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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

A bacterial sensor of plant cell contact controls the transcriptional induction of Ralstonia solanacearum pathogenicity genes  

PubMed Central

The hrp genes of the plant pathogen Ralstonia solanacearum are key pathogenicity determinants; they encode a type III protein secretion machinery involved in the secretion of mediators of the bacterium–plant interaction. These hrp genes are under the genetic control of the hrpB regulatory gene, expression of which is induced when bacteria are co-cultivated with plant cell suspensions. In this study, we used hrp–gfp transcriptional fusions to demonstrate that the expression of the hrpB and type III secretion genes is specifically induced in response to the bacterium–plant cell contact. This contact-dependent induction of hrpB gene expression requires the outer membrane protein PrhA, but not a functional type III secretion apparatus. Genetic evidence indicates that PrhA constitutes the first example of a bacterial receptor for a non-diffusible signal present in the plant cell wall and which triggers the transcriptional activation of bacterial virulence genes.

Aldon, Didier; Brito, Belen; Boucher, Christian; Genin, Stephane

2000-01-01

3

Bacterial Gene Transfer  

NSDL National Science Digital Library

This resource provides detailed instructions for carrying out several laboratory exercises relating to bacterial transformation and conjugation. In this multi-session experiment, students are exposed to various techniques in microbiology, including bacterial transformation and assay and sterile techniques.

Roberta Ellington (Northwestern University;); John Mordacq (Northwestern University;)

1991-01-01

4

Control of bacterial spores.  

PubMed

Bacterial spores are much more resistant than their vegetative counterparts. The most dangerous spore-former is Clostridium botulinum which produces a potent neurotoxin that can prove fatal. The most common food poisoning from a spore-former is caused by C. perfringens. Other food poisoning spore-formers include Bacillus cereus, B. subtilis and B. licheniformis. There are a number of non-pathogenic spore-formers including butyric and thermophilic anaerobes that cause significant economic losses to food producers. Some unusual spoilage complaints have been reported, for example, B. sporothermodurans in UHT milk, Alicyclobacillus acidoterrestris in apple and orange juice and Desulfotomaculum nigrificans in hot vending machines. Control of spore-formers requires an understanding of both the resistance and outgrowth characteristics of the spores. PMID:10885113

Brown, K L

2000-01-01

5

H-NS is a part of a thermally controlled mechanism for bacterial gene regulation.  

PubMed

Temperature is a primary environmental stress to which micro-organisms must be able to adapt and respond rapidly. Whereas some bacteria are restricted to specific niches and have limited abilities to survive changes in their environment, others, such as members of the Enterobacteriaceae, can withstand wide fluctuations in temperature. In addition to regulating cellular physiology, pathogenic bacteria use temperature as a cue for activating virulence gene expression. This work confirms that the nucleoid-associated protein H-NS (histone-like nucleoid structuring protein) is an essential component in thermoregulation of Salmonella. On increasing the temperature from 25 to 37 degrees C, more than 200 genes from Salmonella enterica serovar Typhimurium showed H-NS-dependent up-regulation. The thermal activation of gene expression is extremely rapid and change in temperature affects the DNA-binding properties of H-NS. The reduction in gene repression brought about by the increase in temperature is concomitant with a conformational change in the protein, resulting in the decrease in size of high-order oligomers and the appearance of increasing concentrations of discrete dimers of H-NS. The present study addresses one of the key complex mechanisms by which H-NS regulates gene expression. PMID:15966862

Ono, Shusuke; Goldberg, Martin D; Olsson, Tjelvar; Esposito, Diego; Hinton, Jay C D; Ladbury, John E

2005-10-15

6

H-NS is a part of a thermally controlled mechanism for bacterial gene regulation  

PubMed Central

Temperature is a primary environmental stress to which micro-organisms must be able to adapt and respond rapidly. Whereas some bacteria are restricted to specific niches and have limited abilities to survive changes in their environment, others, such as members of the Enterobacteriaceae, can withstand wide fluctuations in temperature. In addition to regulating cellular physiology, pathogenic bacteria use temperature as a cue for activating virulence gene expression. This work confirms that the nucleoid-associated protein H-NS (histone-like nucleoid structuring protein) is an essential component in thermoregulation of Salmonella. On increasing the temperature from 25 to 37 °C, more than 200 genes from Salmonella enterica serovar Typhimurium showed H-NS-dependent up-regulation. The thermal activation of gene expression is extremely rapid and change in temperature affects the DNA-binding properties of H-NS. The reduction in gene repression brought about by the increase in temperature is concomitant with a conformational change in the protein, resulting in the decrease in size of high-order oligomers and the appearance of increasing concentrations of discrete dimers of H-NS. The present study addresses one of the key complex mechanisms by which H-NS regulates gene expression.

Ono, Shusuke; Goldberg, Martin D.; Olsson, Tjelvar; Esposito, Diego; Hinton, Jay C. D.; Ladbury, John E.

2005-01-01

7

CheA protein, a central regulator of bacterial chemotaxis, belongs to a family of proteins that control gene expression in response to changing environmental conditions.  

PubMed Central

During bacterial chemotaxis, the binding of stimulatory ligands to chemoreceptors at the cell periphery leads to a response at the flagellar motor. Three proteins appear to be required for receptor-mediated control of swimming behavior, the products of the cheA, cheW, and cheY genes. Here we present the complete nucleotide sequence of the Salmonella typhimurium cheA gene together with the purification and characterization of its protein product. The protein is a 73,000 Mr cytoplasmic constituent. Amino acid-sequence comparisons indicate that it belongs to a family of bacterial regulatory proteins including the products of the cpxA, dctB, envZ, ntrB, phoR, phoM, and virA genes. Each member of this family has a conserved domain of approximately equal to 200 residues within its C terminus. We have previously shown that another chemotaxis protein, CheY, represents a domain of protein structure that has been conserved within a second large family of bacterial regulatory proteins. Each protein of the CheA family seems to function as a regulator of a different CheY homologue. Although each pair of proteins appears to produce a specialized response to a distinct type of stimulus, the relationships in primary structure suggest that a similar molecular mechanism may be involved. Images

Stock, A; Chen, T; Welsh, D; Stock, J

1988-01-01

8

CheA protein, a central regulator of bacterial chemotaxis, belongs to a family of proteins that control gene expression in response to changing environmental conditions.  

PubMed

During bacterial chemotaxis, the binding of stimulatory ligands to chemoreceptors at the cell periphery leads to a response at the flagellar motor. Three proteins appear to be required for receptor-mediated control of swimming behavior, the products of the cheA, cheW, and cheY genes. Here we present the complete nucleotide sequence of the Salmonella typhimurium cheA gene together with the purification and characterization of its protein product. The protein is a 73,000 Mr cytoplasmic constituent. Amino acid-sequence comparisons indicate that it belongs to a family of bacterial regulatory proteins including the products of the cpxA, dctB, envZ, ntrB, phoR, phoM, and virA genes. Each member of this family has a conserved domain of approximately equal to 200 residues within its C terminus. We have previously shown that another chemotaxis protein, CheY, represents a domain of protein structure that has been conserved within a second large family of bacterial regulatory proteins. Each protein of the CheA family seems to function as a regulator of a different CheY homologue. Although each pair of proteins appears to produce a specialized response to a distinct type of stimulus, the relationships in primary structure suggest that a similar molecular mechanism may be involved. PMID:3278311

Stock, A; Chen, T; Welsh, D; Stock, J

1988-03-01

9

Expression of Bacterial Genes in Plant Cells  

Microsoft Academic Search

Chimeric bacterial genes conferring resistance to aminoglycoside antibiotics have been inserted into the Agrobacterium tumefaciens tumor-inducing (Ti) plasmid and introduced into plant cells by in vitro transformation techniques. The chimeric genes contain the nopaline synthase 5' and 3' regulatory regions joined to the genes for neomycin phosphotransferase type I or type II. The chimeric genes were cloned into an intermediate

Robert T. Fraley; Stephen G. Rogers; Robert B. Horsch; Patricia R. Sanders; Jeffery S. Flick; Steven P. Adams; Michael L. Bittner; Leslie A. Brand; Cynthia L. Fink; Joyce S. Fry; Gerald R. Galluppi; Sarah B. Goldberg; Nancy L. Hoffmann; Sherry C. Woo

1983-01-01

10

Virus-induced modification of the host cell is required for expression of the bacterial chloramphenicol acetyltransferase gene controlled by a late herpes simplex virus promoter (VP5).  

PubMed Central

The requirements for expression of genes under the control of early (alkaline exonuclease) and late (VP5) herpes simplex virus type 1 (HSV-1) gene promoters were examined in a transient expression assay, using the bacterial chloramphenicol acetyltransferase gene as an expression marker. Both promoters were induced, resulting in the production of high levels of the enzyme upon low-multiplicity infection by HSV-1. S1 nuclease analysis of hybrids between RNA isolated from infected cells containing HSV-1 promoter constructs and marker gene DNA demonstrated normal transcriptional initiation of the marker gene directed by the viral promoters. Viral DNA sequences no more than 125 bases 5' of the putative transcriptional cap site were sufficient for maximum activity of the late promoter. In contrast to expression controlled by the early gene, the late promoter was not active at a measurable level in uninfected cells until DNA sequences between 75 and 125 bases 5' of the transcriptional cap site were deleted. Cotransfection of cells with the expression marker controlled by HSV promoters and a cosmid containing HSV alpha (immediate-early) genes indicated that full expression of both early and late promoters requires the same virus-induced host cell modifications. Inhibition of viral DNA synthesis results in an increased rate of transient expression of marker genes under control of either early or late promoters in contrast to the situation in normal virus infection. These data provide evidence that the normal course of expression of late HSV genes involves negative modulation of potentially active promoters in the infected cell. Images

Costa, R H; Draper, K G; Devi-Rao, G; Thompson, R L; Wagner, E K

1985-01-01

11

Sensory Mechanisms Controlling Bacterial Bioluminescence.  

National Technical Information Service (NTIS)

The goal of this project was to explore the sensory mechanisms which control the expression of bioluminescence in the marine bacterium Vibrio harveyi. Genetic methods were used to discover the genes which encode functions for the production of extracellul...

M. R. Silverman

1999-01-01

12

Persistence drives gene clustering in bacterial genomes  

Microsoft Academic Search

BACKGROUND: Gene clustering plays an important role in the organization of the bacterial chromosome and several mechanisms have been proposed to explain its extent. However, the controversies raised about the validity of each of these mechanisms remind us that the cause of this gene organization remains an open question. Models proposed to explain clustering did not take into account the

Gang Fang; Eduardo PC Rocha; Antoine Danchin

2008-01-01

13

Bacterial plant oncogenes: The rol genes' saga  

Microsoft Academic Search

Therol genes are part of the T-DNA which is transferred byAgrobacterium rhizogenes in plant cells, causing neoplastic growth and differentiation. Each of these bacterial oncogenes deeply influences plant development and is finely regulated once transferred into the plant host. Both from the study of the effects and biochemical function of therol genes and from the analysis of their regulation, important

P. Costantino; I. Capone; M. Cardarelli; A. De Paolis; M. L. Mauro; M. Trovato

1994-01-01

14

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

15

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

2012-03-24

16

Gene flow and bacterial transformation  

SciTech Connect

It is common knowledge that Salmonella which should be removed during the processing of sewage can persist is sewage sludge that is sprayed as agricultural fertilizer. Currently, researchers have found that Salmonella may become nonculturable by conventional means, while remaining viable. The issue raised by this article is the knowledge of lateral gene flow as secure as scientist suppose The author sites several research papers that suggest that intergeneric transformation can and does take place in marine environments such as tropical and subtropical estuaries.

Dixon, B.

1993-07-01

17

REGULATION OF BACTERIAL GENE EXPRESSION BY RIBOSWITCHES  

Microsoft Academic Search

Riboswitches are structured domains that usually reside in the non- coding regions of mRNAs, where they bind metabolites and control gene expression. Like their protein counterparts, these RNA gene control elements form highly specific binding pockets for the target metabolite and undergo allosteric changes in structure. Numerous classes of riboswitches are present in bacteria and they comprise a common and

Wade C. Winkler; Ronald R. Breaker

2005-01-01

18

Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor  

Microsoft Academic Search

Gene expression systems that allow the regula- tion of bacterial genes during an infection are valuable molecular tools but are lacking for myco- bacterial pathogens. We report the development of mycobacterial gene regulation systems that allow controlling gene expression in fast and slow- growing mycobacteria, including Mycobacterium tuberculosis, using anhydrotetracycline (ATc) as inducer. The systems are based on the Escherichia

Sabine Ehrt; Xinzheng V. Guo; Christopher M. Hickey; Marvin Ryou; Mercedes Monteleone; Lee W. Riley; Dirk Schnappinger

2005-01-01

19

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

20

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

21

Artificial bacterial flagella: Fabrication and magnetic control  

NASA Astrophysics Data System (ADS)

Inspired by the natural design of bacterial flagella, we report artificial bacterial flagella (ABF) that have a comparable shape and size to their organic counterparts and can swim in a controllable fashion using weak applied magnetic fields. The helical swimmer consists of a helical tail resembling the dimensions of a natural flagellum and a thin soft-magnetic ``head'' on one end. The swimming locomotion of ABF is precisely controlled by three orthogonal electromagnetic coil pairs. Microsphere manipulation is performed, and the thrust force generated by an ABF is analyzed. ABF swimmers represent the first demonstration of microscopic artificial swimmers that use helical propulsion. Self-propelled devices such as these are of interest in fundamental research and for biomedical applications.

Zhang, Li; Abbott, Jake J.; Dong, Lixin; Kratochvil, Bradley E.; Bell, Dominik; Nelson, Bradley J.

2009-02-01

22

Mechanical Control of Bacterial Cell Shape  

Microsoft Academic Search

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

Hongyuan Jiang; Fangwei Si; William Margolin

2011-01-01

23

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

24

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

25

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

26

Reservoir of bacterial exotoxin genes in the environment.  

PubMed

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. PMID:21318166

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

2011-01-09

27

Growth rate control of adherent bacterial populations.  

PubMed Central

We report a novel in vitro method which, through application of appropriate nutrient limitations, enables growth rate control of adherent bacterial populations. Exponentially growing cells are collected by pressure filtration onto cellulose acetate membranes. Following inversion into the bases of modified fermentors, membranes and bacteria are perfused with fresh medium. Newly formed and loosely attached cells are eluted with spent medium. Steady-state conditions (dependent upon the medium flow rate) at which the adherent bacterial biomass is constant and proportional to the limiting nutrient concentrations are rapidly achieved, and within limits, the growth rate is proportional to the medium flow rate. Scanning electron microscopic studies showed that such populations consist of individual cells embedded within an extracellular polymer matrix. Images

Gilbert, P; Allison, D G; Evans, D J; Handley, P S; Brown, M R

1989-01-01

28

A bacterial gene, fip, required for filamentous bacteriophage fl assembly.  

PubMed Central

An Escherichia coli mutant which does not support the growth of filamentous bacteriophage fl allows phage fl DNA synthesis and gene expression in mutant cells, but progeny particles are not assembled. The mutant cells have no other obvious phenotype. On the basis of experiments with phage containing nonlethal gene I mutations and with mutant fl selected for the ability to grow on mutant bacteria, we propose an interaction between the morphogenetic function encoded by gene I of the phage and the bacterial function altered in this mutant. The bacterial mutation defines a new gene, fip (for filamentous phage production), located near 84.2 min on the E coli chromosome. Images

Russel, M; Model, P

1983-01-01

29

Control of Gram-Negative Bacterial Quorum Sensing with CyclodextrinImmobilized Cellulose Ether Gel  

Microsoft Academic Search

Inclusion complex between cyclodextrins (CDs) and bacterial signal molecules is responsible for inhibitory effects on quorum sensing (QS). Since many bacteria have QS system for controlling gene expression in response to cell population density by means of signal molecules, an intercept of the QS signal onto the CDs can be a general method to control transcription of the QS-regulated genes.

Norihiro Kato; Tomohiro Morohoshi; Tomoyo Nozawa; Hitomi Matsumoto; Tsukasa Ikeda

2006-01-01

30

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

31

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

2011-09-22

32

Gene Testing Helps Sort Out Bacterial, Viral Infections  

MedlinePLUS

... sharing features on this page, please enable JavaScript. Gene Testing Helps Sort Out Bacterial, Viral Infections Results could speed up diagnosis, improve treatment decisions, study authors say (*this news item will not be available after ... and Gene Therapy Viral Infections WEDNESDAY, Sept. 17 ( ...

33

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

34

Implication of gene distribution in the bacterial chromosome for the bacterial cell factory  

Microsoft Academic Search

As bacterial genome sequences accumulate, more and more pieces of data suggest that there is a significant correlation between the distribution of genes along the chromosome and the physical architecture of the cell, suggesting that the map of the cell is in the chromosome. Considering sequences and experimental data indicative of cell compartmentalisation, mRNA folding and turnover, as well as

Eduardo P. C. Rocha; Pascale Guerdoux-Jamet; Ivan Moszer; Alain Viari; Antoine Danchin

2000-01-01

35

Rapid diagnosis of sepsis and bacterial meningitis in children with real-time fluorescent quantitative polymerase chain reaction amplification in the bacterial 16S rRNA gene.  

PubMed

A method for the detection of bacterial pathogens in sepsis and bacterial meningitis with 16S rRNA gene- based real-time fluorescent quantitative polymerase chain reaction (FQ-PCR) is developed. A total of 190 blood specimens and 5 cerebrospinal fluid specimens from neonates with suspected sepsis or bacterial meningitis were evaluated with 16S rRNA gene-based real-time FQ-PCR assay. The positive rate of the real-time FQ-PCR assay was significantly higher (25/195, 12.82%) than that of bacterial culture (15/195, 7.69%; P = .002). When bacterial culture was used as a control, the sensitivity of the real-time FQ-PCR was 100%, the specificity was 94.4%, and Youden's index was 0.944. This study suggests that 16S rRNA gene-based real-time FQ-PCR assay is an important and accurate method in the detection of bacterial pathogens of sepsis and bacterial meningitis and should have a promising usage in the diagnosis of sepsis and bacterial meningitis. PMID:19407210

Chen, Li-Hua; Duan, Qun-Jun; Cai, Mei-Ting; Wu, Yi-Dong; Shang, Shi-Qiang

2009-04-30

36

POLYMERASE CHAIN REACTION AMPLIFICATION OF BACTERIAL 16S rRNA GENES FROM COLD-CUP BIOPSY FORCEPS  

Microsoft Academic Search

PurposeIn looking for a possible infectious cause for interstitial cystitis (IC), we previously determined that bladder tissue specimens from both IC patients and controls were uniformly positive by polymerase chain reaction assay (PCR) for bacterial 16S ribosomal RNA genes from various genera including Escherichia, Propionobacterium, Acinetobacter, and Salmonella. We therefore determined whether the biopsy forceps might be contaminated with bacterial

S. KEAY; C. O. ZHANG; B. R. BALDWIN; R. B. ALEXANDER; J. W. WARREN

1998-01-01

37

Subgingival bacterial colonization profiles correlate with gingival tissue gene expression  

Microsoft Academic Search

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

Panos N Papapanou; Jan H Behle; Moritz Kebschull; Romanita Celenti; Dana L Wolf; Martin Handfield; Paul Pavlidis; Ryan T Demmer

2009-01-01

38

A Discovery Laboratory Investigating Bacterial Gene Regulation  

NSDL National Science Digital Library

This laboratory exercise introduces students to experimental design and gene regulation using different sugar ("food" sources) and an enzyme assay for beta-glalctosidase to identify different E. coli stains with respect to lac operon mutations, then designing their own experiments to study the various aspects of the lac operon.

Robert Moss (Wofford College;)

1999-01-01

39

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

40

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

41

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

42

Determination of the Core of a Minimal Bacterial Gene Set†  

PubMed Central

The availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. Six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minimal metabolic machinery necessary to sustain life was carried out. The proposed minimal genome contains 206 protein-coding genes with all the genetic information necessary for self-maintenance and reproduction in the presence of a full complement of essential nutrients and in the absence of environmental stress. The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed.

Gil, Rosario; Silva, Francisco J.; Pereto, Juli; Moya, Andres

2004-01-01

43

Effects of bacterial ACC deaminase on Brassica napus gene expression.  

PubMed

Plants in association with plant growth-promoting rhizobacteria can benefit from lower plant ethylene levels through the action of the bacterial enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. This enzyme cleaves the immediate biosynthetic precursor of ethylene, ACC. Ethylene is responsible for many aspects of plant growth and development but, under stressful conditions, it exacerbates stress symptoms. The ACC deaminase-containing bacterium Pseudomonas putida UW4 is a potent plant growth-promoting strain and, as such, was used to elaborate the detailed role of bacterial ACC deaminase in Brassica napus (canola) plant growth promotion. Transcriptional changes in bacterially treated canola plants were investigated with the use of an Arabidopsis thaliana oligonucleotide microarray. A heterologous approach was necessary because there are few tools available at present to measure global expression changes in nonmodel organisms, specifically with the sensitivity of microarrays. The results indicate that the transcription of genes involved in plant hormone regulation, secondary metabolism, and stress response was altered in plants by the presence of the bacterium, whereas the upregulation of genes for auxin response factors and the downregulation of stress response genes was observed only in the presence of bacterial ACC deaminase. These results support the suggestion that there is a direct link between ethylene and the auxin response, which has been suggested from physiological studies, and provide more evidence for the stress-reducing benefits of ACC deaminase-expressing plant growth-promoting bacteria. PMID:22352713

Stearns, Jennifer C; Woody, Owen Z; McConkey, Brendan J; Glick, Bernard R

2012-05-01

44

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

45

Proteorhodopsin genes are distributed among divergent marine bacterial taxa  

PubMed Central

Proteorhodopsin (PR) is a retinal-binding bacterial integral membrane protein that functions as a light-driven proton pump. The gene encoding this photoprotein was originally discovered on a large genome fragment derived from an uncultured marine ?-proteobacterium of the SAR86 group. Subsequently, many variants of the PR gene have been detected in marine plankton, via PCR-based gene surveys. It has not been clear, however, whether these different PR genes are widely distributed among different bacterial groups, or whether they have a restricted taxonomic distribution. We report here comparative analyses of PR-bearing genomic fragments recovered directly from planktonic bacteria inhabiting the California coast, the central Pacific Ocean, and waters offshore the Antarctica Peninsula. Sequence analysis of an Antarctic genome fragment harboring PR (ANT32C12) revealed moderate conservation in gene order and identity, compared with a previously reported PR-containing genome fragment from a Monterey Bay ?-proteobacterium (EBAC31A08). Outside the limited region of synteny shared between these clones, however, no significant DNA or protein identity was evident. Analysis of a third PR-containing genome fragment (HOT2C01) from the North Pacific subtropical gyre showed even more divergence from the ?-proteobacterial PR-flanking region. Subsequent phylogenetic and comparative genomic analyses revealed that the Central North Pacific PR-containing genome fragment (HOT2C01) originated from a planktonic ?-proteobacterium. These data indicate that PR genes are distributed among a variety of divergent marine bacterial taxa, including both ?- and ?-proteobacteria. Our analyses also demonstrate the utility of cultivation-independent comparative genomic approaches for assessing gene content and distribution in naturally occurring microbes.

de la Torre, Jose R.; Christianson, Lynne M.; Beja, Oded; Suzuki, Marcelino T.; Karl, David M.; Heidelberg, John; DeLong, Edward F.

2003-01-01

46

Biomimicry of bacterial foraging for distributed optimization and control  

Microsoft Academic Search

We explain the biology and physics underlying the chemotactic (foraging) behavior of E. coli bacteria. We explain a variety of bacterial swarming and social foraging behaviors and discuss the control system on the E. coli that dictates how foraging should proceed. Next, a computer program that emulates the distributed optimization process represented by the activity of social bacterial foraging is

K. M. Passino

2002-01-01

47

Genetic Variation in the ?2-Adrenocepter Gene Is Associated with Susceptibility to Bacterial Meningitis in Adults  

PubMed Central

Recently, the biased ?2-adrenoceptor/?-arrestin pathway was shown to play a pivotal role in crossing of the blood brain barrier by Neisseria meningitidis. We hypothesized that genetic variation in the ?2-adrenoceptor gene (ADRB2) may influence susceptibility to bacterial meningitis. In a prospective genetic association study we genotyped 542 patients with CSF culture proven community acquired bacterial meningitis and 376 matched controls for 2 functional single nucleotide polymorphisms in the ?2-adrenoceptor gene (ADRB2). Furthermore, we analyzed if the use of non-selective beta-blockers, which bind to the ?2-adrenoceptor, influenced the risk of bacterial meningitis. We identified a functional polymorphism in ADRB2 (rs1042714) to be associated with an increased risk for bacterial meningitis (Odds ratio [OR] 1.35, 95% confidence interval [CI] 1.04–1.76; p?=?0.026). The association remained significant after correction for age and was more prominent in patients with pneumococcal meningitis (OR 1.52, 95% CI 1.12–2.07; p?=?0.007). For meningococcal meningitis the difference in genotype frequencies between patients and controls was similar to that in pneumococcal meningitis, but this was not statistically significant (OR 1.43, 95% CI 0.60–3.38; p?=?0.72). Patients with bacterial meningitis had a lower frequency of non-selective beta-blockers use compared to the age matched population (0.9% vs. 1.8%), although this did not reach statistical significance (OR 1.96 [95% CI 0.88–4.39]; p?=?0.09). In conclusion, we identified an association between a genetic variant in the ?2-adrenoceptor and increased susceptibility to bacterial meningitis. The potential benefit of pharmacological treatment targeting the ?2-adrenoceptor to prevent bacterial meningitis in the general population or patients with bacteraemia should be further studied in both experimental studies and observational cohorts.

Adriani, Kirsten S.; Brouwer, Matthijs C.; Baas, Frank; Zwinderman, Aeilko H.; van der Ende, Arie; van de Beek, Diederik

2012-01-01

48

Expression of bacterial cellulase genes in transgenic alfalfa ( Medicago sativa L.), potato ( Solanum tuberosum L.) and tobacco ( Nicotiana tabacum L.)  

Microsoft Academic Search

The genes encoding thermostable cellulases E2 and E3 of Thermomonospora fusca were expressed in plants under the control of the constitutive, hybrid Mac promoter. For both E2 and E3, the genes were modified so as to remove the sequence encoding the bacterial leader peptide. Western blot analysis indicated that expression levels of recombinant cellulase in tobacco lines ranged up to

Thomas Ziegelhoffer; Jessica Will; Sandra Austin-Phillips

1999-01-01

49

Gene regulation mediates host specificity of a bacterial pathogen.  

PubMed

Many bacterial plant pathogens have a gene-for-gene relationship that determines host specificity. However, there are pathogens such as the xylem-limited bacterium Xylella fastidiosa that do not carry genes considered essential for the gene-for-gene model, such as those coding for a type III secretion system and effector molecules. Nevertheless, X.?fastidiosa subspecies are host specific. A comparison of symptom development and host colonization after infection of plants with several mutant strains in two hosts, grapevines and almonds, indicated that X.?fastidiosa virulence mechanisms are similar in those plants. Thus, we tested if modification of gene regulation patterns, by affecting the production of a cell-cell signalling molecule (DSF), impacted host specificity in X.?fastidiosa. Results show that disruption of the rpfF locus, required for DSF synthesis, in a strain incapable of causing disease in grapevines, leads to symptom development in that host. These data are indicative that the core machinery required for the colonization of grapevines is present in that strain, and that changes in gene regulation alone can lead X.?fastidiosa to exploit a novel host. The study of the evolution and mechanisms of host specificity mediated by gene regulation at the genome level could lead to important insights on the emergence of new diseases. PMID:23761371

Killiny, Nabil; Almeida, Rodrigo P P

2011-09-23

50

Overexpression of a bacterial 1-deoxy-D-xylulose 5-phosphate synthase gene in potato tubers perturbs the isoprenoid metabolic network: implications for the control of the tuber life cycle  

Microsoft Academic Search

Potato tubers were engineered to express a bacterial gene encoding 1-deoxy-D-xylulose 5-phosphate synthase (DXS) in order to investigate the effects of perturbation of isoprenoid biosynthesis. Twenty-four independent transgenic lines out of 38 generated produced tubers with significantly elongated shape that also exhibited an early tuber sprouting phenotype. Expression analy- sis of nine transgenic lines (four exhibiting the pheno- type and

Wayne L. Morris; Laurence J. M. Ducreux; Peter Hedden; Steve Millam; Mark A. Taylor

2006-01-01

51

A benefit of high temperature: increased effectiveness of a rice bacterial blight disease resistance gene.  

PubMed

*Continuous planting of crops containing single disease resistance (R) genes imposes a strong selection for virulence in pathogen populations, often rendering the R gene ineffective. Increasing environmental temperatures may complicate R-gene-mediated disease control because high temperatures often promote disease development and reduce R gene effectiveness. Here, performance of one rice bacterial blight disease R gene was assessed in field and growth chamber studies to determine the influence of temperature on R gene effectiveness and durability. *Disease severity and virulence of Xanthomonas oryzae pv. oryzae (Xoo) populations were monitored in field plots planted to rice with and without the bacterial blight R gene Xa7 over 11 yr. The performance of Xa7 was determined in high- and low-temperature regimes in growth chambers. *Rice with Xa7 exhibited less disease than lines without Xa7 over 11 yr, even though virulence of Xoo field populations increased. Xa7 restricted disease more effectively at high than at low temperatures. Other R genes were less effective at high temperatures. *We propose that Xa7 restricts disease and Xoo population size more efficiently in high temperature cropping seasons compared with cool seasons creating fluctuating selection, thereby positively impacting durability of Xa7. PMID:19878463

Webb, K M; Oña, I; Bai, J; Garrett, K A; Mew, T; Vera Cruz, C M; Leach, J E

2009-10-29

52

Bacterial community assembly based on functional genes rather than species  

PubMed Central

The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be “species” (by means of rRNA taxonomy), but rather the more functional level of genes.

Burke, Catherine; Steinberg, Peter; Rusch, Doug; Kjelleberg, Staffan; Thomas, Torsten

2011-01-01

53

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

PubMed

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. PMID:23979428

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

2013-09-02

54

Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation  

PubMed Central

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 member of the NBS-LRR class of plant disease-resistance genes, but quite different from Xa21, another BB-resistance gene isolated from rice. Interestingly, Xa1 gene expression was induced on inoculation with a bacterial pathogen and wound, unlike other isolated resistance genes in plants, which show constitutive expression. The induced expression may be involved in enhancement of resistance against the pathogen.

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

1998-01-01

55

A deficiency in the autophagy gene Atg16L1 enhances resistance to enteric bacterial infection.  

PubMed

Polymorphisms in the essential autophagy gene Atg16L1 have been linked with susceptibility to Crohn's disease, a major type of inflammatory bowel disease (IBD). Although the inability to control intestinal bacteria is thought to underlie IBD, the role of Atg16L1 during extracellular intestinal bacterial infections has not been sufficiently examined and compared to the function of other IBD susceptibility genes, such as Nod2, which encodes a cytosolic bacterial sensor. We find that Atg16L1 mutant mice are resistant to intestinal disease induced by the model bacterial pathogen Citrobacter rodentium. An Atg16L1 deficiency alters the intestinal environment to mediate an enhanced immune response that is dependent on monocytic cells, but this hyperimmune phenotype and its protective effects are lost in Atg16L1/Nod2 double-mutant mice. These results reveal an immunosuppressive function of Atg16L1 and suggest that gene variants affecting the autophagy pathway may have been evolutionarily maintained to protect against certain life-threatening infections. PMID:23954160

Marchiando, Amanda M; Ramanan, Deepshika; Ding, Yi; Gomez, Luis E; Hubbard-Lucey, Vanessa M; Maurer, Katie; Wang, Caihong; Ziel, Joshua W; van Rooijen, Nico; Nuñez, Gabriel; Finlay, B Brett; Mysorekar, Indira U; Cadwell, Ken

2013-08-14

56

Genetics of Bacterial Alginate: Alginate Genes Distribution, Organization and Biosynthesis in Bacteria  

PubMed Central

Bacterial alginate genes are chromosomal and fairly widespread among rRNA homology group I Pseudomonads and Azotobacter. In both genera, the genetic pathway of alginate biosynthesis is mostly similar and the identified genes are identically organized into biosynthetic, regulatory and genetic switching clusters. In spite of these similarities,still there are transcriptional and functional variations between P. aeruginosa and A. vinelandii. In P. aeruginosa all biosynthetic genes except algC transcribe in polycistronic manner under the control of algD promoter while in A. vinelandii, these are organized into many transcriptional units. Of these, algA and algC are transcribed each from two different and algD from three different promoters. Unlike P. aeruginosa, the promoters of these transcriptional units except one of algC and algD are algT-independent. Both bacterial species carry homologous algG gene for Ca2+-independent epimerization. But besides algG, A. vinelandii also has algE1-7 genes which encode C-5-epimerases involved in the complex steps of Ca2+-dependent epimerization. A hierarchy of alginate genes expression under ?22(algT) control exists in P. aeruginosa where algT is required for transcription of the response regulators algB and algR, which in turn are necessary for expression of algD and its downstream biosynthetic genes. Although algTmucABCD genes cluster play similar regulatory roles in both P. aeruginosa and A. vinelandii but unlike, transcription of A. vinelandii, algR is independent of ?22. These differences could be due to the fact that in A. vinelandii alginate plays a role as an integrated part in desiccation-resistant cyst which is not found in P. aeruginosa.

Muhammadi; Ahmed, Nuzhat

2007-01-01

57

Cysteine Biosynthesis Pathway in the Archaeon Methanosarcina barkeri Encoded by Acquired Bacterial Genes?  

Microsoft Academic Search

The pathway of cysteine biosynthesis in archaea is still unexplored. Complementation of a cysteine auxo- trophic Escherichia coli strain NK3 led to the isolation of the Methanosarcina barkeri cysK gene (encoding O-acetylserine (thiol)-lyase-A), which displays great similarity to bacterial cysK genes. Adjacent to cysK is an open reading frame orthologous to bacterial cysE (serine transacetylase) genes. These two genes could

MAKOTO KITABATAKE; MAN WAH SO; DEBRA L. TUMBULA; DIETER SOLL

2000-01-01

58

A statistical model for bacterial speciation triggered by lateral gene transfer  

Microsoft Academic Search

The process of bacterial speciation has been a major unresolved issue in the study of bacterial evolution. It has been proposed that lateral gene transfer and homologous recombination play critical and complementary roles in speciation. We introduce a statistical model, of a population, for the evolution under lateral gene transfer and local homologous recombination. We examine the evolutionary dynamics and

Sunjeet Sidhu; Wequin Peng

2006-01-01

59

RT-qPCR based quantitative analysis of gene expression in single bacterial cells  

Microsoft Academic Search

Recent evidence suggests that cell-to-cell difference at the gene expression level is an order of magnitude greater than previously thought even for isogenic bacterial populations. Such gene expression heterogeneity determines the fate of individual bacterial cells in populations and could also affect the ultimate fate of populations themselves. To quantify the heterogeneity and its biological significance, quantitative methods to measure

Weimin Gao; Weiwen Zhang; Deirdre R. Meldrum

2011-01-01

60

Glucocorticoid Control of Gene Expression.  

National Technical Information Service (NTIS)

The concept that glucocorticoids function at the nuclear level to control expression of specific genes is discussed. The current views on the mechanism of this control are presented and relevant data from different experimental approaches are reported.

F. T. Kenney S. E. Lane K. L. Lee J. N. Ihle

1975-01-01

61

A Combination of Independent Transcriptional Regulators Shapes Bacterial Virulence Gene Expression during Infection  

PubMed Central

Transcriptional regulatory networks are fundamental to how microbes alter gene expression in response to environmental stimuli, thereby playing a critical role in bacterial pathogenesis. However, understanding how bacterial transcriptional regulatory networks function during host-pathogen interaction is limited. Recent studies in group A Streptococcus (GAS) suggested that the transcriptional regulator catabolite control protein A (CcpA) influences many of the same genes as the control of virulence (CovRS) two-component gene regulatory system. To provide new information about the CcpA and CovRS networks, we compared the CcpA and CovR transcriptomes in a serotype M1 GAS strain. The transcript levels of several of the same genes encoding virulence factors and proteins involved in basic metabolic processes were affected in both ?ccpA and ?covR isogenic mutant strains. Recombinant CcpA and CovR bound with high-affinity to the promoter regions of several co-regulated genes, including those encoding proteins involved in carbohydrate and amino acid metabolism. Compared to the wild-type parental strain, ?ccpA and ?covR?ccpA isogenic mutant strains were significantly less virulent in a mouse myositis model. Inactivation of CcpA and CovR alone and in combination led to significant alterations in the transcript levels of several key GAS virulence factor encoding genes during infection. Importantly, the transcript level alterations in the ?ccpA and ?covR?ccpA isogenic mutant strains observed during infection were distinct from those occurring during growth in laboratory medium. These data provide new knowledge regarding the molecular mechanisms by which pathogenic bacteria respond to environmental signals to regulate virulence factor production and basic metabolic processes during infection.

Shelburne, Samuel A.; Olsen, Randall J.; Suber, Bryce; Sahasrabhojane, Pranoti; Sumby, Paul; Brennan, Richard G.; Musser, James M.

2010-01-01

62

Substrate Diffusion Heterogeneity Controls Bacterial Competition and Coexistence  

NASA Astrophysics Data System (ADS)

Diffusion has long been recognized as a key process affecting bacterial physiological functions ranging from nutrient uptake to removal of metabolic waste products. In the vadose zone, significant convective flows are limited and bacteria rely primarily on diffusion for nutrient supply. Even under relatively "wet" conditions (e.g. matric potentials -20 J/kg), soil water is fragmented and exists as thin liquid films or held in crevices imposing constraints on substrate diffusion. Our objective was to investigate the role of diffusion on soil microbial diversity, by focusing on one of the processes that shapes the structure of bacterial communities: competitive interactions. We used a simplified setup, in which the substrate (citrate) fluxes were controlled by different agar gels thicknesses and spatially heterogeneous diffusive pathways were created by an impermeable film with prescribed hole sizes and patterns. Our competition experiments involved two soil bacteria: Burkholderia xenovorans LB400 and Pseudomonas putida KT2440, which were tagged with different constitutive fluorescent markers, allowing for their on line microscopic detection. The growth parameters on citrate of these strains were thoroughly assessed. B. xenovorans LB400 is the weaker competitor. As a result, this strain was outcompeted by KT2440 under high substrate diffusivity and homogeneous conditions. Conversely, the disadvantage of the weakest competitor was not so marked under low substrate diffusivity condition. These results suggest that dry conditions in soil would provide conditions allowing the sustaining of weak bacterial competitors, resulting in the maintenance of high bacterial diversity.

Dechesne, A.; Or, D.; Smets, B. F.

