome of the host, excision, and transfer to a new host by transformation, conjugation or transduction. GEIs play a crucial role in the evolution of a broad spectrum of bacteria as they are involved in the dissemination of variable genes, including antibiotic resistance and virulence genes leading to generation of hospital 'superbugs', as well as catabolic genes leading to formation of new metabolic pathways. Depending on the composition of gene modules, the same type of GEIs can promote survival of pathogenic as well as environmental bacteria. PMID:19178566

Juhas, Mario; van der Meer, Jan Roelof; Gaillard, Muriel; Harding, Rosalind M; Hood, Derek W; Crook, Derrick W

2009-03-01

35

Enhanced resistance against bacterial wilt in transgenic tomato ( Lycopersicon esculentum ) lines expressing the Xa21 gene  

Microsoft Academic Search

To enhance bacterial wilt resistance in tomato plants and simplify the protocol of Agrobacterium tumefaciens mediated gene transfer, parameters affecting transformation efficiency in tomato have been optimized. A. tumefaciens strain EHA101, harboring a recombinant binary expression vector pTCL5 containing the Xa21 gene under the control of the CaMV 35S promoter was used for transformation. Five cultivars of tomato (Rio Grande,

Amber Afroz; Zubeda Chaudhry; Umer Rashid; Ghulam Muhammad Ali; Farhat Nazir; Javaid Iqbal; Muhammad Rashid Khan

2011-01-01

36

Subgingival bacterial colonization profiles correlate with gingival tissue gene expression  

PubMed Central

Background Periodontitis is a chronic inflammatory disease caused by the microbiota of the periodontal pocket. We investigated the association between subgingival bacterial profiles and gene expression patterns in gingival tissues of patients with periodontitis. A total of 120 patients undergoing periodontal surgery contributed with a minimum of two interproximal gingival papillae (range 2-4) from a maxillary posterior region. Prior to tissue harvesting, subgingival plaque samples were collected from the mesial and distal aspects of each tissue sample. Gingival tissue RNA was extracted, reverse-transcribed, labeled, and hybridized with whole-genome microarrays (310 in total). Plaque samples were analyzed using checkerboard DNA-DNA hybridizations with respect to 11 bacterial species. Random effects linear regression models considered bacterial levels as exposure and expression profiles as outcome variables. Gene Ontology analyses summarized the expression patterns into biologically relevant categories. Results Wide inter-species variation was noted in the number of differentially expressed gingival tissue genes according to subgingival bacterial levels: Using a Bonferroni correction (p < 9.15 × 10-7), 9,392 probe sets were differentially associated with levels of Tannerella forsythia, 8,537 with Porphyromonas gingivalis, 6,460 with Aggregatibacter actinomycetemcomitans, 506 with Eikenella corrodens and only 8 with Actinomyces naeslundii. Cluster analysis identified commonalities and differences among tissue gene expression patterns differentially regulated according to bacterial levels. Conclusion Our findings suggest that the microbial content of the periodontal pocket is a determinant of gene expression in the gingival tissues and provide new insights into the differential ability of periodontal species to elicit a local host response.

2009-01-01

37

Genes Necessary for Bacterial Magnetite Biomineralization Identified by Transposon Mutagenesis  

NASA Astrophysics Data System (ADS)

Magnetic bacteria synthesize nanoscale crystals of magnetite in intracellular, membrane-bounded organelles (magnetosomes). These crystals are preserved in the fossil record at least as far back as the late Neoproterozoic and have been tentatively identified in much older rocks (1). This fossil record may provide deep time calibration points for molecular evolution studies once the genes involved in biologically controlled magnetic mineralization (BCMM) are known. Further, a genetic and biochemical understanding of BCMM will give insight into the depositional environment and biogeochemical cycles in which magnetic bacteria play a role. The BCMM process is not well understood, though proteins have been identified from the magnetosome membrane and genetic manipulation and biochemical characterization of these proteins are underway. Most of the proteins currently thought to be involved are encoded within the mam cluster, a large cluster of genes whose products localize to the magnetosome membrane and are conserved among magnetic bacteria (2). In an effort to identify all of the genes necessary for bacterial BCMM, we undertook a transposon mutagenesis of Magnetospirillum magneticum AMB-1. Non-magnetic mutants (MNMs) were identified by growth in liquid culture followed by a magnetic assay. The insertion site of the transposon was identified two ways. First MNMs were screened with a PCR assay to determine if the transposon had inserted into the mam cluster. Second, the transposon was rescued from the mutant DNA and cloned for sequencing. The majority insertion sites are located within the mam cluster. Insertion sites also occur in operons which have not previously been suspected to be involved in magnetite biomineralization. None of the insertion sites have occurred within genes reported from previous transposon mutagenesis studies of AMB-1 (3, 4). Two of the non-mam cluster insertion sites occur in operons containing genes conserved particularly between MS-1 and MC-1. We are undertaking a complementation strategy to demonstrate the necessity of these novel genes in BCMM as well as characterizing the phenotypes of the mutants. 1. S. B. R. Chang, J. F. Stolz, J. L. Kirschvink, S. M. Awramik, Precambrian Res. 43, 305-315 (1989). 2. K. Grünberg, C. Wawer, B. M. Tebo, D. Schüler, Appl. Environ. Microbiol. 67, 4573-4582 (2001). 3. A. T. Wahyudi, H. Takeyama, T. Matsunaga, Appl. Biochem. Biotechnol. 91-3, 147-154 (2001). 4. T. Matsunaga, C. Nakamura, J. G. Burgess, K. Sode, J. Bacteriol. 174, 2748-2753 (1992).

Nash, C. Z.; Komeili, A.; Newman, D. K.; Kirschvink, J. L.

2004-12-01

38

CRISPR-Cas systems: new players in gene regulation and bacterial physiology  

PubMed Central

CRISPR-Cas systems are bacterial defenses against foreign nucleic acids derived from bacteriophages, plasmids or other sources. These systems are targeted in an RNA-dependent, sequence-specific manner, and are also adaptive, providing protection against previously encountered foreign elements. In addition to their canonical function in defense against foreign nucleic acid, their roles in various aspects of bacterial physiology are now being uncovered. We recently revealed a role for a Cas9-based Type II CRISPR-Cas system in the control of endogenous gene expression, a novel form of prokaryotic gene regulation. Cas9 functions in association with two small RNAs to target and alter the stability of an endogenous transcript encoding a bacterial lipoprotein (BLP). Since BLPs are recognized by the host innate immune protein Toll-like Receptor 2 (TLR2), CRISPR-Cas-mediated repression of BLP expression facilitates evasion of TLR2 by the intracellular bacterial pathogen Francisella novicida, and is essential for its virulence. Here we describe the Cas9 regulatory system in detail, as well as data on its role in controlling virulence traits of Neisseria meningitidis and Campylobacter jejuni. We also discuss potential roles of CRISPR-Cas systems in the response to envelope stress and other aspects of bacterial physiology. Since ~45% of bacteria and ~83% of Archaea encode these machineries, the newly appreciated regulatory functions of CRISPR-Cas systems are likely to play broad roles in controlling the pathogenesis and physiology of diverse prokaryotes.

Sampson, Timothy R.; Weiss, David S.

2014-01-01

39

Cloning of pig parotid secretory protein gene upstream promoter and the establishment of a transgenic mouse model expressing bacterial phytase for agricultural phosphorus pollution control.  

PubMed

This study examined the feasibility of using the promoter of the pig parotid secretory protein (PSP) gene for expression of the phytase transgene in mouse models. The pig parotid secretory protein gene is specifically expressed at high levels in the salivary glands. The 10-kb upstream promoter region of the gene necessary for tissue-specific expression has been identified. We have constructed phytase transgenes composed of the appA phytase gene from Escherichia coli driven by the upstream promoter region of the pig PSP gene with a 3' tail of either bovine growth hormone or the pig PSP gene polyadenylation signal. Transgenic mouse models with the construct showed that the upstream region of the pig PSP gene is sufficient for directing the expression of phytase transgenes in the saliva. Expression of salivary phytase reduced fecal phytate by 8.5 and 12.5% in 2 transgenic mouse lines, respectively. These results suggest that the expression of phytase in salivary glands of monogastric animals offers a promising biological approach to relieve the requirement for dietary phosphate supplements and to reduce phosphorus pollution from animal agriculture. PMID:16478942

Yin, H F; Fan, B L; Yang, B; Liu, Y F; Luo, J; Tian, X H; Li, N

2006-03-01

40

Identification of Genes and Gene Products Necessary for Bacterial Bioluminescence  

Microsoft Academic Search

Expression of luminescence in Escherichia coli was recently achieved by cloning genes from the marine bacterium Vibrio fischeri. One DNA fragment on a hybrid plasmid encoded regulatory functions and enzymatic activities necessary for light production. We report the results of a genetic analysis to identify the luminescence genes (lux) that reside on this recombinant plasmid. lux gene mutations were generated

Joanne Engebrecht; Michael Silverman

1984-01-01

41

Limits of Feedback Control in Bacterial Chemotaxis  

PubMed Central

Inputs to signaling pathways can have complex statistics that depend on the environment and on the behavioral response to previous stimuli. Such behavioral feedback is particularly important in navigation. Successful navigation relies on proper coupling between sensors, which gather information during motion, and actuators, which control behavior. Because reorientation conditions future inputs, behavioral feedback can place sensors and actuators in an operational regime different from the resting state. How then can organisms maintain proper information transfer through the pathway while navigating diverse environments? In bacterial chemotaxis, robust performance is often attributed to the zero integral feedback control of the sensor, which guarantees that activity returns to resting state when the input remains constant. While this property provides sensitivity over a wide range of signal intensities, it remains unclear how other parameters such as adaptation rate and adapted activity affect chemotactic performance, especially when considering that the swimming behavior of the cell determines the input signal. We examine this issue using analytical models and simulations that incorporate recent experimental evidences about behavioral feedback and flagellar motor adaptation. By focusing on how sensory information carried by the response regulator is best utilized by the motor, we identify an operational regime that maximizes drift velocity along chemical concentration gradients for a wide range of environments and sensor adaptation rates. This optimal regime is outside the dynamic range of the motor response, but maximizes the contrast between run duration up and down gradients. In steep gradients, the feedback from chemotactic drift can push the system through a bifurcation. This creates a non-chemotactic state that traps cells unless the motor is allowed to adapt. Although motor adaptation helps, we find that as the strength of the feedback increases individual phenotypes cannot maintain the optimal operational regime in all environments, suggesting that diversity could be beneficial.

Hernandez-Nunez, Luis; Emonet, Thierry

2014-01-01

42

Use of a riboswitch-controlled conditional hypomorphic mutation to uncover a role for the essential csrA gene in bacterial autoaggregation.  

PubMed

Essential genes encode biological functions critical for cell survival. Correspondingly, their null mutants are often difficult to obtain, which impedes subsequent genetic and functional analysis. Here, we describe the development and utility of a theophylline-responsive riboswitch that enables target gene expression to be specifically "tuned" from low to high levels, which may be used to generate conditional hypomorphic mutants. Low levels of gene activity in the absence of the ligand (theophylline) permit cell survival, enabling gene activities to be investigated. Normal gene expression levels and wild-type phenotypes can be restored by the addition of the ligand. We demonstrate the utility of this approach with csrA, an essential gene in Escherichia coli that encodes the global regulatory protein CsrA. We placed the theophylline-responsive riboswitch immediately upstream of the csrA ribosome binding site, with the resulting mutant named switch-csrA. Hypomorphism of switch-csrA and its specific responsiveness to theophylline were verified by phenotypic examination and translation analysis. The utility of switch-csrA revealed a previously unidentified function for CsrA, namely its role as a repressor of cellular autoaggregation. Specifically, switch-csrA in the non-ligand-bound form produced low levels of CsrA, and its cells autoaggregated. Theophylline binding induced conformational changes in the riboswitch and permitted efficient csrA translation; consequently, autoaggregation did not occur. Our results indicate that CsrA modulates autoaggregation via the polysaccharide adhesin poly-beta-1,6-N-acetyl-D-glucosamine. In summary, the use of ligand-responsive riboswitches to construct conditional hypomorphic mutants represents a novel approach for investigating the activities of essential genes, which effectively complements traditional genetic approaches. PMID:19706608

Jin, Ye; Watt, Rory M; Danchin, Antoine; Huang, Jian-dong

2009-10-16

43

Bacterial Cellular Engineering by Genome Editing and Gene Silencing  

PubMed Central

Genome editing is an important technology for bacterial cellular engineering, which is commonly conducted by homologous recombination-based procedures, including gene knockout (disruption), knock-in (insertion), and allelic exchange. In addition, some new recombination-independent approaches have emerged that utilize catalytic RNAs, artificial nucleases, nucleic acid analogs, and peptide nucleic acids. Apart from these methods, which directly modify the genomic structure, an alternative approach is to conditionally modify the gene expression profile at the posttranscriptional level without altering the genomes. This is performed by expressing antisense RNAs to knock down (silence) target mRNAs in vivo. This review describes the features and recent advances on methods used in genomic engineering and silencing technologies that are advantageously used for bacterial cellular engineering.

Nakashima, Nobutaka; Miyazaki, Kentaro

2014-01-01

44

Gene expression profiles in febrile children with defined viral and bacterial infection  

PubMed Central

Viral infections are common causes of fever without an apparent source in young children. Despite absence of bacterial infection, many febrile children are treated with antibiotics. Virus and bacteria interact with different pattern recognition receptors in circulating blood leukocytes, triggering specific host transcriptional programs mediating immune response. Therefore, unique transcriptional signatures may be defined that discriminate viral from bacterial causes of fever without an apparent source. Gene expression microarray analyses were conducted on blood samples from 30 febrile children positive for adenovirus, human herpesvirus 6, or enterovirus infection or with acute bacterial infection and 22 afebrile controls. Blood leukocyte transcriptional profiles clearly distinguished virus-positive febrile children from both virus-negative afebrile controls and afebrile children with the same viruses present in the febrile children. Virus-specific gene expression profiles could be defined. The IFN signaling pathway was uniquely activated in febrile children with viral infection, whereas the integrin signaling pathway was uniquely activated in children with bacterial infection. Transcriptional profiles classified febrile children with viral or bacterial infection with better accuracy than white blood cell count in the blood. Similarly accurate classification was shown with data from an independent study using different microarray platforms. Our results support the paradigm of using host response to define the etiology of childhood infections. This approach could be an important supplement to highly sensitive tests that detect the presence of a possible pathogen but do not address its pathogenic role in the patient being evaluated.

Hu, Xinran; Yu, Jinsheng; Crosby, Seth D.; Storch, Gregory A.

2013-01-01

45

Small molecule control of bacterial biofilms  

PubMed Central

Bacterial biofilms are defined as a surface attached community of bacteria embedded in a matrix of extracellular polymeric substances that they have produced. When in the biofilm state, bacteria are more resistant to antibiotics and the host immune response than are their planktonic counterparts. Biofilms are increasingly recognized as being significant in human disease, accounting for 80% of bacterial infections in the body and diseases associated with bacterial biofilms include: lung infections of cystic fibrosis, colitis, urethritis, conjunctivitis, otitis, endocarditis and periodontitis. Additionally, biofilm infections of indwelling medical devices are of particular concern, as once the device is colonized infection is virtually impossible to eradicate. Given the prominence of biofilms in infectious diseases, there has been an increased effort toward the development of small molecules that will modulate bacterial biofilm development and maintenance. In this review, we highlight the development of small molecules that inhibit and/or disperse bacterial biofilms through non-microbicidal mechanisms. The review discuses the numerous approaches that have been applied to the discovery of lead small molecules that mediate biofilm development. These approaches are grouped into: 1) the identification and development of small molecules that target one of the bacterial signaling pathways involved in biofilm regulation, 2) chemical library screening for compounds with anti-biofilm activity, and 3) the identification of natural products that possess anti-biofilm activity, and the chemical manipulation of these natural products to obtain analogues with increased activity.

Worthington, Roberta J.; Richards, Justin J.

2012-01-01

46

Control of intestinal bacterial proliferation in regulation of lifespan in Caenorhabditis elegans  

PubMed Central

Background A powerful approach to understanding complex processes such as aging is to use model organisms amenable to genetic manipulation, and to seek relevant phenotypes to measure. Caenorhabditis elegans is particularly suited to studies of aging, since numerous single-gene mutations have been identified that affect its lifespan; it possesses an innate immune system employing evolutionarily conserved signaling pathways affecting longevity. As worms age, bacteria accumulate in the intestinal tract. However, quantitative relationships between worm genotype, lifespan, and intestinal lumen bacterial load have not been examined. We hypothesized that gut immunity is less efficient in older animals, leading to enhanced bacterial accumulation, reducing longevity. To address this question, we evaluated the ability of worms to control bacterial accumulation as a functional marker of intestinal immunity. Results We show that as adult worms age, several C. elegans genotypes show diminished capacity to control intestinal bacterial accumulation. We provide evidence that intestinal bacterial load, regulated by gut immunity, is an important causative factor of lifespan determination; the effects are specified by bacterial strain, worm genotype, and biologic age, all acting in concert. Conclusions In total, these studies focus attention on the worm intestine as a locus that influences longevity in the presence of an accumulating bacterial population. Further studies defining the interplay between bacterial species and host immunity in C. elegans may provide insights into the general mechanisms of aging and age-related diseases.

2012-01-01

47

Gene recognition from questionable ORFs in bacterial and archaeal genomes.  

PubMed

The ORFs of microbial genomes in annotation files are usually classified into two groups: the first corresponds to known genes; whereas the second includes 'putative', 'probable', 'conserved hypothetical', 'hypothetical', 'unknown' and 'predicted' ORFs etc. Since the annotation is not 100% accurate, it is essential to confirm which ORF of the latter group is coding and which is not. Starting from known genes in the former, this paper describes an improved Z curve method to recognize genes in the latter. Ten-fold cross-validation tests show that the average accuracy of the algorithm is greater than 99% for recognizing the known genes in 57 bacterial and archaeal genomes. The method is then applied to recognize genes of the latter group. The likely non-coding ORFs in each of the 57 bacterial or archaeal genomes studied here are recognized and listed at the website http://tubic.tju.edu.cn/ZCURVE_C_html/noncoding.html. The working mechanism of the algorithm has been discussed in details. A computer program, called ZCURVE_C, was written to calculate a coding score called Z-curve score for ORFs in the above 57 bacterial and archaeal genomes. Coding/non-coding is simply determined by the criterion of Z-curve score > 0/ Z-curve score < 0. A website has been set up to provide the service to calculate the Z-curve score. A user may submit the DNA sequence of an ORF to the server at http://tubic.tju.edu.cn/ZCURVE_C/Default.cgi, and the Z-curve score of the ORF is calculated and returned to the user immediately. PMID:12854962

Chen, Ling-Ling; Zhang, Chun-Ting

2003-08-01

48

Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species.  

PubMed

Ligand-dependent control of gene expression is essential for gene functional analysis, target validation, protein production, and metabolic engineering. However, the expression tools currently available are difficult to transfer between species and exhibit limited mechanistic diversity. Here we demonstrate how the modular architecture of purine riboswitches can be exploited to develop orthogonal and chimeric switches that are transferable across diverse bacterial species, modulating either transcription or translation, to provide tunable activation or repression of target gene expression, in response to synthetic non-natural effector molecules. Our novel riboswitch-ligand pairings are shown to regulate physiologically important genes required for bacterial motility in Escherichia coli and cell morphology in Bacillus subtilis. These findings are relevant for future gene function studies and antimicrobial target validation, while providing new modular and orthogonal regulatory components for deployment in synthetic biology regimes. PMID:24971878

Robinson, Christopher J; Vincent, Helen A; Wu, Ming-Cheng; Lowe, Phillip T; Dunstan, Mark S; Leys, David; Micklefield, Jason

2014-07-30

49

Lateral organ boundaries 1 is a disease susceptibility gene for citrus bacterial canker disease  

PubMed Central

Citrus bacterial canker (CBC) disease occurs worldwide and incurs considerable costs both from control measures and yield losses. Bacteria that cause CBC require one of six known type III transcription activator-like (TAL) effector genes for the characteristic pustule formation at the site of infection. Here, we show that Xanthomonas citri subspecies citri strain Xcc306, with the type III TAL effector gene pthA4 or with the distinct yet biologically equivalent gene pthAw from strain XccAw, induces two host genes, CsLOB1 and CsSWEET1, in a TAL effector-dependent manner. CsLOB1 is a member of the Lateral Organ Boundaries (LOB) gene family of transcription factors, and CsSWEET1 is a homolog of the SWEET sugar transporter and rice disease susceptibility gene. Both TAL effectors drive expression of CsLOB1 and CsSWEET1 promoter reporter gene fusions when coexpressed in citrus or Nicotiana benthamiana. Artificially designed TAL effectors directed to sequences in the CsLOB1 promoter region, but not the CsSWEET1 promoter, promoted pustule formation and higher bacterial leaf populations. Three additional distinct TAL effector genes, pthA*, pthB, and pthC, also direct pustule formation and expression of CsLOB1. Unlike pthA4 and pthAw, pthB and pthC do not promote the expression of CsSWEET1. CsLOB1 expression was associated with the expression of genes associated with cell expansion. The results indicate that CBC-inciting species of Xanthomonas exploit a single host disease susceptibility gene by altering the expression of an otherwise developmentally regulated gene using any one of a diverse set of TAL effector genes in the pathogen populations.

Hu, Yang; Zhang, Junli; Jia, Hongge; Sosso, Davide; Li, Ting; Frommer, Wolf B.; Yang, Bing; White, Frank F.; Wang, Nian; Jones, Jeffrey B.

2014-01-01

50

Environmental and anthropogenic controls over bacterial communities in wetland soils  

PubMed Central

Soil bacteria regulate wetland biogeochemical processes, yet little is known about controls over their distribution and abundance. Bacteria in North Carolina swamps and bogs differ greatly from Florida Everglades fens, where communities studied were unexpectedly similar along a nutrient enrichment gradient. Bacterial composition and diversity corresponded strongly with soil pH, land use, and restoration status, but less to nutrient concentrations, and not with wetland type or soil carbon. Surprisingly, wetland restoration decreased bacterial diversity, a response opposite to that in terrestrial ecosystems. Community level patterns were underlain by responses of a few taxa, especially the Acidobacteria and Proteobacteria, suggesting promise for bacterial indicators of restoration and trophic status.

Hartman, Wyatt H.; Richardson, Curtis J.; Vilgalys, Rytas; Bruland, Gregory L.

2008-01-01

51

Environmental and anthropogenic controls over bacterial communities in wetland soils.  

PubMed

Soil bacteria regulate wetland biogeochemical processes, yet little is known about controls over their distribution and abundance. Bacteria in North Carolina swamps and bogs differ greatly from Florida Everglades fens, where communities studied were unexpectedly similar along a nutrient enrichment gradient. Bacterial composition and diversity corresponded strongly with soil pH, land use, and restoration status, but less to nutrient concentrations, and not with wetland type or soil carbon. Surprisingly, wetland restoration decreased bacterial diversity, a response opposite to that in terrestrial ecosystems. Community level patterns were underlain by responses of a few taxa, especially the Acidobacteria and Proteobacteria, suggesting promise for bacterial indicators of restoration and trophic status. PMID:19004771

Hartman, Wyatt H; Richardson, Curtis J; Vilgalys, Rytas; Bruland, Gregory L

2008-11-18

52

[Expression of the starfish complement component C3 gene homologue under the influence of bacterial lipopolysaccharide].  

PubMed

The fragment of a homologue of complement component C3 gene has been cloned and sequenced from the starfish, Asterias rubens. Phylogenetic analysis of ArC3-like gene demonstrates that ArC3-like gene has close similarity to C3 gene homologues of Deuterostomia invertebrate animals. High level of ArC3-like gene expression was identified in circulating cells (coelomocytes), in a gut's derivate (hepatopancreas) and in male gonada but not in stomach, female gonad and rectal gland of A. rubens starfish. ArC3-like gene expression was shown in all types of starfish coelomocytes: in lymphocyte-like cells, granular and nongranular amebocytes. Injection of bacterial lipopolysaccharide (LPS) solution into the coelomic cavity of starfish leads to the increase of ArC3-like gene expression in coelomocytes and hepatopancreas over the control level of sterile sea water injection. The level of ArC3-like gene expression increased in response to LPS reaching the maximum 6 h after the stimulation, and decreased to basal level 24 h after the stimulation. Injection of LPS solution stimulated the increase of ArC3-like gene expression level in hepatopancreas reaching the maximum 6-12 h after the stimulation, and the level of mRNA of ArC3-like gene had still been increased 48 h after LPS injection. The data demonstrates sustained positive regulation of ArC3-like gene expression under the influence of LPS. PMID:20198861

Mogilenko, D A; Kudriavtsev, I V; Orlov, S V; Kharazova, A D; Polevshchikov, A V

2010-01-01

53

Bacterial syntenies: an exact approach with gene quorum  

PubMed Central

Background The automatic identification of syntenies across multiple species is a key step in comparative genomics that helps biologists shed light both on evolutionary and functional problems. Results In this paper, we present a versatile tool to extract all syntenies from multiple bacterial species based on a clear-cut and very flexible definition of the synteny blocks that allows for gene quorum, partial gene correspondence, gaps, and a partial or total conservation of the gene order. Conclusions We apply this tool to two different kinds of studies. The first one is a search for functional gene associations. In this context, we compare our tool to a widely used heuristic - I-ADHORE - and show that at least up to ten genomes, the problem remains tractable with our exact definition and algorithm. The second application is linked to evolutionary studies: we verify in a multiple alignment setting that pairs of orthologs in synteny are more conserved than pairs outside, thus extending a previous pairwise study. We then show that this observation is in fact a function of the size of the synteny: the larger the block of synteny is, the more conserved the genes are.

2011-01-01

54

MLST revisited: the gene-by-gene approach to bacterial genomics  

PubMed Central

Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria ‘from domain to strain’. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.

Maiden, Martin C. J.; Jansen van Rensburg, Melissa J.; Bray, James E.; Earle, Sarah G.; Ford, Suzanne A.; Jolley, Keith A.; McCarthy, Noel D.

2014-01-01

55

Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments.  

PubMed

In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal patterns in burrow sediments in comparison with surface sediments, suggesting that the burrow provides a unique environment where bacterial gene abundances are influenced directly by macrofaunal activity. In contrast, the abundances of archaeal ammonia oxidizers varied temporally but were not affected by bioturbation, indicating differential responses between bacterial and archaeal ammonia oxidizers to environmental physicochemical controls. This study highlights the importance of bioturbation as a control over the temporal variation in nitrogen-cycling microbial community dynamics within coastal sediments. PMID:24596269

Laverock, B; Tait, K; Gilbert, J A; Osborn, A M; Widdicombe, S

2014-02-01

56

Growth-rate dependent effects on bacterial gene expression  

NASA Astrophysics Data System (ADS)

For fast growing bacteria, which can adapt to wildly different growth conditions, changes in gene expression are often accompanied by changes in growth rates. Because the macroscopic composition of bacteria (e.g., cell size, ribosome concentration, gene copy number) is known to vary greatly for bacteria grown at different rates, significant changes in gene expression may arise 'passively' just due to the growth rate change alone. Towards a quantitative understanding of these passive effects, we analyzed quantitatively available data for the growth rate dependence of various macroscopic parameters affecting gene expression in E. coli, and predicted the growth-rate dependence of gene expression for various simple genetic circuits. For a constitutively expressed gene, the expressed protein concentration is decreased at faster growth, while weak growth-rate dependence is obtained for autorepressing genes and genes under negative control by an autorepressor. We also studied the growth-rate dependence of bistable genetic circuits and determined conditions such that bistability is found over a wide range of growth rates. Our results demonstrate that growth-rate dependent effects play an important role and must be taken into account when analyzing gene expression data under different condition. Buffering against these growth rate dependent effects may be an important requirement underlying the robust operation of endogenous genetic circuits in these bacteria, and should be a prime factor to consider in the design of robust, synthetic circuits.

Klumpp, Stefan

2009-03-01

57

Expression of Xa1, a Bacterial Blight-Resistance Gene in Rice, is Induced by Bacterial Inoculation  

Microsoft Academic Search

The Xa1 gene in rice confers resistance to Japanese race 1 of Xanthomonas oryzae pv. oryzae, the causal pathogen of bacterial blight (BB). We isolated the Xa1 gene by a map-based cloning strategy. The deduced amino acid sequence of the Xa1 gene product contains nucleotide binding sites (NBS) and a new type of leucine-rich repeats (LRR); thus, Xa1 is a

Satomi Yoshimura; Utako Yamanouchi; Yuichi Katayose; Seiichi Toki; Zi-Xuan Wang; Izumi Kono; Nori Kurata; Masahiro Yano; Nobuo Iwata; Takuji Sasaki

1998-01-01

58

Distance Matters: The Impact of Gene Proximity in Bacterial Gene Regulation  

NASA Astrophysics Data System (ADS)

Following recent discoveries of colocalization of downstream-regulating genes in living cells, the impact of the spatial distance between such genes on the kinetics of gene product formation is increasingly recognized. We here show from analytical and numerical analysis that the distance between a transcription factor (TF) gene and its target gene drastically affects the speed and reliability of transcriptional regulation in bacterial cells. For an explicit model system, we develop a general theory for the interactions between a TF and a transcription unit. The observed variations in regulation efficiency are linked to the magnitude of the variation of the TF concentration peaks as a function of the binding site distance from the signal source. Our results support the role of rapid binding site search for gene colocalization and emphasize the role of local concentration differences.

Pulkkinen, Otto; Metzler, Ralf

2013-05-01

59

A versatile element for gene addition in bacterial chromosomes  

PubMed Central

The increasing interest in genetic manipulation of bacterial host metabolic pathways for protein or small molecule production has led to a need to add new genes to a chromosome quickly and easily without leaving behind a selectable marker. The present report describes a vector and four-day procedure that enable site-specific chromosomal insertion of cloned genes in a context insulated from external transcription, usable once in a construction series. The use of rhamnose-inducible transcription from rhaBp allows regulation of the inserted genes independently of the commonly used IPTG and arabinose strategies. Using lacZ as a reporter, we first show that expression from the rhamnose promoter is tightly regulatable, exhibiting very low leakage of background expression compared with background, and moderate rhamnose-induced expression compared with IPTG-induced expression from lacp. Second, the expression of a DNA methyltransferase was used to show that rhamnose regulation yielded on-off expression of this enzyme, such that a resident high-copy plasmid was either fully sensitive or fully resistant to isoschizomer restriction enzyme cleavage. In both cases, growth medium manipulation allows intermediate levels of expression. The vehicle can also be adapted as an ORF-cloning vector.

Sibley, Marion H.; Raleigh, Elisabeth A.

2012-01-01

60

Detecting rare gene transfer events in bacterial populations.  

PubMed

Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research. PMID:24432015

Nielsen, Kaare M; Bøhn, Thomas; Townsend, Jeffrey P

2014-01-01

61

Genes but Not Genomes Reveal Bacterial Domestication of Lactococcus Lactis  

PubMed Central

Background The population structure and diversity of Lactococcus lactis subsp. lactis, a major industrial bacterium involved in milk fermentation, was determined at both gene and genome level. Seventy-six lactococcal isolates of various origins were studied by different genotyping methods and thirty-six strains displaying unique macrorestriction fingerprints were analyzed by a new multilocus sequence typing (MLST) scheme. This gene-based analysis was compared to genomic characteristics determined by pulsed-field gel electrophoresis (PFGE). Methodology/Principal Findings The MLST analysis revealed that L. lactis subsp. lactis is essentially clonal with infrequent intra- and intergenic recombination; also, despite its taxonomical classification as a subspecies, it displays a genetic diversity as substantial as that within several other bacterial species. Genome-based analysis revealed a genome size variability of 20%, a value typical of bacteria inhabiting different ecological niches, and that suggests a large pan-genome for this subspecies. However, the genomic characteristics (macrorestriction pattern, genome or chromosome size, plasmid content) did not correlate to the MLST-based phylogeny, with strains from the same sequence type (ST) differing by up to 230 kb in genome size. Conclusion/Significance The gene-based phylogeny was not fully consistent with the traditional classification into dairy and non-dairy strains but supported a new classification based on ecological separation between “environmental” strains, the main contributors to the genetic diversity within the subspecies, and “domesticated” strains, subject to recent genetic bottlenecks. Comparison between gene- and genome-based analyses revealed little relationship between core and dispensable genome phylogenies, indicating that clonal diversification and phenotypic variability of the “domesticated” strains essentially arose through substantial genomic flux within the dispensable genome.

Passerini, Delphine; Beltramo, Charlotte; Coddeville, Michele; Quentin, Yves; Ritzenthaler, Paul

2010-01-01

62

Bacterial parasite shows potential in disease control  

NSDL National Science Digital Library

This online article reports that researchers have sequenced the complete genome of one strain of Wolbachia pipientis and are gaining new insight into the biology and evolution of Wolbachia-host interactions. It discusses practical applications such as disease and pest control.

Bram, Lon; Scientist, Australian L.

63

Bacterial Bioluminescence: Its Control and Ecological Significance  

NSDL National Science Digital Library

This Microbiological Reviews scholarly article (23-page PDF) presents an overview of data relevant to the ecology of bioluminescent bacteria and the functional importance of light emission. The review article discusses the biochemistry of bioluminescence, taxonomic relationships of luminous bacteria, control of the synthesis and activity of the luminescent system, habitats and distribution of luminous bacteria, functions of bioluminescence, and new perspectives. These perspectives and other specific postulates presented in the article provide new approaches for data collection and experimental work.

Hastings, J. Woodland (John Woodland), 1927-; Nealson, Kenneth H.

2010-03-24

64

NMR Structure of Bacterial Ribosomal Protein L20: Implications for Ribosome Assembly and Translational Control  

Microsoft Academic Search

L20 is a specific protein of the bacterial ribosome, which is involved in the early assembly steps of the 50S subunit and in the feedback control of the expression of its own gene. This dual function involves specific interactions with either the 23S rRNA or its messenger RNA. The solution structure of the free Aquifex aeolicus L20 has been solved.

Sophie Raibaud; Isabelle Lebars; Maude Guillier; Claude Chiaruttini; François Bontems; Alexey Rak; Maria Garber; Frédéric Allemand; Mathias Springer; Frédéric Dardel

2002-01-01

65

Bacterial ?2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?  

PubMed Central

Background Invasive bacteria are known to have captured and adapted eukaryotic host genes. They also readily acquire colonizing genes from other bacteria by horizontal gene transfer. Closely related species such as Helicobacter pylori and Helicobacter hepaticus, which exploit different host tissues, share almost none of their colonization genes. The protease inhibitor ?2-macroglobulin provides a major metazoan defense against invasive bacteria, trapping attacking proteases required by parasites for successful invasion. Results Database searches with metazoan ?2-macroglobulin sequences revealed homologous sequences in bacterial proteomes. The bacterial ?2-macroglobulin phylogenetic distribution is patchy and violates the vertical descent model. Bacterial ?2-macroglobulin genes are found in diverse clades, including purple bacteria (proteobacteria), fusobacteria, spirochetes, bacteroidetes, deinococcids, cyanobacteria, planctomycetes and thermotogae. Most bacterial species with bacterial ?2-macroglobulin genes exploit higher eukaryotes (multicellular plants and animals) as hosts. Both pathogenically invasive and saprophytically colonizing species possess bacterial ?2-macroglobulins, indicating that bacterial ?2-macroglobulin is a colonization rather than a virulence factor. Conclusions Metazoan ?2-macroglobulins inhibit proteases of pathogens. The bacterial homologs may function in reverse to block host antimicrobial defenses. ?2-macroglobulin was probably acquired one or more times from metazoan hosts and has then spread widely through other colonizing bacterial species by more than 10 independent horizontal gene transfers. yfhM-like bacterial ?2-macroglobulin genes are often found tightly linked with pbpC, encoding an atypical peptidoglycan transglycosylase, PBP1C, that does not function in vegetative peptidoglycan synthesis. We suggest that YfhM and PBP1C are coupled together as a periplasmic defense and repair system. Bacterial ?2-macroglobulins might provide useful targets for enhancing vaccine efficacy in combating infections.

Budd, Aidan; Blandin, Stephanie; Levashina, Elena A; Gibson, Toby J

2004-01-01

66

Synthetic Riboswitches That Induce Gene Expression in Diverse Bacterial Species? †  

PubMed Central

We developed a series of ligand-inducible riboswitches that control gene expression in diverse species of Gram-negative and Gram-positive bacteria, including human pathogens that have few or no previously reported inducible expression systems. We anticipate that these riboswitches will be useful tools for genetic studies in a wide range of bacteria.

Topp, Shana; Reynoso, Colleen M. K.; Seeliger, Jessica C.; Goldlust, Ian S.; Desai, Shawn K.; Murat, Dorothee; Shen, Aimee; Puri, Aaron W.; Komeili, Arash; Bertozzi, Carolyn R.; Scott, June R.; Gallivan, Justin P.

2010-01-01

67

[Quorum sensing of genes expression--perspective drug target against bacterial pathogenicity].  

PubMed

Bacteria are capable to sense an increase of cell density population and to reply quickly and coordinately by the induction of special sets of genes. This type of the regulation was named Quorum Sensing (QS); it is based on the effect of low-molecular-weight signaling molecules of different nature (autoinducers) which accumulate in the culture at high density of bacterial population and interact with receptor regulatory proteins. QS systems are the global regulators of bacterial genes expression and play a key role in the control of many metabolic processes in cell including the regulation of virulence of bacteria. Here we review the molecular mechanisms of QS systems functioning in bacteria belonging to different taxonomic groups and discuss the potential of QS regulation as a new drug target for the treatment of bacterial infections. At present this approach is accounted as a new alternative strategy of antimicrobial therapy directed on the development of drugs inhibiting QS regulation and active just against pathogenicity of bacteria (antipathogenic drugs). Such a strategy allows to avoid a wide dissemination of resistant forms of pathogenic bacteria and the formation of biofilms increasing in many times the resistance of bacteria to drug preparations. PMID:16637260

Khmel', I A; Metlitskaia, A Z

2006-01-01

68

Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation  

PubMed Central

Background Ongoing technological advances in genome sequencing are allowing bacterial genomes to be sequenced at ever-lower cost. However, nearly all of these new techniques concomitantly decrease genome quality, primarily due to the inability of their relatively short read lengths to bridge certain genomic regions, e.g., those containing repeats. Fragmentation of predicted open reading frames (ORFs) is one possible consequence of this decreased quality. In this study we quantify ORF fragmentation in draft microbial genomes and its effect on annotation efficacy, and we propose a solution to ameliorate this problem. Results A survey of draft-quality genomes in GenBank revealed that fragmented ORFs comprised > 80% of the predicted ORFs in some genomes, and that increased fragmentation correlated with decreased genome assembly quality. In a more thorough analysis of 25 Streptomyces genomes, fragmentation was especially enriched in some protein classes with repeating, multi-modular structures such as polyketide synthases, non-ribosomal peptide synthetases and serine/threonine kinases. Overall, increased genome fragmentation correlated with increased false-negative Pfam and COG annotation rates and increased false-positive KEGG annotation rates. The false-positive KEGG annotation rate could be ameliorated by linking fragmented ORFs using their orthologs in related genomes. Whereas this strategy successfully linked up to 46% of the total ORF fragments in some genomes, its sensitivity appeared to depend heavily on the depth of sampling of a particular taxon's variable genome. Conclusions Draft microbial genomes contain many ORF fragments. Where these correspond to the same gene they have particular potential to confound comparative gene content analyses. Given our findings, and the rapid increase in the number of microbial draft quality genomes, we suggest that accounting for gene fragmentation and its associated biases is important when designing comparative genomic projects.

2012-01-01

69

Uncovering rate variation of lateral gene transfer during bacterial genome evolution  

Microsoft Academic Search

BACKGROUND: Large scale genome arrangement, such as whole gene insertion\\/deletion, plays an important role in bacterial genome evolution. Various methods have been employed to study the dynamic process of gene insertions and deletions, such as parsimony methods and maximum likelihood methods. Previous maximum likelihood studies have assumed that the rate of gene insertions\\/deletions is constant over different genes. This assumption

Weilong Hao; G. Brian Golding

2008-01-01

70

Sensory components controlling bacterial nitrogen assimilation.  

PubMed

In enteric bacteria, the transcription of the Ntr regulon is regulated by a signal transduction system that measures and transmits information on the nitrogen status of the cell. Four of the components of this signal transduction apparatus have been previously identified, and the roles of these are known, to a first approximation, from studies with purified components. The sensor is a uridylyltransferase/uridylyl-removing enzyme (UTase/UR) that controls the uridylylation state of the PII protein. PII indirectly regulates the transcription of the Ntr regulon by acting through the kinase/phosphatase protein NRII. In the absence of unmodified PII, NRII autophosphorylates on a histidine residue, and these phosphoryl groups are transferred to the transcription factor NRI, resulting in the conversion of NRI to the form able to activate transcription. In the presence of PII and NRII, NRI approximately P is rapidly dephosphorylated, preventing the activation of Ntr transcription. This PII-dependent dephosphorylation of NRI approximately P is referred to as the regulated phosphatase activity. In this report, we describe improved methods for the purification of the UTase/UR and PII, and the crystallization of PII. We also present improved methods for the assay of the activities of the UTase/UR protein and PII. The results of our assays indicate that purified PII is effective in eliciting the regulated phosphatase activity, but does not affect the autophosphorylation of NRII or affect the transfer of phosphoryl groups from NRII approximately P to NRI. In addition, we demonstrate that the elicitation of the regulated phosphatase activity by PII is strongly dependent on the ratio of NRI approximately P to NRI, and that the isolated N-terminal domain of NRI, once phosphorylated, is dephosphorylated by the regulated phosphatase activity. PMID:7874194

Kamberov, E S; Atkinson, M R; Feng, J; Chandran, P; Ninfa, A J

1994-01-01

71

Increased production of cadaverine and anabasine in hairy root cultures of Nicotiana tabacum expressing a bacterial lysine decarboxylase gene  

Microsoft Academic Search

Several hairy root cultures of Nicotiana tabacum varieties, carrying two direct repeats of a bacterial lysine decarboxylase (ldc) gene controlled by the cauliflower mosaic virus (CaMV) 35S promoter expressed LDC activity up to 1 pkat\\/mg protein. Such activity was, for example, sufficient to increase cadaverine levels of the best line SR3\\/1-K1,2 from ca. 50 µg (control cultures) to about 700

Lothar F. Fecker; Christiane Rtigenhagen; Jochen Berlin

1993-01-01

72

GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes  

Microsoft Academic Search

Background: An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing. GeneOrder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of

Srikanth Celamkoti; Sashidhara Kundeti; Anjan Purkayastha; Raja Mazumder; Charles Buck; Donald Seto

2004-01-01

73

Horizontal gene transfer of a bacterial insect toxin gene into the Epichloë fungal symbionts of grasses  

PubMed Central

Horizontal gene transfer is recognized as an important factor in genome evolution, particularly when the newly acquired gene confers a new capability to the recipient species. We identified a gene similar to the makes caterpillars floppy (mcf1 and mcf2) insect toxin genes in Photorhabdus, bacterial symbionts of nematodes, in the genomes of the Epichloë fungi, which are intercellular symbionts of grasses. Infection by Epichloë spp. often confers insect resistance to the grass hosts, largely due to the production of fungal alkaloids. A mcf-like gene is present in all of the Epichloë genome sequences currently available but in no other fungal genomes. This suggests the Epichloë genes were derived from a single lineage-specific HGT event. Molecular dating was used to estimate the time of the HGT event at between 7.2 and 58.8 million years ago. The mcf-like coding sequence from Epichloë typhina subsp. poae was cloned and expressed in Escherichia coli. E. coli cells expressing the Mcf protein were toxic to black cutworms (Agrotis ipsilon), whereas E. coli cells containing the vector only were non-toxic. These results suggest that the Epichloë mcf-like genes may be a component, in addition to the fungal alkaloids, of the insect resistance observed in Epichloë-infected grasses.

Ambrose, Karen V.; Koppenhofer, Albrecht M.; Belanger, Faith C.

2014-01-01

74

Horizontal gene transfer of a bacterial insect toxin gene into the Epichloë fungal symbionts of grasses.  

PubMed

Horizontal gene transfer is recognized as an important factor in genome evolution, particularly when the newly acquired gene confers a new capability to the recipient species. We identified a gene similar to the makes caterpillars floppy (mcf1 and mcf2) insect toxin genes in Photorhabdus, bacterial symbionts of nematodes, in the genomes of the Epichloë fungi, which are intercellular symbionts of grasses. Infection by Epichloë spp. often confers insect resistance to the grass hosts, largely due to the production of fungal alkaloids. A mcf-like gene is present in all of the Epichloë genome sequences currently available but in no other fungal genomes. This suggests the Epichloë genes were derived from a single lineage-specific HGT event. Molecular dating was used to estimate the time of the HGT event at between 7.2 and 58.8 million years ago. The mcf-like coding sequence from Epichloë typhina subsp. poae was cloned and expressed in Escherichia coli. E. coli cells expressing the Mcf protein were toxic to black cutworms (Agrotis ipsilon), whereas E. coli cells containing the vector only were non-toxic. These results suggest that the Epichloë mcf-like genes may be a component, in addition to the fungal alkaloids, of the insect resistance observed in Epichloë-infected grasses. PMID:24990771

Ambrose, Karen V; Koppenhöfer, Albrecht M; Belanger, Faith C

2014-01-01

75

Detection of type III secretion genes as a general indicator of bacterial virulence  

Microsoft Academic Search

Type III secretion systems of Gram-negative bacteria are specific export machineries for virulence factors which allow their translocation to eukaryotic cells. Since they correlate with bacterial pathogenicity, their presence is used as a general indicator of bacterial virulence. By comparing the genetic relationship of the major type III secretion systems we found the family of genes encoding the inner-membrane channel

Katja Stuber; Joachim Frey; André P Burnens; Peter Kuhnert

2003-01-01

76

Marker Assisted Selection of Bacterial Blight Resistance Genes in Rice  

Microsoft Academic Search

Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae is one of the most important diseases affecting rice production in Asia. We were interested in surveying rice genotypes that are popularly used in the Indian breeding program for conferring resistance to bacterial blight, using 11 STMS and 6 STS markers. The basis of selection of these DNA markers was their

A. P. Davierwala; A. P. K. Reddy; M. D. Lagu; P. K. Ranjekar; V. S. Gupta

2001-01-01

77

Peripheral blood RNA gene expression profiling in patients with bacterial meningitis  

PubMed Central

Objectives: The aim of present study was to find genetic pathways activated during infection with bacterial meningitis (BM) and potentially influencing the course of the infection using genome-wide RNA expression profiling combined with pathway analysis and functional annotation of the differential transcription. Methods: We analyzed 21 patients with BM hospitalized in 2008. The control group consisted of 18 healthy subjects. The RNA was extracted from whole blood, globin mRNA was depleted and gene expression profiling was performed using GeneChip Human Gene 1.0 ST Arrays which can assess the transcription of 28,869 genes. Gene expression profile data were analyzed using Bioconductor packages and Bayesian modeling. Functional annotation of the enriched gene sets was used to define the altered genetic networks. We also analyzed whether gene expression profiles depend on the clinical course and outcome. In order to verify the microarray results, the expression levels of ten functionally relevant genes with high statistical significance (CD177, IL1R2, IL18R1, IL18RAP, OLFM4, TLR5, CPA3, FCER1A, IL5RA, and IL7R) were confirmed by quantitative real-time (qRT) PCR. Results: There were 8569 genes displaying differential expression at a significance level of p < 0.05. Following False Discovery Rate (FDR) correction, a total of 5500 genes remained significant at a p-value of < 0.01. Quantitative RT-PCR confirmed the differential expression in 10 selected genes. Functional annotation and network analysis indicated that most of the genes were related to activation of humoral and cellular immune responses (enrichment score 43). Those changes were found in both adults and in children with BM compared to the healthy controls. The gene expression profiles did not significantly depend on the clinical outcome, but there was a strong influence of the specific type of pathogen underlying BM. Conclusion: This study demonstrates that there is a very strong activation of immune response at the transcriptional level during BM and that the type of pathogen influences this transcriptional activation.

Lill, Margit; Koks, Sulev; Soomets, Ursel; Schalkwyk, Leonard C.; Fernandes, Cathy; Lutsar, Irja; Taba, Pille

2013-01-01

78

Evolution of transcription regulatory genes is linked to niche specialization in the bacterial pathogen Streptococcus pyogenes.  

PubMed

Streptococcus pyogenes is a highly prevalent bacterial pathogen, most often giving rise to superficial infections at the throat or skin of its human host. Three genotype-defined subpopulations of strains exhibiting strong tropisms for either the throat or skin (specialists) or having no obvious tissue site preference (generalists) are recognized. Since the microenvironments at the throat and skin are distinct, the signal transduction pathways leading to the control of gene expression may also differ for throat versus skin strains of S. pyogenes. Two loci (mga and rofA/nra) encoding global regulators of virulence gene expression are positioned 300 kb apart on the genome; each contains alleles forming two major sequence clusters of approximately 25 to 30% divergence that are under balancing selection. Strong linkage disequilibrium is observed between sequence clusters of the transcription regulatory loci and the subpopulations of throat and skin specialists, against a background of high recombination rates among housekeeping genes. A taxonomically distinct commensal species (Streptococcus dysgalactiae subspecies equisimilus) shares highly homologous rof alleles. The findings provide strong support for a mechanism underlying niche specialization that involves orthologous replacement of regulatory genes following interspecies horizontal transfer, although the directionality of gene exchange remains unknown. PMID:15937178

Bessen, Debra E; Manoharan, Anand; Luo, Feng; Wertz, John E; Robinson, D Ashley

2005-06-01

79

Emerging frontiers in detection and control of bacterial biofilms.  

