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1

Evolutionary analyses of non-family genes in plants  

SciTech Connect

There are a large number of non-family (NF) genes that do not cluster into families with three or more members per genome. While gene families have been extensively studied, a systematic analysis of NF genes has not been reported. We performed comparative studies on NF genes in 14 plant species. Based on the clustering of protein sequences, we identified ~94,000 NF genes across these species that were divided into five evolutionary groups: Viridiplantae-wide, angiosperm-specific, monocot-specific, dicot-specific, and those that were species-specific. Our analysis revealed that the NF genes resulted largely from less frequent gene duplications and/or a higher rate of gene loss after segmental duplication relative to genes in both low-copy-number families (LF; 3 10 copies per genome) and high-copy-number families (HF; >10 copies). Furthermore, we identified functions enriched in the NF gene set as compared with the HF genes. We found that NF genes were involved in essential biological processes shared by all plant lineages (e.g., photosynthesis and translation), as well as gene regulation and stress responses associated with phylogenetic diversification. In particular, our analysis of an Arabidopsis protein-protein interaction network revealed that hub proteins with the top 10% most connections were over-represented in the NF set relative to the HF set. This research highlights the roles that NF genes may play in evolutionary and functional genomics research.

Ye, Chuyu [ORNL; Li, Ting [ORNL; Yin, Hengfu [ORNL; Weston, David [ORNL; Tuskan, Gerald A [ORNL; Tschaplinski, Timothy J [ORNL; Yang, Xiaohan [ORNL

2013-01-01

2

Evolutionary analyses of non-family genes in plants  

SciTech Connect

There are a large number of non-family (NF) genes that do not cluster into families with three or more members per genome. While gene families have been extensively studied, a systematic analysis of NF genes has not been reported. We performed comparative studies on NF genes in 14 plant species. Based on the clustering of protein sequences, we identified ~94 000 NF genes across these species that were divided into five evolutionary groups: Viridiplantae wide, angiosperm specific, monocot specific, dicot specific, and those that were species specific. Our analysis revealed that the NF genes resulted largely from less frequent gene duplications and/or a higher rate of gene loss after segmental duplication relative to genes in both lowcopy- number families (LF; 3 10 copies per genome) and high-copy-number families (HF; >10 copies). Furthermore, we identified functions enriched in the NF gene set as compared with the HF genes. We found that NF genes were involved in essential biological processes shared by all plant lineages (e.g. photosynthesis and translation), as well as gene regulation and stress responses associated with phylogenetic diversification. In particular, our analysis of an Arabidopsis protein protein interaction network revealed that hub proteins with the top 10% most connections were over-represented in the NF set relative to the HF set. This research highlights the roles that NF genes may play in evolutionary and functional genomics research.

Ye, Chuyu [ORNL; Li, Ting [ORNL; Yin, Hengfu [ORNL; Weston, David [ORNL; Tuskan, Gerald A [ORNL; Tschaplinski, Timothy J [ORNL; Yang, Xiaohan [ORNL

2013-01-01

3

Molecular Evolution of the Plant R Regulatory Gene Family  

PubMed Central

Anthocyanin pigmentation patterns in different plant species are controlled in part by members of the myc-like R regulatory gene family. We have examined the molecular evolution of this gene family in seven plant species. Three regions of the R protein show sequence conservation between monocot and dicot R genes. These regions encode the basic helix-loop-helix domain, as well as conserved N-terminal and C-terminal domains; mean replacement rates for these conserved regions are 1.02 X 10(-9) nonsynonymous nucleotide substitutions per site per year. More than one-half of the protein, however, is diverging rapidly, with nonsynonymous substitution rates of 4.08 X 10(-9) substitutions per site per year. Detailed analysis of R homologs within the grasses (Poaceae) confirm that these variable regions are indeed evolving faster than the flanking conserved domains. Both nucleotide substitutions and small insertion/deletions contribute to the diversification of the variable regions within these regulatory genes. These results demonstrate that large tracts of sequence in these regulatory loci are evolving at a fairly rapid rate.

Purugganan, M. D.; Wessler, S. R.

1994-01-01

4

Evolution of the RALF Gene Family in Plants: Gene Duplication and Selection Patterns  

PubMed Central

Rapid alkalinization factors (RALFs) are plant small peptides that could induce a rapid pH increase in the medium of plant cell suspension culture and play a critical role in plant development. The evolutionary process of the RALF gene family remains unclear. To obtain details of the phylogeny of these genes, this study characterized RALF genes in Arabidopsis, rice, poplar and maize. Phylogenetic trees, evolutionary patterns and molecular evolutionary rates were used to elucidate the evolutionary process of this gene family. In addition, the different signatures of selection, expression patterns, and subcellular localization of RALFs were also analyzed. We found that the RALF gene family had a rapid birth process after the separation of the eudicot and monocot species about 145 million years ago, that tandem duplication played a dominant role in the expansion of Arabidopsis and rice RALF gene family, and that RALFs were under purifying selection according to estimations of the substitution rates of these genes. We also identified a diverse expression pattern of RALF genes and predominant extracellular localization feature of RALF proteins. Our findings shed light on several key differences in RALF gene family evolution among the plant species, which may provide a scaffold for future functional analysis of this family.

Cao, Jun; Shi, Feng

2012-01-01

5

An Automated Method for Rapid Identification of Putative Gene Family Members in Plants  

PubMed Central

Background Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families has become increasingly important. Subfunctionalization via changes in regulatory sequences following duplication (adaptive selection) appears to be a common mechanism of evolution in plants and can be accompanied by purifying selection on the coding region. Such negative selection can be detected by a bias toward synonymous over nonsynonymous substitutions. However, the process of identifying this bias requires many steps usually employing several different software programs. We have simplified the process and significantly shortened the time required by condensing many steps into a few scripts or programs to rapidly identify putative gene family members beginning with a single query sequence. Results In this report we 1) describe the software tools (SimESTs, PCAT, and SCAT) developed to automate the gene family identification, 2) demonstrate the validity of the method by correctly identifying 3 of 4 PAL gene family members from Arabidopsis using EST data alone, 3) identify 2 to 6 CAD gene family members from Glycine max (previously unidentified), and 4) identify 2 members of a putative Glycine max gene family previously unidentified in any plant species. Conclusion Gene families in plants, particularly that subset where purifying selection has occurred in the coding region, can be identified quickly and easily by integrating our software tools and commonly available contig assembly and ORF identification programs.

Frank, Ronald L; Mane, Ajay; Ercal, Fikret

2006-01-01

6

Molecular Evolution of Flower Development: Diversification of the Plant Mads-Box Regulatory Gene Family  

PubMed Central

Floral homeotic genes that control the specification of meristem and organ identity in developing flowers have been isolated from both Arabidopsis thaliana and Antirrhinum majus. Most of these genes belong to a large family of regulatory genes and possess a characteristic DNA binding domain known as the MADS-box. Members of this gene family display primarily floral-specific expression and are homologous to transcription factors found in several animal and fungal species. Molecular evolutionary analyses reveal that there are appreciable differences in the substitution rates between different domains of these plant MADS-box genes. Phylogenetic analyses also demonstrate that members of the plant MADS-box gene family are organized into several distinct gene groups: the AGAMOUS, APETALA3/PISTILLATA and APETALA1/AGL9 groups. The shared evolutionary history of members of a gene group appear to reflect the distinct functional roles these MADS-box genes play in flower development. Molecular evolutionary analyses also suggest that these different gene groups were established in a relatively short span of evolutionary time and that the various floral homeotic loci originated even before the appearance of the flowering plants.

Purugganan, M. D.; Rounsley, S. D.; Schmidt, R. J.; Yanofsky, M. F.

1995-01-01

7

Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom  

PubMed Central

Background As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modification has been a major task for bioenergy feedstock improvement. The study of the evolution and function of lignin biosynthesis genes thus has two-fold implications. First, the lignin biosynthesis pathway provides an excellent model to study the coordinative evolution of a biochemical pathway in plants. Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement. Results We analyzed lignin biosynthesis genes from fourteen plant species and one symbiotic fungal species. Comprehensive comparative genome analysis was carried out to study the distribution, relatedness, and family expansion of the lignin biosynthesis genes across the plant kingdom. In addition, we also analyzed the comparative synteny map between rice and sorghum to study the evolution of lignin biosynthesis genes within the Poaceae family and the chromosome evolution between the two species. Comprehensive lignin biosynthesis gene expression analysis was performed in rice, poplar and Arabidopsis. The representative data from rice indicates that different fates of gene duplications exist for lignin biosynthesis genes. In addition, we also carried out the biomass composition analysis of nine Arabidopsis mutants with both MBMS analysis and traditional wet chemistry methods. The results were analyzed together with the genomics analysis. Conclusion The research revealed that, among the species analyzed, the complete lignin biosynthesis pathway first appeared in moss; the pathway is absent in green algae. The expansion of lignin biosynthesis gene families correlates with substrate diversity. In addition, we found that the expansion of the gene families mostly occurred after the divergence of monocots and dicots, with the exception of the C4H gene family. Gene expression analysis revealed different fates of gene duplications, largely confirming plants are tolerant to gene dosage effects. The rapid expansion of lignin biosynthesis genes indicated that the translation of transgenic lignin modification strategies from model species to bioenergy feedstock might only be successful between the closely relevant species within the same family.

2009-01-01

8

Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants  

PubMed Central

Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor, Zea mays, and Oryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.

Rawal, H. C.; Singh, N. K.; Sharma, T. R.

2013-01-01

9

F-box gene family is expanded in herbaceous annual plants Arabidopsis and rice relative to woody perennial plant Populus  

SciTech Connect

F-box proteins are generally responsible for substrate recognition in the Skp1-Cullin-F-box complexes that are involved in protein degradation via the ubiquitin-26S proteosome pathway. In plants, F-box genes influence a variety of biological processes such as leaf senescence, branching, self-incompatibility and responses to biotic and abiotic stresses. The number of F-box genes in Populus (~320) is less than half that found in Arabidopsis (~660) or rice (~680), even though the total number of genes in Populus is equivalent to that in rice and 1.5 times that in Arabidopsis. We performed comparative genomic analysis between the woody perennial plant Populus and the herbaceous annual plants Arabidopsis and rice in order to explicate the functional implications of this large gene family. Our analyses reveal interspecific differences in genomic distribution, orthologous relationship, intron evolution, protein domain structure and gene expression. The set of F-box genes shared by these three species appear to be involved in core biological processes essential for plant growth and development; lineage-specific differences primarily occurred because of an expansion of the F-box genes via tandem duplications in Arabidopsis and rice. The present study provides insights into the relationship between the structure and composition of the F-box gene family in herbaceous and woody species and their associated developmental and physiological features.

Yang, Xiaohan [ORNL; Kalluri, Udaya C [ORNL; Jawdy, Sara [ORNL; Gunter, Lee E [ORNL; Yin, Tongming [ORNL; Tschaplinski, Timothy J [ORNL; Weston, David [ORNL; Ranjan, Priya [ORNL; Tuskan, Gerald A [ORNL

2008-01-01

10

Functional divergence of the glutathione S-transferase supergene family in Physcomitrella patens reveals complex patterns of large gene family evolution in land plants.  