2005-12-01

63

Improved metabolic action of a bacterial lysine decarboxylase gene in tobacco hairy root cultures by its fusion to a rbcS transit peptide coding sequence  

Microsoft Academic Search

The gene of a bacterial lysine decarboxylase (ldc) fused to arbcS transit peptide coding sequence (tp), and under the control of the CaMV 35S promoter, was expressed in hairy root cultures ofNicotiana tabacum. The fusion of theldc to the targeting signal sequence improved the performance of the bacterial gene in the plant cells in many respects. Nearly all transgenic hairy

S. Herminghaus; D. Tholl; C. Rügenhagen; L. F. Fecker; C. Leuschner

1996-01-01

64

Interaction of two photoreceptors in the regulation of bacterial photosynthesis genes  

PubMed Central

The expression of photosynthesis genes in the facultatively photosynthetic bacterium Rhodobacter sphaeroides is controlled by the oxygen tension and by light quantity. Two photoreceptor proteins, AppA and CryB, have been identified in the past, which are involved in this regulation. AppA senses light by its N-terminal BLUF domain, its C-terminal part binds heme and is redox-responsive. Through its interaction to the transcriptional repressor PpsR the AppA photoreceptor controls expression of photosynthesis genes. The cryptochrome-like protein CryB was shown to affect regulation of photosynthesis genes, but the underlying signal chain remained unknown. Here we show that CryB interacts with the C-terminal domain of AppA and modulates the binding of AppA to the transcriptional repressor PpsR in a light-dependent manner. Consequently, binding of the transcription factor PpsR to its DNA target is affected by CryB. In agreement with this, all genes of the PpsR regulon showed altered expression levels in a CryB deletion strain after blue-light illumination. These results elucidate for the first time how a bacterial cryptochrome affects gene expression.

Metz, Sebastian; Haberzettl, Kerstin; Fruhwirth, Sebastian; Teich, Kristin; Hasewinkel, Christian; Klug, Gabriele

2012-01-01

65

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

66

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

PubMed Central

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 any small genomes. It was originally developed for comparing virus, mitochondrion and chloroplast genomes. This is now extended to small bacterial genomes of sizes less than 2 Mb. Results GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database. It is an updated web-based "on-the-fly" computational tool allowing gene order and synteny comparisons of any two small bacterial genomes. Analyses of several bacterial genomes show that a large amount of gene and genome re-arrangement occurs, as seen with earlier DNA software tools. This can be displayed at the protein level using GeneOrder3.0. Whole genome alignments of genes are presented in both a table and a dot plot. This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences. Conclusions GeneOrder3.0 allows researchers to perform comparative analysis of gene order and synteny in genomes of sizes up to 2 Mb "on-the-fly." Availability: and .

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

2004-01-01

67

Expression of bacterial genes in transgenic tobacco: methods, applications and future prospects  

PubMed Central

Tobacco is the most commonly used plant for expression of transgenes from a variety of organisms, because it is easily grown and transformed, it provides abundant amounts of fresh tissue and has a well-established cell culture system. Many bacterial proteins involved in the synthesis of commercial products are currently engineered for production in tobacco. Bacterial enzymes synthesized in tobacco can enhance protection against abiotic stresses and diseases, and provide a system to test applied strategies such as phytoremediation. Examples of bacterial gene expression in tobacco include production of antigen proteins from several human bacterial pathogens as vaccines, bacterial proteins for enhancing resistance against insects, pathogens and herbicides, and bacterial enzymes for the production of polymers, sugars, and bioethanol. Further improvements in the expression of recombinant proteins and their recovery from tobacco will enhance production and commercial use of these proteins. This review highlights the dynamic use of tobacco in bacterial protein production by examining the most relevant research in this field.

Jube, Sandro

2009-01-01

68

Circuit-level input integration in bacterial gene regulation.  

PubMed

Gene regulatory circuits can receive multiple simultaneous inputs, which can enter the system through different locations. It is thus necessary to establish how these genetic circuits integrate multiple inputs as a function of their relative entry points. Here, we use the dynamic circuit regulating competence for DNA uptake in Bacillus subtilis as a model system to investigate this issue. Specifically, we map the response of single cells in vivo to a combination of (i) a chemical signal controlling the constitutive expression of key competence genes, and (ii) a genetic perturbation in the form of copy number variation of one of these genes, which mimics the level of stress signals sensed by the bacteria. Quantitative time-lapse fluorescence microscopy shows that a variety of dynamical behaviors can be reached by the combination of the two inputs. Additionally, the integration depends strongly on the relative locations where the two perturbations enter the circuit. Specifically, when the two inputs act upon different circuit elements, their integration generates novel dynamical behavior, whereas inputs affecting the same element do not. An in silico bidimensional bifurcation analysis of a mathematical model of the circuit offers good quantitative agreement with the experimental observations, and sheds light on the dynamical mechanisms leading to the different integrated responses exhibited by the gene regulatory circuit. PMID:23572583

Espinar, Lorena; Dies, Marta; Cagatay, Tolga; Süel, Gürol M; Garcia-Ojalvo, Jordi

2013-04-09

69

Identifying essential genes in bacterial metabolic networks with machine learning methods  

Microsoft Academic Search

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

Kitiporn Plaimas; Roland Eils; Rainer König

2010-01-01

70

Computational Bacterial Genome-Wide Analysis of Phylogenetic Profiles Reveals Potential Virulence Genes of Streptococcus agalactiae  

Microsoft Academic Search

The phylogenetic profile of a gene is a reflection of its evolutionary history and can be defined as the differential presence or absence of a gene in a set of reference genomes. It has been employed to facilitate the prediction of gene functions. However, the hypothesis that the application of this concept can also facilitate the discovery of bacterial virulence

Frank Po-Yen Lin; Ruiting Lan; Vitali Sintchenko; Gwendolyn L. Gilbert; Fanrong Kong; Enrico Coiera; Herman Tse

2011-01-01

71

Combinatorial Approach for Fabrication of Coatings to Control Bacterial Adhesion.  

PubMed

Due to the high importance of bacterial infections in medical devices there is an increasing interest in the design of anti-fouling coatings. The application of substrates with controlled chemical gradients to prevent microbial adhesion is presented. We describe here the co-polymerization of poly(ethylene glycol) dimethacrylate with a hyperbranched multimethacrylate (H30MA) using a chemical gradient generator; and the resulting films were characterized with respect to their ability to serve as coating for biomedical devices. The photo-polymerized materials present special surface properties due to the hyperbranched structure of H30MA and phase separation at specific concentrations in the PEGDM matrix. This approach affords the investigation of cell response to a large range of different chemistries on a single sample. Two bacterial strains commonly associated with surgical site infections, Escherichia coli and Pseudomonas aeruginosa, have been cultured on these substrates to study their attachment behaviour. These gradient-coated samples demonstrate less bacterial adhesion at higher concentrations of H30MA, and the adhesion is substantially affected by the extent of surface phase segregation. PMID:21888758

Pedron, S; Peinado, C; Catalina, F; Bosch, P; Anseth, K S; Abrusci, C

2011-08-29

72

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

73

Evolution of Transcription Regulatory Genes Is Linked to Niche Specialization in the Bacterial Pathogen Streptococcus pyogenes†  

PubMed Central

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 ?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.

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

2005-01-01

74

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

75

Differential annotation of tRNA genes with anticodon CAT in bacterial genomes  

Microsoft Academic Search

We have developed three strategies to discriminate among the three types of tRNA genes with anticodon CAT (tRNAIle, elongator tRNAMet and initiator tRNAfMet) in bacterial genomes. With these strategies, we have classified the tRNA genes from 234 bacterial and several organellar genomes. These sequences, in an aligned or unaligned format, may be used for the identification and annotation of tRNA

Francisco J. Silva; Eugeni Belda; Santiago E. Talens

2006-01-01

76

Genes controlling pancreas ontogeny.  

PubMed

The pancreas develops from two separate and independent endodermal primordia. The molecular events supporting the early morphological changes that give rise to the formation of the dorsal and ventral pancreatic buds result from coordinated responses to extrinsic and intrinsic signals. The extrinsic signals are involved in processes dictating whether progenitor cells remain as immature or as committed precursors. After specification, the sequential activation of transcription factors determines cell autonomously the commitment and differentiation of these progenitors. During pancreas development, the roles of extrinsic and intrinsic signals are variable, depending on the particular competence of each progenitor cell. We summarize in this review the main events, at the level of gene expression, which are involved in the early stages of pancreas development. PMID:18956314

Bonal, Claire; Herrera, Pedro L

2008-01-01

77

Bacterial genes in the aphid genome: absence of functional gene transfer from Buchnera to its host.  

PubMed

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,psiLdcA), five rare lipoprotein As (RlpA1-5), N-acetylmuramoyl-L-alanine amidase (AmiD), 1,4-beta-N-acetylmuramidase (bLys), DNA polymerase III alpha chain (psiDnaE), and ATP synthase delta chain (psiAtpH). Buchnera was the apparent source of two highly truncated pseudogenes (psiDnaE and psiAtpH). 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. PMID:20195500

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

2010-02-26

78

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

79

Silencing VP28 gene of white spot syndrome virus of shrimp by bacterially expressed dsRNA.  

PubMed

An in vivo expression system to produce large amounts of virus-derived dsRNAs in bacteria to provide a practical control of white spot syndrome virus (WSSV) in shrimp was developed. The bacterially synthesized dsRNA specific to VP28 gene of WSSV promoted gene-specific interference with the WSSV infection in shrimp. Virus infectivity was significantly reduced in WSSV-challenged shrimp injected with VP28-dsRNA and 100% survival was recorded. The inhibition of the expression of WSSV VP28 gene in experimentally challenged animals by VP28-dsRNA was confirmed by RT-PCR and Western blot analyses. Furthermore, we have demonstrated the efficacy of bacterially expressed VP28-dsRNA to silence VP28 gene expression in SISK cell line transfected with eukaryotic expression vector (pcDNA3.1) inserted with VP28 gene of WSSV. The expression level of VP28 gene in SISK cells was determined by fluorescent microscopy and ELISA. The results showed that the expression was significantly reduced in cells transfected with VP28dsRNA, whereas the cells transected with pcDNA-VP28 alone showed higher expression. The in vivo production of dsRNA using prokaryotic expression system could be an alternative to in vitro method for large-scale production of dsRNA corresponding to VP28 gene of WSSV for practical application to control the WSSV in shrimp farming. PMID:17965920

Sarathi, M; Simon, Martin C; Ahmed, V P Ishaq; Kumar, S Rajesh; Hameed, A S Sahul

2007-10-27

80

A system for the targeted amplification of bacterial gene clusters multiplies antibiotic yield in Streptomyces coelicolor.  

PubMed

Gene clusters found in bacterial species classified as Streptomyces encode the majority of known antibiotics as well as many pharmaceutically active compounds. A site-specific recombination system similar to those that mediate plasmid conjugation was engineered to catalyze tandem amplification of one of these gene clusters in a heterologous Streptomyces species. Three genetic elements were known to be required for DNA amplification in S. kanamyceticus: the oriT-like recombination sites RsA and RsB, and ZouA, a site-specific relaxase similar to TraA proteins that catalyze plasmid transfer. We inserted RsA and RsB sequences into the S. coelicolor genome flanking a cluster of 22 genes (act) responsible for biosynthesis of the polyketide antibiotic actinorhodin. Recombination between RsA and RsB generated zouA-dependent DNA amplification resulting in 4-12 tandem copies of the act gene cluster averaging nine repeats per genome. This resulted in a 20-fold increase in actinorhodin production compared with the parental strain. To determine whether the recombination event required taxon-specific genetic effectors or generalized bacterial recombination (recA), it was also analyzed in the heterologous host Escherichia coli. zouA was expressed under the control of an inducible promoter in wild-type and recA mutant strains. A plasmid was constructed with recombination sites RsA and RsB bordering a drug resistance marker. Induction of zouA expression generated hybrid RsB/RsA sites, evidence of site-specific recombination that occurred independently of recA. ZouA-mediated DNA amplification promises to be a valuable tool for increasing the activities of commercially important biosynthetic, degradative, and photosynthetic pathways in a wide variety of organisms. PMID:21903924

Murakami, Takeshi; Burian, Jan; Yanai, Koji; Bibb, Mervyn J; Thompson, Charles J

2011-09-08

81

A system for the targeted amplification of bacterial gene clusters multiplies antibiotic yield in Streptomyces coelicolor  

PubMed Central

Gene clusters found in bacterial species classified as Streptomyces encode the majority of known antibiotics as well as many pharmaceutically active compounds. A site-specific recombination system similar to those that mediate plasmid conjugation was engineered to catalyze tandem amplification of one of these gene clusters in a heterologous Streptomyces species. Three genetic elements were known to be required for DNA amplification in S. kanamyceticus: the oriT-like recombination sites RsA and RsB, and ZouA, a site-specific relaxase similar to TraA proteins that catalyze plasmid transfer. We inserted RsA and RsB sequences into the S. coelicolor genome flanking a cluster of 22 genes (act) responsible for biosynthesis of the polyketide antibiotic actinorhodin. Recombination between RsA and RsB generated zouA-dependent DNA amplification resulting in 4–12 tandem copies of the act gene cluster averaging nine repeats per genome. This resulted in a 20-fold increase in actinorhodin production compared with the parental strain. To determine whether the recombination event required taxon-specific genetic effectors or generalized bacterial recombination (recA), it was also analyzed in the heterologous host Escherichia coli. zouA was expressed under the control of an inducible promoter in wild-type and recA mutant strains. A plasmid was constructed with recombination sites RsA and RsB bordering a drug resistance marker. Induction of zouA expression generated hybrid RsB/RsA sites, evidence of site-specific recombination that occurred independently of recA. ZouA-mediated DNA amplification promises to be a valuable tool for increasing the activities of commercially important biosynthetic, degradative, and photosynthetic pathways in a wide variety of organisms.

Murakami, Takeshi; Burian, Jan; Yanai, Koji; Bibb, Mervyn J.; Thompson, Charles J.

2011-01-01

82

Expression of exogenously introduced bacterial chloramphenicol acetyltransferase genes in Xenopus laevis embryos before the midblastula transition  

Microsoft Academic Search

Previous papers have reported that DNAs exogenously injected into Xenopus laevis fertilized eggs are expressed only at and after the midblastula transition (MBT). We have injected fertilized eggs of Xenopus laevis with circular plasmids that contained bacterial chloramphenicol acetyltransferase (CAT) genes connected to the promoter of viral genes (pSV2CAT and pAd12.E1aCAT) or the Xenopus cardiac actin gene (actin-CAT fusion gene),

Koichiro Shiokawa; K. Yamana; Yuchang Fu; Yasuo Atsuchi; Keiichi Hosokawa

1990-01-01

83

[Advances in the application research of bacterial ice nucleation active (ina) genes].  

PubMed

For recent years, the research has been focused on the ina gene application in the field of biological ice nucleation. This paper reviewed the application of ina genes in bacterial cell surface display, construction of reporter gene systems, killing insect pests through induced freezing, sensitive detection of pathogenic bacteria contaminating foods, breeding of cold resistant varieties. A brief introduction of the ina gene application in killing insect pests in China was also made in this review. PMID:12385233

Tang, Chao-Rong; Sun, Fu-Zai; Zhao, Ting-Chang

2002-07-01

84

Infection control by antibody disruption of bacterial quorum sensing signaling  

PubMed Central

Summary Quorum sensing (QS) is the process through which bacteria communicate utilizing small diffusible molecules termed autoinducers. It has been demonstrated that QS controls a plethora of microbial processes including the expression of virulence factors. Here, we report an immunopharmacotherapeutic approach for the attenuation of QS in the Gram-positive human pathogen Staphylococcus aureus. An anti-autoinducer monoclonal antibody, AP4-24 H11, was elicited against a rationally-designed hapten, and efficiently inhibited QS in vitro through the sequestration of the autoinducing peptide (AIP)-4 produced by S. aureus RN4850. Importantly, AP4-24H11 suppressed S. aureus pathogenicity in an abscess formation mouse model in vivo and provided complete protection against a lethal S. aureus challenge. These findings provide a strong foundation for further investigations of using immunopharmacotherapy for the treatment of bacterial infections in which QS controls the expression of virulence factors.

Park, Junguk; Jagasia, Reshma; Kaufmann, Gunnar F.; Mathison, John C.; Ruiz, Diana I.; Moss, Jason A.; Meijler, Michael M.; Ulevitch, Richard J.; Janda, Kim D.

2007-01-01

85

Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs  

PubMed Central

Conspectus Riboswitches, which were discovered in the first years of the XXI century, are gene-regulatory mRNA domains that respond to the intracellular concentration of a variety of metabolites and second messengers. They control essential genes in many pathogenic bacteria, and represent a new class of biomolecular target for the development of antibiotics and chemical-biological tools. Five mechanisms of gene regulation are known for riboswitches. Most bacterial riboswitches modulate transcription termination or translation initiation in response to ligand binding. All known examples of eukaryotic riboswitches and some bacterial riboswitches control gene expression by alternative splicing. The glmS riboswitch, widespread in Gram-positive bacteria, is a catalytic RNA activated by ligand binding. Its self-cleavage destabilizes the mRNA of which it is part. Finally, one example of trans-acting riboswitch is known. Three-dimensional (3D) structures have been determined of representatives of thirteen structurally distinct riboswitch classes, providing atomic-level insight into their mechanisms of ligand recognition. While cellular and viral RNAs in general have attracted interest as potential drug targets, riboswitches show special promise due to the diversity and sophistication of small molecule recognition strategies on display in their ligand binding pockets. Moreover, uniquely among known structured RNA domains, riboswitches evolved to recognize small molecule ligands. Structural and biochemical advances in the study of riboswitches provide an impetus for the development of methods for the discovery of novel riboswitch activators and inhibitors. Recent rational drug design efforts focused on select riboswitch classes have yielded a small number of candidate antibiotic compounds, including one active in a mouse model of Staphylococcus aureus infection. The development of high-throughput methods suitable for riboswitch-specific drug discovery is ongoing. A fragment-based screening approach employing equilibrium dialysis that may be generically useful has had early success. Riboswitch-mediated gene regulation is widely employed by bacteria; however, only the thiamine pyrophosphate-responsive riboswitch has thus far been found in eukaryotes. Thus, riboswitches are particularly attractive as targets for antibacterials. Indeed, antimicrobials with previously unknown mechanisms have been found to function by binding riboswitches and leading to aberrant gene expression.

Deigan, Katherine E.; Ferre-D'Amare, Adrian R.

2011-01-01

86

ProTeOn and ProTeOff, new protein devices that inducibly activate bacterial gene expression  

PubMed Central

Using an original workflow, we have modeled, constructed and characterized two new molecular devices that inducibly activate gene expression in Escherichia coli. The devices, prokaryotic-TetOn and prokaryotic-TetOff, were built by fusing an inducible DNA-binding protein domain to a transcription activation domain and constructing a complementary synthetic promoter sequence through which they could control downstream gene expression. In particular, the transactivators were built using variants of the tetracycline repressor, TetR, and the transactivating domain of the LuxR activator. The complementary promoter sequence included TetR’s operator, tetO, and elements of the lux promoter. These specific protein domains and their operator sites were chosen as they have been thoroughly studied and well characterized. First, our methodology began with optimizing the geometry of the molecular components using molecular modeling. We did so to achieve an unprecedented combination of controllable and transactivating function in bacterial organisms. The devices were then built to activate the expression of green fluorescent protein. Their unique function was found to be robustly tight, and activating many-fold increases of expressed gene levels, as measured by flow cytometry experiments. The devices were further characterized with stochastic kinetic models. The new devices presented herein may become useful additions to the molecular toolboxes used by biologists to control bacterial gene expression. The methodology used may also be a foundation for the design, development and characterization of a library of such devices and more complex gene regulatory networks.

Volzing, Katherine; Biliouris, Konstantinos; Kaznessis, Yiannis N.

2012-01-01

87

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

88

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

89

Physical and functional repetition in a bacterial ice nucleation gene  

Microsoft Academic Search

Nucleation of a physical process is distinct from catalysis, and as the function of a protein it is highly unusual. The ability to nucleate ice formation in supercooled water is a property of some members of the bacterial genera Erwinia, Pseudomonas and Xanthomonas1-3. This property is implicated in the ability of bacteria to cause frost injury to plants. Orser et

Robert L. Green; Gareth J. Warren

1985-01-01

90

Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities  

Microsoft Academic Search

The acquisition of new genetic material via horizontal gene transfer allows bacteria to rapidly evolve. One key to estimating the contribution of horizontal gene transfer to bacterial evolution is to quantify the abundance of mobile genetic elements (MGEs) in bacterial communities under varying degrees of selective pressure. We quantified class 1 integrase (intI1) gene abundance in total community DNA extracted

Meredith S Wright; Craig Baker-Austin; Angela H Lindell; Ramunas Stepanauskas; Hatch W Stokes; J Vaun McArthur

2008-01-01

91

[Advances in Detection Technologies of in vivo Expression of Bacterial Virulence Gene.].  

PubMed

The interactions between bacterial pathogens and their hosts is complex. To further our understanding ofathe pathogenesisaof bacterial pathogens, it is necessary to identify bacterial virulence genes that are specifically induced in vivo during infection and probe their regulation in vivo. Toward this end, several technologies, such as in vivo expression technology (IVET), signature-tagged mutagenesis (STM), differential fluorescence induction (DFI), genomic analysis and mapping by in vitro transposition (GAMBIT) and in vivo induced antigen technology (IVIAT), have been developed. The purpose of this reviewais to update the reader on the many advances of these technologies, and to discuss their advantages and disadvantages. PMID:15985422

Chen, Shi-Yong; Mo, Zhao-Lan; Zhang, Zhen-Dong; Zou, Yu-Xia; Xu, Yong-Li; Zhang, Pei-Jun

2005-05-01

92

Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes.  

PubMed

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. PMID:19461975

Arakawa, Kazuharu; Tomita, Masaru

2007-10-09

93

Computational Bacterial Genome-Wide Analysis of Phylogenetic Profiles Reveals Potential Virulence Genes of Streptococcus agalactiae  

PubMed Central

The phylogenetic profile of a gene is a reflection of its evolutionary history and can be defined as the differential presence or absence of a gene in a set of reference genomes. It has been employed to facilitate the prediction of gene functions. However, the hypothesis that the application of this concept can also facilitate the discovery of bacterial virulence factors has not been fully examined. In this paper, we test this hypothesis and report a computational pipeline designed to identify previously unknown bacterial virulence genes using group B streptococcus (GBS) as an example. Phylogenetic profiles of all GBS genes across 467 bacterial reference genomes were determined by candidate-against-all BLAST searches,which were then used to identify candidate virulence genes by machine learning models. Evaluation experiments with known GBS virulence genes suggested good functional and model consistency in cross-validation analyses (areas under ROC curve, 0.80 and 0.98 respectively). Inspection of the top-10 genes in each of the 15 virulence functional groups revealed at least 15 (of 119) homologous genes implicated in virulence in other human pathogens but previously unrecognized as potential virulence genes in GBS. Among these highly-ranked genes, many encode hypothetical proteins with possible roles in GBS virulence. Thus, our approach has led to the identification of a set of genes potentially affecting the virulence potential of GBS, which are potential candidates for further in vitro and in vivo investigations. This computational pipeline can also be extended to in silico analysis of virulence determinants of other bacterial pathogens.

Lin, Frank Po-Yen; Lan, Ruiting; Sintchenko, Vitali; Gilbert, Gwendolyn L.; Kong, Fanrong; Coiera, Enrico

2011-01-01

94

Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions  

Microsoft Academic Search

Riboswitches are structured RNAs typically located in the 5' untranslated regions of bacterial mRNAs that bind metabolites and control gene expression. Most riboswitches sense one metabolite and function as simple genetic switches. However, we found that the 5' region of the Bacillus clausii metE messenger RNA includes two riboswitches that respond to S-adenosylmethionine and coenzyme B12. This tandem arrangement yields

Narasimhan Sudarsan; Ming C. Hammond; Kirsten F. Block; Rüdiger Welz; Jeffrey E. Barrick; Adam Roth; Ronald R. Breaker

2006-01-01

95

Comparative study of differential gene expression in closely related bacterial species by comparative hybridization.  

PubMed

The ability to profile bacterial gene expression has markedly advanced the capacity to understand the molecular mechanisms of pathogenesis, epidemiology, and therapeutics. This advance has been coupled with the development of techniques that enable investigators to identify bacterial specifically expressed genes and promise to open new avenues of functional genomics by allowing researchers to focus on the identified differentially expressed genes. During the past two decades, a number of approaches have been developed to investigate bacterial genes differentially expressed in response to the changing environment, particularly during interaction with their hosts. The most commonly used techniques include in vivo expression technology, signature-tagged mutagenesis, differential fluorescence induction, and cDNA microarrays, which fall into two broad classes: mutagenesis-based technologies and hybridization-based technologies. Selective capture of transcribed sequences, a recently emerging method, is a hybridization-based technique. This technique is powerful in analyzing differential gene expression of the bacteria, with the superb ability to investigate the bacterial species with unknown genomic information. Herein, we describe the application of this technique in a comparative study of the gene expression between two closely related bacteria induced or repressed under a variety of conditions. PMID:22130987

An, Ruisheng; Grewal, Parwinder S

2012-01-01

96

Bacterial gene amplification: implications for the evolution of antibiotic resistance  

Microsoft Academic Search

Recent data suggest that, in response to the presence of antibiotics, gene duplication and amplification (GDA) constitutes an important adaptive mechanism in bacteria. For example, resistance to sulphonamide, trimethoprim and ?-lactams can be conferred by increased gene dosage through GDA of antibiotic hydrolytic enzymes, target enzymes or efflux pumps. Furthermore, most types of antibiotic resistance mechanism are deleterious in the

Linus Sandegren; Dan I. Andersson

2009-01-01

97

Bacterial Community Succession During in situ Uranium Bioremediation: Spatial Similarities Along Controlled Flow Paths  

SciTech Connect

Bacterial community succession was investigated in a field-scale subsurface reactor formed by a series of wells that received weekly ethanol additions to re-circulating groundwater. Ethanol additions stimulated denitrification, metal reduction, sulfate reduction, and U(VI) reduction to sparingly soluble U(IV). Clone libraries of SSU rRNA gene sequences from groundwater samples enabled tracking of spatial and temporal changes over a 1.5 y period. Analyses showed that the communities changed in a manner consistent with geochemical variations that occurred along temporal and spatial scales. Canonical correspondence analysis revealed that the levels of nitrate, uranium, sulfide, sulfate, and ethanol strongly correlated with particular bacterial populations. As sulfate and U(VI) levels declined, sequences representative of sulfate-reducers and metal-reducers were detected at high levels. Ultimately, sequences associated with sulfate-reducing populations predominated, and sulfate levels declined as U(VI) remained at low levels. When engineering controls were compared to the population variation via canonical ordination, changes could be related to dissolved oxygen control and ethanol addition. The data also indicated that the indigenous populations responded differently to stimulation for bio-reduction; however, the two bio-stimulated communities became more similar after different transitions in an idiosyncratic manner. The strong associations between particular environmental variables and certain populations provide insight into the establishment of practical and successful remediation strategies in radionuclide-contaminated environments with respect to engineering controls and microbial ecology.

Hwang, Chiachi; Wu, Weimin; Gentry, Terry J.; Carley, Jack; Corbin, Gail A.; Carroll, Sue L.; Watson, David B.; Jardine, Phil M.; Zhou, Jizhong; Criddle, Craig S.; Fields, Matthew W.

2009-05-22

98

The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces  

PubMed Central

The majority of bacterial genes are located on the leading strand, and the percentage of such genes has a large variation across different bacteria. Although some explanations have been proposed, these are at most partial explanations as they cover only small percentages of the genes and do not even consider the ones biased toward the lagging strand. We have carried out a computational study on 725 bacterial genomes, aiming to elucidate other factors that may have influenced the strand location of genes in a bacterium. Our analyses suggest that (i) genes of some functional categories such as ribosome have higher preferences to be on the leading strands; (ii) genes of some functional categories such as transcription factor have higher preferences on the lagging strands; (iii) there is a balancing force that tends to keep genes from all moving to the leading and more efficient strand and (iv) the percentage of leading-strand genes in an bacterium can be accurately explained based on the numbers of genes in the functional categories outlined in (i) and (ii), genome size and gene density, indicating that these numbers implicitly contain the information about the percentage of genes on the leading versus lagging strand in a genome.

Mao, Xizeng; Zhang, Han; Yin, Yanbin; Xu, Ying

2012-01-01

99

Optimal control and analysis of two-color genomotyping experiments using bacterial multistrain arrays  

PubMed Central

Background Microarray comparative genomic hybridization (aCGH) evaluates the distribution of genes of sequenced bacterial strains among unsequenced strains of the same or related species. As genomic sequences from multiple strains of the same species become available, multistrain microarrays are designed, containing spots for every unique gene in all sequenced strains. To perform two-color aCGH experiments with multistrain microarrays, the choice of control sample can be the genomic DNA of one strain or a mixture of all the strains used in the array design. This important problem has no universally accepted solution. Results We performed a comparative study of the two control sample options with a Streptococcus pneumoniae microarray designed with three fully sequenced strains. We separately hybridized two of these strains (R6 and G54) as test samples using the third strain alone (TIGR4) or a mixture of the three strains as control. We show that for both types of control it is advantageous to analyze spots in separate sets according to their expected control channel signal (5–15% AUC increase). Following this analysis, the use of a mix control leads to higher accuracies (5% increase). This enhanced performance is due to gains in sensitivity (21% increase, p = 0.001) that compensate minor losses in specificity (5% decrease, p = 0.014). Conclusion The use of a single strain control increases the error rate in genes that are part of the accessory genome, where more variation across unsequenced strains is expected, further justifying the use of the mix control.

Pinto, Francisco R; Aguiar, Sandra I; Melo-Cristino, J; Ramirez, Mario

2008-01-01

100

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

2012-02-07

101

Geptop: A Gene Essentiality Prediction Tool for Sequenced Bacterial Genomes Based on Orthology and Phylogeny  

PubMed Central

Integrative genomics predictors, which score highly in predicting bacterial essential genes, would be unfeasible in most species because the data sources are limited. We developed a universal approach and tool designated Geptop, based on orthology and phylogeny, to offer gene essentiality annotations. In a series of tests, our Geptop method yielded higher area under curve (AUC) scores in the receiver operating curves than the integrative approaches. In the ten-fold cross-validations among randomly upset samples, Geptop yielded an AUC of 0.918, and in the cross-organism predictions for 19 organisms Geptop yielded AUC scores between 0.569 and 0.959. A test applied to the very recently determined essential gene dataset from the Porphyromonas gingivalis, which belongs to a phylum different with all of the above 19 bacterial genomes, gave an AUC of 0.77. Therefore, Geptop can be applied to any bacterial species whose genome has been sequenced. Compared with the essential genes uniquely identified by the lethal screening, the essential genes predicted only by Gepop are associated with more protein-protein interactions, especially in the three bacteria with lower AUC scores (<0.7). This may further illustrate the reliability and feasibility of our method in some sense. The web server and standalone version of Geptop are available at http://cefg.uestc.edu.cn/geptop/ free of charge. The tool has been run on 968 bacterial genomes and the results are accessible at the website.

Wei, Wen; Ning, Lu-Wen; Ye, Yuan-Nong; Guo, Feng-Biao

2013-01-01

102

Bacterial IMPDH gene used for the selection of mammalian cell transfectants.  

SciTech Connect

Stable cell transfection is used for the expression of exogenous genes or cDNAs in eukaryotic cells. Selection of these transfectants requires a dominant selectable marker. A variety of such markers has been identified and is currently in use. However, many of these are not suitable for all cell types or require unique conditions. Here we describe a simple and versatile dominant selectable marker that involves bacterial IMP dehydrogenase (IMPDH), an enzyme essential for the replication of mammalian and bacterial cells. Although IMPDH is evolutionarily conserved, the bacterial enzyme is orders of magnitude more resistant to the toxic effect of the drug mycophenolic acid, which is an IMPDH inhibitor. We have demonstrated that transfection of human, monkey or Chinese hamster cell lines with an expression vector containing bacterial IMPDH and mycophenolic acid treatment resulted in the selection of colonies with a strikingly increased resistance to mycophenolic acid toxicity. Analysis of cells derived from these colonies indicated that the acquisition of this resistance was associated with bacterial IMPDH protein expression. As a proof of principle, we showed that mammalian cell transfection with a hicistronic IMPDH/GFP expression vector and mycophenolic acid treatment can he used to successfully select transfectants that express the fluorescent protein. These results indicate that bacterial IMPDH is a practical dominant selectable marker that can be used for the selection of transfectants that express exogenous genes or cDNAs in mammalian cells.

Baccam, M.; Huberman, E.; Energy Systems

2003-06-01

103

[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

104

Genes but Not Genomes Reveal Bacterial Domestication of Lactococcus Lactis  

Microsoft Academic Search

BackgroundThe 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

Delphine Passerini; Charlotte Beltramo; Michele Coddeville; Yves Quentin; Paul Ritzenthaler; Marie-Line Daveran-Mingot; Pascal Le Bourgeois

2010-01-01

105

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

106

Profiling of biodegradation and bacterial 16S rRNA genes in diverse contaminated ecosystems using 60-mer oligonucleotide microarray  

Microsoft Academic Search

We have developed an oligonucleotide microarray for the detection of biodegradative genes and bacterial diversity and tested\\u000a it in five contaminated ecosystems. The array has 60-mer oligonucleotide probes comprising 14,327 unique probes derived from\\u000a 1,057 biodegradative genes and 880 probes representing 110 phylogenetic genes from diverse bacterial communities, and we named\\u000a it as BiodegPhyloChip. The biodegradative genes are involved in

Ashutosh Pathak; Rishi Shanker; Satyendra Kumar Garg; Natesan Manickam

2011-01-01

107

Bacterial diversity of the Inner Mongolian Baer Soda Lake as revealed by 16S rRNA gene sequence analyses  

Microsoft Academic Search

Bacterial diversity associated with Baer Soda Lake in Inner Mongolia of China was investigated using a culture-independent method. Bacterial 16S rRNA gene libraries were generated using bacterial oligonucleotide primers, and 16S rRNA gene sequences of 58 clones were analyzed phylogenetically. The library was dominated by 16S rDNAs of Gram-negative bacteria (24% a-Proteobacteria, 31% ß-Proteobacteria, 33% ?-Proteobacteria, and 2% d-Proteobacteria), with

Yanhe Ma; Weizhou Zhang; Yanfen Xue; Peijin Zhou; Antonio Ventosa; William D. Grant

2004-01-01

108

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

109

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

2011-09-12

110

A functional gene array for detection of bacterial virulence elements  

SciTech Connect

We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.

Jaing, C

2007-11-01

111

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

Microsoft Academic Search

BackgroundThe 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

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

2010-01-01

112

Bacterial ?-galactosidase and human dystrophin genes are expressed in mouse skeletal muscle fibers after ballistic transfection  

Microsoft Academic Search

Ballistic transfection, based on cell and tissue bombardment by the tungsten and gold microparticles covered with the gene DNA, was used for the delivery of a bacterial ?-galactosidase and a full-length cDNA copy of the human dystrophin genes into mouse skeletal muscles. CMV-lacZ, SV40-lacZ, LTR-lacZneo and full-length cDNA dystrophin (pDMD-1, approximately 16 kb) in eukaryotic expression vector pJ OMEGA driven

Alexander V. Zelenin; Victor A. Kolesnikov; Olga A. Tarasenko; Ramin A. Shafei; Inessa A. Zelenina; Vyacheslav V. Mikhailov; Maria L. Semenova; Dmitry V. Kovalenko; Olga V. Artemyeva; Tatyana E. Ivaschenko; Oleg V. Evgrafov; George Dickson; Vladislav S. Baranovand

1997-01-01

113

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs  

PubMed Central

Motivation: Probabilistic logic programming offers a powerful way to describe and evaluate structured statistical models. To investigate the practicality of probabilistic logic programming for structure learning in bioinformatics, we undertook a simplified bacterial gene-finding benchmark in PRISM, a probabilistic dialect of Prolog. Results: We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length modeling and three-state versions of the five model structures. The models are all represented as probabilistic logic programs and evaluated using the PRISM machine learning system in terms of statistical information criteria and gene-finding prediction accuracy, in two bacterial genomes. Neither of our implementations of the two currently most used model structures are best performing in terms of statistical information criteria or prediction performances, suggesting that better-fitting models might be achievable. Availability: The source code of all PRISM models, data and additional scripts are freely available for download at: http://github.com/somork/codonhmm. Contact: soer@ruc.dk Supplementary information: Supplementary data are available at Bioinformatics online.

M?rk, S?ren; Holmes, Ian

2012-01-01

114

Structure-based gene targeting discovery of sphaerimicin, a bacterial translocase?i inhibitor.  

PubMed

Rise and shine: Using a gene-targeting approach aimed at identifying potential L-threonine:uridine-5'-transaldolases that catalyze the formation of (5'S,6'S)-C-glycyluridine, a new bacterial translocase?I inhibitor was discovered from an actinomycete following fermentation optimization. PMID:24014169

Funabashi, Masanori; Baba, Satoshi; Takatsu, Toshio; Kizuka, Masaaki; Ohata, Yasuo; Tanaka, Masahiro; Nonaka, Koichi; Spork, Anatol P; Ducho, Christian; Chen, Wei-Chen Leyla; Van Lanen, Steven G

2013-09-06

115

Host response to respiratory bacterial pathogens as identified by integrated analysis of human gene expression data.  

PubMed

Respiratory bacterial pathogens are one of the leading causes of infectious death in the world and a major health concern complicated by the rise of multi-antibiotic resistant strains. Therapeutics that modulate host genes essential for pathogen infectivity could potentially avoid multi-drug resistance and provide a wider scope of treatment options. Here, we perform an integrative analysis of published human gene expression data generated under challenges from the gram-negative and Gram-positive bacteria pathogens, Pseudomonas aeruginosa and Streptococcus pneumoniae, respectively. We applied a previously described differential gene and pathway enrichment analysis pipeline to publicly available host mRNA GEO datasets resulting from exposure to bacterial infection. We found 72 canonical human pathways common between four GEO datasets, representing P. aeruginosa and S. pneumoniae. Although the majority of these pathways are known to be involved with immune response, we found several interesting new interactions such as the SUMO1 pathway that might have a role in bacterial infections. Furthermore, 36 host-bacterial pathways were also shared with our previous results for respiratory virus host gene expression. Based on our pathway analysis we propose several drug-repurposing opportunities supported by the literature. PMID:24086587

Smith, Steven B; Magid-Slav, Michal; Brown, James R

2013-09-27

116

FUNCTIONAL EXPRESSION OF BACTERIAL ZYMOBACTER PALMAE PYRUVATE DECARBOXYLASE GENE IN LACTIC ACID BACTERIA  

Technology Transfer Automated Retrieval System (TEKTRAN)

In this study, a pyruvate decarboxylase (PDC) gene from bacterial Zymobacter palmae (Zymopdc) was cloned, characterized, and introduced into lactic acid bacteria (LAB) via a shuttle vector pAK80 as part of a research strategy to develop an efficient ethanol producing LAB. Six constructs containing ...

117

Identification and expression profiles of multiple genes in Nile tilapia in response to bacterial infections  

Technology Transfer Automated Retrieval System (TEKTRAN)

To understand the molecular mechanisms involved in response of Nile tilapia (Oreochromis niloticus) to bacterial infection, suppression subtractive cDNA hybridization technique was used to identify upregulated genes in the posterior kidney of Nile tilapia at 6h post infection with Aeromonas hydrophi...