PubMed

Bacteria form surface-attached biofilm communities in nature. In contrast to free-living cells, bacterial cells within biofilms resist sanitizers and antimicrobials. While building biofilms, cells physiologically adapt to sustain the otherwise lethal impacts of a variety of environmental stress conditions. In this development, the production and embedding of cells in extracellular polymeric substances plays a key role. Biofilm bacteria can cause a range of problems to food processing including reduced heat-cold transfer, clogging water pipelines, food spoilage and they may cause infections among consumers. Recent biofilm investigations with the aim of potential control approaches include a combination of bacterial genetics, systems biology, materials and mechanic engineering and chemical biology. PMID:24679251

Tan, Seth Yang-En; Chew, Su Chuen; Tan, Sean Yang-Yi; Givskov, Michael; Yang, Liang

2014-04-01

80

Bacterial Blight of Soybean: Regulation of a Pathogen Gene Determining Host Cultivar Specificity  

Microsoft Academic Search

Soybean cultivars resistant to Pseudomonas syringae pathovar glycinea (Psg), the causal agent of bacterial blight, exhibit a hypersensitive (necrosis) reaction (HR) to infection. Psg strains carrying the avrB gene elicit the HR in soybean cultivars carrying the resistance gene Rpg1. Psg expressing avrB at a high level and capable of eliciting the HR in the absence of de novo bacterial

Thanh V. Huynh; Douglas Dahlbeck; Brian J. Staskawicz

1989-01-01

81

Genes for all metals—a bacterial view of the Periodic Table  

Microsoft Academic Search

  Bacterial chromosomes have genes for transport proteins for inorganic nutrient cations and oxyanions, such as NH4\\u000a +, K+, Mg2+, Co2+, Fe3+, Mn2+, Zn2+ and other trace cations, PO4\\u000a 3-, SO4\\u000a 2- and less abundant oxyanions. Together these account for perhaps a few hundred genes in many bacteria. Bacterial plasmids\\u000a encode resistance systems for toxic metal and metalloid ions including Ag+

S Silver

1998-01-01

82

Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR  

Microsoft Academic Search

DNA marker-assisted selection was used to pyramid four bacterial blight resistance genes, Xa-4, xa-5, xa-13 and Xa-21. Breeding lines with two, three and four resistance genes were developed and tested for resistance to the bacterial blight\\u000a pathogen (Xanthomonas oryzae pv. oryzae). The pyramid lines showed a wider spectrum and a higher level of resistance than lines with only a single

N. Huang; E. R. Angeles; J. Domingo; G. Magpantay; S. Singh; G. Zhang; N. Kumaravadivel; J. Bennett; G. S. Khush

1997-01-01

83

Bacterial Genes in the Aphid Genome: Absence of Functional Gene Transfer from Buchnera to Its Host  

PubMed Central

Genome reduction is typical of obligate symbionts. In cellular organelles, this reduction partly reflects transfer of ancestral bacterial genes to the host genome, but little is known about gene transfer in other obligate symbioses. Aphids harbor anciently acquired obligate mutualists, Buchnera aphidicola (Gammaproteobacteria), which have highly reduced genomes (420–650 kb), raising the possibility of gene transfer from ancestral Buchnera to the aphid genome. In addition, aphids often harbor other bacteria that also are potential sources of transferred genes. Previous limited sampling of genes expressed in bacteriocytes, the specialized cells that harbor Buchnera, revealed that aphids acquired at least two genes from bacteria. The newly sequenced genome of the pea aphid, Acyrthosiphon pisum, presents the first opportunity for a complete inventory of genes transferred from bacteria to the host genome in the context of an ancient obligate symbiosis. Computational screening of the entire A. pisum genome, followed by phylogenetic and experimental analyses, provided strong support for the transfer of 12 genes or gene fragments from bacteria to the aphid genome: three LD–carboxypeptidases (LdcA1, LdcA2,?LdcA), five rare lipoprotein As (RlpA1-5), N-acetylmuramoyl-L-alanine amidase (AmiD), 1,4-beta-N-acetylmuramidase (bLys), DNA polymerase III alpha chain (?DnaE), and ATP synthase delta chain (?AtpH). Buchnera was the apparent source of two highly truncated pseudogenes (?DnaE and ?AtpH). Most other transferred genes were closely related to genes from relatives of Wolbachia (Alphaproteobacteria). At least eight of the transferred genes (LdcA1, AmiD, RlpA1-5, bLys) appear to be functional, and expression of seven (LdcA1, AmiD, RlpA1-5) are highly upregulated in bacteriocytes. The LdcAs and RlpAs appear to have been duplicated after transfer. Our results excluded the hypothesis that genome reduction in Buchnera has been accompanied by gene transfer to the host nuclear genome, but suggest that aphids utilize a set of duplicated genes acquired from other bacteria in the context of the Buchnera–aphid mutualism.

Nikoh, Naruo; McCutcheon, John P.; Kudo, Toshiaki; Miyagishima, Shin-ya; Moran, Nancy A.; Nakabachi, Atsushi

2010-01-01

84

Absence of Spiroplasma or Other Bacterial 16S rRNA Genes in Brain Tissue of Hamsters with Scrapie  

PubMed Central

Spiroplasma spp. have been proposed to be the etiological agents of the transmissible spongiform encephalopathies (TSEs). In a blind study, a panel of 20 DNA samples was prepared from the brains of uninfected hamsters or hamsters infected with the 263K strain of scrapie. The brains of the infected hamsters contained ?1010 infectious doses/g. The coded panel was searched for bacterial 16S rRNA gene sequences, using primers selective for spiroplasma sequences, primers selective for mollicutes in general, and universal bacterial primers. After 35 PCR cycles, no samples were positive for spiroplasma or any other bacterial DNA, while control Spiroplasma mirum genomic DNA, spiked at 1% of the concentration required to account for the scrapie infectivity present, was readily detected. After 70 PCR cycles, nearly all samples yielded amplified products which were homologous to various bacterial 16S rRNA gene sequences, including those of frequent environmental contaminants. These sequences were seen in uninfected as well as infected samples. Because the concentration of scrapie infectivity was at a known high level, it is very unlikely that a bacterial infection at the same concentration could have escaped detection. We conclude that the infectious agent responsible for TSE disease cannot be a spiroplasma or any other eubacterial species.

Alexeeva, Irina; Elliott, Ellen J.; Rollins, Sandra; Gasparich, Gail E.; Lazar, Jozef; Rohwer, Robert G.

2006-01-01

85

Absence of Spiroplasma or other bacterial 16s rRNA genes in brain tissue of hamsters with scrapie.  

PubMed

Spiroplasma spp. have been proposed to be the etiological agents of the transmissible spongiform encephalopathies (TSEs). In a blind study, a panel of 20 DNA samples was prepared from the brains of uninfected hamsters or hamsters infected with the 263K strain of scrapie. The brains of the infected hamsters contained > or =10(10) infectious doses/g. The coded panel was searched for bacterial 16S rRNA gene sequences, using primers selective for spiroplasma sequences, primers selective for mollicutes in general, and universal bacterial primers. After 35 PCR cycles, no samples were positive for spiroplasma or any other bacterial DNA, while control Spiroplasma mirum genomic DNA, spiked at 1% of the concentration required to account for the scrapie infectivity present, was readily detected. After 70 PCR cycles, nearly all samples yielded amplified products which were homologous to various bacterial 16S rRNA gene sequences, including those of frequent environmental contaminants. These sequences were seen in uninfected as well as infected samples. Because the concentration of scrapie infectivity was at a known high level, it is very unlikely that a bacterial infection at the same concentration could have escaped detection. We conclude that the infectious agent responsible for TSE disease cannot be a spiroplasma or any other eubacterial species. PMID:16390954

Alexeeva, Irina; Elliott, Ellen J; Rollins, Sandra; Gasparich, Gail E; Lazar, Jozef; Rohwer, Robert G

2006-01-01

86

Autonomous Bioluminescent Expression of the Bacterial Luciferase Gene Cassette (lux) in a Mammalian Cell Line  

PubMed Central

Background The bacterial luciferase (lux) gene cassette consists of five genes (luxCDABE) whose protein products synergistically generate bioluminescent light signals exclusive of supplementary substrate additions or exogenous manipulations. Historically expressible only in prokaryotes, the lux operon was re-synthesized through a process of multi-bicistronic, codon-optimization to demonstrate for the first time self-directed bioluminescence emission in a mammalian HEK293 cell line in vitro and in vivo. Methodology/Principal Findings Autonomous in vitro light production was shown to be 12-fold greater than the observable background associated with untransfected control cells. The availability of reduced riboflavin phosphate (FMNH2) was identified as the limiting bioluminescence substrate in the mammalian cell environment even after the addition of a constitutively expressed flavin reductase gene (frp) from Vibrio harveyi. FMNH2 supplementation led to a 151-fold increase in bioluminescence in cells expressing mammalian codon-optimized luxCDE and frp genes. When injected subcutaneously into nude mice, in vivo optical imaging permitted near instantaneous light detection that persisted independently for the 60 min length of the assay with negligible background. Conclusions/Significance The speed, longevity, and self-sufficiency of lux expression in the mammalian cellular environment provides a viable and powerful alternative for real-time target visualization not currently offered by existing bioluminescent and fluorescent imaging technologies.

Close, Dan M.; Patterson, Stacey S.; Ripp, Steven; Baek, Seung J.; Sanseverino, John; Sayler, Gary S.

2010-01-01

87

A dual switch controls bacterial enhancer-dependent transcription  

PubMed Central

Bacterial RNA polymerases (RNAPs) are targets for antibiotics. Myxopyronin binds to the RNAP switch regions to block structural rearrangements needed for formation of open promoter complexes. Bacterial RNAPs containing the major variant ?54 factor are activated by enhancer-binding proteins (bEBPs) and transcribe genes whose products are needed in pathogenicity and stress responses. We show that (i) enhancer-dependent RNAPs help Escherichia coli to survive in the presence of myxopyronin, (ii) enhancer-dependent RNAPs partially resist inhibition by myxopyronin and (iii) ATP hydrolysis catalysed by bEBPs is obligatory for functional interaction of the RNAP switch regions with the transcription start site. We demonstrate that enhancer-dependent promoters contain two barriers to full DNA opening, allowing tight regulation of transcription initiation. bEBPs engage in a dual switch to (i) allow propagation of nucleated DNA melting from an upstream DNA fork junction and (ii) complete the formation of the transcription bubble and downstream DNA fork junction at the RNA synthesis start site, resulting in switch region-dependent RNAP clamp closure and open promoter complex formation.

Wiesler, Simone C.; Burrows, Patricia C.; Buck, Martin

2012-01-01

88

A dual switch controls bacterial enhancer-dependent transcription.  

PubMed

Bacterial RNA polymerases (RNAPs) are targets for antibiotics. Myxopyronin binds to the RNAP switch regions to block structural rearrangements needed for formation of open promoter complexes. Bacterial RNAPs containing the major variant ?(54) factor are activated by enhancer-binding proteins (bEBPs) and transcribe genes whose products are needed in pathogenicity and stress responses. We show that (i) enhancer-dependent RNAPs help Escherichia coli to survive in the presence of myxopyronin, (ii) enhancer-dependent RNAPs partially resist inhibition by myxopyronin and (iii) ATP hydrolysis catalysed by bEBPs is obligatory for functional interaction of the RNAP switch regions with the transcription start site. We demonstrate that enhancer-dependent promoters contain two barriers to full DNA opening, allowing tight regulation of transcription initiation. bEBPs engage in a dual switch to (i) allow propagation of nucleated DNA melting from an upstream DNA fork junction and (ii) complete the formation of the transcription bubble and downstream DNA fork junction at the RNA synthesis start site, resulting in switch region-dependent RNAP clamp closure and open promoter complex formation. PMID:22965125

Wiesler, Simone C; Burrows, Patricia C; Buck, Martin

2012-11-01

89

Quantitative Analysis of Bacterial Gene Expression by Using the gusA Reporter Gene System  

PubMed Central

An Azospirillum brasilense Sp7 strain containing a plasmid-borne translational cytN-gusA fusion was grown in a continuous culture to quantitatively evaluate the influence of extracellular signals (such as O2) on expression of the cytNOQP operon. The dissolved oxygen concentration was shifted at regular time intervals before the steady state was reached. The measured ?-glucuronidase activity was used to monitor cytN gene expression. However, as the ?-glucuronidase activity in the experimental setup not only depended on altered transcription of the hybrid gene when the signal was varied but was also influenced by cellular accumulation, degradation, and dilution of the hybrid fusion protein, a mathematical method was developed to describe the intrinsic properties of the dynamic bioprocess. After identification and validation of the mathematical model, the apparent specific rate of expression of the fusion, which was independent of the experimental setup, could be deduced from the model and used to quantify gene expression regulated by extracellular environmental signals. In principle, this approach can be generalized to assess the effects of external signals on bacterial gene expression.

Sun, Jun; Smets, Ilse; Bernaerts, Kristel; Van Impe, Jan; Vanderleyden, Jos; Marchal, Kathleen

2001-01-01

90

A statistical feature of Hurst exponents of essential genes in bacterial genomes.  

PubMed

At present, methods for determining essential genes depend on biochemical experiments. There is therefore a demand for the development of analysis methods and software for identifying essential genes, based on the common features of these genes. In this study, we employed the Hurst exponent as a characteristic parameter and analyzed its distribution among nine bacterial species. We found that most of the significance levels of the Hurst exponents of essential genes were higher than those of the corresponding full-gene-set. Conversely, most of the significance levels of the Hurst exponents of nonessential genes remained unchanged or only increased slightly. Therefore, we propose that this feature represents a restraint for pre- or post-design checking of bacterial essential genes in computer-aided design. PMID:22108754

Liu, Xiao; Wang, Shi-Yuan; Wang, Jia

2012-01-01

91

Seasonal changes in nitrogen-cycle gene abundances and in bacterial communities in acidic forest soils.  

PubMed

The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change. PMID:22752898

Jung, Jaejoon; Yeom, Jinki; Han, Jiwon; Kim, Jisun; Park, Woojun

2012-06-01

92

Bacterial Systems for Tumor-Specific Gene Therapy  

Microsoft Academic Search

This chapter describes the power of genetically engineered bacteria in cancer therapy. In the applications we consider, the\\u000a bacteria are genetically engineered to carry a specific gene into tumors, and on this basis, it can be considered gene therapy.\\u000a However, if gene therapy is defined as the introduction of a gene, or part of a gene, into the cancer cells

J. Martin Brown; Shie-Chau Liu; Jan Theys; Philippe Lambin

93

Relationship between operon preference and functional properties of persistent genes in bacterial genomes  

Microsoft Academic Search

BACKGROUND: Genes in bacteria may be organised into operons, leading to strict co-expression of the genes that participate in the same operon. However, comparisons between different bacterial genomes have shown that much of the operon structure is dynamic on an evolutionary time scale. This indicates that there are opposing effects influencing the tendency for operon formation, and these effects may

Marit S Bratlie; Jostein Johansen; Finn Drabløs

2010-01-01

94

Diversity and expression of nitrogen fixation genes in bacterial symbionts of marine sponges.  

PubMed

Marine sponges contain complex assemblages of bacterial symbionts, the roles of which remain largely unknown. We identified diverse bacterial nifH genes within sponges and found that nifH genes are expressed in sponges. This is the first demonstration of the expression of any protein-coding bacterial gene within a sponge. Two sponges Ircinia strobilina and Mycale laxissima were collected from Key Largo, Florida and had delta(15)N values of c. 0-1 per thousand and 3-4 per thousand respectively. The potential for nitrogen fixation by symbionts was assessed by amplification of nifH genes. Diverse nifH genes affiliated with Proteobacteria and Cyanobacteria were detected, and expression of nifH genes affiliated with those from cyanobacteria was detected. The nifH genes from surrounding seawater were similar to those of Trichodesmium and clearly different from the cyanobacterial nifH genes detected in the two sponges. This study advances understanding of the role of bacterial symbionts in sponges and suggests that provision of fixed nitrogen is a means whereby symbionts benefit sponges in nutrient-limited reef environments. Nitrogen fixation by sponge symbionts is possibly an important source of new nitrogen to the reef environment that heretofore has been neglected and warrants further investigation. PMID:18761667

Mohamed, Naglaa M; Colman, Albert S; Tal, Yossi; Hill, Russell T

2008-11-01

95

More than 9,000,000 Unique Genes in Human Gut Bacterial Community: Estimating Gene Numbers Inside a Human Body  

Microsoft Academic Search

BackgroundEstimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism.Principal FindingsWe presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the

Xing Yang; Lu Xie; Yixue Li; Chaochun Wei; Stefan Bereswill

2009-01-01

96

Isolation of Bacillus amyloliquefaciens S20 and its application in control of eggplant bacterial wilt.  

PubMed

Bacterial strain S20 was isolated and identified as Bacillus amyloliquefaciens based on physiological and biochemical characteristics and a 16S rRNA gene sequence analysis. Strain S20 inhibits the growth of Fusarium oxysporum and Ralstonia solanacearum. Some genes associated with the synthesis of some lipopeptides were detected in strain S20 by PCR. Iturins A were identified as the main antagonistic substrates by analysis with electrospray ionization mass spectrometry/collision-induced dissociation (ESI-MS/CID). Four homologues of iturin A (C13-C16) were identified. Pot experiments showed that the application of strain S20 alone could control eggplant wilt with an efficacy of 25.3% during a 40 day experiment. If strain S20 was used with organic fertilizer, the control efficacy against eggplant wilt reached as high as 70.7%. The application of organic fertilizer alone promotes the growth of R. solanacearum, resulting in a higher wilt incidence than that observed in control plants. The application of strain S20 effectively inhibits R. solanacearum in the rhizosphere soil of eggplant. The combined use of strain S20 and organic fertilizer more effectively controlled R. solanacearum in soil than the use of strain S20 alone. The soil count of strain S20 decreased gradually during the course of the experiment after inoculation. Organic fertilizer was beneficial for the survival of the antagonistic bacterial strain S20; a higher level of these bacteria could be maintained. The application of organic fertilizer with strain S20 increased bacterial diversity in rhizosphere soil. PMID:24632400

Chen, Da; Liu, Xin; Li, Chunyu; Tian, Wei; Shen, Qirong; Shen, Biao

2014-05-01

97

Robust perfect adaptation in bacterial chemotaxis through integral feedback control  

PubMed Central

Integral feedback control is a basic engineering strategy for ensuring that the output of a system robustly tracks its desired value independent of noise or variations in system parameters. In biological systems, it is common for the response to an extracellular stimulus to return to its prestimulus value even in the continued presence of the signal—a process termed adaptation or desensitization. Barkai, Alon, Surette, and Leibler have provided both theoretical and experimental evidence that the precision of adaptation in bacterial chemotaxis is robust to dramatic changes in the levels and kinetic rate constants of the constituent proteins in this signaling network [Alon, U., Surette, M. G., Barkai, N. & Leibler, S. (1998) Nature (London) 397, 168–171]. Here we propose that the robustness of perfect adaptation is the result of this system possessing the property of integral feedback control. Using techniques from control and dynamical systems theory, we demonstrate that integral control is structurally inherent in the Barkai–Leibler model and identify and characterize the key assumptions of the model. Most importantly, we argue that integral control in some form is necessary for a robust implementation of perfect adaptation. More generally, integral control may underlie the robustness of many homeostatic mechanisms.

Yi, Tau-Mu; Huang, Yun; Simon, Melvin I.; Doyle, John

2000-01-01

98

Selection Effects on the Positioning of Genes and Gene Structures from the Interplay of Replication and Transcription in Bacterial Genomes  

PubMed Central

Bacterial chromosomes are partly shaped by the functional requirements for efficient replication, which lead to strand bias as commonly characterized by the excess of guanines over cytosines in the leading strand. Gene structures are also highly organized within bacterial genomes as a result of such functional constraints, displaying characteristic positioning and structuring along the genome. Here we analyze the gene structures in completely sequenced bacterial chromosomes to observe the positional constraints on gene orientation, length, and codon usage with regard to the positions of replication origin and terminus. Selection on these gene features is different in regions surrounding the terminus of replication from the rest of the genome, but the selection could be either positive or negative depending on the species, and these positional effects are partly attributed to the A-T enrichment near the terminus. Characteristic gene structuring relative to the position of replication origin and terminus is commonly observed among most bacterial species with circular chromosomes, and therefore we argue that the highly organized gene positioning as well as the strand bias should be considered for genomics studies of bacteria.

Arakawa, Kazuharu; Tomita, Masaru

2007-01-01

99

Controlling Plant Pathogens with Bacterial/Fungal Antagonist Combinations.  

National Technical Information Service (NTIS)

Fungal/bacterial antagonist combinations, a seed coated with one of the combinations and a plant protected from plant pathogens by one of the combinations. The invention is also a fungal/bacterial antagonist combination comprising a Trichoderma virens fun...

T. D. Johnson

2004-01-01

100

Genetic and functional characterization of the rice bacterial blight disease resistance gene xa5.  

PubMed

Xanthomonas oryzae pv. oryzae is the causal agent of rice bacterial blight, a destructive rice disease worldwide. The gene xa5 provides race-specific resistance to X. oryzae pv. oryzae, and encodes the small subunit of transcription factor IIA. How xa5 functions in bacterial blight resistance is not well understood, and its recessive gene action is disputed. Here we show that xa5 is inherited in a completely recessive manner and the susceptible allele Xa5 is fully dominant. In accordance with this, bacterial growth in heterozygous and homozygous susceptible lines is not significantly different. Further, one allele of Xa5 is sufficient to promote disease in previously resistant plants; additional copies are not predictive of increased lesion length. Surprisingly, a resistant nearly isogenic line (NIL) of an indica variety sustains high levels of bacterial populations compared to the susceptible NIL, yet the resistant plants restrict symptom expression. In contrast, in japonica NILs, bacterial population dynamics differ in resistant and susceptible genotypes. However, both resistant indica and japonica plants delay bacterial movement down the leaf. These results support a model in which xa5-mediated recessive resistance is the result of restricted bacterial movement, but not restricted multiplication. PMID:18944079

Iyer-Pascuzzi, A S; Jiang, H; Huang, L; McCouch, S R

2008-03-01

101

A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes  

PubMed Central

Background Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes.

2014-01-01

102

Rapid identification and cloning of bacterial transferrin and lactoferrin receptor protein genes.  

PubMed Central

The sequences of genes encoding the transferrin and lactoferrin receptor proteins from several bacterial species were analyzed for areas of identity in the predicted protein sequences. Degenerate oligonucleotide primers were designed and tested for their ability to amplify portions of the receptor genes. Primer pairs capable of amplifying products of the tbpA/lbpA or tbpB/lbpB genes from all species possessing these receptors were identified.

Ogunnariwo, J A; Schryvers, A B

1996-01-01

103

The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens.  

PubMed

During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudogenization) and deletion. Here, we examine the evolutionary sequence of gene-death events during the process of genome miniaturization in three bacterial species that have experienced extensive genome reduction: Mycobacterium leprae, Shigella flexneri, and Salmonella typhi. We infer that in all three lineages, the distribution of functional categories is similar in pseudogenes and genes but different from that of absent genes. Based on an analysis of evolutionary distances, we propose a two-step "domino effect" model for reductive genome evolution. The process starts with a gradual gene-by-gene-death sequence of events. Eventually, a crucial gene within a complex pathway or network is rendered nonfunctional triggering a "mass gene extinction" of the dependent genes. In contrast to published reports according to which genes belonging to certain functional categories are prone to nonfunctionalization more frequently and earlier than genes belonging to other functional categories, we could discern no characteristic regularity in the temporal order of function loss. PMID:16237210

Dagan, Tal; Blekhman, Ran; Graur, Dan

2006-02-01

104

Diagnostic microarray for human and animal bacterial diseases and their virulence and antimicrobial resistance genes.  

PubMed

Rapid diagnosis and treatment of disease is often based on the identification and characterization of causative agents derived from phenotypic characteristics. Current methods can be laborious and time-consuming, often requiring many skilled personnel and a large amount of lab space. The objective of our study was to develop a spotted microarray for rapid identification and characterization of bacterial pathogens and their antimicrobial resistance genes. Our spotted microarray consists of 489 70mer probes that detect 40 bacterial pathogens of medical, veterinary and zoonotic importance (including 15 NIAID Category A, B and C pathogens); associated genes that encode resistance for antimicrobial and metal resistance; and DNA elements that are important for horizontal gene transfer among bacteria. High specificity and reliability of the microarray was achieved for bacterial pathogens of animal and human importance by validating MDR pathogenic bacteria as pure cultures or by following their inoculation in complex and highly organic sample matrices, such as soil and manure. PMID:20035807

Peterson, Greg; Bai, Jianfa; Nagaraja, T G; Narayanan, Sanjeev

2010-03-01

105

Bioinformatic Analysis Reveals High Diversity of Bacterial Genes for Laccase-Like Enzymes  

PubMed Central

Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three- domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications.

Ausec, Luka; Zakrzewski, Martha; Goesmann, Alexander; Schluter, Andreas; Mandic-Mulec, Ines

2011-01-01

106

Multiple micro-predators controlling bacterial communities in the environment.  

PubMed

Predator-prey interactions are a main issue in ecological theory, including multispecies predator-prey relationships and intraguild predation. This knowledge is mainly based on the study of plants and animals, while its relevance for microorganisms is not well understood. The three key groups of micro-predators include protists, predatory bacteria and bacteriophages. They greatly differ in size, in prey specificity, in hunting strategies and in the resulting population dynamics. Yet, their potential to jointly control bacterial populations and reducing biomass in complex environments such as wastewater treatment plants is vast. Here, we present relevant ecological concepts and recent findings on micropredators, and propose that an integrative approach to predation at the microscale should be developed enabling the exploitation of this potential. PMID:24598212

Johnke, Julia; Cohen, Yossi; de Leeuw, Marina; Kushmaro, Ariel; Jurkevitch, Edouard; Chatzinotas, Antonis

2014-06-01

107

Cloning, purification, and crystallization of a bacterial gene expression regulator--Hfq protein from Escherichia coli.  

PubMed

Thermostable RNA-binding protein Hfq (also denoted HF1) is a multifunctional expression regulator of many bacterial genes. The regulation takes place both at a translation level (directly) and transcription level (indirectly through the stimulation of bacterial RNA polymerase sigmaS-subunit translation). We have cloned and overexpressed the hfq gene from E. coli and developed a purification procedure for the protein. Using gel filtration and ultracentrifugation techniques it was shown that the obtained Hfq protein is highly homogeneous and well dissolved. It has been crystallized and can be used for structural investigations. PMID:12495429

Vassilieva, I M; Rouzanov, M V; Zelinskaya, N V; Moll, I; Bläsi, U; Garber, M B

2002-11-01

108

A cell cycle and nutritional checkpoint controlling bacterial surface adhesion.  

PubMed

In natural environments, bacteria often adhere to surfaces where they form complex multicellular communities. Surface adherence is determined by the biochemical composition of the cell envelope. We describe a novel regulatory mechanism by which the bacterium, Caulobacter crescentus, integrates cell cycle and nutritional signals to control development of an adhesive envelope structure known as the holdfast. Specifically, we have discovered a 68-residue protein inhibitor of holdfast development (HfiA) that directly targets a conserved glycolipid glycosyltransferase required for holdfast production (HfsJ). Multiple cell cycle regulators associate with the hfiA and hfsJ promoters and control their expression, temporally constraining holdfast development to the late stages of G1. HfiA further functions as part of a 'nutritional override' system that decouples holdfast development from the cell cycle in response to nutritional cues. This control mechanism can limit surface adhesion in nutritionally sub-optimal environments without affecting cell cycle progression. We conclude that post-translational regulation of cell envelope enzymes by small proteins like HfiA may provide a general means to modulate the surface properties of bacterial cells. PMID:24465221

Fiebig, Aretha; Herrou, Julien; Fumeaux, Coralie; Radhakrishnan, Sunish K; Viollier, Patrick H; Crosson, Sean

2014-01-01

109

Detection of bacterial 16S ribosomal RNA genes for forensic identification of vaginal fluid.  

PubMed

To preliminarily evaluate the applicability of bacterial DNA as a marker for the forensic identification of vaginal fluid, we developed and performed PCR-based detection of 16S ribosomal RNA genes of Lactobacillus spp. dominating the vagina and of bacterial vaginosis-related bacteria from DNA extracted from body fluids and stains. As a result, 16S ribosomal RNA genes of Lactobacillus crispatus, Lactobacillus jensenii and Atopobium vaginae were specifically detected in vaginal fluid and female urine samples. Bacterial genes detected in female urine might have originated from contaminated vaginal fluid. In addition, those of Lactobacillus iners, Lactobacillus gasseri and Gardnerella vaginalis were also detected in non-vaginal body fluids such as semen. Because bacterial genes were successfully amplified in DNA samples extracted by using the general procedure for animal tissues without any optional treatments, DNA samples prepared for the identification of vaginal fluid can also be used for personal identification. In conclusion, 16S ribosomal RNA genes of L. crispatus, L. jensenii and A. vaginae could be effective markers for forensic identification of vaginal fluid. PMID:22316585

Akutsu, Tomoko; Motani, Hisako; Watanabe, Ken; Iwase, Hirotaro; Sakurada, Koichi

2012-05-01

110

A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans  

PubMed Central

While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacterial and fungal infection. Using tiling arrays and/or RNA-sequencing, we have characterized the genome-wide transcriptional changes that underlie the host's response to infection by three bacterial (Serratia marcescens, Enterococcus faecalis and otorhabdus luminescens) and two fungal pathogens (Drechmeria coniospora and Harposporium sp.). We developed a flexible tool, the WormBase Converter (available at http://wormbasemanager.sourceforge.net/), to allow cross-study comparisons. The new data sets provided more extensive lists of differentially regulated genes than previous studies. Annotation analysis confirmed that genes commonly up-regulated by bacterial infections are related to stress responses. We found substantial overlaps between the genes regulated upon intestinal infection by the bacterial pathogens and Harposporium, and between those regulated by Harposporium and D. coniospora, which infects the epidermis. Among the fungus-regulated genes, there was a significant bias towards genes that are evolving rapidly and potentially encode small proteins. The results obtained using new methods reveal that the response to infection in C. elegans is determined by the nature of the pathogen, the site of infection and the physiological imbalance provoked by infection. They form the basis for future functional dissection of innate immune signaling. Finally, we also propose alternative methods to identify differentially regulated genes that take into account the greater variability in lowly expressed genes.

Engelmann, Ilka; Griffon, Aurelien; Tichit, Laurent; Montanana-Sanchis, Frederic; Wang, Guilin; Reinke, Valerie; Waterston, Robert H.; Hillier, LaDeana W.; Ewbank, Jonathan J.

2011-01-01

111

Use of Bacterially Expressed dsRNA to Downregulate Entamoeba histolytica Gene Expression  

PubMed Central

Background Modern RNA interference (RNAi) methodologies using small interfering RNA (siRNA) oligonucleotide duplexes or episomally synthesized hairpin RNA are valuable tools for the analysis of gene function in the protozoan parasite Entamoeba histolytica. However, these approaches still require time-consuming procedures including transfection and drug selection, or costly synthetic molecules. Principal Findings Here we report an efficient and handy alternative for E. histolytica gene down-regulation mediated by bacterial double-stranded RNA (dsRNA) targeting parasite genes. The Escherichia coli strain HT115 which is unable to degrade dsRNA, was genetically engineered to produce high quantities of long dsRNA segments targeting the genes that encode E. histolytica ?-tubulin and virulence factor KERP1. Trophozoites cultured in vitro were directly fed with dsRNA-expressing bacteria or soaked with purified dsRNA. Both dsRNA delivery methods resulted in significant reduction of protein expression. In vitro host cell-parasite assays showed that efficient downregulation of kerp1 gene expression mediated by bacterial dsRNA resulted in significant reduction of parasite adhesion and lytic capabilities, thus supporting a major role for KERP1 in the pathogenic process. Furthermore, treatment of trophozoites cultured in microtiter plates, with a repertoire of eighty-five distinct bacterial dsRNA segments targeting E. histolytica genes with unknown function, led to the identification of three genes potentially involved in the growth of the parasite. Conclusions Our results showed that the use of bacterial dsRNA is a powerful method for the study of gene function in E. histolytica. This dsRNA delivery method is also technically suitable for the study of a large number of genes, thus opening interesting perspectives for the identification of novel drug and vaccine targets.

Perdomo, Doranda; Weber, Christian; Guillen, Nancy

2009-01-01

112

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss  

Microsoft Academic Search

BACKGROUND: The bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii, both of which carry homologous virulence gene clusters such as the prfA cluster and clusters of internalin genes. Initial evidence for multiple deletions of the prfA cluster during the evolution of Listeria indicates that this genus provides an interesting model for studying

Henk C den Bakker; Craig A Cummings; Vania Ferreira; Paolo Vatta; Renato H Orsi; Lovorka Degoricija; Melissa Barker; Olga Petrauskene; Manohar R Furtado; Martin Wiedmann

2010-01-01

113

Preparation of a DNA gene probe for detection of mercury resistance genes in gram-negative bacterial communities  

Microsoft Academic Search

A DNA gene probe was prepared to study genetic change mechanisms responsible for adaptation to mercury in natural bacterial communities. The probe was constructed from a 2.6-kilobase NcoI-EcoRI DNA restriction fragment which spans the majority of the mercury resistance operon (mer) in the R-factor R100. The range of specificity of this gene probe was defined by hybridization to the DNA

T. Barkay; D. L. Fouts; B. H. Olson

1985-01-01

114

[Differential expression of genes related to bacterial wilt resistance in peanut (Arachis hypogaea L.)].  

PubMed

Peanut bacterial wilt (BW) caused by Ralstonia solanacearum is one of the most devastating diseases for peanut production in the world. It is believed that breeding and subsequent planting BW-resistant cultivars of peanut (Arachis hypogaea L.) should represent the most effective and economic means of controlling the disease. To illustrate the molecular mechanism of peanut resistant to BW, a BW-resistant cultivar, 'Yuanza 9102', and a BW-sensitive one, 'Zhonghua 12', were infected with Ralstonia solanacearum and differential expression of the genes related to BW-resistance was analyzed using complementary DNA amplified length polymorphism (cDNA-AFLP) technique. The infected 3-leaflet seedlings were followed for 48 h and root samples were taken at 0, 2, 10, 24 and 48 h after inoculation, respectively. A total of 12596 transcript-derived fragments (TDFs) were amplified with 256 primer combinations, including 709 differential expressed TDFs, which were generated from 119 primer combinations. Ninety-eight TDFs were randomly chosen for DNA sequence analysis. BLASTx analysis of the obtained sequences revealed that 40 TDFs encoded gene products associated with energy, transcription, signal transduction, defense, metabolism, cell growth, cell structure or/and protein synthesis. Analysis of the expression of four genes by qRT-PCR verified the results from cDNA-AFLP. Strikingly, one of the identified TDFs, 32-54-1, occurred for 47 times in a known BW-resistant SSH library. These results suggest that resistance to BW in peanut involves multifaceted biochemical and physiological reactions, including regulation of the genes involved in different pathways, such as defense, singal transduction, metabolism, transcription and abiotic stresses. The TDF 32-54-1 was predicted to be closely related to BW resistance in peanut. PMID:21482530

Peng, Wen-Fang; Lv, Jian-Wei; Ren, Xiao-Ping; Huang, Li; Zhao, Xin-Yan; Wen, Qi-Gen; Jiang, Hui-Fang

2011-04-01

115

Interplay of Noisy Gene Expression and Dynamics Explains Patterns of Bacterial Operon Organization  

NASA Astrophysics Data System (ADS)

Bacterial chromosomes are organized into operons -- sets of genes co-transcribed into polycistronic messenger RNA. Hypotheses explaining the emergence and maintenance of operons include proportional co-regulation, horizontal transfer of intact "selfish" operons, emergence via gene duplication, and co-production of physically interacting proteins to speed their association. We hypothesized an alternative: operons can reduce or increase intrinsic gene expression noise in a manner dependent on the post-translational interactions, thereby resulting in selection for or against operons in depending on the network architecture. We devised five classes of two-gene network modules and show that the effects of operons on intrinsic noise depend on class membership. Two classes exhibit decreased noise with co-transcription, two others reveal increased noise, and the remaining one does not show a significant difference. To test our modeling predictions we employed bioinformatic analysis to determine the relationship gene expression noise and operon organization. The results confirm the overrepresentation of noise-minimizing operon architectures and provide evidence against other hypotheses. Our results thereby suggest a central role for gene expression noise in selecting for or maintaining operons in bacterial chromosomes. This demonstrates how post-translational network dynamics may provide selective pressure for organizing bacterial chromosomes, and has practical consequences for designing synthetic gene networks.

Igoshin, Oleg

2011-03-01

116

Retroviral transfer of a bacterial alkyltransferase gene into murine bone marrow protects against chloroethylnitrosourea cytotoxicity.  

PubMed

The chloroethylnitrosoureas (CENUs) are important antineoplastic drugs for which clinical utility has been restricted by the development of severe delayed myelosuppression in most patients. To investigate the potential of DNA repair proteins to reduce bone marrow sensitivity to the CENUs, we transferred the Escherichia coli ada gene, which encodes a Mr 39,000 O6-alkylguanine-DNA alkyltransferase (ATase), into murine bone marrow cells by the use of a high-titer ecotropic retrovirus. The ada-encoded ATase is resistant to O6-benzylguanine (O6-BG), a potent inhibitor of the mammalian ATases, thus affording the bone marrow an additional level of protection against CENUs. In methylcellulose cultures, ada-infected hematopoietic progenitor cells were twice as resistant as uninfected cells to the toxic effects of 1, 3-bis(2-chloroethyl)-1-nitrosourea (BCNU) following treatment with O6-BG. Although showing no obvious protective effects against leukopenia, overexpression of the bacterial ATase activity reduced the severity of anemia and thrombocytopenia in mice treated with O6-BG and BCNU. These effects, which were maximal at a BCNU dose of 12.5 mg/kg, were associated with improved survival when BCNU was given at this dose. At lower BCNU doses cytotoxicity was limited in both transduced and control mice, and at higher doses the protective effect was saturated due to cytotoxicity. These results suggest that ada gene therapy may be a feasible approach to amelioration of delayed myelosuppression following O6-BG plus CENU combination chemotherapy. PMID:9815932

Harris, L C; Marathi, U K; Edwards, C C; Houghton, P J; Srivastava, D K; Vanin, E F; Sorrentino, B P; Brent, T P

1995-11-01

117

Identifying essential genes in bacterial metabolic networks with machine learning methods  

PubMed Central

Background Identifying essential genes in bacteria supports to identify potential drug targets and an understanding of minimal requirements for a synthetic cell. However, experimentally assaying the essentiality of their coding genes is resource intensive and not feasible for all bacterial organisms, in particular if they are infective. Results We developed a machine learning technique to identify essential genes using the experimental data of genome-wide knock-out screens from one bacterial organism to infer essential genes of another related bacterial organism. We used a broad variety of topological features, sequence characteristics and co-expression properties potentially associated with essentiality, such as flux deviations, centrality, codon frequencies of the sequences, co-regulation and phyletic retention. An organism-wise cross-validation on bacterial species yielded reliable results with good accuracies (area under the receiver-operator-curve of 75% - 81%). Finally, it was applied to drug target predictions for Salmonella typhimurium. We compared our predictions to the viability of experimental knock-outs of S. typhimurium and identified 35 enzymes, which are highly relevant to be considered as potential drug targets. Specifically, we detected promising drug targets in the non-mevalonate pathway. Conclusions Using elaborated features characterizing network topology, sequence information and microarray data enables to predict essential genes from a bacterial reference organism to a related query organism without any knowledge about the essentiality of genes of the query organism. In general, such a method is beneficial for inferring drug targets when experimental data about genome-wide knockout screens is not available for the investigated organism.

2010-01-01

118

Measurement of bacterial gene expression in vivo by laser capture microdissection and quantitative real-time RT-PCR.  

PubMed

Due to the relative small number of bacterial pathogens present in an infected host, exploration of pathogen gene expression in vivo is challenging. This study reports the development of a protocol for quantifying bacterial gene expression in vivo in Actinobacillus pleuropneumoniae using laser capture microdissection and real-time quantitative RT-PCR. PMID:17250913

Klitgaard, Kirstine; Jensen, Tim K; Angen, Øystein; Boye, Mette

2007-05-01

119

Systematic chromosomal deletion of bacterial ribosomal protein genes  

PubMed Central

Detailed studies of ribosomal proteins, essential components of the protein biosynthetic machinery, have been hampered by the lack of readily accessible chromosomal deletions of the corresponding genes. Here, we report the systematic genomic deletion of 41 individual ribosomal protein genes in Escherichia coli, which are not included in the Keio collection. Chromosomal copies of these genes were replaced by an antibiotic resistance gene in the presence of an inducible, easy-to-exchange plasmid-born allele. Using this knockout collection, 9 ribosomal proteins (L15, L21, L24, L27, L29, L30, L34, S9 and S17) were found nonessential for survival under induction conditions at various temperatures. Taken together with previous results, this analysis revealed that 22 of the 54 E. coli ribosomal protein genes can be individually deleted from the genome. These strains also allow expression of truncated protein variants to probe the importance of RNA-protein interactions in functional sites of the ribosome. This set of strains should enhance in vivo studies of ribosome assembly/function, and may ultimately allow systematic substitution of ribosomal proteins with RNA.

Shoji, Shinichiro; Dambacher, Corey M.; Shajani, Zahra; Williamson, James R.; Schultz, Peter G.

2011-01-01

120

Systematic chromosomal deletion of bacterial ribosomal protein genes.  

PubMed

Detailed studies of ribosomal proteins (RPs), essential components of the protein biosynthetic machinery, have been hampered by the lack of readily accessible chromosomal deletions of the corresponding genes. Here, we report the systematic genomic deletion of 41 individual RP genes in Escherichia coli, which are not included in the Keio collection. Chromosomal copies of these genes were replaced by an antibiotic resistance gene in the presence of an inducible, easy-to-exchange plasmid-born allele. Using this knockout collection, we found nine RPs (L15, L21, L24, L27, L29, L30, L34, S9, and S17) nonessential for survival under induction conditions at various temperatures. Taken together with previous results, this analysis revealed that 22 of the 54 E. coli RP genes can be individually deleted from the genome. These strains also allow expression of truncated protein variants to probe the importance of RNA-protein interactions in functional sites of the ribosome. This set of strains should enhance in vivo studies of ribosome assembly/function and may ultimately allow systematic substitution of RPs with RNA. PMID:21945294

Shoji, Shinichiro; Dambacher, Corey M; Shajani, Zahra; Williamson, James R; Schultz, Peter G

2011-11-01

121

A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans  

Microsoft Academic Search

While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacterial and fungal infection. Using tiling arrays and\\/or RNA-sequencing, we have characterized the genome-wide transcriptional changes that

Ilka Engelmann; Aurélien Griffon; Laurent Tichit; Frédéric Montañana-Sanchis; Guilin Wang; Valerie Reinke; Robert H. Waterston; LaDeana W. Hillier; Jonathan J. Ewbank

2011-01-01

122

Bacterial Adaptation of Respiration from Oxic to Microoxic and Anoxic Conditions: Redox Control  

PubMed Central

Abstract Under a shortage of oxygen, bacterial growth can be faced mainly by two ATP-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. This bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells can sense and respond to changes in oxygen tension and to the availability of other electron acceptors. Bacteria can sense oxygen by direct interaction of this molecule with a membrane protein receptor (e.g., FixL) or by interaction with a cytoplasmic transcriptional factor (e.g., Fnr). A third type of oxygen perception is based on sensing changes in redox state of molecules within the cell. Redox-responsive regulatory systems (e.g., ArcBA, RegBA/PrrBA, RoxSR, RegSR, ActSR, ResDE, and Rex) integrate the response to multiple signals (e.g., ubiquinone, menaquinone, redox active cysteine, electron transport to terminal oxidases, and NAD/NADH) and activate or repress target genes to coordinate the adaptation of bacterial respiration from oxic to anoxic conditions. Here, we provide a compilation of the current knowledge about proteins and regulatory networks involved in the redox control of the respiratory adaptation of different bacterial species to microxic and anoxic environments. Antioxid. Redox Signal. 16, 819–852.

Bueno, Emilio; Mesa, Socorro; Bedmar, Eulogio J.; Richardson, David J.

2012-01-01

123

Close linkage of a blast resistance gene, Pias(t), with a bacterial leaf blight resistance gene, Xa1-as(t), in a rice cultivar 'Asominori'.  

PubMed

It has long been known that a bacterial leaf blight-resistant line in rice obtained from a crossing using 'Asominori' as a resistant parent also has resistance to blast, but a blast resistance gene in 'Asominori' has not been investigated in detail. In the present study, a blast resistance gene in 'Asominori', tentatively named Pias(t), was revealed to be located within 162-kb region between DNA markers YX4-3 and NX4-1 on chromosome 4 and to be linked with an 'Asominori' allele of the bacterial leaf blight resistance gene Xa1, tentatively named Xa1-as(t). An 'Asominori' allele of Pias(t) was found to be dominant and difference of disease severity between lines having the 'Asominori' allele of Pias(t) and those without it was 1.2 in disease index from 0 to 10. Pias(t) was also closely linked with the Ph gene controlling phenol reaction, suggesting the possibility of successful selection of blast resistance using the phenol reaction. Since blast-resistant commercial cultivars have been developed using 'Asominori' as a parent, Pias(t) is considered to be a useful gene in rice breeding for blast resistance. PMID:23341747

Endo, Takashi; Yamaguchi, Masayuki; Kaji, Ryota; Nakagomi, Koji; Kataoka, Tomomori; Yokogami, Narifumi; Nakamura, Toshiki; Ishikawa, Goro; Yonemaru, Jun-Ichi; Nishio, Takeshi

2012-12-01

124

The Effect of Nitrogen on Disease Development and Gene Expression in Bacterial and Fungal Plant Pathogens  

Microsoft Academic Search

Successful colonisation of plants by pathogens requires efficient utilisation of nutrient resources available in host tissues. Several bacterial and fungal genes are specifically induced during pathogenesis and under nitrogen-limiting conditions in vitro. This suggests that a nitrogen-limiting environment may be one of the cues for disease symptom development during growth of the pathogens in planta. Here we review recent literature

Sandor S. Snoeijers; Alejandro Pérez-García; Matthieu H. A. J. Joosten

2000-01-01

125

A gene expression atlas of the central nervous system based on bacterial artificial chromosomes  

Microsoft Academic Search

The mammalian central nervous system (CNS) contains a remarkable array of neural cells, each with a complex pattern of connections that together generate perceptions and higher brain functions. Here we describe a large-scale screen to create an atlas of CNS gene expression at the cellular level, and to provide a library of verified bacterial artificial chromosome (BAC) vectors and transgenic

Shiaoching Gong; Chen Zheng; Martin L. Doughty; Kasia Losos; Nicholas Didkovsky; Uta B. Schambra; Norma J. Nowak; Alexandra Joyner; Gabrielle Leblanc; Mary E. Hatten; Nathaniel Heintz

2003-01-01

126

Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach  

Microsoft Academic Search

The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relatively unbiased view of its genetic structure and the patterns of ancestry connected to

Jing Tang; William P. Hanage; Christophe Fraser; Jukka Corander

2009-01-01

127

Requirement for an upstream element for optimal transcription of a bacterial tRNA gene  

Microsoft Academic Search

Bacterial promoters are the sites at the 5' end of each gene that bind RNA polymerase and direct the initiation of transcription. The functional elements of Escherichia coli promoters1,2 are two highly conserved sequences, each about six nucleotides long, usually centred at sites -10 and -35, +1 being the initiating nucleotide. We have been interested in the structure of promoters

Angus I. Lamond; Andrew A. Travers

1983-01-01

128

FliZ Is a Global Regulatory Protein Affecting the Expression of Flagellar and Virulence Genes in Individual Xenorhabdus nematophila Bacterial Cells  

PubMed Central

Heterogeneity in the expression of various bacterial genes has been shown to result in the presence of individuals with different phenotypes within clonal bacterial populations. The genes specifying motility and flagellar functions are coordinately regulated and form a complex regulon, the flagellar regulon. Complex interplay has recently been demonstrated in the regulation of flagellar and virulence gene expression in many bacterial pathogens. We show here that FliZ, a DNA-binding protein, plays a key role in the insect pathogen, Xenorhabdus nematophila, affecting not only hemolysin production and virulence in insects, but efficient swimming motility. RNA-Seq analysis identified FliZ as a global regulatory protein controlling the expression of 278 Xenorhabdus genes either directly or indirectly. FliZ is required for the efficient expression of all flagellar genes, probably through its positive feedback loop, which controls expression of the flhDC operon, the master regulator of the flagellar circuit. FliZ also up- or downregulates the expression of numerous genes encoding non-flagellar proteins potentially involved in key steps of the Xenorhabdus lifecycle. Single-cell analysis revealed the bimodal expression of six identified markers of the FliZ regulon during exponential growth of the bacterial population. In addition, a combination of fluorescence-activated cell sorting and RT-qPCR quantification showed that this bimodality generated a mixed population of cells either expressing (“ON state”) or not expressing (“OFF state”) FliZ-dependent genes. Moreover, studies of a bacterial population exposed to a graded series of FliZ concentrations showed that FliZ functioned as a rheostat, controlling the rate of transition between the “OFF” and “ON” states in individuals. FliZ thus plays a key role in cell fate decisions, by transiently creating individuals with different potentials for motility and host interactions.