PubMed

Plant glutathione S-transferases (GSTs) are multifunctional proteins encoded by a large gene family that play major roles in the detoxification of xenobiotics and oxidative stress metabolism. To date, studies on the GST gene family have focused mainly on vascular plants (particularly agricultural plants). In contrast, little information is available on the molecular characteristics of this large gene family in nonvascular plants. In addition, the evolutionary patterns of this family in land plants remain unclear. In this study, we identified 37 GST genes from the whole genome of the moss Physcomitrella patens, a nonvascular representative of early land plants. The 37 P. patens GSTs were divided into 10 classes, including two new classes (hemerythrin and iota). However, no tau GSTs were identified, which represent the largest class among vascular plants. P. patens GST gene family members showed extensive functional divergence in their gene structures, gene expression responses to abiotic stressors, enzymatic characteristics, and the subcellular locations of the encoded proteins. A joint phylogenetic analysis of GSTs from P. patens and other higher vascular plants showed that different class GSTs had distinct duplication patterns during the evolution of land plants. By examining multiple characteristics, this study revealed complex patterns of evolutionary divergence among the GST gene family in land plants. PMID:23188805

Liu, Yan-Jing; Han, Xue-Min; Ren, Lin-Ling; Yang, Hai-Ling; Zeng, Qing-Yin

2012-11-27

11

Plant Receptor-Like Kinase Gene Family: Diversity, Function, and Signaling  

NSDL National Science Digital Library

A basic feature of all biological systems is the ability to sense and process information from chemical signals via cell-surface receptors. One prevalent class of receptors in both plants and animals is the receptor protein kinases. These proteins contain a signal-binding region located outside the cell linked to a region inside the cell called the protein kinase domain. The protein kinase domain transmits information to other cellular components by catalyzing the transfer of a phosphate group from adenosine triphosphate (ATP) to an amino acid residue on the target proteins. In animals and humans, the well-studied family of receptor tyrosine kinases (RTKs) mediates a wide range of signaling events at the cell surface. The importance of receptor protein kinases in plant biology was revealed by the discovery of a family of more than 400 genes coding for receptor-like kinases (RLKs) present in the recently sequenced genome of the model plant Arabidopsis. Unlike most animal RTKs, the plant RLKs use serine and threonine residues in proteins as targets for phosphorylation. Detailed studies of a handful of plant RLK genes have implicated them in the control of plant growth and development and in responses to pathogens. Multiple signals can be sensed by different RLKs, including peptides produced by neighboring cells, steroid hormones, and pathogen cell-wall proteins and carbohydrates. Major challenges for the future will include understanding the wide range of specific signaling functions performed by this large family of receptors and discovering how the information from this multitude of signal initiation points is integrated by the plant's cells.

Shin-Han Shiu (University of Wisconsin-Madison;The Department of Botany REV); Anthony B. Bleecker (University of Wisconsin-Madison;The Department of Botany REV)

2001-12-18

12

Genome-wide identification and analysis of membrane-bound O-acyltransferase (MBOAT) gene family in plants.  

PubMed

Membrane bound O-acyl transferase (MBOAT) family is composed of gene members encoding a variety of acyltransferase enzymes, which play important roles in plant acyl lipid metabolism. Here, we present the first genome-enabled identification and analysis of MBOAT gene models in plants. In total, we identified 136 plant MBOAT sequences from 14 plant species with complete genomes. Phylogenetic relationship analyses suggested the plant MBOAT gene models fell into four major groups, two of which likely encode enzymes of diacylglycerol acyltransferase 1 (DGAT1) and lysophospholipid acyltransferase (LPLAT), respectively, with one-three copies of paralogs present in each of the most plant species. A group of gene sequences, which are homologous to Saccharomyces cerevisiae glycerol uptake proteins (GUP), was identified in plants; copy numbers were conserved, with only one copy represented in each of the most plant species; analyses showed that residues essential for acyltransferases were more prone to be conserved than vertebrate orthologs. Among four groups, one was inferred to emerge in land plants and experience a rapid expansion in genomes of angiosperms, which suggested their important roles in adaptation of plants in lands. Sequence and phylogeny analyses indicated that genes in all four groups encode enzymes with acyltransferases. Comprehensive sequence identification of MBOAT family members and investigation into classification provide a complete picture of the MBOAT gene family in plants, and could shed light into enzymatic functions of different MBOAT genes in plants. PMID:23928653

Wang, Peng; Wang, Zhunian; Dou, Yongchao; Zhang, Xiaoxiao; Wang, Maoyuan; Tian, Xinmin

2013-08-09

13

Molecular Evolution of Flower Development: Diversification of the Plant MADS-Box Regulatory Gene Family  

Microsoft Academic Search

Floral homeotic genes that control the specification of meristem and organ identity in developing flowers have been isolated from both Arabidopsis thaliana and Antirrhinum nwjus. Most of these genes belong to a large family of regulatory genes and possess a characteristic DNA binding domain known as the MADSbox. Members of this gene family display primarily floral-specific expression and are homologous

Michael D. Purugganan; Steven D. Rounsley; Robert J. Schmidt; Martin F. Yanofsky

1995-01-01

14

A Novel Gene Family in Moss (Physcomitrella patens) Shows Sequence Homology and a Phylogenetic Relationship with the TIR-NBS Class of Plant Disease Resistance Genes  

Microsoft Academic Search

  Plant disease resistance (R) genes encode proteins in which several motifs of the nucleotide-binding region (NBS) are highly\\u000a conserved. Using degenerate primers designed according to the kinase 1 (P-loop) and hydrophobic (HD) motifs of the R gene\\u000a NBS domains, homologous sequences were cloned from moss (Physcomitrella patens; phylum Bryophyta) representing an ancient\\u000a nonvascular plant. A novel gene family (PpC) with

Motomu Akita; Jari P. T. Valkonen

2002-01-01

15

Recombination between Diverged Clusters of the Tomato Cf9 Plant Disease Resistance Gene Family  

Microsoft Academic Search

The tomato Cf-4 and Cf-9 genes are the founder members of a large gene family of homologues of Cladosporium fulvum resistance gene Cf-9 (Hcr9 genes), several of which confer resistance against C. fulvum through recognition of different pathogen-encoded avirulence determinants. Three loci of tandemly repeated Hcr9 genes--Southern Cross (SC), Milky Way (MW), and Northern Lights (NL)--are located on the short

Martin Parniske; Jonathan D. G. Jones

1999-01-01

16

Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants.  

PubMed Central

Members of a new inverted repeat element family, named Stowaway, have been found in close association with more than 40 monocotyledonous and dicotyledonous plant genes listed in the GenBank and EMBL nucleic acid data bases. Stowaway elements are characterized by a conserved terminal inverted repeat, small size, target site specificity (TA), and potential form stable DNA secondary structures. Some elements are located at the extreme 3' ends of sequenced cDNAs and supply polyadenylation signals to their host genes. Other elements are in the 5' upstream regions of several genes and appear to contain previously identified cis-acting regulatory domains. Although the Stowaway elements share many structural features with the recently discovered Tourist elements, the two families share no significant sequence similarity. Together, the Stowaway and Tourist families serve to define an important new class of short inverted repeat elements found in possibly all flowering plant genomes.

Bureau, T E; Wessler, S R

1994-01-01

17

Animal and Plant Members of a Gene Family with Similarity to Alkaloid-Synthesizing Enzymes  

Microsoft Academic Search

Here we describe novel members of a gene family which have similarity to strictosidine synthase (SS), one of the key enzymes in the production of monoterpene indole alkaloids. In addition to the first animal member of the family described previously (Drosophila hemomucin), a second Drosophila member has been identified, which appears to differ in subcellular distribution from hemomucin. In Arabidopsis,

Marco Fabbri; Gabriele Delp; Otto Schmidt; Ulrich Theopold

2000-01-01

18

The I2C Family from the Wilt Disease Resistance Locus I2 Belongs to the Nucleotide Binding, Leucine-Rich Repeat Superfamily of Plant Resistance Genes  

Microsoft Academic Search

Characterization of plant resistance genes is an important step in understanding plant defense mechanisms. fusarium oxysporum f sp 1ycopersici is the causal agent of a vascular wilt disease in tomato. Genes conferring resistance to plant vascular diseases have yet to be described molecularly. Members of a new multigene family, complex 12C, were isolated by map-based cloning from the 12 F.

Naomi Ori; Yuval Eshed; Gernot Presting; Dani Zamir; Robert Fluhra

1997-01-01

19

Global Analysis of Ankyrin Repeat Domain C3HC4-Type RING Finger Gene Family in Plants  

PubMed Central

Ankyrin repeat (ANK) C3HC4-type RING finger (RF) genes comprise a large family in plants and play important roles in various physiological processes of plant life. In this study, we identified 187 ANK C3HC4-type RF proteins from 29 species with complete genomes and named the ANK C3HC4-type RF proteins the XB3-like proteins because they are structurally related to the rice (Oryza sativa) XB3. A phylogenetic relationship analysis suggested that the XB3-like genes originated from ferns, and the encoded proteins fell into 3 major groups. Among these groups, we found that the spacing between the metal ligand position 6 and 7, and the conserved residues, which was in addition to the metal ligand amino acids, in the C3HC4-type RF were different. Using a wide range of protein structural analyses, protein models were established, and all XB3-like proteins were found to contain two to seven ANKs and a C3HC4-type RF. The microarray data for the XB3-like genes of Arabidopsis, Oryza sative, Zea mays and Glycine max revealed that the expression of XB3-like genes was in different tissues and during different life stages. The preferential expression of XB3-like genes in specified tissues and the response to phytohormone and abiotic stress treatments of Arabidopsis and Zea mays not only confirmed the microarray analysis data but also demonstrated that the XB3-like proteins play roles in plant growth and development as well as in stress responses. Our data provide a very useful reference for the identification and functional analysis of members of this gene family and also provide a new method for the genome-wide analysis of gene families.

Liu, Shiyang; Yu, Mingli; Su, Hongyan; Shu, Huairui; Li, Xinzheng

2013-01-01

20

Global analysis of ankyrin repeat domain C3HC4-type RING finger gene family in plants.  

PubMed

Ankyrin repeat (ANK) C3HC4-type RING finger (RF) genes comprise a large family in plants and play important roles in various physiological processes of plant life. In this study, we identified 187 ANK C3HC4-type RF proteins from 29 species with complete genomes and named the ANK C3HC4-type RF proteins the XB3-like proteins because they are structurally related to the rice (Oryza sativa) XB3. A phylogenetic relationship analysis suggested that the XB3-like genes originated from ferns, and the encoded proteins fell into 3 major groups. Among these groups, we found that the spacing between the metal ligand position 6 and 7, and the conserved residues, which was in addition to the metal ligand amino acids, in the C3HC4-type RF were different. Using a wide range of protein structural analyses, protein models were established, and all XB3-like proteins were found to contain two to seven ANKs and a C3HC4-type RF. The microarray data for the XB3-like genes of Arabidopsis, Oryza sative, Zea mays and Glycine max revealed that the expression of XB3-like genes was in different tissues and during different life stages. The preferential expression of XB3-like genes in specified tissues and the response to phytohormone and abiotic stress treatments of Arabidopsis and Zea mays not only confirmed the microarray analysis data but also demonstrated that the XB3-like proteins play roles in plant growth and development as well as in stress responses. Our data provide a very useful reference for the identification and functional analysis of members of this gene family and also provide a new method for the genome-wide analysis of gene families. PMID:23516424

Yuan, Xiaowei; Zhang, Shizhong; Liu, Shiyang; Yu, Mingli; Su, Hongyan; Shu, Huairui; Li, Xinzheng

2013-03-13

21

Characterization and evolutionary analysis of a large polygalacturonase gene family in the oomycete plant pathogen Phytophthora cinnamomi.  