118

Host Response to Respiratory Bacterial Pathogens as Identified by Integrated Analysis of Human Gene Expression Data  

PubMed Central

Respiratory bacterial pathogens are one of the leading causes of infectious death in the world and a major health concern complicated by the rise of multi-antibiotic resistant strains. Therapeutics that modulate host genes essential for pathogen infectivity could potentially avoid multi-drug resistance and provide a wider scope of treatment options. Here, we perform an integrative analysis of published human gene expression data generated under challenges from the gram-negative and Gram-positive bacteria pathogens, Pseudomonas aeruginosa and Streptococcus pneumoniae, respectively. We applied a previously described differential gene and pathway enrichment analysis pipeline to publicly available host mRNA GEO datasets resulting from exposure to bacterial infection. We found 72 canonical human pathways common between four GEO datasets, representing P. aeruginosa and S. pneumoniae. Although the majority of these pathways are known to be involved with immune response, we found several interesting new interactions such as the SUMO1 pathway that might have a role in bacterial infections. Furthermore, 36 host-bacterial pathways were also shared with our previous results for respiratory virus host gene expression. Based on our pathway analysis we propose several drug-repurposing opportunities supported by the literature.

Smith, Steven B.; Magid-Slav, Michal; Brown, James R.

2013-01-01

119

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 Central

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.

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

2012-01-01

120

Feedback Control Architecture and the Bacterial Chemotaxis Network  

PubMed Central

Bacteria move towards favourable and away from toxic environments by changing their swimming pattern. This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to ‘reset’ (adapt) the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. The role of this feedback has been studied extensively in the simple chemotaxis pathway of Escherichia coli. However it has been recently found that the majority of bacteria have multiple chemotaxis homologues of the E. coli proteins, resulting in more complex pathways. In this paper we investigate the configuration and role of feedback in Rhodobacter sphaeroides, a bacterium containing multiple homologues of the chemotaxis proteins found in E. coli. Multiple proteins could produce different possible feedback configurations, each having different chemotactic performance qualities and levels of robustness to variations and uncertainties in biological parameters and to intracellular noise. We develop four models corresponding to different feedback configurations. Using a series of carefully designed experiments we discriminate between these models and invalidate three of them. When these models are examined in terms of robustness to noise and parametric uncertainties, we find that the non-invalidated model is superior to the others. Moreover, it has a ‘cascade control’ feedback architecture which is used extensively in engineering to improve system performance, including robustness. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in achieving robust functionality in more complex signalling pathways and in improving their performance.

Hamadeh, Abdullah; Roberts, Mark A. J.; August, Elias; McSharry, Patrick E.; Maini, Philip K.; Armitage, Judith P.; Papachristodoulou, Antonis

2011-01-01

121

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

122

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

PubMed

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. PMID:20921390

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

2010-10-04

123

Identification and analysis of bacterial virulence genes in vivo.  

PubMed Central

Signature-tagged mutagenesis is a mutation-based screening method for the identification of virulence genes of microbial pathogens. Genes isolated by this approach fall into three classes: those with known biochemical function, those of suspected function and some whose functions cannot be predicted from database searches. A variety of in vitro and in vivo methods are available to elucidate the function of genes of the second and third classes. We describe the use of some of these approaches to study the function of the Salmonella pathogenicity island 2 type III secretion system of Salmonella typhimurium. This virulence determinant is required for intracellular survival. Secretion by this system is induced by an acidic pH, and its function may be to alter trafficking of the Salmonella-containing vacuole. Use of a temperature-sensitive non-replicating plasmid and competitive index tests with other genes show that in vivo phenotypes do not always correspond to those predicted from in vitro studies.

Unsworth, K E; Holden, D W

2000-01-01

124

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

125

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

PubMed Central

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 of a wide variety of mercury-resistant bacteria previously shown to possess the mercuric reductase enzyme. All of the tested gram-negative bacteria had DNA sequences homologous to the mer probe, whereas no such homologies were detected in DNA of the gram-positive strains. Thus, the mer probe can be utilized to study gene flow processes in gram-negative bacterial communities. Images

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

1985-01-01

126

Archaeal amoA Genes Outnumber Bacterial amoA Genes in Municipal Wastewater Treatment Plants in Bangkok  

Microsoft Academic Search

The contribution of ammonia-oxidizing archaea (AOA) to nitrogen removal in wastewater treatment plants (WWTPs) remains unknown.\\u000a This study investigated the abundance of archaeal (AOA) and bacterial (ammonia-oxidizing bacteria (AOB)) amoA genes in eight of Bangkok’s municipal WWTPs. AOA amoA genes (3.28?×?107?±?1.74?×?107–2.23?×?1011?±?1.92?×?1011 copies l?1 sludge) outnumbered AOB amoA genes in most of the WWTPs even though the plants’ treatment processes, influent and

Pantip Kayee; Puntipar Sonthiphand; Chaiwat Rongsayamanont; Tawan Limpiyakorn

127

Bacterial Transcription Terminators: The RNA 3?End Chronicles  

Microsoft Academic Search

The process of transcription termination is essential to proper expression of bacterial genes and, in many cases, to the regulation of bacterial gene expression. Two types of bacterial transcriptional terminators are known to control gene expression. Intrinsic terminators dissociate transcription complexes without the assistance of auxiliary factors. Rho-dependent terminators are sites of dissociation mediated by an RNA helicase called Rho.

Jason M. Peters; Abbey D. Vangeloff; Robert Landick

2011-01-01

128

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

129

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

130

Inoculum pretreatment affects bacterial survival, activity and catabolic gene expression during phytoremediation of diesel contaminated soil.  

PubMed

Plant-bacteria partnership is a promising approach for remediating soil contaminated with organic pollutants. The colonization and metabolic activity of an inoculated microorganism depend not only on environmental conditions but also on the physiological condition of the applied microorganisms. This study assessed the influence of different inoculum pretreatments on survival, gene abundance and catabolic gene expression of an applied strain (Pantoea sp. strain BTRH79) in the rhizosphere of ryegrass vegetated in diesel contaminated soil. Maximum bacterium survival, gene abundance and expression were observed in the soil inoculated with bacterial cells that had been pregrown on complex medium, and hydrocarbon degradation and genotoxicity reduction were also high in this soil. These findings propose that use of complex media for growing plant inocula may enhance bacterial survival and colonization and subsequently the efficiency of pollutant degradation. PMID:23399305

Khan, Sumia; Afzal, Muhammad; Iqbal, Samina; Mirza, Muhammad Sajjad; Khan, Qaiser M

2013-02-08

131

Control of the bacterial flora of Brachionus plicatilis and Artemia franciscana by incubation in bacterial suspensions  

Microsoft Academic Search

The accumulation of bacteria in Brachionus plicatilis and Artemia franciscana during a short-term incubation was quantified using immunocolony blot (ICB) and an enzyme-linked immunosorbent assay (ELISA). Four bacterial strains, isolated from turbot and halibut, were grazed effectively by both species when given at high concentrations (?5×107 bacteria ml?1). B. plicatilis accumulated 21–63×103 bacteria per rotifer and A. franciscana up to

Pavlos Makridis; Anders Jon Fjellheim; Jorunn Skjermo; Olav Vadstein

2000-01-01

132

Analysis of Bacterial Communities Associated with Insect Biological Control Agents using Molecular Techniques  

Microsoft Academic Search

Investigations of the diversity of bacterial communities associated with field- collected specimens of two insect biological control agents of spotted knapweed, Agapeta zoegana and Cyphocleonus achates, were made using molecular methods. The objective was to assess the bacterial communities of each insect to evaluate the potential compati- bility of plant pathogenic fungi as a supplement to insect diets for mass

B. A. FREDERICK; A. J. CAESAR

133

The Rhizobium meliloti PII protein, which controls bacterial nitrogen metabolism, affects alfalfa nodule development.  

PubMed

Symbiotic nitrogen fixation involves the development of specialized organs called nodules within which plant photosynthates are exchanged for combined nitrogen of bacterial origin. To determine the importance of bacterial nitrogen metabolism in symbiosis, we have characterized a key regulator of this metabolism in Rhizobium meliloti, the uridylylatable P(II) protein encoded by glnB. We have constructed both a glnB null mutant and a point mutant making nonuridylylatable P(II). In free-living conditions, P(II) is required for expression of the ntrC-dependent gene glnII and for adenylylation of glutamine synthetase I. P(II) is also required for efficient infection of alfalfa but not for expression of nitrogenase. However alfalfa plants inoculated with either glnB mutant are nitrogen-starved in the absence of added combined nitrogen. We hypothesize that P(II) controls expression or activity of a bacteroid ammonium transporter required for a functional nitrogen-fixing symbiosis. Therefore, the P(II) protein affects both Rhizobium nitrogen metabolism and alfalfa nodule development. PMID:9159400

Arcondéguy, T; Huez, I; Tillard, P; Gangneux, C; de Billy, F; Gojon, A; Truchet, G; Kahn, D

1997-05-01

134

Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution  

PubMed Central

We describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. The approach used is based on comparing the evolutionary distances within a set of orthologs to a standard intergenomic distance, which was defined as the median of the distribution of the distances between all one-to-one orthologs. Under the clock-like model, the points on a plot of intergenic distances versus intergenomic distances are expected to fit a straight line. A statistical technique to identify significant deviations from the clock-like behavior is described. For several hundred analyzed orthologous sets representing three well-defined bacterial lineages, the ?-Proteobacteria, the ?-Proteobacteria, and the Bacillus-Clostridium group, the clock-like null hypothesis could not be rejected for ?70% of the sets, whereas the rest showed substantial anomalies. Subsequent detailed phylogenetic analysis of the genes with the strongest deviations indicated that over one-half of these genes probably underwent a distinct form of horizontal gene transfer, xenologous gene displacement, in which a gene is displaced by an ortholog from a different lineage. The remaining deviations from the clock-like model could be explained by lineage-specific acceleration of evolution. The results indicate that although xenologous gene displacement is a major force in bacterial evolution, a significant majority of orthologous gene sets in three major bacterial lineages evolved in accordance with the clock-like model. The approach described here allows rapid detection of deviations from this mode of evolution on the genome scale.

Novichkov, Pavel S.; Omelchenko, Marina V.; Gelfand, Mikhail S.; Mironov, Andrei A.; Wolf, Yuri I.; Koonin, Eugene V.

2004-01-01

135

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

PubMed Central

Background Estimating 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 Findings We presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged. Conclusion By combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future. The list of genomes used in this paper can be found in the supplementary table.

Yang, Xing; Xie, Lu; Li, Yixue; Wei, Chaochun

2009-01-01

136

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

137

The inflammatory bowel disease (IBD) susceptibility genes NOD1 and NOD2 have conserved anti-bacterial roles in zebrafish.  

PubMed

Inflammatory bowel disease (IBD), in the form of Crohn's disease (CD) or ulcerative colitis (UC), is a debilitating chronic immune disorder of the intestine. A complex etiology resulting from dysfunctional interactions between the intestinal immune system and its microflora, influenced by host genetic susceptibility, makes disease modeling challenging. Mutations in NOD2 have the highest disease-specific risk association for CD, and a related gene, NOD1, is associated with UC. NOD1 and NOD2 encode intracellular bacterial sensor proteins acting as innate immune triggers, and represent promising therapeutic targets. The zebrafish has the potential to aid in modeling genetic and environmental aspects of IBD pathogenesis. Here, we report the characterization of the Nod signaling components in the zebrafish larval intestine. The nod1 and nod2 genes are expressed in intestinal epithelial cells and neutrophils together with the Nod signaling pathway genes ripk2, a20, aamp, cd147, centaurin b1, erbin and grim-19. Using a zebrafish embryo Salmonella infection model, morpholino-mediated depletion of Nod1 or Nod2 reduced the ability of embryos to control systemic infection. Depletion of Nod1 or Nod2 decreased expression of dual oxidase in the intestinal epithelium and impaired the ability of larvae to reduce intracellular bacterial burden. This work highlights the potential use of zebrafish larvae in the study of components of IBD pathogenesis. PMID:21729873

Oehlers, Stefan H; Flores, Maria Vega; Hall, Chris J; Swift, Simon; Crosier, Kathryn E; Crosier, Philip S

2011-07-04

138

A bacterial antibiotic-resistance gene that complements the human multidrug-resistance P-glycoprotein gene  

Microsoft Academic Search

Bacteria have developed many fascinating antibiotic-resistance mechanisms,. A protein in Lactococcus lactis, LmrA, mediates antibiotic resistance by extruding amphiphilic compounds from the inner leaflet of the cytoplasmic membrane,. Unlike other known bacterial multidrug-resistance proteins, LmrA is an ATP-binding cassette (ABC) transporter. The human multidrug-resistance P-glycoprotein, encoded by the MDR1 gene, is also an ABC transporter, overexpression of which is one

Hendrik W. van Veen; Richard Callaghan; Loredana Soceneantu; Alessandro Sardini; Wil N. Konings; Christopher F. Higgins

1998-01-01

139

Unexpected effect of a Bacteroides conjugative transposon, CTnDOT, on chromosomal gene expression in its bacterial host  

PubMed Central

Foreign DNA elements such as plasmids and conjugative transposons are constantly entering new bacterial hosts. A possible outcome of such events that has not been considered previously is that regulatory genes carried on some of them might affect the expression of chromosomal genes of the new host. To assess this possibility, we investigated the effect of the Bacteroides conjugative transposon CTnDOT on expression of chromosomal genes in Bacteroides thetaiotaomicron 5482 (BT4001). Most of the upregulated genes were genes of unknown function, but a number of them were associated with a region of the chromosome that contained a putative conjugative transposon, which had been tentatively designated as CTn4-bt. Upregulation of CTn4-bt genes and other chromosomal genes affected by CTnDOT was controlled by two regulatory genes on CTnDOT, rteA and rteB, which encode a two-component regulatory system. Transfer of CTn4-bt was also mediated by rteA and rteB. Three other putative CTns, CTn1-bt, CTn2-bt and CTn3-bt, were mobilized by CTnERL, a CTn closely related to CTnDOT, but genes from CTnERL other than rteA and rteB were also required. Unexpectedly, homologous recombination was required for CTn1-bt, CTn2-bt, CTn3-bt and CTn4-bt to integrate in the recipient. Our results show that regulatory genes on an incoming mobile element can have multiple effects on its new host, including the activation of previously non-transmissible elements.

Moon, Kyung; Sonnenburg, Justin; Salyers, Abigail A

2007-01-01

140

Identification of self-consistent modulons from bacterial microarray expression data with the help of structured regulon gene sets.  

PubMed

Identification of bacterial modulons from series of gene expression measurements on microarrays is a principal problem, especially relevant for inadequately studied but practically important species. Usage of a priori information on regulatory interactions helps to evaluate parameters for regulatory subnetwork inference. We suggest a procedure for modulon construction where a seed regulon is iteratively updated with genes having expression patterns similar to those for regulon member genes. A set of genes essential for a regulon is used to control modulon updating. Essential genes for a regulon were selected as a subset of regulon genes highly related by different measures to each other. Using Escherichia coli as a model, we studied how modulon identification depends on the data, including the microarray experiments set, the adopted relevance measure and the regulon itself. We have found that results of modulon identification are highly dependent on all parameters studied and thus the resulting modulon varies substantially depending on the identification procedure. Yet, modulons that were identified correctly displayed higher stability during iterations, which allows developing a procedure for reliable modulon identification in the case of less studied species where the known regulatory interactions are sparse. PMID:22803819

Permina, Elizaveta A; Medvedeva, Yulia A; Baeck, Pia M; Hegde, Shubhada R; Mande, Shekhar C; Makeev, Vsevolod J

2012-07-18

141

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

2013-08-22

142

Dynamics of Immune System Gene Expression upon Bacterial Challenge and Wounding in a Social Insect (Bombus terrestris)  

PubMed Central

The innate immune system which helps individuals to combat pathogens comprises a set of genes representing four immune system pathways (Toll, Imd, JNK and JAK/STAT). There is a lack of immune genes in social insects (e.g. honeybees) when compared to Diptera. Potentially, this might be compensated by an advanced system of social immunity (synergistic action of several individuals). The bumble bee, Bombus terrestris, is a primitively eusocial species with an annual life cycle and colonies headed by a single queen. We used this key pollinator to study the temporal dynamics of immune system gene expression in response to wounding and bacterial challenge. Antimicrobial peptides (AMP) (abaecin, defensin 1, hymenoptaecin) were strongly up-regulated by wounding and bacterial challenge, the latter showing a higher impact on the gene expression level. Sterile wounding down-regulated TEP A, an effector gene of the JAK/STAT pathway, and bacterial infection influenced genes of the Imd (relish) and JNK pathway (basket). Relish was up-regulated within the first hour after bacterial challenge, but decreased strongly afterwards. AMP expression following wounding and bacterial challenge correlates with the expression pattern of relish whereas correlated expression with dorsal was absent. Although expression of AMPs was high, continuous bacterial growth was observed throughout the experiment. Here we demonstrate for the first time the temporal dynamics of immune system gene expression in a social insect. Wounding and bacterial challenge affected the innate immune system significantly. Induction of AMP expression due to wounding might comprise a pre-adaptation to accompanying bacterial infections. Compared with solitary species this social insect exhibits reduced immune system efficiency, as bacterial growth could not be inhibited. A negative feedback loop regulating the Imd-pathway is suggested. AMPs, the end product of the Imd-pathway, inhibited the up-regulation of the transcription factor relish, which is necessary for effector gene expression.

Erler, Silvio; Popp, Mario; Lattorff, H. Michael G.

2011-01-01

143

Dynamics of immune system gene expression upon bacterial challenge and wounding in a social insect (Bombus terrestris).  

PubMed

The innate immune system which helps individuals to combat pathogens comprises a set of genes representing four immune system pathways (Toll, Imd, JNK and JAK/STAT). There is a lack of immune genes in social insects (e.g. honeybees) when compared to Diptera. Potentially, this might be compensated by an advanced system of social immunity (synergistic action of several individuals). The bumble bee, Bombus terrestris, is a primitively eusocial species with an annual life cycle and colonies headed by a single queen. We used this key pollinator to study the temporal dynamics of immune system gene expression in response to wounding and bacterial challenge.Antimicrobial peptides (AMP) (abaecin, defensin 1, hymenoptaecin) were strongly up-regulated by wounding and bacterial challenge, the latter showing a higher impact on the gene expression level. Sterile wounding down-regulated TEP A, an effector gene of the JAK/STAT pathway, and bacterial infection influenced genes of the Imd (relish) and JNK pathway (basket). Relish was up-regulated within the first hour after bacterial challenge, but decreased strongly afterwards. AMP expression following wounding and bacterial challenge correlates with the expression pattern of relish whereas correlated expression with dorsal was absent. Although expression of AMPs was high, continuous bacterial growth was observed throughout the experiment.Here we demonstrate for the first time the temporal dynamics of immune system gene expression in a social insect. Wounding and bacterial challenge affected the innate immune system significantly. Induction of AMP expression due to wounding might comprise a pre-adaptation to accompanying bacterial infections. Compared with solitary species this social insect exhibits reduced immune system efficiency, as bacterial growth could not be inhibited. A negative feedback loop regulating the Imd-pathway is suggested. AMPs, the end product of the Imd-pathway, inhibited the up-regulation of the transcription factor relish, which is necessary for effector gene expression. PMID:21479237

Erler, Silvio; Popp, Mario; Lattorff, H Michael G

2011-03-29

144

Transcriptional profiling of immune genes in bovine monocyte-derived macrophages exposed to bacterial antigens  

Microsoft Academic Search

The involvement of Toll-like receptors (TLRs) and other immune signalling genes during challenge of bovine macrophages with bacterial products derived from disease-causing bacteria in cattle was investigated. An in vitro cell culture model of bovine monocyte derived macrophages (MDM) was established and these cells were exposed to purified protein derivative (PPD-b) derived from Mycobacterium bovis and to lipopolysachharide (LPS) derived

Maria Taraktsoglou; Urszula Szalabska; David A. Magee; John A. Browne; Torres Sweeney; Eamonn Gormley; David E. MacHugh

2011-01-01

145

Replication Orientation Affects the Rate and Direction of Bacterial Gene Evolution  

Microsoft Academic Search

.   In many bacterial genomes, the leading and lagging strands have different skews in base composition; for example, an excess\\u000a of guanosine compared to cytosine on the leading strand. We find that Chlamydia genes that have switched their orientation relative to the direction of replication, for example by inversion, acquire the\\u000a skew of their new ``host'' strand. In contrast to

Elisabeth R. M. Tillier; Richard A. Collins

2000-01-01

146

Metabolic changes of Brassica rapa transformed with a bacterial isochorismate synthase gene  

Microsoft Academic Search

Metabolome analysis by 1-dimensional proton nuclear magnetic resonance (1H NMR) coupled with multivariate data analysis was carried out in Brassica rapa plants transformed with a gene encoding bacterial isochorismate synthase (ICS). Partial least square-discrimination analysis (PLS-DA) on selected signals suggested that the resonances that were dominant in the transgenic plants corresponded to a glucosinolate (neoglucobrassicin), phenylpropanoids (sinapoyl malate, feruloyl malate,

Sanimah Simoh; Huub J. M. Linthorst; Alfons W. M. Lefeber; Cornelis Erkelens; Hye Kyong Kim; Young Hae Choi; Robert Verpoorte

2010-01-01

147

Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature  

Microsoft Academic Search

Bacterial tmRNA mediates a trans-translation reaction, which permits the recycling of stalled ribosomes and probably also contributes to the regulated expression of a subset of genes. Its action results in the addition of a small number of C-terminal amino acids to protein whose synthesis had stalled and these constitute a proteolytic recognition tag for the degradation of these incompletely synthesized

Brice Felden; Christian Massire; E ric Westhof; John F. Atkins; Raymond F. Gesteland

2001-01-01

148

A novel system for large-scale gene expression analysis: bacterial colonies array.  

PubMed

In the present work, we report the use of bacterial colonies to optimize macroarray technique. The devised system is significantly cheaper than other methods available to detect large-scale differential gene expression. Recombinant Escherichia coli clones containing plasmid-encoded copies of 4,608 individual expressed sequence tag (ESTs) were robotically spotted onto nylon membranes that were incubated for 6 and 12 h to allow the bacteria to grow and, consequently, amplify the cloned ESTs. The membranes were then hybridized with a beta-lactamase gene specific probe from the recombinant plasmid and, subsequently, phosphorimaged to quantify the microbial cells. Variance analysis demonstrated that the spot hybridization signal intensity was similar for 3,954 ESTs (85.8%) after 6 h of bacterial growth. Membranes spotted with bacteria colonies grown for 12 h had 4,017 ESTs (87.2%) with comparable signal intensity but the signal to noise ratio was fivefold higher. Taken together, the results of this study indicate that it is possible to investigate large-scale gene expression using macroarrays based on bacterial colonies grown for 6 h onto membranes. PMID:16538485

Barsalobres-Cavallari, C; De Rosa Júnior, V; Nogueira, F; Ferro, J; Di Mauro, S; Menossi, M; Ulian, E; Silva-Filho, M

2006-03-15

149

Integrated biological control of bacterial speck and spot of tomato under field conditions using foliar biological control agents and plant growth-promoting rhizobacteria  

Microsoft Academic Search

Integration of foliar bacterial biological control agents and plant growth promoting rhizobacteria (PGPR) was investigated to determine whether biological control of bacterial speck of tomato, caused by Pseudomonas syringae pv. tomato, and bacterial spot of tomato, caused by Xanthomonas campestris pv. vesicatoria and Xanthomonas vesicatoria, could be improved. Three foliar biological control agents and two selected PGPR strains were employed

P. Ji; H. L. Campbell; J. W. Kloepper; J. B. Jones; T. V. Suslow; M. Wilson

2006-01-01

150

Integrated biological control of bacterial speck and spot of tomato under Weld conditions using foliar biological control agents and plant growth-promoting rhizobacteria  

Microsoft Academic Search

Integration of foliar bacterial biological control agents and plant growth promoting rhizobacteria (PGPR) was investigated to deter- mine whether biological control of bacterial speck of tomato, caused by Pseudomonas syringae pv. tomato, and bacterial spot of tomato, caused by Xanthomonas campestris pv. vesicatoria and Xanthomonas vesicatoria, could be improved. Three foliar biological control agents and two selected PGPR strains were

P. Ji; H. L. Campbell; J. W. Kloepper; J. B. Jones; T. V. Suslow; M. Wilson

2006-01-01

151

Differential Regulation of Horizontally Acquired and Core Genome Genes by the Bacterial Modulator H-NS  

PubMed Central

Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in response to external stimuli such as osmolarity and temperature. Here we provide evidence that H-NS discriminates and differentially modulates core and HGT DNA. As an example of this, plasmid R27-encoded H-NS protein has evolved to selectively silence HGT genes and does not interfere with core genome regulation. In turn, differential regulation of both gene lineages by resident chromosomal H-NS requires a helper protein: the Hha protein. Tight silencing of HGT DNA is accomplished by H-NS-Hha complexes. In contrast, core genes are modulated by H-NS homoligomers. Remarkably, the presence of Hha-like proteins is restricted to the Enterobacteriaceae. In addition, conjugative plasmids encoding H-NS variants have hitherto been isolated only from members of the family. Thus, the H-NS system in enteric bacteria presents unique evolutionary features. The capacity to selectively discriminate between core and HGT DNA may help to maintain horizontally transmitted DNA in silent form and may give these bacteria a competitive advantage in adapting to new environments, including host colonization.

Aznar, Sonia; Garcia, Jesus; Pons, Miquel; Madrid, Cristina; Juarez, Antonio

2009-01-01

152

Growth of transgenic canola ( Brassica napus cv. Westar) expressing a bacterial1-aminocyclopropane-1-carboxylate (ACC) deaminase gene on high concentrations of salt  

Microsoft Academic Search

Summary  Canola, Brassica napus cv. Westar, was transformed to express a bacterial 1-aminocyclopropane-1-carboxylate (ACC) deaminase (EC 4.1.99.4) gene under\\u000a the transcriptional control of (a) the constitutive and strong 35S promoter from cauliflower mosaic virus, (b) the root-specific promoter of the rolD gene within the T-DNA from the Ri plasmid of Agrobacterium rhizogenes, and (c) the promoter for the pathogenesis-related prb-1b gene

Elena Sergeeva; Saleh Shah; Bernard R. Glick

2006-01-01

153

Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch.  

PubMed

Coenzyme B(12) has a key role in various enzymatic reactions and controls expression of bacterial genes through riboswitches. Here we report the crystal structure of the Symbiobacterium thermophilum B(12) riboswitch bound to its ligand adenosylcobalamin. The riboswitch forms a unique junctional structure with a large ligand-binding pocket tailored for specific recognition of the adenosyl moiety and flanked by structural elements that stabilize the regulatory region and enable control of gene expression. PMID:23064646

Peselis, Alla; Serganov, Alexander

2012-10-14

154

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

155

Control of gene expression in bacteriophage T7: Transcriptional controls  

Microsoft Academic Search

Two transcriptional control mechanisms of T7 can be distinguished both affecting the transcription by E. coli RNA polymerase: An early control and an “early-late” control. In wild type infections, both transcriptional control proteins appear at approximately the same time. Mutations in the early control gene have, therefore, little effect on transcription, if tested in the presence of virus RNA polymerase.

H. Ponta; H. J. Rahmsdorf; S. H. Pai; M. Hirsch-Kauffmann; P. Herrlich; M. Schweiger

1974-01-01

156

Feedback control of gene expression  

Microsoft Academic Search

Although feedback regulation of photosynthesis by carbon metabolites has long been recognized and investigated, its underlying molecular mechanisms remain unclear. The recent discovery that glucose and acetate trigger global repression of maize photosynthetic gene transcription provides the first direct evidence that a fundamental mechanism is used for feedback regulation of photosynthesis in higher plants. The metabolic repression of photosynthetic genes

Jen Sheen

1994-01-01

157

Effective, Broad Spectrum Control of Virulent Bacterial Infections Using Cationic DNA Liposome Complexes Combined with Bacterial Antigens  

PubMed Central

Protection against virulent pathogens that cause acute, fatal disease is often hampered by development of microbial resistance to traditional chemotherapeutics. Further, most successful pathogens possess an array of immune evasion strategies to avoid detection and elimination by the host. Development of novel, immunomodulatory prophylaxes that target the host immune system, rather than the invading microbe, could serve as effective alternatives to traditional chemotherapies. Here we describe the development and mechanism of a novel pan-anti-bacterial prophylaxis. Using cationic liposome non-coding DNA complexes (CLDC) mixed with crude F. tularensis membrane protein fractions (MPF), we demonstrate control of virulent F. tularensis infection in vitro and in vivo. CLDC+MPF inhibited bacterial replication in primary human and murine macrophages in vitro. Control of infection in macrophages was mediated by both reactive nitrogen species (RNS) and reactive oxygen species (ROS) in mouse cells, and ROS in human cells. Importantly, mice treated with CLDC+MPF 3 days prior to challenge survived lethal intranasal infection with virulent F. tularensis. Similarly to in vitro observations, in vivo protection was dependent on the presence of RNS and ROS. Lastly, CLDC+MPF was also effective at controlling infections with Yersinia pestis, Burkholderia pseudomallei and Brucella abortus. Thus, CLDC+MPF represents a novel prophylaxis to protect against multiple, highly virulent pathogens.

Ireland, Robin; Olivares-Zavaleta, Norma; Warawa, Jonathan M.; Gherardini, Frank C.; Jarrett, Clayton; Hinnebusch, B. Joseph; Belisle, John T.; Fairman, Jeffery; Bosio, Catharine M.

2010-01-01

158

Epidemiological effect of gene deployment strategies on bacterial blight of rice.  

PubMed

ABSTRACT Experiments were conducted in farmers' fields at two locations of the irrigated lowlands of Laguna province in southern Luzon island, Philippines, during the wet seasons of 1993 and 1994. Nine rice populations were studied including pure stands, two-component mixtures, two-gene combinations of backcrossed lines containing varying combinations of the bacterial blight resistance genes Xa-4, xa-5, and Xa-10, and a non-isogenic cultivar containing Xa-4 and partial resistance to bacterial blight. The area under the disease progress curve (AUDPC) of both gene combinations studied was significantly less than the single most effective gene of each combination deployed singly. A mixture of a susceptible and a resistant line expressed an AUDPC significantly less than the mean of its component pure stands, but two other mixtures did not. The cultivar IR20, which contains both Xa-4 and partial resistance, reduced the AUDPC by about two-thirds as compared with IR-BB4, which contains Xa-4 and little or no partial resistance. PMID:18945155

Ahmed, H U; Finckh, M R; Alfonso, R F; Mundt, C C

1997-01-01

159

Molecular Breeding of Transgenic Rice Plants Expressing a Bacterial Chlorocatechol Dioxygenase Gene  

Microsoft Academic Search

The cbnA gene encoding the chlorocatechol dioxygenase gene from Ralstonia eutropha NH9 was introduced into rice plants. The cbnA gene was expressed in transgenic rice plants under the control of a modified cauliflower mosaic virus 35S promoter. Western blot analysis using anti-CbnA protein indicated that the cbnA gene was expressed in leaf tissue, roots, culms, and seeds. Transgenic rice calluses

Masami Shimizu; Tetsuya Kimura; Takayoshi Koyama; Katsuhisa Suzuki; Naoto Ogawa; Kiyotaka Miyashita; Kazuo Sakka; Kunio Ohmiya

2002-01-01

160

Assessing the probability of detection of horizontal gene transfer events in bacterial populations.  

PubMed

Experimental approaches to identify horizontal gene transfer (HGT) events of non-mobile DNA in bacteria have typically relied on detection of the initial transformants or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to be detected in a short time frame. Population genetic modeling of the growth dynamics of bacterial genotypes is therefore necessary to account for natural selection and genetic drift during the time lag and to predict realistic time frames for detection with a given sampling design. Here we draw on statistical approaches to population genetic theory to construct a cohesive probabilistic framework for investigation of HGT of exogenous DNA into bacteria. In particular, the stochastic timing of rare HGT events is accounted for. Integrating over all possible event timings, we provide an equation for the probability of detection, given that HGT actually occurred. Furthermore, we identify the key variables determining the probability of detecting HGT events in four different case scenarios that are representative of bacterial populations in various environments. Our theoretical analysis provides insight into the temporal aspects of dissemination of genetic material, such as antibiotic resistance genes or transgenes present in genetically modified organisms. Due to the long time scales involved and the exponential growth of bacteria with differing fitness, quantitative analyses incorporating bacterial generation time, and levels of selection, such as the one presented here, will be a necessary component of any future experimental design and analysis of HGT as it occurs in natural settings. PMID:22363321

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

2012-02-20

161

Sustainable control of pea bacterial blight : approaches for durable genetic resistance and biocontrol by endophytic bacteria  

Microsoft Academic Search

Key-words: bacterial blight, biological control, biodiversity, endophytic bacteria, L-form, pea, PDRl retrotransposon, Pisum sativum, Pisum abyssinicum, Pseudomonas syringae pv. pisi, race specific resistance, race non-specific resistance, Spanish landraces.<\\/font>Pea bacterial blight (Pseudomonas syringae pv. pisi) occurs worldwide and can cause severe damage under cool and wet conditions particularly at the seedling stage in wintersown crops. Seven Ps. syr. pv. pisi races

M. Elvira-Recuenco

2000-01-01

162

Biological control of bacterial spot of tomato using hrp mutants of Xanthomonas campestris pv. vesicatoria  

Microsoft Academic Search

Xanthomonas campestris pv. vesicatoria strain 75-3 hrpG, hrpX, hrpF and hrpE1 mutants were evaluated for control of bacterial spot of tomato under both greenhouse and field conditions. In greenhouse studies, the 75-3 hrp mutants were spray-inoculated onto tomato foliage 48h prior to inoculation of the wild-type pathogen, X. campestris pv. vesicatoria 75-3, and bacterial spot severity was assessed 10 days

W. P. Moss; J. M. Byrne; H. L. Campbell; P. Ji; U. Bonas; J. B. Jones; M. Wilson

2007-01-01

163

Bacterial resistance evolution by recruitment of super-integron gene cassettes.  

PubMed

The capture and spread of antibiotic resistance determinants by integrons underlies the rapid evolution of multiple antibiotic resistance among diverse Gram-negative clinical isolates. The association of multiple resistance integrons (MRIs) with mobile DNA elements facilitates their transit across phylogenetic boundaries and augments the potential impact of integrons on bacterial evolution. Recently, ancestral chromosomal versions, the super-integrons (SIs), were found to be genuine components of the genomes of diverse bacterial species. SIs possess evolutionary characteristics and stockpiles of adaptive functions, including cassettes related to antibiotic resistance determinants previously characterized in clinical isolates, which suggest that MRIs and their resistance genes were originally recruited from SIs and their pool of amassed genes. However, the recombination activity of integrons has never been demonstrated in a bacterium other than Escherichia coli. We introduced a naturally occurring MRI (TpR, SulR) on a conjugative plasmid into Vibrio cholerae, a species known to harbour a SI. We show that MRIs can randomly recruit genes directly from the cache of SI cassettes. By applying a selective constraint for the development of antibiotic resistance, we demonstrate bacterial resistance evolution through the recruitment a novel, but phenotypically silent, chloramphenicol acetyltransferase gene from the V. cholerae SI and its precise insertion into the MRI. The resulting resistance profile (CmR, TpR, SulR) could then be disseminated by conjugation to other clinically relevant pathogens at high frequency. These results demonstrate that otherwise phenotypically sensitive strains may still be a genetic source for the evolution of resistance to clinically relevant antibiotics through integron-mediated recombination events. PMID:11952913

Rowe-Magnus, Dean A; Guerout, Anne-Marie; Mazel, Didier

2002-03-01

164

Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis  

Microsoft Academic Search

Traditionally, evolutionary biologists have viewed mutations within individual genes as the major source of phenotypic variation leading to adaptation through natural selection, and ultimately generating diversity among species. Although such processes must contribute to the initial development of gene functions and their subsequent fine-tuning, changes in genome repertoire, occurring through gene acquisition and deletion, are the major events underlying the

Howard Ochman; Nancy A. Moran

2001-01-01

165

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli  

PubMed Central

Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uniqueness of ORFans within a genome has precluded the use of a comparative approach to examine their function and evolution. However, by identifying sequences unique to monophyletic groups at increasing phylogenetic depths, we can make direct comparisons of the characteristics of ORFans of different ages in the Escherichia coli genome, and establish their functional status and evolutionary rates. Relative to the genes ancestral to ?-Proteobacteria and to those genes distributed sporadically in other prokaryotic species, ORFans in the E. coli lineage are short, A+T rich, and evolve quickly. Moreover, most encode functional proteins. Based on these features, ORFans are not attributable to errors in gene annotation, limitations of current databases, or to failure of methods for detecting homology. Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions.

Daubin, Vincent; Ochman, Howard

2004-01-01

166

Bacterial Community Structure of Acid-Impacted Lakes: What Controls Diversity?? †  

PubMed Central

Although it is recognized that acidification of freshwater systems results in decreased overall species richness of plants and animals, little is known about the response of aquatic microbial communities to acidification. In this study we examined bacterioplankton community diversity and structure in 18 lakes located in the Adirondack Park (in the state of New York in the United States) that were affected to various degrees by acidic deposition and assessed correlations with 31 physical and chemical parameters. The pH of these lakes ranged from 4.9 to 7.8. These studies were conducted as a component of the Adirondack Effects Assessment Program supported by the U.S. Environmental Protection Agency. Thirty-one independent 16S rRNA gene libraries consisting of 2,135 clones were constructed from epilimnion and hypolimnion water samples. Bacterioplankton community composition was determined by sequencing and amplified ribosomal DNA restriction analysis of the clone libraries. Nineteen bacterial classes representing 95 subclasses were observed, but clone libraries were dominated by representatives of the Actinobacteria and Betaproteobacteria classes. Although the diversity and richness of bacterioplankton communities were positively correlated with pH, the overall community composition assessed by principal component analysis was not. The strongest correlations were observed between bacterioplankton communities and lake depth, hydraulic retention time, dissolved inorganic carbon, and nonlabile monomeric aluminum concentrations. While there was not an overall correlation between bacterioplankton community structure and pH, several bacterial classes, including the Alphaproteobacteria, were directly correlated with acidity. These results indicate that unlike more identifiable correlations between acidity and species richness for higher trophic levels, controls on bacterioplankton community structure are likely more complex, involving both direct and indirect processes.

Percent, Sascha F.; Frischer, Marc E.; Vescio, Paul A.; Duffy, Ellen B.; Milano, Vincenzo; McLellan, Maggie; Stevens, Brett M.; Boylen, Charles W.; Nierzwicki-Bauer, Sandra A.