Severac, Dany; Rialle, Stephanie; Longin, Cyrille; Gaudriault, Sophie; Givaudan, Alain

2013-01-01

129

Bacterial metal resistance genes and metal bioavailability in contaminated sediments.  

PubMed

In bacteria a metal may be defined as bioavailable if it crosses the cytoplasmic membrane to reach the cytoplasm. Once inside the cell, specific metal resistance systems may be triggered. In this research, specific metal resistance genes were used to estimate metal bioavailability in sediment microbial communities. Gene levels were measured by quantitative PCR and correlated to metals in sediments using five different protocols to estimate dissolved, particle-adsorbed and occluded metals. The best correlations were obtained with czcA (a Cd/Zn/Co efflux pump) and Cd/Zn adsorbed or occluded in particles. Only adsorbed Co was correlated to czcA levels. We concluded that the measurement of czcA gene levels by quantitative PCR is a promising tool which may complement the classical approaches used to estimate Cd/Zn/Co bioavailability in sediment compartments. PMID:24662000

Roosa, Stéphanie; Wattiez, Ruddy; Prygiel, Emilie; Lesven, Ludovic; Billon, Gabriel; Gillan, David C

2014-06-01

130

Denitrification gene expression in clay-soil bacterial community  

NASA Astrophysics Data System (ADS)

Our contribution in the Italian research project SOILSINK was focused on microbial denitrification gene expression in Mediterranean agricultural soils. In ecosystems with high inputs of nitrogen, such as agricultural soils, denitrification causes a net loss of nitrogen since nitrate is reduced to gaseous forms, which are released into the atmosphere. Moreover, incomplete denitrification can lead to emission of nitrous oxide, a potent greenhouse gas which contributes to global warming and destruction of ozone layer. A critical role in denitrification is played by microorganisms and the ability to denitrify is widespread among a variety of phylogenetically unrelated organisms. Data reported here are referred to wheat cultivation in a clay-rich soil under different environmental impact management (Agugliano, AN, Italy). We analysed the RNA directly extracted from soil to provide information on in situ activities of specific populations. The expression of genes coding for two nitrate reductases (narG and napA), two nitrite reductases (nirS and nirK), two nitric oxide reductases (cnorB and qnorB) and nitrous oxide reductase (nosZ) was analyzed by reverse transcription (RT)-nested PCR. Only napA, nirS, nirK, qnorB and nosZ were detected and fragments sequenced showed high similarity with the corresponding gene sequences deposited in GenBank database. These results suggest the suitability of the method for the qualitative detection of denitrifying bacteria in environmental samples and they offered us the possibility to perform the denaturing gradient gel electrophoresis (DGGE) analyzes for denitrification genes.. Earlier conclusions showed nirK gene is more widely distributed in soil environment than nirS gene. The results concerning the nosZ expression indicated that microbial activity was clearly present only in no-tilled and no-fertilized soils.

Pastorelli, R.; Landi, S.

2009-04-01

131

Secondary metabolites in transgenic tobacco and potato: high accumulation of 4-hydroxybenzoic acid glucosides results from high expression of the bacterial gene ubiC  

Microsoft Academic Search

The bacterial gene ubiC encodes chorismate pyruvate-lyase (CPL), which converts chorismate to 4-hydroxybenzoate (4HB). The ubiC gene was expressed in tobacco (Nicotiana tabacum L., Solanaceae) and potato (Solanum tuberosum L., Solanaceae) under the control of the very strong constitutive plant promotor (ocs3) mas. High accumulation of 4HB glucosides as new, artificial secondary metabolites was observed in the transgenic plants. 4HB

Annegret Köhle; Susanne Sommer; Shu-Ming Li; Lieselotte Schilde-Rentschler; Helga Ninnemann; Lutz Heide

2003-01-01

132

Fate of tetracycline, sulfonamide and fluoroquinolone resistance genes and the changes in bacterial diversity during composting of swine manure.  

PubMed

This study monitored the abundance of antibiotic resistant genes (ARGs) and the bacterial diversity during composting of swine manure spiked with chlortetracycline, sulfadiazine and ciprofloxacin at two different levels and a control without antibiotics. Resistance genes of tetracycline (tetQ, tetW, tetC, tetG, tetZ and tetY), sulfonamide (sul1, sul2, dfrA1 and dfrA7) and fluoroquinolone (gyrA and parC) represented 0.02-1.91%, 0.67-10.28% and 0.00005-0.0002%, respectively, of the total 16S rDNA copies in the initial composting mass. After 28-42 days of composting, these ARGs, except parC, were undetectable in the composting mass indicating that composting is a potential method of manure management. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of bacterial 16S rDNA of the composting mass indicated that the addition of antibiotics up to 100, 20 and 20mg/kg of chlortetracycline, sulfadiazine and ciprofloxacin, respectively, elicited only a transient perturbation and the bacterial diversity was restored in due course of composting. PMID:22537403

Selvam, Ammaiyappan; Xu, Delin; Zhao, Zhenyong; Wong, Jonathan W C

2012-12-01

133

Dissecting specific and global transcriptional regulation of bacterial gene expression  

PubMed Central

Gene expression is regulated by specific transcriptional circuits but also by the global expression machinery as a function of growth. Simultaneous specific and global regulation thus constitutes an additional—but often neglected—layer of complexity in gene expression. Here, we develop an experimental-computational approach to dissect specific and global regulation in the bacterium Escherichia coli. By using fluorescent promoter reporters, we show that global regulation is growth rate dependent not only during steady state but also during dynamic changes in growth rate and can be quantified through two promoter-specific parameters. By applying our approach to arginine biosynthesis, we obtain a quantitative understanding of both specific and global regulation that allows accurate prediction of the temporal response to simultaneous perturbations in arginine availability and growth rate. We thereby uncover two principles of joint regulation: (i) specific regulation by repression dominates the transcriptional response during metabolic steady states, largely repressing the biosynthesis genes even when biosynthesis is required and (ii) global regulation sets the maximum promoter activity that is exploited during the transition between steady states.

Gerosa, Luca; Kochanowski, Karl; Heinemann, Matthias; Sauer, Uwe

2013-01-01

134

In an early branching metazoan, bacterial colonization of the embryo is controlled by maternal antimicrobial peptides  

PubMed Central

Early embryos of many organisms develop outside the mother and are immediately confronted with myriads of potential colonizers. How these naive developmental stages control and shape the bacterial colonization is largely unknown. Here we show that early embryonic stages of the basal metazoan Hydra are able to control bacterial colonization by using maternal antimicrobial peptides. Antimicrobial peptides of the periculin family selecting for a specific bacterial colonization during embryogenesis are produced in the oocyte and in early embryos. If overexpressed in hydra ectodermal epithelial cells, periculin1a drastically reduces the bacterial load, indicating potent antimicrobial activity. Unexpectedly, transgenic polyps also revealed that periculin, in addition to bactericidal activity, changes the structure of the bacterial community. These findings delineate a role for antimicrobial peptides both in selecting particular bacterial partners during development and as important components of a “be prepared” strategy providing transgenerational protection.

Fraune, Sebastian; Augustin, Rene; Anton-Erxleben, Friederike; Wittlieb, Jorg; Gelhaus, Christoph; Klimovich, Vladimir B.; Samoilovich, Marina P.; Bosch, Thomas C. G.

2010-01-01

135

Differential gene expression in bacterial symbionts from loliginid squids demonstrates variation between mutualistic and environmental niches  

PubMed Central

Summary Luminescent bacteria (?-Proteobacteria: Vibrionaceae) are found in complex bilobed light organs of both sepiolid and loliginid squids (Mollusca: Cephalopoda). Despite the existence of multiple strain colonization between Vibrio bacteria and loliginid squids, specificity at the genus level still exists and may influence interactions between symbiotic and free-living stages of the symbiont. The environmentally transmitted behaviour of Vibrio symbionts bestows a certain degree of recognition that exists prior and subsequent to the colonization process. Therefore, we identified bacterial genes required for successful colonization of loliginid light organs by examining transcripts solely expressed in either the light organ or free-living stages. Selective capture of transcribed sequences (SCOTS) was used to differentiate genes expressed by the same bacterium when thriving in two different environments (i.e. loliginid light organs and seawater). Genes specific for squid light organs included vulnibactin synthetase, outer membrane protein W and dihydroxy dehydratase, which have been associated with the maintenance of bacterial host associations in other systems. In contrast, genes that were solely expressed in the free-living condition consisted of transcripts recognized as important factors for bacterial survival in the environment. These transcripts included genes for methyl accepting chemotaxis proteins, arginine decarboxylase and chitinase. These results provide valuable information regarding mechanisms determining specificity, establishment, and maintenance of bacteria–squid associations.

Guerrero-Ferreira, Ricardo C.; Nishiguchi, Michele K.

2010-01-01

136

Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins.  

PubMed

Most proteins comprise one or several domains. New domain architectures can be created by combining previously existing domains. The elementary events that create new domain architectures may be categorized into three classes, namely domain(s) insertion or deletion (indel), exchange and repetition. Using 'DomainTeam', a tool dedicated to the search for microsyntenies of domains, we quantified the relative contribution of these events. This tool allowed us to collect homologous bacterial genes encoding proteins that have obviously evolved by modular assembly of domains. We show that indels are the most frequent elementary events and that they occur in most cases at either the N- or C-terminus of the proteins. As revealed by the genomic neighbourhood/context of the corresponding genes, we show that a substantial number of these terminal indels are the consequence of gene fusions/fissions. We provide evidence showing that the contribution of gene fusion/fission to the evolution of multi-domain bacterial proteins is lower-bounded by 27% and upper-bounded by 64%. We conclude that gene fusion/fission is a major contributor to the evolution of multi-domain bacterial proteins. PMID:16601004

Pasek, Sophie; Risler, Jean-Loup; Brézellec, Pierre

2006-06-15

137

Horizontal gene transfer and the evolution of bacterial and archaeal population structure.  

PubMed

Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat-association of nascent populations. Further, we hypothesize that subpopulations can evolve through local gene-exchange networks by tapping into a gene pool that is adaptive towards local, continuously changing organismic interactions and is, to a large degree, responsible for the observed rapid gene turnover. Overall, these insights help to explain how bacteria and archaea form populations that display both ecological cohesion and high genomic diversity. PMID:23332119

Polz, Martin F; Alm, Eric J; Hanage, William P

2013-03-01

138

Horizontal Gene Transfer and the Evolution of Bacterial and Archaeal Population Structure  

PubMed Central

Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat association of nascent populations. Further, we hypothesize that subpopulations can evolve through local gene exchange networks by tapping into a gene pool that is adaptive towards local, continuously changing organismic interactions and is, to a large degree, responsible for the observed rapid gene turnover. Overall, these insights help explain how bacteria and archaea form populations that display both ecological cohesion and high genomic diversity.

Alm, Eric J.; Hanage, William P.

2013-01-01

139

Role of starvation genes in the survival of deep subsurface bacterial communities. Final report  

SciTech Connect

The investigation dealt with several aspects of subsurface bacterial survival and their nature. Mutants of Pseudomonas putida, a common environmental bacterium with counterparts in the subsurface, were isolated by transposon mutagenesis. These mutants were highly sensitive to starvation stress. Reporter gene fusions also showed that these genes were starvation genes since they were induced several fold when the cultures were started. Since the regulatory religions (promoters) of starvation genes are of interest in bioremediation and in experiments designed to understand the roles of starvation genes in the maintenance of microbial community structure, the promoter of one of these genes (pstarv1, contained in strain MK107) was characterized in detail. As a preliminary to these studies, the growth characteristics of Pseudomonas putida MK1 and MK107 were compared for cells growing in batch cultures or as an attached monolayer in microstat cultures.

Matin, A. [Stanford Univ., CA (United States). Dept. of Microbiology and Immunology; Schmidt, T. [Michigan State Univ., East Lansing, MI (United States). Dept. of Microbiology; Caldwell, D. [Univ. of Saskatchewan, Saskatoon, Saskatchewan (Canada). Dept. of Microbiology

1998-11-01

140

Reduced Set of Virulence Genes Allows High Accuracy Prediction of Bacterial Pathogenicity in Humans  

PubMed Central

Although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. The advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes, for both known human pathogenic and non-pathogenic strains; this information is now available to investigate genetic features that determine pathogenic phenotypes in bacteria. In this work we determined presence/absence patterns of different virulence-related genes among more than finished bacterial genomes from both human pathogenic and non-pathogenic strains, belonging to different taxonomic groups (i.e: Actinobacteria, Gammaproteobacteria, Firmicutes, etc.). An accuracy of 95% using a cross-fold validation scheme with in-fold feature selection is obtained when classifying human pathogens and non-pathogens. A reduced subset of highly informative genes () is presented and applied to an external validation set. The statistical model was implemented in the BacFier v1.0 software (freely available at ), that displays not only the prediction (pathogen/non-pathogen) and an associated probability for pathogenicity, but also the presence/absence vector for the analyzed genes, so it is possible to decipher the subset of virulence genes responsible for the classification on the analyzed genome. Furthermore, we discuss the biological relevance for bacterial pathogenesis of the core set of genes, corresponding to eight functional categories, all with evident and documented association with the phenotypes of interest. Also, we analyze which functional categories of virulence genes were more distinctive for pathogenicity in each taxonomic group, which seems to be a completely new kind of information and could lead to important evolutionary conclusions.

Iraola, Gregorio; Vazquez, Gustavo; Spangenberg, Lucia; Naya, Hugo

2012-01-01

141

Bacterial Control of Aquatic Algal Populations - Phase II.  

National Technical Information Service (NTIS)

Experiments are described utilizing the bacterial species Bdellovibrio bacteriovorus and Myxococcus xanthus to inhibit and subsequently lyse the cyanobacterial species, Phormidium luridum. Culture supernatants of B. bacteriovorus were shown to inhibit the...

J. C. Burnham

1981-01-01

142

Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.  

PubMed

Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. We identified 24, single-copy, ubiquitous genes suitable for this phylogenetic analysis. We used two approaches to combine the data for the 24 genes. First, we concatenated alignments of all genes into a single alignment from which a Maximum Likelihood (ML) tree was inferred using RAxML. Second, we used a relatively new approach to combining gene data, Bayesian Concordance Analysis (BCA), as implemented in the BUCKy software, in which the results of 24 single-gene phylogenetic analyses are used to generate a "primary concordance" tree. A comparison of the concatenated ML tree and the primary concordance (BUCKy) tree reveals that the two approaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene. After comparing the results and the methods used, we conclude that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes. PMID:23638103

Lang, Jenna Morgan; Darling, Aaron E; Eisen, Jonathan A

2013-01-01

143

Bacterial and fungal chitinase chiJ orthologs evolve under different selective constraints following horizontal gene transfer  

PubMed Central

Background Certain bacteria from the genus Streptomyces are currently used as biological control agents against plant pathogenic fungi. Hydrolytic enzymes that degrade fungal cell wall components, such as chitinases, are suggested as one possible mechanism in biocontrol interactions. Adaptive evolution of chitinases are previously reported for plant chitinases involved in defence against fungal pathogens, and in fungal chitinases involved in fungal-fungal interactions. In this study we investigated the molecular evolution of chitinase chiJ in the bacterial genus Streptomyces. In addition, as chiJ orthologs are previously reported in certain fungal species as a result from horizontal gene transfer, we conducted a comparative study of differences in evolutionary patterns between bacterial and fungal taxa. Findings ChiJ contained three sites evolving under strong positive selection and four groups of co-evolving sites. Regions of high amino acid diversity were predicted to be surface-exposed and associated with coil regions that connect certain ?-helices and ?-strands in the family 18 chitinase TIM barrel structure, but not associated with the catalytic cleft. The comparative study with fungal ChiJ orthologs identified three regions that display signs of type 1 functional divergence, where unique adaptations in the bacterial and fungal taxa are driven by positive selection. Conclusions The identified surface-exposed regions of chitinase ChiJ where sequence diversification is driven by positive selection may putatively be related to functional divergence between bacterial and fungal orthologs. These results show that ChiJ orthologs have evolved under different selective constraints following the horizontal gene transfer event.

2012-01-01

144

Could bacteriophages transfer antibiotic resistance genes from environmental bacteria to human-body associated bacterial populations?  

PubMed Central

Environments without any contact with anthropogenic antibiotics show a great abundance of antibiotic resistance genes that use to be chromosomal and are part of the core genes of the species that harbor them. Some of these genes are shared with human pathogens where they appear in mobile genetic elements. Diversity of antibiotic resistance genes in non-contaminated environments is much greater than in human and animal pathogens, and in environments contaminated with antibiotic from anthropogenic activities. This suggests the existence of some bottleneck effect for the mobilization of antibiotic resistance genes among different biomes. Bacteriophages have characteristics that make them suitable vectors between different biomes, and as well for transferring genes from biome to biome. Recent metagenomic studies and detection of bacterial genes by genomic techniques in the bacteriophage fraction of different microbiota provide indirect evidences that the mobilization of genes mediated by phages, including antibiotic resistance genes, is far more relevant than previously thought. Our hypothesis is that bacteriophages might be of critical importance for evading one of the bottlenecks, the lack of ecological connectivity that modulates the pass of antibiotic resistance genes from natural environments such as waters and soils, to animal and human microbiomes. This commentary concentrates on the potential importance of bacteriophages in transferring resistance genes from the environment to human and animal body microbiomes, but there is no doubt that transduction occurs also in body microbiomes.

Muniesa, Maite; Colomer-Lluch, Marta; Jofre, Juan

2013-01-01

145

Bacterial chitinase with phytopathogen control capacity from suppressive soil revealed by functional metagenomics.  

PubMed

Plant disease caused by fungal pathogens results in vast crop damage globally. Microbial communities of soil that is suppressive to fungal crop disease provide a source for the identification of novel enzymes functioning as bioshields against plant pathogens. In this study, we targeted chitin-degrading enzymes of the uncultured bacterial community through a functional metagenomics approach, using a fosmid library of a suppressive soil metagenome. We identified a novel bacterial chitinase, Chi18H8, with antifungal activity against several important crop pathogens. Sequence analyses show that the chi18H8 gene encodes a 425-amino acid protein of 46 kDa with an N-terminal signal peptide, a catalytic domain with the conserved active site F175DGIDIDWE183, and a chitinase insertion domain. Chi18H8 was expressed (pGEX-6P-3 vector) in Escherichia coli and purified. Enzyme characterization shows that Chi18H8 has a prevalent chitobiosidase activity with a maximum activity at 35 °C at pH lower than 6, suggesting a role as exochitinase on native chitin. To our knowledge, Chi18H8 is the first chitinase isolated from a metagenome library obtained in pure form and which has the potential to be used as a candidate agent for controlling fungal crop diseases. Furthermore, Chi18H8 may also answer to the demand for novel chitin-degrading enzymes for a broad range of other industrial processes and medical purposes. PMID:24121932

Hjort, Karin; Prest, Ilaria; Elväng, Annelie; Marinell, Flavia; Sjöling, Sara

2014-03-01

146

Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens.  

PubMed

Mobile genetic elements (MGEs) encoding virulence and resistance genes are widespread in bacterial pathogens, but it has remained unclear how they occasionally jump to new host species. Staphylococcus aureus clones exchange MGEs such as S. aureus pathogenicity islands (SaPIs) with high frequency via helper phages. Here we report that the S. aureus ST395 lineage is refractory to horizontal gene transfer (HGT) with typical S. aureus but exchanges SaPIs with other species and genera including Staphylococcus epidermidis and Listeria monocytogenes. ST395 produces an unusual wall teichoic acid (WTA) resembling that of its HGT partner species. Notably, distantly related bacterial species and genera undergo efficient HGT with typical S. aureus upon ectopic expression of S. aureus WTA. Combined with genomic analyses, these results indicate that a 'glycocode' of WTA structures and WTA-binding helper phages permits HGT even across long phylogenetic distances thereby shaping the evolution of Gram-positive pathogens. PMID:23965785

Winstel, Volker; Liang, Chunguang; Sanchez-Carballo, Patricia; Steglich, Matthias; Munar, Marta; Bröker, Barbara M; Penadés, Jose R; Nübel, Ulrich; Holst, Otto; Dandekar, Thomas; Peschel, Andreas; Xia, Guoqing

2013-01-01

147

Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens  

PubMed Central

Mobile genetic elements (MGEs) encoding virulence and resistance genes are widespread in bacterial pathogens, but it has remained unclear how they occasionally jump to new host species. Staphylococcus aureus clones exchange MGEs such as S. aureus pathogenicity islands (SaPIs) with high frequency via helper phages. Here we report that the S. aureus ST395 lineage is refractory to horizontal gene transfer (HGT) with typical S. aureus but exchanges SaPIs with other species and genera including Staphylococcus epidermidis and Listeria monocytogenes. ST395 produces an unusual wall teichoic acid (WTA) resembling that of its HGT partner species. Notably, distantly related bacterial species and genera undergo efficient HGT with typical S. aureus upon ectopic expression of S. aureus WTA. Combined with genomic analyses, these results indicate that a ‘glycocode’ of WTA structures and WTA-binding helper phages permits HGT even across long phylogenetic distances thereby shaping the evolution of Gram-positive pathogens.

Winstel, Volker; Liang, Chunguang; Sanchez-Carballo, Patricia; Steglich, Matthias; Munar, Marta; Broker, Barbara M.; Penades, Jose R.; Nubel, Ulrich; Holst, Otto; Dandekar, Thomas; Peschel, Andreas; Xia, Guoqing

2013-01-01

148

Upslope dissolved organic matter controls bacterial activity through shifts in community composition  

NASA Astrophysics Data System (ADS)

Water moving through heterogeneous catchments supplies distinct down-slope bacterial communities with dissolved organic matter (DOM) of distinct chemical composition. Yet interactions between DOM sources and bacterial communities are not well understood at the catchment level. To investigate how upslope DOM influences bacterial activity and community composition, we used mesocosm experiments to manipulate DOM source from along a toposequence fed to down-slope bacteria. We measured bacterial production (BP) throughout the experiment and characterized DOM chemistry and bacterial community composition (using denaturing gradient gel electrophoresis of 16S rRNA) at the beginning and end of the experiment. Compared to lake controls, lake bacteria fed soil water DOM had higher integrated BP (420%) and DOC-specific BP (532%). Addition of upslope DOM to lake bacteria shifted community composition in the direction of the community from which the DOM originated relative to controls. Results demonstrated a surprisingly complete functional redundancy among natural soil, stream, and lake water communities, and showed that DOM controlled the level of bacterial activity, but only through alterations in bacterial community composition. We suggest that water flow through catchments will govern these interactions by influencing contact time between DOM and bacterial communities.

Judd, K. E.; Crump, B. C.; Kling, G. W.

2005-05-01

149

Bacterial gene expression detected in human faeces by reverse transcription-PCR  

Microsoft Academic Search

A method to isolate and specifically detect bacterial messenger RNA (mRNA) in human faeces is presented. The surface layer protein gene slpA of Lactobacillus acidophilus ATCC 4356T was chosen as a model system because it is transcribed at a high level to a relatively stable mRNA (Boot et al., 1996, J. Bacteriol. 178, 5388–5394). A simulation of the recovery of

Nora A. Fitzsimons; Antoon D. L. Akkermans; Willem M. de Vos; Elaine E. Vaughan

2003-01-01

150

Fine mapping of a resistance gene to bacterial leaf pustule in soybean  

Microsoft Academic Search

Soybean bacterial leaf pustule (BLP) is a prevalent disease caused by Xanthomonas axonopodis pv. glycines. Fine mapping of the BLP resistant gene, rxp, is needed to select BLP resistant soybean cultivars by marker-assisted selection (MAS). We used a total of 227 recombinant\\u000a inbred lines (RILs) derived from a cross between ‘Taekwangkong’ (BLP susceptible) and ‘Danbaekkong’ (BLP resistant) for rxp fine

Dong Hyun Kim; Kil Hyun Kim; Kyujung Van; Moon Young Kim; Suk-Ha Lee

2010-01-01

151

Sequence Tagged Site Marker-Assisted Selection for Three Bacterial Blight Resistance Genes in Rice  

Microsoft Academic Search

identification of DNA markers linked to desirable genes or QTL affecting target traits is a prerequisite for MAS. IR65598-112 and the two sister lines IR65600-42 and IR65600-96 Conventional breeding brought major increases in are promising new plant type (NPT) rice lines with high yield potential. rice production through the modern high-yielding varie- However, these lines are susceptible to bacterial blight

A. C. Sanchez; D. S. Brar; N. Huang; Z. Li; G. S. Khush

2000-01-01

152

CONJUGAL GENE TRANSFER IN THE RHIZOSPHERE OF WATER GRASS (ECHINOCHLORA CRUSGALLI): INFLUENCE OF ROOT EXUDATE AND BACTERIAL ACTIVITY  

EPA Science Inventory

The premise that genetic exchange is primarily localized in niches characterized by dense bacterial populations and high availability of growth substrates was tested by relating conjugal gene transfer of an RP4 derivative to availability of root exudates and bacterial metabolic a...

153

Anti-inflammatory effect and prostate gene expression profiling of steryl ferulate on experimental rats with non-bacterial prostatitis.  

PubMed

Steryl ferulate (SF) is a bioactive mixture extracted from rice bran and shows higher inhibitory activity against inflammation than the corresponding free sterols. In this study, the aim was to investigate the anti-inflammatory effect and prostate gene expression profiling of SF using a Xiaozhiling-induced non-bacterial prostatitis (NBP) rat model. The anti-inflammatory effect was evaluated by prostate weight, prostate index, acid phosphatase, density of lecithin corpuscles (DLC), white blood cell count (WBC), and prostatic histologic section. Prostate gene expression profiling was assessed by a cDNA microarray and validated by quantitative real-time PCR of five selected genes. Pathway analysis and Gene ontology (GO) analysis were applied to determine the roles of these differentially expressed genes involved in these biological pathways or GO terms. SF treatment could significantly inhibit prostate weight, prostate index, total acid phosphatase, prostatic acid phosphatase and WBC, suppress the severity of histological lesion and increase the DLC. Compared with the control group, the SF treatment group contained 238 up-regulated genes and 111 down-regulated genes. GO analysis demonstrated that the most significant expression genes were closely related to the terms of fibrinolysis, inflammatory response, high-density lipoprotein particle, protein-lipid complex, enzyme inhibitor activity, peptidase inhibitor activity and others. Canonical pathway analysis indicated five pathways were significantly regulated, which were associated with inflammation and tumorgenesis. In conclusion, SF may be used as a health supplement to prevent NBP, in that it could inhibit prostate inflammation in NBP patients by affecting the expression of genes in the related GO terms and pathways. PMID:24686498

Hu, Yinzhou; Xiong, Lina; Huang, Weisu; Cai, Huafang; Luo, Yanxi; Zhang, Ying; Lu, Baiyi

2014-06-28

154

Ras GTPase-like protein MglA, a controller of bacterial social-motility in Myxobacteria, has evolved to control bacterial predation by Bdellovibrio.  

PubMed

Bdellovibrio bacteriovorus invade Gram-negative bacteria in a predatory process requiring Type IV pili (T4P) at a single invasive pole, and also glide on surfaces to locate prey. Ras-like G-protein MglA, working with MglB and RomR in the deltaproteobacterium Myxococcus xanthus, regulates adventurous gliding and T4P-mediated social motility at both M. xanthus cell poles. Our bioinformatic analyses suggested that the GTPase activating protein (GAP)-encoding gene mglB was lost in Bdellovibrio, but critical residues for MglA(Bd) GTP-binding are conserved. Deletion of mglA(Bd) abolished prey-invasion, but not gliding, and reduced T4P formation. MglA(Bd) interacted with a previously uncharacterised tetratricopeptide repeat (TPR) domain protein Bd2492, which we show localises at the single invasive pole and is required for predation. Bd2492 and RomR also interacted with cyclic-di-GMP-binding receptor CdgA, required for rapid prey-invasion. Bd2492, RomR(Bd) and CdgA localize to the invasive pole and may facilitate MglA-docking. Bd2492 was encoded from an operon encoding a TamAB-like secretion system. The TamA protein and RomR were found, by gene deletion tests, to be essential for viability in both predatory and non-predatory modes. Control proteins, which regulate bipolar T4P-mediated social motility in swarming groups of deltaproteobacteria, have adapted in evolution to regulate the anti-social process of unipolar prey-invasion in the "lone-hunter" Bdellovibrio. Thus GTP-binding proteins and cyclic-di-GMP inputs combine at a regulatory hub, turning on prey-invasion and allowing invasion and killing of bacterial pathogens and consequent predatory growth of Bdellovibrio. PMID:24721965

Milner, David S; Till, Rob; Cadby, Ian; Lovering, Andrew L; Basford, Sarah M; Saxon, Emma B; Liddell, Susan; Williams, Laura E; Sockett, R Elizabeth

2014-04-01

155

Ras GTPase-Like Protein MglA, a Controller of Bacterial Social-Motility in Myxobacteria, Has Evolved to Control Bacterial Predation by Bdellovibrio  

PubMed Central

Bdellovibrio bacteriovorus invade Gram-negative bacteria in a predatory process requiring Type IV pili (T4P) at a single invasive pole, and also glide on surfaces to locate prey. Ras-like G-protein MglA, working with MglB and RomR in the deltaproteobacterium Myxococcus xanthus, regulates adventurous gliding and T4P-mediated social motility at both M. xanthus cell poles. Our bioinformatic analyses suggested that the GTPase activating protein (GAP)-encoding gene mglB was lost in Bdellovibrio, but critical residues for MglABd GTP-binding are conserved. Deletion of mglABd abolished prey-invasion, but not gliding, and reduced T4P formation. MglABd interacted with a previously uncharacterised tetratricopeptide repeat (TPR) domain protein Bd2492, which we show localises at the single invasive pole and is required for predation. Bd2492 and RomR also interacted with cyclic-di-GMP-binding receptor CdgA, required for rapid prey-invasion. Bd2492, RomRBd and CdgA localize to the invasive pole and may facilitate MglA-docking. Bd2492 was encoded from an operon encoding a TamAB-like secretion system. The TamA protein and RomR were found, by gene deletion tests, to be essential for viability in both predatory and non-predatory modes. Control proteins, which regulate bipolar T4P-mediated social motility in swarming groups of deltaproteobacteria, have adapted in evolution to regulate the anti-social process of unipolar prey-invasion in the “lone-hunter” Bdellovibrio. Thus GTP-binding proteins and cyclic-di-GMP inputs combine at a regulatory hub, turning on prey-invasion and allowing invasion and killing of bacterial pathogens and consequent predatory growth of Bdellovibrio.

Milner, David S.; Till, Rob; Cadby, Ian; Lovering, Andrew L.; Basford, Sarah M.; Saxon, Emma B.; Liddell, Susan; Williams, Laura E.; Sockett, R. Elizabeth

2014-01-01

156

Sticky Situations: Key Components That Control Bacterial Surface Attachment  

PubMed Central

The formation of bacterial biofilms is initiated by cells transitioning from the free-swimming mode of growth to a surface. This review is aimed at highlighting the common themes that have emerged in recent research regarding the key components, signals, and cues that aid in the transition and those involved in establishing a more permanent surface association during initial attachment.

Petrova, Olga E.

2012-01-01

157

Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene.  

PubMed

Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an increasingly important yield constraint in this staple crop. A mesophyll colonizer, Xoc differs from X. oryzae pv. oryzae (Xoo), which invades xylem to cause bacterial blight of rice. Both produce multiple distinct TAL effectors, type III-delivered proteins that transactivate effector-specific host genes. A TAL effector finds its target(s) via a partially degenerate code whereby the modular effector amino acid sequence identifies nucleotide sequences to which the protein binds. Virulence contributions of some Xoo TAL effectors have been shown, and their relevant targets, susceptibility (S) genes, identified, but the role of TAL effectors in leaf streak is uncharacterized. We used host transcript profiling to compare leaf streak to blight and to probe functions of Xoc TAL effectors. We found that Xoc and Xoo induce almost completely different host transcriptional changes. Roughly one in three genes upregulated by the pathogens is preceded by a candidate TAL effector binding element. Experimental analysis of the 44 such genes predicted to be Xoc TAL effector targets verified nearly half, and identified most others as false predictions. None of the Xoc targets is a known bacterial blight S gene. Mutational analysis revealed that Tal2g, which activates two genes, contributes to lesion expansion and bacterial exudation. Use of designer TAL effectors discriminated a sulfate transporter gene as the S gene. Across all targets, basal expression tended to be higher than genome-average, and induction moderate. Finally, machine learning applied to real vs. falsely predicted targets yielded a classifier that recalled 92% of the real targets with 88% precision, providing a tool for better target prediction in the future. Our study expands the number of known TAL effector targets, identifies a new class of S gene, and improves our ability to predict functional targeting. PMID:24586171

Cernadas, Raul A; Doyle, Erin L; Niño-Liu, David O; Wilkins, Katherine E; Bancroft, Timothy; Wang, Li; Schmidt, Clarice L; Caldo, Rico; Yang, Bing; White, Frank F; Nettleton, Dan; Wise, Roger P; Bogdanove, Adam J

2014-02-01

158

Control of gene expression by type III secretory activity  

PubMed Central

Summary The bacterial flagellum and the highly related injectisome (or needle complex) are among the most complicated multi-protein structures found in Gram-negative microorganisms. The assembly of both structures is dependent upon a type III secretion system. An interesting regulatory feature unique to these systems is the coordination of gene expression with type III secretory activity. This means of regulation ensures that secretion substrates are expressed only when required during the assembly process or upon completion of the fully functional structure. Prominent within the regulatory scheme are secreted proteins and type III secretion chaperones that exert effects on gene expression at the transcriptional and post-transcriptional levels. Although the major structural components of the flagellum and injectisome systems are highly conserved, recent studies reveal diversity in the mechanisms used by secretion substrates and chaperones to control gene expression.

Brutinel, Evan D.; Yahr, Timothy L.

2008-01-01

159

Gene expression in gut symbiotic organ of stinkbug affected by extracellular bacterial symbiont.  

PubMed

The bean bug Riptortus pedestris possesses a specialized symbiotic organ in a posterior region of the midgut, where numerous crypts harbor extracellular betaproteobacterial symbionts of the genus Burkholderia. Second instar nymphs orally acquire the symbiont from the environment, and the symbiont infection benefits the host by facilitating growth and by occasionally conferring insecticide resistance. Here we performed comparative transcriptomic analyses of insect genes expressed in symbiotic and non-symbiotic regions of the midgut dissected from Burkholderia-infected and uninfected R. pedestris. Expression sequence tag analysis of cDNA libraries and quantitative reverse transcription PCR identified a number of insect genes expressed in symbiosis- or aposymbiosis-associated patterns. For example, genes up-regulated in symbiotic relative to aposymbiotic individuals, including many cysteine-rich secreted protein genes and many cathepsin protease genes, are likely to play a role in regulating the symbiosis. Conversely, genes up-regulated in aposymbiotic relative to symbiotic individuals, including a chicken-type lysozyme gene and a defensin-like protein gene, are possibly involved in regulation of non-symbiotic bacterial infections. Our study presents the first transcriptomic data on gut symbiotic organ of a stinkbug, which provides initial clues to understanding of molecular mechanisms underlying the insect-bacterium gut symbiosis and sheds light on several intriguing commonalities between endocellular and extracellular symbiotic associations. PMID:23691247

Futahashi, Ryo; Tanaka, Kohjiro; Tanahashi, Masahiko; Nikoh, Naruo; Kikuchi, Yoshitomo; Lee, Bok Luel; Fukatsu, Takema

2013-01-01

160

Importance of Combinatorial Gene Control  

NSDL National Science Digital Library

A hypothetical scheme illustrating how combinations of a few gene regulatory proteins can generate many different cell types during development. In this simple scheme a "decision" to make a new gene regulatory protein (shown as a numbered circle) is made after each cell division. Repetition of this simple rule enables eight cell types (A through H) to be created using only three different regulatory proteins. Each of these hypothetical cell types would then express different genes, as dictated by the combination of gene regulatory proteins that are present within it.

BEGIN:VCARD VERSION:2.1 FN:Bruce Alberts N:Alberts;Bruce REV:2005-04-16 END:VCARD; BEGIN:VCARD VERSION:2.1 FN:Dennis Bray N:Bray;Dennis REV:2005-04-16 END:VCARD; BEGIN:VCARD VERSION:2.1 FN:Alexander Johnson N:Johnson;Alexander REV:2005-04-16 END:VCARD; BEGIN:VCARD VERSION:2.1 FN:Julian Lewis N:Lewis;Julian REV:2005-04-16 END:VCARD; BEGIN:VCARD VERSION:2.1 FN:Martin Raff N:Raff;Martin REV:2005-04-16 END:VCARD; BEGIN:VCARD VERSION:2.1 FN:Keith Roberts N:Roberts;Keith REV:2005-04-16 END:VCARD

1998-07-01

161

Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics  

PubMed Central

Antibiotics such as erythromycin and rifampicin, at low concentrations, alter global bacterial transcription patterns as measured by the stimulation or inhibition of a variety of promoter–lux reporter constructs in a Salmonella typhimurium library. Analysis of a 6,500-clone library indicated that as many as 5% of the promoters may be affected, comprising genes for a variety of functions, as well as a significant fraction of genes with no known function. Studies of a selection of the reporter clones showed that stimulation varied depending on the nature of the antibiotic, the promoter, and what culture medium was used; the response differed on solid as compared with liquid media. Transcription was markedly reduced in antibiotic-resistant hosts, but the presence of mutations deficient in stress responses such as SOS or universal stress did not prevent antibiotic-induced modulation. The results show that small molecules may have contrasting effects on bacteria depending on their concentration: either the modulation of bacterial metabolism by altering transcription patterns or the inhibition of growth by the inhibition of specific target functions. Both activities could play important roles in the regulation of microbial communities. These studies indicate that the detection of pharmaceutically useful natural product inhibitors could be effectively achieved by measuring activation of transcription at low concentrations in high-throughput assays using appropriate bacterial promoter–reporter constructs.

Goh, Ee-Been; Yim, Grace; Tsui, Wayne; McClure, JoAnn; Surette, Michael G.; Davies, Julian

2002-01-01

162

Canine Uterine Bacterial Infection Induces Upregulation of Proteolysis-Related Genes and Downregulation of Homeobox and Zinc Finger Factors  

PubMed Central

Background Bacterial infection with the severe complication of sepsis is a frequent and serious condition, being a major cause of death worldwide. To cope with the plethora of occurring bacterial infections there is therefore an urgent need to identify molecular mechanisms operating during the host response, in order both to identify potential targets for therapeutic intervention and to identify biomarkers for disease. Here we addressed this issue by studying global gene expression in uteri from female dogs suffering from spontaneously occurring uterine bacterial infection. Principal Findings The analysis showed that almost 800 genes were significantly (p<0.05) upregulated (>2-fold) in the uteri of diseased animals. Among these were numerous chemokine and cytokine genes, as well as genes associated with inflammatory cell extravasation, anti-bacterial action, the complement system and innate immune responses, as well as proteoglycan-associated genes. There was also a striking representation of genes associated with proteolysis. Robust upregulation of immunoglobulin components and genes involved in antigen presentation was also evident, indicating elaboration of a strong adaptive immune response. The bacterial infection was also associated with a significant downregulation of almost 700 genes, of which various homeobox and zinc finger transcription factors were highly represented. Conclusions/Significance Together, these finding outline the molecular patterns involved in bacterial infection of the uterus. The study identified altered expression of numerous genes not previously implicated in bacterial disease, and several of these may be evaluated for potential as biomarkers of disease or as therapeutic targets. Importantly, since humans and dogs show genetic similarity and develop diseases that share many characteristics, the molecular events identified here are likely to reflect the corresponding situation in humans afflicted by similar disease.

Hagman, Ragnvi; Ronnberg, Elin; Pejler, Gunnar

2009-01-01

163

Copper control of bacterial nitrous oxide emission and its impact on vitamin B12-dependent metabolism  

PubMed Central

Global agricultural emissions of the greenhouse gas nitrous oxide (N2O) have increased by around 20% over the last 100 y, but regulation of these emissions and their impact on bacterial cellular metabolism are poorly understood. Denitrifying bacteria convert nitrate in soils to inert di-nitrogen gas (N2) via N2O and the biochemistry of this process has been studied extensively in Paracoccus denitrificans. Here we demonstrate that expression of the gene encoding the nitrous oxide reductase (NosZ), which converts N2O to N2, is regulated in response to the extracellular copper concentration. We show that elevated levels of N2O released as a consequence of decreased cellular NosZ activity lead to the bacterium switching from vitamin B12-dependent to vitamin B12-independent biosynthetic pathways, through the transcriptional modulation of genes controlled by vitamin B12 riboswitches. This inhibitory effect of N2O can be rescued by addition of exogenous vitamin B12.

Sullivan, Matthew J.; Gates, Andrew J.; Appia-Ayme, Corinne; Rowley, Gary; Richardson, David J.

2013-01-01

164

Prominent down-regulation of storage protein genes after bacterial challenge in eri-silkworm, Samia cynthia ricini.  

PubMed

We constructed two independent cDNA libraries from the fat body of Escherichia coli- or Candida albicans-challenged eri-silkworm Samia cynthia ricini larvae. We performed comparative expressed sequence tag (EST) analysis of the two cDNA libraries and found that two putative storage protein genes, ScSP1 and ScSP2, were markedly repressed by E. coli injection as compared with C. albicans injection. By quantitative real-time RT-PCR analysis, we showed that ScSP1 mRNA significantly reduced to 1/32-1/3 in the fat body of the female larvae, and ScSP2 mRNA reduced to 1/7-1/3 and 1/22-1/5 in the females and males, respectively, 12-36 h after E. coli injection as compared with PBS injection. In addition, SDS-PAGE analysis revealed that the accumulation of both the ScSP proteins in the larval hemolymph apparently decreased up to 36 h after E. coli injection. However, the amounts of the two ScSP proteins returned to the same level as those in the larvae injected with PBS by 48 h after injection, showing that the reduction in ScSPs caused by the bacterial challenge was transient. Moreover, potential binding sites for the Drosophila Rel/NF-kappaB protein Dorsal were found in the 5' upstream regulatory regions of ScSP1 and ScSP2, suggesting the participation of the Rel/NF-kappaB proteins in controlling the bacterial suppression of the ScSP genes. These results suggested the hypothesis that S. c. ricini has a genetic program to shut down temporarily dispensable gene expression in order to induce an acute and efficient expression of immune-related genes. These findings may provide new insight into the innate immune system in lepidopteran insects. PMID:18064702

Meng, Yan; Omuro, Naoko; Funaguma, Shunsuke; Daimon, Takaaki; Kawaoka, Shinpei; Katsuma, Susumu; Shimada, Toru

2008-01-01

165

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists.  

PubMed

Characterizing ecological relationships between viruses, bacteria and protists in the ocean are critical to understanding ecosystem function, yet these relationships are infrequently investigated together. We evaluated these relationships through microbial association network analysis of samples collected approximately monthly from March 2008 to January 2011 in the surface ocean (0-5 m) at the San Pedro Ocean Time series station. Bacterial, T4-like myoviral and protistan communities were described by Automated Ribosomal Intergenic Spacer Analysis and terminal restriction fragment length polymorphism of the gene encoding the major capsid protein (g23) and 18S ribosomal DNA, respectively. Concurrent shifts in community structure suggested similar timing of responses to environmental and biological parameters. We linked T4-like myoviral, bacterial and protistan operational taxonomic units by local similarity correlations, which were then visualized as association networks. Network links (correlations) potentially represent synergistic and antagonistic relationships such as viral lysis, grazing, competition or other interactions. We found that virus-bacteria relationships were more cross-linked than protist-bacteria relationships, suggestive of increased taxonomic specificity in virus-bacteria relationships. We also found that 80% of bacterial-protist and 74% of bacterial-viral correlations were positive, with the latter suggesting that at monthly and seasonal timescales, viruses may be following their hosts more often than controlling host abundance. PMID:24196323

Chow, Cheryl-Emiliane T; Kim, Diane Y; Sachdeva, Rohan; Caron, David A; Fuhrman, Jed A

2014-04-01

166

Bacterial foraging-based PI controller of inverter-based distributed generators  

Microsoft Academic Search

This paper introduces a new optimal technique to estimate the PI gains for current regulated inverter control. The PI controller tuning is accomplished using bacterial foraging optimization (BFO) algorithm to reduce voltage and current harmonic distortions and comply with the local grid requirements and interconnection standards. Robust and decoupled active and reactive power control is achieved. The investigation is conducted

Ahmed G. Agamy; Ali H. Kasem Alaboudy; Hossam E. Mostafa; Mahmud Y. Fekry

2011-01-01

167

Bacterial origin of a diverse family of UDP-glycosyltransferase genes in the Tetranychus urticae genome.  

PubMed

UDP-glycosyltransferases (UGTs) catalyze the conjugation of a variety of small lipophilic molecules with uridine diphosphate (UDP) sugars, altering them into more water-soluble metabolites. Thereby, UGTs play an important role in the detoxification of xenobiotics and in the regulation of endobiotics. Recently, the genome sequence was reported for the two-spotted spider mite, Tetranychus urticae, a polyphagous herbivore damaging a number of agricultural crops. Although various gene families implicated in xenobiotic metabolism have been documented in T. urticae, UGTs so far have not. We identified 80 UGT genes in the T. urticae genome, the largest number of UGT genes in a metazoan species reported so far. Phylogenetic analysis revealed that lineage-specific gene expansions increased the diversity of the T. urticae UGT repertoire. Genomic distribution, intron-exon structure and structural motifs in the T. urticae UGTs were also described. In addition, expression profiling after host-plant shifts and in acaricide resistant lines supported an important role for UGT genes in xenobiotic metabolism. Expanded searches of UGTs in other arachnid species (Subphylum Chelicerata), including a spider, a scorpion, two ticks and two predatory mites, unexpectedly revealed the complete absence of UGT genes. However, a centipede (Subphylum Myriapoda) and a water flea and a crayfish (Subphylum Crustacea) contain UGT genes in their genomes similar to insect UGTs, suggesting that the UGT gene family might have been lost early in the Chelicerata lineage and subsequently re-gained in the tetranychid mites. Sequence similarity of T. urticae UGTs and bacterial UGTs and their phylogenetic reconstruction suggest that spider mites acquired UGT genes from bacteria by horizontal gene transfer. Our findings show a unique evolutionary history of the T. urticae UGT gene family among other arthropods and provide important clues to its functions in relation to detoxification and thereby host adaptation. PMID:24727020

Ahn, Seung-Joon; Dermauw, Wannes; Wybouw, Nicky; Heckel, David G; Van Leeuwen, Thomas

2014-07-01

168

The heat-shock-regulated grpE gene of Escherichia coli is required for bacterial growth at all temperatures but is dispensable in certain mutant backgrounds.  

PubMed Central

Previous work has established that the grpE+ gene product is a heat shock protein that is essential for bacteriophage lambda growth at all temperatures and for Escherichia coli growth at temperatures above 43 degrees C. Here it is shown that the grpE+ gene product is essential for bacterial viability at all temperatures. The strategy required constructing a grpE deletion derivative carrying a selectable chloramphenicol drug resistance marker provided by an omega insertion and showing that this deletion construct can be crossed into the bacterial chromosome if and only if a functional grpE+ gene is present elsewhere in the same cell. As a control, the same omega insertion could be placed immediately downstream of the grpE+ coding sequence without any observable effects on host growth. This result demonstrates that the inability to construct a grpE-deleted E. coli strain is not simply due to a lethal polar effect on neighboring gene expression. Unexpectedly, it was found that the grpE deletion derivative could be crossed into the bacterial chromosome in a strain that was defective in DnaK function. Further analysis showed that it was not the lack of DnaK function per se that allowed E. coli to tolerate a deletion in the grpE+ gene. Rather, it was the presence of unknown extragenic suppressors of a dnaK mutation that somehow compensated for the deficiency in both DnaK and GrpE function. Images

Ang, D; Georgopoulos, C

1989-01-01

169

A novel ion-beam-mutation effect application in identification of gene involved in bacterial antagonism to fungal infection of ornamental crops  

NASA Astrophysics Data System (ADS)

This work is on a novel application of ion beam effect on biological mutation. Bacillus licheniformis (B. licheniformis) is a common soil bacterium with an antagonistic effect on Curcuma alismatifolia Gagnep. and Chrysanthemum indicum Linn. In an attempt to control fungal diseases of local crops by utilizing B. licheniformis, we carried out gene analysis of the bacterium to understand the bacterial antagonistic mechanism. The bacterial cells were bombarded to induce mutations using nitrogen ion beam. After ion bombardment, DNA analysis revealed that the modified polymorphism fragment present in the wild type was missing in a bacterial mutant which lost the antifungal activity. The fragments conserved in the wild type but lost in the mutant bacteria was identified to code for the thioredoxin reductase (TrxR) gene. The gene analysis showed that the TrxR gene from B. licheniformis had the expression of the antagonism to fungi in a synchronous time evolution with the fungus inhibition when the bacteria were co-cultivated with the fungi. The collective results indicate the TrxR gene responsible for the antagonism of bacteria B. licheniformis to fungal infection.

Mahadtanapuk, S.; Teraarusiri, W.; Nanakorn, W.; Yu, L. D.; Thongkumkoon, P.; Anuntalabhochai, S.