PubMed

Polygalacturonases (PGs) are secreted by fungal pathogens during saprophytic and parasitic growth, and their degradation of pectin in the plant cell wall is believed to play a major role in tissue invasion and maceration. In this study, PG activity was demonstrated in culture filtrates of the oomycete plant pathogen, Phytophthora cinnamomi. A P. cinnamomi pg gene fragment amplified using degenerate primers based on conserved regions in fungal and plant PGs was used to isolate 17 complete P. cinnamomi pg genes and pseudogenes from a genomic library and partial sequence for another two genes. Gel blotting of genomic DNA indicated that there may be even more pg genes in the P. cinnamomi genome. P. cinnamomi pg gene sequences were expressed in PG-deficient yeast and found to confer PG activity, thereby confirming their functional identity. The predicted mature P. cinnamomi PGs fall into subgroups that exhibit large differences in the extent of N-glycosylation, isoelectric points, and N- and C-terminal structure. Evidence for birth-and-death and reticulate evolution in the P. cinnamomi pg gene family was obtained, and some codons for surface exposed residues in the P. cinnamomi PGs were shown to have been subject to diversifying selection. Contrary to accepted phylogenies for other proteins, phylogenetic analysis of the P. cinnamomi PGs revealed a closer relationship with PGs from true fungi than with those from plants. PMID:12236597

Götesson, Arvid; Marshall, Jerry S; Jones, David A; Hardham, Adrienne R

2002-09-01

22

Functional analyses of three ASMT gene family members in rice plants.  

PubMed

N-acetylserotonin methyltransferase (ASMT) is the final enzyme in a biosynthetic pathway that produces melatonin. ASMT may play a rate-limiting role in the production of this bioactive molecule in plants. There are three ASMT genes (ASMT1-ASMT3) in the rice genome, but only ASMT1 has been functionally characterized. A major barrier to further progress in characterizing these genes has been a failure of functional expression within the Escherichia coli. Purified recombinant ASMT2 and ASMT3 are inactive in ASMT enzyme catalysis. To determine the biological functions of ASMT2 and ASMT3, we first overexpressed them in rice calli, which resulted in enhanced production of melatonin in the respective transgenic calli. To further corroborate the functions of ASMT2 and ASMT3 as ASMT genes, we generated stable transgenic rice plants. ASMT enzyme activity was increased in comparison with the wild type in T2 homozygous transgenic rice plants expressing three ASMT genes independently. When seedlings were treated with 1 mm N-acetylserotonin (NAS), leaf melatonin contents were higher in the three transgenic lines than in the wild type. There were no significant differences between the transgenic lines and the wild type without this treatment. ASMT1 and ASMT2 transcripts were highly expressed in stems and flowers, but ASMT3 was barely detectable in any of the plant organs. All three ASMT mRNAs were simultaneously induced in treatments with abscisic and methyl jasmonic acids. PMID:24033370

Park, Sangkyu; Byeon, Yeong; Back, Kyoungwhan

2013-09-03

23

Torn at the Genes One Family's Debate Over Genetically Altered Plants  

NSDL National Science Digital Library

The setting for this case is the family dinner table, where a heated discussion about genetically altered foods is taking place. Marsha Cumberland’s brother-in-law has joined the family for dinner. Ed is an industry official whose job it is to decide whether or not new products need pre-market approval by the FDA. He has just returned from a conference on transgenic foods.  When it turns out that some of the food on the dinner table is genetically modified, a debate ensues with different members of the family at different ends of the spectrum. Written for an introductory biology course, the case considers the scientific and ethical issues of genetically altered plants.

Nelson, Jennifer; Herreid, Clyde F.

2000-01-01

24

The autophagy-associated Atg8 gene family operates both under favourable growth conditions and under starvation stresses in Arabidopsis plants  

Microsoft Academic Search

Arabidopsis plants possess a family of nine AtAtg8 gene homologues of the yeast autophagy-associated Apg8\\/Aut7 gene. To gain insight into how these genes function in plants, first, the expression patterns of five AtAtg8 homologues were analysed in young Arabidop- sis plants grown under favourable growth conditions or following exposure to prolonged darkness or sugar starvation. Promoters, plus the entire coding

Silvia Slavikova; Galia Shy; Youli Yao; Rina Glozman; Hanna Levanony; Shmuel Pietrokovski; Zvulun Elazar; Gad Galili

2005-01-01

25

Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family.  

PubMed

Plastids are DNA-containing organelles unique to plant cells. In Arabidopsis, one-third of the genes required for embryo development encode plastid-localized proteins. To help understand the role of plastids in embryogenesis and postembryonic development, we characterized proteins of the mitochondrial transcription termination factor (mTERF) family, which in animal models, comprises DNA-binding regulators of mitochondrial transcription. Of 35 Arabidopsis mTERF proteins, 11 are plastid-localized. Genetic complementation shows that at least one plastidic mTERF, BELAYA SMERT' (BSM), is required for embryogenesis. The main postembryonic phenotypes of genetic mosaics with the bsm mutation are severe abnormalities in leaf development. Mutant bsm cells are albino, are compromised in growth, and suffer defects in global plastidic gene expression. The bsm phenotype could be phenocopied by inhibition of plastid translation with spectinomycin. Plastid translation is essential for cell viability in dicotyledonous species such as tobacco but not in monocotyledonous maize. Here, genetic interactions between BSM and the gene encoding plastid homomeric acetyl-CoA carboxylase ACC2 suggest that there is a functional redundancy in malonyl-CoA biosynthesis that permits bsm cell survival in Arabidopsis. Overall, our results indicate that biosynthesis of malonyl-CoA and plastid-derived systemic growth-promoting compounds are the processes that link plant development and plastid gene expression. PMID:21464319

Babiychuk, Elena; Vandepoele, Klaas; Wissing, Josef; Garcia-Diaz, Miguel; De Rycke, Riet; Akbari, Hana; Joubès, Jérôme; Beeckman, Tom; Jänsch, Lothar; Frentzen, Margrit; Van Montagu, Marc C E; Kushnir, Sergei

2011-04-04

26

Plant F-Box Protein Evolution Is Determined by Lineage-Specific Timing of Major Gene Family Expansion Waves  

PubMed Central

F-box proteins (FBPs) represent one of the largest and fastest evolving gene/protein families in the plant kingdom. The FBP superfamily can be divided in several subfamilies characterized by different C-terminal protein-protein interaction domains that recruit targets for proteasomal degradation. Hence, a clear picture of their phylogeny and molecular evolution is of special interest for the general understanding of evolutionary histories of multi-domain and/or large protein families in plants. In an effort to further understand the molecular evolution of F-box family proteins, we asked whether the largest subfamily in Arabidopsis thaliana, which carries a C-terminal F-box associated domain (FBA proteins) shares evolutionary patterns and signatures of selection with other FBPs. To address this question, we applied phylogenetic and molecular evolution analyses in combination with the evaluation of transcriptional profiles. Based on the 2219 FBA proteins we de novo identified in 34 completely sequenced plant genomes, we compared their evolutionary patterns to a previously analyzed large subfamily carrying C-terminal kelch repeats. We found that these two large FBP subfamilies generally tend to evolve by massive waves of duplication, followed by sequence conservation of the F-box domain and sequence diversification of the target recruiting domain. We conclude that the earlier in evolutionary time a major wave of expansion occurred, the more pronounced these selection signatures are. As a consequence, when performing cross species comparisons among FBP subfamilies, significant differences will be observed in the selective signatures of protein-protein interaction domains. Depending on the species, the investigated subfamilies comprise up to 45% of the complete superfamily, indicating that other subfamilies possibly follow similar modes of evolution.

Quint, Marcel

2013-01-01

27

Characterization of P69E and P69F, Two Differentially Regulated Genes Encoding New Members of the Subtilisin-Like Proteinase Family from Tomato Plants  

PubMed Central

Subtilisin-like proteins represent an ancient family of serine proteases that are extremely widespread in living organisms. We report here the structure and genomic organization of two new transcriptionally active genes encoding proteins that belong to the P69 family of subtilisin-like proteases from tomato (Lycopersicon esculentum) plants. The two new members, P69E and P69F, are organized in a cluster and arranged in a tandem form. mRNA expression analysis and studies of transgenic Arabidopsis plants transformed with promoter-?-glucuronidase fusions for each of these two genes revealed that they are differentially regulated, with each showing a highly specific mRNA expression pattern. P69E mRNA is expressed only in roots, while P69F mRNA is expressed only in hydathodes. A comparison of all the P69 amino acid sequences, gene structure, expression profiles, and clustered organization suggests a working model for P69 gene family evolution.

Jorda, Lucia; Conejero, Vicente; Vera, Pablo

2000-01-01

28

Knock-down of a member of the isoflavone reductase gene family impairs plant growth and nodulation in Phaseolus vulgaris.  

PubMed

Flavonoids and isoflavonoids participate in the signaling exchange between roots of legumes and nitrogen-fixing rhizobia and can promote division of cortical cells during nodule formation by inhibiting auxin transport. Here, we report the characterization of a member of the common bean isoflavone reductase (EC 1.3.1.45, PvIFR1) gene family, an enzyme that participates in the last steps of the biosynthetic pathway of isoflavonoids. Transcript levels of PvIFR1 were detected preferentially in the susceptible zone of roots, augmented upon nitrogen starvation and in response to Rhizobium etli inoculation at very early stages of the interaction. Knockdown of PvIFR1 mediated by RNA interference (RNAi) in common bean composite plants resulted in a reduction of shoot and root length. Furthermore, reduction of PvIFR1 mRNAs also affected growth of lateral roots after emergence, a stage in which auxins are required to establish a persistent meristem. Upon inoculation, the number of nodules formed by different strains of R. etli was significantly lower in IFR RNAi than in control roots. Transcript levels of two auxin-regulated genes are consistent with lower levels of auxin in PvIFR1 silenced roots. These results suggest a complex role of PvIFR1 during plant growth, root development and symbiosis, all processes in which auxin transport is involved. PMID:23644278

Rípodas, Carolina; Via, Virginia Dalla; Aguilar, O Mario; Zanetti, María Eugenia; Blanco, Flavio Antonio

2013-04-16

29

Three orthologs in rice, Arabidopsis, and Populus encoding starch branching enzymes (SBEs) are different from other SBE gene families in plants.  