2008-01-01

167

Bacterial social engagements  

Microsoft Academic Search

Quorum sensing is a process that enables bacteria to communicate using secreted signaling molecules called autoinducers. This process enables a population of bac- teria to regulate gene expression collectively and, there- fore, control behavior on a community-wide scale. Quorum sensing is widespread in the bacterial world and, generally, processes controlled by quorum sensing are unproductive when undertaken by an individual

Jennifer M. Henke; Bonnie L. Bassler

2004-01-01

168

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

169

10. Development of component technologies for control of bacterial wilt in potato  

Microsoft Academic Search

Research strategies to control potato bacterial wilt (Ralstonia solanacearum) were conducted in Pangalengan subdistrict in West Java from January to December 2001. Activities were done to determine the following: 1) status of Ralstonia solanacearum in farmers' and experimental fields, 2) effects of control components including seed selection during storage, crop rotation, field sanitation, mulching, and manuring with beneficial organisms added,

Oni Setiani Gunawan; Z. Abidin; R. S. Basuki; A. Dimyati; A. Asgar; Elske van de Fliert

170

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

PubMed Central

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 these rare drug candidates, the putative pederin biosynthesis genes were cloned from total DNA of Paederus fuscipes beetles, which use this compound for chemical defense. Sequence analysis of the gene cluster and adjacent regions revealed the presence of ORFs with typical bacterial architecture and homologies. The ped cluster, which is present only in beetle specimens with high pederin content, is located on a 54-kb region bordered by transposase pseudogenes and encodes a mixed modular polyketide synthase/nonribosomal peptide synthetase. Notably, none of the modules contains regions with homology to acyltransferase domains, but two copies of isolated monodomain acyltransferase genes were found at the upstream end of the cluster. In line with an involvement in pederin biosynthesis, the upstream cluster region perfectly mirrors pederin structure. The unexpected presence of additional polyketide synthase/nonribosomal peptide synthetase modules reveals surprising insights into the evolutionary relationship between pederin-type pathways in beetles and sponges.

Piel, Jorn

2002-01-01

171

The effects of pneumoperitoneum and controlled ventilation on peritoneal lymphatic bacterial clearance: experimental results in rats  

PubMed Central

OBJECTIVE: To evaluate the effect of pneumoperitoneum, both alone and in combination with controlled ventilation, on peritoneal lymphatic bacterial clearance using a rat bacterial peritonitis model. METHOD: A total of 69 male Wistar rats were intraperitoneally inoculated with an Escherichia coli solution (109 colony-forming units (cfu)/mL) and divided into three groups of 23 animals each: A (control group), B (pneumoperitoneum under 5 mmHg of constant pressure), and C (endotracheal intubation, controlled ventilation, and pneumoperitoneum as in Group B). The animals were sacrificed after 30 min under these conditions, and blood, mediastinal ganglia, lungs, peritoneum, liver, and spleen cultures were performed. RESULTS: Statistical analyses comparing the number of cfu/sample in each of the cultures showed that no differences existed between the three groups. CONCLUSION: Based on our results, we concluded that pneumoperitoneum, either alone or in association with mechanical ventilation, did not modify the bacterial clearance through the diaphragmatic lymphatic system of the peritoneal cavity.

Casaroli, Armando Angelo; Mimica, Lycia M. J.; Fontes, Belchor; Rasslan, Samir

2011-01-01

172

[Molecular mapping of a bacterial blight resistance gene Xa-25 in rice].  

PubMed

Xa-25 was a bacterial blight resistance gene identified in a somaclonal mutant HX-3. A doubled-haploid (DH) population including 129 stable lines was derived from anther culture of a typical japanica 02428 and a typical indica HX-3 cross. The bacterial blight strain Zhe173, a typical bacterial blight strain in Yangtze River valley, was used to test the resistance or susceptible of the DH population lines, and the results showed that the resistance lines and susceptible lines were 62 and 67, respectively. A total of 300 SSR primer pairs covering 12 rice chromosomes were used for polymorphism survey of 02428 and HX-3. Among these primers, 74 showed polymorphism between the parents. Using these polymorphic SSR markers, bulked segregant analysis was conducted on the DH population. As the result, Xa-25 was located at the terminal region of the long arm of chromosome 4 between the two SSR markers RM6748 and RM1153, the map distance between Xa-25 and the two SSR markers was 9.3 cM and 3.0 cM, respectively. PMID:15759866

Gao, Dong-Ying; Liu, Ai-Min; Zhou, Yi-Hong; Cheng, Yan-Jun; Xiang, Yang-Hai; Sun, Li-Hua; Zhai, Wen-Xue

2005-02-01

173

mRNA Composition and Control of Bacterial Gene Expression  

Microsoft Academic Search

lacZ) was measured (i) in a relA 1 background during exponential growth at different rates and (ii) in relA 1 and DrelA derivatives of Escherichia coli B\\/r after induction of a mild stringent or a relaxed response to raise or lower, respectively, the level of ppGpp. Expression from all three promoters was stimulated during slow exponential growth or at elevated

S.-T. Liang; Y.-C. Xu; P. Dennis; H. Bremer

2000-01-01

174

Modulation of gene expression via disruption of NF-kappaB signaling by a bacterial small molecule.  

PubMed

The control of innate immune responses through activation of the nuclear transcription factor NF-kappaB is essential for the elimination of invading microbial pathogens. We showed that the bacterial N-(3-oxo-dodecanoyl) homoserine lactone (C12) selectively impairs the regulation of NF-kappaB functions in activated mammalian cells. The consequence is specific repression of stimulus-mediated induction of NF-kappaB-responsive genes encoding inflammatory cytokines and other immune regulators. These findings uncover a strategy by which C12-producing opportunistic pathogens, such as Pseudomonas aeruginosa, attenuate the innate immune system to establish and maintain local persistent infection in humans, for example, in cystic fibrosis patients. PMID:18566250

Kravchenko, Vladimir V; Kaufmann, Gunnar F; Mathison, John C; Scott, David A; Katz, Alexander Z; Grauer, David C; Lehmann, Mandy; Meijler, Michael M; Janda, Kim D; Ulevitch, Richard J

2008-06-19

175

Plasmids expressing the herpes simplex virus thymidine kinase gene in mammalian and bacterial cells  

Microsoft Academic Search

Two plasmids containing either the complete thymidine kinase gene of Herpes simplex virus type I (pSK2) or the gene without the remote control sequence (pSK1) just behind the lac promoter and the first codons of the lacZ gene were constructed. Both plasmids efficiently transform mouse Ltk- cells as well as E. coli tk- cells to the Tk+ phenotype and are

Michael Strauss; Udo Kiessling; Ruth Kähler

1983-01-01

176

Medium-dependent control of the bacterial growth rate.  

PubMed

By combining results from previous studies of nutritional up-shifts we here re-investigate how bacteria adapt to different nutritional environments by adjusting their macromolecular composition for optimal growth. We demonstrate that, in contrast to a commonly held view the macromolecular composition of bacteria does not depend on the growth rate as an independent variable, but on three factors: (i) the genetic background (i.e. the strain used), (ii) the physiological history of the bacteria used for inoculation of a given growth medium, and (iii) the kind of nutrients in the growth medium. These factors determine the ribosome concentration and the average rate of protein synthesis per ribosome, and thus the growth rate. Immediately after a nutritional up-shift, the average number of ribosomes in the bacterial population increases exponentially with time at a rate which eventually is attained as the final post-shift growth rate of all cell components. After a nutritional up-shift from one minimal medium to another minimal medium of higher nutritional quality, ribosome and RNA polymerase syntheses are co-regulated and immediately increase by the same factor equal to the increase in the final growth rate. However, after an up-shift from a minimal medium to a medium containing all 20 amino acids, RNA polymerase and ribosome syntheses are no longer coregulated; a smaller rate of synthesis of RNA polymerase is compensated by a gradual increase in the fraction of free RNA polymerase, possibly due to a gradual saturation of mRNA promoters. We have also analyzed data from a recent publication, in which it was concluded that the macromolecular composition in terms of RNA/protein and RNA/DNA ratios is solely determined by the effector molecule ppGpp. Our analysis indicates that this is true only in special cases and that, in general, medium adaptation also depends on factors other than ppGpp. PMID:23228516

Ehrenberg, Måns; Bremer, Hans; Dennis, Patrick P

2012-12-07

177

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

178

A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History  

PubMed Central

It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data. For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogies by using a BLAST reciprocal best hit definition of orthology. In addition, concatenation of sequences of different genes as well as building of consensus trees only consider the few genes that are shared among all organisms. Here we present an attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny. This led us to perform a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny. We then used this core of genes to infer a tree. This phylogeny presents several differences with the rRNA phylogeny, notably for the position of hyperthermophilic bacteria.

Daubin, Vincent; Gouy, Manolo; Perriere, Guy

2002-01-01

179

The Tzs protein and exogenous cytokinin affect virulence gene expression and bacterial growth of Agrobacterium tumefaciens.  

PubMed

The soil phytopathogen Agrobacterium tumefaciens causes crown gall disease in a wide range of plant species. The neoplastic growth at the infection sites is caused by transferring, integrating, and expressing transfer DNA (T-DNA) from A. tumefaciens into plant cells. A trans-zeatin synthesizing (tzs) gene is located in the nopaline-type tumor-inducing plasmid and causes trans-zeatin production in A. tumefaciens. Similar to known virulence (Vir) proteins that are induced by the vir gene inducer acetosyringone (AS) at acidic pH 5.5, Tzs protein is highly induced by AS under this growth condition but also constitutively expressed and moderately upregulated by AS at neutral pH 7.0. We found that the promoter activities and protein levels of several AS-induced vir genes increased in the tzs deletion mutant, a mutant with decreased tumorigenesis and transient transformation efficiencies, in Arabidopsis roots. During AS induction and infection of Arabidopsis roots, the tzs deletion mutant conferred impaired growth, which could be rescued by genetic complementation and supplementing exogenous cytokinin. Exogenous cytokinin also repressed vir promoter activities and Vir protein accumulation in both the wild-type and tzs mutant bacteria with AS induction. Thus, the tzs gene or its product, cytokinin, may be involved in regulating AS-induced vir gene expression and, therefore, affect bacterial growth and virulence during A. tumefaciens infection. PMID:23593941

Hwang, Hau-Hsuan; Yang, Fong-Jhih; Cheng, Tun-Fang; Chen, Yi-Chun; Lee, Ying-Ling; Tsai, Yun-Long; Lai, Erh-Min

2013-09-01

180

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

2012-07-14

181

Viral and nanoflagellate control of bacterial production in the East China Sea summer 2011  

NASA Astrophysics Data System (ADS)

This study investigated spatial patterns in bacterial, viral, nanoflagellate abundance and the loss of bacterial production due to viral lysis and nanoflagellate grazing across the surface water of East China Sea (ECS) during the summer (1-12 July) of 2011. Abundance of bacteria ranged from 1.3 × 105 to 12.4 × 105 cells mL-1, with the highest value found in surface coastal waters, coinciding with a peak in Chl a concentrations. Spatial variations in bacterial growth rates ranged from 0.029 to 0.071 h-1, the highest growth rate near the river mouth of the Changjiang River. Nanoflagellate grazing was responsible for most of the bacterial mortality, accounting for 59% of total mortality within the plume (salinity <31) and 66% outside the plume (salinity >31) on average. Variation in viral lysis was associated with environmental gradients and bacterial abundance. We found a balance budget between bacterial losses due to both bacterivory and viral infection and production, which suggests strong top-down control of bacteria in the ECS during the summer.

Tsai, An-Yi; Gong, Gwo-Ching; Huang, Jun-Kai; Lin, Yun-Chi

2013-03-01

182

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

PubMed Central

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 flowing 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 on biodegradable chitin and a nonnutritional silicon surface, respectively, detached to become part of the free-living population in the bulk aqueous phase. Specific surface-associated growth rates that included the cells that subsequently detached from the substrata varied depending on the nutritional value of the substratum and during the period of surface colonization. Specific growth rates of 3.79 and 2.83 day?1 were obtained when cells first began to proliferate on a pure chitin film and a silicon surface, respectively. Later, when cell densities on the surface and detached cells as CFU in the bulk aqueous phase achieved a quasi-steady state, specific growth rates decreased to 1.08 and 0.79 day?1 on the chitin and silicon surfaces, respectively. Virtually all of the cells that detached from either the chitin or the silicon surfaces and the majority of cells associated with the chitin surface over the 200-h period of surface colonization displayed no detectable expression of the chitin-degrading genes chiA and chiB. Cells displaying high levels of chiA-chiB expression were detected only on the chitin surface and then only clustered in discrete areas of the surface. Surface-associated, differential gene expression and displacement of bacterial production from surfaces represent adaptations at the population level that promote efficient utilization of limited resources and dispersal of progeny to maximize access to new sources of energy and maintenance of the population.

Baty, Ace M.; Eastburn, Callie C.; Techkarnjanaruk, Somkiet; Goodman, Amanda E.; Geesey, Gill G.

2000-01-01

183

Bacteriophages for detection and control of bacterial pathogens in food and food-processing environment.  

PubMed

This chapter presents recent advances in bacteriophage research and their application in the area of food safety. Section 1 describes general facts on phage biology that are relevant to their application for control and detection of bacterial pathogens in food and environmental samples. Section 2 summarizes the recently acquired data on application of bacteriophages to control growth of bacterial pathogens and spoilage organisms in food and food-processing environment. Section 3 deals with application of bacteriophages for detection and identification of bacterial pathogens. Advantages of bacteriophage-based methods are presented and their shortcomings are discussed. The chapter is intended for food scientist and food product developers, and people in food inspection and health agencies with the ultimate goal to attract their attention to the new developing technology that has a tremendous potential in providing means for producing wholesome and safe food. PMID:23034118

Brovko, Lubov Y; Anany, Hany; Griffiths, Mansel W

2012-01-01

184

Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning  

Microsoft Academic Search

Techniques based on amplification of 16S rRNA genes for comparing bacterial communities are now widely used in microbial ecology, but calibration of these techniques with traditional tools, such as cultivation, has been conspicuously absent. In this study, we compared levels of bacterial community diversity in two pinyon rhizosphere soil samples and two between-tree (interspace) soil samples by analyzing 179 cultivated

JOHN DUNBAR; SHANNON TAKALA; SUSAN M. BARNS; JODY A. DAVIS; CHERYL R. KUSKE

1999-01-01

185

Terrestrial Runoff Controls the Bacterial Community Composition of Biofilms along a Water Quality Gradient in the Great Barrier Reef  

PubMed Central

16S rRNA gene molecular analysis elucidated the spatiotemporal distribution of bacterial biofilm communities along a water quality gradient. Multivariate statistics indicated that terrestrial runoff, in particular dissolved organic carbon and chlorophyll a concentrations, induced shifts of specific bacterial communities between locations and seasons, suggesting microbial biofilms could be suitable bioindicators for water quality.

Wild, Christian; Uthicke, Sven

2012-01-01

186

Dissection of a Type I Interferon Pathway in Controlling Bacterial Intracellular Infection in Mice  

PubMed Central

Defense mechanisms against intracellular bacterial pathogens are incompletely understood. Our study characterizes a type I IFN-dependent cell-autonomous defense pathway directed against Legionella pneumophila, an intracellular model organism and frequent cause of pneumonia. We show that macrophages infected with L. pneumophila produced IFN? in a STING- and IRF3-dependent manner. Paracrine type I IFNs stimulated up-regulation of IFN-stimulated genes and a cell-autonomous defense pathway acting on replicating and non-replicating Legionella within their specialized vacuole. Our infection experiments in mice lacking receptors for type I and/or II IFNs show that type I IFNs contribute to expression of IFN-stimulated genes and to bacterial clearance as well as resistance in L. pneumophila pneumonia in addition to type II IFN. Overall, our study shows that paracrine type I IFNs mediate defense against L. pneumophila, and demonstrates a protective role of type I IFNs in in vivo infections with intracellular bacteria.

Lippmann, Juliane; Muller, Holger; Naujoks, Jan; Tabeling, Christoph; Shin, Sunny; Witzenrath, Martin; Hellwig, Katharina; Kirschning, Carsten J.; Taylor, Gregory A.; Barchet, Winfried; Bauer, Stefan; Suttorp, Norbert; Roy, Craig R.; Opitz, Bastian

2011-01-01

187

Facilitation of Bacterial Adaptation to Chlorothalonil-Contaminated Sites by Horizontal Transfer of the Chlorothalonil Hydrolytic Dehalogenase Gene?  

PubMed Central

Horizontal transfer of the chlorothalonil hydrolytic dehalogenase gene (chd) is proposed based on the high conservation of the chd gene and its close association with a novel insertion sequence, ISOcsp1, in 16 isolated chlorothalonil-dechlorinating strains belonging to eight different genera. The ecological role of horizontal gene transfer is assumed to facilitate bacterial adaptation to chlorothalonil-contaminated sites, through detoxification of chlorothalonil to less toxic 2,4,5-trichloro-6-hydroxybenzene-1,3-dicarbonitrile.

Liang, Bin; Wang, Guangli; Zhao, Yanfu; Chen, Kai; Li, Shunpeng; Jiang, Jiandong

2011-01-01

188

Genetic engineering of shikonin biosynthesis hairy root cultures of Lithospermum erythrorhizon transformed with the bacterial ubiC gene  

Microsoft Academic Search

The biosynthetic pathway to 4-hydroxybenzoate (4HB), a precursor of the naphthoquinone pigment shikonin, was modified in Lithospermum erythrorhizon hairy root cultures by introduction of the bacterial gene ubiC. This gene of Escherichia coli encodes chorismate pyruvate-lyase (CPL), an enzyme that converts chorismate into 4HB and is not normally present in plants. The ubiC gene was fused to the sequence for

Susanne Sommer; Annegret Köhle; Kazufumi Yazaki; Koichiro Shimomura; Andreas Bechthold; Lutz Heide

1999-01-01

189

Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths  

Microsoft Academic Search

Bacterial community succession was investigated in a field-scale subsurface reactor formed by a series of wells that received weekly ethanol additions to re-circulating groundwater. Ethanol additions stimulated denitrification, metal reduction, sulfate reduction and U(VI) reduction to sparingly soluble U(IV). Clone libraries of SSU rRNA gene sequences from groundwater samples enabled tracking of spatial and temporal changes over a 1.5-year period.

Chiachi Hwang; Weimin Wu; Terry J Gentry; Jack Carley; Gail A Corbin; Sue L Carroll; David B Watson; Phil M Jardine; Jizhong Zhou; Craig S Criddle; Matthew W Fields

2009-01-01

190

Nontarget effects of bacterial biological control agents on soil Protozoa  

Microsoft Academic Search

Biological control agents (BCAs) have gained increasing interest as an alternative to chemical pesticides in agriculture. Before widespread environmental use, risk assessment of effects on target and non-target organisms are needed. However, the knowledge about the effect of BCAs on non-target soil Protozoa is insufficient to support thorough risk assessment. In this study we report on the effects of Pseudomonas

Karen Stevnbak Andersen; Anne Winding

2004-01-01

191

Robust perfect adaptation in bacterial chemotaxis through integral feedback control  

Microsoft Academic Search

Integral feedback control is a basic engineering strategy for en- suring that the output of a system robustly tracks its desired value independent of noise or variations in system parameters. In bio- logical 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

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

2002-01-01

192

Altered temperature induction sensitivity of the lambda p R \\/cI857 system for controlled gene E expression in Escherichia coli  

Microsoft Academic Search

Cell lysis of Gram-negative bacteria can be efficiently achieved by expression of the cloned lysis gene E of bacteriophage PhiX174. Gene E expression is tightly controlled by the rightward V pR promoter and the temperature-sensitive repressor cI857 on lysis plasmid pAW12. The resulting empty bacterial cell envelopes, called bacterial ghosts, are currently under investigation as candidate vaccines. Expression of gene

Wolfgang Jechlinger; Michael P. Szostak; Angela Witte; Werner Lubitz

1999-01-01

193

Factors influencing efficacy of plastic shelters for control of bacterial blight of lilac  

Technology Transfer Automated Retrieval System (TEKTRAN)

Plastic shelters are thought to manage bacterial blight by protecting plants from rain and/or frost. In February to April 2008 and 2009, we studied the contribution of frost protection to efficacy of this cultural control practice. Lilacs in 1-gallon pots were exposed to four treatments: 1) plants...

194

Bacterial supplementation in the irritable bowel syndrome. A randomised doubleblind placebo-controlled crossover study  

Microsoft Academic Search

Background. Symptoms of at least a subgroup of patients with irritable bowel syndrome may be associated with an alteration in gut flora. Studies on bacterial based therapy have yielded mixed results.Aims. To determine if oral administration of the probiotic Lactobacillus casei strain GG under randomized placebo controlled conditions improves symptoms in irritable bowel syndrome patients with bloating related symptoms.Patients. A

M. A. O'Sullivan; C. A. O'Morain

2000-01-01

195

High-Throughput Bioluminescence-Based Mutant Screening Strategy for Identification of Bacterial Virulence Genes?  

PubMed Central

A high-throughput bioluminescence screening procedure for identification of virulence genes in bacteria was developed and applied to the fish pathogen Edwardsiella ictaluri. A random transposon mutant library expressing bioluminescence was constructed and robotically arrayed on 384-well plates. Mutants were cultivated and mixed with catfish serum and neutrophils in 96-well plates, and bioluminescence was used to detect mutants that are more susceptible to killing by these host factors. The virulence and vaccine efficacy of selected mutants were determined in channel catfish. Transposon insertion sites in 13 mutants attenuated in the natural host were mapped to the E. ictaluri genome. Ten unique genes were mutated, including genes encoding a negative regulator of sigmaE activity, a glycine cleavage system protein, tricarboxylic acid cycle enzymes, an O polysaccharide biosynthesis enzyme, proteins encoded on the native plasmid pEI1, and a fimbrial chaperon protein. Three of these mutants were found to have potential as live attenuated vaccines. This study demonstrates a novel application of bioluminescence to identify bacterial genes required for host resistance; as a result, efficacious and genetically defined live attenuated vaccine candidates were developed.

Karsi, Attila; Gulsoy, Nagihan; Corb, Erin; Dumpala, Pradeep R.; Lawrence, Mark L.

2009-01-01

196

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

197

Gene network dynamics controlling keratinocyte migration  

Microsoft Academic Search

Translation of large-scale data into a coherent model that allows one to simulate, predict and control cellular behavior is far from being resolved. Assuming that long-term cellular behavior is reflected in the gene expression kinetics, we infer a dynamic gene regulatory network from time-series measurements of DNA microarray data of hepatocyte growth factor-induced migration of primary human keratinocytes. Transferring the

Hauke Busch; David Camacho-Trullio; Zbigniew Rogon; Kai Breuhahn; Peter Angel; Roland Eils; Axel Szabowski

2008-01-01

198

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

199

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

200

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

2012-06-29

201

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

202

Genes and co-expression modules common to drought and bacterial stress responses in Arabidopsis and rice.  

PubMed

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. PMID:24130868

Shaik, Rafi; Ramakrishna, Wusirika

2013-10-10

203

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

204

Controlling autonomous underwater floating platforms using bacterial fermentation.  

PubMed

Biogenic gas has a wide range of energy applications from being used as a source for crude bio-oil components to direct ignition for heating. The current study describes the use of biogenic gases from Clostridium acetobutylicum for a new application-renewable ballast regeneration for autonomous underwater devices. Uninterrupted (continuous) and blocked flow (pressurization) experiments were performed to determine the overall biogas composition and total volume generated from a semirigid gelatinous matrix. For stopped flow experiments, C. acetobutylicum generated a maximum pressure of 55 psi over 48 h composed of 60 % hydrogen gas when inoculated in a 5 % agar (w/v) support with 5 % glucose (w/v) in the matrix. Typical pressures over 24 h at 318 K ranged from 10 to 33 psi. These blocked flow experiments show for the first time the use of microbial gas production as a way to repressurize gas cylinders. Continuous flow experiments successfully demonstrated how to deliver biogas to an open ballast control configuration for deployable underwater platforms. This study is a starting point for engineering and microbiology investigations of biogas which will advance the integration of biology within autonomous systems. PMID:22851013

Biffinger, Justin C; Fitzgerald, Lisa A; Howard, Erinn C; Petersen, Emily R; Fulmer, Preston A; Wu, Peter K; Ringeisen, Bradley R

2012-08-01

205

Fine mapping and analysis of a candidate gene in tomato accession PI128216 conferring hypersensitive resistance to bacterial spot race T3.  

PubMed

Bacterial spot caused by Xanthomonas euvesicatoria, X. vesicatoria, X. perforans and X. gardneri is one of the most destructive diseases in tomatoes (Solanum lycopersicum L.) growing in tropical and subtropical regions. Exploring resistance genes from diverse germplasm and incorporating them into cultivated varieties are critical for controlling this disease. The S. pimpinellifolium accession PI128216 was reported to carry the Rx4 gene on chromosome 11 conferring hypersensitivity and field resistance to race T3. To facilitate the use of marker-assisted selection in breeding and map-based cloning of the gene, an F(2) population derived from a cross between the susceptible variety OH88119 and the resistant accession PI128216 was created for fine mapping of the Rx4 gene. Using 18 markers developed through various approaches, we mapped the gene to a 45.1-kb region between two markers pcc17 and pcc14 on chromosome 11. A NBS-LRR class of resistance gene was identified as the candidate for the Rx4 gene based on annotation results from the International Tomato Annotation Group. Comparison of the genomic DNA sequences of the Rx4 alleles in PI128216 and OH88119 revealed a 6-bp insertion/deletion (InDel) and eight SNPs. The InDel marker was successfully used to distinguish resistance and susceptibility in 12 tomato lines. These results will facilitate cloning the Rx4 gene and provide a useful tool for marker-assisted selection of this gene in tomato breeding programs. PMID:22038434

Pei, Chengcheng; Wang, Hui; Zhang, Jieyun; Wang, Yuanyuan; Francis, David M; Yang, Wencai

2011-10-22

206

Ingestion of bacterially expressed double-stranded RNA inhibits gene expression in planarians  

PubMed Central

Freshwater planarian flatworms are capable of regenerating complete organisms from tiny fragments of their bodies; the basis for this regenerative prowess is an experimentally accessible stem cell population that is present in the adult planarian. The study of these organisms, classic experimental models for investigating metazoan regeneration, has been revitalized by the application of modern molecular biological approaches. The identification of thousands of unique planarian ESTs, coupled with large-scale whole-mount in situ hybridization screens, and the ability to inhibit planarian gene expression through double-stranded RNA-mediated genetic interference, provide a wealth of tools for studying the molecular mechanisms that regulate tissue regeneration and stem cell biology in these organisms. Here we show that, as in Caenorhabditis elegans, ingestion of bacterially expressed double-stranded RNA can inhibit gene expression in planarians. This inhibition persists throughout the process of regeneration, allowing phenotypes with disrupted regenerative patterning to be identified. These results pave the way for large-scale screens for genes involved in regenerative processes.

Newmark, Phillip A.; Reddien, Peter W.; Cebria, Francesc; Alvarado, Alejandro Sanchez

2003-01-01

207

SNP detection in transforming growth factor-beta1 gene using bacterial magnetic particles.  

PubMed

A single nucleotide polymorphism (SNP) within the transforming growth factor-beta1 (TGF-beta1) gene was detected by hybridization-based method using bacterial magnetic particles (BMPs). TGF-beta1 is commonly associated with a single base change resulting in a Leu(10)-->Pro (T(869)-->C) polymorphism and is a genetic marker for susceptibility to osteoporosis. Short (9 bases) and specific probes were designed to detect SNP in TGF-beta1. Detection probes were immobilized on BMPs using cross-linking reagents. TGF-beta1 PCR products (139 bp) were labeled with the fluorescent dye coumarin and hybridized with detection probes on BMPs. Complementary hybridized targets gave over four times higher fluorescent intensities, compared with one base mismatched hybridizations. The SNP genotype was successfully discriminated using this technique. PMID:12706579

Ota, Hiroyuki; Takeyama, Haruko; Nakayama, Hideki; Katoh, Takahiko; Matsunaga, Tadashi

2003-05-01

208

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

209

Control mechanisms of plastid gene expression  

SciTech Connect

Plastid DNAs of higher plants contain approximately 150 genes that encode RNAs and proteins for genetic and photosynthetic functions of the organelle. Results published in the last few years illustrate that the spatial and temporal expression of these plastid genes is regulated, in part, at the transcriptional level, but that developmentally controlled changes in mRNA stability, translational activity, and protein phosphorylation also have an important role in the control of plastid functions. This comprehensive review summarizes and discusses the mechanisms by which regulation of gene expression is exerted at the transcriptional and post-transcriptional levels. It provides an overview of our current knowledge, but also emphasizes areas that are controversial and in which information on regulatory mechanisms is still incomplete. 455 refs., 3 figs., 3 tabs.

Gruissem, W.; Tonkyn, J.C. [Univ. of California, Berkeley, CA (United States)

1993-12-31

210

Integrity of bacterial genomic DNA after autoclaving: possible implications for horizontal gene transfer and clinical waste management.  

PubMed

Current autoclaving practices are designed to kill bacteria. Little is known about the effect of autoclaving on the integrity of bacterial genomic DNA. An experiment was performed to examine the effect of standard autoclaving on the integrity of bacterial DNA, employing polymerase chain reaction (PCR) as an indicator of DNA integrity. Amplifiable PCR signal was observed at t = 10, 20 and 30 min autoclaving time for Pseudomonas aeruginosa NCTC 10662; at t = 10, 20, 30 and 40 min for Salmonella Nottingham NCTC 7832; and at t = 10 and 20 min for Escherichia coli NCTC 9001. Careful consideration should therefore be given to residual molecular artefacts in future risk and environmental impact assessments, where the legacy of residual genomic DNA from dead bacterial and higher organisms may act as a potential reservoir, thereby feeding horizontal gene transfer scenarios in viable cells with potential hazardous genes of virulence, persistence or antibiotic resistance characteristics. PMID:23333146

Yap, J M; Goldsmith, C E; Moore, J E

2013-01-16

211

{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)

1995-10-01

212

Transition Metals in Control of Gene Expression  

NASA Astrophysics Data System (ADS)

Metalloproteins play structural and catalytic roles in gene expression. The metalloregulatory proteins are a subclass that exerts metal-responsive control of genes involved in respiration, metabolism, and metal-specific homeostasis or stress-response systems, such as iron uptake and storage, copper efflux, and mercury detoxification. Two allosteric mechanisms for control of gene expression were first discovered in metalloregulatory systems: an iron-responsive translational control mechanism for ferritin production and a mercury-responsive DNA-distortion mechanism for transcriptional control of detoxification genes. These otherwise unrelated mechanisms give rise to a rapid physiological response when metal ion concentrations exceed a dangerous threshold. Molecular recognition in these allosteric metal ion receptors is achieved through atypical coordination geometries, cluster formation, or complexes with prosthetic groups, such as sulfide and heme. Thus, many of the inorganic assemblies that otherwise buttress the structure of biopolymers or catalyze substrate transformation in active sites of enzymes have also been adapted to serve sensor functions in the metalloregulatory proteins. Mechanistic studies of these metal-sensor protein interactions are providing new insights into fundamental aspects of inorganic chemistry, molecular biology, and cellular physiology.

O'Halloran, Thomas V.

1993-08-01

213

A gene transfer system based on the homologous pyrG gene and efficient expression of bacterial genes in Aspergillus oryzae.  

PubMed

A homologous transformation system for Aspergillus oryzae is described. The system is based on an A. oryzae strain deficient in orotidine-5'-phosphate decarboxylase (pyrG) and the vector pAO4-2, which contains a functional A. oryzae pyrG gene as selection marker. Transformation of the A. oryzae pyrG mutant with circular pAO4-2 resulted in the appearance of Pyr+ transformants at a frequency of up to 20 per micrograms of DNA, whereas with linear pAO4-2 up to 200 transformants per micrograms DNA were obtained. In 75% of the Pyr+ transformants recombination events had occurred at the pyrG locus, most of which (90%) resulted in insertion of one or two copies of the vector and the others (10%) in a replacement of the mutant allele by the wild-type allele. Vector pAO4-2 is also capable of transforming a corresponding mutant of Aspergillus niger. This transformation system was used to introduce into A. oryzae the heterologous and non-selectable bacterial genes lacZ, encoding beta-galactosidase, and uidA, encoding beta-glucuronidase. Using the Aspergillus nidulans gpdA promoter to drive bacterial gene expression in A. oryzae, relatively high levels of activity, as well as protein per se, as judged by western blot analyses, were obtained. PMID:2688930

de Ruiter-Jacobs, Y M; Broekhuijsen, M; Unkles, S E; Campbell, E I; Kinghorn, J R; Contreras, R; Pouwels, P H; van den Hondel, C A

1989-09-01

214

Induction of hemolin gene expression by bacterial cell wall components in eri-silkworm, Samia cynthia ricini  

Microsoft Academic Search

A cDNA clone encoding hemolin was isolated from fat body of immunized Samia cynthia ricini larvae based on subtractive suppression hybridization method. The cDNA encodes 413 amino acid residue open reading frame with an 18 residue predicted signal peptide. The expression of the gene was strongly induced in fat body and midgut by an injection of bacterial cells or peptidoglycans,

Yanyuan Bao; Yoshiaki Yamano; Isao Morishima

2007-01-01

215

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

216

Genes involved in the control of tumor progression and their possible use for gene therapy  

Microsoft Academic Search

Summary Three major groups of genes may be used for cancer gene therapy: (i ) oncogenes and tumor suppressor genes; ( ii ) genes involved in the control of tumor progression and metastasis; and ( iii ) genes encoding proteins protecting the organism from tumor cells. Each group contains numerous genes, and the discovery of new important genes is an

Georgii P. Georgiev; Sergei L. Kiselev; Evgenii M. Lukanidin

217

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system  

PubMed Central

The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease that participates in the CRISPR-Cas immune defense against prokaryotic viruses. We describe the use of a Cas9 nuclease mutant that retains DNA-binding activity and can be engineered as a programmable transcription repressor by preventing the binding of the RNA polymerase (RNAP) to promoter sequences or as a transcription terminator by blocking the running RNAP. In addition, a fusion between the omega subunit of the RNAP and a Cas9 nuclease mutant directed to bind upstream promoter regions can achieve programmable transcription activation. The simple and efficient modulation of gene expression achieved by this technology is a useful asset for the study of gene networks and for the development of synthetic biology and biotechnological applications.

Bikard, David; Jiang, Wenyan; Samai, Poulami; Hochschild, Ann; Zhang, Feng; Marraffini, Luciano A.

2013-01-01

218

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system.  

PubMed

The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease that participates in the CRISPR-Cas immune defense against prokaryotic viruses. We describe the use of a Cas9 nuclease mutant that retains DNA-binding activity and can be engineered as a programmable transcription repressor by preventing the binding of the RNA polymerase (RNAP) to promoter sequences or as a transcription terminator by blocking the running RNAP. In addition, a fusion between the omega subunit of the RNAP and a Cas9 nuclease mutant directed to bind upstream promoter regions can achieve programmable transcription activation. The simple and efficient modulation of gene expression achieved by this technology is a useful asset for the study of gene networks and for the development of synthetic biology and biotechnological applications. PMID:23761437

Bikard, David; Jiang, Wenyan; Samai, Poulami; Hochschild, Ann; Zhang, Feng; Marraffini, Luciano A

2013-06-12

219

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

220

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

221

Deletion of the gene for subunit III leads to defective assembly of bacterial cytochrome oxidase.  

PubMed Central

COIII is one of the major subunits in the mitochondrial and a bacterial cytochrome c oxidase, cytochrome aa3. It does not contain any of the enzyme's redox-active metal centres and can be removed from the enzyme without major changes in its established functions. We have deleted the COIII gene from Paracoccus denitrificans. The mutant still expresses spectroscopically detectable enzyme almost as the wild-type, but its cytochrome c oxidase activity is much lower. From 50 to 80% of cytochrome a is reduced and its absorption maximum is 2-3 nm blue-shifted. The EPR signal of ferric cytochrome a is heterogeneous indicating the presence of multiple cytochrome a species. Proteolysis of the membrane-bound oxidase shows new cleavage sites both in COI and COII. DEAE-chromatography of solubilized enzyme yields fractions that contain a COI + COII complex and in addition haem-binding, free COI as well as free COII. The mutant phenotype can be complemented by introducing the COIII gene back to cells in a plasmid vector. We conclude that cytochrome oxidase assembles inefficiently in the absence of COIII and that this subunit may facilitate a late step in the assembly. The different oxidase species in the mutant represent either accumulating intermediates of the assembly pathway or dissociation products of a labile COI + COII complex and its conformational variants. Images

Haltia, T; Finel, M; Harms, N; Nakari, T; Raitio, M; Wikstrom, M; Saraste, M

1989-01-01

222

Bacterial magnetic particles as a novel and efficient gene vaccine delivery system.  

PubMed

DNA vaccination is an attractive approach for eliciting antigen-specific immunity. In this study, we used magnetosomes (bacterial magnetic particles, BMPs) as carriers of a recombinant DNA composed of a secondary lymphoid tissue chemokine, human papillomavirus type E7 (HPV-E7) and Ig-Fc fragment (pSLC-E7-Fc) to generate a gene vaccine (BMP-V) for tumour immunotherapy. The results indicate that BMPs linked to DNA more efficiently in phosphate-buffered saline (pH=4-5) than in physiological saline. Efficient transfection of BMP-V in vitro and in vivo was achieved when a 600-mT static magnetic field was applied for 10 min. In a mouse tumour model, subcutaneous injection of BMP-V (5 ?g, × 3 at 4-day intervals) plus magnetic exposure elicited systemic HPV-E7-specific immunity leading to significant tumour inhibition. The treated mice tolerated BMP-V immunisation well with no toxic side effects, as shown by histopathological examinations of major internal organs. Taken together, these results suggest that BMP can be used as a gene carrier to elicit a systemic immune response. PMID:22170341

Tang, Y-S; Wang, D; Zhou, C; Ma, W; Zhang, Y-Q; Liu, B; Zhang, S

2011-12-15

223

Bacterial magnetic particles as a novel and efficient gene vaccine delivery system  

PubMed Central

DNA vaccination is an attractive approach for eliciting antigen-specific immunity. In this study, we used magnetosomes (bacterial magnetic particles, BMPs) as carriers of a recombinant DNA composed of a secondary lymphoid tissue chemokine, human papillomavirus type E7 (HPV-E7) and Ig-Fc fragment (pSLC-E7-Fc) to generate a gene vaccine (BMP-V) for tumour immunotherapy. The results indicate that BMPs linked to DNA more efficiently in phosphate-buffered saline (pH=4–5) than in physiological saline. Efficient transfection of BMP-V in vitro and in vivo was achieved when a 600-mT static magnetic field was applied for 10?min. In a mouse tumour model, subcutaneous injection of BMP-V (5??g, × 3 at 4-day intervals) plus magnetic exposure elicited systemic HPV-E7-specific immunity leading to significant tumour inhibition. The treated mice tolerated BMP-V immunisation well with no toxic side effects, as shown by histopathological examinations of major internal organs. Taken together, these results suggest that BMP can be used as a gene carrier to elicit a systemic immune response.