2014-05-01

170

A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria reveals a lineage-specific distribution in a soil clay fraction  

Microsoft Academic Search

We designed an oligonucleotide microarray using probe sequences based upon a phylogenetic analysis of 16S rRNA genes recovered from members of the bacterial division Acidobacteria. A total of 42,194 oligonucleotide probes targeting members of the Acidobacteria division at multiple phylogenetic levels were included on a high-density microarray. Positive control hybridizations revealed a linear relationship between hybridization signal and template concentration,

Mark R. Liles; Ozgur Turkmen; Brian F. Manske; Mingzi Zhang; Jean-Marie Rouillard; Isabelle George; Teri Balser; Nedret Billor; Robert M. Goodman

2010-01-01

171

Generation of a Complete Single-Gene Knockout Bacterial Artificial Chromosome Library of Cowpox Virus and Identification of Its Essential Genes  

PubMed Central

Cowpox virus (CPXV) belongs to the genus Orthopoxvirus in the Poxviridae family. It infects a broad range of vertebrates and can cause zoonotic infections. CPXV has the largest genome among the orthopoxviruses and is therefore considered to have the most complete set of genes of all members of the genus. Since CPXV has also become a model for studying poxvirus genetics and pathogenesis, we created and characterized a complete set of single gene knockout bacterial artificial chromosome (BAC) clones of the CPXV strain Brighton Red. These mutants allow a systematic assessment of the contribution of single CPXV genes to the outcome of virus infection and replication, as well as to the virus host range. A full-length BAC clone of CPXV strain Brighton Red (pBRF) harboring the gene expressing the enhanced green fluorescent protein under the control of a viral late promoter was modified by introducing the mrfp1 gene encoding the monomeric red fluorescent protein driven by a synthetic early vaccinia virus promoter. Based on the modified BAC (pBRFseR), a library of targeted knockout mutants for each single viral open reading frame (ORF) was generated. Reconstitution of infectious virus was successful for 109 of the 183 mutant BAC clones, indicating that the deleted genes are not essential for virus replication. In contrast, 74 ORFs were identified as essential because no virus progeny was obtained upon transfection of the mutant BAC clones and in the presence of a helper virus. More than 70% of all late CPXV genes belonged to this latter group of essential genes.

Xu, Zhiyong; Zikos, Dimitrios; Osterrieder, Nikolaus

2014-01-01

172

Biological controls on bacterial populations in ballast water during ocean transit.  

PubMed

Bacteria (and viruses) numerically dominate ballast water communities, but what controls their population dynamics during transit is largely unexplored. Here, bacterial abundance, net and intrinsic growth rates, and grazing mortality were determined during a trans-Atlantic voyage. The effects of grazing pressure by microzooplankton on heterotrophic bacteria during transit were determined for source port, mid-ocean exchange (MOE), and six-day-old source port ballast water. When the grazer component was removed, bacterial abundances significantly increased. Additionally, we determined that the grazer-mediated mortality for ballast water originating from ports was greater than MOE water and that mortality decreased over time for the source port ballast water. This study shows that bacterial populations in transit are controlled by microzooplankton grazing. If these findings are representative of ballast water environments, they suggest that if the grazing component is selectively removed by various treatment methods, bacterial populations may increase; this could have environmental and human health consequences. PMID:24246652

Seiden, Jennica M; Rivkin, Richard B

2014-01-15

173

Bacterial Dimethylsulfoniopropionate Degradation Genes in the Oligotrophic North Pacific Subtropical Gyre  

PubMed Central

Dimethylsulfoniopropionate (DMSP) is an organic sulfur compound that is rapidly metabolized by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methiolpropionate. The abundance and diversity of genes encoding bacterial DMS production (dddP) and demethylation (dmdA) were measured in the North Pacific subtropical gyre (NPSG) between May 2008 and February 2009 at Station ALOHA (22°45?N, 158°00?W) at two depths: 25 m and the deep chlorophyll maximum (DCM; ?100 m). The highest abundance of dmdA genes was in May 2008 at 25 m, with ?16.5% of cells harboring a gene in one of the eight subclades surveyed, while the highest abundance of dddP genes was in July 2008 at 25 m, with ?2% of cells harboring a gene. The dmdA gene pool was consistently dominated by homologs from SAR11 subclades, which was supported by findings in metagenomic data sets derived from Station ALOHA. Expression of the SAR11 dmdA genes was low, with typical transcript:gene ratios between 1:350 and 1:1,400. The abundance of DMSP genes was statistically different between 25 m and the DCM and correlated with a number of environmental variables, including primary production, photosynthetically active radiation, particulate DMSP, and DMS concentrations. At 25 m, dddP abundance was positively correlated with pigments that are diagnostic of diatoms; at the DCM, dmdA abundance was positively correlated with temperature. Based on gene abundance, we hypothesize that SAR11 bacterioplankton dominate DMSP cycling in the oligotrophic NPSG, with lesser but consistent involvement of other members of the bacterioplankton community.

Varaljay, Vanessa A.; Gifford, Scott M.; Wilson, Samuel T.; Sharma, Shalabh; Karl, David M.

2012-01-01

174

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer  

USGS Publications Warehouse

Background: Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results: Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion: We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer. ?? 2009 Pearson et al; licensee BioMed Central Ltd.

Pearson, T.; Giffard, P.; Beckstrom-Sternberg, S.; Auerbach, R.; Hornstra, H.; Tuanyok, A.; Price, E. P.; Glass, M. B.; Leadem, B.; Beckstrom-Sternberg, J. S.; Allan, G. J.; Foster, J. T.; Wagner, D. M.; Okinaka, R. T.; Sim, S. H.; Pearson, O.; Wu, Z.; Chang, J.; Kaul, R.; Hoffmaster, A. R.; Brettin, T. S.; Robison, R. A.; Mayo, M.; Gee, J. E.; Tan, P.; Currie, B. J.; Keim, P.

2009-01-01

175

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer  

PubMed Central

Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.

2009-01-01

176

Analysis of gene expression levels in individual bacterial cells without image segmentation  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer We present a method for extracting gene expression data from images of bacterial cells. Black-Right-Pointing-Pointer The method does not employ cell segmentation and does not require high magnification. Black-Right-Pointing-Pointer Fluorescence and phase contrast images of the cells are correlated through the physics of phase contrast. Black-Right-Pointing-Pointer We demonstrate the method by characterizing noisy expression of comX in Streptococcus mutans. -- Abstract: Studies of stochasticity in gene expression typically make use of fluorescent protein reporters, which permit the measurement of expression levels within individual cells by fluorescence microscopy. Analysis of such microscopy images is almost invariably based on a segmentation algorithm, where the image of a cell or cluster is analyzed mathematically to delineate individual cell boundaries. However segmentation can be ineffective for studying bacterial cells or clusters, especially at lower magnification, where outlines of individual cells are poorly resolved. Here we demonstrate an alternative method for analyzing such images without segmentation. The method employs a comparison between the pixel brightness in phase contrast vs fluorescence microscopy images. By fitting the correlation between phase contrast and fluorescence intensity to a physical model, we obtain well-defined estimates for the different levels of gene expression that are present in the cell or cluster. The method reveals the boundaries of the individual cells, even if the source images lack the resolution to show these boundaries clearly.

Kwak, In Hae; Son, Minjun [Physics Department, University of Florida, P.O. Box 118440, Gainesville, FL 32611-8440 (United States)] [Physics Department, University of Florida, P.O. Box 118440, Gainesville, FL 32611-8440 (United States); Hagen, Stephen J., E-mail: sjhagen@ufl.edu [Physics Department, University of Florida, P.O. Box 118440, Gainesville, FL 32611-8440 (United States)

2012-05-11

177

High-throughput platform for the discovery of elicitors of silent bacterial gene clusters.  

PubMed

Over the past decade, bacterial genome sequences have revealed an immense reservoir of biosynthetic gene clusters, sets of contiguous genes that have the potential to produce drugs or drug-like molecules. However, the majority of these gene clusters appear to be inactive for unknown reasons prompting terms such as "cryptic" or "silent" to describe them. Because natural products have been a major source of therapeutic molecules, methods that rationally activate these silent clusters would have a profound impact on drug discovery. Herein, a new strategy is outlined for awakening silent gene clusters using small molecule elicitors. In this method, a genetic reporter construct affords a facile read-out for activation of the silent cluster of interest, while high-throughput screening of small molecule libraries provides potential inducers. This approach was applied to two cryptic gene clusters in the pathogenic model Burkholderia thailandensis. The results not only demonstrate a prominent activation of these two clusters, but also reveal that the majority of elicitors are themselves antibiotics, most in common clinical use. Antibiotics, which kill B. thailandensis at high concentrations, act as inducers of secondary metabolism at low concentrations. One of these antibiotics, trimethoprim, served as a global activator of secondary metabolism by inducing at least five biosynthetic pathways. Further application of this strategy promises to uncover the regulatory networks that activate silent gene clusters while at the same time providing access to the vast array of cryptic molecules found in bacteria. PMID:24808135

Seyedsayamdost, Mohammad R

2014-05-20

178

High-throughput platform for the discovery of elicitors of silent bacterial gene clusters  

PubMed Central

Over the past decade, bacterial genome sequences have revealed an immense reservoir of biosynthetic gene clusters, sets of contiguous genes that have the potential to produce drugs or drug-like molecules. However, the majority of these gene clusters appear to be inactive for unknown reasons prompting terms such as “cryptic” or “silent” to describe them. Because natural products have been a major source of therapeutic molecules, methods that rationally activate these silent clusters would have a profound impact on drug discovery. Herein, a new strategy is outlined for awakening silent gene clusters using small molecule elicitors. In this method, a genetic reporter construct affords a facile read-out for activation of the silent cluster of interest, while high-throughput screening of small molecule libraries provides potential inducers. This approach was applied to two cryptic gene clusters in the pathogenic model Burkholderia thailandensis. The results not only demonstrate a prominent activation of these two clusters, but also reveal that the majority of elicitors are themselves antibiotics, most in common clinical use. Antibiotics, which kill B. thailandensis at high concentrations, act as inducers of secondary metabolism at low concentrations. One of these antibiotics, trimethoprim, served as a global activator of secondary metabolism by inducing at least five biosynthetic pathways. Further application of this strategy promises to uncover the regulatory networks that activate silent gene clusters while at the same time providing access to the vast array of cryptic molecules found in bacteria.

Seyedsayamdost, Mohammad R.

2014-01-01

179

The role of horizontal gene transfer in the evolution of selected foodborne bacterial pathogens.  

PubMed

Bacteria use various ways to transfer genetic information. These methods include: conjugation, which requires cell to cell contact between cells, transduction, which is bacteriophage-facilitated transfer of genetic information, and transformation, which is the uptake of free DNA from the environment. Usually the genes to be transferred lie on mobile genetic elements, pieces of DNA that encode proteins important to facilitate movement of DNA within or between genomes. This review highlights the transfer methods and the role of the assorted mobile genetic elements in the evolution of four foodborne bacterial pathogens: Escherichia coli O157:H7, Salmonella, Staphylococcus aureus and Listeria monocytogenes. PMID:18420329

Kelly, B G; Vespermann, A; Bolton, D J

2009-05-01

180

Comparing wastewater chemicals, indicator bacteria concentrations, and bacterial pathogen genes as fecal pollution indicators.  

PubMed

The objective of this study was to compare fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli [EC], and enterococci [ENT]) concentrations with a wide array of typical organic wastewater chemicals and selected bacterial genes as indicators of fecal pollution in water samples collected at or near 18 surface water drinking water intakes. Genes tested included esp (indicating human-pathogenic ENT) and nine genes associated with various animal sources of shiga-toxin-producing EC (STEC). Fecal pollution was indicated by genes and/or chemicals for 14 of the 18 tested samples, with little relation to FIB standards. Of 13 samples with <50 EC 100 mL(-1), human pharmaceuticals or chemical indicators of wastewater treatment plant effluent occurred in six, veterinary antibiotics were detected in three, and stx1 or stx2 genes (indicating varying animal sources of STEC) were detected in eight. Only the EC eaeA gene was positively correlated with FIB concentrations. Human-source fecal pollution was indicated by the esp gene and the human pharmaceutical carbamazepine in one of the nine samples that met all FIB recreational water quality standards. Escherichia coli rfbO157 and stx2c genes, which are typically associated with cattle sources and are of potential human health significance, were detected in one sample in the absence of tested chemicals. Chemical and gene-based indicators of fecal contamination may be present even when FIB standards are met, and some may, unlike FIB, indicate potential sources. Application of multiple water quality indicators with variable environmental persistence and fate may yield greater confidence in fecal pollution assessment and may inform remediation decisions. PMID:19141815

Haack, Sheridan K; Duris, Joseph W; Fogarty, Lisa R; Kolpin, Dana W; Focazio, Michael J; Furlong, Edward T; Meyer, Michael T

2009-01-01

181

Simultaneous amplification of two bacterial genes: more reliable method of Helicobacter pylori detection in microbial rich dental plaque samples.  

PubMed

Polymerase Chain reaction (PCR) assay is considered superior to other methods for detection of Helicobacter pylori (H. pylori) in oral cavity; however, it also has limitations when sample under study is microbial rich dental plaque. The type of gene targeted and number of primers used for bacterial detection in dental plaque samples can have a significant effect on the results obtained as there are a number of closely related bacterial species residing in plaque biofilm. Also due to high recombination rate of H. pylori some of the genes might be down regulated or absent. The present study was conducted to determine the frequency of H. pylori colonization of dental plaque by simultaneously amplifying two genes of the bacterium. One hundred dental plaque specimens were collected from dyspeptic patients before their upper gastrointestinal endoscopy and presence of H. pylori was determined through PCR assay using primers targeting two different genes of the bacterium. Eighty-nine of the 100 samples were included in final analysis. With simultaneous amplification of two bacterial genes 51.6% of the dental plaque samples were positive for H. pylori while this prevalence increased to 73% when only one gene amplification was used for bacterial identification. Detection of H. pylori in dental plaque samples is more reliable when two genes of the bacterium are simultaneously amplified as compared to one gene amplification only. PMID:20512648

Chaudhry, Saima; Idrees, Muhammad; Izhar, Mateen; Butt, Arshad Kamal; Khan, Ayyaz Ali

2011-01-01

182

The use of chimeric gene constructs to express a bacterial endoglucanase in mammalian cells.  

PubMed

The synthesis and secretion of a truncated Clostridium thermocellum endoglucanase (EGE') encoded by the celE' gene was investigated in Chinese hamster ovary (CHO) cells. Fusion genes consisting of the human growth hormone (hGH) gene and celE', transcribed from the SV40 early enhancer/promoter, were constructed and stably transfected into CHO cells. A gene consisting of celE' inserted into the first exon of the hGH gene resulted in the synthesis of truncated proteins (less than or equal to 22 kDa) lacking endoglucanase activity. Cloning celE' into the second exon of the hGH gene, resulted in the synthesis and secretion of a 50 kDa protein with endoglucanase activity. A 50 kDa protein was also synthesised by cells transfected with celE' cloned into the fifth exon of the hGH gene. However, despite a 5-fold increase in enzyme activity compared to the exon 2 transfected cell line less than 40% of the protein was secreted. Constructs devoid of introns, in which celE' was fused to the SV40 early promoter and to the rabbit beta-globin polyadenylation sequence resulted in a 2-18-fold increase in endoglucanase activity compared to the constructs containing introns. In addition more than 75% of the synthesised protein was secreted. Analyses of EGE' encoded mRNA from the transfected cell lines suggests that the presence of introns results in the aberrant splicing of message by the use of cryptic splice sites in the celE' gene. These results demonstrate that introns are not required for the efficient expression of a bacterial endoglucanase in mammalian cells, rather introns appear to reduce expression of the encoded protein. PMID:1314095

Hall, J; Hirst, B H; Hazlewood, G P; Gilbert, H J

1992-04-01

183

Bacterial start site prediction  

Microsoft Academic Search

With the growing number of completely sequenced bacterial genes, accurate gene prediction in bacterial genomes remains an important problem. Although the existing tools predict genes in bacterial genomes with high overall accuracy, their ability to pinpoint the translation start site remains unsatisfactory. In this paper, we present a novel approach to bacterial start site prediction that takes into account multiple

Sridhar S. Hannenhalli; William S. Hayes; Artemis G. Hatzigeorgiou; James W. Fickett

1999-01-01

184

Detecting the Molecular Signature of Social Conflict: Theory and a Test with Bacterial Quorum Sensing Genes  

PubMed Central

Extending social evolution theory to the molecular level opens the door to an unparalleled abundance of data and statistical tools for testing alternative hypotheses about the long-term evolutionary dynamics of cooperation and conflict. To this end, we take a collection of known sociality genes (bacterial quorum sensing [QS] genes), model their evolution in terms of patterns that are detectable using gene sequence data, and then test model predictions using available genetic data sets. Specifically, we test two alternative hypotheses of social conflict: (1) the “adaptive” hypothesis that cheaters are maintained in natural populations by frequency-dependent balancing selection as an evolutionarily stable strategy and (2) the “evolutionary null” hypothesis that cheaters are opposed by purifying kin selection yet exist transiently because of their recurrent introduction into populations by mutation (i.e., kin selection-mutation balance). We find that QS genes have elevated within- and among-species sequence variation, nonsignificant signatures of natural selection, and putatively small effect sizes of mutant alleles, all patterns predicted by our evolutionary null model but not by the stable cheater hypothesis. These empirical findings support our theoretical prediction that QS genes experience relaxed selection due to nonclonality of social groups, conditional expression, and the individual-level advantage enjoyed by cheaters. Furthermore, cheaters are evolutionarily transient, persisting in populations because of their recurrent introduction by mutation and not because they enjoy a frequency-dependent fitness advantage.

Van Dyken, J. David; Wade, Michael J.

2014-01-01

185

Organomercurials removal by heterogeneous merB genes harboring bacterial strains.  

PubMed

Organomercury lyase (MerB) is a key enzyme in bacterial detoxification and bioremediation of organomercurials. However, the merB gene is often considered as an ancillary component of the mer operon because there is zero to three merB genes in different mer operons identified so far. In this study, organomercurials' removal abilities of native mercury-resistant bacteria that have one or multiple merB genes were examined. Each heterogeneous merB genes from these bacteria was further cloned into Escherichia coli to investigate the substrate specificity of each MerB enzyme. The merB1 gene from Bacillus megaterium MB1 conferred the highest volatilization ability to methylmercury chloride, ethylmercury chloride, thimerosal and p-chloromercuribenzoate, while the merB3 from B. megaterium MB1 conferred the fastest mercury volatilization activity to p-chloromercuribenzoate. The substrate specificities among these MerB enzymes show the necessity for selecting the appropriate bacteria strains or MerB enzymes to apply them in bioremediation engineering for cleaning up specific organomercurial contaminations. PMID:20541123

Chien, Mei-Fang; Narita, Masaru; Lin, Kuo-Hsing; Matsui, Kazuaki; Huang, Chieh-Chen; Endo, Ginro

2010-07-01

186

Development of candidate gene markers associated to common bacterial blight resistance in common bean.  

PubMed

Common bacterial blight (CBB), caused by Xanthomonas axonopodis pv. phaseoli (Xap), is a major yield-limiting factor of common bean (Phaseolus vulgaris L.) production around the world. Two major CBB-resistant quantitative trait loci (QTL), linked to the sequence characterized amplified region markers BC420 and SU91, are located at chromosomes 6 and 8, respectively. Using map-based cloning approach, four bacterial artificial chromosome (BAC) clones from the BC420-QTL locus and one BAC clone containing SU91 were sequenced by Roche 454 technique and subsequently assembled using merged assemblies from three different programs. Based on the quality of the assembly, only the sequences of BAC 32H6 and 4K7 were used for candidate gene marker (CGM) development and candidate gene (CG) selection. For the BC420-QTL locus, 21 novel genes were predicted in silico by FGENESH using Medicago gene model, whereas 16 genes were identified in the SU91-QTL locus. For each putative gene, one or more primer pairs were designed and tested in the contrasting near isogenic lines. Overall, six and nine polymorphic markers were found in the SU91- and BC420-QTL loci, respectively. Afterwards, association mapping was conducted in a breeding population of 395 dry bean lines to discover marker-trait associations. Two CGMs per each locus showed better association with CBB resistance than the BC420 and SU91 markers, which include BC420-CG10B and BC420-CG14 for BC420_QTL locus, and SU91-CG10 and SU91-CG11 for SU91_QTL locus. The strong associations between CBB resistance and the CGs 10 and 14 from BC420_QTL locus and the CGs 10 and 11 from SU91_QTL locus indicate that the genes 10 and 14 from the BC420 locus are potential CGs underlying the BC420_QTL locus, whereas the genes 10 and 11 from the SU91 locus are potential CGs underlying the SU91_QTL locus. The superiority of SU91-CG11 was further validated in a recombinant inbred line population Sanilac × OAC 09-3. Thus, co-dominant CGMs, BC420-CG14 and SU91-CG11, are recommended to replace BC420 and SU91 for marker-assisted selection of common bean with resistance to CBB. PMID:22798059

Shi, Chun; Yu, Kangfu; Xie, Weilong; Perry, Gregory; Navabi, Alireza; Pauls, K Peter; Miklas, Phillip N; Fourie, Deidré

2012-11-01

187

Emergence of collective territorial defense in bacterial communities: horizontal gene transfer can stabilize microbiomes.  

PubMed

Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving a varied metabolic repertoire of the constituent species. In other words horizontal transfer of resistance genes makes a community compatible in terms of exoproducts and capable to maintain a varied and mature metagenome. The same property may allow microbiota to protect a host organism, or if used as a microbial therapy, to purge pathogens and restore a protective environment. PMID:24755769

Juhász, János; Kertész-Farkas, Attila; Szabó, Dóra; Pongor, Sándor

2014-01-01

188

Recruitment in the sea: bacterial genes required for inducing larval settlement in a polychaete worm  

PubMed Central

Metamorphically competent larvae of the marine tubeworm Hydroides elegans can be induced to metamorphose by biofilms of the bacterium Pseudoalteromonas luteoviolacea strain HI1. Mutational analysis was used to identify four genes that are necessary for metamorphic induction and encode functions that may be related to cell adhesion and bacterial secretion systems. No major differences in biofilm characteristics, such as biofilm cell density, thickness, biomass and EPS biomass, were seen between biofilms composed of P. luteoviolacea (HI1) and mutants lacking one of the four genes. The analysis indicates that factors other than those relating to physical characteristics of biofilms are critical to the inductive capacity of P. luteoviolacea (HI1), and that essential inductive molecular components are missing in the non-inductive deletion-mutant strains.

Huang, Ying; Callahan, Sean; Hadfield, Michael G.

2012-01-01

189

Emergence of Collective Territorial Defense in Bacterial Communities: Horizontal Gene Transfer Can Stabilize Microbiomes  

PubMed Central

Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving a varied metabolic repertoire of the constituent species. In other words horizontal transfer of resistance genes makes a community compatible in terms of exoproducts and capable to maintain a varied and mature metagenome. The same property may allow microbiota to protect a host organism, or if used as a microbial therapy, to purge pathogens and restore a protective environment.

Szabo, Dora; Pongor, Sandor

2014-01-01

190

Bacterial expression system with tightly regulated gene expression and plasmid copy number  

Microsoft Academic Search

A new Escherichia coli host\\/vector system has been engineered to allow tight and uniform modulation of gene expression and ? origin (ori) plasmid copy number. Regulation of ? ori plasmid copy number is achieved through arabinose-inducible expression of the necessary Rep protein, ?, whose gene was integrated into the chromosome of the host strain under control of the PBAD promoter. ?

Lisa M. Bowers; Kathleen LaPoint; Larry Anthony; Anna Pluciennik; Marcin Filutowicz

2004-01-01

191

Application of nanotechnology to control bacterial adhesion and patterning on material surfaces  

PubMed Central

Bacterial adhesion and biofilm formation on surfaces raises health hazard issues in the medical environment. Previous studies of bacteria adhesion have focused on observations in their natural/native environments. Recently, surface science has contributed in advancing the understanding of bacterial adhesion by providing ideal platforms that attempt to mimic the bacteria's natural environments, whilst also enabling concurrent control, selectivity and spatial control of bacterial adhesion. In this review, we will look at techniques of how nanotechnology is used to control cell adhesion on a planar scale, in addition to describing the use of nanotools for cell micropatterning. Additionally, it will provide a general background of common methods for nanoscale modification enabling biologist unfamiliar with nanotechnology to enter the field.

Costello, Cait M.; Yeung, Chun L.; Rawson, Frankie J.; Mendes, Paula M.

2012-01-01

192

Multiple Genes Affect Sensitivity of Caenorhabditis elegans to the Bacterial Pathogen Microbacterium nematophilum  

PubMed Central

Interactions with bacteria play a major role in immune responses, ecology, and evolution of all animals, but they have been neglected until recently in the case of C. elegans. We report a genetic investigation of the interaction of C. elegans with the nematode-specific pathogen Microbacterium nematophilum, which colonizes the rectum and causes distinctive tail swelling in its host. A total of 121 mutants with altered response to infection were isolated from selections or screens for a bacterially unswollen (Bus) phenotype, using both chemical and transposon mutagenesis. Some of these correspond to known genes, affecting either bacterial adhesion or colonization (srf-2, srf-3, srf-5) or host swelling response (sur-2, egl-5). Most mutants define 15 new genes (bus-1–bus-6, bus-8, bus-10, bus-12–bus-18). The majority of these mutants exhibit little or no rectal infection when challenged with the pathogen and are probably altered in surface properties such that the bacteria can no longer infect worms. A number have corresponding alterations in lectin staining and cuticle fragility. Most of the uninfectable mutants grow better than wild type in the presence of the pathogen, but the sur-2 mutant is hypersensitive, indicating that the tail-swelling response is associated with a specific defense mechanism against this pathogen.

Gravato-Nobre, Maria J.; Nicholas, Hannah R.; Nijland, Reindert; O'Rourke, Delia; Whittington, Deborah E.; Yook, Karen J.; Hodgkin, Jonathan

2005-01-01

193

An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing.  

PubMed

Rhizobium-induced root nodules are specialized organs for symbiotic nitrogen fixation. Indeterminate-type nodules are formed from an apical meristem and exhibit a spatial zonation which corresponds to successive developmental stages. To get a dynamic and integrated view of plant and bacterial gene expression associated with nodule development, we used a sensitive and comprehensive approach based upon oriented high-depth RNA sequencing coupled to laser microdissection of nodule regions. This study, focused on the association between the model legume Medicago truncatula and its symbiont Sinorhizobium meliloti, led to the production of 942 million sequencing read pairs that were unambiguously mapped on plant and bacterial genomes. Bioinformatic and statistical analyses enabled in-depth comparison, at a whole-genome level, of gene expression in specific nodule zones. Previously characterized symbiotic genes displayed the expected spatial pattern of expression, thus validating the robustness of our approach. We illustrate the use of this resource by examining gene expression associated with three essential elements of nodule development, namely meristem activity, cell differentiation and selected signaling processes related to bacterial Nod factors and redox status. We found that transcription factor genes essential for the control of the root apical meristem were also expressed in the nodule meristem, while the plant mRNAs most enriched in nodules compared with roots were mostly associated with zones comprising both plant and bacterial partners. The data, accessible on a dedicated website, represent a rich resource for microbiologists and plant biologists to address a variety of questions of both fundamental and applied interest. PMID:24483147

Roux, Brice; Rodde, Nathalie; Jardinaud, Marie-Françoise; Timmers, Ton; Sauviac, Laurent; Cottret, Ludovic; Carrère, Sébastien; Sallet, Erika; Courcelle, Emmanuel; Moreau, Sandra; Debellé, Frédéric; Capela, Delphine; de Carvalho-Niebel, Fernanda; Gouzy, Jérôme; Bruand, Claude; Gamas, Pascal

2014-03-01

194

Involvement of the cell-specific pigment genes pks and sult in bacterial defense response of sea urchins Strongylocentrotus intermedius.  

PubMed

Bacterial infections are one of the most important problems in mass aquaculture, causing the loss of millions of juvenile organisms. We isolated 22 bacterial strains from the cavity fluid of the sea urchin Strongylocentrotus pallidus and used phylogenetic analysis based on 16S rRNA gene sequences to separate the bacterial strains into 9 genera (Aliivibrio, Bizionia, Colwellia, Olleya, Paenibacillus, Photobacterium, Pseudoalteromonas, Shewanella, and Vibrio). Incubating Strongylocentrotus intermedius larvae with a strain from each of the 9 bacterial genera, we investigated the viability of the larvae, the amount of pigment cells, and the level of polyketide synthase (pks) and sulfotransferase (sult) gene expression. Results of the assay on sea urchin development showed that all bacterial strains, except Pseudoalteromonas and Bizionia, suppressed sea urchin development (resulting in retardation of the embryos' development with cellular disorders) and reduced cell viability. We found that pks expression in the sea urchin larvae after incubation with the bacteria of 9 tested genera was significantly increased, while the sult expression was increased only after the treatment with Pseudoalteromonas and Shewanella. Shikimic acid, which is known to activate the biosynthesis of naphthoquinone pigments, increased the tolerance of the sea urchin embryos to the bacteria. In conclusion, we show that the cell-specific pigment genes pks and sult are involved in the bacterial defense response of sea urchins. PMID:23548362

Kiselev, Konstantin V; Ageenko, Natalya V; Kurilenko, Valeria V

2013-03-26

195

RNAi knock-down of the Litopenaeus vannamei Toll gene (LvToll) significantly increases mortality and reduces bacterial clearance after challenge with Vibrio harveyi.  

PubMed

In this study, we used real-time PCR to simultaneously monitor the responses of 12 key genes of the shrimp innate immune system in Litopenaeus vannamei after challenge with Vibrio harveyi. In the proPO activating system, we found that proPO was up-regulated (3.3x control at 36hpi). The hemolymph clotting genes transglutaminase (TGase) and clotting protein were also up-regulated, as were 5 genes in the antimicrobial peptide system (ALF, Crustin, Lyz, PEN2 and PEN4), with only PEN3 showing no significant changes. In the antioxidant defense system, SOD was slightly elevated while GPx was substantially down-regulated. In the pattern recognition receptor system, at 24hpi, the Toll gene (LvToll) showed the highest relative increase in expression level of all the investigated genes (15x greater than the sterile seawater control). In the second part of this study, when LvToll was knocked down by RNAi silencing, there was no effect on either survival rates or bacterial number in unchallenged shrimp. There was also no difference in mortality rates between control shrimp and LvToll-silenced shrimp when these two groups were challenged with a viral pathogen (white spot syndrome virus; WSSV). However, when LvToll-silenced shrimp were challenged by V. harveyi, there was a significant increase in mortality and bacterial CFU counts. We note that the increase in bacterial CFU count occurred even though treatment with EGFP dsRNA had the opposite effect of reducing the CFU counts. We conclude that LvToll is an important factor in the shrimp innate immune response to acute V. harveyi infection, but not to WSSV. PMID:19698743

Han-Ching Wang, Kc; Tseng, Chun-Wei; Lin, Han-You; Chen, I-Tung; Chen, Ya-Hui; Chen, Yi-Min; Chen, Tzong-Yueh; Yang, Huey-Lang

2010-01-01

196

Control of bacterial growth by temperature and organic matter in the Western Arctic  

NASA Astrophysics Data System (ADS)

Temperature is thought to have a disproportionate role in controlling bacterial growth in perennially cold waters like the Western Arctic Ocean. One impact of temperature is that bacteria in cold waters may require more dissolved organic material (DOM) in order to approach growth rates observed at higher temperatures (the Wiebe-Pomeroy hypothesis). To explore these issues, this study examined the effect of DOM additions and temperatures shifts on bacterial assemblages during short (2 h) and long (up to 10 days) incubations. We found that the temperature response for bacterial assemblages in the Western Arctic was similar to that observed in temperate waters; the Q10 values for leucine and thymidine incorporation were 3.1±2.6 and 1.9±0.56, respectively, not significantly different from values observed in the equatorial Pacific Ocean. In contrast to what would be predicted from the Wiebe-Pomeroy hypothesis, the impact of DOM additions on leucine incorporation either was the same or greater at higher, not lower temperatures. Increasing the incubation temperature did stimulate leucine incorporation more quickly than did DOM additions, but DOM seems as important as temperature in controlling bacterial growth. Leucine incorporation rates per cell (an index of community growth rates) observed in these experiments varied greatly and approached rates observed in waters warmer by 25 °C. These results suggest that the role of temperature in controlling bacterial growth in the Western Arctic is similar to that in low-latitude ocean.

Kirchman, David L.; Malmstrom, Rex R.; Cottrell, Matthew T.

2005-12-01

197

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss  

PubMed Central

Background The bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii, both of which carry homologous virulence gene clusters such as the prfA cluster and clusters of internalin genes. Initial evidence for multiple deletions of the prfA cluster during the evolution of Listeria indicates that this genus provides an interesting model for studying the evolution of virulence and also presents practical challenges with regard to definition of pathogenic strains. Results To better understand genome evolution and evolution of virulence characteristics in Listeria, we used a next generation sequencing approach to generate draft genomes for seven strains representing Listeria species or clades for which genome sequences were not available. Comparative analyses of these draft genomes and six publicly available genomes, which together represent the main Listeria species, showed evidence for (i) a pangenome with 2,032 core and 2,918 accessory genes identified to date, (ii) a critical role of gene loss events in transition of Listeria species from facultative pathogen to saprotroph, even though a consistent pattern of gene loss seemed to be absent, and a number of isolates representing non-pathogenic species still carried some virulence associated genes, and (iii) divergence of modern pathogenic and non-pathogenic Listeria species and strains, most likely circa 47 million years ago, from a pathogenic common ancestor that contained key virulence genes. Conclusions Genome evolution in Listeria involved limited gene loss and acquisition as supported by (i) a relatively high coverage of the predicted pan-genome by the observed pan-genome, (ii) conserved genome size (between 2.8 and 3.2 Mb), and (iii) a highly syntenic genome. Limited gene loss in Listeria did include loss of virulence associated genes, likely associated with multiple transitions to a saprotrophic lifestyle. The genus Listeria thus provides an example of a group of bacteria that appears to evolve through a loss of virulence rather than acquisition of virulence characteristics. While Listeria includes a number of species-like clades, many of these putative species include clades or strains with atypical virulence associated characteristics. This information will allow for the development of genetic and genomic criteria for pathogenic strains, including development of assays that specifically detect pathogenic Listeria strains.

2010-01-01

198

Presence of a bacterial-like citrate synthase gene in Tetrahymena thermophila: recent lateral gene transfers (LGT) or multiple gene losses subsequent to a single ancient LGT?  

PubMed

Citrate synthase is the initial enzyme in the tricarboxylic acid cycle of mitochondria. In plants and fungi, it is the second isozyme in the glyoxylate cycle of peroxisomes (or glyoxysomes), and it is also present in bacteria. Some of the biochemical reactions in the glyoxylate cycle of the ciliated protozoan Tetrahymena pyriformis depend upon mitochondrial enzymes, as T. pyriformis lacks some glyoxysome-specific enzymes. Here we demonstrate a new citrate synthase gene from Tetrahymena thermophila that is different from the mitochondrial counterpart. A potential peroxysome-targeted signal was detected in the N-terminus, suggesting the localization of the enzyme in peroxysomes. Phylogenetic analysis placed the Tetrahymena sequence in a clade consisting of a few sequences from eukaryotes such as cellular slime molds and two land plants, near a green sulfur bacterium and many proteobacteria as a sister group but not in a mitochondrial clade. Southern blot analysis revealed that this type of gene was absent from distantly related ciliates and other species of Tetrahymena except for the closest species, T. mallaccensis. The scattered presence of the bacterial-like genes among distantly related eukaryotes suggests three alternative interpretations of acquisition of the novel glyoxysomal citrate synthase gene via lateral gene transfer (LGT). (1). Some eukaryotes independently acquired the gene from a common bacterium or closely related bacteria via LGT. (2). A hypothetical eukaryote once acquired the gene, which was thereafter independently transferred from the eukaryote to other eukaryotes. (3). A single event of LGT (or duplication) occurred in a certain common ancestor of eukaryotes, followed by multiple losses in many eukaryotic lineages during the subsequent evolution. Considering the monophyly of the bacterial-like eukaryotic citrate synthase genes, the first model is somewhat unlikely, even though it is not impossible. The second and third models can rationally explain the present observation, so these models are discussed in some detail. PMID:15170257

Mukai, Atsushi; Endoh, Hiroshi

2004-05-01

199

Multiple gene loci affecting genetic background-controlled disease resistance conferred by R gene Xa3 \\/ Xa26 in rice  

Microsoft Academic Search

The function of bacterial-blight resistance gene Xa3\\/Xa26 in rice is influenced by genetic background; the Oryza sativa L. ssp. japonica background can increase Xa3\\/Xa26 expression, resulting in an enhanced resistance. To identify whether Xa3\\/Xa26 transcript level is the only factor contributing to genetic background-controlled resistance, we screened an F2 population that was developed from a cross between Oryza sativa L.

Yan Zhou; Yinglong Cao; Yi Huang; Weibo Xie; Caiguo Xu; Xianghua Li; Shiping Wang

2009-01-01

200

Activating the expression of bacterial cryptic genes by rpoB mutations in RNA polymerase or by rare earth elements.  

PubMed

Since bacteria were found to contain genes encoding enzymes that synthesize a plethora of potential secondary metabolites, interest has grown in the activation of these cryptic pathways. Homologous and heterologous expression of these cryptic secondary metabolite-biosynthetic genes, often "silent" under ordinary laboratory fermentation conditions, may lead to the discovery of novel secondary metabolites. We review current progress on this topic, describing concepts for activating silent genes. We especially focus on genetic manipulation of transcription and translation, as well as the utilization of rare earth elements as a novel method to activate the silent genes. The possible roles of silent genes in bacterial physiology are also discussed. PMID:24127067

Ochi, Kozo; Tanaka, Yukinori; Tojo, Shigeo

2014-02-01

201

Identification and Expression Analysis of a Gene Encoding a Bacterial-Type Phosphoenolpyruvate Carboxylase from Arabidopsis and Rice1  

PubMed Central

Phosphoenolpyruvate carboxylase (PEPC) is distributed in plants and bacteria but is not found in fungi and animal cells. Important motifs for enzyme activity and structure are conserved in plant and bacterial PEPCs, with the exception of a phosphorylation domain present at the N terminus of all plant PEPCs reported so far, which is absent in the bacterial enzymes. Here, we describe a gene from Arabidopsis, stated as Atppc4, encoding a PEPC, which shows more similarity to Escherichia coli than to plant PEPCs. Interestingly, this enzyme lacks the phosphorylation domain, hence indicating that it is a bacterial-type PEPC. Three additional PEPC genes are present in Arabidopsis, stated as Atppc1, Atppc2, and Atppc3, encoding typical plant-type enzymes. As most plant PEPC genes, Atppc1, Atppc2, and Atppc3 are formed by 10 exons interrupted by nine introns. In contrast, Atppc4 gene has an unusual structure formed by 20 exons. A bacterial-type PEPC gene was also identified in rice (Oryza sativa), stated as Osppc-b, therefore showing the presence of this type of PEPC in monocots. The phylogenetic analysis suggests that both plant-type and bacterial-type PEPCs diverged early during the evolution of plants from a common ancestor, probably the PEPC from ?-proteobacteria. The diversity of plant-type PEPCs in C3, C4, and Crassulacean acid metabolism plants is indicative of the evolutionary success of the regulation by phosphorylation of this enzyme. Although at a low level, the bacterial-type PEPC genes are expressed in Arabidopsis and rice.

Sanchez, Rosario; Cejudo, Francisco Javier

2003-01-01

202

Genome-wide analysis of defense-responsive genes in bacterial blight resistance of rice mediated by the recessive R gene xa13  

Microsoft Academic Search

Defense responses triggered by dominant and recessive disease resistance ( R) genes are presumed to be regulated by different molecular mechanisms. In order to characterize the genes activated in defense responses against bacterial blight mediated by the recessive R gene xa13, two pathogen-induced subtraction cDNA libraries were constructed using the resistant rice line IRBB13—which carries xa13 —and its susceptible, near-isogenic,

Z. Chu; Y. Ouyang; J. Zhang; H. Yang; S. Wang

2004-01-01

203

Multicopy Integration of Heterologous Genes, Using the Lactococcal Group II Intron Targeted to Bacterial Insertion Sequences†  

PubMed Central

Group II introns are mobile genetic elements that can be redirected to invade specific genes. Here we describe the use of the lactococcal group II intron, Ll.ltrB, to achieve multicopy delivery of heterologous genes into the genome of Lactococcus lactis IL1403-UCD without the need for selectable markers. Ll.ltrB was retargeted to invade three transposase genes, the tra gene found in IS904 (tra904), tra981, and tra983, of which 9, 10, and 14 copies, respectively, were present in IL1403-UCD. Intron invasion of tra904, tra981, and tra983 allele groups occurred at high frequencies, and individual segregants possessed anywhere from one to nine copies of intron in the respective tra alleles. To achieve multicopy delivery of a heterologous gene, a green fluorescent protein (GFP) marker was cloned into the tra904-targeted Ll.ltrB, and the resultant intron (Ll.ltrB::GFP) was induced to invade the L. lactis tra904 alleles. Segregants possessing Ll.ltrB::GFP in three, four, five, six, seven, and eight copies in different tra904 alleles were obtained. In general, increasing the chromosomal copy number of Ll.ltrB::GFP resulted in strains expressing successively higher levels of GFP. However, strains possessing the same number of Ll.ltrB::GFP copies within different sets of tra904 alleles exhibited differential GFP expression, and segregants possessing seven or eight copies of Ll.ltrB::GFP grew poorly upon induction, suggesting that GFP expression from certain combinations of alleles was detrimental. The highest level of GFP expression was observed from a specific six-copy variant that produced GFP at a level analogous to that obtained with a multicopy plasmid. In addition, the high level of GFP expression was stable for over 120 generations. This work demonstrates that stable multicopy integration of heterologous genes can be readily achieved in bacterial genomes with group II intron delivery by targeting repeated elements.

Rawsthorne, Helen; Turner, Kevin N.; Mills, David A.

2006-01-01

204

Assessment of Bacterial bph Gene in Amazonian Dark Earth and Their Adjacent Soils  

PubMed Central

Amazonian Anthrosols are known to harbour distinct and highly diverse microbial communities. As most of the current assessments of these communities are based on taxonomic profiles, the functional gene structure of these communities, such as those responsible for key steps in the carbon cycle, mostly remain elusive. To gain insights into the diversity of catabolic genes involved in the degradation of hydrocarbons in anthropogenic horizons, we analysed the bacterial bph gene community structure, composition and abundance using T-RFLP, 454-pyrosequencing and quantitative PCR essays, respectively. Soil samples were collected in two Brazilian Amazon Dark Earth (ADE) sites and at their corresponding non-anthropogenic adjacent soils (ADJ), under two different land use systems, secondary forest (SF) and manioc cultivation (M). Redundancy analysis of T-RFLP data revealed differences in bph gene structure according to both soil type and land use. Chemical properties of ADE soils, such as high organic carbon and organic matter, as well as effective cation exchange capacity and pH, were significantly correlated with the structure of bph communities. Also, the taxonomic affiliation of bph gene sequences revealed the segregation of community composition according to the soil type. Sequences at ADE sites were mostly affiliated to aromatic hydrocarbon degraders belonging to the genera Streptomyces, Sphingomonas, Rhodococcus, Mycobacterium, Conexibacter and Burkholderia. In both land use sites, shannon's diversity indices based on the bph gene data were higher in ADE than ADJ soils. Collectively, our findings provide evidence that specific properties in ADE soils shape the structure and composition of bph communities. These results provide a basis for further investigations focusing on the bio-exploration of novel enzymes with potential use in the biotechnology/biodegradation industry.

Brossi, Maria Julia de Lima; Mendes, Lucas William; Germano, Mariana Gomes; Lima, Amanda Barbosa; Tsai, Siu Mui

2014-01-01

205

Assessment of Bacterial bph Gene in Amazonian Dark Earth and Their Adjacent Soils.  

PubMed

Amazonian Anthrosols are known to harbour distinct and highly diverse microbial communities. As most of the current assessments of these communities are based on taxonomic profiles, the functional gene structure of these communities, such as those responsible for key steps in the carbon cycle, mostly remain elusive. To gain insights into the diversity of catabolic genes involved in the degradation of hydrocarbons in anthropogenic horizons, we analysed the bacterial bph gene community structure, composition and abundance using T-RFLP, 454-pyrosequencing and quantitative PCR essays, respectively. Soil samples were collected in two Brazilian Amazon Dark Earth (ADE) sites and at their corresponding non-anthropogenic adjacent soils (ADJ), under two different land use systems, secondary forest (SF) and manioc cultivation (M). Redundancy analysis of T-RFLP data revealed differences in bph gene structure according to both soil type and land use. Chemical properties of ADE soils, such as high organic carbon and organic matter, as well as effective cation exchange capacity and pH, were significantly correlated with the structure of bph communities. Also, the taxonomic affiliation of bph gene sequences revealed the segregation of community composition according to the soil type. Sequences at ADE sites were mostly affiliated to aromatic hydrocarbon degraders belonging to the genera Streptomyces, Sphingomonas, Rhodococcus, Mycobacterium, Conexibacter and Burkholderia. In both land use sites, shannon's diversity indices based on the bph gene data were higher in ADE than ADJ soils. Collectively, our findings provide evidence that specific properties in ADE soils shape the structure and composition of bph communities. These results provide a basis for further investigations focusing on the bio-exploration of novel enzymes with potential use in the biotechnology/biodegradation industry. PMID:24927167

Brossi, Maria Julia de Lima; Mendes, Lucas William; Germano, Mariana Gomes; Lima, Amanda Barbosa; Tsai, Siu Mui

2014-01-01

206

Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase.  

PubMed Central

In spite of much effort, no one has succeeded in isolating and characterizing the enzyme(s) responsible for synthesis of cellulose, the major cell wall polymer of plants. We have characterized two cotton (Gossypium hirsutum) cDNA clones and identified one rice (Oryza sativa) cDNA that are homologs of the bacterial celA genes that encode the catalytic subunit of cellulose synthase. Three regions in the deduced amino acid sequences of the plant celA gene products are conserved with respect to the proteins encoded by bacterial celA genes. Within these conserved regions, there are four highly conserved subdomains previously suggested to be critical for catalysis and/or binding of the substrate UDP-glucose (UDP-Glc). An overexpressed DNA segment of the cotton celA1 gene encodes a polypeptide fragment that spans these domains and binds UDP-Glc, while a similar fragment having one of these domains deleted does not. The plant celA genes show little homology at the N- and C-terminal regions and also contain two internal insertions of sequence, one conserved and one hypervariable, that are not found in the bacterial gene sequences. Cotton celA1 and celA2 genes are expressed at high levels during active secondary wall cellulose synthesis in developing cotton fibers. Genomic Southern blot analyses in cotton demonstrate that celA forms a small gene family. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5

Pear, J R; Kawagoe, Y; Schreckengost, W E; Delmer, D P; Stalker, D M

1996-01-01

207

Artificial bacterial flagella for remote-controlled targeted single-cell drug delivery.  

PubMed

An approach for batch preparation of liposome-functionalized microdevices is demonstrated for remotely controlled single-cell drug delivery. The liposome functionalized artificial bacterial flagella exhibit corkscrew swimming in 3D with micrometer positioning precision by applying an external rotating magnetic field. The devices are also capable of delivering water-soluble drugs to single cells in vitro. PMID:24616145

Mhanna, Rami; Qiu, Famin; Zhang, Li; Ding, Yun; Sugihara, Kaori; Zenobi-Wong, Marcy; Nelson, Bradley J

2014-05-01

208

Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome.  

PubMed

When groups of related bacterial genomes are compared, the number of core genes found in all genomes is usually much less than the mean genome size, whereas the size of the pangenome (the set of genes found on at least one of the genomes) is much larger than the mean size of one genome. We analyze 172 complete genomes of Bacilli and compare the properties of the pangenomes and core genomes of monophyletic subsets taken from this group. We then assess the capabilities of several evolutionary models to predict these properties. The infinitely many genes (IMG) model is based on the assumption that each new gene can arise only once. The predictions of the model depend on the shape of the evolutionary tree that underlies the divergence of the genomes. We calculate results for coalescent trees, star trees, and arbitrary phylogenetic trees of predefined fixed branch length. On a star tree, the pangenome size increases linearly with the number of genomes, as has been suggested in some previous studies, whereas on a coalescent tree, it increases logarithmically. The coalescent tree gives a better fit to the data, for all the examples we consider. In some cases, a fixed phylogenetic tree proved better than the coalescent tree at reproducing structure in the gene frequency spectrum, but little improvement was gained in predictions of the core and pangenome sizes. Most of the data are well explained by a model with three classes of gene: an essential class that is found in all genomes, a slow class whose rate of origination and deletion is slow compared with the time of divergence of the genomes, and a fast class showing rapid origination and deletion. Although the majority of genes originating in a genome are in the fast class, these genes are not retained for long periods, and the majority of genes present in a genome are in the slow or essential classes. In general, we show that the IMG model is useful for comparison with experimental genome data both for species level and widely divergent taxonomic groups. Software implementing the described formulae is provided at http://github.com/rec3141/pangenome. PMID:22752048

Collins, R Eric; Higgs, Paul G

2012-11-01

209

Genes and Co-Expression Modules Common to Drought and Bacterial Stress Responses in Arabidopsis and Rice  

PubMed Central

Plants are simultaneously exposed to multiple stresses resulting in enormous changes in the molecular landscape within the cell. Identification and characterization of the synergistic and antagonistic components of stress response mechanisms contributing to the cross talk between stresses is of high priority to explore and enhance multiple stress responses. To this end, we performed meta-analysis of drought (abiotic), bacterial (biotic) stress response in rice and Arabidopsis by analyzing a total of 386 microarray samples belonging to 20 microarray studies and identified approximately 3100 and 900 DEGs in rice and Arabidopsis, respectively. About 38.5% (1214) and 28.7% (272) DEGs were common to drought and bacterial stresses in rice and Arabidopsis, respectively. A majority of these common DEGs showed conserved expression status in both stresses. Gene ontology enrichment analysis clearly demarcated the response and regulation of various plant hormones and related biological processes. Fatty acid metabolism and biosynthesis of alkaloids were upregulated and, nitrogen metabolism and photosynthesis was downregulated in both stress conditions. WRKY transcription family genes were highly enriched in all upregulated gene sets while ‘CO-like’ TF family showed inverse relationship of expression between drought and bacterial stresses. Weighted gene co-expression network analysis divided DEG sets into multiple modules that show high co-expression and identified stress specific hub genes with high connectivity. Detection of consensus modules based on DEGs common to drought and bacterial stress revealed 9 and 4 modules in rice and Arabidopsis, respectively, with conserved and reversed co-expression patterns.