PubMed

Starch branching enzymes (SBEs) play important roles in plant starch synthesis. Three orthologs encoding SBEs in rice, Arabidopsis thaliana, and Populus trichocarpa are described. Putative amino acid sequences of these three SBE genes show approximately 30% identity to those of SBEI and SBEII from plants such as maize, barley, and wheat. More interestingly, they share approximately 31% amino acid sequence identity with those of glycogen-branching enzymes from such animals as mouse, horse, and monkey. The three genes have similar genomic structures, but their structural features are quite different from those of genes of both SBEI and SBEII families in plants. Based on phylogenetic analysis and genomic structure comparison, it is proposed that the three SBE genes represent a new family of SBEs. PMID:17698298

Han, Yuepeng; Sun, Feng-Jie; Rosales-Mendoza, Sergio; Korban, Schuyler S

2007-07-17

30

The ROOT DETERMINED NODULATION1 gene regulates nodule number in roots of Medicago truncatula and defines a highly conserved, uncharacterized plant gene family.  

PubMed

The formation of nitrogen-fixing nodules in legumes is tightly controlled by a long-distance signaling system in which nodulating roots signal to shoot tissues to suppress further nodulation. A screen for supernodulating Medicago truncatula mutants defective in this regulatory behavior yielded loss-of-function alleles of a gene designated ROOT DETERMINED NODULATION1 (RDN1). Grafting experiments demonstrated that RDN1 regulatory function occurs in the roots, not the shoots, and is essential for normal nodule number regulation. The RDN1 gene, Medtr5g089520, was identified by genetic mapping, transcript profiling, and phenotypic rescue by expression of the wild-type gene in rdn1 mutants. A mutation in a putative RDN1 ortholog was also identified in the supernodulating nod3 mutant of pea (Pisum sativum). RDN1 is predicted to encode a 357-amino acid protein of unknown function. The RDN1 promoter drives expression in the vascular cylinder, suggesting RDN1 may be involved in initiating, responding to, or transporting vascular signals. RDN1 is a member of a small, uncharacterized, highly conserved gene family unique to green plants, including algae, that we have named the RDN family. PMID:21742814

Schnabel, Elise L; Kassaw, Tessema K; Smith, Lucinda S; Marsh, John F; Oldroyd, Giles E; Long, Sharon R; Frugoli, Julia A

2011-07-08

31

Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes  

Microsoft Academic Search

Metal cation homeostasis is essential for plant nutrition and resistance to toxic heavy metals. Many plant metal transporters remain to be identified at the molecular level. In the present study, we have isolated AtNramp cDNAs from Arabidopsis and show that these genes complement the phenotype of a metal uptake deficient yeast strain, smf1. AtNramps show homology to the Nramp gene

Sébastien Thomine; Rongchen Wang; John M. Ward; Nigel M. Crawford; Julian I. Schroeder

2000-01-01

32

Transcriptional profiling of the PDR gene family in rice roots in response to plant growth regulators, redox perturbations and weak organic acid stresses.  

PubMed

The role of plant pleiotropic drug resistance (PDR) type ATP-binding cassette (ABC) transporters remains poorly understood. We characterized the expression of the rice pleiotropic drug resistance (PDR) gene family in roots, where PDR transporters are believed to have major functions. A prototypical oligonucleotide array was developed containing 70-mers chosen in the gene-specific 3' untranslated regions of the rice PDR genes, other full-molecule rice ABC transporter genes and relevant marker genes. Jasmonates, which are involved in plant defense and secondary metabolism, proved major inducers of PDR gene expression. Over half of the PDR genes were JA-induced in roots of rice; OsPDR9 to the highest level. Salicylic acid, involved in plant pathogen defense, markedly induced the expression of OsPDR20. OsPDR20 was cDNA cloned and characterized. Abscisic acid, typically involved in water deficit responses, particularly induced OsPDR3 in roots and shoot and OsPDR6 in rice leaves. OsPDR9 and OsPDR20 were furthermore up-regulated in response to dithiothreitol- or glutathione-induced redox perturbations. Exogenous application of the weak organic acids lactic acid, malic acid, and citric acid differentially induced the expression of OsPDR3, OsPDR8, OsPDR9 and OsPDR20 in rice seedling roots. This transcriptional survey represents a guide for the further functional analysis of individual PDR transporters in roots of rice. PMID:18830621

Moons, Ann

2008-09-17

33

Family miridae - the plant bugs  

Technology Transfer Automated Retrieval System (TEKTRAN)

Presented for the true bug family Miridae (Hemiptera: Heteroptera), commonly called plant bugs, is an overview of the classification, morphology, habitats and host plants, life history and habits, economic importance, and natural enemies. Adult illustrations providing examples of seven of the eight...

34

Characterization of Homeodomain-Leucine Zipper Genes in the Fern Ceratopteris richardii and the Evolution of the Homeodomain-Leucine Zipper Gene Family in Vascular Plants  

Microsoft Academic Search

The homeodomain-leucine zipper (HD-Zip) genes encode transcription factors that are characterized by the presence of both a homeodomain and a leucine zipper motif. They belong to the homeobox gene superfamily and have been reported only from flowering plants. This article is the first report on the fern HD-Zip genes (named Crhb1-Crhb11) isolated from the homosporous fern Ceratopteris richardii. Phylogenetic analyses

Kumi Aso; Masahiro Kato; Jo Ann Banks; Mitsuyasu Hasebe

35

Fast Plants and Families I  

NSDL National Science Digital Library

Description: This is an investigation describing the procedure for looking at a seed pod from a mature Fast Plant with a dry pod by sandwiching the pod between layers of clear tape, then exploring the sibling seeds. Questions that might be considered:- In how many ways can you describe the pod (the mother)? Are the pods from one plant more like each other than they are like the pods from other plants? What about the siblings from a single pod? - Do all the seeds in a pod have the same father? - How much variation is there within and between families of Fast Plants? - How much does the environment affect the variation in Fast Plants, e.g. the number of seeds per pod, style length, plant height, days to first flowering, etc? - Is there any relationship between the length of the seed pod and its position on the maternal plant?

Program, The W.

36

[Plant Trihelix transcription factors family].  

PubMed

The Trihelix transcription factor family has raised great concerns only in recent years. It was named after its conserved DNA binding domain containing three tandem helix (helix-loop-helix-loop-helix), which could bind specifically with GT element, a light-responsive DNA element. So, this family is also known as GT factors. At the early stage of study, the knowledge of this family was only confined to their functions in regulation of light-responsive genes. However, recent researches indicated that Trihelix family also plays important roles in different growth and development processes involving flowers, stomata, trichomes, embryos, and seeds, as well as roles in response to abiotic and biotic stresses. This review mainly focused on the structural characteristics, classification, and the latest functional research progresses on the Trihelix family. PMID:23262102

Luo, Jun-Ling; Zhao, Na; Lu, Chang-Ming

2012-12-01

37

The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes  

Microsoft Academic Search

The Mi locus of tomato confers resistance to root knot nematodes. Tomato DNA spanning the locus was isolated as bacterial artificial chromosome clones, and 52 kb of contiguous DNA was sequenced. Three open reading frames were identified with similarity to cloned plant disease resistance genes. Two of them, Mi-1.1 and Mi-1.2 , appear to be intact genes; the third is

Stephen B. Milligan; John Bodeau; Jafar Yaghoobi; Isgouhi Kaloshian; Pim Zabel; Valerie M. Williamson

1998-01-01

38

Family selection in plant breeding  

Microsoft Academic Search

Plant breeding programmes rarely take explicit practical account of the two sources of genetic variance, namely between and within full-sib families, even though existence of these two sources of variation has long been recognised. This paper refers to inbred and clonal crops, not to outbred, seed-propagated species. Theory suggests that the two variances should be of similar size, sometimes very

N. W. Simmonds

1996-01-01

39

Testing Times for Plant Family Recognition  

ERIC Educational Resources Information Center

|Plant families are the level of the taxonomic hierarchy that many biologists use to organise their understanding of plant diversity. Consequently, from many perspectives, it is very useful to be able to recognise the major plant families "on sight". To this end numerous books and web sites have described and illustrated plant families, but few…

Burrows, Geoffrey E.

2010-01-01

40

The insect SNMP gene family  

Microsoft Academic Search

SNMPs are membrane proteins observed to associate with chemosensory neurons in insects; in Drosophila melanogaster, SNMP1 has been shown to be essential for the detection of the pheromone cis-vaccenyl acetate (CVA). SNMPs are one of three insect gene clades related to the human fatty acid transporter CD36. We previously characterized the CD36 gene family in 4 insect Orders that effectively

Richard G. Vogt; Natalie E. Miller; Rachel Litvack; Richard A. Fandino; Jackson Sparks; Jon Staples; Robert Friedman; Joseph C. Dickens

2009-01-01

41

Gene targeting in plants  

PubMed Central

Although the generation of transgenic plants is now routine, the integration of foreign genetic information has so far been at random sites in the genome. We now present evidence for directed integration into a predicted location in the host plant genome. Protoplasts of transgenic tobacco (Nicotiana tabaccum) plants carrying copies of a partial, non-functional drug-resistance gene in the nuclear DNA were used as recipients for DNA molecules containing the missing part of the gene. Molecular and genetic data confirm the integration of the foreign DNA through homologous recombination within overlapping parts of the protein coding region, resulting in the formation of an active gene in the host chromosome. This approach is referred to as gene targeting. The gene targeting frequency (the number of drug-resistant clones resulting from gene correction compared to the number of resistant clones from parallel experiments with a similar non-interrupted hybrid gene) was 0.5-4.2×10-4. These experiments demonstrate the possibility of producing transgenic plants with desired modifications to a specific nuclear gene. Images

Paszkowski, Jerzy; Baur, Markus; Bogucki, Augustyn; Potrykus, Ingo

1988-01-01

42

A member of a new plant gene family encoding a meprin and TRAF homology (MATH) domain-containing protein is involved in restriction of long distance movement of plant viruses.  

PubMed

Restriction of long distance movement of several potyviruses in Arabidopsis thaliana is controlled by at least three dominant restricted TEV movement (RTM) genes, named RTM1, RTM2 and RTM3 and acts as a non conventional resistance. RTM1 encodes a protein belonging to the jacalin family and RTM2 encodes a protein which has similarities to small heat shock proteins. The recent cloning of RTM3 which encodes a protein belonging to an unknown protein family of 29 members which has a meprin and TRAF homology (MATH) domain in its N-terminal region and a coiled-coil (CC) domain at its C-terminal end is an important breakthrough for a better understanding of this resistance process. Not only the third gene involved in this resistance has been identified and has allowed revealing a new gene family in plant but the discovery that the RTM3 protein interacts directly with RTM1 strongly suggests that the RTM proteins form a multimeric complex. However, these data also highlight striking similarities of the RTM resistance with the well known R-gene mediated resistance. PMID:20930558

Cosson, Patrick; Sofer, Luc; Schurdi-Levraud, Valérie; Revers, Frédéric

2010-10-01

43

Proteinase Inhibitor from Ginkgo Seeds Is a Member of the Plant Nonspecific Lipid Transfer Protein Gene Family1  

PubMed Central

A 9-kD proteinase inhibitor was isolated from the seeds of ginkgo (Ginkgo biloba) and purified to homogeneity. This protein was revealed to partial-noncompetitively inhibit the aspartic acid proteinase pepsin and the cysteine proteinase papain (inhibition constant = 10?5–10?4 m). The cDNA of the inhibitor was revealed to contain a 357-bp open reading frame encoding a 119-amino acid protein with a potential signal peptide (27 residues), indicating that this protein is synthesized as a preprotein and secreted outside the cells. Semiquantitative reverse transcription-polymerase chain reaction revealed that this gene expresses only in seeds, not in stems, leaves, and roots, suggesting that the protein is involved in seed development and/or germination. The inhibitor showed about 40% sequence homology with type-I nonspecific lipid transfer protein (nsLTP1) from other plant species. Actually, this inhibitor exerted both lipid transfer activity and lipid-binding activity, while the protein did not show any antifungal and antibacterial activities. Furthermore, the site-directed mutagenesis study using a recombinant ginkgo nsLTP1 revealed that proline (Pro)-79 and phenylalanine-80 are important on phospholipid transfer activity and that Pro-79 and isoleucine-82 are essential for the binding activity toward cis-unsaturated fatty acids. On the other hand, the ?-helical content of P79A and F80A mutants was significantly lower than that of the wild-type protein. It was noteworthy that the papain-inhibitory activity of P79A and F80A mutants was elevated twice as much as that of the wild-type protein. In summary, we concluded that Pro-79 plays a critical role in both the lipid transfer and binding activities of ginkgo nsLTP1.