Tang, Y-S; Wang, D; Zhou, C; Ma, W; Zhang, Y-Q; Liu, B; Zhang, S

2012-01-01

224

Microbial Control of the Culture of Artemia Juveniles through Preemptive Colonization by Selected Bacterial Strains  

PubMed Central

The use of juvenile Artemia as feed in aquaculture and in the pet shop industry has been getting more attention during the last decade. In this study, the use of selected bacterial strains to improve the nutritional value of dry food for Artemia juveniles and to obtain control of the associated microbial community was examined. Nine bacterial strains were selected based on their positive effects on survival and/or growth of Artemia juveniles under monoxenic culture conditions, while other strains caused no significant effect, significantly lower rates of survival and/or growth, or even total mortality of the Artemia. The nine selected strains were used to preemptively colonize the culture water of Artemia juveniles. Xenic culture of Artemia under suboptimal conditions yielded better survival and/or growth rates when they were grown in the preemptively colonized culture medium than when grown in autoclaved seawater. The preemptive colonization of the culture water had a drastic influence on the microbial communities that developed in the culture water or that were associated with the Artemia, as determined with Biolog GN community-level physiological profiles. Chemotaxonomical characterization based on fatty acid methyl ester analysis of bacterial isolates recovered from the culture tanks was performed, and a comparison with the initially introduced strains was made. Finally, several modes of action for the beneficial effect of the bacterial strains are proposed.

Verschuere, Laurent; Rombaut, Geert; Huys, Geert; Dhont, Jean; Sorgeloos, Patrick; Verstraete, Willy

1999-01-01

225

Control of Bacterial Motility by Environmental Factors in Polarly Flagellated and Peritrichous Bacteria Isolated from Lake Baikal  

Microsoft Academic Search

Despite numerous studies on bacterial motility, little is known about the regulation of this process by environmental factors in natural isolates. In this study we investigated the control of bacterial motility in response to environmental parameters in two strains isolated from the natural habitat of Lake Baikal. Morphological characterization, carbon source utilization, fermentation analysis, and sequence comparison of 16S rRNA

O. A. Soutourina; E. A. Semenova; V. V. Parfenova; A. Danchin; P. Bertin

2001-01-01

226

DNA sequencing of the gene encoding a bacterial superantigen, Yersinia pseudotuberculosis-derived mitogen (YPM), and characterization of the gene product, cloned YPM  

Microsoft Academic Search

Previously, we found a novel bacterial superantigen from Yersinia pseudotuberculosis, designated Y. pseudotuberculosis-derived mitogen (YPM). In the present study, we analyzed the DNA sequence of the gene encoding YPM. The YPM gene was cloned into a plasmid vector pMW119 and expressed in Escherichia coli DH10B. Like the native YPM, the cloned YPM required the expression of MHC class II molecules

Tohru Miyoshi-Akiyama; Hidehito Kato; Takehiko Uchiyama

1995-01-01

227

The evolution of the bacterial luciferase gene cassette (lux) as a real-time bioreporter.  

PubMed

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. PMID:22368493

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

2012-01-11

228

Bacteriophages of Staphylococcus aureus efficiently package various bacterial genes and mobile genetic elements including SCCmec with different frequencies.  

PubMed

Staphylococcus aureus is a serious human and veterinary pathogen in which new strains with increasing virulence and antimicrobial resistance occur due to acquiring new genes by horizontal transfer. It is generally accepted that temperate bacteriophages play a major role in gene transfer. In this study, we proved the presence of various bacterial genes of the S.?aureus COL strain directly within the phage particles via qPCR and quantified their packaging frequency. Non-parametric statistical analysis showed that transducing bacteriophages ?11, ?80 and ?80? of serogroup B, in contrast to serogroup A bacteriophage ?81, efficiently package selected chromosomal genes localized in 4 various loci of the chromosome and 8 genes carried on variable elements, such as staphylococcal cassette chromosome SCCmec, staphylococcal pathogenicity island SaPI1, genomic islands vSa? and vSa?, and plasmids with various frequency. Bacterial gene copy number per ng of DNA isolated from phage particles ranged between 1.05?×?10(2) for the tetK plasmid gene and 3.86?×?10(5) for the SaPI1 integrase gene. The new and crucial finding that serogroup B bacteriophages can package concurrently ccrA1 (1.16?×?10(4)) and mecA (1.26?×?10(4)) located at SCCmec type I into their capsids indicates that generalized transduction plays an important role in the evolution and emergence of new methicillin-resistant clones. PMID:23757132

Mašla?ová, Ivana; Doška?, Ji?í; Varga, Marian; Kuntová, Lucie; Mužík, Jan; Malúšková, Denisa; R?ži?ková, Vladislava; Pant??ek, Roman

2012-09-03

229

Finding immune gene expression differences induced by marine bacterial pathogens in the deep-sea hydrothermal vent mussel Bathymodiolus azoricus  

NASA Astrophysics Data System (ADS)

The deep-sea hydrothermal vent mussel Bathymodiolus azoricus lives in a natural environment characterized by extreme conditions of hydrostatic pressure, temperature, pH, high concentrations of heavy metals, methane and hydrogen sulphide. The deep-sea vent biological systems represent thus the opportunity to study and provide new insights into the basic physiological principles that govern the defense mechanisms in vent animals and to understand how they cope with microbial infections. Hence, the importance of understanding this animal's innate defense mechanisms, by examining its differential immune gene expressions toward different pathogenic agents. In the present study, B. azoricus mussels were infected with single suspensions of marine bacterial pathogens, consisting of Vibrio splendidus, Vibrio alginolyticus, or Vibrio anguillarum, and a pool of these Vibrio strains. Flavobacterium suspensions were also used as an irrelevant bacterium. Gene expression analyses were carried out using gill samples from animals dissected at 12 h and 24 h post-infection times by means of quantitative-Polymerase Chain Reaction aimed at targeting several immune genes. We also performed SDS-PAGE protein analyses from the same gill tissues. We concluded that there are different levels of immune gene expression between the 12 h and 24 h exposure times to various bacterial suspensions. Our results from qPCR demonstrated a general pattern of gene expression, decreasing from 12 h over 24 h post-infection. Among the bacteria tested, Flavobacterium is the microorganism species inducing the highest gene expression level in 12 h post-infections animals. The 24 h infected animals revealed, however, greater gene expression levels, using V. splendidus as the infectious agent. The SDS-PAGE analysis also pointed at protein profile differences between 12 h and 24 h, particularly around a protein area, of 18 KDa molecular mass, where most dissimilarities were found. Multivariate analyses demonstrated that immune genes, as well as experimental infections, clustered in discrete groups in accordance with the patterns observed in gene expression changes induced by bacterial pathogens.

Martins, E.; Queiroz, A.; Serrão Santos, R.; Bettencourt, R.

2013-02-01

230

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

231

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

232

Expression in plants of two bacterial antibiotic resistance genes after protoplast transformation with a new plant expression vector.  

PubMed Central

Two bacterial antibiotic resistance genes, one coding for the neomycin phosphotransferase (NPT I) from Tn903, and the other coding for the chloramphenicol acetyltransferase from Tn9 were used as plant selectable markers. Both genes were introduced into the Nicotiana tabacum genome in a new plant expression vector, using the direct gene transfer method. The vector pDH51, used in these experiments contains a plant expression unit as a movable cassette, consisting of the strong cauliflower mosaic virus (CaMV) 35S RNA promoter and transcription terminator separated by a polylinker containing several unique restriction sites. Images

Pietrzak, M; Shillito, R D; Hohn, T; Potrykus, I

1986-01-01

233

Impact of dibenzofuran\\/dibenzo- p -dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations  

Microsoft Academic Search

The impact of dibenzofuran (DF) and dibenzo-p-dioxin (DD) on the changes in bacterial community structure and the transition of catabolic genes were studied using forest\\u000a soil. The bacterial community structure of soil suspensions amended with 1 µg\\/g of either DF or DD was analyzed by 16S rRNA\\u000a and functional gene sequencing. To analyze the functional genes in the communities, we targeted

Nobutada Kimura; Yoichi Kamagata

2009-01-01

234

Functional characterization of the bacterial iac genes for degradation of the plant hormone indole-3-acetic acid.  

PubMed

Pseudomonas putida 1290 is a model organism for the study of bacterial degradation of the plant hormone indole-3-acetic acid (IAA). This property is encoded by the iac gene cluster. Insertional inactivation and/or deletion of individual iac genes and heterologous expression of the gene cluster in Escherichia coli were combined with mass spectrometry to demonstrate that iac-based degradation of IAA is likely to involve 2-hydroxy-IAA, 3-hydroxy-2-oxo-IAA, and catechol as intermediates. The first gene of the cluster, iacA encodes for the first step in the pathway, and also can convert indole to indoxyl to produce the blue pigment indigo. Transcriptional profiling of iac genes in P. putida 1290 revealed that they were induced in the presence of IAA. Based on results with an iacR knockout, we propose that this gene codes for a repressor of iacA expression and that exposure to IAA relieves this repression. Transformation of P. putida KT2440 (which cannot degrade IAA) with the iac gene cluster conferred the ability to grow on IAA as a sole source of carbon and energy, but not the ability to chemotaxi towards IAA. We could show such tactic response for P. putida 1290, thus representing the first demonstration of bacterial chemotaxis towards IAA. We discuss the ecological significance of our findings, and specifically the following question: under what circumstances do bacteria with the ability to degrade, recognize, and move towards IAA have a selective advantage? PMID:23881445

Scott, Jeness C; Greenhut, Isaac V; Leveau, Johan H J

2013-07-24

235

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

236

Genetic control of bacterial suicide: regulation of the induction of PBSX in Bacillus subtilis.  

PubMed Central

PBSX is a phage-like bacteriocin (phibacin) of Bacillus subtilis 168. Bacteria carrying the PBSX genome are induced by DNA-damaging agents to lyse and produce PBSX particles. The particles cannot propagate the PBSX genome. The particles produced by this suicidal response kill strains nonlysogenic for PBSX. A 5.2-kb region which controls the induction of PBSX has been sequenced. The genes identified include the previously identified repressor gene xre and a positive control factor gene, pcf. Pcf is similar to known sigma factors and acts at the late promoter PL, which has been located distal to pcf. The first two genes expressed from the late promoter show homology to genes encoding the subunits of phage terminases. Images

McDonnell, G E; Wood, H; Devine, K M; McConnell, D J

1994-01-01

237

Bacterial Bioluminescence Regulates Expression of a Host Cryptochrome Gene in the Squid-Vibrio Symbiosis  

PubMed Central

ABSTRACT 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.

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

2013-01-01

238

Single nucleotide polymorphism genotyping of aldehyde dehydrogenase 2 gene using a single bacterial magnetic particle.  

PubMed

A single nucleotide polymorphism (SNP) genotyping for aldehyde dehydrogenase 2 gene (ALDH2) has been developed by using a nano-sized magnetic particle, which was synthesized intracellularly by magnetic bacteria. Streptavidin-immobilized on bacterial magnetic particles (BMPs) were prepared using biotin labeled cross-linkers reacting with the amine group on BMPs. ALDH2 fragments from genomic DNA were amplified using a TRITC labeled primer and biotin labeled primer pair, and conjugated onto BMP surface by biotin-streptavidin interaction. PCR product-BMP complex was observed at a single particle level by fluorescence microscopy. These complexes were treated with restriction enzyme, specifically digesting the wild-type sequence of ALDH2 (normal allele of ALDH2). The homozygous (ALDH2*1/*1), heterozygous (ALDH2*1/*2), and mutant (ALDH2*2/*2) genotypes were discriminated by three fluorescence patterns of each particle. SNP genotyping of ALDH2 has been successfully achieved at a single particle level using BMP. PMID:12706576

Yoshino, Tomoko; Tanaka, Tsuyoshi; Takeyama, Haruko; Matsunaga, Tadashi

2003-05-01

239

Bacterial control on the structure of As-Fe oxy-hydroxides in acid mine drainage.  

NASA Astrophysics Data System (ADS)

Nano-crystalline or amorphous iron oxy-hydroxides are kinetically favored with respect to stable crystalline phases in low temperature environments. Therefore, they frequently occur as transient phases in Earth's surface environments. They exhibit very-high surface areas (few 100 cm2/g) and thus play a key role in the geochemical cycles of minor and trace elements, including toxic elements as arsenic. Natural low-temperature iron oxides also potentially host biological signatures since they can form through various biologically driven reactions. In the present communication, we compare the mineralogy and crystal chemistry of biogenic As-rich iron precipitates synthesized using various acidophilic bacterial strain isolated from an exceptionally arsenic-rich acid mine drainage [1]. XAS, XRD, SEM and TEM investigation of these highly reactive nano-minerals obtained in controlled conditions allows to better constrain their mechanisms of formation. Our data show that the enzymatic oxidation of Fe(II) and/or As(III) play a key role in controlling the nature of the mineral species precipitating in acid mine drainage. We show that the nature of mineral species forming from solutions can be directly determined by the metabolic activity of specific bacterial strains. This influence is thought to be primarily indirect, bacteria controlling the rate of Fe(II) and As(III) oxidation reactions, which in turn leads to various Fe(III) and As(V) super-saturation conditions. These latter parameters are crucial in controlling the structure of nano-crystalline As-Fe low temperature minerals. 1- Morin et al. (2003) Bacterial formation of tooeleite and mixed As(III)/(V)-Fe(III) gels in the Carnoulès acid mine drainage, France. A XANES, XRD and SEM study. Environ. Sci. and Technol. 37,1705-1712.

Morin, G.; Lebrun, S.; Juillot, F.; Casiot, C.; Bruneel, O.; Belin, S.; Proux, O.; Brown, G. E.; Guyot, F.; Calas, G.

2004-12-01

240

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

241

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

242

Single nucleotide polymorphism detection in aldehyde dehydrogenase 2 (ALDH2) gene using bacterial magnetic particles based on dissociation curve analysis.  

PubMed

Single nucleotide polymorphism (SNP) detection for aldehyde dehydrogenase 2 (ALDH2) gene based on DNA thermal dissociation curve analysis was successfully demonstrated using an automated system with bacterial magnetic particles (BMPs) by developing a new method for avoiding light scattering caused by nanometer-size particles when using commercially available fluorescent dyes such as FITC, Cy3, and Cy5 as labeling chromophores. Biotin-labeled PCR products in ALDH2, two allele-specific probes (Cy3-labeled detection probe for ALDH2*1 and Cy5-labeled detection probe for ALDH2*2), streptavidin-immobilized BMPs (SA-BMPs) were simultaneously mixed. The mixture was denatured at 70 degrees C for 3 min, cooled slowly to 25 degrees C, and incubated for 10 min, allowing the DNA duplex to form between Cy3- or Cy5-labeled detection probes and biotin-labeled PCR products on SA-BMPs. Then duplex DNA-BMP complex was heated to 58 degrees C, a temperature determined by dissociation curve analysis and a dissociated single-base mismatched detection probe was removed at the same temperature under precise control. Furthermore, fluorescence signal from the detection probe was liberated into the supernatant from completely matched duplex DNA-BMP complex by heating to 80 degrees C and measured. In the homozygote target DNA (ALDH2*1/*1 and ALDH2*2/*2), the fluorescence signals from single-base mismatched were decreased to background level, indicating that mismatched hybridization was efficiently removed by the washing process. In the heterozygote target DNA (ALDH2*1/*2), each fluorescence signals was at a similar level. Therefore, three genotypes of SNP in ALDH2 gene were detected using the automated detection system with BMPs. PMID:15329927

Maruyama, Kohei; Takeyama, Haruko; Nemoto, Etsuo; Tanaka, Tsuyoshi; Yoda, Kiyoshi; Matsunaga, Tadashi

2004-09-20

243

Culturable bacterial microflora associated with nectarine fruit and their potential for control of brown rot.  

PubMed

Microflora of fruit surfaces have been the best source of antagonists against fungi causing postharvest decay of fruit. However, there is little information on microflora colonizing surfaces of fruits other than grape, apple, and citrus. We characterized bacterial microflora on nectarine fruit surfaces from the early stage of development until harvest. Identification of bacterial strains was made using MIDI (fatty acid methyl ester analysis) and Biolog systems. Biolog identified 35% and MIDI 53% of the strains. Thus results from MIDI were used to determine the frequency of occurrence of genera and species. The most frequently occurring genera were Curtobacterium (21.31%), followed by Pseudomonas (19.99%), Microbacterium (13.57%), Clavibacter (9.69%), Pantoea (6.59%), and Enterobacter (4.26%). The frequency of isolations of some bacteria - for example, the major pseudomonads (Pseudomonas syringae, Pseudomonas putida, and Pseudomonas savastanoi) or Pantoea agglomerans - tended to decline as fruit developed. As Pseudomonas declined, Curtobacterium became more dominant. Time of isolation was a significant factor in the frequency of occurrence of different bacteria, indicating succession of the genera. Throughput screening of the bacterial strains against Monilinia fructicola on nectarine fruit resulted in the detection of strains able to control brown rot. The 10 best-performing antagonistic strains were subjected to secondary screening. Four strains reduced decay severity by more than 50% (51.7%-91.4% reduction) at the high pathogen inoculum concentration of 105 conidia/mL. PMID:20657618

Janisiewicz, Wojciech J; Buyer, Jeffrey S

2010-06-01

244

Evolution of bacterial flora in burn wounds: key role of environmental disinfection in control of infection  

PubMed Central

Bacterial flora in burn patients undergoes change over period of time and is dependent upon many factors. Study of burn flora is not only helpful in locating entry of multidrug resistant bacterial strains into the unit’s usual flora but also in determining current antibiotic susceptibilities. Since no studies are available from India that have studied sequential emergence of different microorganisms in burn wound, present study was carried out to study evolution of bacterial flora in burn wounds and its correlation with invasive wound infection. Environmental sampling was also carried out for possible sources of infection. Patients with 20-70% of total burn surface were enrolled and followed up for entire duration of stay. Clinical & treatment details were noted. Surface wound swabs were collected on first, third, seventh, tenth and fourteenth day post admission. Environmental sampling was done every three months. Of 215 wound swabs collected from 71 patients, 72 were sterile and 143 yielded 214 isolates. Colonization rates were 33% on first day, 94% on 7th day and 100% by 14th day. 42% swabs grew gram negative bacteria. Overall Staphylococcus aureus was the predominant isolate (45%) followed by Pseudomonas aeruginosa (13.9%), beta hemolytic Streptococci (9.4%). Maximum invasive infections were seen at the seventh day. A high level of environmental contamination was seen with S. aureus, a substantial portion being MRSA. Better control of environmental contamination and disinfection along with rigorous hand washing and barrier precautions are recommended to prevent infection of wounds.

Taneja, Neelam; Chari, PS; Singh, Malkit; Singh, Gagandeep; Biswal, Manisha; Sharma, Meera

2013-01-01

245

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

246

The use of the luxA gene of the bacterial luciferase operon as a reporter gene  

Microsoft Academic Search

Bacterial luciferase can be assayed rapidly and with high sensitivity both in vivo and in vitro. Here we demonstrate that the N-terminal hydrophobic domain of the a catalytic subunit of the luciferase enzyme is indispensable for enzyme activity, although N-terminal translational fusions with full luciferase activity can be obtained. Bacterial luciferase is therefore ideally suited as a reporter enzyme for

Olof Olsson; Csaba Koncz; Aladar A. Szalay

1988-01-01

247

Quorum-sensing regulation of gene expression: Fundamental and applied aspects and the role in bacterial communication  

Microsoft Academic Search

Quorum sensing (QS) is a specific type of regulation of gene expression in bacteria; it is dependent on the population density.\\u000a QS systems include two obligate components: a low-molecular-weight regulator (autoinducer), readily diffusible through the\\u000a cytoplasmic membrane, and a regulatory receptor protein, which interacts with the regulator. As the bacterial population reaches\\u000a a critical level of density, autoinducers accumulate to

I. A. Khmel

2006-01-01

248

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

249

Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning  

PubMed Central

Techniques based on amplification of 16S rRNA genes for comparing bacterial communities are now widely used in microbial ecology, but calibration of these techniques with traditional tools, such as cultivation, has been conspicuously absent. In this study, we compared levels of bacterial community diversity in two pinyon rhizosphere soil samples and two between-tree (interspace) soil samples by analyzing 179 cultivated bacterial isolates and 801 16S rRNA genes amplified from extracted soil DNA. Phylotypes were defined by performing a restriction fragment length polymorphism analysis of 16S rRNA gene sequences with the enzymes RsaI and BstUI. The average level of 16S rRNA gene sequence similarity of members of a phylotype was 86.6% based on an analysis of partial sequences. A total of 498 phylotypes were identified among the 16S ribosomal DNA (rDNA) clones, while 34 phylotypes occurred among the cultivated isolates. Analysis of sequences from a subset of the phylotypes showed that at least seven bacterial divisions were represented in the clone libraries, whereas the isolates represented only three. The phylotype richness, frequency distribution (evenness), and composition of the four culture collections and the four clone libraries were investigated by using a variety of diversity indices. Although cultivation and 16S rRNA cloning analyses gave contradictory descriptions of the relative phylotype richness for one of the four environments, the two methods identified qualitatively consistent relationships when levels of evenness were compared. The levels of phylotype similarity between communities were uniformly low (15 to 31%). Both methods consistently indicated that one environment was distinct from the other three. Our data illustrate that while 16S rDNA cloning and cultivation generally describe similar relationships between soil microbial communities, significant discrepancies can occur.

Dunbar, John; Takala, Shannon; Barns, Susan M.; Davis, Jody A.; Kuske, Cheryl R.

1999-01-01

250

A Non-Synonymous Coding Variant (L616F) in the TLR5 Gene Is Potentially Associated with Crohn's Disease and Influences Responses to Bacterial Flagellin  

PubMed Central

Background and Objectives Although numerous studies have implicated TLR5, or its ligands, bacterial flagellins, in the pathogenesis of Crohn's disease (CD), genome-wide association studies (GWAS) have not reported associations with the TLR5 gene. We aimed to examine potential CD-associated TLR5 variants and assess whether they modified inflammatory responses to bacterial flagellins. Methods and Principal Results A two-stage study was carried out. In stage 1, we genotyped tagging single-nucleotide polymorphisms (tag-SNPs) in the TLR5 gene in a sample of CD cases (<20 years of age, N?=?566) and controls (N?=?536). Single SNP and haplotype analysis was carried out. In Stage 2, we assessed the functional significance of potential CD-associated variant(s) vis-à-vis effects on the inflammatory response to bacterial flagellin using HEK293T cells. We observed marginal association between a non-synonymous coding SNP rs5744174 (p?=?0.05) and CD. Associations between SNP rs851139 that is in high linkage disequilibrium (LD) with SNP rs5744174 were also suggested (p?=?0.07). Haplotype analysis revealed that a 3 marker haplotype was significantly associated with CD (p?=?0.01). Functional studies showed that the risk allele (616F) (corresponding to the C allele of SNP rs5744174) conferred significantly greater production of CCL20 in response to a range of flagellin doses than the comparator allele (616L). Conclusions Our findings suggest that a non-synonymous coding variation in the TLR5 gene may confer modest susceptibility for CD.

Sheridan, Jared; Mack, David R.; Amre, Devendra K.; Israel, David M.; Cherkasov, Artem; Li, Huifang; Grimard, Guy; Steiner, Theodore S.

2013-01-01

251

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

252

INFLUENCE OF ROOT EXUDATES AND BACTERIAL METABOLIC ACTIVITY ON APPARENT CONJUGAL GENE TRANSFER FREQUENCIES IN THE RHIZOSPHERE OF WATER GRASS (ECHINOCLORA CRUSGALLI)  

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...

253

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

2012-11-02

254

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

255

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

2013-08-18

256

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

2012-06-11

257

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

258

Antisense Suppression of a (+)-?-Cadinene Synthase Gene in Cotton Prevents the Induction of This Defense Response Gene during Bacterial Blight Infection But Not Its Constitutive Expression1[w  

PubMed Central

In cotton (Gossypium hirsutum) the enzyme (+)-?-cadinene synthase (CDNS) catalyzes the first committed step in the biosynthesis of cadinane-type sesquiterpenes, such as gossypol, that provide constitutive and inducible protection against pests and diseases. A cotton cDNA clone encoding CDNS (cdn1-C4) was isolated from developing embryos and functionally characterized. Southern analysis showed that CDNS genes belong to a large multigene family, of which five genomic clones were studied, including three pseudogenes and one gene that may represent another subfamily of CDNS. CDNS expression was shown to be induced in cotton infected with either the bacterial blight or verticillium wilt pathogens. Constructs for the constitutive or seed-specific antisense suppression of cdn1-C4 were introduced into cotton by Agrobacterium-mediated transformation. Gossypol levels were not reduced in the seeds of transformants with either construct, nor was the induction of CDNS expression affected in stems of the constitutive antisense plants infected with Verticillium dahliae Kleb. However, the induction of CDNS mRNA and protein in response to bacterial blight infection of cotyledons was completely blocked in the constitutive antisense plants. These results suggest that cdn1-C4 may be involved specifically in the bacterial blight response and that the CDNS multigene family comprises a complex set of genes differing in their temporal and spatial regulation and responsible for different branches of the cotton sesquiterpene pathway.

Townsend, Belinda J.; Poole, Andrew; Blake, Christopher J.; Llewellyn, Danny J.

2005-01-01

259

Pretranslational control of Menkes disease gene expression.  

PubMed

The gene for Menkes disease codes for a Cu-transporting ATPase that regulates Cu homeostasis in all tissues with the exception of adult liver. The basis for developmental or tissue-specific regulation at present is not understood. To learn if the regulation is associated with the promoter, we cloned and sequenced a 2.2 kb genomic DNA fragment flanking exon 1. When ligated into a pGL2 luciferase reporter gene construct, the 2.2 kb showed promoter activity, but not nearly to the extent of a 1.3 kb fragment previously reporter by Levinson et al. Sequence analysis of the nucleotides spanning the region between 1.3 kb and 2.2 kb revealed a 13-nucleotide motif ACACAAAAAAATA 2059 bp upstream from the start site that duplicated the 'hunchback' binding site, a key site controlling developmental gene expression in Drosophila. Eliminating 129 bp containing the hunchback site (Hb) from the 5' end of the 2.2 kb stimulated promoter activity, suggesting the Hb site was basically suppressive. When ligated upstream of an SV40 and tested in SY5Y cells, however, the SV40 promoter activity was strongly stimulated, which conflicts with the site being suppressive. Mutating the site in the 2.2 kb weakened the promoter activity in SY5Y and HepG2 cells and a fragment with mutated sequence ligated upstream of the SV40 cancelled the activation of SV40 promoter activity. All data suggested the Hb site was a positive controlling site for Cu-ATPase expression. Nuclear extracts from SY5Y and HepG2 cells were observed to bind to a 106 bp probe with the Hb site in a gel-shift assay. Only SY5Y proteins, however, showed a slower moving shift band indicative of a secondary interaction. A probe with mutated sequences displayed the same shift pattern, suggesting other sites in the 106 bp DNA strand were also recognizing the nuclear proteins. A Southwestern analysis suggested that proteins of 125 kD, 70 kD, 50 kD and 42 kD bound to the wild type probe; a 60 kD and all with the exception of the 42 kD bound to the mutant probe. The data support the conclusion that the distal promoter of the Menkes disease gene contains elements that interact in combinatorial fashion to regulate Cu-ATPase expression and that tissue specificity may lie with the quantity or types of distinct DNA binding proteins in the nucleus. PMID:12572664

Harris, Edward D; Reddy, Manchi C M; Majumdar, Sudeep; Cantera, Mariela

2003-03-01

260

Characterization of gtf, a Glucosyltransferase Gene in the Genomes of Pediococcus parvulus and Oenococcus oeni, Two Bacterial Species Commonly Found in Wine?  

PubMed Central

“Ropiness” is a bacterial alteration in wines, beers, and ciders, caused by ?-glucan-synthesizing pediococci. A single glucosyltransferase, Gtf, controls ropy polysaccharide synthesis. In this study, we show that the corresponding gtf gene is also present on the chromosomes of several strains of Oenococcus oeni isolated from nonropy wines. gtf is surrounded by mobile elements that may be implicated in its integration into the chromosome of O. oeni. gtf is expressed in all the gtf+ strains, and ?-glucan is detected in the majority of these strains. Part of this ?-glucan accumulates around the cells forming a capsule, while the other part is liberated into the medium together with heteropolysaccharides. Most of the time, this polymer excretion does not lead to ropiness in a model medium. In addition, we show that wild or recombinant bacterial strains harboring a functional gtf gene (gtf+) are more resistant to several stresses occurring in wine (alcohol, pH, and SO2) and exhibit increased adhesion capacities compared to their gtf mutant variants.

Dols-Lafargue, Marguerite; Lee, Hyo Young; Le Marrec, Claire; Heyraud, Alain; Chambat, Gerard; Lonvaud-Funel, Aline

2008-01-01

261

DNA sequencing of the gene encoding a bacterial superantigen, Yersinia pseudotuberculosis-derived mitogen (YPM), and characterization of the gene product, cloned YPM  

SciTech Connect

Previously, we found a novel bacterial superantigen from Yersinia pseudotuberculosis, designated Y. pseudotuberculosis-derived mitogen (YPM). In the present study, we analyzed the DNA sequence of the gene encoding YPM. The YPM gene was cloned into a plasmid vector pMW119 and expressed in Escherichia coli DH10B. Like the native YPM, the cloned YPM required the expression of MHC class II molecules on accessory cells in the induction of IL-2 production by human T cells. TCR-V{beta} repertoire of human T cells reactive with the cloned YPM was V{beta}3, V{beta}9, V{beta}13.1, and V{beta}13.2. This repertoire is the same as that of T cells reactive with the native YPM. These results indicate that the cloned YPM expressed in E. coli is identical to the native YPM. Sequencing of the YPM gene revealed that the gene contained an open reading frame of 456 base pairs encoding a precursor form of 151 amino acid residues with m.w. 16,679 that is processed into a mature form of 131 amino acid residues with m.w. 14,529. Homology analysis revealed that the homology of amino acid sequence is quite low among YPM and other well known bacterial superantigens. We designated the gene encoding YPM as ypm. 30 refs., 5 figs., 2 tabs.

Miyoshi-Akiyama, Tohru; Kato, Hidehito; Uchiyama, Takehiko [Tokyo Women`s Medical College (Japan)] [and others

1995-05-15

262

Identification of Genes Controlled by Quorum Sensing in Pseudomonas aeruginosa  

Microsoft Academic Search

Bacteria communicate with each other to coordinate expression of specific genes in a cell density-dependent fashion, a phenomenon called quorum sensing and response. Although we know that quorum sensing via acyl-homoserine lactone (HSL) signals controls expression of several virulence genes in the human pathogen Pseudomonas aeruginosa, the number and types of genes controlled by quorum sensing have not been studied

Marvin Whiteley; Kimberly M. Lee; E. P. Greenberg

1999-01-01

263

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

264

Linezolid Exerts Greater Bacterial Clearance but No Modification of Host Lung Gene Expression Profiling: A Mouse MRSA Pneumonia Model  

PubMed Central

Background Linezolid (LZD) is beneficial to patients with MRSA pneumonia, but whether and how LZD influences global host lung immune responses at the mRNA level during MRSA-mediated pneumonia is still unknown. Methods A lethal mouse model of MRSA pneumonia mediated by USA300 was employed to study the influence of LZD on survival, while the sublethal mouse model was used to examine the effect of LZD on bacterial clearance and lung gene expression during MRSA pneumonia. LZD (100mg/kg/day, IP) was given to C57Bl6 mice for three days. On Day 1 and Day 3 post infection, bronchoalveolar lavage fluid (BALF) protein concentration and levels of cytokines including IL6, TNF?, IL1?, Interferon-? and IL17 were measured. In the sublethal model, left lungs were used to determine bacterial clearance and right lungs for whole-genome transcriptional profiling of lung immune responses. Results LZD therapy significantly improved survival and bacterial clearance. It also significantly decreased BALF protein concentration and levels of cytokines including IL6, IL1?, Interferon-? and IL17. No significant gene expression changes in the mouse lungs were associated with LZD therapy. Conclusion LZD is beneficial to MRSA pneumonia, but it does not modulate host lung immune responses at the transcriptional level.

Chen, Jiwang; Feng, Gang; Song, Yang; Wardenburg, Juliane B.; Lin, Simon; Inoshima, Ichiro; Otto, Michael; Wunderink, Richard G.

2013-01-01

265

A mutation within the leucine-rich repeat domain of the Arabidopsis disease resistance gene RPS5 partially suppresses multiple bacterial and downy mildew resistance genes.  

PubMed Central

Recognition of pathogens by plants is mediated by several distinct families of functionally variable but structurally related disease resistance (R) genes. The largest family is defined by the presence of a putative nucleotide binding domain and 12 to 21 leucine-rich repeats (LRRs). The function of these LRRs has not been defined, but they are speculated to bind pathogen-derived ligands. We have isolated a mutation in the Arabidopsis RPS5 gene that indicates that the LRR region may interact with other plant proteins. The rps5-1 mutation causes a glutamate-to-lysine substitution in the third LRR and partially compromises the function of several R genes that confer bacterial and downy mildew resistance. The third LRR is relatively well conserved, and we speculate that it may interact with a signal transduction component shared by multiple R gene pathways.

Warren, R F; Henk, A; Mowery, P; Holub, E; Innes, R W

1998-01-01

266

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

National Technical Information Service (NTIS)

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 wer...

A. Matin T. Schmidt D. Caldwell

1998-01-01

267

Dominant gene for common bean resistance to common bacterial blight caused by Xanthomonas axonopodis pv. phaseoli  

Microsoft Academic Search

The common bacterial blight pathogen [Xanthomonas axonopodis pv. phaseoli (Xap)] is a limiting factor for common bean (Phaseolus vulgaris L.) production worldwide and resistance to the pathogen in most commercial cultivars is inadequate. Variability in virulence\\u000a of the bacterial pathogen has been observed in strains isolated from Puerto Rico and Central America. A few common bean lines\\u000a show a differential

Mildred Zapata; James S. Beaver; Timothy G. Porch

2011-01-01

268

Eukaryotic control on bacterial cell cycle and differentiation in the Rhizobium-legume symbiosis  

PubMed Central

Symbiosis between legumes and Rhizobium bacteria leads to the formation of root nodules where bacteria in the infected plant cells are converted into nitrogen-fixing bacteroids. Nodules with a persistent meristem are indeterminate, whereas nodules without meristem are determinate. The symbiotic plant cells in both nodule types are polyploid because of several cycles of endoreduplication (genome replication without mitosis and cytokinesis) and grow consequently to extreme sizes. Here we demonstrate that differentiation of bacteroids in indeterminate nodules of Medicago and related legumes from the galegoid clade shows remarkable similarity to host cell differentiation. During bacteroid maturation, repeated DNA replication without cytokinesis results in extensive amplification of the entire bacterial genome and elongation of bacteria. This finding reveals a positive correlation in prokaryotes between DNA content and cell size, similar to that in eukaryotes. These polyploid bacteroids are metabolically functional but display increased membrane permeability and are nonviable, because they lose their ability to resume growth. In contrast, bacteroids in determinate nodules of the nongalegoid legumes lotus and bean are comparable to free-living bacteria in their genomic DNA content, cell size, and viability. Using recombinant Rhizobium strains nodulating both legume types, we show that bacteroid differentiation is controlled by the host plant. Plant factors present in nodules of galegoid legumes but absent from nodules of nongalegoid legumes block bacterial cell division and trigger endoreduplication cycles, thereby forcing the endosymbionts toward a terminally differentiated state. Hence, Medicago and related legumes have evolved a mechanism to dominate the symbiosis.

Mergaert, Peter; Uchiumi, Toshiki; Alunni, Benoit; Evanno, Gwenaelle; Cheron, Angelique; Catrice, Olivier; Mausset, Anne-Elisabeth; Barloy-Hubler, Frederique; Galibert, Francis; Kondorosi, Adam; Kondorosi, Eva

2006-01-01

269

Nucleotide sequence of the narL gene that is involved in global regulation of nitrate controlled respiratory genes of Escherichia coli.  

PubMed Central

The DNA sequence was determined for the narL gene of Escherichia coli. This gene is involved in global regulation of a number of nitrate controlled genes including frdABCD, tor, narGHJI, and adhE which are associated with bacterial respiration and fermentation. Comparison of the deduced amino acid sequence of narL to that of other bacterial genes revealed significant homologies to the phoB, ompR, and virG gene products based on the presence of similar protein domains. These DNA binding proteins are members of two-component regulatory systems. The similarities suggest that narL may also participate in such a two-component regulatory system and that the narR gene, which lies upstream of narL, may encode a second component required for nitrate control of gene regulation. In vitro protein synthesis experiments using a narL plasmid identified a putative NarL protein of 29 kDa in size consistent with the DNA sequence analysis. Primer extension experiments revealed the presence of two 5' termini for narL mRNA, and indicates that transcription may be complex. Images

Gunsalus, R P; Kalman, L V; Stewart, R R

1989-01-01

270

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

271

Construction of improved vectors and cassettes containing gusA and antibiotic resistance genes for studies of transcriptional activity and bacterial localization  

Microsoft Academic Search

Broad-host-range, conjugative vectors with a constitutively expressed gusA gene combined with different antibiotic resistance (tetracycline, gentamicin, kanamycin) genes have been constructed. These plasmids are designed for tracking Gram-negative bacterial strains without the risk of random mutagenesis. We also constructed a set of cassettes containing a promoterless gusA gene linked with different antibiotic resistance genes for making transcriptional fusions and for

Jerzy Wielbo; Anna Skorupska

2001-01-01

272

Root transcriptome analysis of Arabidopsis thaliana exposed to beneficial Bacillus subtilis FB17 rhizobacteria revealed genes for bacterial recruitment and plant defense independent of malate efflux.  