Shaik, Rafi; Ramakrishna, Wusirika

2013-01-01

210

Combinatorial Control of Gene Expression  

PubMed Central

The complexity and diversity of eukaryotic organisms are a feat of nature's engineering. Pulling the strings of such an intricate machinery requires an even more masterful and crafty approach. Only the number and type of responses that they generate exceed the staggering proportions of environmental signals perceived and processed by eukaryotes. Hence, at first glance, the cell's sparse stockpile of controlling factors does not seem remotely adequate to carry out this response. The question as to how eukaryotes sense and respond to environmental cues has no single answer. It is an amalgamation, an interplay between several processes, pathways, and factors—a combinatorial control. A short description of some of the most important elements that operate this entire conglomerate is given in this paper.

Bhattacharjee, Soumya; Renganaath, Kaushik; Mehrotra, Rajesh; Mehrotra, Sandhya

2013-01-01

211

Bacterial Filament Formation, a Defense Mechanism against Flagellate Grazing, Is Growth Rate Controlled in Bacteria of Different Phyla  

PubMed Central

A facultatively filamentous bacterium was isolated from eutrophic lake water and was identified as Flectobacillus sp. strain MWH38 (a member of the Cytophaga-Flavobacterium-Bacteroides phylum) by comparative 16S rRNA gene sequence analysis. Filament formation by Flectobacillus sp. strain MWH38 and filament formation by Flectobacillus major, the closest known relative of strain MWH38, were studied in chemostat cultures under grazing pressure by the bacterivorous flagellate Ochromonas sp. strain DS and without predation at several growth rates. The results clearly demonstrated that filament formation by the two flectobacilli is growth rate controlled and thus independent of the presence of a predator. However, flagellate grazing positively influenced bacterial growth rates by decreasing bacterial biomass and thus indirectly stimulated filament formation. The results of investigations of cell elongation and filament formation by Comamonas acidovorans PX54 (a member of the ? subclass of the class Proteobacteria) supported the recent proposal that in this species the mechanism of filament formation is growth rate controlled. The finding that the grazing defense mechanism consisting of filament formation is growth rate controlled in the flectobacilli investigated and C. acidovorans PX54 (i.e., in bacteria belonging to divergent evolutionary phyla) may indicate that this mechanism is a phylogenetically widely distributed defense strategy against grazing.

Hahn, Martin W.; Moore, Edward R. B.; Hofle, Manfred G.

1999-01-01

212

Bacterial filament formation, a defense mechanism against flagellate grazing, is growth rate controlled in bacteria of different phyla.  

PubMed

A facultatively filamentous bacterium was isolated from eutrophic lake water and was identified as Flectobacillus sp. strain MWH38 (a member of the Cytophaga-Flavobacterium-Bacteroides phylum) by comparative 16S rRNA gene sequence analysis. Filament formation by Flectobacillus sp. strain MWH38 and filament formation by Flectobacillus major, the closest known relative of strain MWH38, were studied in chemostat cultures under grazing pressure by the bacterivorous flagellate Ochromonas sp. strain DS and without predation at several growth rates. The results clearly demonstrated that filament formation by the two flectobacilli is growth rate controlled and thus independent of the presence of a predator. However, flagellate grazing positively influenced bacterial growth rates by decreasing bacterial biomass and thus indirectly stimulated filament formation. The results of investigations of cell elongation and filament formation by Comamonas acidovorans PX54 (a member of the beta subclass of the class Proteobacteria) supported the recent proposal that in this species the mechanism of filament formation is growth rate controlled. The finding that the grazing defense mechanism consisting of filament formation is growth rate controlled in the flectobacilli investigated and C. acidovorans PX54 (i.e., in bacteria belonging to divergent evolutionary phyla) may indicate that this mechanism is a phylogenetically widely distributed defense strategy against grazing. PMID:9872755

Hahn, M W; Moore, E R; Höfle, M G

1999-01-01

213

Distribution of alginate genes in bacterial isolates from corroded metal surfaces.  

PubMed

The distribution of alginate genes encoding biosynthesis of alginate was examined for bacterial isolates associated with corrosive biofilms recovered from source water, cooling lines, and reactor surfaces of a nuclear power plant. A total of 120 diverse Gram-positive and -negative isolates were obtained. Using DNA:DNA hybridization, 11 isolates were shown to contain sequences homologous to structural (algD, algG, alg-76) and/or regulatory (albB) alginate biosynthetic genes derived from an alginate-producing cystic fibrosis isolate of Pseudomonas aeruginosa (FRD1). Identification of isolates was accomplished by fatty acids methyl esters (FAME) analysis and the Biolog identification system. Nine of the twelve isolates were identified as various Pseudomonas spp., and two additional Gram-negative isolates were tentatively identified as Aeromonas veronii and Stenotrophomonas maltophilia. The remaining isolate was identified as a Gram-positive Bacillus pumilus. The results of the investigation extend current knowledge on the distribution of alginate biosynthetic genes in environmental isolates and permits the development of a more environmentally realistic model system to investigate the role of exopolymer production in biofilm formation and biocorrosion processes. PMID:24190336

Wallace, W H; Rice, J F; White, D C; Sayler, G S

1994-05-01

214

Bacterial Diversity in Oral Samples of Children in Niger with Acute Noma, Acute Necrotizing Gingivitis, and Healthy Controls  

PubMed Central

Background Noma is a gangrenous disease that leads to severe disfigurement of the face with high morbidity and mortality, but its etiology remains unknown. Young children in developing countries are almost exclusively affected. The purpose of the study was to record and compare bacterial diversity in oral samples from children with or without acute noma or acute necrotizing gingivitis from a defined geographical region in Niger by culture-independent molecular methods. Methods and Principal Findings Gingival samples from 23 healthy children, nine children with acute necrotizing gingivitis, and 23 children with acute noma (both healthy and diseased oral sites) were amplified using “universal” PCR primers for the 16 S rRNA gene and pooled according to category (noma, healthy, or acute necrotizing gingivitis), gender, and site status (diseased or control site). Seven libraries were generated. A total of 1237 partial 16 S rRNA sequences representing 339 bacterial species or phylotypes at a 98–99% identity level were obtained. Analysis of bacterial composition and frequency showed that diseased (noma or acute necrotizing gingivitis) and healthy site bacterial communities are composed of similar bacteria, but differ in the prevalence of a limited group of phylotypes. Large increases in counts of Prevotella intermedia and members of the Peptostreptococcus genus are associated with disease. In contrast, no clear-cut differences were found between noma and non-noma libraries. Conclusions Similarities between acute necrotizing gingivitis and noma samples support the hypothesis that the disease could evolve from acute necrotizing gingivitis in certain children for reasons still to be elucidated. This study revealed oral microbiological patterns associated with noma and acute necrotizing gingivitis, but no evidence was found for a specific infection-triggering agent.

Stadelmann, Benoit; Baratti-Mayer, Denise; Gizard, Yann; Mombelli, Andrea; Pittet, Didier; Schrenzel, Jacques

2012-01-01

215

Evolutionary optimization of sequence kernels for detection of bacterial gene starts.  

PubMed

Oligo kernels for biological sequence classification have a high discriminative power. A new parameterization for the K-mer oligo kernel is presented, where all oligomers of length K are weighted individually. The task specific choice of these parameters increases the classification performance and reveals information about discriminative features. For adapting the multiple kernel parameters based on cross-validation the covariance matrix adaptation evolution strategy is proposed. It is applied to optimize the trimer oligo kernels for the detection of bacterial gene starts. The resulting kernels lead to higher classification rates, and the adapted parameters reveal the importance of particular triplets for classification, for example of those occurring in the Shine-Dalgarno Sequence. PMID:18098369

Mersch, Britta; Glasmachers, Tobias; Meinicke, Peter; Igel, Christian

2007-10-01

216

Light without substrate amendment: the bacterial luciferase gene cassette as a mammalian bioreporter  

NASA Astrophysics Data System (ADS)

Bioluminescent production represents a facile method for bioreporter detection in mammalian tissues. The lack of endogenous bioluminescent reactions in these tissues allows for high signal to noise ratios even at low signal strength compared to fluorescent signal detection. While the luciferase enzymes commonly employed for bioluminescent detection are those from class Insecta (firefly and click beetle luciferases), these are handicapped in that they require concurrent administration of a luciferin compound to elicit a bioluminescent signal. The bacterial luciferase (lux) gene cassette offers the advantages common to other bioluminescent proteins, but is simultaneously capable of synthesizing its own luciferin substrates using endogenously available cellular compounds. The longstanding shortcoming of the lux cassette has been its recalcitrance to function in the mammalian cellular environment. This paper will present an overview of the work completed to date to overcome this limitation and provide examples of mammalian lux-based bioreporter technologies that could provide the framework for advanced, biomedically relevant real-time sensor development.

Close, Dan M.; Xu, Tingting; Smartt, Abby E.; Jegier, Pat; Ripp, Steven A.; Sayler, Gary S.

2011-05-01

217

Chronic Dermatomycoses of the Foot as Risk Factors for Acute Bacterial Cellulitis of the Leg: A Case-Control Study  

Microsoft Academic Search

Objective: To assess the role of foot dermatomycosis (tinea pedis and onychomycosis) and other candidate risk factors in the development of acute bacterial cellulitis of the leg. Methods: A case-control study, including 243 patients (cases) with acute bacterial cellulitis of the leg and 467 controls, 2 per case, individually matched for gender, age (±5 years), hospital and admission date (±2

Jean-Claude Roujeau; Bardur Sigurgeirsson; Hans-Christian Korting; Helmut Kerl; Carle Paul

2004-01-01

218

Human Gut Bacterial Communities Are Altered by Addition of Cruciferous Vegetables to a Controlled Fruit- and Vegetable-Free Diet1–3  

PubMed Central

In the human gut, commensal bacteria metabolize food components that typically serve as energy sources. These components have the potential to influence gut bacterial community composition. Cruciferous vegetables, such as broccoli and cabbage, contain distinctive compounds that can be utilized by gut bacteria. For example, glucosinolates can be hydrolyzed by certain bacteria, and dietary fibers can be fermented by a range of species. We hypothesized that cruciferous vegetable consumption would alter growth of certain bacteria, thereby altering bacterial community composition. We tested this hypothesis in a randomized, crossover, controlled feeding study. Fecal samples were collected from 17 participants at the end of 2 14-d intake periods: a low-phytochemical, low-fiber basal diet (i.e. refined grains without fruits or vegetables) and a high (“double”) cruciferous vegetable diet [basal diet + 14 g cruciferous vegetables/(kg body weight?d)]. Fecal bacterial composition was analyzed by the terminal restriction fragment length polymorphism (tRFLP) method using the bacterial 16S ribosomal RNA gene and nucleotide sequencing. Using blocked multi-response permutation procedures analysis, we found that overall bacterial community composition differed between the 2 consumption periods (? = 0.603; P = 0.011). The bacterial community response to cruciferous vegetables was individual-specific, as revealed by nonmetric multidimensional scaling ordination analysis. Specific tRFLP fragments that characterized each of the diets were identified using indicator species analysis. Putative species corresponding to these fragments were identified through gene sequencing as Eubacterium hallii, Phascolarctobacterium faecium, Burkholderiales spp., Alistipes putredinis, and Eggerthella spp. In conclusion, human gut bacterial community composition was altered by cruciferous vegetable consumption, which could ultimately influence gut metabolism of bioactive food components and host exposure to these compounds.

Li, Fei; Hullar, Meredith A. J.; Schwarz, Yvonne; Lampe, Johanna W.

2009-01-01

219

Genome-wide identification of Streptococcus pneumoniae genes essential for bacterial replication during experimental meningitis.  

PubMed

Meningitis is the most serious of invasive infections caused by the Gram-positive bacterium Streptococcus pneumoniae. Vaccines protect only against a limited number of serotypes, and evolving bacterial resistance to antimicrobials impedes treatment. Further insight into the molecular pathogenesis of invasive pneumococcal disease is required in order to enable the development of new or adjunctive treatments and/or pneumococcal vaccines that are efficient across serotypes. We applied genomic array footprinting (GAF) in the search for S. pneumoniae genes that are essential during experimental meningitis. A total of 6,000 independent TIGR4 marinerT7 transposon mutants distributed over four libraries were injected intracisternally into rabbits, and cerebrospinal fluid (CSF) was collected after 3, 9, and 15 h. Microarray analysis of mutant-specific probes from CSF samples and inocula identified 82 and 11 genes mutants of which had become attenuated or enriched, respectively, during infection. The results point to essential roles for capsular polysaccharides, nutrient uptake, and amino acid biosynthesis in bacterial replication during experimental meningitis. The GAF phenotype of a subset of identified targets was followed up by detailed studies of directed mutants in competitive and noncompetitive infection models of experimental rat meningitis. It appeared that adenylosuccinate synthetase, flavodoxin, and LivJ, the substrate binding protein of a branched-chain amino acid ABC transporter, are relevant as targets for future therapy and prevention of pneumococcal meningitis, since their mutants were attenuated in both models of infection as well as in competitive growth in human cerebrospinal fluid in vitro. PMID:21041497

Molzen, T E; Burghout, P; Bootsma, H J; Brandt, C T; van der Gaast-de Jongh, Christa E; Eleveld, M J; Verbeek, M M; Frimodt-Møller, N; Østergaard, C; Hermans, P W M

2011-01-01

220

Influence of Uranium on Bacterial Communities: A Comparison of Natural Uranium-Rich Soils with Controls  

PubMed Central

This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing gradient gel electrophoresis (DGGE) revealed the presence of a complex population in both control and uranium-rich samples. However, bacterial communities inhabiting uraniferous soils exhibited specific fingerprints that were remarkably stable over time, in contrast to populations from nearby control samples. Representatives of Acidobacteria, Proteobacteria, and seven others phyla were detected in DGGE bands specific to uraniferous samples. In particular, sequences related to iron-reducing bacteria such as Geobacter and Geothrix were identified concomitantly with iron-oxidizing species such as Gallionella and Sideroxydans. All together, our results demonstrate that uranium exerts a permanent high pressure on soil bacterial communities and suggest the existence of a uranium redox cycle mediated by bacteria in the soil.

Mondani, Laure; Benzerara, Karim; Carriere, Marie; Christen, Richard; Mamindy-Pajany, Yannick; Fevrier, Laureline; Marmier, Nicolas; Achouak, Wafa; Nardoux, Pascal; Berthomieu, Catherine; Chapon, Virginie

2011-01-01

221

Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0  

PubMed Central

Background The growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling. Findings GeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the visualization of synteny by plotting protein similarity scores between two genomes and it also provides visual annotation of "hypothetical" proteins from older archived genomes based on more recent annotations. Conclusions The web-based software tool GeneOrder4.0 is a user-friendly application that has been updated to allow the rapid analysis of synteny and gene order in large bacterial genomes. It is developed with the wet-bench researcher in mind.

2010-01-01

222

{open_quotes}Horizontal{close_quotes} gene transfer from a transgenic potato line to a bacterial pathogen (Erwinia chrysanthemi) occurs - if at all - at an extremely low frequency  

SciTech Connect

The frequency of possible {open_quotes}horizontal{close_quotes} gene transfer between a plant and a tightly associated bacterial pathogen was studied in a model system consisting of transgenic Solanum tuberosum, containing a {beta}-lactamase gene linked to a pBR322 origin of replication, and Erwinia chrysanthemi. This experimental system offers optimal conditions for the detection of possible horizontal gene transfer events, even when they occur at very low frequency. Horizontal gene transfer was not detected under conditions mimicking a {open_quotes}natural{close_quotes} infection. The gradual, stepwise alteration of artificial, positive control conditions to idealized natural conditions, however, allowed the characterization of factors that affected gene transfer, and revealed a gradual decrease of the gene transfer frequency from 6.3 x 10{sup -2} under optimal control conditions to a calculated 2.0 x 10{sub -17} under idealized natural conditions. These data, in combination with other published studies, argue that horizontal gene transfer is so rare as to be essentially irrelevant to any realistic assessment of the risk involved in release experiments involving transgenic plants. 22 refs., 3 figs., 2 tabs.

Schlueter, K.; Fuetterer, J.; Potrykus, I. [Institute of Plant Sciences, Zuerich (Switzerland)] [Institute of Plant Sciences, Zuerich (Switzerland)

1995-10-01

223

Control of Local Bacterial Soft Tissue Contamination by Adequate Microvascular Response is Critically Dependent on the Extent of Bacterial Challenge  

Microsoft Academic Search

Background: Local cellular and humoral defense mechanisms play a significant role in combating local bacterial infection. The effectiveness of these mechanisms is directly related to an intact vascular system. The objective of this study was to elucidate the effect of local bacterial challenge on the host tissue microvascular response and nutritive perfusion. Material and Methods: The hamster dorsal skin fold

Clayton N. Kraft; Martin Hansis; Michael D. Menger; Hans-Georg Sahl; Brigitte Vollmar

2001-01-01

224

Diversity and analysis of bacterial terpene synthases.  

PubMed

Terpenoid compounds are generally considered to be plant or fungal metabolites, although a small number of odorous terpenoid metabolites of bacterial origin have been known for many years. Recently, extensive bacterial genome sequencing and bioinformatic analysis of deduced bacterial proteins using a profile hidden Markov model have revealed more than a hundred distinct predicted terpene synthase genes. Although some of these synthase genes might be silent in the parent microorganisms under normal laboratory culture conditions, the controlled overexpression of these genes in a versatile heterologous host has made it possible to identify the biochemical function of cryptic genes and isolate new terpenoid metabolites. PMID:22999173

Yamada, Yuuki; Cane, David E; Ikeda, Haruo

2012-01-01

225

Regularities of the location of genes having different functions and of some other nucleotide sequences in the bacterial chromosome  

Microsoft Academic Search

The review considers the results of genomic research performed over the last decade that shed light on the location in the\\u000a bacterial chromosomes of genes having different functions. A tendency towards polarity of the chromosome composition is observed:\\u000a vitally important genes tend to be concentrated in the region of replication origin (oriC), and their concentration decreases\\u000a toward the region of

A. A. Prozorov

2007-01-01

226

Fine mapping of the rice bacterial blight resistance gene Xa-4 and its co-segregation marker  

Microsoft Academic Search

An F2 population developed from theXa-4 near isogenic lines, IR24 and IRBB4, was used for fine mapping of the rice bacterial blight resistance gene,Xa-4. Some restriction fragment length polymorphism (RFLP) markers on the high-density map constructed by Harushima et al. and\\u000a the amplified DNA fragments homologous to the conserved domains of plant disease resistance (R) genes were used to construct

Wenming Wang; Yongli Zhou; Guanhuai Jiang; Bojun Ma; Xuewei Chen; Qi Zhang; Lihuang Zhu; Wenxue Zhai

2000-01-01

227

STS and microsatellite marker-assisted selection for bacterial blight resistance and waxy genes in rice, Oryza sativa L  

Microsoft Academic Search

DNA marker-assisted selection was employed to select Xa-21 bacterial blight resistance and waxy (Wx) genes. Genotypes with both genes were selected from four F2 populations involving indica × indica, indica × intermediate and japonica × indica crosses. With the assistance of PCR marker,\\u000a 13 true breeding lines carrying Xa-21 were identified from F2 generation of IRBB 21 × G 11353

J. Ramalingam; H. S. Basharat; G. Zhang

2002-01-01

228

Pyramiding of two bacterial blight resistance and a semidwarfing gene in Type 3 Basmati using marker-assisted selection  

Microsoft Academic Search

A traditional Type 3 Basmati rice cultivar grown in India is tall and lodges even under low nitrogen fertilizer dose. In addition\\u000a to lodging, it is highly susceptible to several diseases and pests including bacterial blight (BB). BB resistance genes (Xa21 and xa13) and a semidwarfing gene (sd-1) were pyramided in Type 3 Basmati from a rice cultivar PR106-P2 using

Deepak Rajpurohit; Rahul Kumar; Mankesh Kumar; Priyanka Paul; Anjali Awasthi; P. Osman Basha; Anju Puri; Tripta Jhang; Kuldeep Singh; Harcharan Singh Dhaliwal

2011-01-01

229

Distinct Ectomycorrhizospheres Share Similar Bacterial Communities as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes  

PubMed Central

Analysis of the 16S rRNA gene sequences generated from Xerocomus pruinatus and Scleroderma citrinum ectomycorrhizospheres revealed that similar bacterial communities inhabited the two ectomycorrhizospheres in terms of phyla and genera, with an enrichment of the Burkholderia genus. Compared to the bulk soil habitat, ectomycorrhizospheres hosted significantly more Alpha-, Beta-, and Gammaproteobacteria.

Oger, P.; Morin, E.; Frey-Klett, P.

2012-01-01

230

Glycosylation Genes Expressed in Seam Cells Determine Complex Surface Properties and Bacterial Adhesion to the Cuticle of Caenorhabditis elegans  

PubMed Central

The surface of the nematode Caenorhabditis elegans is poorly understood but critical for its interactions with the environment and with pathogens. We show here that six genes (bus-2, bus-4, and bus-12, together with the previously cloned srf-3, bus-8, and bus-17) encode proteins predicted to act in surface glycosylation, thereby affecting disease susceptibility, locomotory competence, and sexual recognition. Mutations in all six genes cause resistance to the bacterial pathogen Microbacterium nematophilum, and most of these mutations also affect bacterial adhesion and biofilm formation by Yersinia species, demonstrating that both infection and biofilm formation depend on interaction with complex surface carbohydrates. A new bacterial interaction, involving locomotory inhibition by a strain of Bacillus pumilus, reveals diversity in the surface properties of these mutants. Another biological property—contact recognition of hermaphrodites by males during mating—was also found to be impaired in mutants of all six genes. An important common feature is that all are expressed most strongly in seam cells, rather than in the main hypodermal syncytium, indicating that seam cells play the major role in secreting surface coat and consequently in determining environmental interactions. To test for possible redundancies in gene action, the 15 double mutants for this set of genes were constructed and examined, but no synthetic phenotypes were observed. Comparison of the six genes shows that each has distinctive properties, suggesting that they do not act in a linear pathway.

Gravato-Nobre, Maria J.; Stroud, Dave; O'Rourke, Delia; Darby, Creg; Hodgkin, Jonathan

2011-01-01

231

Bacterial Competition Reveals Differential Regulation of the pks Genes by Bacillus subtilis  

PubMed Central

Bacillus subtilis is adaptable to many environments in part due to its ability to produce a broad range of bioactive compounds. One such compound, bacillaene, is a linear polyketide/nonribosomal peptide. The pks genes encode the enzymatic megacomplex that synthesizes bacillaene. The majority of pks genes appear to be organized as a giant operon (>74 kb from pksC-pksR). In previous work (P. D. Straight, M. A. Fischbach, C. T. Walsh, D. Z. Rudner, and R. Kolter, Proc. Natl. Acad. Sci. U. S. A. 104:305–310, 2007, doi:10.1073/pnas.0609073103), a deletion of the pks operon in B. subtilis was found to induce prodiginine production by Streptomyces coelicolor. Here, colonies of wild-type B. subtilis formed a spreading population that induced prodiginine production from Streptomyces lividans, suggesting differential regulation of pks genes and, as a result, bacillaene. While the parent colony showed widespread induction of pks expression among cells in the population, we found the spreading cells uniformly and transiently repressed the expression of the pks genes. To identify regulators that control pks genes, we first determined the pattern of pks gene expression in liquid culture. We next identified mutations in regulatory genes that disrupted the wild-type pattern of pks gene expression. We found that expression of the pks genes requires the master regulator of development, Spo0A, through its repression of AbrB and the stationary-phase regulator, CodY. Deletions of degU, comA, and scoC had moderate effects, disrupting the timing and level of pks gene expression. The observed patterns of expression suggest that complex regulation of bacillaene and other antibiotics optimizes competitive fitness for B. subtilis.

Vargas-Bautista, Carol; Rahlwes, Kathryn

2014-01-01

232

Messing with Bacterial Quorum Sensing  

PubMed Central

Quorum sensing is widely recognized as an efficient mechanism to regulate expression of specific genes responsible for communal behavior in bacteria. Several bacterial phenotypes essential for the successful establishment of symbiotic, pathogenic, or commensal relationships with eukaryotic hosts, including motility, exopolysaccharide production, biofilm formation, and toxin production, are often regulated by quorum sensing. Interestingly, eukaryotes produce quorum-sensing-interfering (QSI) compounds that have a positive or negative influence on the bacterial signaling network. This eukaryotic interference could result in further fine-tuning of bacterial quorum sensing. Furthermore, recent work involving the synthesis of structural homologs to the various quorum-sensing signal molecules has resulted in the development of additional QSI compounds that could be used to control pathogenic bacteria. The creation of transgenic plants that express bacterial quorum-sensing genes is yet another strategy to interfere with bacterial behavior. Further investigation on the manipulation of quorum-sensing systems could provide us with powerful tools against harmful bacteria.

Gonzalez, Juan E.; Keshavan, Neela D.

2006-01-01

233

RNA-dependent control of gene amplification  

PubMed Central

We exploit the unusual genome organization of the ciliate cell to analyze the control of specific gene amplification during a nuclear differentiation process. Ciliates contain two types of nuclei within one cell, the macronucleus and the micronucleus; and after sexual reproduction a new macronucleus is formed from a micronuclear derivative. During macronuclear differentiation, most extensive DNA reorganization, elimination, and fragmentation processes occur, resulting in a macronucleus containing short DNA molecules (nanochromosomes) representing individual genetic units and each being present in high copy number. It is believed that these processes are controlled by small nuclear RNAs but also by a template derived from the old macronucleus. We first describe the exact copy numbers of selected nanochromosomes in the macronucleus, and define the timing during nuclear differentiation at which copy number is determined. This led to the suggestion that DNA processing and copy number control may be closely related mechanisms. Degradation of an RNA template derived from the macronucleus leads to significant decrease in copy number, whereas injection of additional template molecules results in an increase in copy number and enhanced expression of the corresponding gene. These observations can be incorporated into a mechanistic model about an RNA-dependent epigenetic regulation of gene copy number during nuclear differentiation. This highlights that RNA, in addition to its well-known biological functions, can also be involved in the control of gene amplification.

Heyse, Gero; Jonsson, Franziska; Chang, Wei-Jen; Lipps, Hans J.

2010-01-01

234

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ  

PubMed Central

The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/PrrA two-component system with a central role in redox regulation in R. sphaeroides. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA.

Mank, Nils N.; Berghoff, Bork A.; Hermanns, Yannick N.; Klug, Gabriele

2012-01-01

235

Sludge as a potential important source of antibiotic resistance genes in both the bacterial and bacteriophage fractions.  

PubMed

The emergence and prevalence of antibiotic resistance genes (ARGs) in the environment is a serious global health concern. ARGs found in bacteria can become mobilized in bacteriophage particles in the environment. Sludge derived from secondary treatment in wastewater treatment plants (WWTPs) constitutes a concentrated pool of bacteria and phages that are removed during the treatment process. This study evaluates the prevalence of ARGs in the bacterial and phage fractions of anaerobic digested sludge; five ARGs (blaTEM, blaCTX-M, qnrA, qnrS, and sul1) are quantified by qPCR. Comparison between the wastewater and sludge revealed a shift in the prevalence of ARGs (blaTEM and sul1 became more prevalent in sludge), suggesting there is a change in the bacterial and phage populations from wastewater to those selected during the secondary treatment and the later anaerobic mesophilic digestion of the sludge. ARGs densities were higher in the bacterial than in the phage fraction, with high densities in both fractions; particularly for blaTEM and sul1 (5 and 8 log10 gene copies (GC)/g, respectively, in bacterial DNA; 5.5 and 4.4 log10 GC/g, respectively, in phage DNA). These results question the potential agricultural uses of treated sludge, as it could contribute to the spread of ARGs in the environment and have an impact on the bacterial communities of the receiving ecosystem. PMID:24873655

Calero-Cáceres, William; Melgarejo, Ana; Colomer-Lluch, Marta; Stoll, Claudia; Lucena, Francisco; Jofre, Juan; Muniesa, Maite

2014-07-01

236

Antitumor activity of mutant bacterial cytosine deaminase gene for colon cancer  

PubMed Central

AIM: To evaluate bacterial cytosine deaminase (bCD) mutant D314A and 5-fluorocytosine (5-FC) for treatment of colon cancer in a mouse model. METHODS: Recombinant lentivirus vectors that contained wild-type bCD gene (bCDwt), and bCD mutant D314A gene (bCD-D314A) with green fluorescence protein gene were constructed and used to infect human colon carcinoma LoVo cells, to generate stable transfected cells, LoVo/null, LoVo/bCDwt or LoVo/bCD-D314A. These were injected subcutaneously into Balb/c nude mice to establish xenograft models. Two weeks post-LoVo cell inoculation, PBS or 5-FC (500 mg/kg) was administered by intraperitoneal (i.p.) injection once daily for 14 d. On the day after LoVo cell injection, mice were monitored daily for tumor volume and survival. RESULTS: Sequence analyses confirmed the construction of recombinant lentiviral plasmids that contained bCDwt or bCD-D314A. The lentiviral vector had high efficacy for gene delivery, and RT-PCR showed that bCDwt or bCD-D314A gene was transferred to LoVo cells. Among these treatment groups, gene delivery or 5-FC administration alone had no effect on tumor growth. However, bCDwt/5-FC or bCD-D314A/5-FC treatment inhibited tumor growth and prolonged survival of mice significantly (P < 0.05). Importantly, the tumor volume in the bCD-D314A/5-FC-treated group was lower than that in the bCDwt/5-FC group (P < 0.05), and bCD-D314A plus 5-FC significantly prolonged survival of mice in comparison with bCDwt plus 5-FC (P < 0.05). CONCLUSION: The bCD mutant D314A enhanced significantly antitumor activity in human colon cancer xenograft models, which provides a promising approach for human colon carcinoma therapy.

Deng, Long-Ying; Wang, Jian-Ping; Gui, Zhi-Fu; Shen, Li-Zong

2011-01-01

237

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution  

PubMed Central

Background The genetic network involved in the bacterial cell cycle is poorly understood even though it underpins the remarkable ability of bacteria to proliferate. How such network evolves is even less clear. The major aims of this work were to identify and examine the genes and pathways that are differentially expressed during the Caulobacter crescentus cell cycle, and to analyze the evolutionary features of the cell cycle network. Results We used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many genes previously unknown for their cell cycle regulation, includes almost half of the genes involved in primary metabolism, suggesting that these “house-keeping” genes are not constitutively transcribed during the cell cycle, as often assumed. Gene and module co-expression clustering reveal co-regulated pathways and suggest functionally coupled genes. In addition, an evolutionary analysis of the cell cycle network shows a high correlation between co-expression and co-evolution. Most co-expression modules have strong phylogenetic signals, with broadly conserved genes and clade-specific genes predominating different substructures of the cell cycle co-expression network. We also found that conserved genes tend to determine the expression profile of their module. Conclusion We describe the first phylogenetic and single-nucleotide-resolution transcriptomic analysis of a bacterial cell cycle network. In addition, the study suggests how evolution has shaped this network and provides direct biological network support that selective pressure is not on individual genes but rather on the relationship between genes, which highlights the importance of integrating phylogenetic analysis into biological network studies.

2013-01-01

238

The Evolution of the Bacterial Luciferase Gene Cassette (lux) as a Real-Time Bioreporter  

PubMed Central

The bacterial luciferase gene cassette (lux) is unique among bioluminescent bioreporter systems due to its ability to synthesize and/or scavenge all of the substrate compounds required for its production of light. As a result, the lux system has the unique ability to autonomously produce a luminescent signal, either continuously or in response to the presence of a specific trigger, across a wide array of organismal hosts. While originally employed extensively as a bacterial bioreporter system for the detection of specific chemical signals in environmental samples, the use of lux as a bioreporter technology has continuously expanded over the last 30 years to include expression in eukaryotic cells such as Saccharomyces cerevisiae and even human cell lines as well. Under these conditions, the lux system has been developed for use as a biomedical detection tool for toxicity screening and visualization of tumors in small animal models. As the technologies for lux signal detection continue to improve, it is poised to become one of the first fully implantable detection systems for intra-organismal optical detection through direct marriage to an implantable photon-detecting digital chip. This review presents the basic biochemical background that allows the lux system to continuously autobioluminesce and highlights the important milestones in the use of lux-based bioreporters as they have evolved from chemical detection platforms in prokaryotic bacteria to rodent-based tumorigenesis study targets. In addition, the future of lux imaging using integrated circuit microluminometry to image directly within a living host in real-time will be introduced and its role in the development of dose/response therapeutic systems will be highlighted.

Close, Dan; Xu, Tingting; Smartt, Abby; Rogers, Alexandra; Crossley, Robert; Price, Sarah; Ripp, Steven; Sayler, Gary

2012-01-01

239

Systematic 16S rRNA Gene Sequencing of Atypical Clinical Isolates Identified 27 New Bacterial Species Associated with Humans  

PubMed Central

Clinical microorganisms isolated during a 5-year study in our hospital that could not be identified by conventional criteria were studied by 16S rRNA gene sequence analysis. Each isolate yielded a ?1,400-bp sequence containing <5 ambiguities which was compared with the GenBank 16S rRNA gene library; 1,404 such isolates were tested, and 120 were considered unique (27 isolates) or rare (?10 cases reported in the literature) human pathogens. Eleven new species, “Actinobaculum massiliae,” “Candidatus Actinobaculum timonae,” Paenibacillus sanguinis, “Candidatus Bacteroides massiliae,” Chryseobacterium massiliae, “Candidatus Chryseobacterium timonae,” Paenibacillus massiliensis, “Candidatus Peptostreptococcus massiliae,” “Candidatus Prevotella massiliensis,” Rhodobacter massiliensis, and “Candidatus Veillonella atypica” were identified. Sixteen species were obtained from humans for the first time. Our results show the important role that 16S rRNA gene sequence-based bacterial identification currently plays in recognizing unusual and emerging bacterial diseases.

Drancourt, M.; Berger, P.; Raoult, D.

2004-01-01

240

A bacterial view of the periodic table: genes and proteins for toxic inorganic ions.  

PubMed

Essentially all bacteria have genes for toxic metal ion resistances and these include those for Ag+, AsO2-, AsO4(3-), Cd2+ Co2+, CrO4(2-), Cu2+, Hg2+, Ni2+, Pb2+, TeO3(2-), Tl+ and Zn2+. The largest group of resistance systems functions by energy-dependent efflux of toxic ions. Fewer involve enzymatic transformations (oxidation, reduction, methylation, and demethylation) or metal-binding proteins (for example, metallothionein SmtA, chaperone CopZ and periplasmic silver binding protein SilE). Some of the efflux resistance systems are ATPases and others are chemiosmotic ion/proton exchangers. For example, Cd2+-efflux pumps of bacteria are either inner membrane P-type ATPases or three polypeptide RND chemiosmotic complexes consisting of an inner membrane pump, a periplasmic-bridging protein and an outer membrane channel. In addition to the best studied three-polypeptide chemiosmotic system, Czc (Cd2+, Zn2+, and Co2), others are known that efflux Ag+, Cu+, Ni2+, and Zn2+. Resistance to inorganic mercury, Hg2+ (and to organomercurials, such as CH3Hg+ and phenylmercury) involve a series of metal-binding and membrane transport proteins as well as the enzymes mercuric reductase and organomercurial lyase, which overall convert more toxic to less toxic forms. Arsenic resistance and metabolizing systems occur in three patterns, the widely-found ars operon that is present in most bacterial genomes and many plasmids, the more recently recognized arr genes for the periplasmic arsenate reductase that functions in anaerobic respiration as a terminal electron acceptor, and the aso genes for the periplasmic arsenite oxidase that functions as an initial electron donor in aerobic resistance to arsenite. PMID:16133099

Silver, Simon; Phung, Le T

2005-12-01

241

Plant chromatin: development and gene control.  

PubMed

It is increasingly clear that chromatin is not just a device for packing DNA within the nucleus but also a dynamic material that changes as cellular environments alter. The precise control of chromatin modification in response to developmental and environmental cues determines the correct spatial and temporal expression of genes. Here, we review exciting discoveries that reveal chromatin participation in many facets of plant development. These include: chromatin modification from embryonic and meristematic development to flowering and seed formation, the involvement of DNA methylation and chromatin in controlling invasive DNA and in maintenance of epigenetic states, and the function of chromatin modifying and remodeling complexes such as SWI/SNF and histone acetylases and deacetylases in gene control. Given the role chromatin structure plays in every facet of plant development, chromatin research will undoubtedly be integral in both basic and applied plant biology. PMID:11891760

Li, Guofu; Hall, Timothy C; Holmes-Davis, Rachel

2002-03-01

242

Control of gene expression in trypanosomes.  

PubMed Central

Trypanosomes are protozoan agents of major parasitic diseases such as Chagas' disease in South America and sleeping sickness of humans and nagana disease of cattle in Africa. They are transmitted to mammalian hosts by specific insect vectors. Their life cycle consists of a succession of differentiation and growth phases requiring regulated gene expression to adapt to the changing extracellular environment. Typical of such stage-specific expression is that of the major surface antigens of Trypanosoma brucei, procyclin in the procyclic (insect) form and the variant surface glycoprotein (VSG) in the bloodstream (mammalian) form. In trypanosomes, the regulation of gene expression is effected mainly at posttranscriptional levels, since primary transcription of most of the genes occurs in long polycistronic units and is constitutive. The transcripts are processed by transsplicing and polyadenylation under the influence of intergenic polypyrimidine tracts. These events show some developmental regulation. Untranslated sequences of the mRNAs seem to play a prominent role in the stage-specific control of individual gene expression, through a modulation of mRNA abundance. The VSG and procyclin transcription units exhibit particular features that are probably related to the need for a high level of expression. The promoters and RNA polymerase driving the expression of these units resemble those of the ribosomal genes. Their mutually exclusive expression is ensured by controls operating at several levels, including RNA elongation. Antigenic variation in the bloodstream is achieved through DNA rearrangements or alternative activation of the telomeric VSG gene expression sites. Recent discoveries, such as the existence of a novel nucleotide in telomeric DNA and the generation of point mutations in VSG genes, have shed new light on the mechanisms and consequences of antigenic variation.

Vanhamme, L; Pays, E

1995-01-01

243

Cloning the bacterial bphC gene into Nicotiana tabacum to improve the efficiency of phytoremediation of polychlorinated biphenyls  

PubMed Central

The aim of this work was to construct transgenic plants with increased capabilities to degrade organic pollutants, such as polychlorinated biphenyls. The environmentally important gene of bacterial dioxygenase, the bphC gene, was chosen to clone into a plant of Nicotiana tabacum. The chosen bphC gene encodes 2,3-dihydroxybiphenyl-1,2-dioxygenase, which cleaves the aromatic ring of dihydroxybiphenyl, and we cloned it in fusion with the gene for ?-glucuronidase (GUS), luciferase (LUC) or with a histidine tail. Several genetic constructs were designed and prepared and the possible expression of desired proteins in tobacco plants was studied by transient expression. We used genetic constructs successfully expressing dioxygenase's genes we used for preparation of transgenic tobacco plants by agrobacterial infection. The presence of transgenic DNA , mRNA and protein was determined in parental and the first filial generation of transgenic plants with the bphC gene. Properties of prepared transgenic plants will be further studied.

Novakova, Martina; Mackova, Martina; Antosova, Zuzana; Viktorova, Jitka; Szekeres, Miklos; Demnerova, Katerina

2010-01-01

244

Application of a Microcomputer-Based System to Control and Monitor Bacterial Growth  

PubMed Central

A modular microcomputer-based system was developed to control and monitor various modes of bacterial growth. The control system was composed of an Apple II Plus microcomputer with 64-kilobyte random-access memory; a Cyborg ISAAC model 91A multichannel analog-to-digital and digital-to-analog converter; paired MRR-1 pH, pO2, and foam control units; and in-house-designed relay, servo control, and turbidimetry systems. To demonstrate the flexibility of the system, we grew bacteria under various computer-controlled and monitored modes of growth, including batch, turbidostat, and chemostat systems. The Apple-ISAAC system was programmed in Labsoft BASIC (extended Applesoft) with an average control program using ca. 6 to 8 kilobytes of memory and up to 30 kilobytes for datum arrays. This modular microcomputer-based control system was easily coupled to laboratory scale fermentors for a variety of fermentations.

Titus, Jeffrey A.; Luli, Gregory W.; Dekleva, Michael L.; Strohl, William R.

1984-01-01

245

Application of a microcomputer-based system to control and monitor bacterial growth.  

PubMed

A modular microcomputer-based system was developed to control and monitor various modes of bacterial growth. The control system was composed of an Apple II Plus microcomputer with 64-kilobyte random-access memory; a Cyborg ISAAC model 91A multichannel analog-to-digital and digital-to-analog converter; paired MRR-1 pH, pO(2), and foam control units; and in-house-designed relay, servo control, and turbidimetry systems. To demonstrate the flexibility of the system, we grew bacteria under various computer-controlled and monitored modes of growth, including batch, turbidostat, and chemostat systems. The Apple-ISAAC system was programmed in Labsoft BASIC (extended Applesoft) with an average control program using ca. 6 to 8 kilobytes of memory and up to 30 kilobytes for datum arrays. This modular microcomputer-based control system was easily coupled to laboratory scale fermentors for a variety of fermentations. PMID:16346462

Titus, J A; Luli, G W; Dekleva, M L; Strohl, W R

1984-02-01

246

The role of bacterial grazers in controlling oxic and anoxic decomposition of organic matter  

SciTech Connect

One prominent theory describing the relation between productivity, O[sub 2], and carbon preservation is that anoxic decomposition is intrinsically slower than oxic decomposition and thus results in the accumulation of organic matter in anoxic sediments and waters. However, several past studies suggest that differences in the intrinsic rates of decomposition between the two types of systems are small. Measurement of the microbial metabolism of individual radiolabeled compounds in the oxic and anoxic waters of stratified water bodies provides further evidence of this. This lack of a rate difference suggests the need for further explanation of the controls on carbon preservation. One possible explanation is that animal-poor anoxic sediments may sequester organic matter as bacterial biomass or as bacterial-derived products in the absence of bacterial grazers. Thus, differences in the numbers and diversity of organisms that graze upon bacteria between oxic and anoxic sediments may explain part of the difference in carbon preservation rates that have been observed between the two types of systems. The absence of bacterial grazers in compacted sediments could also explain why organic carbon is preserved in deep oxic and ancient sediments.

Lee, C. (State Univ. of New York, Stony Brook, NY (United States). Marine Sciences Research Center)

1992-01-01

247

14. GENE PUMPING STATION CONTROL ROOM AS SEEN FROM MAIN ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

14. GENE PUMPING STATION CONTROL ROOM AS SEEN FROM MAIN STATION MANAGER'S CONTROL DESK. ELECTRICAL CONTROL INDICATORS AND CONTROLS FOR REGULATING ELECTRICITY INTO PLANT AS WELL AS SYNCHRONIZING STARTUP OF PUMPS. - Gene Pump Plant, South of Gene Wash Reservoir, 2 miles west of Whitsett Pump Plant, Parker Dam, San Bernardino County, CA

248

Using bacterial extract along with differential gene expression in Acropora millepora larvae to decouple the processes of attachment and metamorphosis.  

PubMed

Biofilms of the bacterium Pseudoalteromonas induce metamorphosis of acroporid coral larvae. The bacterial metabolite tetrabromopyrrole (TBP), isolated from an extract of Pseudoalteromonas sp. associated with the crustose coralline alga (CCA) Neogoniolithon fosliei, induced coral larval metamorphosis (100%) with little or no attachment (0-2%). To better understand the molecular events and mechanisms underpinning the induction of Acropora millepora larval metamorphosis, including cell proliferation, apoptosis, differentiation, migration, adhesion and biomineralisation, two novel coral gene expression assays were implemented. These involved the use of reverse-transcriptase quantitative PCR (RT-qPCR) and employed 47 genes of interest (GOI), selected based on putative roles in the processes of settlement and metamorphosis. Substantial differences in transcriptomic responses of GOI were detected following incubation of A. millepora larvae with a threshold concentration and 10-fold elevated concentration of TBP-containing extracts of Pseudoalteromonas sp. The notable and relatively abrupt changes of the larval body structure during metamorphosis correlated, at the molecular level, with significant differences (p<0.05) in gene expression profiles of 24 GOI, 12 hours post exposure. Fourteen of those GOI also presented differences in expression (p<0.05) following exposure to the threshold concentration of bacterial TBP-containing extract. The specificity of the bacterial TBP-containing extract to induce the metamorphic stage in A. millepora larvae without attachment, using a robust, low cost, accurate, ecologically relevant and highly reproducible RT-qPCR assay, allowed partially decoupling of the transcriptomic processes of attachment and metamorphosis. The bacterial TBP-containing extract provided a unique opportunity to monitor the regulation of genes exclusively involved in the process of metamorphosis, contrasting previous gene expression studies that utilized cues, such as crustose coralline algae, biofilms or with GLW-amide neuropeptides that stimulate the entire onset of larval metamorphosis and attachment. PMID:22655067

Siboni, Nachshon; Abrego, David; Seneca, Francois; Motti, Cherie A; Andreakis, Nikos; Tebben, Jan; Blackall, Linda L; Harder, Tilmann

2012-01-01

249

Using Bacterial Extract along with Differential Gene Expression in Acropora millepora Larvae to Decouple the Processes of Attachment and Metamorphosis  

PubMed Central

Biofilms of the bacterium Pseudoalteromonas induce metamorphosis of acroporid coral larvae. The bacterial metabolite tetrabromopyrrole (TBP), isolated from an extract of Pseudoalteromonas sp. associated with the crustose coralline alga (CCA) Neogoniolithon fosliei, induced coral larval metamorphosis (100%) with little or no attachment (0–2%). To better understand the molecular events and mechanisms underpinning the induction of Acropora millepora larval metamorphosis, including cell proliferation, apoptosis, differentiation, migration, adhesion and biomineralisation, two novel coral gene expression assays were implemented. These involved the use of reverse-transcriptase quantitative PCR (RT-qPCR) and employed 47 genes of interest (GOI), selected based on putative roles in the processes of settlement and metamorphosis. Substantial differences in transcriptomic responses of GOI were detected following incubation of A. millepora larvae with a threshold concentration and 10-fold elevated concentration of TBP-containing extracts of Pseudoalteromonas sp. The notable and relatively abrupt changes of the larval body structure during metamorphosis correlated, at the molecular level, with significant differences (p<0.05) in gene expression profiles of 24 GOI, 12 hours post exposure. Fourteen of those GOI also presented differences in expression (p<0.05) following exposure to the threshold concentration of bacterial TBP-containing extract. The specificity of the bacterial TBP-containing extract to induce the metamorphic stage in A. millepora larvae without attachment, using a robust, low cost, accurate, ecologically relevant and highly reproducible RT-qPCR assay, allowed partially decoupling of the transcriptomic processes of attachment and metamorphosis. The bacterial TBP-containing extract provided a unique opportunity to monitor the regulation of genes exclusively involved in the process of metamorphosis, contrasting previous gene expression studies that utilized cues, such as crustose coralline algae, biofilms or with GLW-amide neuropeptides that stimulate the entire onset of larval metamorphosis and attachment.

Siboni, Nachshon; Abrego, David; Seneca, Francois; Motti, Cherie A.; Andreakis, Nikos; Tebben, Jan; Blackall, Linda L.; Harder, Tilmann

2012-01-01

250

Expression of antimicrobial peptide genes in Bombyx mori gut modulated by oral bacterial infection and development.  