Sawano, Yoriko; Hatano, Ken-ichi; Miyakawa, Takuya; Komagata, Hideki; Miyauchi, Yumiko; Yamazaki, Hiroshi; Tanokura, Masaru

2008-01-01

44

Gene Linkage and Familial Behavioral Characteristics.  

National Technical Information Service (NTIS)

The identification of genes influencing behavioral traits by relating the pattern of phenotypes in a family to the transmission of marker genes having a known Mendelian pattern of inheritance was studied. Families selected for two or more siblings with pr...

L. R. Weitkamp

1981-01-01

45

Structure and expression of the maize (Zea mays L.) SUN-domain protein gene family: evidence for the existence of two divergent classes of SUN proteins in plants  

PubMed Central

Background The nuclear envelope that separates the contents of the nucleus from the cytoplasm provides a surface for chromatin attachment and organization of the cortical nucleoplasm. Proteins associated with it have been well characterized in many eukaryotes but not in plants. SUN (Sad1p/Unc-84) domain proteins reside in the inner nuclear membrane and function with other proteins to form a physical link between the nucleoskeleton and the cytoskeleton. These bridges transfer forces across the nuclear envelope and are increasingly recognized to play roles in nuclear positioning, nuclear migration, cell cycle-dependent breakdown and reformation of the nuclear envelope, telomere-led nuclear reorganization during meiosis, and karyogamy. Results We found and characterized a family of maize SUN-domain proteins, starting with a screen of maize genomic sequence data. We characterized five different maize ZmSUN genes (ZmSUN1-5), which fell into two classes (probably of ancient origin, as they are also found in other monocots, eudicots, and even mosses). The first (ZmSUN1, 2), here designated canonical C-terminal SUN-domain (CCSD), includes structural homologs of the animal and fungal SUN-domain protein genes. The second (ZmSUN3, 4, 5), here designated plant-prevalent mid-SUN 3 transmembrane (PM3), includes a novel but conserved structural variant SUN-domain protein gene class. Mircroarray-based expression analyses revealed an intriguing pollen-preferred expression for ZmSUN5 mRNA but low-level expression (50-200 parts per ten million) in multiple tissues for all the others. Cloning and characterization of a full-length cDNA for a PM3-type maize gene, ZmSUN4, is described. Peptide antibodies to ZmSUN3, 4 were used in western-blot and cell-staining assays to show that they are expressed and show concentrated staining at the nuclear periphery. Conclusions The maize genome encodes and expresses at least five different SUN-domain proteins, of which the PM3 subfamily may represent a novel class of proteins with possible new and intriguing roles within the plant nuclear envelope. Expression levels for ZmSUN1-4 are consistent with basic cellular functions, whereas ZmSUN5 expression levels indicate a role in pollen. Models for possible topological arrangements of the CCSD-type and PM3-type SUN-domain proteins are presented.

2010-01-01

46

Phylogenetic and Structural Relationships of the PR5 Gene Family Reveal an Ancient Multigene Family Conserved in Plants and Select Animal Taxa  

Microsoft Academic Search

Pathogenesis-related group 5 (PR5) plant proteins include thaumatin, osmotin, and related proteins, many of which have antimicrobial\\u000a activity. The recent discovery of PR5-like (PR5-L) sequences in nematodes and insects raises questions about their evolutionary\\u000a relationships. Using complete plant genome data and discovery of multiple insect PR5-L sequences, phylogenetic comparisons\\u000a among plants and animals were performed. All PR5\\/PR5-L protein sequences were

Robert G. Shatters; Laura M. Boykin; Stephen L. Lapointe; Wayne B. Hunter; A. A. Weathersbee

2006-01-01

47

Identification of a novel gene family, paralogs of inhibitor of apoptosis proteins present in plants, fungi, and animals  

Microsoft Academic Search

Only few orthologs of animal apoptosis regulators have been found in plants. Recently, the ectopic expression of mammalian inhibitor of apoptosis proteins (IAPs) has been shown to affect plant programmed cell death. Here, we identified two novel proteins homologous to ArabidopsisthalianaIAP-like protein (AtILP) 1 and 2 by applying an improved motif searching method. Furthermore, homologs of AtILP1 were found to

K. Higashi; R. Takasawa; A. Yoshimori; T. Goh; S. Tanuma; K. Kuchitsu

2005-01-01

48

Organization and differential activation of a gene family encoding the plant defense enzyme chalcone synthase in Phaseolus vulgaris  

Microsoft Academic Search

Chalcone synthase (CHS) catalyzes the first and key regulatory step in the branch pathway of phenylpropanoid biosynthesis specific for synthesis of ubiquitous flavonoid pigments and UV protectants. In bean (Phaseolus vulgaris L.) and other members of the Leguminoseae, chalcone synthase is also involved in the synthesis of the isoflavonoid-derived phytoalexin antibiotics characteristic of this family. We have demonstrated that the

Thomas B. Ryder; Susan A. Hedrick; John N. Bell; Xaiowu Liang; Steven D. Clouse; Christopher J. Lamb

1987-01-01

49

Isolation of disease resistance genes from crop plants  

Microsoft Academic Search

The recent cloning of several resistance genes from diverse plant species, in combination with various technical advances, has provided new opportunities for accessing the great diversity of disease resistance genes in crop plants. Many resistance genes probably belong to clusters of large multigene families encoding receptor-like proteins that have evolved to have different specificities. The isolation of genes from crop

Richard W Michelmore

1995-01-01

50

The Nme gene family in fish.  

PubMed

The Nme gene family, also known as Nm23 or NDPK, is a very ancient gene family that can be found in all kingdoms of life. In the late eighties, a gene of the Nme family, NME1, was identified as the first metastatic suppressor gene, resulting in a major interest for this family. Due to the complexity of the family, the need for a unified and evolutionary-supported gene nomenclature was recently stressed by the scientific community. Based on a complete evolutionary history study of the gene family in metazoans and vertebrates, a unified nomenclature was recently proposed and accepted by gene nomenclature consortia. In addition to its well-documented role in tumor metastasis, members of the Nme family are also involved in a wide variety of cellular and physiological processes. Available data in non-mammalian species remain, however, scarce with the noticeable exception of Drosophila in which a major role in development was reported. In fish, very few studies have specifically investigated the role of nme genes. Several transcriptomic and proteomic studies have, however, revealed the expression of nme genes in various fish organs and tissues, in mature oocytes, and during embryonic development. Altogether, interest for the Nme gene family in fish is growing and new functions/roles in fish biology are expected to be discovered in the forthcoming years. Here, we briefly review the current knowledge of the Nme family in fish. PMID:22484598

Desvignes, T; Fostier, A; Fauvel, C; Bobe, J

2012-04-08

51

Auxin-Responsive Genes AIR12 Code for a New Family of Plasma Membrane b-Type Cytochromes Specific to Flowering Plants1[C][W][OA  

PubMed Central

We report here on the identification of the major plasma membrane (PM) ascorbate-reducible b-type cytochrome of bean (Phaseolus vulgaris) and soybean (Glycine max) hypocotyls as orthologs of Arabidopsis (Arabidopsis thaliana) AIR12 (for auxin induced in root cultures). Soybean AIR12, which is glycosylated and glycosylphosphatidylinositol-anchored to the external side of the PM in vivo, was expressed in Pichia pastoris in a recombinant form, lacking the glycosylphosphatidylinositol modification signal and purified from the culture medium. Recombinant AIR12 is a soluble protein predicted to fold into a ?-sandwich domain and belonging to the DOMON (for dopamine ?-monooxygenase N terminus) domain superfamily. It is shown to be a b-type cytochrome with a symmetrical ?-band at 561 nm, fully reduced by ascorbate, and fully oxidized by monodehydroascorbate radical. AIR12 is a high-potential cytochrome b showing a wide bimodal dependence from the redox potential between +80 mV and +300 mV. Optical absorption and electron paramagnetic resonance analysis indicate that AIR12 binds a single, highly axial low-spin heme, likely coordinated by methionine-91 and histidine-76, which are strongly conserved in AIR12 sequences. Phylogenetic analyses reveal that the auxin-responsive genes AIR12 represent a new family of PM b-type cytochromes specific to flowering plants. Circumstantial evidence suggests that AIR12 may interact with other redox partners within the PM to constitute a redox link between cytoplasm and apoplast.

Preger, Valeria; Tango, Nunzio; Marchand, Christophe; Lemaire, Stephane D.; Carbonera, Donatella; Di Valentin, Marilena; Costa, Alex; Pupillo, Paolo; Trost, Paolo

2009-01-01

52

Three orthologs in rice, Arabidopsis, and Populus encoding starch branching enzymes (SBEs) are different from other SBE gene families in plants  

Microsoft Academic Search

Starch branching enzymes (SBEs) play important roles in plant starch synthesis. Three orthologs encoding SBEs in rice, Arabidopsis thaliana, and Populus trichocarpa are described. Putative amino acid sequences of these three SBE genes show ?30% identity to those of SBEI and SBEII from plants such as maize, barley, and wheat. More interestingly, they share ?31% amino acid sequence identity with

Yuepeng Han; Feng-Jie Sun; Sergio Rosales-Mendoza; Schuyler S. Korban

2007-01-01

53

Gene family matters: expanding the HGNC resource.  