PubMed

Our previous work has demonstrated that Arabidopsis thaliana can actively recruit beneficial rhizobacteria Bacillus subtilis strain FB17 (hereafter FB17) through an unknown shoot-to-root long-distance signaling pathway post a foliar bacterial pathogen attack. However, it is still not well understood which genetic targets FB17 affects in plants. Microarray analysis of A. thaliana roots treated with FB17 post 24 h of treatment showed 168 and 129 genes that were up- and down-regulated, respectively, compared with the untreated control roots. Those up-regulated include auxin-regulated genes as well as genes involved in metabolism, stress response, and plant defense. In addition, other defense-related genes, as well as cell-wall modification genes were also down-regulated with FB17 colonization. Expression patterns of 20 selected genes were analyzed by semi-quantitative RT-PCR, validating the microarray results. A. thaliana insertion mutants were used against FB17 to further study the functional response of the differentially expressed genes. Five mutants for the up-regulated genes were tested for FB17 colonization, three (at3g28360, at3g20190 and at1g21240) mutants showed decreased FB17 colonization on the roots while increased FB17 titers was seen with three mutants of the down-regulated genes (at3g27980, at4g19690 and at5g56320). Further, these mutants for up-regulated genes and down-regulated genes were foliar infected with Pseudomonas syringae pv. tomato (hereafter PstDC3000) and analyzed for Aluminum activated malate transporter (ALMT1) expression which showed that ALMT1 may be the key regulator for root FB17 colonization. Our microarray showed that under natural condition, FB17 triggers plant responses in a manner similar to known plant growth-promoting rhizobacteria and to some extent also suppresses defense-related genes expression in roots, enabling stable colonization. The possible implication of this study opens up a new dialogin terms of how beneficial microbes regulate plant genetic response for mutualistic associations. PMID:23794026

Lakshmanan, Venkatachalam; Castaneda, Rafael; Rudrappa, Thimmaraju; Bais, Harsh P

2013-06-23

273

A single regulatory gene is sufficient to alter bacterial host range  

PubMed Central

Microbial symbioses are essential for the normal development and growth of animals1,2,3. Often, symbionts must be acquired from the environment during each generation, and identification of the relevant symbiotic partner against a myriad of unwanted relationships is a formidable task4. While examples of this specificity are well-documented, the genetic mechanisms governing it are poorly characterized5. Here we show that the two-component sensor kinase RscS is necessary and sufficient for conferring efficient colonization of Euprymna scolopes squid by bioluminescent Vibrio fischeri from the North Pacific Ocean. In the squid symbiont V. fischeri ES114, RscS controls light-organ colonization by inducing the Syp exopolysaccharide, a mediator of biofilm formation during initial infection. A genome-level comparison revealed that rscS, while present in squid symbionts, is absent from the fish symbiont V. fischeri MJ11. We found that heterologous expression of RscS in strain MJ11 conferred the ability to colonize E. scolopes in a manner comparable to that of natural squid isolates. Furthermore, phylogenetic analyses support an important role for rscS in the evolution of the squid symbiosis. Our results demonstrate that a regulatory gene can alter the host range of animal-associated bacteria. We show that, by encoding a regulator and not an effector that interacts directly with the host, a single gene can contribute to the evolution of host specificity by switching “on” pre-existing capabilities for interaction with animal tissue.

Mandel, Mark J.; Wollenberg, Michael S.; Stabb, Eric V.; Visick, Karen L.; Ruby, Edward G.

2009-01-01

274

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

275

Alternatives to antibiotics for the control of bacterial disease in aquaculture.  

PubMed

The wide and frequent use of antibiotics in aquaculture has resulted in the development and spread of antibiotic resistance. Because of the health risks associated with the use of antibiotics in animal production, there is a growing awareness that antibiotics should be used with more care. This is reflected in the recent implementation of more strict regulations on the prophylactic use of antibiotics and the presence of antibiotic residues in aquaculture products. For a sustainable further development of the aquaculture industry, novel strategies to control bacterial infections are needed. This review evaluates several alternative biocontrol measures that have emerged recently. Most of these methods are still in research phase; few have been tested in real aquaculture settings. It is important to further develop different strategies that could be combined or used in rotation in order to maximise the chance of successfully protecting the animals and to prevent resistance development. PMID:21489864

Defoirdt, Tom; Sorgeloos, Patrick; Bossier, Peter

2011-04-12

276

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

277

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

SciTech Connect

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{sup 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.

Hjort, K.; Bergstrom, M.; Adesina, M.F.; Jansson, J.K.; Smalla, K.; Sjoling, S.

2009-09-01

278

Design of a new universal real-time PCR system targeting the tuf gene for the enumeration of bacterial counts in food.  

PubMed

A novel universal real-time PCR, consisting of newly designed oligonucleotide subsets, was designed for a bacterial housekeeping gene encoding the peptide elongation factor Tu. Specificity and universality were confirmed in 66 bacterial strains, including 51 genera and 63 species. The amplification kinetics of tuf gene-targeted real-time quantitative PCR were consistent in a wide range of bacterial species tested. A calibration curve (r(2) = 0.97) was produced for the estimation of bacterial counts, based on measurements of representative inoculations with 10-fold serial dilutions of the cells of representative bacterial species. Linear regression analysis of the real-time PCR-derived bacterial counts and aerobic plate counts, in a total 149 samples consisting of 25 minced meat, 34 fresh-cut vegetables, and 90 fish, exhibited a high correlation (r(2) = 0.84, 0.87, and 0.95, respectively) over the range of 3.0 to 9.0 log CFU/g. In total, the difference between the two methods was less than 0.5 log in 75 of these samples, and in the remaining 74 samples, the difference was 0.5 to 1.0 log. Presently, our tuf gene-targeted real-time quantitative PCR assay achieves a rapid (within 2 h) estimation of bacterial counts of 3.0 to 9.0 log CFU/g, in a practical manner. PMID:20377955

Tanaka, Yuichiro; Takahashi, Hajime; Simidu, Usio; Kimura, Bon

2010-04-01

279

[Colonization and disease control and fruit preservation functions of endophytic bacterial strains in lychee].  

PubMed

By spraying the GFP-marked endophytic bacterial strains BS-2-gfp and TB2-gfp, this paper studied their colonization in lychee organs and the functions of the strains in disease control and fruit preservation. The BS-2-gfp and TB2-gfp could colonize and propagate in lychee leaves, flowers, un-matured fruits, and matured fruits, and transfer from the flowers to un-matured fruits. The colonization of BS-2-gfp and TB2-gfp in lychee leaves varied with season and growth stage, being larger in quantity and longer in duration in spring than in autumn. The colonization quantity and duration of the strains also differed in other organs. Both the BS-2-gfp and the TB2-gfp could be isolated and recovered from lychee leaves after 37 d inoculation, the BS-2-gfp could not be isolated from the flowers after inoculation for 10 d, and the BS-2-gfp and TB2-gfp had the largest colonization quantity in matured fruits. The colonization quantity of TB2-gfp in lychee pericarp reached to the maximum (1.90 x 10(6) CFU x g(-1) FM) when the disease index of litchi downy blight had a sharp increase, and, compared with BS-2-gfp, the TB2-gfp had better fruit preservation efficiency, and its colonization quantity in lychee pericarp was also higher. It was suggested that there was a positive correlation between the colonization quantity of test bacterial strains in lychee pericarp and the disease control and fruit preservation effect. PMID:22097379

Cai, Xue-qing; Chen, Wei; Lin, Na; Lin, Tong; Hu, Fang-ping

2011-08-01

280

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

PubMed Central

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.

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

2007-01-01

281

Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences.  

PubMed Central

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, a number of the sequences were similar to those of the order Verrucomicrobiales. However, few of the sequence types are closely related to those of characterized species. The relative contributions of the groups of sequences differed among the lakes, suggesting that bacterial population structure varies and that it may be possible to relate aquatic bacterial community structure to water chemistry.

Hiorns, W D; Methe, B A; Nierzwicki-Bauer, S A; Zehr, J P

1997-01-01

282

Induction of hemolin gene expression by bacterial cell wall components in eri-silkworm, Samia cynthia ricini.  

PubMed

A cDNA clone encoding hemolin was isolated from fat body of immunized Samia cynthia ricini larvae based on subtractive suppression hybridization method. The cDNA encodes 413 amino acid residue open reading frame with an 18 residue predicted signal peptide. The expression of the gene was strongly induced in fat body and midgut by an injection of bacterial cells or peptidoglycans, but very weakly by lipopolysaccharide. The mRNA expression in the fat body was detected as early as 3 h post-injection, and reached the peak level at 12 h. PMID:17126583

Bao, Yanyuan; Yamano, Yoshiaki; Morishima, Isao

2006-10-17

283

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

284

Use of a bacterial expression vector to map the varicella-zoster virus major glycoprotein gene, gC.  

PubMed Central

The genome of varicella-zoster virus (VZV) encodes at least three major glycoprotein genes. Among viral gene products, the gC gene products are the most abundant glycoproteins and induce a substantial humoral immune response (Keller et al., J. Virol. 52:293-297, 1984). We utilized two independent approaches to map the gC gene. Small fragments of randomly digested VZV DNA were inserted into a bacterial expression vector. Bacterial colonies transformed by this vector library were screened serologically for antigen expression with monoclonal antibodies to gC. Hybridization of the plasmid DNA from a gC antigen-positive clone revealed homology to the 3' end of the VZV Us segment. In addition, mRNA from VZV-infected cells was hybrid selected by a set of VZV DNA recombinant plasmids and translated in vitro, and polypeptide products were immunoprecipitated by convalescent zoster serum or by monoclonal antibodies to gC. This analysis revealed that the mRNA encoding a 70,000-dalton polypeptide precipitable by anti-gC antibodies mapped to the HindIII C fragment, which circumscribes the entire Us region. We conclude that the VZV gC glycoprotein gene maps to the 3' end of the Us region and is expressed as a 70,000-dalton primary translational product. These results are consistent with the recently reported DNA sequence of Us (A.J. Davison, EMBO J. 2:2203-2209, 1983). Furthermore, glycosylation appears not to be required for a predominant portion of the antigenicity of gC glycoproteins. We also report the tentative map assignments for eight other VZV primary translational products. Images

Ellis, R W; Keller, P M; Lowe, R S; Zivin, R A

1985-01-01

285

Control of Stochasticity in Eukaryotic Gene Expression  

Microsoft Academic Search

Noise, or random fluctuations, in gene expression may produce variability in cellular behavior. To measure the noise intrinsic to eukaryotic gene expression, we quantified the differences in expression of two alleles in a diploid cell. We found that such noise is gene-specific and not dependent on the regulatory pathway or absolute rate of expression. We propose a model in which

Jonathan M. Raser; Erin K. O'Shea

2004-01-01

286

A bacterial artificial chromosome (BAC) library of Malus floribunda 821 and contig construction for positional cloning of the apple scab resistance gene Vf  

Microsoft Academic Search

The apple scab resistance gene Vf, originating from the wild species Malus floribunda 821, has been incorporated into a wide variety of apple cultivars through a classical breeding program. With the aim of isolating the Vf gene, a bacterial artificial chromosome (BAC) library consisting of 31 584 clones has been constructed from M. floribunda 821. From the analysis of 88

Mingliang Xu; Junqi Song; Zhukuan Cheng; Jiming Jiang; Schuyler S. Korban

2001-01-01

287

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

288

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

289

Evolution of Transcription Regulatory Genes Is Linked to Niche Specialization in the Bacterial Pathogen Streptococcus pyogenes  

Microsoft Academic Search

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

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

2005-01-01

290

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

291

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

2013-07-24

292

DNA bridging and antibridging: a role for bacterial nucleoid-associated proteins in regulating the expression of laterally acquired genes.  

PubMed

Horizontal DNA transfer plays a major role in the evolution of bacteria. It allows them to acquire new traits rapidly and these may confer fitness advantages as the bacteria compete with others in the environment. Historically, the mechanisms of horizontal DNA transfer, chiefly conjugation, transformation and transduction, have received a great deal of attention. Less attention has been focused on the regulatory problems that may accompany the acquisition of new genes by lateral routes. How are these genes integrated into the existing regulatory circuits of the cell? Does a process of 'plug-and-play' operate, or are the new genes silenced pending the evolution of regulatory mechanisms that make their expression not only safe but also beneficial to both the gene and its new host? Recent research shows that bacterial nucleoid-associated proteins such as H-NS, HU and Fis are important contributors to the processes of regulatory integration that accompany horizontal gene transfer. A key emerging theme is the antagonism that exists between the DNA-protein-DNA bridging activity of the H-NS repressor and the DNA-bending and DNA-wrapping activities of regulatory proteins that oppose H-NS. PMID:19207739

Dorman, Charles J; Kane, Kelly A

2008-12-22

293

Analysis of extracellular alginate lyase and its gene from a marine bacterial strain, Pseudoalteromonas atlantica AR06.  

PubMed

Pseudoalteromonas atlantica AR06 is a marine bacterial strain that can utilize alginate as a sole source of carbon and energy. The extracellular protein fraction prepared from the AR06 cultivation media exhibited alginate lyase activity to depolymerize the alginate molecules having homopolymeric and heteropolymeric forms of mannuronate and guluronate so as to mainly convert into the dimer to tetramer. A DNA fragment encoding a portion of alginate lyase was amplified from AR06 genomic DNA by PCR using a set of degenerated primers, and then the whole alginate lyase gene, named alyA, and its flanking regions were obtained from a cosmid library of AR06 genomic DNA. The alyA mutant of AR06 showed (1) the loss of alginate depolymerization activity on alginate agar plate and (2) significant growth defects in alginate minimal medium; these defects were complemented by the introduction of the alyA gene. Furthermore, zymography and biochemical analyses revealed that three extracellular protein bands of AR06 had alginate lyase activities and that all three protein bands were derived from the nascent alyA gene product. These results clearly indicated that the alyA gene greatly contributes to the assimilation of alginate in AR06. The transcription of the alyA gene was induced by the presence of alginate in minimal medium, but its obvious induction was not observed in rich medium even in the presence of alginate. PMID:19844705

Matsushima, Ryoji; Danno, Hiroko; Uchida, Motoharu; Ishihara, Kenji; Suzuki, Toshiyuki; Kaneniwa, Masaki; Ohtsubo, Yoshiyuki; Nagata, Yuji; Tsuda, Masataka

2009-10-21

294

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.

295

Use of a bacterial expression vector to identify the gene encoding a major core protein of vaccinia virus.  

PubMed Central

The DNA sequence of a vaccinia virus late gene contains an open reading frame that corresponds to the 28,000-dalton (28K) polypeptide made by in vitro translation of hybrid-selected mRNA. To further characterize the protein product of this late gene, we cloned a segment of DNA containing part of the open reading frame into a bacterial expression vector. The fusion protein produced from this vector, containing 151 amino acids of the predicted vaccinia virus protein, was used to immunize rabbits. The resulting antiserum specifically bound to a major 25K structural protein that is localized in the core of vaccinia virions, as well as to a 28K protein found in infected cells. Pulse-chase experiments indicated that the 25K core protein is originally made as a 28K precursor. Images

Weir, J P; Moss, B

1985-01-01

296

A red beet (Beta vulgaris) UDP-glucosyltransferase gene induced by wounding, bacterial infiltration and oxidative stress.  

PubMed

Mechanical wounding, infiltration with P. syringae or A. tumefaciens, and exposure to an H(2)O(2)-generating system (Glc/Glc oxidase) induce betacyanin synthesis in red beet (Beta vulgaris) leaves. These conditions also induced the expression of BvGT, a gene encoding a glucosyltransferase (GT) from Beta vulgaris. BvGT has a high similarity to Dorotheanthus bellidiformis betanidin-5 GT involved in betacyanin synthesis. Furthermore, the transient expression of a BvGT antisense construct resulted in the reduction of BvGT transcript accumulation and betanin synthesis, suggesting a role for this gene product in betacyanin glucosylation. In addition, the NADPH oxidase inhibitor, diphenylene iodonium (DPI), inhibited the accumulation of the BvGT transcript in response to infiltration with Agrobacterium tumefaciens. Hence, this result suggests that ROS produced by a plasma membrane NADPH oxidase may act as a signal to induce BvGT expression, necessary for betanin synthesis after wounding and bacterial infiltration. PMID:15582929

Sepúlveda-Jiménez, Gabriela; Rueda-Benítez, Patricia; Porta, Helena; Rocha-Sosa, Mario

2004-12-06

297

Transformation of Japanese persimmon (Diospyros kaki Thunb.) with a bacterial gene for choline oxidase  

Microsoft Academic Search

This report describes the first successful genetic engineering of tolerance to salt in an agriculturally important species of woody plants by Agrobacterium-mediated transformation with the codA gene of Arthrobacter globiformis. This gene encodes choline oxidase, which catalyzes the oxidation of choline to glycinebetaine. The binary plasmid vector pGC95.091, containing a kanamycin-resistance gene (nptII), a gene for ß-glucuronidase (gusA) and the

Mei Gao; Atsushi Sakamoto; Keisuke Miura; Norio Murata; Akira Sugiura; Ryutaro Tao

2000-01-01

298

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

Microsoft Academic Search

Background  Invasive bacteria are known to have captured and adapted eukaryotic host genes. They also readily acquire colonizing genes\\u000a 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

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

2004-01-01

299

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

300

Phylogenetic diversity of bacterial symbionts of Solemya hosts based on comparative sequence analysis of 16S rRNA genes.  

PubMed Central

The bacterial endosymbionts of two species of the bivalve genus Solemya from the Pacific Ocean, Solemya terraeregina and Solemya pusilla, were characterized. Prokaryotic cells resembling gram-negative bacteria were observed in the gills of both host species by transmission electron microscopy. The ultrastructure of the symbiosis in both host species is remarkably similar to that of all previously described Solemya spp. By using sequence data from 16S rRNA, the identity and evolutionary origins of the S. terraeregina and S. pusilla symbionts were also determined. Direct sequencing of PCR-amplified products from host gill DNA with primers specific for Bacteria 16S rRNA genes gave a single, unambiguous sequence for each of the two symbiont species. In situ hybridization with symbiont-specific oligonucleotide probes confirmed that these gene sequences belong to the bacteria residing in the hosts gills. Phylogenetic analyses of the 16S rRNA gene sequences by both distance and parsimony methods identify the S. terraeregina and S. pusilla symbionts as members of the gamma subdivision of the Proteobacteria. In contrast to symbionts of other bivalve families, which appear to be monophyletic, the S. terraeregina and S. pusilla symbionts share a more recent common ancestry with bacteria associating endosymbiotically with bivalves of the superfamily Lucinacea than with other Solemya symbionts (host species S. velum, S. occidentalis, and S. reidi). Overall, the 16S rRNA gene sequence data suggest that the symbionts of Solemya hosts represent at least two distinct bacterial lineages within the gamma-Proteobacteria. While it is increasingly clear that all extant species of Solemya live in symbiosis with specific bacteria, the associations appear to have multiple evolutionary origins.

Krueger, D M; Cavanaugh, C M

1997-01-01

301

Terminal restriction pattern analysis of 16S rRNA genes for the characterization of bacterial communities of activated sludge.  

PubMed

A culture-independent molecular technique using terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes was applied to the characterization of bacterial communities of activated sludge taken from different municipal sewage treatment plants. 16S rDNA fragments from the bulk DNA of sludge were amplified by PCR with a Cy5-labeled forward primer corresponding to nucleotide positions 8 to 27 and a reverse primer complementary to positions 907 to 926 in the Escherichia coli numbering system. The 16S rDNAs thus obtained were digested with tetrameric restriction enzymes and analyzed using a Pharmacia automated DNA sequencer. A preliminary study on a model DNA mixture prepared from different bacterial species showed that the fluorescence intensity of terminal fragments (T-RFs) of 16S rDNAs amplified and detected was directly proportional to the 16S rRNA gene copy number rather than the amount of genomic DNA of each species present. 16S rDNA fragments amplified from the sludges and digested with HhaI usually generated at least 60 T-RFs, among which T-RFs of around 208 bp were the most abundant regardless of the time or area sampled. Southern blot hybridization with oligonucleotide probes specific to the 5' terminal regions of the 16S rDNA of different phylogenetic groups indicated that the T-RFs of around 208 bp were derived from members of the beta subclass of the class Proteobacteria. Hybridization with a probe specific to the class Actinobacteria failed to detect any appreciable signal. These results did not agree fully with those obtained by quinone profiling. The usefulness and limitations of the T-RFLP method for monitoring bacterial population dynamics in activated sludge were discussed. PMID:16232834

Hiraishi, A; Iwasaki, M; Shinjo, H

2000-01-01

302

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

303

Role of gene order in developmental control of human gamma- and beta-globin gene expression.  

PubMed

To determine the effect of gene order on globin gene developmental regulation, we produced transgenic mice containing two tandemly arranged gamma- or beta-globin or gamma beta- and beta gamma-globin genes linked to a 2.5-kb cassette containing sequences of the locus control region (LCR). Analysis of constructs containing two identical gamma or beta genes assessed the effect of gene order on globin gene expression, while analysis of constructs containing tandemly arranged gamma and beta genes assessed any additional effects of the trans-acting environment. When two gamma genes were tandemly linked to the LCR, expression from the proximal gamma gene was three- to fourfold higher than expression from the distal gamma gene, and the ratio of proximal to distal gene expression remained unchanged throughout development. Similarly, when two beta genes were tandemly linked to the LCR, the proximal beta gene was predominantly expressed throughout development. These results indicate that proximity to LCR increases gene expression, perhaps by influencing the frequency of interaction between the LCR and globin gene promoters. An arrangement where the gamma gene was proximal and the beta gene distal to the LCR resulted in predominant gamma-gene expression in the embryo. When the order was reversed and the gamma gene was placed distally to the LCR, gamma-gene expression in the embryo was still up to threefold higher than expression of the LCR-proximal beta gene. These findings suggest that the embryonic trans-acting environment interacts preferentially with the gamma genes irrespective of their order or proximity to the LCR. We conclude that promoter competition rather than gene order plays the major role in globin gene switching. PMID:8336720

Peterson, K R; Stamatoyannopoulos, G

1993-08-01

304

Direct transcriptional control of the plasminogen activator gene of Yersinia pestis by the cyclic AMP receptor protein.  

PubMed

Horizontal gene transfer events followed by proper regulatory integration of a gene drive rapid evolution of bacterial pathogens. A key event in the evolution of the highly virulent plague bacterium Yersinia pestis was the acquisition of plasmid pPCP1, which carries the plasminogen activator gene, pla. This promoted the bubonic form of the disease by increasing bacterial dissemination from flea bite sites and incidentally enhanced replication in respiratory airways during pneumonic infection. We determined that expression of pla is controlled by the global regulator cyclic AMP (cAMP) receptor protein (Crp). This transcription factor is well conserved among distantly related bacteria, where it acts as a soluble receptor for the ubiquitous signaling molecule cAMP and controls a global network of metabolic and stress-protective genes. Crp has a similar physiological role in Y. pestis since loss of its function resulted in an inability to metabolize a variety of nonglucose substrates. Activation of pla expression requires a transcription activation element of the pla promoter that serves as a Crp binding site. Crp interaction with this site was demonstrated to occur only in the presence of cAMP. Alteration of the Crp binding site nucleotide sequence prevented in vitro formation of Crp-DNA complexes and inhibited in vivo expression of pla. The placement of pla under direct regulatory control of Crp highlights how highly adapted pathogens integrate laterally acquired genes to coordinate virulence factor expression with global gene networks to maintain homeostasis through the infectious life cycle. PMID:17933899

Kim, Tae-Jong; Chauhan, Sadhana; Motin, Vladimir L; Goh, Ee-Been; Igo, Michele M; Young, Glenn M

2007-10-12

305

Inflammatory cytokine gene expression in human periodontal ligament fibroblasts stimulated with bacterial lipopolysaccharides.  

PubMed Central

The effects of Porphyromonas gingivalis lipopolysaccharide (P-LPS) and Escherichia coli lipopolysaccharide (E-LPS) on the gene expression and production of inflammatory cytokines of human periodontal ligament fibroblasts (HPLF) were examined by a Northern (RNA blot) assay and enzyme-linked immunosorbent assay, respectively. mRNAs for interleukin-6 (IL-6), IL-8, and transforming growth factor beta (TGF-beta) were detected in HPLF cells, but IL-1 alpha, IL-1 beta, tumor necrosis factor alpha, transforming growth factor alpha, and granulocyte-macrophage colony-stimulating factor were not detected by reverse transcription-PCR. The expression of TGF-beta mRNA was not influenced by either LPS. P-LPS (1 to 10 micrograms/ml) and E-LPS (100 micrograms/ml) markedly stimulated the expression of IL-6 and IL-8 mRNAs compared with the control. The synthesis of IL-6 and IL-8 was also stimulated by 10 and 100 micrograms of both LPSs per ml, but IL-8 synthesis was not stimulated with E-LPS at 1 microgram/ml. Secretion of IL-6 and IL-8 into the culture medium was detected at 6 and 3 h, respectively, after exposure to P-LPS (10 micrograms/ml). These findings suggested that P. gingivalis leads to periodontal tissue destruction and alveolar bone resorption through IL-6 and IL-8 released from HPLF cells stimulated with its LPS.

Yamaji, Y; Kubota, T; Sasaguri, K; Sato, S; Suzuki, Y; Kumada, H; Umemoto, T

1995-01-01

306

Bacterial infections associated with cancer: possible implication in etiology with special reference to lateral gene transfer  

Microsoft Academic Search

Bacteria are capable of exchanging DNA between each other and even from other organisms including human, but what will be\\u000a the fate of such exchange? Enigmatic association between bacterial infections and cancer is also demonstrated recently with\\u000a unknown exact cause and effect mechanism. This enigma may be resolved not in all but in few cases with the view of horizontal

Abdul Arif Khan; Abhinav Shrivastava

2010-01-01

307

Dose–response relationships and statistical performance of a battery of bacterial gene profiling assays  

Microsoft Academic Search

Because of increasing awareness and legislative demands, there is a demand for the development and use of biological assays\\u000a for the assessment of the toxicity of chemicals, environmental samples. Recently, a growing number of bacterial reporter assays\\u000a have been developed and implemented. Nevertheless, little data is published on the performance of these assays in terms of\\u000a analytical parameters. We present

F. Dardenne; I. Nobels; W. De Coen; R. Blust

2007-01-01

308

Control of Stochasticity in Eukaryotic Gene Expression  

NASA Astrophysics Data System (ADS)

Noise, or random fluctuations, in gene expression may produce variability in cellular behavior. To measure the noise intrinsic to eukaryotic gene expression, we quantified the differences in expression of two alleles in a diploid cell. We found that such noise is gene-specific and not dependent on the regulatory pathway or absolute rate of expression. We propose a model in which the balance between promoter activation and transcription influences the variability in messenger RNA levels. To confirm the predictions of our model, we identified both cis- and trans-acting mutations that alter the noise of gene expression. These mutations suggest that noise is an evolvable trait that can be optimized to balance fidelity and diversity in eukaryotic gene expression.

Raser, Jonathan M.; O'Shea, Erin K.

2004-06-01

309

Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations  

Microsoft Academic Search

BACKGROUND: Genome scans are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation, but on their own, they are often helpless at identifying the specific gene(s) or mutation(s) targeted by selection. This shortcoming is hopefully bound to disappear in the near future, thanks to the wealth of new genomic resources that are currently being developed

Aurélie Bonin; Margot Paris; Guillaume Tetreau; Jean-Philippe David; Laurence Després

2009-01-01

310

Self-Organization in High-Density Bacterial Colonies: Efficient Crowd Control  

Microsoft Academic Search

Colonies of bacterial cells can display complex collective dynamics, frequently culminating in the formation of biofilms and other ordered super-structures. Recent studies suggest that to cope with local environmental challenges, bacterial cells can actively seek out small chambers or cavities and assemble there, engaging in quorum sensing behavior. By using a novel microfluidic device, we showed that within chambers of

HoJung Cho; Henrik Jönsson; Kyle Campbell; Pontus Melke; Joshua W Williams; Bruno Jedynak; Ann M Stevens; Alex Groisman; Andre Levchenko

2007-01-01

311

Fuzzy logic controllers generated by pseudo-bacterial genetic algorithm with adaptive operator  

Microsoft Academic Search

This paper presents a new genetic operator called adaptive operator to improve local portions of chromesomes. This new operator is implemented in a pseudo-bacterial genetic algorithm (PBGA). The PBGA was proposed by the authors as a new approach combining a genetic algorithm (GA) with a local improvement mechanism inspired by a process in bacterial genetics. The PBGA was applied for

N. E. Nawa; T. Hashiyama; T. Furuhashi; Y. Uchikawa

1997-01-01

312

Organic matter bioavailability controls the active bacterial fraction in deep-sea sediments  

Microsoft Academic Search

Deep-sea sediments, covering more than 60% of the earth surface, represent the largest Earth's ecosystem. Bacteria are the most abundant component and the major players of biogeochemical transformations. However, the knowledge of the physiological and metabolic state of bacterial cells in deep-sea sediments is still extremely poor, thus limiting our actual comprehension of bacterial role on C cycling and early

G. M. Luna; L. Giuliano; R. Danovaro

2003-01-01

313

A bacterial artificial chromosome (BAC) library for sunflower, and identification of clones containing genes for putative transmembrane receptors.  

PubMed

Sunflower (Helianthus annuus L.) is an economically important oil seed crop with an estimated genome size of 3000 Mb. We have constructed a bacterial artificial chromosome (BAC) library for sunflower, which represents an estimated 4- to 5-fold coverage of the genome. Nuclei isolated from young leaves were used as a source of high-molecular-weight DNA and a partial restriction endonuclease digestion protocol was used to cleave the DNA. A random sample of 60 clones indicated an average insert size of 80 kb, implying a 95% probability of recovering any specific sequence of interest. The library was screened with chloroplast DNA probes. Only 0.1% of the clones were identified to be of chloroplast origin, indicating that contamination with organellar DNAs is very low. The utility of the library was evaluated by screening for the presence of genes for putative transmembrane receptors sharing epidermal growth factor (EGF) and integrin-like domains. First, a homologous sunflower EST (HaELP1) was obtained by degenerate RT-PCR cloning, using Arabidopsis thaliana genes (AtELP) as a source of consensus sequences. Three different BACs yielded positive hybridization signals when HaELP1 was used as a probe. BAC subcloning and sequencing demonstrated the presence of two different loci putatively homologous to genes for transmembrane proteins with EGF- and integrin-like domains from sunflower. This work demonstrates the suitability of the library for homology map-based cloning of sunflower genes and physical mapping of the sunflower genome. PMID:11862492

Gentzbittel, L; Abbott, A; Galaud, J P; Georgi, L; Fabre, F; Liboz, T; Alibert, G

2001-12-19

314

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

315

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.  

PubMed

Taxonomic classification of the thousands-millions of 16S rRNA gene sequences generated in microbiome studies is often achieved using a naïve Bayesian classifier (for example, the Ribosomal Database Project II (RDP) classifier), due to favorable trade-offs among automation, speed and accuracy. The resulting classification depends on the reference sequences and taxonomic hierarchy used to train the model; although the influence of primer sets and classification algorithms have been explored in detail, the influence of training set has not been characterized. We compared classification results obtained using three different publicly available databases as training sets, applied to five different bacterial 16S rRNA gene pyrosequencing data sets generated (from human body, mouse gut, python gut, soil and anaerobic digester samples). We observed numerous advantages to using the largest, most diverse training set available, that we constructed from the Greengenes (GG) bacterial/archaeal 16S rRNA gene sequence database and the latest GG taxonomy. Phylogenetic clusters of previously unclassified experimental sequences were identified with notable improvements (for example, 50% reduction in reads unclassified at the phylum level in mouse gut, soil and anaerobic digester samples), especially for phylotypes belonging to specific phyla (Tenericutes, Chloroflexi, Synergistetes and Candidate phyla TM6, TM7). Trimming the reference sequences to the primer region resulted in systematic improvements in classification depth, and greatest gains at higher confidence thresholds. Phylotypes unclassified at the genus level represented a greater proportion of the total community variation than classified operational taxonomic units in mouse gut and anaerobic digester samples, underscoring the need for greater diversity in existing reference databases. PMID:21716311

Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth E

2011-06-30

316

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys  

PubMed Central

Taxonomic classification of the thousands–millions of 16S rRNA gene sequences generated in microbiome studies is often achieved using a naïve Bayesian classifier (for example, the Ribosomal Database Project II (RDP) classifier), due to favorable trade-offs among automation, speed and accuracy. The resulting classification depends on the reference sequences and taxonomic hierarchy used to train the model; although the influence of primer sets and classification algorithms have been explored in detail, the influence of training set has not been characterized. We compared classification results obtained using three different publicly available databases as training sets, applied to five different bacterial 16S rRNA gene pyrosequencing data sets generated (from human body, mouse gut, python gut, soil and anaerobic digester samples). We observed numerous advantages to using the largest, most diverse training set available, that we constructed from the Greengenes (GG) bacterial/archaeal 16S rRNA gene sequence database and the latest GG taxonomy. Phylogenetic clusters of previously unclassified experimental sequences were identified with notable improvements (for example, 50% reduction in reads unclassified at the phylum level in mouse gut, soil and anaerobic digester samples), especially for phylotypes belonging to specific phyla (Tenericutes, Chloroflexi, Synergistetes and Candidate phyla TM6, TM7). Trimming the reference sequences to the primer region resulted in systematic improvements in classification depth, and greatest gains at higher confidence thresholds. Phylotypes unclassified at the genus level represented a greater proportion of the total community variation than classified operational taxonomic units in mouse gut and anaerobic digester samples, underscoring the need for greater diversity in existing reference databases.

Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth E

2012-01-01

317

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

318

Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies.  

PubMed

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. PMID:22880076

Vasileiadis, Sotirios; Puglisi, Edoardo; Arena, Maria; Cappa, Fabrizio; Cocconcelli, Pier S; Trevisan, Marco

2012-08-06

319

Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat.  

PubMed

Northern peatlands represent a major global carbon store harbouring approximately one-third of the global reserves of soil organic carbon. A large proportion of these peatlands consists of acidic Sphagnum-dominated ombrotrophic bogs, which are characterized by extremely low rates of plant debris decomposition. The degradation of cellulose, the major component of Sphagnum-derived litter, was monitored in long-term incubation experiments with acidic (pH 4.0) peat extracts. This process was almost undetectable at 10°C and occurred at low rates at 20°C, while it was significantly accelerated at both temperature regimes by the addition of available nitrogen. Cellulose breakdown was only partially inhibited in the presence of cycloheximide, suggesting that bacteria participated in this process. We aimed to identify these bacteria by a combination of molecular and cultivation approaches and to determine the factors that limit their activity in situ. The indigenous bacterial community in peat was dominated by Alphaproteobacteria and Acidobacteria. The addition of cellulose induced a clear shift in the community structure towards an increase in the relative abundance of the Bacteroidetes. Increasing temperature and nitrogen availability resulted in a selective development of bacteria phylogenetically related to Cytophaga hutchinsonii (94-95% 16S rRNA gene sequence similarity), which densely colonized microfibrils of cellulose. Among isolates obtained from this community only some subdivision 1 Acidobacteria were capable of degrading cellulose, albeit at a very slow rate. These Acidobacteria represent indigenous cellulolytic members of the microbial community in acidic peat and are easily out-competed by Cytophaga-like bacteria under conditions of increased nitrogen availability. Members of the phylum Firmicutes, known to be key players in cellulose degradation in neutral habitats, were not detected in the cellulolytic community enriched at low pH. PMID:21564458

Pankratov, Timofey A; Ivanova, Anastasia O; Dedysh, Svetlana N; Liesack, Werner

2011-05-12

320

Locus control regions and gene therapy  

Microsoft Academic Search

Gene therapy is a procedure in which exogenous genetic material is\\u000aintroduced into the cells of a patient in order to correct an genetic error or\\u000ato provide the cells of the patient with a new functional property.\\u000aCorrection can be achieved by gene targeting via homologous\\u000arecombination, at present achieved with very low efficiency (reviewed in\\u000aYanez and Porter

D. D. Drabek

1999-01-01

321

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

322

Surface-mediated gene transfer from nanocomposites of controlled texture  

NASA Astrophysics Data System (ADS)

Safe and efficient gene delivery would have great potential in gene therapy and tissue engineering, but synthetic biomaterial surfaces endowed with efficient gene-transferring functions do not yet exist. Inspired by naturally occurring biomineralization processes, we co-precipitated DNA with inorganic minerals onto cell-culture surfaces. The DNA/mineral nanocomposite surfaces obtained not only supported cell growth but also provided high concentrations of DNA in the immediate microenvironment of the cultured cells. Gene transfer from the engineered surfaces was as efficient as an optimized commercial lipid transfection reagent; in addition, the extent of gene transfer was adjustable by varying the mineral composition. DNA/mineral nanocomposite surfaces represent a promising system for enhancing gene transfer and controlling the extent of gene transfer for various biomedical applications, including tissue engineering or gene therapy of bone.

Shen, Hong; Tan, Jian; Saltzman, W. Mark

2004-08-01

323

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

324

EVALUATION OF BIOTIC AND TREATMENT FACTORS RELATING TO BACTERIAL CONTROL OF ZEBRA MUSSELS  

SciTech Connect

Testing over the last quarter has indicated the following regarding control of zebra mussels with bacterium Pseudomonas fluorescens strain CL0145A: (1) the concentration of bacteria suspended in water is directly correlated with mussel kill; (2) the ratio of bacterial mass per mussel, if too low, could limit mussel kill; a treatment must be done at a high enough ratio so that mussels do not deplete all the suspended bacteria before the end of the desired exposure period; (3) bacteria appear to lose almost all their toxicity after suspension for 24 hr in highly oxygenated water; (4) in a recirculating pipe system, the same percentage mussel kill will be achieved irrespective of whether all the bacteria are applied at once or divided up and applied intermittently in smaller quantities over a 10-hr period. Since this is the fourth quarterly report, a summation of all test results over the last twelve months is provided as a table in this report. The table includes the above-mentioned fourth-quarter results.

Daniel P. Molloy

2002-04-30

325

Effervescent fast-disintegrating bacterial formulation for biological control of rice sheath blight.  

PubMed

A lack of effective, easily applied and stable formulation has been a major obstacle to widespread use of biocontrol agents for control of rice sheath blight. In this study, effervescent fast-disintegrating granules containing endospores of Bacillus megaterium were developed for use either by broadcast or spray application. The formulation composed of lactose, polyvinyl pyrrolidone K-30 (PVP, K-30) and effervescent base (citric acid, tartaric acid and sodium bicarbonate). The number of living bacteria in effervescent granules that performed mycelial growth inhibition was in the range of 10(9) CFU/g after 12 months storage at room temperature. The number of viable bacteria after applying into the water and spraying on the rice seedling for 7 days in the greenhouse tests were also satisfactory high (10(9) CFU/g of granules and 10(6) CFU/g of plant, respectively). The scanning electron microscope (SEM) was used to observe bacterial antagonist on the surface of leaf sheath and leaf blade after spraying with formulation. Effervescent formulation applied either broadcasting or spraying reduced incidence of sheath blight disease in the greenhouse experiments. PMID:17428569

Wiwattanapatapee, R; Chumthong, A; Pengnoo, A; Kanjanamaneesathian, M

2007-02-02

326

Traffic Control of Bacteria-Derived Molecules: A New System of Host-Bacterial Crosstalk  

PubMed Central

Virulent microorganisms, such as pathogenic bacteria and viruses, are recognized by pattern recognition receptors (PRRs), including toll-like receptors (TLRs) and nucleotide-binding oligomerization-domain proteins (NODs), and induce inflammatory responses in mammalian hosts. Conversely, commensal bacteria and probiotics, which symbiotically confer health benefits on the host organisms, can lodge in the host intestinal tract without inducing intestinal inflammation. Recent advances in investigations concerning host-microbial interactions have shown that some effector molecules secreted from beneficial bacteria activate cell survival pathways, such as those mediated by p38 MAPK and Akt, and bring health benefits to mammalian hosts. It is noteworthy that such bacteria-derived molecules are taken into the intestinal epithelia through a transport or endocytosis system, thereafter exhibiting their beneficial effects. Understanding this traffic control process can aid in the comprehension of host and microbe interactions and may provide new insight to clarify the pathogenesis of intestinal disorders. This paper highlights the intestinal trafficking systems of bacteria-derived molecules that affect the bacterial functions and modulate epithelial signaling cascades. The latter mechanism may contribute to the maintenance of intestinal homeostasis by improving the host damage induced by virulence factors and various disease states.

Konishi, Hiroaki; Fujiya, Mikihiro; Kohgo, Yutaka

2013-01-01

327

Creation of a bacterial cell controlled by a chemically synthesized genome.  