PubMed

Although Bombyx mori systematic immunity is extensively studied, little is known about the silkworm's intestine-specific responses to bacterial infection. Antimicrobial peptides (AMPs) gene expression analysis of B. mori intestinal tissue to oral infection with the Gram-positive (Staphylococcus aureus) and -negative (Escherichia coli) bacteria revealed that there is specificity in the interaction between host immune responses and parasite types. Neither Att1 nor Leb could be stimulated by S. aureus and E. coli. However, CecA1, Glo1, Glo2, Glo3, Glo4 and Lys, could only be trigged by S. aureus. On the contrary, E. coli stimulation caused the decrease in the expression of CecA1, Glo3 and Glo4 in some time points. Interestingly, there is regional specificity in the silkworm local gut immunity. During the immune response, the increase in Def, Hem and LLP3 was only detected in the foregut and midgut. For CecB1, CecD, LLP2 and Mor, after orally administered with E. coli, the up-regulation was only limited in the midgut and hindgut. CecE was the only AMP that positively responses to the both bacteria in all the testing situations. With development, the expression levels of the AMPs were also changed dramatically. That is, at spinning and prepupa stages, a large increase in the expression of CecA1, CecB1, CecD, CecE, Glo1, Glo2, Glo3, Glo4, Leb, Def, Hem, Mor and Lys was detected in the gut. Unexpectedly, in addition to the IMD pathway genes, the Toll and JAK/STAT pathway genes in the silkworm gut can also be activated by microbial oral infection. But in the developmental course, corresponding to the increase in expression of AMPs at spinning and prepupa stages, only the Toll pathway genes in the gut exhibit the similar increasing trend. Our results imply that the immune responses in the silkworm gut are synergistically regulated by the Toll, JAK/STAT and IMD pathways. However, as the time for approaching pupation, the Toll pathway may play a role in the AMPs expression. PMID:20600274

Wu, Shan; Zhang, Xiaofeng; He, Yongqiang; Shuai, Jiangbing; Chen, Xiaomei; Ling, Erjun

2010-11-01

251

Bacterial bioluminescence regulates expression of a host cryptochrome gene in the squid-Vibrio symbiosis.  

PubMed

The symbiosis between the squid Euprymna scolopes and its luminous symbiont, Vibrio fischeri, is characterized by daily transcriptional rhythms in both partners and daily fluctuations in symbiont luminescence. In this study, we sought to determine whether symbionts affect host transcriptional rhythms. We identified two transcripts in host tissues (E. scolopes cry1 [escry1] and escry2) that encode cryptochromes, proteins that influence circadian rhythms in other systems. Both genes cycled daily in the head of the squid, with a pattern similar to that of other animals, in which expression of certain cry genes is entrained by environmental light. In contrast, escry1 expression cycled in the symbiont-colonized light organ with 8-fold upregulation coincident with the rhythms of bacterial luminescence, which are offset from the day/night light regime. Colonization of the juvenile light organ by symbionts was required for induction of escry1 cycling. Further, analysis with a mutant strain defective in light production showed that symbiont luminescence is essential for cycling of escry1; this defect could be complemented by presentation of exogenous blue light. However, blue-light exposure alone did not induce cycling in nonsymbiotic animals, but addition of molecules of the symbiont cell envelope to light-exposed animals did recover significant cycling activity, showing that light acts in synergy with other symbiont features to induce cycling. While symbiont luminescence may be a character specific to rhythms of the squid-vibrio association, resident microbial partners could similarly influence well-documented daily rhythms in other systems, such as the mammalian gut. PMID:23549919

Heath-Heckman, Elizabeth A C; Peyer, Suzanne M; Whistler, Cheryl A; Apicella, Michael A; Goldman, William E; McFall-Ngai, Margaret J

2013-01-01

252

Identification of Burkholderia cenocepacia genes required for bacterial survival in vivo.  

PubMed

Burkholderia cenocepacia (formerly Burkholderia cepacia complex genomovar III) causes chronic lung infections in patients with cystic fibrosis. In this work, we used a modified signature-tagged mutagenesis (STM) strategy for the isolation of B. cenocepacia mutants that cannot survive in vivo. Thirty-seven specialized plasposons, each carrying a unique oligonucleotide tag signature, were constructed and used to examine the survival of 2,627 B. cenocepacia transposon mutants, arranged in pools of 37 unique mutants, after a 10-day lung infection in rats by using the agar bead model. The recovered mutants were screened by real-time PCR, resulting in the identification of 260 mutants which presumably did not survive within the lungs. These mutants were repooled into smaller pools, and the infections were repeated. After a second screen, we isolated 102 mutants unable to survive in the rat model. The location of the transposon in each of these mutants was mapped within the B. cenocepacia chromosomes. We identified mutations in genes involved in cellular metabolism, global regulation, DNA replication and repair, and those encoding bacterial surface structures, including transmembrane proteins and cell surface polysaccharides. Also, we found 18 genes of unknown function, which are conserved in other bacteria. A subset of 12 representative mutants that were individually examined using the rat model in competition with the wild-type strain displayed reduced survival, confirming the predictive value of our STM screen. This study provides a blueprint to investigate at the molecular level the basis for survival and persistence of B. cenocepacia within the airways. PMID:15213146

Hunt, Tracey A; Kooi, Cora; Sokol, Pamela A; Valvano, Miguel A

2004-07-01

253

Lysis-deficient phages as novel therapeutic agents for controlling bacterial infection  

PubMed Central

Background Interest in phage therapy has grown over the past decade due to the rapid emergence of antibiotic resistance in bacterial pathogens. However, the use of bacteriophages for therapeutic purposes has raised concerns over the potential for immune response, rapid toxin release by the lytic action of phages, and difficulty in dose determination in clinical situations. A phage that kills the target cell but is incapable of host cell lysis would alleviate these concerns without compromising efficacy. Results We developed a recombinant lysis-deficient Staphylococcus aureus phage P954, in which the endolysin gene was rendered nonfunctional by insertional inactivation. P954, a temperate phage, was lysogenized in S. aureus strain RN4220. The native endolysin gene on the prophage was replaced with an endolysin gene disrupted by the chloramphenicol acetyl transferase (cat) gene through homologous recombination using a plasmid construct. Lysogens carrying the recombinant phage were detected by growth in presence of chloramphenicol. Induction of the recombinant prophage did not result in host cell lysis, and the phage progeny were released by cell lysis with glass beads. The recombinant phage retained the endolysin-deficient genotype and formed plaques only when endolysin was supplemented. The host range of the recombinant phage was the same as that of the parent phage. To test the in vivo efficacy of the recombinant endolysin-deficient phage, immunocompromised mice were challenged with pathogenic S. aureus at a dose that results in 80% mortality (LD80). Treatment with the endolysin-deficient phage rescued mice from the fatal S. aureus infection. Conclusions A recombinant endolysin-deficient staphylococcal phage has been developed that is lethal to methicillin-resistant S. aureus without causing bacterial cell lysis. The phage was able to multiply in lytic mode utilizing a heterologous endolysin expressed from a plasmid in the propagation host. The recombinant phage effectively rescued mice from fatal S. aureus infection. To our knowledge this is the first report of a lysis-deficient staphylococcal phage.

2011-01-01

254

Bacterial symbiosis and paratransgenic control of vector-borne Chagas disease.  

PubMed

The triatomine vectors of Chagas disease are obligate haematophagous insects, feeding on vertebrate blood throughout their entire developmental cycle. As a result of obtaining their nutrition from a single food source, their diet is devoid of certain vitamins and nutrients. Consequently, these insects harbour populations of bacterial symbionts within their intestinal tract, which provide the required nutrients that are lacking from their diet. We have isolated and characterised symbiont cultures from various triatomine species and developed a method for genetically transforming them. We can then reintroduce them into their original host species, thereby producing stable paratransgenic insects in which we are able to express heterologous gene products. Using this methodology, we have generated paratransgenic Rhodnius prolixus that are refractory for infection with Trypanosoma cruzi. Two examples of potentially refractory genes are currently being expressed in paratransgenic insects. These include the insect immune peptide cecropin A and active single chain antibody fragments. We have also developed an approach that would allow introduction of genetically modified bacterial symbionts into natural populations of Chagas disease vectors. This approach utilises the coprophagic behaviour of these insects, which is the way in which the symbionts are transmitted among bug populations in nature. The production and ultimate release of transgenic or paratransgenic insects for public health applications is potentially very promising but also worthy of much careful consideration with respect to environmental, political, and human safety concerns. PMID:11334952

Beard, C B; Dotson, E M; Pennington, P M; Eichler, S; Cordon-Rosales, C; Durvasula, R V

2001-05-01

255

Bacterial rRNA Genes Associated with Soil Suppressiveness against the Plant-Parasitic Nematode Heterodera schachtii  

Microsoft Academic Search

The goal of this study was to identify bacteria involved in soil suppressiveness against the plant-parasitic nematode Heterodera schachtii. Since H. schachtii cysts isolated from the suppressive soil can transfer this beneficial property to nonsuppressive soils, analysis of the cyst-associated microorganisms should lead to the identification of the causal organisms. Our experimental approach was to identify bacterial rRNA genes (rDNA)

Bei Yin; Lea Valinsky; Xuebiao Gao; J. Ole Becker; James Borneman

2003-01-01

256

Detection of the organophosphate degrading gene opdA in the newly isolated bacterial strain Bacillus pumilus W1  

Microsoft Academic Search

The toxicity of organophosphates to a wide range of organisms necessitates the study of their degradation. We designed a study\\u000a to isolate an organophosphate-degrading bacterium and to detect the gene involved in the hydrolysis of organophosphates. The\\u000a bacterial strain was isolated by the enrichment culture technique from organophosphate-contaminated soil, It was identified\\u000a as Bacillus pumilus W1 based on its biochemical

Muhammad Ali; Tatheer Alam Naqvi; Maria Kanwal; Faisal Rasheed; Abdul Hameed; Safia Ahmed

257

Transgenic control of perforin gene expression  

SciTech Connect

Perforin is a pore-forming effector molecule of CTL and NK cells. To characterize perforin gene expression and its transcriptional control mechanisms in vivo, expression of a cell surface tag, i.e., human CD4, was driven by 5.1 kb of the murin perforin 5{prime} flanking and promoter region in transgenic mice. Six out of seven transgenic lines expressed the perforin-tag hybrid gene at low to intermediate levels, depending on the integration site. Transgene expression occurred in all cells that physiologically are able to express perforin. At the whole organ level, significant amounts of transgenic mRNA and endogenous perforin mRNA were co-expressed in the lymphoid organs, as well as in the lung, the ileum, the oviduct/uterus, and the bone marrow. At the single cell level, the perforin tag was present on NK cells and on CD8{sup +}, as well as on CD4{sup +} cells. Also targeted were Thy-1.2{sup +} {gamma}{delta} T cells, but not Thy-1.2{sup -} {gamma}{delta} T cells, B cells, nor monocytes. During thymic T cell development, transgene expression occurred in double negative (CD4{sup -}CD8{sup -}) thymocytes and was detected at all subsequent stages, but exceeded the expression levels of the endogenous gene in the thymus. In conclusion, the analyzed perforin 5{prime} flanking and promoter region contains important cis-acting sequences that restrict perforin expression to T cells and NK cells, and therefore provides a unique tool for manipulating T cell and/or Nk cell-mediated immune responses in transgenic mice. On the other hand, the normal control of perforin gene expression involves at least one additional negative control mechanism that was not mediated by the transgenic promoter and upstream region. This control restricts perforin gene expression in thymically developing T cells and in most resting peripheral T cells, but can be released upon T cell activation. 43 refs., 7 figs., 1 tab.

Lichtenheld, M.G.; Podack, E.R.; Levy, R.B. [Univ. of Miami, FL (United States)

1995-03-01

258

Posttranscriptional Control of Gene Expression in Yeast  

PubMed Central

Studies of the budding yeast Saccharomyces cerevisiae have greatly advanced our understanding of the posttranscriptional steps of eukaryotic gene expression. Given the wide range of experimental tools applicable to S. cerevisiae and the recent determination of its complete genomic sequence, many of the key challenges of the posttranscriptional control field can be tackled particularly effectively by using this organism. This article reviews the current knowledge of the cellular components and mechanisms related to translation and mRNA decay, with the emphasis on the molecular basis for rate control and gene regulation. Recent progress in characterizing translation factors and their protein-protein and RNA-protein interactions has been rapid. Against the background of a growing body of structural information, the review discusses the thermodynamic and kinetic principles that govern the translation process. As in prokaryotic systems, translational initiation is a key point of control. Modulation of the activities of translational initiation factors imposes global regulation in the cell, while structural features of particular 5? untranslated regions, such as upstream open reading frames and effector binding sites, allow for gene-specific regulation. Recent data have revealed many new details of the molecular mechanisms involved while providing insight into the functional overlaps and molecular networking that are apparently a key feature of evolving cellular systems. An overall picture of the mechanisms governing mRNA decay has only very recently begun to develop. The latest work has revealed new information about the mRNA decay pathways, the components of the mRNA degradation machinery, and the way in which these might relate to the translation apparatus. Overall, major challenges still to be addressed include the task of relating principles of posttranscriptional control to cellular compartmentalization and polysome structure and the role of molecular channelling in these highly complex expression systems.

McCarthy, John E. G.

1998-01-01

259

Lies and deception in bacterial gene regulation: the roles of nucleic acid decoys.  

PubMed

Bacteria use intricately interconnected mechanisms acting at the transcriptional and post-transcriptional level to adjust gene expression to their needs. An intriguing example found in the chitosugar utilization systems of Escherichia coli and Salmonella is uncovered in a study by Plumbridge and colleagues. Three transcription factors (TFs), a small regulatory RNA (sRNA) and a sRNA trap cooperate to set thresholds and dynamics in regulation of chitosugar utilization. Specifically, under inducing conditions a decoy site on the polycistronic chitobiose (chbBCARFG) mRNA sequesters sRNA ChiX, which represses synthesis of the separately encoded chitoporin ChiP. Base-pairing of ChiX with its decoy has no role for the chb genes themselves when the mRNA is in excess. In the absence of substrate, however, this base-pairing tightly represses chbC encoding a subunit of the chitosugar transporter. Thus, one and the same sRNA/mRNA interaction serves different regulatory functions under different environmental conditions. The employment of RNA decoys to control the activities of post-transcriptional regulators themselves is an increasingly recognized mechanism in gene regulation. Another observation in the current study highlights the possibility that decoy sites might even exist on the DNA controlling the availability of TFs for their target promoters. PMID:24707963

Göpel, Yvonne; Görke, Boris

2014-05-01

260

Recent progress in biointerfaces with controlled bacterial adhesion by using chemical and physical methods.  

PubMed

Biointerfaces with the controlled adhesion of bacteria are highly important, owing to their wide applications, which range from decreasing the probability of infection to promoting higher efficiency and sensitivity in biocatalysts and biosensors. In this Focus Review, we summarize the recent progress in chemically and physically designed biointerfaces with controlled bacterial adhesion. On one hand, several smart-responsive biointerfaces that can be switched between bacteria-adhesive states and bacteria-resistant states by applying an external stimulus have been rationally designed and developed for adhering and detaching bacteria, whilst, on the other hand, the adhesive behavior of bacteria can be controlled by regulating the topography of the biointerface. In addition, new technologies (i.e., biosensors) and materials (i.e., graphene) provide promising approaches for efficiently controlling the adhesion of bacteria for practical applications. PMID:24866966

Meng, Jingxin; Zhang, Pengchao; Wang, Shutao

2014-08-01

261

Reference Gene Selection for Insect Expression Studies Using Quantitative Real-Time PCR: The Head of the Honeybee, Apis mellifera , After a Bacterial Challenge  

Microsoft Academic Search

In this study an important and often neglected aspect of gene expression studies in insects, the validation of appropriate reference genes with stable expression levels between sample groups, is addressed. Although in this paper the reference gene selection for the honeybee, Apis mellifera L. (Hymenoptera: Apidae) head was tested in the context of bacterial challenge with Escherichia coli, this work

Bieke Scharlaken; Dirk C. de Graaf; Karen Goossens; Marleen Brunain; Luc J. Peelman; Frans J. Jacobs

2008-01-01

262

Construction of a 1.2Mb contig including the citrus tristeza virus resistance gene locus using a bacterial artificial chromosome library of Poncirus trifoliata (L.) Raf  

Microsoft Academic Search

The citrus tristeza virus resistance gene ( Ctv) is a single dominant gene in Poncirus trifoliata, a sexually compatible relative of citrus. To clone this gene, a bacterial artificial chromosome (BAC) library has been constructed from an individual plant that was homozygous for Ctv. This library contains 45 696 clones with an average insert size of 80 kb, corresponding to

Zhong-Nan Yang; Xin-Rong Ye; Sandong Choi; Joe Molina; Francis Moonan; Rod A. Wing; Mikeal L. Roose; T. Erik Mirkov

2001-01-01

263

Combinatorial Transcription Control in Gene Regulation  

NASA Astrophysics Data System (ADS)

We develop a simple thermodynamic model for the regulation of gene transcription and explore the limits of combinatorial control. Our model is based on the ``regulated recruitment'' mechanism [M. Ptashne and A. Gann, Nature 386 (1997) 569], assuming weak contact interaction between the regulatory proteins together with specific protein-DNA interactions. We further assume "programmability" in the strengths of these interactions within a biophysically allowed range [U. Gerland, J.D. Moroz, and T.Hwa, PNAS 99 (2002) 12015], through the choices and the locations of the protein-binding DNA sequences in the regulatory region. Within our thermodynamic model, we demonstrate the implementability of various binary logic functions (including XOR) by computing the degree of gene transcription (output) for all combinations of regulatory protein concentrations (input).

Hwa, Terence; Buchler, Nicolas E.; Gerland, Ulrich

2003-03-01

264

Biological control of rice bacterial blight by plant-associated bacteria producing 2,4-diacetylphloroglucinol.  

PubMed

Certain plant-associated strains of fluorescent Pseudomonas spp. are known to produce the antimicrobial antibiotic 2,4-diacetylphloroglucinol (DAPG). It has antibacterial, antifungal, antiviral, and antihelminthic properties and has played a significant role in the biological control of tobacco, wheat, and sugar beet diseases. It has never been reported from India and has not been implicated in the biological suppression of a major disease of the rice crop. Here, we report that a subpopulation of 27 strains of plant-associated Pseudomonas fluorescens screened in a batch of 278 strains of fluorescent pseudomonads produced DAPG. The DAPG production was detected by a PCR-based screening method that used primers Phl2a and Phl2b and amplified a 745-bp fragment characteristic of DAPG. HPLC, 1H NMR, and IR analyses provided further evidence for its production. We report also that this compound inhibited the growth of the devastating rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae in laboratory assays and suppressed rice bacterial blight up to 59%-64% in net-house and field experiments. Tn5 mutants defective in DAPG production (Phl-) of P. fluorescens PTB 9 were much less effective in their suppression of rice bacterial blight. PMID:16541159

Velusamy, Palaniyandi; Immanuel, J Ebenezar; Gnanamanickam, Samuel S; Thomashow, Linda

2006-01-01

265

Quantification of yeast and bacterial gene transcripts in retail cheeses by reverse transcription-quantitative PCR.  

PubMed

The cheese microbiota contributes to a large extent to the development of the typical color, flavor, and texture of the final product. Its composition is not well defined in most cases and varies from one cheese to another. The aim of the present study was to establish procedures for gene transcript quantification in cheeses by reverse transcription-quantitative PCR. Total RNA was extracted from five smear-ripened cheeses purchased on the retail market, using a method that does not involve prior separation of microbial cells. 16S rRNA and malate:quinone oxidoreductase gene transcripts of Corynebacterium casei, Brevibacterium aurantiacum, and Arthrobacter arilaitensis and 26S rRNA and beta tubulin gene transcripts of Geotrichum candidum and Debaryomyces hansenii could be detected and quantified in most of the samples. Three types of normalization were applied: against total RNA, against the amount of cheese, and against a reference gene. For the first two types of normalization, differences of reverse transcription efficiencies from one sample to another were taken into account by analysis of exogenous control mRNA. No good correlation was found between the abundances of target mRNA or rRNA transcripts and the viable cell concentration of the corresponding species. However, in most cases, no mRNA transcripts were detected for species that did not belong to the dominant species. The applications of gene expression measurement in cheeses containing an undefined microbiota, as well as issues concerning the strategy of normalization and the assessment of amplification specificity, are discussed. PMID:23124230

Monnet, Christophe; Straub, Cécile; Castellote, Jessie; Onesime, Djamila; Bonnarme, Pascal; Irlinger, Françoise

2013-01-01

266

Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression  

PubMed Central

Background In bacteria, the weak correlations at the genome scale between mRNA and protein levels suggest that not all mRNAs are translated with the same efficiency. To experimentally explore mRNA translational level regulation at the systemic level, the detailed translational status (translatome) of all mRNAs was measured in the model bacterium Lactococcus lactis in exponential phase growth. Results Results demonstrated that only part of the entire population of each mRNA species was engaged in translation. For transcripts involved in translation, the polysome size reached a maximum of 18 ribosomes. The fraction of mRNA engaged in translation (ribosome occupancy) and ribosome density were not constant for all genes. This high degree of variability was analyzed by bioinformatics and statistical modeling in order to identify general rules of translational regulation. For most of the genes, the ribosome density was lower than the maximum value revealing major control of translation by initiation. Gene function was a major translational regulatory determinant. Both ribosome occupancy and ribosome density were particularly high for transcriptional regulators, demonstrating the positive role of translational regulation in the coordination of transcriptional networks. mRNA stability was a negative regulatory factor of ribosome occupancy and ribosome density, suggesting antagonistic regulation of translation and mRNA stability. Furthermore, ribosome occupancy was identified as a key component of intracellular protein levels underlining the importance of translational regulation. Conclusions We have determined, for the first time in a bacterium, the detailed translational status for all mRNAs present in the cell. We have demonstrated experimentally the high diversity of translational states allowing individual gene differentiation and the importance of translation-level regulation in the complex process linking gene expression to protein synthesis.

2012-01-01

267

Copy Number Variation of the Beta Defensin Gene Cluster on Chromosome 8p Influences the Bacterial Microbiota within the Nasopharynx of Otitis-Prone Children.  

PubMed

As there is increasing evidence that aberrant defensin expression is related to susceptibility for infectious disease and inflammatory disorders, we sought to determine if copy number of the beta-defensin gene cluster located on chromosome 8p23.1 (DEFB107, 106, 105, 104, 103, DEFB4 and SPAG11), that shows copy number variation as a block, was associated with susceptibility to otitis media (OM). The gene DEFB103 within this complex encodes human beta defensin-3 (hBD-3), an antimicrobial peptide (AP) expressed by epithelial cells that line the mammalian airway, important for defense of mucosal surfaces and previously shown to have bactericidal activity in vitro against multiple human pathogens, including the three that predominate in OM. To this end, we conducted a retrospective case-control study of 113 OM prone children and 267 controls aged five to sixty months. We identified the copy number of the above defined beta-defensin gene cluster (DEFB-CN) in each study subject by paralogue ratio assays. The mean DEFB-CN was indistinguishable between subjects classified as OM prone based on a recent history of multiple episodes of OM and control subjects who had no history of OM (4.4±0.96 versus 4.4±1.08, respectively: Odds Ratio [OR]: 1.16 (95% CI: 0.61, 2.20). Despite a lack of direct association, we observed a statistically significant correlation between DEFB-CN and nasopharyngeal bacterial colonization patterns. Collectively, our findings suggested that susceptibility to OM might be mediated by genetic variation among individuals, wherein a DEFB-CN less than 4 exerts a marked influence on the microbiota of the nasopharynx, specifically with regard to colonization by the three predominant bacterial pathogens of OM. PMID:24867293

Jones, Eric A; Kananurak, Anchasa; Bevins, Charles L; Hollox, Edward J; Bakaletz, Lauren O

2014-01-01

268

Copy Number Variation of the Beta Defensin Gene Cluster on Chromosome 8p Influences the Bacterial Microbiota within the Nasopharynx of Otitis-Prone Children  

PubMed Central

As there is increasing evidence that aberrant defensin expression is related to susceptibility for infectious disease and inflammatory disorders, we sought to determine if copy number of the beta-defensin gene cluster located on chromosome 8p23.1 (DEFB107, 106, 105, 104, 103, DEFB4 and SPAG11), that shows copy number variation as a block, was associated with susceptibility to otitis media (OM). The gene DEFB103 within this complex encodes human beta defensin-3 (hBD-3), an antimicrobial peptide (AP) expressed by epithelial cells that line the mammalian airway, important for defense of mucosal surfaces and previously shown to have bactericidal activity in vitro against multiple human pathogens, including the three that predominate in OM. To this end, we conducted a retrospective case-control study of 113 OM prone children and 267 controls aged five to sixty months. We identified the copy number of the above defined beta-defensin gene cluster (DEFB-CN) in each study subject by paralogue ratio assays. The mean DEFB-CN was indistinguishable between subjects classified as OM prone based on a recent history of multiple episodes of OM and control subjects who had no history of OM (4.4±0.96 versus 4.4±1.08, respectively: Odds Ratio [OR]: 1.16 (95% CI: 0.61, 2.20). Despite a lack of direct association, we observed a statistically significant correlation between DEFB-CN and nasopharyngeal bacterial colonization patterns. Collectively, our findings suggested that susceptibility to OM might be mediated by genetic variation among individuals, wherein a DEFB-CN less than 4 exerts a marked influence on the microbiota of the nasopharynx, specifically with regard to colonization by the three predominant bacterial pathogens of OM.

Bevins, Charles L.; Hollox, Edward J.; Bakaletz, Lauren O.

2014-01-01

269

Molecular chemotherapy of pancreatic cancer using novel mutant bacterial cytosine deaminase gene.  

PubMed

The combination of molecular chemotherapy with radiation therapy has the potential to become a powerful approach for treatment of pancreatic cancer. We have developed an adenoviral vector (AdbCD-D314A) encoding a mutant bacterial cytosine deaminase (bCD) gene, which converts the prodrug 5-fluorocytosine (5-FC) into the active drug 5-fluorouracil. The aim of this study was to investigate AdbCD-D314A/5-FC-mediated cytotoxicity in vitro and therapeutic efficacy in vivo alone and in combination with radiation against human pancreatic cancer cells and xenografts. AdbCD-D314A/5-FC-mediated cytotoxicity alone and in combination with radiation was analyzed using crystal violet inclusion and clonogenic survival assays. CD enzyme activity was determined by measuring conversion of [3H]5-FC to [3H]5-fluorouracil after adenoviral infection of pancreatic cancer cells in vitro and pancreatic tumor xenografts by TLC. S.c. pancreatic tumor xenografts were used to evaluate the therapeutic efficacy of AdbCD-D314A/5-FC molecular chemotherapy in combination with radiation therapy. AdbCD-D314A infection resulted in increased 5-FC-mediated pancreatic cancer cell killing that correlated with significantly enhanced CD enzyme activity compared with AdbCDwt encoding wild-type of bCD. Animal studies showed significant inhibition of growth of human pancreatic tumors treated with AdbCD-D314A/5-FC in comparison with AdbCDwt/5-FC. Also, a significantly greater inhibition of growth of Panc2.03 and MIA PaCA-2 tumor xenografts was produced by the combination of AdbCD-D314A/5-FC with radiation compared with either agent alone. The results indicate that the combination of AdbCD-D314A/5-FC molecular chemotherapy with radiation therapy significantly enhanced cytotoxicity of pancreatic cancer cells in vitro and increased therapeutic efficacy against human pancreatic tumor xenografts. PMID:18790765

Kaliberova, Lyudmila N; Della Manna, Debbie L; Krendelchtchikova, Valentina; Black, Margaret E; Buchsbaum, Donald J; Kaliberov, Sergey A

2008-09-01

270

In Situ-Synthesized Virulence and Marker Gene Biochip for Detection of Bacterial Pathogens in Water? †  

PubMed Central

Pathogen detection tools with high reliability are needed for various applications, including food and water safety and clinical diagnostics. In this study, we designed and validated an in situ-synthesized biochip for detection of 12 microbial pathogens, including a suite of pathogens relevant to water safety. To enhance the reliability of presence/absence calls, probes were designed for multiple virulence and marker genes (VMGs) of each pathogen, and each VMG was targeted by an average of 17 probes. Hybridization of the biochip with amplicon mixtures demonstrated that 95% of the initially designed probes behaved as predicted in terms of positive/negative signals. The probes were further validated using DNA obtained from three different types of water samples and spiked with pathogen genomic DNA at decreasing relative abundance. Excellent specificity for making presence/absence calls was observed by using a cutoff of 0.5 for the positive fraction (i.e., the fraction of probes yielding a positive signal for a given VMG). A split multiplex PCR design for simultaneous amplification of the VMGs resulted in a detection limit of between 0.1 and 0.01% relative abundance, depending on the type of pathogen and the VMG. Thermodynamic analysis of the hybridization patterns obtained with DNA from the different water samples demonstrated that probes with a hybridization Gibbs free energy of approximately ?19.3 kcal/mol provided the best trade-off between sensitivity and specificity. The developed biochip may be used to detect the described bacterial pathogens in water samples when parallel and specific detection is required.

Miller, Sarah M.; Tourlousse, Dieter M.; Stedtfeld, Robert D.; Baushke, Samuel W.; Herzog, Amanda B.; Wick, Lukas M.; Rouillard, Jean Marie; Gulari, Erdogan; Tiedje, James M.; Hashsham, Syed A.

2008-01-01

271

Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola  

Microsoft Academic Search

BACKGROUND: Non-host resistance in rice to its bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), mediated by a maize NBS-LRR type R gene, Rxo1 shows a typical hypersensitive reaction (HR) phenotype, but the molecular mechanism(s) underlying this type of non-host resistance remain largely unknown. RESULTS: A microarray experiment was performed to reveal the molecular mechanisms underlying HR of rice to Xoc

Yong-Li Zhou; Mei-Rong Xu; Ming-Fu Zhao; Xue-Wen Xie; Ling-Hua Zhu; Bin-Ying Fu; Zhi-Kang Li

2010-01-01

272

Metabolite profiles of rice cultivars containing bacterial blight-resistant genes are distinctive from susceptible rice.  

PubMed

The metabolic changes of bacterial blight-resistant line C418/Xa23 generated by molecular marker-assisted selection (n= 12), transgenic variety C418-Xa21 generated by using the Agrobacterium-mediated system (n= 12), and progenitor cultivar C418 (n= 12) were monitored using gas chromatography/mass spectrometry. The validation, discrimination, and establishment of correlative relationships between metabolite signals were performed by cluster analysis, principal component analysis, and partial least squares-discriminant analysis. Significant and unintended changes were observed in 154 components in C418/Xa23 and 48 components in C418-Xa21 compared with C418 (P< 0.05, Fold change > 2.0). The most significant decreases detected (P< 0.001) in both C418/Xa23 and C418-Xa21 were in three amino acids: glycine, tyrosine, and alanine, and four identified metabolites: malic acid, ferulic acid, succinic acid, and glycerol. Linoleic acid was increased specifically in C418/Xa23 which was derived from traditional breeding. This line, possessing a distinctive metabolite profile as a positive control, shows more differences vs. the parental than the transgenic line. Only succinic acid that falls outside the boundaries of natural variability between the two non-transgenic varieties C418 and C418/Xa23 should be further investigated with respect to safety or nutritional impact. PMID:22687573

Wu, Jiao; Yu, Haichuan; Dai, Haofu; Mei, Wenli; Huang, Xin; Zhu, Shuifang; Peng, Ming

2012-08-01

273

Hemoglobin Biosynthesis in Vitreoscilla stercoraria DW: Cloning, Expression, and Characterization of a New Homolog of a Bacterial Globin Gene  

PubMed Central

In the strictly aerobic, gram-negative bacterium Vitreoscilla strain C1, oxygen-limited growth conditions create a more than 50-fold increase in the expression of a homodimeric heme protein which was recognized as the first bacterial hemoglobin (Hb). The recently determined crystal structure of Vitreoscilla Hb has indicated that the heme pocket of microbial globins differs from that of eukaryotic Hbs. In an attempt to understand the diverse functions of Hb-like proteins in prokaryotes, we have cloned and characterized the gene (vgb) encoding an Hb-like protein from another strain of Vitreoscilla, V. stercoraria DW. Several silent changes were observed within the coding region of the V. stercoraria vgb gene. Apart from that, V. stercoraria Hb exhibited interesting differences between the A and E helices. Compared to its Hb counterpart from Vitreoscilla strain C1, the purified preparation of V. stercoraria Hb displays a slower autooxidation rate. The differences between Vitreoscilla Hb and V. stercoraria Hb were mapped onto the three-dimensional structure of Vitreoscilla Hb, which indicated that the four changes, namely, Ile7Val, Ile9Thr, Ile10Ser, and Leu62Val, present within the V. stercoraria Hb fall in the region where the A and E helices contact each other. Therefore, alteration in the relative orientation of the A and E helices and the corresponding conformational change in the heme binding pocket of V. stercoraria Hb can be correlated to its slower autooxidation rate. In sharp contrast to the oxygen-regulated biosynthesis of Hb in Vitreoscilla strain C1, production of Hb in V. stercoraria has been found to be low and independent of oxygen control, which is supported by the absence of a fumarate and nitrate reductase regulator box within the V. stercoraria vgb promoter region. Thus, the regulation mechanisms of the Hb-encoding gene appear to be quite different in the two closely related species of Vitreoscilla. The relatively slower autooxidation rate of V. stercoraria Hb, lack of oxygen sensitivity, and constitutive production of Hb suggest that it may have some other function(s) in the cellular physiology of V. stercoraria DW, together with facilitated oxygen transport, predicted for earlier reported Vitreoscilla Hb.

Joshi, Meenal; Mande, Shekhar; Dikshit, Kanak L.

1998-01-01

274

Control of bacterial biofilm growth on surfaces by nanostructural mechanics and geometry  

NASA Astrophysics Data System (ADS)

Surface-associated communities of bacteria, called biofilms, pervade natural and anthropogenic environments. Mature biofilms are resistant to a wide range of antimicrobial treatments and therefore pose persistent pathogenic threats. The use of surface chemistry to inhibit biofilm growth has been found to only transiently affect initial attachment. In this work, we investigate the tunable effects of physical surface properties, including high-aspect-ratio (HAR) surface nanostructure arrays recently reported to induce long-range spontaneous spatial patterning of bacteria on the surface. The functional parameters and length scale regimes that control such artificial patterning for the rod-shaped pathogenic species Pseudomonas aeruginosa are elucidated through a combinatorial approach. We further report a crossover regime of biofilm growth on a HAR nanostructured surface versus the nanostructure effective stiffness. When the 'softness' of the hair-like nanoarray is increased beyond a threshold value, biofilm growth is inhibited as compared to a flat control surface. This result is consistent with the mechanoselective adhesion of bacteria to surfaces. Therefore by combining nanoarray-induced bacterial patterning and modulating the effective stiffness of the nanoarray—thus mimicking an extremely compliant flat surface—bacterial mechanoselective adhesion can be exploited to control and inhibit biofilm growth.

Epstein, A. K.; Hochbaum, A. I.; Kim, Philseok; Aizenberg, J.

2011-12-01

275

Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes  

PubMed Central

Background Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Methodology/Principal Findings Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. Conclusions This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

2013-01-01

276

Low-shear modeled microgravity: a global environmental regulatory signal affecting bacterial gene expression, physiology, and pathogenesis  

NASA Technical Reports Server (NTRS)

Bacteria inhabit an impressive variety of ecological niches and must adapt constantly to changing environmental conditions. While numerous environmental signals have been examined for their effect on bacteria, the effects of mechanical forces such as shear stress and gravity have only been investigated to a limited extent. However, several important studies have demonstrated a key role for the environmental signals of low shear and/or microgravity in the regulation of bacterial gene expression, physiology, and pathogenesis [Chem. Rec. 1 (2001) 333; Appl. Microbiol. Biotechnol. 54 (2000) 33; Appl. Environ. Microbiol. 63 (1997) 4090; J. Ind. Microbiol. 18 (1997) 22; Curr. Microbiol. 34(4) (1997) 199; Appl. Microbiol. Biotechnol. 56(3-4) (2001) 384; Infect Immun. 68(6) (2000) 3147; Cell 109(7) (2002) 913; Appl. Environ. Microbiol. 68(11) (2002) 5408; Proc. Natl. Acad. Sci. U. S. A. 99(21) (2002) 13807]. The response of bacteria to these environmental signals, which are similar to those encountered during prokaryotic life cycles, may provide insight into bacterial adaptations to physiologically relevant conditions. This review focuses on the current and potential future research trends aimed at understanding the effect of the mechanical forces of low shear and microgravity analogues on different bacterial parameters. In addition, this review also discusses the use of microgravity technology to generate physiologically relevant human tissue models for research in bacterial pathogenesis.

Nickerson, Cheryl A.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; LeBlanc, Carly L.; Honer zu Bentrup, Kerstin; Hammond, Timothy; Pierson, Duane L.

2003-01-01

277

Nature of bacterial colonization influences transcription of mucin genes in mice during the first week of life  

PubMed Central

Background Postnatal regulation of the small intestinal mucus layer is potentially important in the development of adult gut functionality. We hypothesized that the nature of bacterial colonization affects mucus gene regulation in early life. We thus analyzed the influence of the presence of a conventional microbiota as well as two selected monocolonizing bacterial strains on the transcription of murine genes involved in mucus layer development during the first week of life. Mouse pups (N?=?8/group) from differently colonized dams: Germ-free (GF), conventional specific pathogen free (SPF), monocolonized with either Lactobacillus acidophilus NCFM (Lb) or Escherichia coli Nissle (Ec) were analyzed by qPCR on isolated ileal tissue sections from postnatal days 1 and 6 (PND1, PND6) after birth with respect to: (i) transcription of specific genes involved in mucus production (Muc1-4, Tff3) and (ii) amounts of 16S rRNA of Lactobacillus and E. coli. Quantification of 16S rRNA genes was performed to obtain a measure for amounts of colonized bacteria. Results We found a microbiota-independent transcriptional increase of all five mucus genes from PND1 to PND6. Furthermore, the relative level of transcription of certain mucus genes on PND1 was increased by the presence of bacteria. This was observed for Tff3 in the SPF, Ec, and Lb groups; for Muc2 in SPF; and for Muc3 and Muc4 in Ec and Lb, respectively. Detection of bacterial 16S rRNA genes levels above the qPCR detection level occurred only on PND6 and only for some of the colonized animals. On PND6, we found significantly lower levels of Muc1, Muc2 and Muc4 gene transcription for Lb animals with detectable Lactobacillus levels as compared to animals with Lactobacillus levels below the detection limit. Conclusions In summary, our data show that development of the expression of genes encoding secreted (Muc2/Tff3) and membrane-bound (Muc1/Muc3/Muc4) mucus regulatory proteins, respectively, is distinct and that the onset of this development may be accelerated by specific groups of bacteria present or absent at the mucosal site.

2012-01-01

278

Comprehensive Analysis of Bacterial Flora in Postoperative Maxillary Cyst Fluid by 16S rRNA Gene and Culture Methods  

PubMed Central

Intracystic fluid was aseptically collected from 11 patients with postoperative maxillary cyst (POMC), and DNA was extracted from the POMC fluid. Bacterial species were identified by sequencing after cloning of approximately 580?bp of the 16S rRNA gene. Identification of pathogenic bacteria was also performed by culture methods. The phylogenetic identity was determined by sequencing 517–596?bp in each of the 1139 16S rRNA gene clones. A total of 1114 clones were classified while the remaining 25 clones were unclassified. A total of 103 bacterial species belonging to 42 genera were identified in POMC fluid samples by 16S rRNA gene analysis. Species of Prevotella (91%), Neisseria (73%), Fusobacterium (73%), Porphyromonas (73%), and Propionibacterium (73%) were found to be highly prevalent in all patients. Streptococcus mitis (64%), Fusobacterium nucleatum (55%), Propionibacterium acnes (55%), Staphylococcus capitis (55%), and Streptococcus salivarius (55%) were detected in more than 6 of the 11 patients. The results obtained by the culture method were different from those obtained by 16S rRNA gene analysis, but both approaches may be necessary for the identification of pathogens, especially of bacteria that are difficult to detect by culture methods, and the development of rational treatments for patients with POMC.

Sano, Naoto; Yamashita, Yoshio; Fukuda, Kazumasa; Taniguchi, Hatsumi; Goto, Masaaki; Miyamoto, Hiroshi

2012-01-01

279

Bacterial colonization factors control specificity and stability of the gut microbiota.  

PubMed

Mammals harbour a complex gut microbiome, comprising bacteria that confer immunological, metabolic and neurological benefits. Despite advances in sequence-based microbial profiling and myriad studies defining microbiome composition during health and disease, little is known about the molecular processes used by symbiotic bacteria to stably colonize the gastrointestinal tract. We sought to define how mammals assemble and maintain the Bacteroides, one of the most numerically prominent genera of the human microbiome. Here we find that, whereas the gut normally contains hundreds of bacterial species, germ-free mice mono-associated with a single Bacteroides species are resistant to colonization by the same, but not different, species. To identify bacterial mechanisms for species-specific saturable colonization, we devised an in vivo genetic screen and discovered a unique class of polysaccharide utilization loci that is conserved among intestinal Bacteroides. We named this genetic locus the commensal colonization factors (ccf). Deletion of the ccf genes in the model symbiont, Bacteroides fragilis, results in colonization defects in mice and reduced horizontal transmission. The ccf genes of B. fragilis are upregulated during gut colonization, preferentially at the colonic surface. When we visualize microbial biogeography within the colon, B. fragilis penetrates the colonic mucus and resides deep within crypt channels, whereas ccf mutants are defective in crypt association. Notably, the CCF system is required for B. fragilis colonization following microbiome disruption with Citrobacter rodentium infection or antibiotic treatment, suggesting that the niche within colonic crypts represents a reservoir for bacteria to maintain long-term colonization. These findings reveal that intestinal Bacteroides have evolved species-specific physical interactions with the host that mediate stable and resilient gut colonization, and the CCF system represents a novel molecular mechanism for symbiosis. PMID:23955152

Lee, S Melanie; Donaldson, Gregory P; Mikulski, Zbigniew; Boyajian, Silva; Ley, Klaus; Mazmanian, Sarkis K

2013-09-19

280

Control of expression of silk protein genes  

Microsoft Academic Search

At least three silk genes are specifically expressed in the posterior, and five other genes in middle, silk glands. The products of genes active in PSG include fibroin, L-chain fibroin and P25 protein. PSG genes as well as the Ser-1 gene, differing in structure, exhibit a striking degree of homology of their 5? flanking sequences. This suggests the presence of

Krystyna Grzelak

1995-01-01

281

Spatial and Temporal Variations in Chitinolytic Gene Expression and Bacterial Biomass Production during Chitin Degradation  

Microsoft Academic Search

Growth of the chitin-degrading marine bacterium S91 on solid surfaces under oligotrophic conditions was accompanied by the displacement of a large fraction of the surface-derived bacterial production into the flow- ing bulk aqueous phase, irrespective of the value of the surface as a nutrient source. Over a 200-h period of surface colonization, 97 and 75% of the bacterial biomass generated

ACE M. BATY; CALLIE C. EASTBURN; SOMKIET TECHKARNJANARUK; AMANDA E. GOODMAN; GILL G. GEESEY

2000-01-01

282

Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice  

PubMed Central

Background The next big challenge in human genetics is understanding the 98% of the genome that comprises non-coding DNA. Hidden in this DNA are sequences critical for gene regulation, and new experimental strategies are needed to understand the functional role of gene-regulation sequences in health and disease. In this study, we build upon our HuGX ('high-throughput human genes on the X chromosome’) strategy to expand our understanding of human gene regulation in vivo. Results In all, ten human genes known to express in therapeutically important brain regions were chosen for study. For eight of these genes, human bacterial artificial chromosome clones were identified, retrofitted with a reporter, knocked single-copy into the Hprt locus in mouse embryonic stem cells, and mouse strains derived. Five of these human genes expressed in mouse, and all expressed in the adult brain region for which they were chosen. This defined the boundaries of the genomic DNA sufficient for brain expression, and refined our knowledge regarding the complexity of gene regulation. We also characterized for the first time the expression of human MAOA and NR2F2, two genes for which the mouse homologs have been extensively studied in the central nervous system (CNS), and AMOTL1 and NOV, for which roles in CNS have been unclear. Conclusions We have demonstrated the use of the HuGX strategy to functionally delineate non-coding-regulatory regions of therapeutically important human brain genes. Our results also show that a careful investigation, using publicly available resources and bioinformatics, can lead to accurate predictions of gene expression.

2013-01-01

283

Expression of nitric oxide synthase (NOS) genes in channel catfish is highly regulated and time dependent after bacterial challenges.  

PubMed

Nitric oxide is well known for its roles in immune responses. As such, its synthesizing enzymes have been extensively studied from various species including some teleost fish species. However, the NOS genes have not been characterized in channel catfish (Ictalurus punctatus). In this study, we identified and characterized three NOS genes including one NOS1 and two NOS2 genes in channel catfish. Comparing with the NOS genes from other fish species, the catfish NOS genes are highly conserved in their structural features. Phylogenetic and syntenic analyses allowed determination of NOS1 and NOS2 genes of channel catfish and their orthology relationships. Syntenic analysis, as well as the phylogenetic analysis, indicated that the two NOS2 genes of catfish were lineage-specific duplication. The NOS genes were broadly expressed in most tested tissues, with NOS1 being expressed at the highest levels in the brain, NOS2b1 highly expressed in the skin and gill, and NOS2b2 lowly expressed in most of the tested tissues. The most striking findings of this study was that the expression of the NOS genes are highly regulated after bacterial infection, with time-dependent expression patterns that parallel the migration of macrophages. After Edwardsiella ictaluri challenge, dramatically different responses among the three NOS genes were observed. NOS1 was only significantly in the skin early after infection, while NOS2b1 was rapidly upregulated in gill, but more up-regulated in trunk kidney with the progression of the disease, suggesting such differences in gene expression may be reflective of the migration of macrophages among various tissues of the infected fish. In contrast to NOS1 and NOS2b1, NOS2b2 was normally expressed at very low levels, but it is induced in the brain and liver while significantly down-regulated in most other tissues. PMID:24560653

Yao, Jun; Li, Chao; Zhang, Jiaren; Liu, Shikai; Feng, Jianbin; Wang, Ruijia; Li, Yun; Jiang, Chen; Song, Lin; Chen, Ailu; Liu, Zhanjiang

2014-07-01

284

Bacillus thuringiensis Suppresses Bacterial wilt Disease Caused by Ralstonia solanacearum with Systemic Induction of Defense-Related Gene Expression in Tomato  

PubMed Central

Bacillus thuringiensis is a naturally abundant Gram-positive bacterium and a well-known, effective bio-insecticide. Recently, B. thuringiensis has attracted considerable attention as a potential biological control agent for the suppression of plant diseases. In this study, the bacterial wilt disease-suppressing activity of B. thuringiensis was examined in tomato plants. Treatment of tomato roots with B. thuringiensis culture followed by challenge inoculation with Ralstonia solanacearum suppressed the development of wilt symptoms to less than one third of the control. This disease suppression in tomato plants was reproduced by pretreating their roots with a cell-free filtrate (CF) that had been fractionated from B. thuringiensis culture by centrifugation and filtration. In tomato plants challenge-inoculated with R. solanacearum after pretreatment with CF, the growth of R. solanacearum in stem tissues clearly decreased, and expression of defense-related genes such as PR-1, acidic chitinase, and ?-1,3-glucanase was induced in stem and leaf tissues. Furthermore, the stem tissues of tomato plants with their roots were pretreated with CF exhibited resistance against direct inoculation with R. solanacearum. Taken together, these results suggest that treatment of tomato roots with the CF of B. thuringiensis systemically suppresses bacterial wilt through systemic activation of the plant defense system.

Hyakumachi, Mitsuro; Nishimura, Mitsuyoshi; Arakawa, Tatsuyuki; Asano, Shinichiro; Yoshida, Shigenobu; Tsushima, Seiya; Takahashi, Hideki

2013-01-01

285

Development of a bacterial artificial chromosome (BAC) recombineering procedure using galK-untranslated region (UTR) for the mutation of diploid genes.  

PubMed

Bacterial artificial chromosome (BAC) recombineering using galK selection allows DNA cloned in Escherichia coli to be modified without introducing an unwanted selectable marker at the modification site. Genomes of some herpesviruses have a pair of inverted repeat sequences that makes it very difficult to introduce mutations into diploid (duplicate) genes using the galK selection method. To mutate diploid genes, we developed a galK-UTR BAC recombineering procedure that blocks one copy of the target diploid gene by insertion of a galK untranslated region (UTR), which enables the simple mutation of the other copy. The blocked copy can then be replaced with an UTR-specific primer pair. The IR2 gene of equine herpesvirus 1 (EHV-1) maps within both the internal (IR) and terminal repeat (TR) of the genomic short region and is expressed at low levels because its promoter is TATA-less. Both IR2 promoters in EHV-1 BAC were replaced with a mutant IR2 promoter containing three Sp1-binding motifs and a consensus TATA box by galK-UTR BAC recombineering. The expression level of the IR2 protein controlled by the modified promoter increased approximately 4-fold as compared to that of wild-type EHV-1. The galK-UTR method will provide a useful tool in studies of herpesviruses. PMID:22407056

Dai, Gan; Kim, Seongman; O'Callaghan, Dennis J; Kim, Seong K

2012-06-01

286

Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin  

PubMed Central

Through their metabolic activities, microbial populations mediate the impact of high gradient regions on ecological function and productivity of the highly dynamic Columbia River coastal margin (CRCM). A 2226-probe oligonucleotide DNA microarray was developed to investigate expression patterns for microbial genes involved in nitrogen and carbon metabolism in the CRCM. Initial experiments with the environmental microarrays were directed toward validation of the platform and yielded high reproducibility in multiple tests. Bioinformatic and experimental validation also indicated that >85% of the microarray probes were specific for their corresponding target genes and for a few homologs within the same microbial family. The validated probe set was used to query gene expression responses by microbial assemblages to environmental variability. Sixty-four samples from the river, estuary, plume, and adjacent ocean were collected in different seasons and analyzed to correlate the measured variability in chemical, physical and biological water parameters to differences in global gene expression profiles. The method produced robust seasonal profiles corresponding to pre-freshet spring (April) and late summer (August). Overall relative gene expression was high in both seasons and was consistent with high microbial abundance measured by total RNA, heterotrophic bacterial production, and chlorophyll a. Both seasonal patterns involved large numbers of genes that were highly expressed relative to background, yet each produced very different gene expression profiles. April patterns revealed high differential gene expression in the coastal margin samples (estuary, plume and adjacent ocean) relative to freshwater, while little differential gene expression was observed along the river-to-ocean transition in August. Microbial gene expression profiles appeared to relate, in part, to seasonal differences in nutrient availability and potential resource competition. Furthermore, our results suggest that highly-active particle-attached microbiota in the Columbia River water column may perform dissimilatory nitrate reduction (both dentrification and DNRA) within anoxic particle microniches.