PubMed

ABSTRACT: The HUGO Gene Nomenclature Committee (HGNC) assigns approved gene symbols to human loci. There are currently over 33,000 approved gene symbols, the majority of which represent protein-coding genes, but we also name other locus types such as non-coding RNAs, pseudogenes and phenotypic loci. Where relevant, the HGNC organise these genes into gene families and groups. The HGNC website http://www.genenames.org/ is an online repository of HGNC-approved gene nomenclature and associated resources for human genes, and includes links to genomic, proteomic and phenotypic information. In addition to this, we also have dedicated gene family web pages and are currently expanding and generating more of these pages using data curated by the HGNC and from information derived from external resources that focus on particular gene families. Here, we review our current online resources with a particular focus on our gene family data, using it to highlight our new Gene Symbol Report and gene family data downloads. PMID:23245209

Daugherty, Louise C; Seal, Ruth L; Wright, Mathew W; Bruford, Elspeth A

2012-07-01

54

Transcription Factor Families Have Much Higher Expansion Rates in Plants than in Animals  

Microsoft Academic Search

Transcription factors (TFs), which are central to the regulation of gene expression, are usually members of multigene families. In plants, they are involved in diverse processes such as developmental control and elicitation of defense and stress responses. To investigate if differences exist in the expansion patterns of TF gene families between plants and other eukaryotes, we first used Arabidopsis (Arabidopsis

Shin-Han Shiu; Ming-Che Shih; Wen-Hsiung Li

2005-01-01

55

The Evolution of Mammalian Gene Families  

PubMed Central

Gene families are groups of homologous genes that are likely to have highly similar functions. Differences in family size due to lineage-specific gene duplication and gene loss may provide clues to the evolutionary forces that have shaped mammalian genomes. Here we analyze the gene families contained within the whole genomes of human, chimpanzee, mouse, rat, and dog. In total we find that more than half of the 9,990 families present in the mammalian common ancestor have either expanded or contracted along at least one lineage. Additionally, we find that a large number of families are completely lost from one or more mammalian genomes, and a similar number of gene families have arisen subsequent to the mammalian common ancestor. Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees, including changes likely driven by adaptive natural selection. Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic “revolving door” of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.

Demuth, Jeffery P.; Bie, Tijl De; Stajich, Jason E.; Cristianini, Nello; Hahn, Matthew W.

2006-01-01

56

Multiple inter-kingdom horizontal gene transfers in the evolution of the phosphoenolpyruvate carboxylase gene family.  

PubMed

Pepcase is a gene encoding phosphoenolpyruvate carboxylase that exists in bacteria, archaea and plants,playing an important role in plant metabolism and development. Most plants have two or more pepcase genes belonging to two gene sub-families, while only one gene exists in other organisms. Previous research categorized one plant pepcase gene as plant-type pepcase (PTPC) while the other as bacteria-type pepcase (BTPC) because of its similarity with the pepcase gene found in bacteria. Phylogenetic reconstruction showed that PTPC is the ancestral lineage of plant pepcase, and that all bacteria, protistpepcase and BTPC in plants are derived from a lineage of pepcase closely related with PTPC in algae. However, their phylogeny contradicts the species tree and traditional chronology of organism evolution. Because the diversification of bacteria occurred much earlier than the origin of plants, presumably all bacterialpepcase derived from the ancestral PTPC of algal plants after divergingfrom the ancestor of vascular plant PTPC. To solve this contradiction, we reconstructed the phylogeny of pepcase gene family. Our result showed that both PTPC and BTPC are derived from an ancestral lineage of gamma-proteobacteriapepcases, possibly via an ancient inter-kingdom horizontal gene transfer (HGT) from bacteria to the eukaryotic common ancestor of plants, protists and cellular slime mold. Our phylogenetic analysis also found 48other pepcase genes originated from inter-kingdom HGTs. These results imply that inter-kingdom HGTs played important roles in the evolution of the pepcase gene family and furthermore that HGTsare a more frequent evolutionary event than previouslythought. PMID:23251445

Peng, Yingmei; Cai, Jing; Wang, Wen; Su, Bing

2012-12-12

57

Heterochronic genes in plant evolution and development  

PubMed Central

Evolution of morphology includes evolutionary shifts of developmental processes in space or in time. Heterochronic evolution is defined as a temporal shift. The concept of heterochrony has been very rewarding to investigators of both animal and plant developmental evolution, because it has strong explanatory power when trying to understand morphological diversity. While for animals, extensive literature on heterochrony developed along with the field of evolution of development, in plants the concept has been applied less often and is less elaborately developed. Yet novel genetic findings highlight heterochrony as a developmental and evolutionary process in plants. Similar to what has been found for the worm Caenorhabditis, a heterochronic gene pathway controlling developmental timing has been elucidated in flowering plants. Two antagonistic microRNA’s miR156 and miR172 target two gene families of transcription factors, SQUAMOSA PROMOTOR BINDING PROTEIN-LIKE and APETALA2-like, respectively. Here, we propose that this finding now allows the molecular investigation of cases of heterochronic evolution in plants. We illustrate this point by examining microRNA expression patterns in the Antirrhinum majus incomposita and choripetala heterochronic mutants. Some of the more beautiful putative cases of heterochronic evolution can be found outside flowering plants, but little is known about the extent of conservation of this flowering plant pathway in other land plants. We show that the expression of an APETALA2-like gene decreases with age in a fern species. This contributes to the idea that ferns share some heterochronic gene functions with flowering plants.

Geuten, Koen; Coenen, Heleen

2013-01-01

58

A Bayesian model for gene family evolution  

PubMed Central

Background A birth and death process is frequently used for modeling the size of a gene family that may vary along the branches of a phylogenetic tree. Under the birth and death model, maximum likelihood methods have been developed to estimate the birth and death rate and the sizes of ancient gene families (numbers of gene copies at the internodes of the phylogenetic tree). This paper aims to provide a Bayesian approach for estimating parameters in the birth and death model. Results We develop a Bayesian approach for estimating the birth and death rate and other parameters in the birth and death model. In addition, a Bayesian hypothesis test is developed to identify the gene families that are unlikely under the birth and death process. Simulation results suggest that the Bayesian estimate is more accurate than the maximum likelihood estimate of the birth and death rate. The Bayesian approach was applied to a real dataset of 3517 gene families across genomes of five yeast species. The results indicate that the Bayesian model assuming a constant birth and death rate among branches of the phylogenetic tree cannot adequately explain the observed pattern of the sizes of gene families across species. The yeast dataset was thus analyzed with a Bayesian heterogeneous rate model that allows the birth and death rate to vary among the branches of the tree. The unlikely gene families identified by the Bayesian heterogeneous rate model are different from those given by the maximum likelihood method. Conclusions Compared to the maximum likelihood method, the Bayesian approach can produce more accurate estimates of the parameters in the birth and death model. In addition, the Bayesian hypothesis test is able to identify unlikely gene families based on Bayesian posterior p-values. As a powerful statistical technique, the Bayesian approach can effectively extract information from gene family data and thereby provide useful information regarding the evolutionary process of gene families across genomes.

2011-01-01

59

Lineage-specific expansion of IFIT gene family: an insight into coevolution with IFN gene family.  

PubMed

In mammals, IFIT (Interferon [IFN]-induced proteins with Tetratricopeptide Repeat [TPR] motifs) family genes are involved in many cellular and viral processes, which are tightly related to mammalian IFN response. However, little is known about non-mammalian IFIT genes. In the present study, IFIT genes are identified in the genome databases from the jawed vertebrates including the cartilaginous elephant shark but not from non-vertebrates such as lancelet, sea squirt and acorn worm, suggesting that IFIT gene family originates from a vertebrate ancestor about 450 million years ago. IFIT family genes show conserved gene structure and gene arrangements. Phylogenetic analyses reveal that this gene family has expanded through lineage-specific and species-specific gene duplication. Interestingly, IFN gene family seem to share a common ancestor and a similar evolutionary mechanism; the function link of IFIT genes to IFN response is present early since the origin of both gene families, as evidenced by the finding that zebrafish IFIT genes are upregulated by fish IFNs, poly(I:C) and two transcription factors IRF3/IRF7, likely via the IFN-stimulated response elements (ISRE) within the promoters of vertebrate IFIT family genes. These coevolution features creates functional association of both family genes to fulfill a common biological process, which is likely selected by viral infection during evolution of vertebrates. Our results are helpful for understanding of evolution of vertebrate IFN system. PMID:23818968

Liu, Ying; Zhang, Yi-Bing; Liu, Ting-Kai; Gui, Jian-Fang

2013-06-20

60

The mammalian aldehyde oxidase gene family  

PubMed Central

Aldehyde oxidases (EC 1.2.3.1) are a small group of structurally conserved cytosolic proteins represented in both the animal and plant kingdoms. In vertebrates, aldehyde oxidases constitute the small sub-family of molybdo-flavoenzymes, along with the evolutionarily and structurally related protein, xanthine oxidoreductase. These enzymes require a molybdo-pterin cofactor (molybdenum cofactor, MoCo) and flavin adenine dinucleotide for their catalytic activity. Aldehyde oxidases have broad substrate specificity and catalyse the hydroxylation of N-heterocycles and the oxidation of aldehydes to the corresponding acid. In humans, a single aldehyde oxidase gene (AOX1) and two pseudogenes clustering on a short stretch of chromosome 2q are known. In other mammals, a variable number of structurally conserved aldehyde oxidase genes has been described. Four genes (Aox1, Aox3, Aox4 and Aox3l1), coding for an equivalent number of catalytically active enzymes, are present in the mouse and rat genomes. Although human AOX1 and its homologous proteins are best known as drug metabolising enzymes, the physiological substrate(s) and function(s) are as yet unknown. The present paper provides an update of the available information on the evolutionary history, tissue- and cell-specific distribution and function of mammalian aldehyde oxidases.

2009-01-01

61

Gene encoding plant asparagine synthetase  

DOEpatents

The identification and cloning of the gene(s) for plant asparagine synthetase (AS), an important enzyme involved in the formation of asparagine, a major nitrogen transport compound of higher plants is described. Expression vectors constructed with the AS coding sequence may be utilized to produce plant AS; to engineer herbicide resistant plants, salt/drought tolerant plants or pathogen resistant plants; as a dominant selectable marker; or to select for novel herbicides or compounds useful as agents that synchronize plant cells in culture. The promoter for plant AS, which directs high levels of gene expression and is induced in an organ specific manner and by darkness, is also described. The AS promoter may be used to direct the expression of heterologous coding sequences in appropriate hosts.

Coruzzi, Gloria M. (New York, NY); Tsai, Fong-Ying (New York, NY)

1993-10-26

62

The ?-Tubulin Gene Family in Humans  

Microsoft Academic Search

Despite the central role of ?-tubulin in the organization of the microtubule cytoskeleton, the ?-tubulin gene family in humans has not been characterized. We now report the identification of a second expressed human ?-tubulin gene (TUBG2) and a ?-tubulin pseudogene (TUBG1P) in addition to the previously identified ?-tubulin gene (TUBG1). Evidence from Southern hybridizations suggests that there are probably no

Dawnne O'Neal Wise; Ralf Krahe; Berl R. Oakley

2000-01-01

63

Gene Family Evolution across 12 Drosophila Genomes  

Microsoft Academic Search

Comparison of whole genomes has revealed large and frequent changes in the size of gene families. These changes occur because of high rates of both gene gain (via duplication) and loss (via deletion or pseudogenization), as well as the evolution of entirely new genes. Here we use the genomes of 12 fully sequenced Drosophila species to study the gain and

Matthew W. Hahn; Mira V. Han; Sang-Gook Han

2007-01-01

64

Evolution of the mammalian lysozyme gene family  

PubMed Central

Background Lysozyme c (chicken-type lysozyme) has an important role in host defense, and has been extensively studied as a model in molecular biology, enzymology, protein chemistry, and crystallography. Traditionally, lysozyme c has been considered to be part of a small family that includes genes for two other proteins, lactalbumin, which is found only in mammals, and calcium-binding lysozyme, which is found in only a few species of birds and mammals. More recently, additional testes-expressed members of this family have been identified in human and mouse, suggesting that the mammalian lysozyme gene family is larger than previously known. Results Here we characterize the extent and diversity of the lysozyme gene family in the genomes of phylogenetically diverse mammals, and show that this family contains at least eight different genes that likely duplicated prior to the diversification of extant mammals. These duplicated genes have largely been maintained, both in intron-exon structure and in genomic context, throughout mammalian evolution. Conclusions The mammalian lysozyme gene family is much larger than previously appreciated and consists of at least eight distinct genes scattered around the genome. Since the lysozyme c and lactalbumin proteins have acquired very different functions during evolution, it is likely that many of the other members of the lysozyme-like family will also have diverse and unexpected biological properties.