PubMed

We report the design, synthesis, and assembly of the 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication. PMID:20488990

Gibson, Daniel G; Glass, John I; Lartigue, Carole; Noskov, Vladimir N; Chuang, Ray-Yuan; Algire, Mikkel A; Benders, Gwynedd A; Montague, Michael G; Ma, Li; Moodie, Monzia M; Merryman, Chuck; Vashee, Sanjay; Krishnakumar, Radha; Assad-Garcia, Nacyra; Andrews-Pfannkoch, Cynthia; Denisova, Evgeniya A; Young, Lei; Qi, Zhi-Qing; Segall-Shapiro, Thomas H; Calvey, Christopher H; Parmar, Prashanth P; Hutchison, Clyde A; Smith, Hamilton O; Venter, J Craig

2010-05-20

328

Organization and control of genes encoding catabolic enzymes in Rhizobiaceae  

SciTech Connect

Rhizobiaceae, a diverse bacterial group comprising rhizobia and agrobacteria, symbiotic partnership with plants form nitrogen-fixing nodules on plant roots or are plant pathogens. Phenolic compounds produced by plants serve as inducers of rhizobial nodulation genes and agrobacterial virulence genes reflect their capacity to utilize numerous aromatics, including phenolics, as a source of carbon and energy. In many microbes the aerobic degradation of numerous aromatic compounds to tricarboxylic acid cycle intermediates is achieved by the [beta]-ketoadipate pathway. Our initial studies focused on the organization and regulation of the ketoadipate pathway in Agrobacterium tumefaciens. We have cloned, identified and characterized a novel regulatory gene that modulates expression of an adjacent pca (protocatechuate) structural gene, pcaD. Regulation of pcaD is mediated by the regulatory gene, termed pcaQ, in concert with the intermediate [beta]-carboxy-cis,cis-muconate. [beta]-carboxy-cis,cismuconate is an unstable chemical, not marketed commercially, and it is unlikely to permeate Escherichia coli cells if supplied in media. Because of these factors, characterization of pcaQ in E. coli required an in vivo delivery system for [beta]-carboxycis,cis-muconate. This was accomplished by designing an E. coli strain that expressed an Acinetobacter calcoaceticus pcaA gene for conversion of protocatechuate to [beta]-carboxy-cis,cis-muconate.

Parke, D.; Ornston, L.N.

1993-03-01

329

The Effects of Individual PCB Congeners on the Soil Bacterial Community Structure and the Abundance of Biphenyl Dioxygenase Genes  

PubMed Central

Polychlorinated biphenyls (PCBs) are toxic environmental contaminants that represent a class of 209 congeners characterized by different degree of chlorination and substitution patterns. Most of experimental studies about microbial degradation of PCBs have been conducted on PCB mixtures, even though evidence accumulated in bacteria and other organisms shows that exposure to different congeners may have different biological effects. Microcosm experiments were conducted using aerobic agitated soil slurries individually exposed to PCB congeners with different degrees of chlorination: PCB-3, 15, 28, and 77, and the commercial mixture Aroclor 1242. After four weeks of incubation, PCBs were analyzed by gas chromatography/mass spectrometry (GC/MS) showing different transformation extents: With the exception of PCB-15 that was not significantly transformed (7%), biodegradation rates decreased with the degree of chlorination, from 75% for PCB-3 to 22% for PCB-77 and Aroclor 1242. The bacterial abundance, as measured by colony counting and 16S rDNA quantification by real-time PCR, was lower (of about 40%) in soil microcosms exposed to the higher-chlorinated congeners, PCB-28, PCB-77, and Aroclor 1242, as compared to non-exposed soils and soils exposed to the lower-chlorinated congeners, PCB-3 and PCB-15. The relative abundance of different taxonomic groups, as determined by real-time PCR, revealed an increase of ?-Proteobacteria and Actinobacteria in all microcosms exposed to PCBs, as compared with non-exposed soil. In addition, exposure to PCB-77 and Aroclor 1242 resulted in a higher abundance of ?-Proteobacteria and Acidobacteria. Globally, these results suggest that exposure to PCBs (and especially to higher-chlorinated congeners and Aroclor 1242) selected bacterial groups involving most known PCB degraders, i.e., ?-Proteobacteria and Acidobacteria. The quantification of biphenyl dioxygenase (BPH) genes - involved in the aerobic degradation of PCBs - using real-time PCR showed that exposure to all PCB congeners and Aroclor 1242 resulted in a marked increase of two out of the four BPH genes tested, similarly suggesting the selection of PCB-degrading bacteria. This paper showed that exposure to different PCB congeners leads to different structures of the soil bacterial community and BPH genes expression patterns.

Correa, Paola A.; Lin, LianShin; Just, Craig L.; Hu, Dingfei; Hornbuckle, Keri C.; Schnoor, Jerald L.; Van Aken, Benoit

2009-01-01

330

Temporal and spatial coexistence of archaeal and bacterial amoA genes and gene transcripts in Lake Lucerne.  

PubMed

Despite their crucial role in the nitrogen cycle, freshwater ecosystems are relatively rarely studied for active ammonia oxidizers (AO). This study of Lake Lucerne determined the abundance of both amoA genes and gene transcripts of ammonia-oxidizing archaea (AOA) and bacteria (AOB) over a period of 16 months, shedding more light on the role of both AO in a deep, alpine lake environment. At the surface, at 42 m water depth, and in the water layer immediately above the sediment, AOA generally outnumbered AOB. However, in the surface water during summer stratification, when both AO were low in abundance, AOB were more numerous than AOA. Temporal distribution patterns of AOA and AOB were comparable. Higher abundances of amoA gene transcripts were observed at the onset and end of summer stratification. In summer, archaeal amoA genes and transcripts correlated negatively with temperature and conductivity. Concentrations of ammonium and oxygen did not vary enough to explain the amoA gene and transcript dynamics. The observed herbivorous zooplankton may have caused a hidden flux of mineralized ammonium and a change in abundance of genes and transcripts. At the surface, AO might have been repressed during summer stratification due to nutrient limitation caused by active phytoplankton. PMID:23533328

Vissers, Elisabeth W; Anselmetti, Flavio S; Bodelier, Paul L E; Muyzer, Gerard; Schleper, Christa; Tourna, Maria; Laanbroek, Hendrikus J

2013-03-05

331

The Use of Artificial MicroRNA Technology to Control Gene Expression in Arabidopsis thaliana.  

PubMed

In plants, double-stranded RNA (dsRNA) is an effective trigger of RNA silencing, and several classes of endogenous small RNA (sRNA), processed from dsRNA substrates by DICER-like (DCL) endonucleases, are essential in controlling gene expression. One such sRNA class, the microRNAs (miRNAs) control the expression of closely related genes to regulate all aspects of plant development, including the determination of leaf shape, leaf polarity, flowering time, and floral identity. A single miRNA sRNA silencing signal is processed from a long precursor transcript of nonprotein-coding RNA, termed the primary miRNA (pri-miRNA). A region of the pri-miRNA is partially self-complementary allowing the transcript to fold back onto itself to form a stem-loop structure of imperfectly dsRNA. Artificial miRNA (amiRNA) technology uses endogenous pri-miRNAs, in which the miRNA and miRNA* (passenger strand of the miRNA duplex) sequences have been replaced with corresponding amiRNA/amiRNA* sequences that direct highly efficient RNA silencing of the targeted gene. Here, we describe the rules for amiRNA design, as well as outline the PCR and bacterial cloning procedures involved in the construction of an amiRNA plant expression vector to control target gene expression in Arabidopsis thaliana. PMID:24057368

Eamens, Andrew L; McHale, Marcus; Waterhouse, Peter M

2014-01-01

332

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

333

Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota  

PubMed Central

The publicly available annotated archaeal genome sequences (23 complete and three partial annotations, October 2005) were searched for the presence of potential two-component open reading frames (ORFs) using gene category lists and BLASTP. A total of 489 potential two-component genes were identified from the gene category lists and BLASTP. Two-component genes were found in 14 of the 21 Euryarchaeal sequences (October 2005) and in neither the Crenarchaeota nor the Nanoarchaeota. A total of 20 predicted protein domains were identified in the putative two-component ORFs that, in addition to the histidine kinase and receiver domains, also includes sensor and signalling domains. The detailed structure of these putative proteins is shown, as is the distribution of each class of two-component genes in each species. Potential members of orthologous groups have been identified, as have any potential operons containing two or more two-component genes. The number of two-component genes in those Euryarchaeal species which have them seems to be linked more to lifestyle and habitat than to genome complexity, with most examples being found in Methanospirillum hungatei, Haloarcula marismortui, Methanococcoides burtonii and the mesophilic Methanosarcinales group. The large numbers of two-component genes in these species may reflect a greater requirement for internal regulation. Phylogenetic analysis of orthologous groups of five different protein classes, three probably involved in regulating taxis, suggests that most of these ORFs have been inherited vertically from an ancestral Euryarchaeal species and point to a limited number of key horizontal gene transfer events.

Ashby, Mark K.

2006-01-01

334

Bacterial quorum sensing: its role in virulence and possibilities for its control.  

PubMed

Quorum sensing is a process of cell-cell communication that allows bacteria to share information about cell density and adjust gene expression accordingly. This process enables bacteria to express energetically expensive processes as a collective only when the impact of those processes on the environment or on a host will be maximized. Among the many traits controlled by quorum sensing is the expression of virulence factors by pathogenic bacteria. Here we review the quorum-sensing circuits of Staphylococcus aureus, Bacillus cereus, Pseudomonas aeruginosa, and Vibrio cholerae. We outline these canonical quorum-sensing mechanisms and how each uniquely controls virulence factor production. Additionally, we examine recent efforts to inhibit quorum sensing in these pathogens with the goal of designing novel antimicrobial therapeutics. PMID:23125205

Rutherford, Steven T; Bassler, Bonnie L

2012-11-01

335

Mobilizable narrow host range plasmids as natural suicide vectors enabling horizontal gene transfer among distantly related bacterial species.  

PubMed

Klebsiella pneumoniae 287-w carries three small narrow host range (NHR) plasmids (pIGMS31, pIGMS32, and pIGRK), which could be maintained in several closely related species of Gammaproteobacteria, but not in Alphaproteobacteria. The plasmids contain different mobilization systems (MOB), whose activity in Escherichia coli was demonstrated in the presence of the helper transfer system originating from plasmid RK2. The MOBs of pIGMS31 and pIGMS32 are highly conserved in many bacterial plasmids (members of the MOB family), while the predicted MOB of pIGRK has a unique structure, encoding a protein similar to phage-related integrases. The MOBs of pIGMS31 and pIGMS32 enabled the transfer of heterologous replicons from E. coli into both gammaproteobacterial and alphaproteobacterial hosts, which suggests that these NHR plasmids contain broad host range MOB systems. Such plasmids therefore represent efficient carrier molecules, which may act as natural suicide vectors promoting the spread of diverse genetic information (including other types of mobile elements, e.g. resistance transposons) among evolutionarily distinct bacterial species. Thus, mobilizable NHR plasmids may play a much more important role in horizontal gene transfer than previously thought. PMID:22092700

Smorawinska, Maria; Szuplewska, Magdalena; Zaleski, Piotr; Wawrzyniak, Pawe?; Maj, Anna; Plucienniczak, Andrzej; Bartosik, Dariusz

2011-11-02

336

Quantitative polymerase chain reaction (PCR) assays for a bacterial thiaminase I gene and the thiaminase-producing bacterium Paenibacillus thiaminolyticus.  

USGS Publications Warehouse

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.

Richter, C. A.; Wright-Osment, M. K.; Zajicek, J. L.; Honeyfield, D. C.; Tillitt, D. E.

2009-01-01

337

Assessment of the Importance of Similarity in Carbon Source Utilization Profiles between the Biological Control Agent and the Pathogen in Biological Control of Bacterial Speck of Tomato  

Microsoft Academic Search

Bacterial speck of tomato, caused by Pseudomonas syringae pv. tomato, was used to determine whether similarity in carbon source utilization between a preemptive biological control agent and the pathogen was significant in determining the ability of the bacterium to suppress disease. Similarity in carbon source utilization was quantified as the ratio of the number of tomato carbon sources utilized in

Pingsheng Ji; Mark Wilson

2002-01-01

338

Inhibition of fungal growth in planta and in vitro by transgenic tobacco expressing a bacterial nonheme chloroperoxidase gene  

Microsoft Academic Search

Transgenic tobacco plants producing chloroperoxidase (CPO-P), encoded by a novel gene from Pseudomonas pyrrocinia, were obtained by Agrobacterium-mediated transformation. Successful transformation was shown by PCR, Southern, northern and western blot analyses, and assays\\u000a of CPO-P enzyme activity. Extracts from plants transformed with the CPO-P gene significantly reduced Aspergillus flavus colonies by up to 100% compared with extracts from control plants

K. Rajasekaran; J. W. Cary; T. J. Jacks; K. D. Stromberg; T. E. Cleveland

2000-01-01

339

Expression of a bacterial gene in transgenic plants confers resistance to the herbicide phenmedipham  

Microsoft Academic Search

Tobacco plants were genetically engineered to express a detoxifying pathway for the herbicide phenmedipham. A gene fromArthrobacter oxidans strain P52 that encodes an enzyme catalysing the hydrolytic cleavage of the carbamate compound phenmedipham has recently been cloned and sequenced. The coding sequence was fused with a cauliflower mosaic virus 35S promoter and introduced into tobacco plants byAgrobacterium-mediated gene transfer. Transgenic

Wolfgang R. Streber; Ulrike Kutschka; Frank Thomas; Hans-Dieter Pohlenz

1994-01-01

340

Lines of Evidence for Horizontal Gene Transfer of a Phenazine Producing Operon into Multiple Bacterial Species  

Microsoft Academic Search

Phenazines are secondary metabolites with broad-spectrum antibiotic activity against bacteria, fungi, and eukaryotes. In pseudomonad\\u000a species, a conserved seven-gene phenazine operon (phzABCDEFG) is required for the conversion of chorismic acid to the broad-spectrum antibiotic phenazine-1-carboxylate. Previous\\u000a analyses of genes involved in phenazine production from nonpseudomonad species uncovered a high degree of sequence similarity\\u000a to pseudomonad homologues. The analyses undertaken in

David A. Fitzpatrick

2009-01-01

341

Evidence for the bacterial origin of genes encoding fermentation enzymes of the amitochondriate protozoan parasite Entamoeba histolytica.  

PubMed Central

Entamoeba histolytica is an amitochondriate protozoan parasite with numerous bacterium-like fermentation enzymes including the pyruvate:ferredoxin oxidoreductase (POR), ferredoxin (FD), and alcohol dehydrogenase E (ADHE). The goal of this study was to determine whether the genes encoding these cytosolic E. histolytica fermentation enzymes might derive from a bacterium by horizontal transfer, as has previously been suggested for E. histolytica genes encoding heat shock protein 60, nicotinamide nucleotide transhydrogenase, and superoxide dismutase. In this study, the E. histolytica por gene and the adhE gene of a second amitochondriate protozoan parasite, Giardia lamblia, were sequenced, and their phylogenetic positions were estimated in relation to POR, ADHE, and FD cloned from eukaryotic and eubacterial organisms. The E. histolytica por gene encodes a 1,620-amino-acid peptide that contained conserved iron-sulfur- and thiamine pyrophosphate-binding sites. The predicted E. histolytica POR showed fewer positional identities to the POR of G. lamblia (34%) than to the POR of the enterobacterium Klebsiella pneumoniae (49%), the cyanobacterium Anabaena sp. (44%), and the protozoan Trichomonas vaginalis (46%), which targets its POR to anaerobic organelles called hydrogenosomes. Maximum-likelihood, neighbor-joining, and parsimony analyses also suggested as less likely E. histolytica POR sharing more recent common ancestry with G. lamblia POR than with POR of bacteria and the T. vaginalis hydrogenosome. The G. lamblia adhE encodes an 888-amino-acid fusion peptide with an aldehyde dehydrogenase at its amino half and an iron-dependent (class 3) ADH at its carboxy half. The predicted G. lamblia ADHE showed extensive positional identities to ADHE of Escherichia coli (49%), Clostridium acetobutylicum (44%), and E. histolytica (43%) and lesser identities to the class 3 ADH of eubacteria and yeast (19 to 36%). Phylogenetic analyses inferred a closer relationship of the E. histolytica ADHE to bacterial ADHE than to the G. lamblia ADHE. The 6-kDa FD of E. histolytica and G. lamblia were most similar to those of the archaebacterium Methanosarcina barkeri and the delta-purple bacterium Desulfovibrio desulfuricans, respectively, while the 12-kDa FD of the T. vaginalis hydrogenosome was most similar to the 12-kDa FD of gamma-purple bacterium Pseudomonas putida. E. histolytica genes (and probably G. lamblia genes) encoding fermentation enzymes therefore likely derive from bacteria by horizontal transfer, although it is not clear from which bacteria these amebic genes derive. These are the first nonorganellar fermentation enzymes of eukaryotes implicated to have derived from bacteria.

Rosenthal, B; Mai, Z; Caplivski, D; Ghosh, S; de la Vega, H; Graf, T; Samuelson, J

1997-01-01

342

Cancer genes and the pathways they control  

Microsoft Academic Search

The revolution in cancer research can be summed up in a single sentence: cancer is, in essence, a genetic disease. In the last decade, many important genes responsible for the genesis of various cancers have been discovered, their mutations precisely identified, and the pathways through which they act characterized. The purposes of this review are to highlight examples of progress

Bert Vogelstein; Kenneth W Kinzler

2004-01-01

343

Misexpression screen delineates novel genes controlling Drosophila lifespan.  

PubMed

In an initial preliminary screen we identified factors associated with controlling Drosophila aging by examining longevity in adults where EP elements induced over-expression or antisense-RNA at genes adjacent to each insertion. Here, we study 45 EP lines that initially showed at least 10% longer mean lifespan than controls. These 45 lines and a daughterless (da)-Gal4 stock were isogenized into a CS10 wild-type background. Sixteen EP lines corresponding to 15 genes significantly extended lifespan when their target genes were driven by da-Gal4. In each case, the target genes were seen to be over-expressed. Independently derived UAS-gene transgenic stocks were available or made for two candidates: ImpL2 which is ecdysone-inducible gene L2, and CG33138, 1,4-alpha-glucan branching enzyme. With both, adult lifespan was increased upon over-expression via the GeneSwitch inducible Gal4 driver system. Several genes in this set of 15 correspond to previously discovered longevity assurance systems such as insulin/IGF-1 signaling, gene silencing, and autophagy; others suggest new potential mechanisms for the control of aging including mRNA synthesis and maturation, intracellular vesicle trafficking, and neuroendocrine regulation. PMID:22366109

Paik, Donggi; Jang, Yeo Gil; Lee, Young Eun; Lee, Young Nam; Yamamoto, Rochelle; Gee, Heon Yung; Yoo, Seungmin; Bae, Eunkyung; Min, Kyung-Jin; Tatar, Marc; Park, Joong-Jean

2012-02-24

344

Identification of Brucella melitensis 16M genes required for bacterial survival in the caprine host.  

PubMed

Brucella species are gram-negative bacteria which belong to alpha-Proteobacteria family. These organisms are zoonotic pathogens that induce abortion and sterility in domestic mammals and chronic infections in humans known as Malta fever. The virulence of Brucella is dependent upon its ability to enter and colonize the cells in which it multiplies. The genetic basis of this aspect is poorly understood. Signature-tagged mutagenesis (STM) was used to identify potential Brucella virulence factors. PCR amplification has been used in place of DNA hybridization to identify the STM-generated attenuated mutants. A library of 288 Brucella melitensis 16M tagged mini-Tn5 Km2 mutants, in 24 pools, was screened for its ability to colonize spleen, lymph nodes and liver of goats at three weeks post-i.v. infection. This comparative screening identified 7 mutants (approximately 5%) which were not recovered from the output pool in goats. Some genes were known virulence genes involved in biosynthesis of LPS (lpsA gene) or in intracellular survival (the virB operon). Other mutants included ones which had a disrupted gene homologous to flgF, a gene coding for the basal-body rod of the flagellar apparatus, and another with a disruption in a gene homologous to ppk which is involved in the biosynthesis of inorganic polyphosphate (PolyP) from ATP. Other genes identified encoded factors involved in DNA metabolism and oxidoreduction metabolism. Using STM and the caprine host for screening, potential virulence determinants in B. melitensis have been identified. PMID:17090391

Zygmunt, Michel S; Hagius, Sue D; Walker, Joel V; Elzer, Philip H

2006-10-16

345

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.

346

Evolution of Bacterial Phosphoglycerate Mutases: Non-Homologous Isofunctional Enzymes Undergoing Gene Losses, Gains and Lateral Transfers  

PubMed Central

Background The glycolytic phosphoglycerate mutases exist as non-homologous isofunctional enzymes (NISE) having independent evolutionary origins and no similarity in primary sequence, 3D structure, or catalytic mechanism. Cofactor-dependent PGM (dPGM) requires 2,3-bisphosphoglycerate for activity; cofactor-independent PGM (iPGM) does not. The PGM profile of any given bacterium is unpredictable and some organisms such as Escherichia coli encode both forms. Methods/Principal Findings To examine the distribution of PGM NISE throughout the Bacteria, and gain insight into the evolutionary processes that shape their phyletic profiles, we searched bacterial genome sequences for the presence of dPGM and iPGM. Both forms exhibited patchy distributions throughout the bacterial domain. Species within the same genus, or even strains of the same species, frequently differ in their PGM repertoire. The distribution is further complicated by the common occurrence of dPGM paralogs, while iPGM paralogs are rare. Larger genomes are more likely to accommodate PGM paralogs or both NISE forms. Lateral gene transfers have shaped the PGM profiles with intradomain and interdomain transfers apparent. Archaeal-type iPGM was identified in many bacteria, often as the sole PGM. To address the function of PGM NISE in an organism encoding both forms, we analyzed recombinant enzymes from E. coli. Both NISE were active mutases, but the specific activity of dPGM greatly exceeded that of iPGM, which showed highest activity in the presence of manganese. We created PGM null mutants in E. coli and discovered the ?dPGM mutant grew slowly due to a delay in exiting stationary phase. Overexpression of dPGM or iPGM overcame this defect. Conclusions/Significance Our biochemical and genetic analyses in E. coli firmly establish dPGM and iPGM as NISE. Metabolic redundancy is indicated since only larger genomes encode both forms. Non-orthologous gene displacement can fully account for the non-uniform PGM distribution we report across the bacterial domain.

Foster, Jeremy M.; Davis, Paul J.; Raverdy, Sylvine; Sibley, Marion H.; Raleigh, Elisabeth A.; Kumar, Sanjay; Carlow, Clotilde K. S.

2010-01-01

347

Rapid induction by wounding and bacterial infection of an S gene family receptor-like kinase gene in Brassica oleracea.  

PubMed Central

A receptor-like kinase, SRK, has been implicated in the autoincompatible response that leads to the rejection of self-pollen in Brassica plants. SRK is encoded by one member of a multigene family, which includes several receptor-like kinase genes with patterns of expression very different from that of SRK but of unknown function. Here, we report the characterization of a novel member of the Brassica S gene family, SFR2. RNA gel blot analysis demonstrated that SFR2 mRNA accumulated rapidly in response both to wounding and to infiltration with either of two bacteria: Xanthomonas campestris, a pathogen, and Escherichia coli, a saprophyte. SFR2 mRNA also accumulated rapidly after treatment with salicylic acid, a molecule that has been implicated in plant defense response signaling pathways. A SFR2 promoter and reporter gene fusion was introduced into tobacco and was shown to be induced by bacteria of another genus, Ralstonia (Pseudomonas) solanacearum. The accumulation of SFR2 mRNA in response to wounding and pathogen invasion is typical of a gene involved in the defense responses of the plant. The rapidity of SFR2 mRNA accumulation is consistent with SFR2 playing a role in the signal transduction pathway that leads to induction of plant defense proteins, such as pathogenesis-related proteins or enzymes of phenylpropanoid metabolism.

Pastuglia, M; Roby, D; Dumas, C; Cock, J M

1997-01-01

348

Control of globin gene expression during development and erythroid differentiation  

PubMed Central

Extensive studies during the last 30 years have led to considerable understanding of cellular and molecular control of hemoglobin switching. Cell biology studies in the 1970s defined the control of globin genes during erythroid differentiation and led to development of therapies for sickle cell disease. Molecular investigations of the last 20 years have delineated the two basic mechanisms that control globin gene activity during development—autonomous silencing and gene competition. Studies of hemoglobin switching have provided major insights on the control of gene loci by remote regulatory elements. Research in this field has an impact on understanding regulatory mechanisms in general and is of particular importance for eventual development of molecular cures for sickle cell disease and ? thalassemia.

Stamatoyannopoulos, George

2010-01-01

349

Neural Route of Cerebral Listeria monocytogenes Murine Infection: Role of Immune Response Mechanisms in Controling Bacterial Neuroinvasion  

PubMed Central

The pathologic features of cerebral Listeria monocytogenes infection strongly suggest that besides hematogenous spread, bacteria might also spread via a neural route. We propose that after snout infection of recombination activating gene 1 (RAG-1)-deficient mice, L. monocytogenes spreads to the brain via a neural route. The neural route of invasion is suggested by (i) the immunostaining of L. monocytogenes in the trigeminal ganglia (TG) and brain stem but not in other areas of the brain; (ii) the kinetics of bacterial loads in snout, TG, and brain; and (iii) the increased resistance of mice infected with a plcB bacterial mutant (unable to spread from cell to cell). Gamma interferon (IFN-?) plays a protective role in neuroinvasion; inducible nitric oxide synthase (iNOS) accounts only partially for the protection, as shown by a comparison of the susceptibilities of IFN-? receptor (IFN-?R)-deficient, iNOS-deficient, and wild-type mice to snout infection with L. monocytogenes. The dramatically enhanced susceptibility of RAG-1-deficient, IFN-?R gene-deficient mice indicated the overall importance of innate immune cells in the release of protective levels of IFN-?. The source of IFN-? appeared to be NK cells, as shown by use of RAG-1-deficient, ?-chain receptor gene-deficient mice; NK cells played a relevant protective role in neuroinvasion through a perforin-independent mechanism. In vitro evidence indicated that IFN-? can directly induce bacteriostatic mechanisms in neural tissue.

Jin, Yuxuan; Dons, Lone; Kristensson, Krister; Rottenberg, Martin E.

2001-01-01

350

Direct Transcriptional Control of the Plasminogen Activator Gene of Yersinia pestis by the Cyclic AMP Receptor Protein  

Microsoft Academic Search

Horizontal gene transfer events followed by proper regulatory integration of a gene drive rapid evolution of bacterial pathogens. A key event in the evolution of the highly virulent plague bacterium Yersinia pestis was the acquisition of plasmid pPCP1, which carries the plasminogen activator gene, pla. This promoted the bubonic form of the disease by increasing bacterial dissemination from flea bite

Tae-Jong Kim; Sadhana Chauhan; Vladimir L. Motin; Ee-Been Goh; Michele M. Igo; Glenn M. Young

2007-01-01

351

The L6 Gene for Flax Rust Resistance 1s Related to the Arabidopsis Bacterial Resistance Gene RPSP and the Tobacco Vira1 Resistance Gene N  

Microsoft Academic Search

The L6 rust resistance gene from flax was cloned after tagging with the maize transposable element Aclivator. The gene is predicted to encode two products of 1294 and 705 amino acids that result from alternatively spliced transcripts. The longer product is similar to the products of two other plant disease resistance genes, the tobacco mosaic virus resistance gene N of

Gregory J. Lawrence; E. Jean Finnegan; Michael A. AyliffeIb; Jeffrey G. Ellisai

1995-01-01

352

Impact of dibenzofuran/dibenzo-p-dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations.  

PubMed

The impact of dibenzofuran (DF) and dibenzo-p-dioxin (DD) on the changes in bacterial community structure and the transition of catabolic genes were studied using forest soil. The bacterial community structure of soil suspensions amended with 1 microg/g of either DF or DD was analyzed by 16S rRNA and functional gene sequencing. To analyze the functional genes in the communities, we targeted a gene sequence that functions as the binding site of Rieske iron sulfur center common to ring-hydroxylating dioxygenases (RHDs) for monocyclic, bicyclic, and tricyclic aromatic compounds. The gene fragments were polymerase chain reaction-amplified from DNAs extracted from soil suspensions spiked with either DF or DD, cloned, and sequenced (70 clones). Bacterial community analysis based on 16S rRNA genes revealed that specific 16S rRNA gene sequences, in particular, phylotypes within alpha-Proteobacteria, increased in the soil suspension amended with DF or DD. RHD gene-based functional community analysis showed that, in addition to two groups of RHD genes that were also detected in unamended soil suspensions, another two groups of RHD genes, each of which is specific to DF- and DD-amended soil, respectively, emerged to a great extent. The DD-specific genotype is phylogenetically distant from any known RHDs. These results strongly suggest that soil microbial community potentially harbors a wide array of organisms having diverse RHDs including those previously unknown, and that they could quickly respond to an impact of contamination of hazardous chemicals by changing the microbial community and gene diversity. PMID:19513710

Kimura, Nobutada; Kamagata, Yoichi

2009-06-10

353

Diaphragm Used with Replens Gel and Risk of Bacterial Vaginosis: Results from a Randomized Controlled Trial  

PubMed Central

Background. Bacterial vaginosis (BV) has been linked to female HIV acquisition and transmission. We investigated the effect of providing a latex diaphragm with Replens and condoms compared to condom only on BV prevalence among participants enrolled in an HIV prevention trial. Methods. We enrolled HIV-seronegative women and obtained a vaginal swab for diagnosis of BV using Nugent's criteria; women with BV (score 7–10) were compared to those with intermediate (score 4–6) and normal flora (score 0–3). During quarterly follow-up visits over 12–24 months a vaginal Gram stain was obtained. The primary outcome was serial point prevalence of BV during followup. Results. 528 participants were enrolled; 213 (40%) had BV at enrollment. Overall, BV prevalence declined after enrollment in women with BV at baseline (OR = 0.4, 95% CI 0.29–.56) but did not differ by intervention group. In the intention-to-treat analysis BV prevalence did not differ between the intervention and control groups for women who had BV (OR = 1.01, 95% CI 0.52–1.94) or for those who did not have BV (OR = 1.21, 95% CI 0.65–2.27) at enrollment. Only 2.1% of participants were treated for symptomatic BV and few women (5–16%) were reported using anything else but water to cleanse the vagina over the course of the trial. Conclusions. Provision of the diaphragm, Replens, and condoms did not change the risk of BV in comparison to the provision of condoms alone.

Cohen, Craig R.; Cheng, Su-Chun; Shiboski, Stephen; Chipato, Tsungai; Matu, Martin; Mwangi, James; Mutimutema, Monalisa E. S.; Tuveson, Jennifer; Kamba, Mavis; Padian, Nancy; van der Straten, Ariane

2012-01-01

354

A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes  

Microsoft Academic Search

Background  Archaeal and bacterial genomes contain a number of genes of foreign origin that arose from recent horizontal gene transfer,\\u000a but the role of integrative elements (IEs), such as viruses, plasmids, and transposable elements, in this process has not\\u000a been extensively quantified. Moreover, it is not known whether IEs play an important role in the origin of ORFans (open reading\\u000a frames

Diego Cortez; Patrick Forterre; Simonetta Gribaldo

2009-01-01

355

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

356

Design and Evaluation of Useful Bacterium-Specific PCR Primers That Amplify Genes Coding for Bacterial 16S rRNA  

PubMed Central

We report the design and evaluation of PCR primers 63f and 1387r for amplification of 16S rRNA genes from bacteria. Their specificity and efficacy were tested systematically with a variety of bacterial species and environmental samples. They were found to be more useful for 16S rRNA gene amplification in ecological and systematic studies than PCR amplimers that are currently more generally used.

Marchesi, Julian R.; Sato, Takuichi; Weightman, Andrew J.; Martin, Tracey A.; Fry, John C.; Hiom, Sarah J.; Wade, William G.

1998-01-01

357

Diversity and abundance of the bacterial 16S rRNA gene sequences in forestomach of alpacas ( Lama pacos) and sheep ( Ovis aries)  

Microsoft Academic Search

Two bacterial 16S rRNA gene clone libraries were constructed from the forestomach of alpacas and sheep fed alfalfa. After the amplification using the universal 16S rRNA gene primers, equal quantities of PCR products from the same species were mixed and used to construct the two libraries. Sequence analysis showed that the 60 clones from alpacas were divided into 27 phylotypes

Cai-Xia Pei; Qiang Liu; Chang-Sheng Dong; HongQuan Li; Jun-Bing Jiang; Wen-Jun Gao

2010-01-01

358

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

359

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

360

Causes and effects of N-terminal codon bias in bacterial genes.  

PubMed

Most amino acids are encoded by multiple codons, and codon choice has strong effects on protein expression. Rare codons are enriched at the N terminus of genes in most organisms, although the causes and effects of this bias are unclear. Here, we measure expression from >14,000 synthetic reporters in Escherichia coli and show that using N-terminal rare codons instead of common ones increases expression by ~14-fold (median 4-fold). We quantify how individual N-terminal codons affect expression and show that these effects shape the sequence of natural genes. Finally, we demonstrate that reduced RNA structure and not codon rarity itself is responsible for expression increases. Our observations resolve controversies over the roles of N-terminal codon bias and suggest a straightforward method for optimizing heterologous gene expression in bacteria. PMID:24072823

Goodman, Daniel B; Church, George M; Kosuri, Sriram

2013-09-26

361

Identification and characterization of a Salmonella typhimurium oxygen-regulated gene required for bacterial internalization.  

PubMed Central

Growth of Salmonella typhimurium in a low-oxygen environment induces the ability of these bacteria to enter mammalian cells. We have carried out a search for invasion genes that are expressed under low-oxygen conditions by using Tn5lacZY transcriptional fusions. Several noninvasive oxygen-regulated lacZY insertion strains have been identified. The invasion defect in one of these noninvasive S. typhimurium strains, BJ66, has been complemented by introduction of a cosmid (pBDJ125) from an S. typhimurium SL1344 gene bank. A 1.9-kb EcoRV DNA fragment subcloned from this cosmid, containing a single open reading frame (orgA), restores the ability of BJ66 to invade mammalian cells. Comparative searches of the GenBank and EMBL sequence data banks with the nucleotide sequence of the gene and deduced amino acid sequence of the protein reveal no significant similarities. Interestingly, hybridization of an orgA gene probe with a P22 chromosomal mapping library demonstrated that the orgA gene maps to a region on the chromosome between 57.5 and 60 min where other Salmonella invasion genes have been mapped. Other enteroinvasive bacteria (Shigella flexneri, Escherichia coli, Yersinia spp., and Listeria monocytogenes) lack sequences which cross hybridize to the probe. We have compared the virulence of S. typhimurium SL1344 and an isogenic orgA mutant in a mouse model of typhoid fever. The orgA mutant was as virulent as the wild-type strain was when inoculated intraperitoneally but is significantly reduced (> 60-fold) in its ability to cause disease by an oral route of infection. Images

Jones, B D; Falkow, S

1994-01-01

362

Specific expression of antimicrobial peptide and HSP70 genes in response to heat-shock and several bacterial challenges in mussels  

Microsoft Academic Search

Defensin, mytilin and myticin are antimicrobial peptides (AMP) involved in mussel innate immunity. Their in vitro antibacterial activity is different according to the targeted bacterial species. To determine if this specificity is correlated to different regulations of gene expressions, adult mussels were challenged in vivo with either Vibrio splendidus LGP32, Vibrio anguillarum, Micrococcus lysodeikticus or by heat shock. RNAs were

Cinzia Cellura; Mylène Toubiana; Nicolò Parrinello; Philippe Roch

2007-01-01

363

Bacteroides fragilis Transfer Factor Tn5520: the Smallest Bacterial Mobilizable Transposon Containing Single Integrase and Mobilization Genes That Function in Escherichia coli  

Microsoft Academic Search

Many bacterial genera, including Bacteroides spp., harbor mobilizable transposons, a class of transfer factors that carry genes for conjugal DNA transfer and, in some cases, antibiotic resistance. Mobilizable transposons are capable of inserting into and mobilizing other, nontransferable plasmids and are implicated in the dissem- ination of antibiotic resistance. This paper presents the isolation and characterization of Tn5520, a new

GAYATRI VEDANTAM; THOMAS J. NOVICKI; DAVID W. HECHT

1999-01-01

364

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

365

CONSTRUCTION OF A HEXAPLOID WHEAT (TRITICUM AESTIVUM L.) BACTERIAL ARTIFICIAL CHROMOSOME LIBRARY AND IDENTIFICATION OF CANDIDATE BAC CLONES CONTAINING STRIPE RUST RESISTANCE GENE MARKERS  

Technology Transfer Automated Retrieval System (TEKTRAN)

A hexaploid wheat (Triticum astivum L.) bacterial artificial chromosome (BAC) library was constructed for the positional cloning of the wheat strip rust resistance gene Yr5. The Yr5 near-isogenic line were used to isolate the high molecular weight DNA as intact nuclei. The HindIII partial restrict...