Smith, Maria W.; Herfort, Lydie; Tyrol, Kaitlin; Suciu, Dominic; Campbell, Victoria; Crump, Byron C.; Peterson, Tawnya D.; Zuber, Peter; Baptista, Antonio M.; Simon, Holly M.

2010-01-01

287

Proteomics as a Quality Control Tool of Pharmaceutical Probiotic Bacterial Lysate Products  

PubMed Central

Probiotic bacteria have a wide range of applications in veterinary and human therapeutics. Inactivated probiotics are complex samples and quality control (QC) should measure as many molecular features as possible. Capillary electrophoresis coupled to mass spectrometry (CE/MS) has been used as a multidimensional and high throughput method for the identification and validation of biomarkers of disease in complex biological samples such as biofluids. In this study we evaluate the suitability of CE/MS to measure the consistency of different lots of the probiotic formulation Pro-Symbioflor which is a bacterial lysate of heat-inactivated Escherichia coli and Enterococcus faecalis. Over 5000 peptides were detected by CE/MS in 5 different lots of the bacterial lysate and in a sample of culture medium. 71 to 75% of the total peptide content was identical in all lots. This percentage increased to 87–89% when allowing the absence of a peptide in one of the 5 samples. These results, based on over 2000 peptides, suggest high similarity of the 5 different lots. Sequence analysis identified peptides of both E. coli and E. faecalis and peptides originating from the culture medium, thus confirming the presence of the strains in the formulation. Ontology analysis suggested that the majority of the peptides identified for E. coli originated from the cell membrane or the fimbrium, while peptides identified for E. faecalis were enriched for peptides originating from the cytoplasm. The bacterial lysate peptides as a whole are recognised as highly conserved molecular patterns by the innate immune system as microbe associated molecular pattern (MAMP). Sequence analysis also identified the presence of soybean, yeast and casein protein fragments that are part of the formulation of the culture medium. In conclusion CE/MS seems an appropriate QC tool to analyze complex biological products such as inactivated probiotic formulations and allows determining the similarity between lots.

Klein, Gunter; Schanstra, Joost P.; Hoffmann, Janosch; Mischak, Harald; Siwy, Justyna; Zimmermann, Kurt

2013-01-01

288

Expression of a Synthesized Gene Encoding Cationic Peptide Cecropin B in Transgenic Tomato Plants Protects against Bacterial Diseases?  

PubMed Central

The cationic lytic peptide cecropin B (CB), isolated from the giant silk moth (Hyalophora cecropia), has been shown to effectively eliminate Gram-negative and some Gram-positive bacteria. In this study, the effects of chemically synthesized CB on plant pathogens were investigated. The S50s (the peptide concentrations causing 50% survival of a pathogenic bacterium) of CB against two major pathogens of the tomato, Ralstonia solanacearum and Xanthomonas campestris pv. vesicatoria, were 529.6 ?g/ml and 0.29 ?g/ml, respectively. The CB gene was then fused to the secretory signal peptide (sp) sequence from the barley ?-amylase gene, and the new construct, pBI121-spCB, was used for the transformation of tomato plants. Integration of the CB gene into the tomato genome was confirmed by PCR, and its expression was confirmed by Western blot analyses. In vivo studies of the transgenic tomato plant demonstrated significant resistance to bacterial wilt and bacterial spot. The levels of CB expressed in transgenic tomato plants (?0.05 ?g in 50 mg of leaves) were far lower than the S50 determined in vitro. CB transgenic tomatoes could therefore be a new mode of bioprotection against these two plant diseases with significant agricultural applications.

Jan, Pey-Shynan; Huang, Hsu-Yuang; Chen, Hueih-Min

2010-01-01

289

Heterologous expression of genes in bacterial, fungal, animal and plant cells  

Microsoft Academic Search

Analysis of gene function is of central importance for the understanding of physiological processes. Expression of genes in heterologous organisms has allowed the isolation of many important genes (e.g. for nutrient uptake and transport) and has contributed a lot to the functional analysis of the gene products. For animal research, expression in Xenopus oocytes and cell cultures are predominant techniques,

W. B. Frommer; O. Ninnemann

1995-01-01

290

Gene Expression Analysis of TREM1 and GRK2 in Polymorphonuclear Leukocytes as the Surrogate Biomarkers of Acute Bacterial Infections  

PubMed Central

Objective: In the acute stage of infectious diseases such as pneumonia and sepsis, sequelae hypercytokinemia and cytokine storm are often observed simultaneously. During bacterial infections, activated polymorphonuclear leukocytes (PMNs) cause inflammation and organ dysfunction in severely ill patients. Gene expression of the triggering receptor on myeloid cells (TREM)-1 and G-coupled-protein receptor kinase (GRK)-2 in PMNs isolated from patients was analysed to identify genes correlated with the severity of pathophysiological conditions. Methods: mRNA levels of TREM1 and GRK2 in the PMNs from 26 patients (13 with pneumonia, 5 with severe sepsis, and 8 with septic shock) were analysed by using quantitative real-time PCR. The synthesised soluble form (s)TREM-1 was incubated with normal PMNs to investigate its biological functions in vitro. Results: Copies of TREM1 transcript were 0.7- to 2.1-fold higher in patients with pneumonia compared to those of normal subjects; the average fold-change was 1.1-fold. The mRNA levels of patients suffering from severe sepsis and septic shock were 0.34- and 0.33-fold lower compared to those of healthy subjects, respectively. TREM1 mRNA levels in 5 of 26 patients in convalescent stages recovered to normal levels. The mRNA levels of GRK2 in the PMNs of patients were also downregulated. The synthesised sTREM-1 upregulated the mRNA levels of TREM1 in normal PMNs. Conclusions: TREM1 mRNA levels were inversely correlated with the severity of pathophysiological conditions in acute bacterial infections. The gene expression levels of TREM1 in PMNs isolated from patients with bacterial infections may be used as a surrogate biomarker for determining the severity.

Ubagai, Tsuneyuki; Nakano, Ryuichi; Kikuchi, Hirotoshi; Ono, Yasuo

2014-01-01

291

Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil.  

PubMed

Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study, we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF(103) of the isolate Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used. PMID:19922433

Hjort, Karin; Bergström, Maria; Adesina, Modupe F; Jansson, Janet K; Smalla, Kornelia; Sjöling, Sara

2010-02-01

292

Characterization of bacterial operons consisting of two tubulins and a kinesin-like gene by the novel Two-Step Gene Walking method.  

PubMed

Tubulins are still considered as typical proteins of Eukaryotes. However, more recently they have been found in the unusual bacteria Prosthecobacter (btubAB). In this study, the genomic organization of the btub-genes and their genomic environment were characterized by using the newly developed Two-Step Gene Walking method. In all investigated Prosthecobacters, btubAB are organized in a typical bacterial operon. Strikingly, all btub-operons comprise a third gene with similarities to kinesin light chain sequences. The genomic environments of the characterized btub-operons are always different. This supports the hypothesis that this group of genes represents an independent functional unit, which was acquired by Prosthecobacter via horizontal gene transfer. The newly developed Two-Step Gene Walking method is based on randomly primed polymerase chain reaction (PCR). It presents a simple workflow, which comprises only two major steps--a Walking-PCR with a single specific outward pointing primer (step 1) and the direct sequencing of its product using a nested specific primer (step 2). Two-Step Gene Walking proved to be highly efficient and was successfully used to characterize over 20 kb of sequence not only in pure culture but even in complex non-pure culture samples. PMID:17942428

Pilhofer, Martin; Bauer, Andreas Peter; Schrallhammer, Martina; Richter, Lothar; Ludwig, Wolfgang; Schleifer, Karl-Heinz; Petroni, Giulio

2007-01-01

293

Designer gene networks: Towards fundamental cellular control  

NASA Astrophysics Data System (ADS)

The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model formulation leads to computational and analytical approaches relevant to nonlinear dynamics and statistical physics. We first review the relevant work on synthetic gene networks, highlighting the important experimental findings with regard to genetic switches and oscillators. We then present the derivation of a deterministic model describing the temporal evolution of the concentration of protein in a single-gene network. Bistability in the steady-state protein concentration arises naturally as a consequence of autoregulatory feedback, and we focus on the hysteretic properties of the protein concentration as a function of the degradation rate. We then formulate the effect of an external noise source which interacts with the protein degradation rate. We demonstrate the utility of such a formulation by constructing a protein switch, whereby external noise pulses are used to switch the protein concentration between two values. Following the lead of earlier work, we show how the addition of a second network component can be used to construct a relaxation oscillator, whereby the system is driven around the hysteresis loop. We highlight the frequency dependence on the tunable parameter values, and discuss design plausibility. We emphasize how the model equations can be used to develop design criteria for robust oscillations, and illustrate this point with parameter plots illuminating the oscillatory regions for given parameter values. We then turn to the utilization of an intrinsic cellular process as a means of controlling the oscillations. We consider a network design which exhibits self-sustained oscillations, and discuss the driving of the oscillator in the context of synchronization. Then, as a second design, we consider a synthetic network with parameter values near, but outside, the oscillatory boundary. In this case, we show how resonance can lead to the induction of oscillations and amplification of a cellular signal. Finally, we construct a toggle switch from positive regulatory elements, and compare the switching properties for this network with those of a network constructed using negative regulation. Our results demonstrate the utility of model analysis in the construction of synthetic gene regulatory networks.

Hasty, Jeff; Isaacs, Farren; Dolnik, Milos; McMillen, David; Collins, J. J.

2001-03-01

294

Environmental controlling mechanisms on bacterial abundance in the South China Sea inferred from generalized additive models (GAMs)  

NASA Astrophysics Data System (ADS)

We modeled the abundance distribution of heterotrophic bacteria collected from 4 cruises in the northern South China Sea using generalized additive models to infer the underlying mechanisms controlling bacterial abundance and to predict bacterial abundance using environmental parameters that can be easily obtained. We incorporated spatial coordinates, depth, month, chlorophyll (Chl) a concentration, temperature, salinity, nutricline and mixed layer depth in the model, which captures the main features of the observations and explains 88% of the total variation of bacterial abundance. The most important factor affecting bacterial abundance is chlorophyll, followed by salinity and nutricline depth, reflecting the importance of carbon and nutrient sources to bacteria. Bacterial abundance shows a unimodal relationship with temperature and decreases with depth. All the functions are nonlinear. After controlling environmental parameters, bacterial abundances are higher in fall and winter than in spring and summer and usually show an onshore-offshore decreasing gradient, which probably signify transportation pathways of terrestrial organic matter to the sea via atmospheric deposition. Comparisons of variograms between raw data and residuals of the model show that positive autocorrelation at small scales is induced by both environmental similarity and geographic proximity, while the negative autocorrelation at large scales is mostly contributed by environmental similarity in remote water masses.

Chen, Bingzhang; Liu, Hongbin; Huang, Bangqin

2012-08-01

295

Gradient-based optimization of kernel-target alignment for sequence kernels applied to bacterial gene start detection.  

PubMed

Biological data mining using kernel methods can be improved by a task-specific choice of the kernel function. Oligo kernels for genomic sequence analysis have proven to have a high discriminative power and to provide interpretable results. Oligo kernels that consider subsequences of different lengths can be combined and parameterized to increase their flexibility. For adapting these parameters efficiently, gradient-based optimization of the kernel-target alignment is proposed. The power of this new, general model selection procedure and the benefits of fitting kernels to problem classes are demonstrated by adapting oligo kernels for bacterial gene start detection. PMID:17473315

Igel, Christian; Glasmachers, Tobias; Mersch, Britta; Pfeifer, Nico; Meinicke, Peter

2007-01-01

296

Refined identification of Vibrio bacterial flora from Acanthasther planci based on biochemical profiling and analysis of housekeeping genes.  

PubMed

We used a polyphasic approach for precise identification of bacterial flora (Vibrionaceae) isolated from crown-of-thorns starfish (COTS) from Lizard Island (Great Barrier Reef, Australia) and Guam (U.S.A., Western Pacific Ocean). Previous 16S rRNA gene phylogenetic analysis was useful to allocate and identify isolates within the Photobacterium, Splendidus and Harveyi clades but failed in the identification of Vibrio harveyi-like isolates. Species of the V harveyi group have almost indistinguishable phenotypes and genotypes, and thus, identification by standard biochemical tests and 16S rRNA gene analysis is commonly inaccurate. Biochemical profiling and sequence analysis of additional topA and mreB housekeeping genes were carried out for definitive identification of 19 bacterial isolates recovered from sick and wild COTS. For 8 isolates, biochemical profiles and topA and mreB gene sequence alignments with the closest relatives (GenBank) confirmed previous 16S rRNA-based identification: V. fortis and Photobacterium eurosenbergii species (from wild COTS), and V natriegens (from diseased COTS). Further phylogenetic analysis based on topA and mreB concatenated sequences served to identify the remaining 11 V harveyi-like isolates: V. owensii and V. rotiferianus (from wild COTS), and V. owensii, V. rotiferianus, and V. harveyi (from diseased COTS). This study further confirms the reliability of topA-mreB gene sequence analysis for identification of these close species, and it reveals a wider distribution range of the potentially pathogenic V. harveyi group. PMID:22013751

Rivera-Posada, J A; Pratchett, M; Cano-Gomez, A; Arango-Gomez, J D; Owens, L

2011-09-01

297

Bacterial genome instability.  

PubMed

Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease. PMID:24600039

Darmon, Elise; Leach, David R F

2014-03-01

298

Cloning and characterization of the biosynthetic gene cluster of the bacterial RNA polymerase inhibitor tirandamycin from marine-derived Streptomyces sp. SCSIO1666  

Microsoft Academic Search

Tirandamycins are bacterial RNA polymerase inhibitors holding great potential for antibacterial agent design. To elucidate the biosynthetic machinery and generate new derivatives, the tirandamycin biosynthetic gene cluster was cloned and sequenced from marine-derived Streptomyces sp. SCSIO1666. The biosynthetic gene cluster of tirandamycin spans a DNA region of ?56kb and consists of 15 open reading frames (ORFs) which encode three type

Xuhua Mo; Zhongwen Wang; Bo Wang; Junying Ma; Hongbo Huang; Xinpeng Tian; Si Zhang; Changsheng Zhang; Jianhua Ju

2011-01-01

299

Posttranscriptional control of gene expression: a genome-wide perspective  

Microsoft Academic Search

Gene expression is regulated at multiple levels, and cells need to integrate and coordinate different layers of control to implement the information in the genome. Post-transcriptional levels of regulation such as tran- script turnover and translational control are an integral part of gene expression and might rival the sophisti- cation and importance of transcriptional control. Micro- array-based methods are increasingly

Juan Mata; Samuel Marguerat; Jürg Bähler

2005-01-01

300

Organ specificity in the circadian control of plant gene expression.  

PubMed

Of the many plant genes whose expressions are controlled by the circadian clock, one of the phosphoenolpyruvate carboxylase kinase genes in soya bean (Glycine max) exhibits the unusual property that its control is organ-specific--it is under circadian control in leaves but not in roots. Preliminary experiments suggest that the same is true for at least one gene in Arabidopsis thaliana. It will be important to define the extent and function of this phenomenon and the underlying mechanism. PMID:16246016

Sullivan, S; Shenton, M; Nimmo, H G

2005-11-01

301

Regulated bioluminescence as a tool for bioremediation process monitoring and control of bacterial cultures  

SciTech Connect

An effective on-line monitoring technique for toxic waste bioremediation using bioluminescent microorganisms has demonstrated great potential for the description and optimization of biological processes. The lux genes of the bacterium Vibrio Fascheri are used by this species to produce visible light. The lux genes can be genetically fused to the control region of a catabolic gene, with the result that bioluminescence is produced whenever the catabolic gene is induced. Thus the detection of light from a sample (monoculture, consortium, or bioreactor) indicates that genetic expression from a specific gene is occurring. We have used this technique to monitor biodegradation of specific contaminants from waste sites. For these studies, fusions between the lux genes and the operons for naphthalene (nah) and toluene/xylene (xyl) degradation were constructed. Strains carrying one of these fusions respond sensitively and specifically to target substrates. Bioluminescence from these cultures can be rapidly measured in a non-destructive and non-invasive manner. The potential for this technique in this and other biological systems is discussed. 7 refs., 3 figs.

Burlage, R.S. [Oak Ridge National Lab., TN (United States); Heitzer, A.; DiGrazia, P.M. [Tennessee Univ., Knoxville, TN (United States). Center for Environmental Biotechnology

1991-12-01

302

Regulated bioluminescence as a tool for bioremediation process monitoring and control of bacterial cultures  

SciTech Connect

An effective on-line monitoring technique for toxic waste bioremediation using bioluminescent microorganisms has demonstrated great potential for the description and optimization of biological processes. The lux genes of the bacterium Vibrio Fascheri are used by this species to produce visible light. The lux genes can be genetically fused to the control region of a catabolic gene, with the result that bioluminescence is produced whenever the catabolic gene is induced. Thus the detection of light from a sample (monoculture, consortium, or bioreactor) indicates that genetic expression from a specific gene is occurring. We have used this technique to monitor biodegradation of specific contaminants from waste sites. For these studies, fusions between the lux genes and the operons for naphthalene (nah) and toluene/xylene (xyl) degradation were constructed. Strains carrying one of these fusions respond sensitively and specifically to target substrates. Bioluminescence from these cultures can be rapidly measured in a non-destructive and non-invasive manner. The potential for this technique in this and other biological systems is discussed. 7 refs., 3 figs.

Burlage, R.S. (Oak Ridge National Lab., TN (United States)); Heitzer, A.; DiGrazia, P.M. (Tennessee Univ., Knoxville, TN (United States). Center for Environmental Biotechnology)

1991-01-01

303

Bacterial genes induced within the nodule during the Rhizobium-legume symbiosis  

Microsoft Academic Search

Summary During the symbiosis between the bacterium Rhizo- bium meliloti and plants such as alfalfa, the bacteria elicit the formation of nodules on the roots of host plants. The bacteria infect the nodule, enter the cyto- plasm of plant cells and differentiate into a distinct cell type called a bacteroid, which is capable of fixing atmospheric nitrogen. To discover bacterial

Valerie Oke; Sharon R. Long

1999-01-01

304

A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles  

Microsoft Academic Search

Many drug candidates from marine and terrestrial invertebrates are suspected metabolites of uncultured bacterial symbionts. The antitumor polyketides of the pederin family, isolated from beetles and sponges, are an example. Drug development from such sources is commonly hampered by low yields and the difficulty of sustaining invertebrate cultures. To obtain insight into the true producer and find alternative supplies of

Jörn Piel

2002-01-01

305

Bacterial Diversity in Adirondack Mountain Lakes as Revealed by 16S rRNA Gene Sequences  

Microsoft Academic Search

Bacterial communities of seven lakes in the Adirondack Mountains of New York State were characterized by amplification and sequencing of 16S ribosomal DNA. Analysis of over 100 partial sequences revealed a diverse collection of lineages, largely of the class Proteobacteria (19% alpha subdivision, 31% beta subdivision, and 9% gamma subdivision), the phylum Cytophaga-Flavobacteria-Bacteroides (15%), and the order Actinomycetales (18%). Additionally,

WILLIAM D. HIORNS; BARBARA A. METHE; SANDRA A. NIERZWICKI-BAUER; JONATHAN P. ZEHR; Darrin Fresh

1997-01-01

306

A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors  

NASA Astrophysics Data System (ADS)

Bacterial chemoreceptors are widely used as a model system for elucidating the molecular mechanisms of transmembrane signalling and have provided a detailed understanding of how ligand binding by the receptor modulates the activity of its associated kinase CheA. However, the mechanisms by which conformational signals move between signalling elements within a receptor dimer and how they control kinase activity remain unknown. Here, using long molecular dynamics simulations, we show that the kinase-activating cytoplasmic tip of the chemoreceptor fluctuates between two stable conformations in a signal-dependent manner. A highly conserved residue, Phe396, appears to serve as the conformational switch, because flipping of the stacked aromatic rings of an interacting F396-F396? pair in the receptor homodimer takes place concomitantly with the signal-related conformational changes. We suggest that interacting aromatic residues, which are common stabilizers of protein tertiary structure, might serve as rotameric molecular switches in other biological processes as well.

Ortega, Davi R.; Yang, Chen; Ames, Peter; Baudry, Jerome; Parkinson, John S.; Zhulin, Igor B.

2013-12-01

307

Membrane Proteases in the Bacterial Protein Secretion and Quality Control Pathway  

PubMed Central

Summary: Proteolytic cleavage of proteins that are permanently or transiently associated with the cytoplasmic membrane is crucially important for a wide range of essential processes in bacteria. This applies in particular to the secretion of proteins and to membrane protein quality control. Major progress has been made in elucidating the structure-function relationships of many of the responsible membrane proteases, including signal peptidases, signal peptide hydrolases, FtsH, the rhomboid protease GlpG, and the site 1 protease DegS. These enzymes employ very different mechanisms to cleave substrates at the cytoplasmic and extracytoplasmic membrane surfaces or within the plane of the membrane. This review highlights the different ways that bacterial membrane proteases degrade their substrates, with special emphasis on catalytic mechanisms and substrate delivery to the respective active sites.

Wang, Peng; van Dijl, Jan Maarten

2012-01-01

308

Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection.  

PubMed

Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Shigella spp., Campylobacter jejuni, Salmonella enterica, and Aeromonas spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected Shigella spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens. PMID:23884998

Lindsay, Brianna; Pop, Mihai; Antonio, Martin; Walker, Alan W; Mai, Volker; Ahmed, Dilruba; Oundo, Joseph; Tamboura, Boubou; Panchalingam, Sandra; Levine, Myron M; Kotloff, Karen; Li, Shan; Magder, Laurence S; Paulson, Joseph N; Liu, Bo; Ikumapayi, Usman; Ebruke, Chinelo; Dione, Michel; Adeyemi, Mitchell; Rance, Richard; Stares, Mark D; Ukhanova, Maria; Barnes, Bret; Lewis, Ian; Ahmed, Firoz; Alam, Meer Taifur; Amin, Ruhul; Siddiqui, Sabbir; Ochieng, John B; Ouma, Emmanuel; Juma, Jane; Mailu, Eunice; Omore, Richard; O'Reilly, Ciara E; Hannis, James; Manalili, Sheri; Deleon, Jonna; Yasuda, Irene; Blyn, Lawrence; Ranken, Raymond; Li, Feng; Housley, Roberta; Ecker, David J; Hossain, M Anowar; Breiman, Robert F; Morris, J Glenn; McDaniel, Timothy K; Parkhill, Julian; Saha, Debasish; Sampath, Rangarajan; Stine, O Colin; Nataro, James P

2013-10-01

309

Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection  

PubMed Central

Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Shigella spp., Campylobacter jejuni, Salmonella enterica, and Aeromonas spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected Shigella spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens.

Pop, Mihai; Antonio, Martin; Walker, Alan W.; Mai, Volker; Ahmed, Dilruba; Oundo, Joseph; Tamboura, Boubou; Panchalingam, Sandra; Levine, Myron M.; Kotloff, Karen; Li, Shan; Magder, Laurence S.; Paulson, Joseph N.; Liu, Bo; Ikumapayi, Usman; Ebruke, Chinelo; Dione, Michel; Adeyemi, Mitchell; Rance, Richard; Stares, Mark D.; Ukhanova, Maria; Barnes, Bret; Lewis, Ian; Ahmed, Firoz; Alam, Meer Taifur; Amin, Ruhul; Siddiqui, Sabbir; Ochieng, John B.; Ouma, Emmanuel; Juma, Jane; Mailu, Eunice; Omore, Richard; O'Reilly, Ciara E.; Hannis, James; Manalili, Sheri; DeLeon, Jonna; Yasuda, Irene; Blyn, Lawrence; Ranken, Raymond; Li, Feng; Housley, Roberta; Ecker, David J.; Hossain, M. Anowar; Breiman, Robert F.; Morris, J. Glenn; McDaniel, Timothy K.; Parkhill, Julian; Saha, Debasish; Sampath, Rangarajan; Stine, O. Colin; Nataro, James P.

2013-01-01

310

Diversity of endophytic bacteria in Malaysian plants as revealed by 16S rRNA encoding gene sequence based method of bacterial identification.  

PubMed

Bacterial endophytes do have several potential applications in pharmacy, medicine and agricultural biotech industry. The main objective of this study was to understand types of bacterial endophytes associated with dicotyledonous (dicot) and monocotyledonous (monocot) plant species. Isolation of the endophytic bacteria was performed using surface-sterilized various tissue samples, and identification of the endophytic bacterial isolates (EBIs) was completed using 16S rRNA encoding gene sequence similarity based method. In total, 996 EBIs were isolated and identified from 1055 samples of 31 monocot and 65 dicot plant species from Peninsular Malaysia. The 996 EBIs represented 71 different types of bacterial species. Twelve (12) out of 71 species are reported as endophytes for the first time. We conclude that diverse types of bacterial endophytes are associated with dicot and monocot plants, and could be useful in pharmacy, medicine and agricultural biotechnology for various potential applications. PMID:24396249

Loh, Chye Ying; Tan, Yin Yin; Rohani, Rahim; Weber, Jean-Frédéric F; Bhore, Subhash Janardhan

2013-09-01

311

Bacterial cell wall synthesis gene uppP is required for Burkholderia colonization of the Stinkbug Gut.  

PubMed

To establish a host-bacterium symbiotic association, a number of factors involved in symbiosis must operate in a coordinated manner. In insects, bacterial factors for symbiosis have been poorly characterized at the molecular and biochemical levels, since many symbionts have not yet been cultured or are as yet genetically intractable. Recently, the symbiotic association between a stinkbug, Riptortus pedestris, and its beneficial gut bacterium, Burkholderia sp., has emerged as a promising experimental model system, providing opportunities to study insect symbiosis using genetically manipulated symbiotic bacteria. Here, in search of bacterial symbiotic factors, we targeted cell wall components of the Burkholderia symbiont by disruption of uppP gene, which encodes undecaprenyl pyrophosphate phosphatase involved in biosynthesis of various bacterial cell wall components. Under culture conditions, the ?uppP mutant showed higher susceptibility to lysozyme than the wild-type strain, indicating impaired integrity of peptidoglycan of the mutant. When administered to the host insect, the ?uppP mutant failed to establish normal symbiotic association: the bacterial cells reached to the symbiotic midgut but neither proliferated nor persisted there. Transformation of the ?uppP mutant with uppP-encoding plasmid complemented these phenotypic defects: lysozyme susceptibility in vitro was restored, and normal infection and proliferation in the midgut symbiotic organ were observed in vivo. The ?uppP mutant also exhibited susceptibility to hypotonic, hypertonic, and centrifugal stresses. These results suggest that peptidoglycan cell wall integrity is a stress resistance factor relevant to the successful colonization of the stinkbug midgut by Burkholderia symbiont. PMID:23747704

Kim, Jiyeun Kate; Lee, Ho Jin; Kikuchi, Yoshitomo; Kitagawa, Wataru; Nikoh, Naruo; Fukatsu, Takema; Lee, Bok Luel

2013-08-01

312

SearchDOGS Bacteria, Software That Provides Automated Identification of Potentially Missed Genes in Annotated Bacterial Genomes.  

PubMed

We report the development of SearchDOGS Bacteria, software to automatically detect missing genes in annotated bacterial genomes by combining BLAST searches with comparative genomics. Having successfully applied the approach to yeast genomes, we redeveloped SearchDOGS to function as a standalone, downloadable package, requiring only a set of GenBank annotation files as input. The software automatically generates a homology structure using reciprocal BLAST and a synteny-based method; this is followed by a scan of the entire genome of each species for unannotated genes. Results are provided in a HTML interface, providing coordinates, BLAST results, syntenic location, omega values (Ka/Ks, where Ks is the number of synonymous substitutions per synonymous site and Ka is the number of nonsynonymous substitutions per nonsynonymous site) for protein conservation estimates, and other information for each candidate gene. Using SearchDOGS Bacteria, we identified 155 gene candidates in the Shigella boydii sb227 genome, including 56 candidates of length < 60 codons. SearchDOGS Bacteria has two major advantages over currently available annotation software. First, it outperforms current methods in terms of sensitivity and is highly effective at identifying small or highly diverged genes. Second, as a freely downloadable package, it can be used with unpublished or confidential data. PMID:24659774

Ohéigeartaigh, Seán S; Armisén, David; Byrne, Kevin P; Wolfe, Kenneth H

2014-06-01

313

Discrete cyclic di-GMP-dependent control of bacterial predation versus axenic growth in Bdellovibrio bacteriovorus.  

PubMed

Bdellovibrio bacteriovorus is a Delta-proteobacterium that oscillates between free-living growth and predation on Gram-negative bacteria including important pathogens of man, animals and plants. After entering the prey periplasm, killing the prey and replicating inside the prey bdelloplast, several motile B. bacteriovorus progeny cells emerge. The B. bacteriovorus HD100 genome encodes numerous proteins predicted to be involved in signalling via the secondary messenger cyclic di-GMP (c-di-GMP), which is known to affect bacterial lifestyle choices. We investigated the role of c-di-GMP signalling in B. bacteriovorus, focussing on the five GGDEF domain proteins that are predicted to function as diguanylyl cyclases initiating c-di-GMP signalling cascades. Inactivation of individual GGDEF domain genes resulted in remarkably distinct phenotypes. Deletion of dgcB (Bd0742) resulted in a predation impaired, obligately axenic mutant, while deletion of dgcC (Bd1434) resulted in the opposite, obligately predatory mutant. Deletion of dgcA (Bd0367) abolished gliding motility, producing bacteria capable of predatory invasion but unable to leave the exhausted prey. Complementation was achieved with wild type dgc genes, but not with GGAAF versions. Deletion of cdgA (Bd3125) substantially slowed predation; this was restored by wild type complementation. Deletion of dgcD (Bd3766) had no observable phenotype. In vitro assays showed that DgcA, DgcB, and DgcC were diguanylyl cyclases. CdgA lacks enzymatic activity but functions as a c-di-GMP receptor apparently in the DgcB pathway. Activity of DgcD was not detected. Deletion of DgcA strongly decreased the extractable c-di-GMP content of axenic Bdellovibrio cells. We show that c-di-GMP signalling pathways are essential for both the free-living and predatory lifestyles of B. bacteriovorus and that obligately predatory dgcC- can be made lacking a propensity to survive without predation of bacterial pathogens and thus possibly useful in anti-pathogen applications. In contrast to many studies in other bacteria, Bdellovibrio shows specificity and lack of overlap in c-di-GMP signalling pathways. PMID:22319440

Hobley, Laura; Fung, Rowena K Y; Lambert, Carey; Harris, Maximilian A T S; Dabhi, Jayesh M; King, Simon S; Basford, Sarah M; Uchida, Kaoru; Till, Robert; Ahmad, Rashidah; Aizawa, Shin-Ichi; Gomelsky, Mark; Sockett, R Elizabeth

2012-02-01

314

Quantitative PCR Monitoring of Antibiotic Resistance Genes and Bacterial Pathogens in Three European Artificial Groundwater Recharge Systems? †  

PubMed Central

Aquifer recharge presents advantages for integrated water management in the anthropic cycle, namely, advanced treatment of reclaimed water and additional dilution of pollutants due to mixing with natural groundwater. Nevertheless, this practice represents a health and environmental hazard because of the presence of pathogenic microorganisms and chemical contaminants. To assess the quality of water extracted from recharged aquifers, the groundwater recharge systems in Torreele, Belgium, Sabadell, Spain, and Nardò, Italy, were investigated for fecal-contamination indicators, bacterial pathogens, and antibiotic resistance genes over the period of 1 year. Real-time quantitative PCR assays for Helicobacter pylori, Yersinia enterocolitica, and Mycobacterium avium subsp. paratuberculosis, human pathogens with long-time survival capacity in water, and for the resistance genes ermB, mecA, blaSHV-5, ampC, tetO, and vanA were adapted or developed for water samples differing in pollutant content. The resistance genes and pathogen concentrations were determined at five or six sampling points for each recharge system. In drinking and irrigation water, none of the pathogens were detected. tetO and ermB were found frequently in reclaimed water from Sabadell and Nardò. mecA was detected only once in reclaimed water from Sabadell. The three aquifer recharge systems demonstrated different capacities for removal of fecal contaminators and antibiotic resistance genes. Ultrafiltration and reverse osmosis in the Torreele plant proved to be very efficient barriers for the elimination of both contaminant types, whereas aquifer passage followed by UV treatment and chlorination at Sabadell and the fractured and permeable aquifer at Nardò posed only partial barriers for bacterial contaminants.

Bockelmann, Uta; Dorries, Hans-Henno; Ayuso-Gabella, M. Neus; Salgot de Marcay, Miquel; Tandoi, Valter; Levantesi, Caterina; Masciopinto, Costantino; Van Houtte, Emmanuel; Szewzyk, Ulrich; Wintgens, Thomas; Grohmann, Elisabeth

2009-01-01

315

Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes  

Microsoft Academic Search

Bacterial communities are important catalysts in the production of composts. Here, it was analysed whether the diversity of bacteria in finished composts is stable and specific for the production process. Single-strand conformation polymorphism (SSCP) based on polymerase chain reaction amplified partial 16S rRNA genes was used to profile and analyse bacterial communities found in total DNA extracted from finished composts.

Letizia Fracchia; Anja B. Dohrmann; Maria Giovanna Martinotti; Christoph C. Tebbe

2006-01-01

316

Analysis of RogB-controlled virulence mechanisms and gene repression in Streptococcus agalactiae.  

PubMed

Streptococcus agalactiae is the leading cause of bacterial sepsis and meningitis in neonates and also the causative agent of different serious infections in immunocompromised adults. The wide range of diseases that are caused by S. agalactiae suggests regulatory mechanisms that control the formation of specific virulence factors in these bacteria. The present study describes a gene from S. agalactiae, designated rogB, encoding a protein with significant similarity to members of the RofA-like protein (RALP) family of transcriptional regulators. Disruption of the rogB gene in the genome of S. agalactiae resulted in mutant strain RGB1, which was impaired in its ability to bind to fibrinogen and fibronectin. Mutant RGB1 also exhibited a reduced adherence to human epithelial cells but did not show an altered invasion of eukaryotic cells. By real-time PCR analysis, mutant RGB1 revealed an increased expression of the cpsA gene, encoding a regulator of capsule gene expression. However, strain RGB1 exhibited a reduced expression of the rogB gene and of two adjacent genes, encoding putative virulence factors in S. agalactiae. Furthermore, mutant RGB1 was impaired in the expression of the fbsA gene, coding for a fibrinogen receptor from S. agalactiae. The altered gene expression in mutant RGB1 could be restored by plasmid-mediated expression of rogB, confirming a RogB deficiency as the cause for the observed changes in virulence gene expression in S. agalactiae. Reporter gene studies with a promotorless luciferase gene fused to fbsA allowed a growth-dependent analysis of fbsA expression in S. agalactiae. These reporter gene studies also suggest that RogB exerts a positive effect on fbsA expression in S. agalactiae. PMID:12933848

Gutekunst, Heike; Eikmanns, Bernhard J; Reinscheid, Dieter J

2003-09-01

317

BB Seminar: Detecting gene-gene interactions in genome-wide case-control studies  

Cancer.gov

Gene-gene interactions have long been recognized to be fundamentally important to understand genetic causes of complex disease traits. At present, identifying gene-gene interactions from genome-wide case-control studies is computationally and methodologically challenging. In this talk, we introduce a new method, named Boolean Operation based Screening and Testing(BOOST). To discover unknown gene-gene interactions that underlie complex diseases, BOOST allows examining all pair-wise interactions in genome-wide case-control studies in a remarkably fast manner.

318

Flow calorimetry and dielectric spectroscopy to control the bacterial conversion of toxic substrates into polyhydroxyalcanoates.  

PubMed

The microbial conversion of toxic substrates into valuable products in continuous culture requires the equivalent of a tight rope walk between formation of the desired product and intoxication of the microbial catalyst. The condition of the latter is reflected immediately by changes in heat flow rate and beta-dispersion in an electrical RF field. Therefore, these were applied to the example of the continuous growth-associated synthesis of polyhydroxyalcanoates (PHA) from phenol by the bacterial strain Variovorax paradoxus DSM 4065. By controlling the supply of phenol to the chemostat, the rates of degradation, biomass formation, and synthesis of target product, respectively, were increasingly elevated until the onset of poisoning the organisms. The boundary between the maximum rates and the initiation of intoxication coincided with a sudden change in the heat flux. Using this occurrence, it was possible to develop a control strategy and test it successfully for a time period of 80 h. After 40 h the process stabilized at mean values, i.e., at rates of 92% phenol degradation, 100% biomass formation, and 70 - 75% of PHA formation compared with the situation shortly before poisoning the organisms. Using a moving-average technique to filter the raw dielectric spectroscope data, changes were followed in biomass concentration of approximately 100 mg/L. However, this technique was not sensitive or rapid enough to control the process. PMID:14760695

Maskow, Thomas; Olomolaiye, Dayo; Breuer, Uta; Kemp, Richard

2004-03-01

319

Controlled delivery of bioactive molecules into live cells using the bacterial mechanosensitive channel MscL  

PubMed Central

Bacterial mechanosensitive channels are some of the largest pores in nature. In particular, MscL, with a pore diameter > 25 Å, allows passage of large organic ions and small proteins. Functional MscL reconstitution into lipids has been proposed for applications in vesicular-based drug release. Here we show that these channels can be functionally expressed in mammalian cells to afford rapid controlled uptake of membrane impermeable molecules. We first demonstrate that MscL gating in response to increased membrane tension is preserved in mammalian cell membranes. Molecular delivery is controlled by adopting an established method of MscL charge-induced activation. We then determine pore size limitations using fluorescently labeled model cargoes. Finally, we activate MscL to introduce the cell-impermeable bi-cyclic peptide phalloidin, a specific marker for actin filaments, into cells. We propose that MscL will be a useful tool for gated and controlled delivery of bioactive molecules into cells.

Doerner, Julia F.; Febvay, Sebastien; Clapham, David E.

2013-01-01

320

Use of sulfite and hydrogen peroxide to control bacterial contamination in ethanol fermentation.  

PubMed Central

Lactic acid bacteria isolated from an industrial-scale ethanol fermentation process were used to evaluate sulfite as a bacterial-contamination control agent in a cell-recycled continuous ethanol fermentation process. The viabilities of bacteria were decreased by sulfite at concentrations of 100 to 400 mg liter-1, while sulfite at the same concentrations did not change the viability of the Saccharomyces cerevisiae strain used in this process. Sulfite was effective only in the presence of oxygen. Bacteria showed differences in their susceptibilities to sulfite. Facultatively heterofermentative Lactobacillus casei 4-3 was more susceptible than was obligatory heterofermentative Lactobacillus fermentum 7-1. The former showed higher enzyme activities involved in the production and consumption of hydrogen peroxide than did the latter. The viability of L. fermentum 7-1 could be selectively controlled by hydrogen peroxide at concentrations of 1 to 10 mM. Based on these findings, it is hypothesized that the sulfur trioxide radical anions formed by peroxidase in the presence of hydrogen peroxide are responsible for the control of contaminating bacteria. Sulfite did not kill the yeast strain, which has catalase to degrade hydrogen peroxide. A cell-recycled continuous ethanol fermentation process was run successfully with sulfite treatments.

Chang, I S; Kim, B H; Shin, P K

1997-01-01

321

Intrinsic and extrinsic approaches for detecting genes in a bacterial genome.  

PubMed Central

The unannotated regions of the Escherichia coli genome DNA sequence from the EcoSeq6 database, totaling 1,278 'intergenic' sequences of the combined length of 359,279 basepairs, were analyzed using computer-assisted methods with the aim of identifying putative unknown genes. The proposed strategy for finding new genes includes two key elements: i) prediction of expressed open reading frames (ORFs) using the GeneMark method based on Markov chain models for coding and non-coding regions of Escherichia coli DNA, and ii) search for protein sequence similarities using programs based on the BLAST algorithm and programs for motif identification. A total of 354 putative expressed ORFs were predicted by GeneMark. Using the BLASTX and TBLASTN programs, it was shown that 208 ORFs located in the unannotated regions of the E. coli chromosome are significantly similar to other protein sequences. Identification of 182 ORFs as probable genes was supported by GeneMark and BLAST, comprising 51.4% of the GeneMark 'hits' and 87.5% of the BLAST 'hits'. 73 putative new genes, comprising 20.6% of the GeneMark predictions, belong to ancient conserved protein families that include both eubacterial and eukaryotic members. This value is close to the overall proportion of highly conserved sequences among eubacterial proteins, indicating that the majority of the putative expressed ORFs that are predicted by GeneMark, but have no significant BLAST hits, nevertheless are likely to be real genes. The majority of the putative genes identified by BLAST search have been described since the release of the EcoSeq6 database, but about 70 genes have not been detected so far. Among these new identifications are genes encoding proteins with a variety of predicted functions including dehydrogenases, kinases, several other metabolic enzymes, ATPases, rRNA methyltransferases, membrane proteins, and different types of regulatory proteins. Images

Borodovsky, M; Rudd, K E; Koonin, E V

1994-01-01

322

Sequential expression of bacterial virulence and plant defense genes during infection of tomato with Clavibacter michiganensis subsp. michiganensis.  

PubMed

The molecular interactions between Clavibacter michiganensis subsp. michiganensis and tomato plant were studied by following the expression of bacterial virulence and host-defense genes during early stages of infection. The C. michiganensis subsp. michiganensis genes included the plasmid-borne cellulase (celA) and the serine protease (pat-1), and the serine proteases chpC and ppaA, residing on the chp/tomA pathogenicity island (PAI). Gene expression was measured following tomato inoculation with Cmm382 (wild type), Cmm100 (lacking the plasmids pCM1 and pCM2), and Cmm27 (lacking the PAI). Transcriptional analysis revealed that celA and pat-1 were significantly induced in Cmm382 at initial 12 to 72 h, whereas chpC and ppaA were highly expressed only 96 h after inoculation. Interdependence between the expression of chromosomal and of plasmid-located genes was revealed: expression of celA and pat-1 was substantially reduced in the absence of the chp/tomA PAI, whereas chpC and ppaA expressions were reduced in the absence of the virulence plasmids. Transcription of chromosomal genes involved in cell wall degradation (i.e., pelA1, celB, xysA, and xysB), was also induced at early stages of infection. Expression of the host-defense genes, chitinase class II and pathogenesis-related protein-5 isoform was induced in the absence of the PAI at early stages of infection, suggesting that PAI-located genes are involved in suppression of tomato basal defenses. PMID:20128699

Chalupowicz, L; Cohen-Kandli, M; Dror, O; Eichenlaub, R; Gartemann, K-H; Sessa, G; Barash, I; Manulis-Sasson, S

2010-03-01

323

Bacterial hrp and Avirulence Genes are Key Determinants in Plant-Pathogen Interactions  

Microsoft Academic Search

Among the 1600 different species known in the bacterial kingdom only a small number are plant pathogenic. In fact, most pathogens\\u000a can only infect a limited number of host plant species. On the other hand, many bacteria live in the plant’s phyllosphere\\u000a and rhizosphere without causing any harm. To be successful as a pathogen, i.e., live on the expense of

Ulla Bonas; Guido Van den Ackerveken

324

[Determination of 16S rRNA gene sequence for a new ANAMMOX bacterial species].  

PubMed

The anaerobic ammonium oxidation (ANAMMOX) activity of the sludge was about 9.84 x 10(-4) mg x (mg x h)(-1) by measuring the simultaneous consumption of ammonium and nitrite under anoxic conditions in the batch tests. The consumption of NO2(-) -N and NH4+ -N was 1.311 for ANAMMOX bacteria. The partial 16S rDNA sequence was obtained by using molecule biology methods. Crude DNA of the total bacteria in granular sludge from EGSB reactor was extracted and purified. Then, PCR amplification by using specific primer, clone and sequence determination was performed. ANAMMOX bacterial species(anaerobic ammonium-oxidizing Planctomycete cquenviron-1) which was enrichment cultivated from EGSB reactor were the same genera with Candidatus "Anammoxoglobus propionicus" and Candidatus "Jettenia asiatica" by analyzing phylogenetic tree. The maximum identities of anaerobic ammonium-oxidizing Planctomycete cquenviron-1 with other ANAMMOX bacterial species was about 93%. The results showed that a new ANAMMOX bacterial species which was enrichment cultivated from EGSB reactor was found and anaerobic ammonium-oxidizing Planctomycete cquenviron-1 was denominated. PMID:18613522

Zu, Bo; Zhang, Dai-jun; Yan, Qing

2008-02-01

325

Dynamics of Xanthomonas oryzae pv. oryzae Populations in Korea and Their Relationship to Known Bacterial Blight Resistance Genes.  

PubMed

ABSTRACT Developing resistant cultivars requires an understanding of the dynamics of the pathogen populations as well as the genetics of host resistance. Bacterial leaf blight (BB), caused by the vascular pathogen Xanthomonas oryzae pv. oryzae, has become one of the most devastating diseases of rice. We demonstrate here the quantitative analyses of responses of near-isogenic lines carrying various BB resistance (R) genes and R-gene combinations against 16 X. oryzae pv. oryzae isolates representing Korean BB pathotypes. The estimated main effects of each R gene against the 16 isolates identified prominent differences in BB pathotypes between Korea and other countries. Three major aspects of our quantitative observations and statistical analysis are (i) strong and broad resistance of xa5; (ii) independent and additive genetic actions of Xa4, xa5, and Xa21 under digenic or trigenic status; and (iii) a strong quantitative complementation effect contributed by the functional alleles of Xa4 and Xa21. We conclude that the pyramid line containing genes Xa4, xa5, and Xa21 would be the most promising and valuable genotype for improving Korean japonica cultivars for BB resistance. PMID:18943752

Jeung, J U; Heu, S G; Shin, M S; Vera Cruz, C M; Jena, K K

2006-08-01

326

Characterization of transgenic tobacco plants containing bacterial bphC gene and study of their phytoremediation ability.  

PubMed

Genetically modified plants can serve as an efficient tool for remediation of diverse dangerous pollutants of the environment such as pesticides, heavy metals, explosives and persistent organic compounds. Transgenic lines of Nicotiana tabacum containing bacterial bphC gene from the degradation pathway of polychlorinated biphenyls (PCBs) were tested. The product of the bphC gene - enzyme 2,3-dihydroxybiphenyl-1,2-dioxygenase is responsible for cleaving of the biphenyl ring. The presence of bphC gene in transgenic plants was detected on DNA, RNA and protein level. The expression of the bphC/His gene was verified afterpurification of the enzyme from plants by affinity chromatography followed by a Western blot and immunochemical assay. The enzyme activity of isolated protein was detected. Efficient transformation of 2,3-DHB by transgenic plants was achieved and the lines also exhibited high production of biomass. The transgenic plants were more tolerant to the commercial PCBs mixture Delor 103 than non-transgenic tobacco. And finally, the higher decrease of total PCB content and especially congener 28 in real contaminated soil from a dumpsite was determined after cultivation of transgenic plant in comparison with nontransgenic tobacco. The substrate specificity of transgenic plants was the same as substrate specificity of BphC enzyme. PMID:24933894

Viktorovtá, Jitka; Novakova, Martina; Trbolova, Ladislava; Vrchotova, Blanka; Lovecka, Petra; Mackova, Martina; Macek, Tomas

2014-01-01

327

Two genes with similarity to bacterial response regulators are rapidly and specifically induced by cytokinin in Arabidopsis  

NASA Technical Reports Server (NTRS)

Cytokinins are central regulators of plant growth and development, but little is known about their mode of action. By using differential display, we identified a gene, IBC6 (for induced by cytokinin), from etiolated Arabidopsis seedlings, that is induced rapidly by cytokinin. The steady state level of IBC6 mRNA was elevated within 10 min by the exogenous application of cytokinin, and this induction did not require de novo protein synthesis. IBC6 was not induced by other plant hormones or by light. A second Arabidopsis gene with a sequence highly similar to IBC6 was identified. This IBC7 gene also was induced by cytokinin, although with somewhat slower kinetics and to a lesser extent. The pattern of expression of the two genes was similar, with higher expression in leaves, rachises, and flowers and lower transcript levels in roots and siliques. Sequence analysis revealed that IBC6 and IBC7 are similar to the receiver domain of bacterial two-component response regulators. This homology, coupled with previously published work on the CKI1 histidine kinase homolog, suggests that these proteins may play a role in early cytokinin signaling.