2011-01-01

65

Gene family evolution across 12 Drosophila genomes.  

PubMed

Comparison of whole genomes has revealed large and frequent changes in the size of gene families. These changes occur because of high rates of both gene gain (via duplication) and loss (via deletion or pseudogenization), as well as the evolution of entirely new genes. Here we use the genomes of 12 fully sequenced Drosophila species to study the gain and loss of genes at unprecedented resolution. We find large numbers of both gains and losses, with over 40% of all gene families differing in size among the Drosophila. Approximately 17 genes are estimated to be duplicated and fixed in a genome every million years, a rate on par with that previously found in both yeast and mammals. We find many instances of extreme expansions or contractions in the size of gene families, including the expansion of several sex- and spermatogenesis-related families in D. melanogaster that also evolve under positive selection at the nucleotide level. Newly evolved gene families in our dataset are associated with a class of testes-expressed genes known to have evolved de novo in a number of cases. Gene family comparisons also allow us to identify a number of annotated D. melanogaster genes that are unlikely to encode functional proteins, as well as to identify dozens of previously unannotated D. melanogaster genes with conserved homologs in the other Drosophila. Taken together, our results demonstrate that the apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss. It is likely that this genomic revolving door has played a large role in shaping the morphological, physiological, and metabolic differences among species. PMID:17997610

Hahn, Matthew W; Han, Mira V; Han, Sang-Gook

2007-11-01

66

Gene Family Evolution across 12 Drosophila Genomes  

PubMed Central

Comparison of whole genomes has revealed large and frequent changes in the size of gene families. These changes occur because of high rates of both gene gain (via duplication) and loss (via deletion or pseudogenization), as well as the evolution of entirely new genes. Here we use the genomes of 12 fully sequenced Drosophila species to study the gain and loss of genes at unprecedented resolution. We find large numbers of both gains and losses, with over 40% of all gene families differing in size among the Drosophila. Approximately 17 genes are estimated to be duplicated and fixed in a genome every million years, a rate on par with that previously found in both yeast and mammals. We find many instances of extreme expansions or contractions in the size of gene families, including the expansion of several sex- and spermatogenesis-related families in D. melanogaster that also evolve under positive selection at the nucleotide level. Newly evolved gene families in our dataset are associated with a class of testes-expressed genes known to have evolved de novo in a number of cases. Gene family comparisons also allow us to identify a number of annotated D. melanogaster genes that are unlikely to encode functional proteins, as well as to identify dozens of previously unannotated D. melanogaster genes with conserved homologs in the other Drosophila. Taken together, our results demonstrate that the apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss. It is likely that this genomic revolving door has played a large role in shaping the morphological, physiological, and metabolic differences among species.

Hahn, Matthew W; Han, Mira V; Han, Sang-Gook

2007-01-01

67

Plant resistance gene  

US Patent & Trademark Office Database

Disclosed are isolated nucleic acid molecules from Solanum tuberosum which are capable of conferring resistance against plant pathogens including Phytophthora infestans. Transgenic plants and plant cells comprising the nucleic acid molecules are also disclosed.

2008-10-14

68

TCP genes: a family snapshot ten years later.  

PubMed

TCP genes encode plant-specific transcription factors with a bHLH motif that allows DNA binding and protein-protein interactions. The TCP gene family has five members in the lycophytes and >20 members in the eudicots. Gene duplication and diversification has generated two clades (class I and II) with slightly different TCP domains. Here, we summarize our current knowledge of the evolution of this family, their regulation, the biochemical activity of their proteins and the biological function of some members, in particular, in the control of cell proliferation in developing tissues. Increasing knowledge of the functions of TCP genes should enable their use as tools to modulate plant growth patterns and to generate novel morphologies in species of agronomical interest. PMID:19963426

Martín-Trillo, Mar; Cubas, Pilar

2009-12-04

69

Dynamic Actin Gene Family Evolution in Primates  

PubMed Central

Actin is one of the most highly conserved proteins and plays crucial roles in many vital cellular functions. In most eukaryotes, it is encoded by a multigene family. Although the actin gene family has been studied a lot, few investigators focus on the comparison of actin gene family in relative species. Here, the purpose of our study is to systematically investigate characteristics and evolutionary pattern of actin gene family in primates. We identified 233 actin genes in human, chimpanzee, gorilla, orangutan, gibbon, rhesus monkey, and marmoset genomes. Phylogenetic analysis showed that actin genes in the seven species could be divided into two major types of clades: orthologous group versus complex group. Codon usages and gene expression patterns of actin gene copies were highly consistent among the groups because of basic functions needed by the organisms, but much diverged within species due to functional diversification. Besides, many great potential pseudogenes were found with incomplete open reading frames due to frameshifts or early stop codons. These results implied that actin gene family in primates went through “birth and death” model of evolution process. Under this model, actin genes experienced strong negative selection and increased the functional complexity by reproducing themselves.

Zhu, Liucun; Zhang, Ying; Hu, Yijun; Wen, Tieqiao; Wang, Qiang

2013-01-01

70

PLANT SCIENCES: Plant Genes on Steroids  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. Plants, like animals, use steroid hormones to regulate their development. However, in plants, the steroid hormone is bound by a receptor at the cell surface instead of a nuclear receptor. In a Perspective, Sablowski and Harberd discuss studies published here (He et al.) and elsewhere that provide the missing link between binding of the steroid by its receptor and changes in the expression of target genes.

Robert Sablowski (John Innes Centre;Department of Cell and Developmental Biology); Nicholas P. Harberd (John Innes Centre;Department of Cell and Developmental Biology)

2005-03-11

71

7 CFR 201.56-12 - Miscellaneous plant families.  

Code of Federal Regulations, 2013 CFR

...Administration of the Act § 201.56-12 Miscellaneous plant families. Kinds of seed by family: Carrot family, Apiaceae (Umbelliferae)âcarrot, celery, celeriac, dill, parsley, parsnip; Hemp family, Cannabaceaeâhemp;...

2013-01-01

72

Genomic and expression analysis of glycosyl hydrolase family 35 genes from rice (Oryza sativa L.)  

Microsoft Academic Search

BACKGROUND: Many plant ?-galactosidases (Bgals) have been well characterized and their deduced biological functions mainly involve degradation of structural pectins, xyloglucans or arabinogalactoproteins in plant cell walls. However, gene multiplicity in glycosyl hydrolase family 35 (GH35), to which these proteins belong, implies diverse functions. In this study, the gene multiplicity, apparent evolutionary relationships and transcript expression of rice Bgal genes

Waraporn Tanthanuch; Mallika Chantarangsee; Janjira Maneesan; James Ketudat-Cairns

2008-01-01

73

Direct gene transfer to plants  

PubMed Central

Evidence for direct, gene-mediated stable genetic transformation of plant cells of Nicotiana tabacum is presented. A selectable hybrid gene comprising the protein coding region of the Tn5 aminoglycoside phosphotransferase type II gene under control of cauliflower mosaic virus gene VI expression signals was introduced into plant protoplasts as part of an Escherichia coli plasmid. The gene was stably integrated into plant genomic DNA and constitutively expressed in selected, drug resistant, protoplast-derived cell clones. The mode of integration of the foreign gene into the plant genome resembled that observed for DNA transfection of mammalian cells. Plants regenerated from transformed cell lines were phenotypically normal and fertile, and they maintained and expressed the foreign gene throughout the development of vegetative and generative organs. Microspores, grown in anther culture, developed into resistant and sensitive haploid plantlets. Genetic crossing analysis of one of the transformed plants revealed the presence of one dominant trait for kanamycin resistance segregating in a Mendelian fashion in the F1 generation. ImagesFig. 2.Fig. 3.Fig. 4.Fig. 5.Fig. 6.

Paszkowski, Jerzy; Shillito, Raymond D.; Saul, Michael; Mandak, Vaclav; Hohn, Thomas; Hohn, Barbara; Potrykus, Ingo

1984-01-01

74

Direct gene transfer to plants.  

PubMed

Evidence for direct, gene-mediated stable genetic transformation of plant cells of Nicotiana tabacum is presented. A selectable hybrid gene comprising the protein coding region of the Tn5 aminoglycoside phosphotransferase type II gene under control of cauliflower mosaic virus gene VI expression signals was introduced into plant protoplasts as part of an Escherichia coli plasmid. The gene was stably integrated into plant genomic DNA and constitutively expressed in selected, drug resistant, protoplast-derived cell clones. The mode of integration of the foreign gene into the plant genome resembled that observed for DNA transfection of mammalian cells. Plants regenerated from transformed cell lines were phenotypically normal and fertile, and they maintained and expressed the foreign gene throughout the development of vegetative and generative organs. Microspores, grown in anther culture, developed into resistant and sensitive haploid plantlets. Genetic crossing analysis of one of the transformed plants revealed the presence of one dominant trait for kanamycin resistance segregating in a Mendelian fashion in the F(1) generation. PMID:16453573

Paszkowski, J; Shillito, R D; Saul, M; Mandák, V; Hohn, T; Hohn, B; Potrykus, I

1984-12-01

75

Structure of homeobox-leucine zipper genes suggests a model for the evolution of gene families.  