366

Changes in Bacterial Populations and in Biphenyl Dioxygenase Gene Diversity in a Polychlorinated Biphenyl-Polluted Soil after Introduction of Willow Trees for Rhizoremediation  

Microsoft Academic Search

The aim of this study was to analyze the structural and functional changes occurring in a polychlorinated- biphenyl (PCB)-contaminated soil ecosystem after the introduction of a suitable host plant for rhizoremedia- tion (Salix viminalis). We have studied the populations and phylogenetic distribution of key bacterial groups (Alpha- and Betaproteobacteria, Acidobacteria, and Actinobacteria) and the genes encoding iron-sulfur protein (ISP) subunits

Daniel Aguirre de Carcer; M. Martin; Ulrich Karlson; Rafael Rivilla

2007-01-01

367

Cytokine responses in primary chicken embryo intestinal cells infected with Campylobacter jejuni strains of human and chicken origin and the expression of bacterial virulence-associated genes  

Microsoft Academic Search

BACKGROUND: Campylobacter jejuni is a major cause of inflammatory diarrhoea in humans and is considered a commensal of the gastroenteric tract of the avian host. However, little is known about the interaction between C. jejuni and the avian host including the cytokine responses and the expression of the bacterial genes. We have investigated the invasiveness of primary chicken embryo intestinal

Yi-Ping Li; Hanne Ingmer; Mogens Madsen; Dang D Bang

2008-01-01

368

Genetic variation in the interleukin-8 gene promoter and vaginal concentrations of interleukin-8 are not associated with bacterial vaginosis during pregnancy  

Microsoft Academic Search

Interleukin-8 (IL-8) may play a role in the activation of the vaginal immune system during bacterial vaginosis. However, contradictory results were obtained regarding the involvement of IL-8 in the immunological response during bacteria vaginosis. These apparently contradictory results could be due to different genetic variations of the study groups. Since some gene polymorphisms may affect the level of IL-8 production,

Laura Diaz-Cueto; Adrian Cuica-Flores; Francisco Ziga-Cordero; Miguel E. Arechavaleta-Velasco; Fabian Arechavaleta-Velasco

2005-01-01

369

Photosynthetic redox control of nuclear gene expression  

Microsoft Academic Search

Chloroplasts contain 3000-4000 different proteins but only a small subset of them is encoded in the plastid genome while the majority is encoded in the nucleus. Expression of these genes therefore requires a high degree of co-ordination between nucleus and chloro- plast. This is achieved by a bilateral information ex- change between both compartments including nucleus-to-plastid (anterograde) and plastid-to-nucleus (retrograde)

Vidal Fey; Raik Wagner; Katharina Brautigam; Thomas Pfannschmidt

2005-01-01

370

Efficacy of Chloramine-T to Control Mortality in Freshwater-Reared Salmonids Diagnosed with Bacterial Gill Disease  

Microsoft Academic Search

Bacterial gill disease (BGD), caused by Flavobacterium branchiophilum and other species of yellow-pigmented, filamentous bacteria, is a common and potentially catastrophic disease of hatchery (freshwater)-reared fish. Chloramine-T (Chl-T) is a biocide proven effective for controlling mortality in freshwater-reared fish diagnosed with BGD. However, Chl-T is not approved by the U.S. Food and Drug Administration for such use. To generate data

James D. Bowker; Daniel G. Carty; Larry Telles; Bob David; David Oviedo

2008-01-01

371

Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample  

SciTech Connect

Numerous investigations applying the cloning and sequencing of rRNA genes (rDNAs) to the study of marine bacterioplankton diversity have shown that the sequences of genes cloned directly from environmental DNA do not correspond to the genes of cultured marine taxa. These results have been interpreted as support for the hypothesis that the most abundant heterotrophic marine bacterioplankton species are not readily culturable by commonly used methods. However, an alternative explanation is that marine bacterioplankton can be easily cultured but are not well represented in sequence databases. To further examine this question, we compared the small-subunit (SSU) rDNAs of 127 cellular clones isolated from a water sample collected off the Oregon coast to 58 bacterial SSU rDNAs cloned from environmental DNAs from the same water sample. The results revealed little overlap between partial SSU rDNA sequences from the cellular clones and the environmental clone library. An exception was the SSU rDNA sequence recovered from a cellular clone belonging to the Pseudomonas subgroup of the {gamma} subclass of the class Proteobacteria, which was related to a single gene cloned directly from the same water sample (OCS181) (similarity, 94.6%). In addition, partial SSU rDNA sequences from three of the cultured strains matched a novel rDNA clone related to the {gamma} subclass of the Proteobacteria found previously in an environmental clone library from marine aggregates (AGG53) (similarity, 94.3 to 99.6%). Our results support the hypothesis that many of the most abundant bacterioplankton species are not readily culturable by standard methods but also show that heterotrophic bacterioplankton that are culturable on media with high organic contents include many strains for which SSU rDNA sequences are not available in sequence databases. 34 refs., 4 figs., 3 tabs.

Suzuki, M.T.; Rappe, M.S.; Haimberger, Z.W. [Oregon State Univ., Corvallis, OR (United States)] [and others

1997-03-01

372

Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample.  

PubMed Central

Numerous investigations applying the cloning and sequencing of rRNA genes (rDNAs) to the study of marine bacterioplankton diversity have shown that the sequences of genes cloned directly from environmental DNA do not correspond to the genes of cultured marine taxa. These results have been interpreted as support for the hypothesis that the most abundant heterotrophic marine bacterioplankton species are not readily culturable by commonly used methods. However, an alternative explanation is that marine bacterioplankton can be easily cultured but are not well represented in sequence databases. To further examine this question, we compared the small-subunit (SSU) rDNAs of 127 cellular clones isolated from a water sample collected off the Oregon coast to 58 bacterial SSU rDNAs cloned from environmental DNAs from the same water sample. The results revealed little overlap between partial SSU rDNA sequences from the cellular clones and the environmental clone library. An exception was the SSU rDNA sequence recovered from a cellular clone belonging to the Pseudomonas subgroup of the gamma subclass of the class Proteobacteria, which was related to a single gene cloned directly from the same water sample (OCS181) (similarity, 94.6%). In addition, partial SSU rDNA sequences from three of the cultured strains matched a novel rDNA clone related to the gamma subclass of the Proteobacteria found previously in an environmental clone library from marine aggregates (AGG53) (similarity, 94.3 to 99.6%). Our results support the hypothesis that many of the most abundant bacterioplankton species are not readily culturable by standard methods but also show that heterotrophic bacterioplankton that are culturable on media with high organic contents include many strains for which SSU rDNA sequences are not available in sequence databases.

Suzuki, M T; Rappe, M S; Haimberger, Z W; Winfield, H; Adair, N; Strobel, J; Giovannoni, S J

1997-01-01

373

Simple F Test Reveals Gene-Gene Interactions in Case-Control Studies  

PubMed Central

Missing heritability is still a challenge for Genome Wide Association Studies (GWAS). Gene-gene interactions may partially explain this residual genetic influence and contribute broadly to complex disease. To analyze the gene-gene interactions in case-control studies of complex disease, we propose a simple, non-parametric method that utilizes the F-statistic. This approach consists of three steps. First, we examine the joint distribution of a pair of SNPs in cases and controls separately. Second, an F-test is used to evaluate the ratio of dependence in cases to that of controls. Finally, results are adjusted for multiple tests. This method was used to evaluate gene-gene interactions that are associated with risk of Type 2 Diabetes among African Americans in the Howard University Family Study. We identified 18 gene-gene interactions (P < 0.0001). Compared with the commonly-used logistical regression method, we demonstrate that the F-ratio test is an efficient approach to measuring gene-gene interactions, especially for studies with limited sample size.

Chen, Guanjie; Yuan, Ao; Zhou, Jie; Bentley, Amy R.; Adeyemo, Adebowale; Rotimi, Charles N.

2012-01-01

374

rho Dependent Transcription Termination of a Bacterial Operon is Antagonized by an Extrachromosomal Gene Product  

Microsoft Academic Search

The psu gene product of ``phasmid'' (phageplasmid) P4 acts as a transcription antitermination factor in trans and in cis, respectively, within the morphogenic operons of its P2 phage helper during lytic viral development and on P4 itself during the establishment stage of its alternative mode of propagation as a plasmid. Here we show that psu also antagonizes activity of the

Rosalba Lagos; Ru-Zhang Jiang; Seung Kim; Richard Goldstein

1986-01-01

375

Influence of temperature regimes on resistance gene-mediated response to rice bacterial blight  

Technology Transfer Automated Retrieval System (TEKTRAN)

Increasing temperatures could reduce yield growth rate of rice by 10% in several rice production areas. Similarly, higher temperatures are predicted to accelerate the breakdown of plant disease resistance through higher disease pressure or altered resistance (R) gene effectiveness in many host-path...

376

Inactivation of expression of several genes in a variety of bacterial species by EGS technology  

PubMed Central

The expression of gene products in bacteria can be inhibited by the use of RNA external guide sequences (EGSs) that hybridize to a target mRNA. Endogenous RNase P cleaves the mRNA in the complex, making it inactive. EGSs participate in this biochemical reaction as the data presented here show. They promote mRNA cleavage at the expected site and sometimes at other secondary sites. Higher-order structure must affect these reactions if the cleavage does not occur at the defined site, which has been determined by techniques based on their ability to find sites that are accessible to the EGS oligonucleotides. Sites defined by a random EGS technique occur as expected. Oligonucleotides made up primarily of defined or random nucleotides are extremely useful in inhibiting expression of the gyrA and rnpA genes from several different bacteria or the cat gene that determines resistance to chloramphenicol in Escherichia coli. An EGS made up of a peptide-phosphorodiamidate morpholino oligonucleotide (PPMO) does not cleave at the same site as an unmodified RNA EGS for reasons that are only partly understood. However, PPMO-EGSs are useful in inhibiting the expression of targeted genes from Gram-negative and Gram-positive organisms during ordinary growth in broth and may provide a basis for broad-spectrum antibiotics.

Shen, Ning; Ko, Jae-hyeong; Xiao, Gaoping; Wesolowski, Donna; Shan, Ge; Geller, Bruce; Izadjoo, Mina; Altman, Sidney

2009-01-01

377

Inactivation of expression of several genes in a variety of bacterial species by EGS technology.  

PubMed

The expression of gene products in bacteria can be inhibited by the use of RNA external guide sequences (EGSs) that hybridize to a target mRNA. Endogenous RNase P cleaves the mRNA in the complex, making it inactive. EGSs participate in this biochemical reaction as the data presented here show. They promote mRNA cleavage at the expected site and sometimes at other secondary sites. Higher-order structure must affect these reactions if the cleavage does not occur at the defined site, which has been determined by techniques based on their ability to find sites that are accessible to the EGS oligonucleotides. Sites defined by a random EGS technique occur as expected. Oligonucleotides made up primarily of defined or random nucleotides are extremely useful in inhibiting expression of the gyrA and rnpA genes from several different bacteria or the cat gene that determines resistance to chloramphenicol in Escherichia coli. An EGS made up of a peptide-phosphorodiamidate morpholino oligonucleotide (PPMO) does not cleave at the same site as an unmodified RNA EGS for reasons that are only partly understood. However, PPMO-EGSs are useful in inhibiting the expression of targeted genes from Gram-negative and Gram-positive organisms during ordinary growth in broth and may provide a basis for broad-spectrum antibiotics. PMID:19416872

Shen, Ning; Ko, Jae-hyeong; Xiao, Gaoping; Wesolowski, Donna; Shan, Ge; Geller, Bruce; Izadjoo, Mina; Altman, Sidney

2009-04-30

378

Bacterial acid phosphatase gene fusions useful as targets for cloning-dependent insertional inactivation.  

PubMed

The Morganella morganii phoC gene, encoding a class A acid phosphatase, was used to generate gene fusions with modified amino-terminal moieties of the Escherichia coli lacZ gene carrying a multiple-cloning site flanked by phage-specific promoters and recognition sites for universal sequencing primers. The corresponding hybrid proteins retained a PhoC-like enzymatic activity which is easily detectable by a plate histochemical assay, rendering similar gene fusions potentially useful as targets for cloning-dependent insertional inactivation. Cloning experiments performed in plasmids carrying similar lacZ-phoC fusions confirmed their usefulness as cloning vectors for direct screening of recombinants. As compared to conventional lacZ alpha-complementation-based vectors, which can only be used in E. coli hosts carrying specific lacZ mutations, the lacZ-phoC fusion-based vectors can be used in combination with any E. coli host and require a less expensive histochemical assay for screening of recombinants, while retaining all the advantageous features that made the former so popular as general purpose cloning vehicles. PMID:9548775

Thaller, M C; Berlutti, F; Schippa, S; Selan, L; Rossolini, G M

379

Magnetic field-controlled gene expression in encapsulated cells  

PubMed Central

Cell and gene therapies have an enormous range of potential applications, but as for most other therapies, dosing is a critical issue, which makes regulated gene expression a prerequisite for advanced strategies. Several inducible expression systems have been established, which mainly rely on small molecules as inducers, such as hormones or antibiotics. The application of these inducers is difficult to control and the effects on gene regulation are slow. Here we describe a novel system for induction of gene expression in encapsulated cells. This involves the modification of cells to express potential therapeutic genes under the control of a heat inducible promoter and the co-encapsulation of these cells with magnetic nanoparticles. These nanoparticles produce heat when subjected to an alternating magnetic field; the elevated temperatures in the capsules then induce gene expression. In the present study we define the parameters of such systems and provide proof-of-principle using reporter gene constructs. The fine-tuned heating of nanoparticles in the magnetic field allows regulation of gene expression from the outside over a broad range and within short time. Such a system has great potential for advancement of cell and gene therapy approaches.

Ortner, Viktoria; Kaspar, Cornelius; Halter, Christian; Tollner, Lars; Mykhaylyk, Olga; Walzer, Johann; Gunzburg, Walter H.; Dangerfield, John A.; Hohenadl, Christine; Czerny, Thomas

2012-01-01

380

Nonsporulating bacterial species contain DNA sequences homologous to the Bacillus spore-specific C-protein gene.  

PubMed

Genes for small, acid-soluble spore proteins (SASPs) are ubiquitous among the spore-forming bacteria and are expressed only during sporulation. Although they perform the function of amino acid storage in spores, the members of the SASP-C multigene family probably serve additional functions, so that similar sequences might be present in non-spore-formers. Using the SASP-C gene (ssp-c) as a hybridization probe, restriction digests of whole genomic DNA from seven nonsporulating bacterial species were examined for similar sequences. Hybridization was found in four species: Streptococcus pyogenes, Staphylococcus aureus, Neisseria sicca, and Mycobacterium phlei, indicating the presence of similar sequences in some, but not all, of the non-spore-formers. In each of these positive species, multiple bands hybridized. A 4.5-kb hybridizing fragment from S. pyogenes and a 9.0-kb hybridizing fragment from M. phlei have been cloned and partially sequenced. These fragments show substantial DNA sequence homology to ssp-c and their deduced amino acid sequences show substantial homology to SASP-C. PMID:1848527

Vocero-Villeta, A M; Schilling, D M; Fliss, E R

1991-02-01

381

Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing  

PubMed Central

Climate warming may induce shifts in soil microbial communities possibly altering the long-term carbon mineralization potential of soils. We assessed the response of the bacterial community in a forest soil to experimental soil warming (+4 °C) in the context of seasonal fluctuations. Three experimental plots were sampled in the fourth year of warming in summer and winter and compared to control plots by 16S rRNA gene pyrosequencing. We sequenced 17 308 amplicons per sample and analysed operational taxonomic units at genetic distances of 0.03, 0.10 and 0.25, with respective Good's coverages of 0.900, 0.977 and 0.998. Diversity indices did not differ between summer, winter, control or warmed samples. Summer and winter samples differed in community structure at a genetic distance of 0.25, corresponding approximately to phylum level. This was mainly because of an increase of Actinobacteria in winter. Abundance patterns of dominant taxa (> 0.06% of all reads) were analysed individually and revealed, that seasonal shifts were coherent among related phylogenetic groups. Seasonal community dynamics were subtle compared to the dynamics of soil respiration. Despite a pronounced respiration response to soil warming, we did not detect warming effects on community structure or composition. Fine-scale shifts may have been concealed by the considerable spatial variation.

Kuffner, Melanie; Hai, Brigitte; Rattei, Thomas; Melodelima, Christelle; Schloter, Michael; Zechmeister-Boltenstern, Sophie; Jandl, Robert; Schindlbacher, Andreas; Sessitsch, Angela

2012-01-01

382

Analysis of Bacterial Community Structure in Sulfurous-Oil-Containing Soils and Detection of Species Carrying Dibenzothiophene Desulfurization (dsz) Genes  

PubMed Central

The selective effects of sulfur-containing hydrocarbons, with respect to changes in bacterial community structure and selection of desulfurizing organisms and genes, were studied in soil. Samples taken from a polluted field soil (A) along a concentration gradient of sulfurous oil and from soil microcosms treated with dibenzothiophene (DBT)-containing petroleum (FSL soil) were analyzed. Analyses included plate counts of total bacteria and of DBT utilizers, molecular community profiling via soil DNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and detection of genes that encode enzymes involved in the desulfurization of hydrocarbons, i.e., dszA, dszB, and dszC.Data obtained from the A soil showed no discriminating effects of oil levels on the culturable bacterial numbers on either medium used. Generally, counts of DBT degraders were 10- to 100-fold lower than the total culturable counts. However, PCR-DGGE showed that the numbers of bands detected in the molecular community profiles decreased with increasing oil content of the soil. Analysis of the sequences of three prominent bands of the profiles generated with the highly polluted soil samples suggested that the underlying organisms were related to Actinomyces sp., Arthrobacter sp., and a bacterium of uncertain affiliation. dszA, dszB, and dszC genes were present in all A soil samples, whereas a range of unpolluted soils gave negative results in this analysis. Results from the study of FSL soil revealed minor effects of the petroleum-DBT treatment on culturable bacterial numbers and clear effects on the DBT-utilizing communities. The molecular community profiles were largely stable over time in the untreated soil, whereas they showed a progressive change over time following treatment with DBT-containing petroleum. Direct PCR assessment revealed the presence of dszB-related signals in the untreated FSL soil and the apparent selection of dszA- and dszC-related sequences by the petroleum-DBT treatment. PCR-DGGE applied to sequential enrichment cultures in DBT-containing sulfur-free basal salts medium prepared from the A and treated FSL soils revealed the selection of up to 10 distinct bands. Sequencing a subset of these bands provided evidence for the presence of organisms related to Pseudomonas putida, a Pseudomonas sp., Stenotrophomonas maltophilia, and Rhodococcus erythropolis. Several of 52 colonies obtained from the A and FSL soils on agar plates with DBT as the sole sulfur source produced bands that matched the migration of bands selected in the enrichment cultures. Evidence for the presence of dszB in 12 strains was obtained, whereas dszA and dszC genes were found in only 7 and 6 strains, respectively. Most of the strains carrying dszA or dszC were classified as R. erythropolis related, and all revealed the capacity to desulfurize DBT. A comparison of 37 dszA sequences, obtained via PCR from the A and FSL soils, from enrichments of these soils, and from isolates, revealed the great similarity of all sequences to the canonical (R. erythropolis strain IGTS8) dszA sequence and a large degree of internal conservation. The 37 sequences recovered were grouped in three clusters. One group, consisting of 30 sequences, was minimally 98% related to the IGTS8 sequence, a second group of 2 sequences was slightly different, and a third group of 5 sequences was 95% similar. The first two groups contained sequences obtained from both soil types and enrichment cultures (including isolates), but the last consisted of sequences obtained directly from the polluted A soil.

Duarte, Gabriela Frois; Rosado, Alexandre Soares; Seldin, Lucy; de Araujo, Welington; van Elsas, Jan Dirk

2001-01-01

383

Metabolism of 2,4-dichlorophenol in tobacco engineered with bacterial degradative genes  

SciTech Connect

The potential use of plants in toxic waste remediation has been overlooked. While chlorophenols are relatively slowly metabolized in Nicotiana tabacum var. Xanthi leaf extracts, chlorocatechols are rapidly metabolized, presumably by polyphenol oxidases. Our initial focus has been the fate of 2,4-dichlorophenol (2,4DCP) in var. Xanthi plants which express a bacterial 2,4DCP hydroxylase, which converts 2,4DCP to 3,5-dichlorocatechol. The roots of wild type and 2,4DCP hydroxylase transgenic plants growing in hydroponics were exposed to {sup 14}C-2,4DCP. Approximately 95% of {sup 14}C-2,4DCP metabolites remained in the roots when exposed to 2,4DCP. Upon extraction of root tissue, three major metabolites were found in untransformed plants and four major metabolites in transformed plants. Upon digestion with beta-D-glucosidase, these metabolites disappeared concomitant with the appearance of free 2,4DCP in wild type plants and 2,4DCP and 3,5-dichlorocatechol in transgenic plants. It is apparent that the chlorophenols are not readily available substrates for polyphenol oxidases in whole plants.

Perkins, E.J.; Sekine, M.; Gordon, M.P. (Univ. of Washington, Seattle (USA))

1990-05-01

384

Dose-response relationships and statistical performance of a battery of bacterial gene profiling assays.  

PubMed

Because of increasing awareness and legislative demands, there is a demand for the development and use of biological assays for the assessment of the toxicity of chemicals, environmental samples. Recently, a growing number of bacterial reporter assays have been developed and implemented. Nevertheless, little data is published on the performance of these assays in terms of analytical parameters. We present results on a battery of 14 transgenic Escherichia coli strains carrying different promoter::reporter fusions. Growth characteristics and basal expression levels were modeled and fitted, data show that growth curves should be taken into account during test development. Our study shows that the induction profiles reflect the mode of action, e.g., paraquat clearly induces the soxRS operon. The sensitivity of the assay compares well to that of whole organism tests, e.g., fish and Daphnia for polar organics. Metal toxicity is detected less efficiently, e.g., cadmium is detected near the LC50 of carp, considered a relatively insensitive species towards cadmium. The assay variability ranges from 10 to 40% depending on the strain, comparable to that of other bioassays. The variability was shown to be determined by the intrinsic traits of the promoter-strain combination, not by operating conditions. PMID:17225096

Dardenne, F; Nobels, I; De Coen, W; Blust, R

2007-01-16

385

Bacterial rheotaxis  

PubMed Central

The motility of organisms is often directed in response to environmental stimuli. Rheotaxis is the directed movement resulting from fluid velocity gradients, long studied in fish, aquatic invertebrates, and spermatozoa. Using carefully controlled microfluidic flows, we show that rheotaxis also occurs in bacteria. Excellent quantitative agreement between experiments with Bacillus subtilis and a mathematical model reveals that bacterial rheotaxis is a purely physical phenomenon, in contrast to fish rheotaxis but in the same way as sperm rheotaxis. This previously unrecognized bacterial taxis results from a subtle interplay between velocity gradients and the helical shape of flagella, which together generate a torque that alters a bacterium's swimming direction. Because this torque is independent of the presence of a nearby surface, bacterial rheotaxis is not limited to the immediate neighborhood of liquid–solid interfaces, but also takes place in the bulk fluid. We predict that rheotaxis occurs in a wide range of bacterial habitats, from the natural environment to the human body, and can interfere with chemotaxis, suggesting that the fitness benefit conferred by bacterial motility may be sharply reduced in some hydrodynamic conditions.

Marcos; Fu, Henry C.; Powers, Thomas R.; Stocker, Roman

2012-01-01

386

Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes  

NASA Astrophysics Data System (ADS)

Horizontal and vertical variations in bacterial community composition were examined in samples collected during two Joint Global Ocean Flux Study (JGOFS) Arabian Sea cruises in 1995. The cruises, 11 months apart, took place during two consecutive NE Monsoon periods (January and December). Bacteria were harvested by filtration from samples collected in the mixed layer, mid-water, and deep sea at stations across the study area. Total bacterial community genomic DNA was analyzed by PCR amplification of 16S rRNA gene fragments, followed by denaturing gradient gel electrophoresis (DGGE). In total, 20 DGGE bands reflecting unique or varying phylotypes were excised, cloned and sequenced. Amplicons were dominated by bacterial groups commonly found in oceanic waters (e.g., the SAR11 cluster of ?-Proteobacteria and cyanobacteria), but surprisingly none of the sequenced amplicons were related to ?-Proteobacteria or to members of the Cytophaga-Flavobacter-Bacteroides phylum. Amplicons related to magnetotactic bacteria were found for the first time in pelagic oceanic waters. The DGGE banding patterns revealed a dominance of ?15 distinguishable amplicons in all samples. In the mixed layer the bacterial community was dominated by the same ?15 phylotypes at all stations, but unique phylotypes were found with increasing depth. Except for cyanobacteria, comparison of the bacterial community composition in surface waters from January and December 1995 showed only minor differences, despite significant differences in environmental parameters. These data suggest a horizontal homogeneity and some degree of seasonal predictability of bacterial community composition in the Arabian Sea.

Riemann, Lasse; Steward, Grieg F.; Fandino, Laura B.; Campbell, Lisa; Landry, Michael R.; Azam, Farooq

1999-08-01

387

Rapid qualitative characterization of bacterial community in eutrophicated wastewater stabilization plant by T-RFLP method based on 16S rRNA genes.  

PubMed

Waste stabilization ponds are a simple, low-cost extensive process for treating wastewater, and well adapted to low socio-economic conditions in developing countries where the microbial populations in these systems are not well characterized. The phylogenetic bacterial community structure within a Tunisian wastewater stabilization plant treating domestic wastewater was assessed by Terminal Restriction Fragment Length Polymorphism method targeting 16S rRNA genes and by the APLAUS+ software of the Microbial Community Analysis (MiCA) web based tool. The dimeric enzymatic digestion with HaeIII and HinfI restriction enzymes revealed high bacterial diversity within the plant where 11 bacterial phyla were identified. The total bacterial community structure includes bacteria catalysing nitrogen and phosphorus removal and bacteria involved in the sulfur cycle. The bacterial community was characterized by the dominance of Proteobacteria which was the most populous phylum (60%) followed by the Actinobacteria (20%), the Firmicutes (10.3%), the Bacteroidetes (2.3%), the Nitrospira (2.2%). Minor bacterial phyla groups occupied smaller fractions such as Chloroflexi, Deferribacteres and Verrumicrobia. T-RFLP analysis revealed also that The Proteobacteria phylum was characterized by the dominance of bacteria of The Gammaproteobacteria class. PMID:22806789

Belila, Abdelaziz; Snoussi, Mejdi; Hassan, Abdennaceur

2011-06-10

388

Frequency of genes in aromatic and aliphatic hydrocarbon biodegradation pathways within bacterial populations from Alaskan sediments.  

PubMed

A significant proportion of the naturally occurring hydrocarbon-degrading populations within Alaskan sediments affected by the Exxon Valdez oil spill had both the xylE and alkB genes and could convert hexadecane and naphthalene to carbon dioxide; a greater proportion of the population had xylE than had alkB, reflecting the composition of the residual oil at the time of sampling; nearly equal populations with xylE alone, alkB alone, and xylE + alkB genes together were found after exposure to fresh crude oil; populations with xylE lacking alkB increased after enrichment on naphthalene. Thus, the genotypes of hydrocarbon-degrading populations reflected the composition of the hydrocarbons to which they were exposed. PMID:7804909

Sotsky, J B; Greer, C W; Atlas, R M

1994-11-01

389

Mammalian cell entry genes in Streptomyces may provide clues to the evolution of bacterial virulence  

PubMed Central

Understanding the evolution of virulence is key to appreciating the role specific loci play in pathogenicity. Streptomyces species are generally non-pathogenic soil saprophytes, yet within their genome we can find homologues of virulence loci. One example of this is the mammalian cell entry (mce) locus, which has been characterised in Mycobacterium tuberculosis. To investigate the role in Streptomyces we deleted the mce locus and studied its impact on cell survival, morphology and interaction with other soil organisms. Disruption of the mce cluster resulted in virulence towards amoebae (Acanthamoeba polyphaga) and reduced colonization of plant (Arabidopsis) models, indicating these genes may play an important role in Streptomyces survival in the environment. Our data suggest that loss of mce in Streptomyces spp. may have profound effects on survival in a competitive soil environment, and provides insight in to the evolution and selection of these genes as virulence factors in related pathogenic organisms.

Clark, Laura C.; Seipke, Ryan F.; Prieto, Pilar; Willemse, Joost; van Wezel, Gilles P.; Hutchings, Matthew I.; Hoskisson, Paul A.

2013-01-01

390

Locus control region mediated regulation of adult ?-globin gene expression  

PubMed Central

Many genes residing in gene clusters and expressed in a differentiation or developmental-stage specific manner are regulated by locus control regions (LCRs). These complex genetic regulatory elements are often composed of several DNAse I hypersensitive sites (HS sites) that function together to regulate the expression of several cis-linked genes. Particularly well characterized is the LCR associated with the ?-globin gene locus. The ?-globin LCR consists of five HS sites that are located upstream of the ?-like globin genes. Recent data demonstrate that the LCR is required for the association of the ?-globin gene locus with transcription foci or factories. The observation that RNA polymerase II associates with the LCR in erythroid progenitor or hematopoietic stem cells which do not express the globin genes suggests that the LCR is always in an accessible chromatin configuration during differentiation of erythroid cells. We propose that erythroid specific factors together with ubiquitous proteins mediate a change in chromatin configuration that juxtaposes the globin genes and the LCR. The proximity then facilitates the transfer of activities from the LCR to the globin genes. In this article we will discuss recent observations regarding ?-globin locus activation with a particular emphasis on LCR mediated activation of adult ?-globin gene expression.

Liang, Shermi; Moghimi, Babak; Yang, Thomas P.; Strouboulis, John; Bungert, Jorg

2009-01-01

391

Expression of the bacterial ipt gene in Physcomitrella rescues mutations in budding and in plastid division  

Microsoft Academic Search

.   Development of Physcomitrella patens (Hedw.) B.S.G. starts with a filamentous protonema growing by apical cell division. As a developmental switch, some subapical\\u000a cells produce three-faced apical cells, the so-called buds, which grow to form leafy shoots, the gametophores. Application\\u000a of cytokinins enhances bud formation but no subsequent gametophore development in several mosses. We used the ipt gene of Agrobacterium

Kirsten Reutter; Rainer Atzorn; Birgit Hadeler; Thomas Schmülling; Ralf Reski

1998-01-01

392

Fluoroquinolones compared with ?-lactam antibiotics for the treatment of acute bacterial sinusitis: a meta-analysis of randomized controlled trials  

PubMed Central

Background The presumed superiority of newer fluoroquinolones for the treatment of acute bacterial sinusitis is based on laboratory data but has not yet been established on clinical grounds. Methods We performed a meta-analysis of randomized controlled trials comparing the effectiveness and safety of fluoroquinolones and ?-lactams in acute bacterial sinusitis. Results We identified 8 randomized controlled trials investigating the newer “respiratory” fluoroquinolones moxifloxacin, levofloxacin and gatifloxacin. In the primary effectiveness analysis involving 2133 intention-to-treat patients from 5 randomized controlled trials, the extent of clinical cure and improvement did not differ between fluoroquinolones and ?-lactams (odds ratio [OR] 1.09, 95% confidence interval [CI] 0.85–1.39) at the test-of-cure assessment, which varied from 10 to 31 days after the start of treatment. Fluoroquinolones were associated with an increased chance of clinical success among the clinically evaluable patients in all of the randomized controlled trials (OR 1.29, 95% CI 1.03–1.63) and in 4 blinded randomized controlled trials (OR 1.45, 95% CI 1.05–2.00). There was no statistically significant difference between fluoroquinolones and amoxicillin–clavulanate (OR 1.24, 95% CI 0.93–1.65). Eradication or presumed eradication of the pathogens isolated before treatment was more likely with fluoroquinolone treatment than with ?-lactam treatment (OR 2.11, 95% CI 1.09–4.08). In the primary safety analysis, adverse events did not differ between treatments (OR 1.17, 95% CI 0.86–1.59). However, more adverse events occurred with fluoroquinolone use than with ?-lactam use in 2 blinded randomized controlled trials. The associations described here were generally consistent when we included 3 additional studies involving other fluoroquinolones (ciprofloxacin and sparfloxacin) in the analysis. Interpretation In the treatment of acute bacterial sinusitis, newer fluoroquinolones conferred no benefit over ?-lactam antibiotics. The use of fluoroquinolones as first-line therapy cannot be endorsed.

Karageorgopoulos, Drosos E.; Giannopoulou, Konstantina P.; Grammatikos, Alexandros P.; Dimopoulos, George; Falagas, Matthew E.

2008-01-01

393

From amplification to gene in thyroid cancer: a high-resolution mapped bacterial-artificial-chromosome resource for cancer chromosome aberrations guides gene discovery after comparative genome hybridization.  

PubMed Central

Chromosome rearrangements associated with neoplasms provide a rich resource for definition of the pathways of tumorigenesis. The power of comparative genome hybridization (CGH) to identify novel genes depends on the existence of suitable markers, which are lacking throughout most of the genome. We now report a general approach that translates CGH data into higher-resolution genomic-clone data that are then used to define the genes located in aneuploid regions. We used CGH to study 33 thyroid-tumor DNAs and two tumor-cell-line DNAs. The results revealed amplifications of chromosome band 2p21, with less-intense amplification on 2p13, 19q13.1, and 1p36 and with least-intense amplification on 1p34, 1q42, 5q31, 5q33-34, 9q32-34, and 14q32. To define the 2p21 region amplified, a dense array of 373 FISH-mapped chromosome 2 bacterial artificial chromosomes (BACs) was constructed, and 87 of these were hybridized to a tumor-cell line. Four BACs carried genomic DNA that was amplified in these cells. The maximum amplified region was narrowed to 3-6 Mb by multicolor FISH with the flanking BACs, and the minimum amplicon size was defined by a contig of 420 kb. Sequence analysis of the amplified BAC 1D9 revealed a fragment of the gene, encoding protein kinase C epsilon (PKCepsilon), that was then shown to be amplified and rearranged in tumor cells. In summary, CGH combined with a dense mapped resource of BACs and large-scale sequencing has led directly to the definition of PKCepsilon as a previously unmapped candidate gene involved in thyroid tumorigenesis.

Chen, X; Knauf, J A; Gonsky, R; Wang, M; Lai, E H; Chissoe, S; Fagin, J A; Korenberg, J R

1998-01-01

394

326. Zinc Finger Protein Targeted Epigenetic Gene Regulation: Toward Directed Long-Term Gene Control  

Microsoft Academic Search

Zinc finger protein transcription factors (ZFP TFs) are capable of regulating the expression of any endogenous gene, potentially providing direct therapeutics for the treatment of disease. To extend this approach we have coupled the versatility and specificity of the ZFP DNA binding domain with non-classical effector domains implicated in long-term, epigenetic control of gene expression. The use of epigenetic mechanisms

Andrew R. McNamara; Andrew W. Snowden; Philip D. Gregory

2004-01-01

395

Metagenomic analysis of the 1-aminocyclopropane-1-carboxylate deaminase gene (acdS) operon of an uncultured bacterial endophyte colonizing Solanum tuberosum L.  

PubMed

Deamination of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is a key plant-beneficial trait found in many plant growth-promoting bacteria. In this study, we analysed ACC deaminase genes (acdS) of bacterial endophytes colonizing field-grown potato plants. PCR analysis revealed the presence of two types of acdS genes, the dominant one showing high homology to an acdS gene derived from Pseudomonas fluorescens. Construction, functional screening and sequence analysis of metagenomic libraries revealed clones containing the acdS gene identified in the PCR library. Sequence analysis of one metagenomic clone identified the entire acdS operon of an uncultivated endophyte and revealed that the acdS gene is coupled upstream with an acdR transcriptional regulator gene as previously found in P. putida strain UW4 (Grichko and Glick 2000). However, in-silico analysis of 195 fully sequenced, acdS-containing bacterial genomes revealed that the majority of strains, including numerous strains belonging to the genus Pseudomonas, do not contain an acdR regulatory gene in the vicinity of the acdS gene or elsewhere in the genome. The acdR (+)-acdS (+) operon was exclusively found in several Alpha- and Betaproteobacteria most prominently in the genus Burkholderia. PMID:21523387

Nikolic, Branislav; Schwab, Helmut; Sessitsch, Angela

2011-04-27

396

Two HMGB1 genes from grass carp Ctenopharyngodon idella mediate immune responses to viral/bacterial PAMPs and GCRV challenge.  

PubMed

High mobility group box 1 (HMGB1) is a nuclear weapon in the immune arsenal and a master regulator of innate immunity, at the crossroads between innate and adaptive immunity. To clarify the immune characterizations of HMGB1 in fishes, two co-orthologs of HMGB1 (CiHMGB1a and CiHMGB1b) were identified in grass carp Ctenopharyngodon idella by local EST database searching and RACE techniques. mRNA expressions of the two HMGB1 genes are widespread in fifteen tissues investigated. The transcripts of CiHMGB1a and CiHMGB1b were significantly up-regulated and reached peak at 24h post GCRV challenge in spleen and head kidney tissues (P<0.05). The modulations are slow post-bacterial PAMP stimulations by contrast with those after viral PAMP or GCRV challenge. They are inhibited by bacterial PAMPs, but are enhanced by viral PAMP or virus. mRNA expression of CiHMGB1a is high and strongly modulated by nucleic acids and transcription of CiHMGB1b is low and mildly regulated by nucleic acids and capsids of GCRV. The over-expression vectors were constructed and transfected into C. idella kidney cell line to obtain stably expressing recombinant proteins. In HMGB1 over-expressed cells, mRNA expressions of IPS-1, MyD88 and Mx1 were down-regulated, whereas TRIF was found to be up-regulated and IFN-I showed no change in its expression. After GCRV challenge, the transcripts of IPS-1, MyD88 and Mx1 were up-regulated, while IFN-I showed down-regulation, and TRIF showed up-regulation after an initial phase of decline. The titer assay demonstrated no antiviral activity of HMGB1s. The results indicated mRNA expressions of HMGB1a and HMGB1b are enhanced by GCRV or viral PAMP, and are inhibited by bacterial PAMPs; HMGB1a and HMGB1b collaborate with each other and play important roles in modulating the innate immune responses, although without direct antiviral effect; the immune network triggered by HMGB1 work together in concert to maintain homeostasis. PMID:23228458

Yang, Chunrong; Peng, Limin; Su, Jianguo

2012-12-07

397

Use of Genomics To Identify Bacterial Undecaprenyl Pyrophosphate Synthetase: Cloning, Expression, and Characterization of the Essential uppS Gene  

PubMed Central

The prenyltransferase undecaprenyl pyrophosphate synthetase (di-trans,poly-cis-decaprenylcistransferase; EC 2.5.1.31) was purified from the soluble fraction of Escherichia coli by TSK-DEAE, ceramic hydroxyapatite, TSK-ether, Superdex 200, and heparin-Actigel chromatography. The protein was labeled with the photolabile analogue of the farnesyl pyrophosphate analogue (E,E)-[1-3H]-(2-diazo-3-trifluoropropionyloxy)geranyl diphos-phate and was detected on a sodium dodecyl sulfate-polyacrylamide gel as a protein with an apparent molecular mass of 29 kDa. This protein band was cut out from the gel, trypsin digested, and subjected to matrix-assisted laser desorption ionization mass spectrometric analysis. Comparison of the experimental data with computer-simulated trypsin digest data for all E. coli proteins yielded a single match with a protein of unassigned function (SWISS-PROT Q47675; YAES_ECOLI). Sequences with strong similarity indicative of homology to this protein were identified in 25 bacterial species, in Saccharomyces cerevisiae, and in Caenorhabditis elegans. The homologous genes (uppS) were cloned from E. coli, Haemophilus influenzae, and Streptococcus pneumoniae, expressed in E. coli as amino-terminal His-tagged fusion proteins, and purified over a Ni2+ affinity column. An untagged version of the E. coli uppS gene was also cloned and expressed, and the protein purified in two chromatographic steps. We were able to detect Upp synthetase activity for all purified enzymes. Further, biochemical characterization revealed no differences between the recombinant untagged E. coli Upp synthetase and the three His-tagged fusion proteins. All enzymes were absolutely Triton X-100 and MgCl2 dependent. With the use of a regulatable gene disruption system, we demonstrated that uppS is essential for growth in S. pneumoniae R6.

Apfel, Christian M.; Takacs, Bela; Fountoulakis, Michael; Stieger, Martin; Keck, Wolfgang

1999-01-01

398

Use of genomics to identify bacterial undecaprenyl pyrophosphate synthetase: cloning, expression, and characterization of the essential uppS gene.  

PubMed

The prenyltransferase undecaprenyl pyrophosphate synthetase (di-trans,poly-cis-decaprenylcistransferase; EC 2.5.1.31) was purified from the soluble fraction of Escherichia coli by TSK-DEAE, ceramic hydroxyapatite, TSK-ether, Superdex 200, and heparin-Actigel chromatography. The protein was labeled with the photolabile analogue of the farnesyl pyrophosphate analogue (E, E)-[1-3H]-(2-diazo-3-trifluoropropionyloxy)geranyl diphosphate and was detected on a sodium dodecyl su