Brandstatter, I.; Kieber, J. J.; Evans, M. L. (Principal Investigator)

1998-01-01

328

Soil Bacterial Diversity Screening Using Single 16S rRNA Gene V Regions Coupled with Multi-Million Read Generating Sequencing Technologies  

PubMed Central

The novel multi-million read generating sequencing technologies are very promising for resolving the immense soil 16S rRNA gene bacterial diversity. Yet they have a limited maximum sequence length screening ability, restricting studies in screening DNA stretches of single 16S rRNA gene hypervariable (V) regions. The aim of the present study was to assess the effects of properties of four consecutive V regions (V3-6) on commonly applied analytical methodologies in bacterial ecology studies. Using an in silico approach, the performance of each V region was compared with the complete 16S rRNA gene stretch. We assessed related properties of the soil derived bacterial sequence collection of the Ribosomal Database Project (RDP) database and concomitantly performed simulations based on published datasets. Results indicate that overall the most prominent V region for soil bacterial diversity studies was V3, even though it was outperformed in some of the tests. Despite its high performance during most tests, V4 was less conserved along flanking sites, thus reducing its ability for bacterial diversity coverage. V5 performed well in the non-redundant RDP database based analysis. However V5 did not resemble the full-length 16S rRNA gene sequence results as well as V3 and V4 did when the natural sequence frequency and occurrence approximation was considered in the virtual experiment. Although, the highly conserved flanking sequence regions of V6 provide the ability to amplify partial 16S rRNA gene sequences from very diverse owners, it was demonstrated that V6 was the least informative compared to the rest examined V regions. Our results indicate that environment specific database exploration and theoretical assessment of the experimental approach are strongly suggested in 16S rRNA gene based bacterial diversity studies.

Vasileiadis, Sotirios; Puglisi, Edoardo; Arena, Maria; Cappa, Fabrizio; Cocconcelli, Pier S.; Trevisan, Marco

2012-01-01

329

The different potential of sponge bacterial symbionts in N? release indicated by the phylogenetic diversity and abundance analyses of denitrification genes, nirK and nosZ.  

PubMed

Nitrogen cycle is a critical biogeochemical process of the oceans. The nitrogen fixation by sponge cyanobacteria was early observed. Until recently, sponges were found to be able to release nitrogen gas. However the gene-level evidence for the role of bacterial symbionts from different species sponges in nitrogen gas release is limited. And meanwhile, the quanitative analysis of nitrogen cycle-related genes of sponge microbial symbionts is relatively lacking. The nirK gene encoding nitrite reductase which catalyzes soluble nitrite into gas NO and nosZ gene encoding nitrous oxide reductase which catalyzes N?O into N? are two key functional genes in the complete denitrification pathway. In this study, using nirK and nosZ genes as markers, the potential of bacterial symbionts in six species of sponges in the release of N2 was investigated by phylogenetic analysis and real-time qPCR. As a result, totally, 2 OTUs of nirK and 5 OTUs of nosZ genes were detected by gene library-based saturated sequencing. Difference phylogenetic diversity of nirK and nosZ genes were observed at OTU level in sponges. Meanwhile, real-time qPCR analysis showed that Xestospongia testudinaria had the highest abundance of nosZ gene, while Cinachyrella sp. had the greatest abundance of nirK gene. Phylogenetic analysis showed that the nirK and nosZ genes were probably of Alpha-, Beta-, and Gammaproteobacteria origin. The results from this study suggest that the denitrification potential of bacteria varies among sponges because of the different phylogenetic diversity and relative abundance of nosZ and nirK genes in sponges. Totally, both the qualitative and quantitative analyses of nirK and nosZ genes indicated the different potential of sponge bacterial symbionts in the release of nitrogen gas. PMID:23762300

Zhang, Xia; He, Liming; Zhang, Fengli; Sun, Wei; Li, Zhiyong

2013-01-01

330

Nucleotide and partner-protein control of bacterial replicative helicase structure and function.  

PubMed

Cellular replication forks are powered by ring-shaped, hexameric helicases that encircle and unwind DNA. To better understand the molecular mechanisms and control of these enzymes, we used multiple methods to investigate the bacterial replicative helicase, DnaB. A 3.3 Å crystal structure of Aquifex aeolicus DnaB, complexed with nucleotide, reveals a newly discovered conformational state for this motor protein. Electron microscopy and small angle X-ray scattering studies confirm the state seen crystallographically, showing that the DnaB ATPase domains and an associated N-terminal collar transition between two physical states in a nucleotide-dependent manner. Mutant helicases locked in either collar state are active but display different capacities to support critical activities such as duplex translocation and primase-dependent RNA synthesis. Our findings establish the DnaB collar as an autoregulatory hub that controls the ability of the helicase to transition between different functional states in response to both nucleotide and replication initiation/elongation factors. PMID:24373746

Strycharska, Melania S; Arias-Palomo, Ernesto; Lyubimov, Artem Y; Erzberger, Jan P; O'Shea, Valerie L; Bustamante, Carlos J; Berger, James M

2013-12-26

331

A refinery sludge deposition site: presence of nahH and alkJ genes and crude oil biodegradation ability of bacterial isolates.  

PubMed

204 bacterial isolates from four Greek refinery sludge deposition sites were investigated for the presence of nahH and alkJ genes encoding key enzymes of both aromatic and aliphatic hydrocarbon degradation pathways by PCR and DNA hybridisation. Members of Pseudomonas, Acinetobacter, Bacillus, Rhodococcus and Arthrobacter play important role in bioremediation processes in sandy/loam soil contaminated with oil and nahH and alkJ genes were present in the 73% of the isolates. Consortia of bacterial isolates that were used for biodegradation of aliphatic and aromatic hydrocarbons in crude oil using liquid cultures exhibited rates from 35% to 48% within 10 days of incubation. PMID:18688575

Arvanitis, Nikolaos; Katsifas, Efstathios A; Chalkou, Kalliopi I; Meintanis, Christos; Karagouni, Amalia D

2008-12-01

332

Molecular aspects of the E. coli nucleoid protein, H-NS: a central controller of gene regulatory networks  

Microsoft Academic Search

The nucleoid-associated protein H-NS has a central role in the structuring and control of the enteric bacterial chromosome. This protein has been demonstrated to contribute to the regulation of expression for approximately thirty genes. In this article, the molecular aspects of H-NS structure and function are briefly reviewed. H-NS contains at least two independent structural domains: a C-terminal domain, involved

Roy M. Williams; Sylvie Rimsky

1997-01-01

333

Bacterial Bioluminescence: Isolation and Expression of the Luciferase Genes from Vibrio harveyi  

Microsoft Academic Search

Genes for the luciferase enzyme of Vibrio harveyi were isolated in Escherichia coli by a general method in which nonluminous, transposon insertion mutants were used. Conditions necessary for light production in E. coli were examined. Stimulation of transcription of the genes for luciferase (lux A and lux B) was required for efficient synthesis of luciferase. To enhance transcription bacteriophage promoter

Robert Belas; Alan Mileham; Daniel Cohn; Marcia Hilmen; Melvin Simon; Michael Silverman

1982-01-01

334

Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4  

Microsoft Academic Search

BACKGROUND: The universal ribosomal protein S4 is essential for the initiation of small subunit ribosomal assembly and translational accuracy. Being part of the information processing machinery of the cell, the gene for S4 is generally thought of as being inherited vertically and has been used in concatenated gene phylogenies. Here we report the evolution of ribosomal protein S4 in relation

Ke Chen; Elijah Roberts; Zaida Luthey-Schulten

2009-01-01

335

Control of Flagellar Gene Regulation in Legionella pneumophila and Its Relation to Growth Phase? †  

PubMed Central

The bacterial pathogen Legionella pneumophila responds to environmental changes by differentiation. At least two forms are well described: replicative bacteria are avirulent; in contrast, transmissive bacteria express virulence traits and flagella. Phenotypic analysis, Western blotting, and electron microscopy of mutants of the regulatory genes encoding RpoN, FleQ, FleR, and FliA demonstrated that flagellin expression is strongly repressed and that the mutants are nonflagellated in the transmissive phase. Transcriptome analyses elucidated that RpoN, together with FleQ, enhances transcription of 14 out of 31 flagellar class II genes, which code for the basal body, hook, and regulatory proteins. Unexpectedly, FleQ independent of RpoN enhances the transcription of fliA encoding sigma 28. Expression analysis of a fliA mutant showed that FliA activates three out of the five remaining flagellar class III genes and the flagellar class IV genes. Surprisingly, FleR does not induce but inhibits expression of at least 14 flagellar class III genes on the transcriptional level. Thus, we propose that flagellar class II genes are controlled by FleQ and RpoN, whereas the transcription of the class III gene fliA is controlled in a FleQ-dependent but RpoN-independent manner. However, RpoN and FleR might influence flagellin synthesis on a posttranscriptional level. In contrast to the commonly accepted view that enhancer-binding proteins such as FleQ always interact with RpoN to fullfill their regulatory functions, our results strongly indicate that FleQ regulates gene expression that is RpoN dependent and RpoN independent. Finally, FliA induces expression of flagellar class III and IV genes leading to the complete synthesis of the flagellum.

Albert-Weissenberger, Christiane; Sahr, Tobias; Sismeiro, Odile; Hacker, Jorg; Heuner, Klaus; Buchrieser, Carmen

2010-01-01

336

R gene-controlled host specificity in the legume-rhizobia symbiosis  

PubMed Central

Leguminous plants can enter into root nodule symbioses with nitrogen-fixing soil bacteria known as rhizobia. An intriguing but still poorly understood property of the symbiosis is its host specificity, which is controlled at multiple levels involving both rhizobial and host genes. It is widely believed that the host specificity is determined by specific recognition of bacterially derived Nod factors by the cognate host receptor(s). Here we describe the positional cloning of two soybean genes Rj2 and Rfg1 that restrict nodulation with specific strains of Bradyrhizobium japonicum and Sinorhizobium fredii, respectively. We show that Rj2 and Rfg1 are allelic genes encoding a member of the Toll-interleukin receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class of plant resistance (R) proteins. The involvement of host R genes in the control of genotype-specific infection and nodulation reveals a common recognition mechanism underlying symbiotic and pathogenic host–bacteria interactions and suggests the existence of their cognate avirulence genes derived from rhizobia. This study suggests that establishment of a root nodule symbiosis requires the evasion of plant immune responses triggered by rhizobial effectors.

Yang, Shengming; Tang, Fang; Gao, Muqiang; Krishnan, Hari B.; Zhu, Hongyan

2010-01-01

337

Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing.  

PubMed

Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and 'Solibacterales' and negatively with lineages such as Chloroflexi 'Ellin6529'. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data. PMID:24245591

Lopes, Ana R; Manaia, Célia M; Nunes, Olga C

2014-03-01

338

Two classes of glutathione S-transferase genes with different response profiles to bacterial challenge in Venerupis philippinarum.  

PubMed

Glutathione S-transferase (GST) is major cytosolic detoxification enzymes involved in many pathological and physiological processes. In the present study, two classes of GSTs (VpGST-1 and VpGST-2) were cloned from Venerupis philippinarum haemocytes by cDNA library and RACE approaches. Sequence alignments and phylogenetic analysis together supported that they belonged to a new member of sigma and pi classes GSTs protein family, respectively. The expression profiles of these two genes under Vibrio anguillarum challenge were investigated by quantitative RT-PCR. The bacterial challenge could significantly up-regulate the mRNA expression of both VpGST-1 and VpGST-2 with larger amplitude in VpGST-2, and the feedback speed for VpGST-2 was more rapid than that of VpGST-1. The differences in the response to bacterial challenge indicated that they were functional diversity and probably played cooperative roles in mediating the Vibrio challenge in clam. PMID:22119575

Li, Chenghua; Su, Xiurong; Li, Ye; Li, Taiwu; Sun, Chongjie; Zhou, Tingting; Liu, Haipeng

2012-01-01

339

Mechanisms that control bacterial populations in continuous-flow culture models of mouse large intestinal flora.  

PubMed

A previous study had established that anaerobic continuous-flow (CF) cultures of conventional mouse cecal flora were able to maintain the in vivo ecological balance among the indigenous bacterial species tested. This paper describes experiments designed to determine the mechanisms which control the population sizes of these species in such CF cultures. One strain each of Escherichia coli, Fusobacterium sp., and Eubacterium sp. were studied. Growth of these strains in filtrates of CF cultures was considerably more rapid than in the CF cultures themselves, indicating that the inhibitory activity had been lost in the process of filtration. Growth rates to match those in CF cultures could be obtained, however, by restoring the original levels of H(2)S in the culture filtrates. The inhibitory effect of H(2)S in filtrates and in dialysates of CF cultures could be abolished by adding glucose or pyruvate, but not formate or lactate. The fatty acids present in CF cultures matched those in the cecum of conventional mice in both quality and concentration. These acids could not account for the slow rates of growth of the tested strains in CF cultures, but they did cause a marked increase in the initial lag phase of E. coli growth. The results obtained are compatible with the hypothesis that the populations of most indigenous intestinal bacteria are controlled by one or a few nutritional substrates which a given strain can utilize most efficiently in the presence of H(2)S and at the prevailing conditions of pH and anaerobiosis. This hypothesis consequently implies that the populations of enterobacteria, such as the E. coli strain tested, and those of the predominant anaerobes are controlled by analogous mechanisms. PMID:6339388

Freter, R; Brickner, H; Botney, M; Cleven, D; Aranki, A

1983-02-01

340

Quantitative polymerase chain reaction (PCR) assays for a bacterial thiaminase I gene and the thiaminase-producing bacterium Paenibacillus thiaminolyticus.  

PubMed

The thiaminase I enzyme produced by the gram-positive bacterium Paenibacillus thiaminolyticus isolated from the viscera of Lake Michigan alewives Alosa pseudoharengus is currently the only defined source of the thiaminase activity linked to thiamine (vitamin B1) deficiency in early mortality syndrome (EMS) in the larvae of Great Lakes salmonines. Diets of alewife or isolated strains of P. thiaminolyticus mixed in a semipurified diet and fed to lake trout Salvelinus namaycush have been shown to produce EMS in fry. We utilized quantitative polymerase chain reaction (Q-PCR) to aid in studies of the sources of P. thiaminolyticus and thiaminase I. Quantitative PCR assays were established to detect the thiaminase I gene of P. thiaminolyticus, the 16S rRNA gene from most species of bacteria, and the 16S rRNA gene specifically from P. thiaminolyticus and a few closely related taxa. The Q-PCR assays are linear over at least six orders of magnitude and can detect the thiaminase I gene of P. thiaminolyticus from as few as 1,000 P. thiaminolyticus cells/g of sample or the Paenibacillus 16S rRNA gene from as few as 100 P. thiaminolyticus cells/g of sample. The initial results from alewife viscera samples with high thiaminase activity yielded unexpectedly low densities of P. thiaminolyticus cells; Paenibacillus thiaminolyticus was detectable in 2 of 6 alewife viscera tested at densities on the order of 100 cells/g out of 100,000,000 total bacterial cells/g. The low numbers of P. thiaminolyticus detected suggest that alewives contain additional non-P. thiaminolyticus sources of thiaminase activity. PMID:20218497

Richter, Catherine A; Wright-Osment, Maureen K; Zajicek, James L; Honeyfield, Dale C; Tillitt, Donald E

2009-12-01

341

Cysteine Metabolism-Related Genes and Bacterial Resistance to Potassium Tellurite? †  

PubMed Central

Tellurite exerts a deleterious effect on a number of small molecules containing sulfur moieties that have a recognized role in cellular oxidative stress. Because cysteine is involved in the biosynthesis of glutathione and other sulfur-containing compounds, we investigated the expression of Geobacillus stearothermophilus V cysteine-related genes cobA, cysK, and iscS and Escherichia coli cysteine regulon genes under conditions that included the addition of K2TeO3 to the culture medium. Results showed that cell tolerance to tellurite correlates with the expression level of the cysteine metabolic genes and that these genes are up-regulated when tellurite is present in the growth medium.

Fuentes, Derie E.; Fuentes, Eugenia L.; Castro, Miguel E.; Perez, Jose M.; Araya, Manuel A.; Chasteen, Thomas G.; Pichuantes, Sergio E.; Vasquez, Claudio C.

2007-01-01

342

Analysis of developmental control genes using virus-induced gene silencing.  

PubMed

A consistent challenge in studying the evolution of developmental processes has been the problem of explicitly assessing the function of developmental control genes in diverse species. In recent years, virus-induced gene silencing (VIGS) has proved to be remarkably adaptable and efficient in silencing developmental control genes in species across the angiosperms. Here we describe proven protocols for Nicotiana benthamiana and Papaver somniferum, representing a core and basal eudicot species. PMID:23386295

Geuten, Koen; Viaene, Tom; Vekemans, Dries; Kourmpetli, Sofia; Drea, Sinead

2013-01-01

343

Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation.  

PubMed

Barcode-based 16S rRNA gene pyrosequencing showed that the kimchi microbiome was dominated by six lactic acid bacteria (LAB), Leuconostoc (Lc.) mesenteroides, Lactobacillus (Lb.) sakei, Weissella (W.) koreensis, Lc. gelidum, Lc. carnosum, and Lc. gasicomitatum. Therefore, we used completed genome sequences of representatives of these bacteria to investigate metatranscriptomic gene-expression profiles during kimchi fermentation. Total mRNA was extracted from kimchi samples taken at five time points during a 29 day-fermentation. Nearly all (97.7%) of the metagenome sequences that were recruited on all LAB genomes of GenBank mapped onto the six LAB strains; this high coverage rate indicated that this approach for assessing processes carried out by the kimchi microbiome was valid. Expressed mRNA sequences (as cDNA) were determined using Illumina GA IIx. Assignment of mRNA sequences to metabolic genes using MG-RAST revealed the prevalence of carbohydrate metabolism and lactic acid fermentation. The mRNA sequencing reads were mapped onto genomes of the six LAB strains, which showed that Lc. mesenteroides was most active during the early-stage fermentation, whereas gene expression by Lb. sakei and W. koreensis was high during later stages. However, gene expression by Lb. sakei decreased rapidly at 25 days of fermentation, which was possibly caused by bacteriophage infection of the Lactobacillus species. Many genes related to carbohydrate transport and hydrolysis and lactate fermentation were actively expressed, which indicated typical heterolactic acid fermentation. Mannitol dehydrogenase-encoding genes (mdh) were identified from all Leuconostoc species and especially Lc. mesenteroides, which harbored three copies (two copies on chromosome and one copy on plasmid) of mdh with different expression patterns. These results contribute to knowledge of the active populations and gene expression in the LAB community responsible for an important fermentation process. PMID:23558201

Jung, Ji Young; Lee, Se Hee; Jin, Hyun Mi; Hahn, Yoonsoo; Madsen, Eugene L; Jeon, Che Ok

2013-05-15

344

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes  

PubMed Central

Background Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes. Results This paper describes a new prokaryotic genefinding algorithm based on a comprehensive statistical model of protein coding Open Reading Frames (ORFs) and Translation Initiation Sites (TISs). The former is based on a linguistic "Entropy Density Profile" (EDP) model of coding DNA sequence and the latter comprises several relevant features related to the translation initiation. They are combined to form a so-called Multivariate Entropy Distance (MED) algorithm, MED 2.0, that incorporates several strategies in the iterative program. The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes. Conclusion Results of extensive tests show that MED 2.0 achieves a competitive high performance in the gene prediction for both 5' and 3' end matches, compared to the current best prokaryotic gene finders. The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. Furthermore, the genome-specific parameters given by MED 2.0 match with the current understanding of prokaryotic genomes and may serve as tools for comparative genomic studies. In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation.

Zhu, Huaiqiu; Hu, Gang-Qing; Yang, Yi-Fan; Wang, Jin; She, Zhen-Su

2007-01-01

345

Detection of antibiotic-related genes from bacterial biocontrol agents with polymerase chain reaction.  

PubMed

Pseudomonas chlororaphis PA23, Pseudomonas spp. strain DF41, and Bacillus amyloliquefaciens BS6 consistently inhibit infection of canola petals by Sclerotinia sclerotiorum in both greenhouse and field experiments. Bacillus thuringiensis BS8, Bacillus cereus L, and Bacillus mycoides S have shown significant inhibition against S. sclerotiorum on plate assays. The presence of antibiotic biosynthetic or self-resistance genes in these strains was investigated with polymerase chain reaction and, in one case, Southern blotting. Thirty primers were used to amplify (i) antibiotic biosythetic genes encoding phenazine-1-carboxylic acid, 2,4-diacetylphloroglucinol, pyoluteorin, and pyrrolnitrin, and (ii) the zwittermicin A self-resistance gene. Our findings revealed that the fungal antagonist P. chlororaphis PA23 contains biosynthetic genes for phenazine-1-carboxylic acid and pyrrolnitrin. Moreover, production of these compounds was confirmed by high performance liquid chromatography. Pseudomonas spp. DF41 and B. amyloliquefaciens BS6 do not appear to harbour genes for any of the antibiotics tested. Bacillus thuringiensis BS8, B. cereus L, and B. mycoides S contain the zwittermicin A self-resistance gene. This is the first report of zmaR in B. mycoides. PMID:16699573

Zhang, Y; Fernando, W G D; de Kievit, T R; Berry, C; Daayf, F; Paulitz, T C

2006-05-01

346

TnAraOut, a transposon-based approach to identify and characterize essential bacterial genes.  

PubMed

Identification of genes that encode essential products provides a promising approach to validation of new antibacterial drug targets. We have developed a mariner-based transposon, TnAraOut, that allows efficient identification and characterization of essential genes by transcriptionally fusing them to an outward-facing, arabinose-inducible promoter, PBAD, located at one end of the transposon. In the absence of arabinose, such TnAraOut fusion strains display pronounced growth defects. Of a total of 16 arabinose-dependent TnAraOut mutants characterized in Vibrio cholerae, four were found to carry insertions upstream of known essential genes (gyrB, proRS, ileRS, and aspRS) whereas the other strains carried insertions upstream of known and hypothetical genes not previously shown to encode essential gene products. One of the essential genes identified by this analysis appears to be unique to V. cholerae and thus may represent an example of a species-specific drug target. PMID:10888841

Judson, N; Mekalanos, J J

2000-07-01

347

Antibiotic-Induced Replication Stress Triggers Bacterial Competence by Increasing Gene Dosage near the Origin.  

PubMed

Streptococcus pneumoniae (pneumococcus) kills nearly 1 million children annually, and the emergence of antibiotic-resistant strains poses a serious threat to human health. Because pneumococci can take up DNA from their environment by a process called competence, genes associated with antibiotic resistance can rapidly spread. Remarkably, competence is activated in response to several antibiotics. Here, we demonstrate that antibiotics targeting DNA replication cause an increase in the copy number of genes proximal to the origin of replication (oriC). As the genes required for competence initiation are located near oriC, competence is thereby activated. Transcriptome analyses show that antibiotics targeting DNA replication also upregulate origin-proximal gene expression in other bacteria. This mechanism is a direct, intrinsic consequence of replication fork stalling. Our data suggest that evolution has conserved the oriC-proximal location of important genes in bacteria to allow for a robust response to replication stress without the need for complex gene-regulatory pathways. PAPERCLIP: PMID:24725406

Slager, Jelle; Kjos, Morten; Attaiech, Laetitia; Veening, Jan-Willem

2014-04-10

348

Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces  

PubMed Central

Background Bacterial leaf blight (BLB) caused by the vascular pathogen Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases leading to crop failure in rice growing countries. A total of 37 resistance genes against Xoo has been identified in rice. Of these, ten BLB resistance genes have been mapped on rice chromosomes, while 6 have been cloned, sequenced and characterized. Diversity analysis at the resistance gene level of this disease is scanty, and the landraces from West Bengal and North Eastern states of India have received little attention so far. The objective of this study was to assess the genetic diversity at conserved domains of 6 BLB resistance genes in a set of 22 rice accessions including landraces and check genotypes collected from the states of Assam, Nagaland, Mizoram and West Bengal. Results In this study 34 pairs of primers were designed from conserved domains of 6 BLB resistance genes; Xa1, xa5, Xa21, Xa21(A1), Xa26 and Xa27. The designed primer pairs were used to generate PCR based polymorphic DNA profiles to detect and elucidate the genetic diversity of the six genes in the 22 diverse rice accessions of known disease phenotype. A total of 140 alleles were identified including 41 rare and 26 null alleles. The average polymorphism information content (PIC) value was 0.56/primer pair. The DNA profiles identified each of the rice landraces unequivocally. The amplified polymorphic DNA bands were used to calculate genetic similarity of the rice landraces in all possible pair combinations. The similarity among the rice accessions ranged from 18% to 89% and the dendrogram produced from the similarity values was divided into 2 major clusters. The conserved domains identified within the sequenced rare alleles include Leucine-Rich Repeat, BED-type zinc finger domain, sugar transferase domain and the domain of the carbohydrate esterase 4 superfamily. Conclusions This study revealed high genetic diversity at conserved domains of six BLB resistance genes in a set of 22 rice accessions. The inclusion of more genotypes from remote ecological niches and hotspots holds promise for identification of further genetic diversity at the BLB resistance genes.

2014-01-01

349

Composite films of poly(vinyl alcohol)-chitosan-bacterial cellulose for drug controlled release.  

PubMed

Mono and multilayer composite films of poly(vinyl alcohol)-chitosan-bacterial cellulose (PVA/chitosan/BC) have been prepared to achieve controlled release of ibuprofen sodium salt (IbuNa) as model drug. The composite films have been characterized by Fourier transformed infrared spectroscopy (FTIR) and X-ray diffraction (XRD). Surface morphology was investigated by scanning electron microscopy (SEM). Equilibrium swelling was measured in water at two different pH values and in vitro release of IbuNa in pH 1.2 and pH 7.4 media was studied. The release experiments revealed that drug release is pH sensitive. The release kinetics of IbuNa could be described by the Fickian model of diffusion with a good agreement. The IbuNa release rate was decreasing for all the films as the BC concentration was increased in the films composition, the decrease being higher for the multilayer films. PMID:24769089

Pavaloiu, Ramona-Daniela; Stoica-Guzun, Anicuta; Stroescu, Marta; Jinga, Sorin Ion; Dobre, Tanase

2014-07-01

350

Effective strategy for pyramiding three bacterial blight resistance genes into fine grain rice cultivar, Samba Mahsuri, using sequence tagged site markers.  

PubMed

Bacterial leaf blight (BB) of rice is a major disease limiting rice production in several rice growing regions of the world. The pathogen, Xanthomonas oryzae pv oryzae, causing the disease is highly virulent to rice crops and is capable of evolving new races. Breeding efforts to incorporate single BB resistant gene often leads to resistance breakdown within a short period. To overcome such breakdown of resistance and develop germplasm with durable disease resistance, we have introgressed three bacterial blight resistance genes, xa5, xa13, and Xa21 into a fine grain rice variety, Samba Mahsuri, using sequence tagged site (STS) markers linked to these genes. Since the efficiency of the STS markers linked to recessive genes to detect homozygotes is less than 100%, we adopted four different pyramiding schemes to minimize loss of recessive resistance genes in advanced backcross generations. Pyramiding scheme A in which a two-gene Samba Mahsuri pyramid line containing Xa21 and xa5 genes was crossed with the Samba Mahsuri line having xa13 gene alone was found to be most effective in preventing the loss of an important recessive gene xa13. We further demonstrated that there was no yield penalty due to pyramiding of multiple genes into the elite indica rice variety. PMID:20349335

Kottapalli, Kameswara Rao; Lakshmi Narasu, M; Jena, Kshirod K

2010-07-01

351

Addition of transcription activator-like effector binding sites to a pathogen strain-specific rice bacterial blight resistance gene makes it effective against additional strains and against bacterial leaf streak.  

PubMed

Xanthomonas transcription activator-like (TAL) effectors promote disease in plants by binding to and activating host susceptibility genes. Plants counter with TAL effector-activated executor resistance genes, which cause host cell death and block disease progression. We asked whether the functional specificity of an executor gene could be broadened by adding different TAL effector binding elements (EBEs) to it. We added six EBEs to the rice Xa27 gene, which confers resistance to strains of the bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) that deliver the TAL effector AvrXa27. The EBEs correspond to three other effectors from Xoo strain PXO99(A) and three from strain BLS256 of the bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc). Stable integration into rice produced healthy lines exhibiting gene activation by each TAL effector, and resistance to PXO99(A) , a PXO99(A) derivative lacking AvrXa27, and BLS256, as well as two other Xoo and 10 Xoc strains virulent toward wildtype Xa27 plants. Transcripts initiated primarily at a common site. Sequences in the EBEs were found to occur nonrandomly in rice promoters, suggesting an overlap with endogenous regulatory sequences. Thus, executor gene specificity can be broadened by adding EBEs, but caution is warranted because of the possible coincident introduction of endogenous regulatory elements. PMID:22747776

Hummel, Aaron W; Doyle, Erin L; Bogdanove, Adam J

2012-09-01

352

In situ synthesis of size-controlled, stable silver nanoparticles within ultrashort peptide hydrogels and their anti-bacterial properties.  

PubMed

We have developed a silver-releasing biomaterial with promising potential for wound healing applications. The material is made of ultrashort peptides which can self-assemble in water to form hydrogels. Silver nanoparticles (Ag NPs) were synthesized in situ within the biomaterial, using only UV irradiation and no additional chemical reducing agents. The synthetic strategy allows precise control of the nanoparticle size, with the network of peptide fibers preventing aggregation of Ag NPs. The biomaterial shows increased mechanical strength compared to the hydrogel control. We observed a sustained release of Ag NPs over a period of 14 days. This is a crucial prerequisite for effective anti-bacterial therapy. The ability to inhibit bacterial growth was tested using different bacterial strains, namely gram-negative Escherichia coli and Pseudomonas aeruginosa and gram-positive Staphylococcus aureus. Inhibition of bacterial growth was observed for all strains. The best results were obtained for Pseudomonas aeruginosa which is known for exhibiting multidrug resistance. Biocompatibility studies on HDFa cells, using Ag NP-containing hydrogels, did not show any significant influence on cell viability. We propose this silver-releasing hydrogel as an excellent biomaterial with great potential for applications in wound healing due to its low silver content, sustained silver nanoparticle release and biocompatibility. PMID:24933510

Reithofer, Michael R; Lakshmanan, Anupama; Ping, Andy T K; Chin, Jia M; Hauser, Charlotte A E

2014-08-01

353

Bacterial morphogenes  

Microsoft Academic Search

Cell shape is not the product of a particular gene or protein, but the result of the collective actions of many of them. These\\u000a are involved in several processes, including peptidoglycan precursor synthesis, peptidoglycan synthesis and recycling, cell\\u000a elongation, cell septation and division site selection. The analysis of the “morphogene” content of several bacterial genomes\\u000a suggests that there are three

Jesús Mingorance; Anabel Rico; Paulino GÓmez-Puertas

354

Bacterial Biosynthetic Gene Clusters Encoding the Anti-cancer Haterumalide Class of Molecules  

PubMed Central

Haterumalides are halogenated macrolides with strong antitumor properties, making them attractive targets for chemical synthesis. Unfortunately, current synthetic routes to these molecules are inefficient. The potent haterumalide, oocydin A, was previously identified from two plant-associated bacteria through its high bioactivity against plant pathogenic fungi and oomycetes. In this study, we describe oocydin A (ooc) biosynthetic gene clusters identified by genome sequencing, comparative genomics, and chemical analysis in four plant-associated enterobacteria of the Serratia and Dickeya genera. Disruption of the ooc gene cluster abolished oocydin A production and bioactivity against fungi and oomycetes. The ooc gene clusters span between 77 and 80 kb and encode five multimodular polyketide synthase (PKS) proteins, a hydroxymethylglutaryl-CoA synthase cassette and three flavin-dependent tailoring enzymes. The presence of two free-standing acyltransferase proteins classifies the oocydin A gene cluster within the growing family of trans-AT PKSs. The amino acid sequences and organization of the PKS domains are consistent with the chemical predictions and functional peculiarities associated with trans-acyltransferase PKS. Based on extensive in silico analysis of the gene cluster, we propose a biosynthetic model for the production of oocydin A and, by extension, for other members of the haterumalide family of halogenated macrolides exhibiting anti-cancer, anti-fungal, and other interesting biological properties.

Matilla, Miguel A.; Stockmann, Henning; Leeper, Finian J.; Salmond, George P. C.

2012-01-01

355

An intron-encoded protein assists RNA splicing of multiple similar introns of different bacterial genes.  

PubMed

Four group II introns were found in an unusually intron-rich dnaN gene (encoding the beta subunit of DNA polymerase III) of the cyanobacterium Trichodesmium erythraeum, and they have strong similarities to two introns of the RIR gene (encoding ribonucleotide reductase) of the same organism. Of these six introns, only the RIR-3 intron encodes a maturase protein and showed efficient RNA splicing when expressed in Escherichia coli cells. The other five introns do not encode a maturase protein and did not show RNA splicing in E. coli. But these maturase-less introns showed efficient RNA splicing when the RIR-3 intron-encoded maturase protein was co-expressed from a freestanding gene in the same cell. These findings demonstrated that an intron-encoded protein could function as a general maturase for multiple introns of different genes. Major implications may include an intron-mediated co-regulation of the different genes and a resemblance of the evolutionary origin of spliceosomal introns. PMID:16150738

Meng, Qing; Wang, Yanfei; Liu, Xiang-Qin

2005-10-21

356

The Pto kinase conferring resistance to tomato bacterial speck disease interacts with proteins that bind a cis-element of pathogenesis-related genes  

Microsoft Academic Search

In tomato, the Pto kinase confers resistance to bacterial speck disease by recognizing the expression of a corresponding avirulence gene, avrPto, in the pathogen Pseudomonas syringae pv. tomato. Using the yeast two-hybrid system, we have identified three genes, Pti4, Pti5 and Pti6, that encode proteins that physically interact with the Pto kinase. Pti4\\/5\\/6 each encode a protein with characteristics that

Jianmin Zhou; Xiaoyan Tang; Gregory B. Martin

1997-01-01

357

Analysis of differentially expressed genes in response to bacterial stimulation in hemocytes of the carpet-shell clam Ruditapes decussatus: Identification of new antimicrobial peptides  

Microsoft Academic Search

Suppression subtractive hybridization was used to identify differentially expressed genes in hemocytes from carpet-shell clam Ruditapes decussatus stimulated with a mixture of dead bacterial strains. Putative function could be assigned to 100 of the 253 sequenced cDNAs. Based on sequence homologies, 3.16% of the total identified genes were possibly related to immune functions. Clam myticin isoforms 1, 2 and 3,

Camino Gestal; Marímar Costa; Antonio Figueras; Beatriz Novoa

2007-01-01

358

Particle-bombardment-mediated co-transformation of elite Chinese rice cultivars with genes conferring resistance to bacterial blight and sap-sucking insect pests  

Microsoft Academic Search

.   Transgenic rice plants were generated using particle bombardment to simultaneously introduce the rice Xa21 gene effective against bacterial blight and the Galanthus nivalis agglutinin (snowdrop lectin; gna) gene effective against sap-sucking insect pests, specifically the brown plant hopper. Using three plasmids, we co-transformed\\u000a 5- to 10-d-old, mature seed-derived rice (Oryza sativa L.) callus of two elite Chinese rice cultivars,

Kexuan Tang; Porntip Tinjuangjun; Yanan Xu; Xiaofen Sun; John A. Gatehouse; Pamela C. Ronald; Huaxiong Qi; Xinggui Lu; Paul Christou; Ajay Kohli

1999-01-01

359

Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker-assisted selection into indica rice cultivar PR106  

Microsoft Academic Search

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major disease of rice in several countries. Three BB resistance genes, xa5, xa13 and Xa21, were pyramided into cv. PR106, which is widely grown in Punjab, India, using marker-assisted selection. Lines of PR106 with\\u000a pyramided genes were evaluated after inoculation with 17 isolates of the pathogen

S. Singh; J. S. Sidhu; N. Huang; Y. Vikal; Z. Li; D. S. Brar; H. S. Dhaliwal; G. S. Khush

2001-01-01

360

Identification of Bacterial Species Associated with the Sheep Scab Mite (Psoroptes ovis) by Using Amplified Genes Coding for 16S rRNA  

PubMed Central

This was the first molecular study of the bacterial flora of the sheep scab mite (Psoroptes ovis). A sequence analysis of genes coding for 16S rRNA revealed that Serratia marcescens and bacteria closely related to Staphylococcus intermedius or Staphylococcus chromogens and Alloiococcus otitidis were present. These bacteria were associated with skin lesions, dermatitis, and otitis media caused by P. ovis.

Hogg, J. C.; Lehane, M. J.

1999-01-01

361

Plant nuclear gene knockout reveals a role in plastid division for the homolog of the bacterial cell division protein FtsZ, an ancestral tubulin  

Microsoft Academic Search

Little is known about the division of eukaryotic cell organelles and up to now neither in animals nor in plants has a gene product been shown to mediate this process. A cDNA encoding a homolog of the bacterial cell division protein FtsZ, an ancestral tubulin, was isolated from the eukaryote Physcomitrella patens and used to disrupt efficiently the genomic locus

S IRKKA SCHOLZ; S VEN KRUSE; V OLKER SPETH; RALF RESKI

1998-01-01

362

Plant Nuclear Gene Knockout Reveals a Role in Plastid Division for the Homolog of the Bacterial Cell Division Protein FtsZ, an Ancestral Tubulin  

Microsoft Academic Search

Little is known about the division of eukaryotic cell organelles and up to now neither in animals nor in plants has a gene product been shown to mediate this process. A cDNA encoding a homolog of the bacterial cell division protein FtsZ, an ancestral tubulin, was isolated from the eukaryote Physcomitrella patens and used to disrupt efficiently the genomic locus

Rene Strepp; Sirkka Scholz; Sven Kruse; Volker Speth; Ralf Reski

1998-01-01

363

Short-term effect of elevated temperature on the abundance and diversity of bacterial and archaeal amoA genes in Antarctic Soils.  

PubMed

Global warming will have far-reaching effects on our ecosystem. However, its effects on Antarctic soils have been poorly explored. To assess the effects of warming on microbial abundance and community composition, we sampled Antarctic soils from the King George Island in the Antarctic Peninsula and incubated these soils at elevated temperatures of 5°C and 8°C for 14 days. The reduction in total organic carbon and increase in soil respiration were attributed to the increased proliferation of Bacteria, Fungi, and Archaea. Interestingly, bacterial ammonia monooxygenase (amoA) genes were predominant over archaeal amoA, unlike in many other environments reported previously. Phylogenetic analyses of bacterial and archaeal amoA communities via clone libraries revealed that the diversity of amoA genes in Antarctic ammonia-oxidizing prokaryotic communities were temperature-insensitive. Interestingly, our data also showed that the amoA of Antarctic ammonia-oxidizing bacteria (AOB) communities differed from previously described amoA sequences of cultured isolates and clone library sequences, suggesting the presence of novel Antarctic-specific AOB communities. Denitrification-related genes were significantly reduced under warming conditions, whereas the abundance of amoA and nifH increased. Barcoded pyrosequencing of the bacterial 16S rRNA gene revealed that Proteobacteria, Acidobacteria, and Actinobacteria were the major phyla in Antarctic soils and the effect of short-term warming on the bacterial community was not apparent. PMID:23751559

Han, Jiwon; Jung, Jaejoon; Park, Minsuk; Hyun, Seunghun; Park, Woojun

2013-09-28

364

Identification and Phylogenetic Analysis of Heme Synthesis Genes in Trypanosomatids and Their Bacterial Endosymbionts  

PubMed Central

It has been known for decades that some insect-infecting trypanosomatids can survive in culture without heme supplementation while others cannot, and that this capability is associated with the presence of a betaproteobacterial endosymbiont in the flagellate's cytoplasm. However, the specific mechanisms involved in this process remained obscure. In this work, we sequence and phylogenetically analyze the heme pathway genes from the symbionts and from their hosts, as well as from a number of heme synthesis-deficient Kinetoplastida. Our results show that the enzymes responsible for synthesis of heme are encoded on the symbiont genomes and produced in close cooperation with the flagellate host. Our evidence suggests that this synergistic relationship is the end result of a history of extensive gene loss and multiple lateral gene transfer events in different branches of the phylogeny of the Trypanosomatidae.

Alves, Joao M. P.; Voegtly, Logan; Matveyev, Andrey V.; Lara, Ana M.; da Silva, Flavia Maia; Serrano, Myrna G.; Buck, Gregory A.; Teixeira, Marta M. G.; Camargo, Erney P.

2011-01-01

365

Differentiation of bacterial 16S rRNA genes and intergenic regions and Mycobacterium tuberculosis katG genes by structure-specific endonuclease cleavage.  

PubMed

We describe here a new approach for analyzing nucleic acid sequences using a structure-specific endonuclease, Cleavase I. We have applied this technique to the detection and localization of mutations associated with isoniazid resistance in Mycobacterium tuberculosis and for differentiating bacterial genera, species and strains. The technique described here is based on the observation that single strands of DNAs can assume defined conformations, which can be detected and cleaved by structure-specific endonucleases such as Cleavase I. The patterns of fragments produced are characteristic of the sequences responsible for the structure, so that each DNA has its own structural fingerprint. Amplicons, containing either a single 5'-fluorescein or 5'-tetramethyl rhodamine label were generated from a 620-bp segment of the katG gene of isoniazid-resistant and -sensitive M. tuberculosis, the 5' 350 bp of the 16S rRNA genes of Escherichia coli O157:H7, Salmonella typhimurium, Salmonella enteritidis, Salmonella arizonae, Shigella sonnei, Shigella dysenteriae, Campylobacter jejuni, staphylococcus, hominis, Staphylococcus warneri, and Staphylococcus aureus and an approximately 550-bp DNA segment comprising the intergenic region between the 16S and 23S rRNA genes of Salmonella typhimurium, Salmonella enteritidis, Salmonella arizonae, Shigella sonnei, and Shigella dysenteriae serotypes 1, 2, and 8. Changes in the structural fingerprints of DNA fragments derived from the katG genes of isoniazid-resistant M. tuberculosis isolates were clearly identified and could be mapped to the site of the actual mutation relative to the labeled end. Bland patterns which clearly differentiated bacteria to the level of genus and, in some cases, species were generated from the 16S genes. Cleavase I analysis of the intergenic regions of Salmonella and Shigella species differentiated genus, species, and serotypes. Structural fingerprinting by digestion with Cleavase I is a rapid, simple, and sensitive method for analyzing nucleic acid sequences and may find wide utility in microbial analysis. PMID:8940459

Brow, M A; Oldenburg, M C; Lyamichev, V; Heisler, L M; Lyamicheva, N; Hall, J G; Eagan, N J; Olive, D M; Smith, L M; Fors, L; Dahlberg, J E

1996-12-01

366

[Phytase activity in some groups of bacteria. Search for and cloning of genes for bacterial phytases].  

PubMed

A search for phytase genes in 9 Bacillus strains from the collection of IMGAN was implemented. The growth optimum of strains IX-22, IX-12B, K17-2, K18, IMG I, IMG II, M4 and M8 was 50-60 degrees C; the optimal growth temperature for Bacillus sp. 790 was 45-47 degrees C. According to the sequence data of 16S RNA genes, Bacillus sp. 790 belongs to the B. subtilis/amyloliquefaciens group. The other 8 strains were identified as B. licheniformis. Selection of Bacillus strains, potentially containing the phytase genes, was performed via PCR with primers designed on the basis of the conserved sequence regions of the phyA gene from B. amyloliquefaciens FZB45 with chromosomal DNA being used as the template. The nucleotide sequences of all PCR fragments showed a high level of homology to the known Bacillus phytase genes. The gene libraries of B. licheniformis M8 and B. amyloliquefaciens 790 in E. coli were constructed and phytase-containing clones were selected from them. Twenty-four Pseudomonas strains of different species, 5 Xanthomonas maltophilia strains and 1 Xanthomonas malvacearum (all from the mentioned collection) were tested for phytase activity. Such activity was found in 13 Pseudomonas strains and in 6 Xanthomonas strains. The accumulation of phytase in Pseudomonas was shown to take place at later (over 2 days') growth stages. The optimum pH for phytase from 3 Pseudomonas strains were established. The enzymes were found to be most active at pH 5.5. PMID:15024999

Shedova, E N; Berezina, O V; Khmel', I A; Lipasova, V A; Borriss, R; Velikodvorskaia, G A

2004-01-01

367

Globally dispersed mobile drug-resistance genes in Gram-negative bacterial isolates from patients with bloodstream infections in a US urban general hospital  

PubMed Central

Mobile drug-resistance genes with identical nucleic acid sequences carried by multidrug-resistant Escherichia coli strains that cause community-acquired infections are becomingly increasingly dispersed worldwide. Over a 2-year period, we analysed Gram-negative bacterial (GNB) pathogens from the blood of inpatients at an urban public hospital to determine what proportion of these isolates carried such globally dispersed drug-resistance genes. Of 376 GNB isolates, 167 (44?%) were Escherichia coli, 50 (13?%) were Klebsiella pneumoniae, 25 (7?%) were Pseudomonas aeruginosa, 25 (7?%) were Proteus mirabilis and 20 (5?%) were Enterobacter cloacae; the remainder (24?%) comprised 26 different GNB species. Among E. coli isolates, class 1 integrons were detected in 64 (38?%). The most common integron gene cassette configuration was dfrA17-aadA5, found in 30 (25?%) of 119 drug-resistant E. coli isolates and in one isolate of Moraxella morganii. Extended-spectrum ?-lactamase (ESBL) genes were found in 16 E. coli isolates (10?%). These genes with identical sequences were found in nearly 40?% of bloodstream E. coli isolates in the study hospital, as well as in a variety of bacterial species from clinical and non-clinical sources worldwide. Thus, a substantial proportion of bloodstream infections among hospitalized patients were caused by E. coli strains carrying drug-resistance genes that are dispersed globally in a wide variety of bacterial species.

Adams-Sapper, S.; Sergeevna-Selezneva, J.; Tartof, S.; Raphael, E.; Diep, B. An; Perdreau-Remington, F.

2012-01-01

368

GenePRIMP: A software quality control tool  

ScienceCinema

Amrita Pati of the DOE Joint Genome Institute's Genome Biology group describes the software tool GenePRIMP and how it fits into the quality control pipeline for microbial genomics. Further details regarding GenePRIMP appear in a paper published online May 2, 2010 in Nature Methods.

Amrita Pati

2010-09-01

369

GenePRIMP: A software quality control tool  

SciTech Connect

Amrita Pati of the DOE Joint Genome Institute's Genome Biology group describes the software tool GenePRIMP and how it fits into the quality control pipeline for microbial genomics. Further details regarding GenePRIMP appear in a paper published online May 2, 2010 in Nature Methods.

Amrita Pati

2010-05-05

370

Evaluation of environmental bacterial contamination and procedures to control cross infection in a sample of Italian dental surgeries  

PubMed Central

OBJECTIVES—To perform a pilot study on bacterial contamination in some dental surgeries (n=51) in a local health unit in Brescia (Lombardy Region, Italy) and to evaluate the procedures to control cross infection used by the personnel to reduce the risk of infection in dental practice.?METHODS—A survey was carried out by interviewing 133 dental personnel with a questionnaire on the procedures used to control infection. The autoclaves, chemical baths (chemiclaves), and ovens present in the surgeries were tested for sterilisation efficiency with a spore test, and already packed and sterilised instruments were randomly sampled and tested for sterility. Microbial contamination of air, surface, and dental unit water samples were also studied.?RESULTS—The dental personnel did not generally follow the principal procedures for infection control: 30% of personnel were not vaccinated against hepatitis B virus, infected instruments were often not decontaminated, periodic checks of autoclave efficiency were lacking, and the knowledge of disinfection mechanisms and procedures was incomplete. High bacteriological contamination of water at dental surgeries was often found and total bacteriological counts in air samples were high. Surface studies showed widespread bacterial contamination.?CONCLUSIONS—On the basis of these results, an educational programme for the prevention of infective hazards has been prepared and carried out. The results of this pilot study will be used for planning a national survey.???Keywords: dental surgeries; bacterial contamination; cross infection control procedures

Monarca, S.; Grottolo, M.; Renzi, D.; Paganelli, C.; Sapelli, P.; Zerbini, I.; Nardi, G.

2000-01-01

371

Resource Availability and Spatial Heterogeneity Control Bacterial Community Response to Nutrient Enrichment in Lakes  

PubMed Central

The diversity and composition of ecological communities often co-vary with ecosystem productivity. However, the relative importance of productivity, or resource abundance, versus the spatial distribution of resources in shaping those ecological patterns is not well understood, particularly for the bacterial communities that underlie most important ecosystem functions. Increasing ecosystem productivity in lakes has been shown to influence the composition and ecology of bacterial communities, but existing work has only evaluated the effect of increasing resource supply and not heterogeneity in how those resources are distributed. We quantified how bacterial communities varied with the trophic status of lakes and whether community responses differed in surface and deep habitats in response to heterogeneity in nutrient resources. Using ARISA fingerprinting, we found that bacterial communities were more abundant, richer, and more distinct among habitats as lake trophic state and vertical heterogeneity in nutrients increased, and that spatial resource variation produced habitat specific responses of bacteria in response to increased productivity. Furthermore, changes in communities in high nutrient lakes were not produced by turnover in community composition but from additional taxa augmenting core bacterial communities found in lower productivity lakes. These data suggests that bacterial community responses to nutrient enrichment in lakes vary spatially and are likely influenced disproportionately by rare taxa.

Jankowski, KathiJo; Schindler, Daniel E.; Horner-Devine, M. Claire

2014-01-01

372

Self-organization in high-density bacterial colonies: efficient crowd control.  

PubMed

Colonies of bacterial cells can display complex collective dynamics, frequently culminating in the formation of biofilms and other ordered super-structures. Recent stu