PubMed Central

Homeobox genes are present in both plants and animals. Homeobox-leucine zipper genes, however, have been identified thus far only in the small mustard plant Arabidopsis thaliana. This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events. To better understand this gene family, we isolated several sequences containing the homeobox-leucine zipper motif and carried out a comparative analysis of nine homeobox-leucine zipper genes (HAT1, HAT2, HAT3, HAT4, HAT5, HAT7, HAT9, HAT14, and HAT22). Gene structures, sequence comparisons, and chromosomal locations suggest a simple model for the evolution of these genes. The model postulates that a primordial homeobox gene acquired a leucine zipper by exon capture. The nascent homeobox-leucine zipper gene then appears to have undergone a series of gene duplication and chromosomal translocation events, leading to the formation of the HAT gene family. This work has general implications for the evolution of regulatory genes. Images

Schena, M; Davis, R W

1994-01-01

76

Evaluation of candidate genes for familial brachydactyly  

Microsoft Academic Search

Type A1 brachydactyly in humans is a recognisable syndrome characterised by shortening of the middle phalanx of all digits with occasional fusion of the middle and terminal phalanges. The purpose of this study was to evaluate candidate genes for type A1 brachydactyly in two families with multiple affected members. Several classes of genes have been implicated in the control of

J M Mastrobattista; P Dollé; S H Blanton; H Northrup

1995-01-01

77

Chromosomal evolution in the plant family Solanaceae  

Microsoft Academic Search

BACKGROUND: Over the past decades, extensive comparative mapping research has been performed in the plant family Solanaceae. The recent identification of a large set of single-copy conserved orthologous (COSII) markers has greatly accelerated comparative mapping studies among major solanaceous species including tomato, potato, eggplant, pepper and diploid Nicotiana species (as well as tetraploid tobacco). The large amount of comparative data

Feinan Wu; Steven D Tanksley

2010-01-01

78

The shape of human gene family phylogenies  

PubMed Central

Background The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies. Results We find that gene duplication has produced gene family trees significantly less balanced than expected from a simple model of the process, and less balanced than species phylogenies: the opposite to what might be expected under the 2R hypothesis. Conclusion While other explanations are plausible, we suggest that the greater imbalance of gene family trees than species trees is due to the prevalence of tandem duplications over regional duplications during the evolution of the human genome.

Cotton, James A; Page, Roderic DM

2006-01-01

79

Sorghum phosphoenolpyruvate carboxylase gene family: structure, function and molecular evolution.  

PubMed

Although housekeeping functions have been shown for the phosphoenolpyruvate carboxylase (EC 4.1.1.31, PEPC) in plants and in prokaryotes, PEPC is mainly known for its specific role in the primary photosynthetic CO2 fixation in C4 and CAM plants. We have shown that in Sorghum, a monocotyledonous C4 plant, the enzyme is encoded in the nucleus by a small multigene family. Here we report the entire nucleotide sequence (7.5 kb) of the third member (CP21) that completes the structure of the Sorghum PEPC gene family. Nucleotide composition, CpG islands and GC content of the three Sorghum PEPC genes are analysed with respect to their possible implications in the regulation of expression. A study of structure/function and phylogenetic relationships based on the compilation of all PEPC sequences known so far is presented. Data demonstrated that: (1) the different forms of plant PEPC have very similar primary structures, functional and regulatory properties, (2) neither apparent amino acid sequences nor phylogenetic relationships are specific for the C4 and CAM PEPCs and (3) expression of the different genes coding for the Sorghum PEPC isoenzymes is differently regulated (i.e. by light, nitrogen source) in a spatial and temporal manner. These results suggest that the main distinguishing feature between plant PEPCs is to be found at the level of genes expression rather than in their primary structure. PMID:8443342

Lepiniec, L; Keryer, E; Philippe, H; Gadal, P; Crétin, C

1993-02-01

80

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa  

Microsoft Academic Search

BACKGROUND: NAC (NAM, ATAF1\\/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no

Ruibo Hu; Guang Qi; Yingzhen Kong; Dejing Kong; Qian Gao; Gongke Zhou

2010-01-01

81

Heterochronic genes in plant evolution and development.  

PubMed

Evolution of morphology includes evolutionary shifts of developmental processes in space or in time. Heterochronic evolution is defined as a temporal shift. The concept of heterochrony has been very rewarding to investigators of both animal and plant developmental evolution, because it has strong explanatory power when trying to understand morphological diversity. While for animals, extensive literature on heterochrony developed along with the field of evolution of development, in plants the concept has been applied less often and is less elaborately developed. Yet novel genetic findings highlight heterochrony as a developmental and evolutionary process in plants. Similar to what has been found for the worm Caenorhabditis, a heterochronic gene pathway controlling developmental timing has been elucidated in flowering plants. Two antagonistic microRNA's miR156 and miR172 target two gene families of transcription factors, SQUAMOSA PROMOTOR BINDING PROTEIN-LIKE and APETALA2-like, respectively. Here, we propose that this finding now allows the molecular investigation of cases of heterochronic evolution in plants. We illustrate this point by examining microRNA expression patterns in the Antirrhinum majus incomposita and choripetala heterochronic mutants. Some of the more beautiful putative cases of heterochronic evolution can be found outside flowering plants, but little is known about the extent of conservation of this flowering plant pathway in other land plants. We show that the expression of an APETALA2-like gene decreases with age in a fern species. This contributes to the idea that ferns share some heterochronic gene functions with flowering plants. PMID:24093023

Geuten, Koen; Coenen, Heleen

2013-09-25

82

Transcriptional gene silencing in plants  

Microsoft Academic Search

The review presents current data on molecular genetic mechanisms of suppression of the gene (transgene) expression in plants\\u000a at the transcriptional level. The stages of RNA-directed DNA methylation are discussed in detail. Mutations affecting transcriptional\\u000a gene inactivation without altering nucleotide sequence methylation are described.

T. V. Marenkova; E. V. Deineko

2010-01-01

83

The aspartate-family pathway of plants  

PubMed Central

The Asp family pathway of plants is highly important from a nutritional standpoint because it leads to the synthesis of the four essential amino acids Lys, Thr, Met and Ile. These amino acids are not synthesized by human and its monogastric livestock and should be supplemented in their diets. Among the Asp-family amino acids, Lys is considered as the nutritionally most important essential amino acid because its level is most limiting in cereal grains, representing the largest source of plant foods and feeds worldwide. Metabolic engineering approaches led to significant increase in Lys level in seeds by enhancing its synthesis and reducing its catabolism. However, results from the model plant Arabidopsis showed that this approach may retard seed germination due to a major negative effect on the levels of a number of TCA cycle metabolites that associate with cellular energy. In the present review, we discuss the regulatory metabolic link of the Asp-family pathway with the TCA cycle and its biological significance upon exposure to stress conditions that cause energy deprivation. In addition, we also discuss how deep understanding of the regulatory metabolic link of the Asp-family pathway with energy and stress regulation can be used to improve Lys level in seeds of important crop species, minimizing the interference with the cellular energy status and plant-stress interaction. This review thus provides an example showing how deep understanding the inter-regulation of metabolism with plant stress physiology can lead to successful nutritional improvements with minimal negative effect on plant growth and response to stressful environments.

2011-01-01

84

Familial Hypercholesterolemia: The Lipids or the Genes?  

Microsoft Academic Search

Familial Hypercholesterolemia (FH) is a common cause of premature cardiovascular disease and is often undiagnosed in young\\u000a people. Although the disease is diagnosed clinically by high LDL cholesterol levels and family history, to date there are\\u000a no single internationally accepted criteria for the diagnosis of FH. Several genes have been shown to be involved in FH; yet\\u000a determining the implications

Akl C Fahed; Georges M Nemer

2011-01-01

85

Analysis of Brassica rapa ESTs: gene discovery and expression patterns of AP2/ERF family genes.  

PubMed

Chinese cabbage (Brassica rapa subsp. pekinensis) is among the most important vegetables and is widely cultivated in world. Genes in the AP2/ERF family encode transcriptional regulators that serve a variety of functions in the plants. Expressed sequence tags (ESTs) are created by partially sequencing randomly isolated gene transcripts and have proved valuable in molecular biology. Starting from the database with 142 947 ESTs of B. rapa, 62 putative AP2/ERF family genes were identified by in silico cloning using the conserved AP2/ERF domain amino acid sequence of Arabidopsis thaliana as a probe. Based on the number of AP2/ERF domains and functions of the genes, the AP2/ERF transcription factors from B. rapa were classified into four subfamilies (DREB, ERF, AP2 and RAV). Using large-scale available EST information as a source of expression data for digital expression profiling, differentially detected genes were identified among diverse plant tissues. Roots contained the largest number of transcripts of the AP2/ERF family genes, followed by leaves and seeds. Only a few of the 62 AP2/ERF family genes were detected in all tissues: most were detected only in some tissues but not in others. The maximum detected was that of BraERF-B2-5, and it was recorded from seed tissue. PMID:19701799

Zhuang, Jing; Xiong, Ai-Sheng; Peng, Ri-He; Gao, Feng; Zhu, Bo; Zhang, Jian; Fu, Xiao-Yan; Jin, Xiao-Feng; Chen, Jian-Min; Zhang, Zhen; Qiao, Yu-Shan; Yao, Quan-Hong

2009-08-23

86

A novel family of small proteins that affect plant development  

SciTech Connect

The DVL genes represent a new group of plant proteins that influence plant growth and development. Overexpression of DVL1, and other members of the DVL family, causes striking phenotypic changes. The DVL proteins share sequence homology in their C-terminal half. Point mutations in the C-terminal domain show it is necessary and deletion studies demonstrate the C-terminal domain is sufficient to confer the overexpression phenotypes. The phenotypes observed, and the conservation of the protein sequence in the plant kingdom, does suggest the DVL proteins have a role in modulating plant growth and development. Our working hypothesis is the DVL proteins function as regulators of cellular signaling pathways that control growth and development.

John Charles Walker

2011-04-29

87

RTM3, which controls long-distance movement of potyviruses, is a member of a new plant gene family encoding a meprin and TRAF homology domain-containing protein.  

PubMed

Restriction of long-distance movement of several potyviruses in Arabidopsis (Arabidopsis thaliana) is controlled by at least three dominant restricted TEV movement (RTM) genes, named RTM1, RTM2, and RTM3. RTM1 encodes a protein belonging to the jacalin family, and RTM2 encodes a protein that has similarities to small heat shock proteins. In this article, we describe the positional cloning of RTM3, which encodes a protein belonging to an undescribed protein family of 29 members that has a meprin and TRAF homology (MATH) domain in its amino-terminal region and a coiled-coil domain at its carboxy-terminal end. Involvement in the RTM resistance system is the first biological function experimentally identified for a member of this new gene family in plants. Our analyses showed that the coiled-coil domain is not only highly conserved between RTM3-homologous MATH-containing proteins but also in proteins lacking a MATH domain. The cluster organization of the RTM3 homologs in the Arabidopsis genome suggests the role of duplication events in shaping the evolutionary history of this gene family, including the possibility of deletion or duplication of one or the other domain. Protein-protein interaction experiments revealed RTM3 self-interaction as well as an RTM1-RTM3 interaction. However, no interaction has been detected involving RTM2 or the potyviral coat protein previously shown to be the determinant necessary to overcome the RTM resistance. Taken together, these observations strongly suggest the RTM proteins might form a multiprotein complex in the resistance mechanism to block the long-distance movement of potyviruses. PMID:20584941

Cosson, Patrick; Sofer, Luc; Le, Quang Hien; Léger, Valérie; Schurdi-Levraud, Valérie; Whitham, Steven A; Yamamoto, Miki L; Gopalan, Suresh; Le Gall, Olivier; Candresse, Thierry; Carrington, James C; Revers, Frédéric

2010-06-28

88

Analysis of Brassica rapa ESTs: gene discovery and expression patterns of AP2\\/ERF family genes  

Microsoft Academic Search

Chinese cabbage (Brassica rapa subsp. pekinensis) is among the most important vegetables and is widely cultivated in world. Genes in the AP2\\/ERF family encode transcriptional\\u000a regulators that serve a variety of functions in the plants. Expressed sequence tags (ESTs) are created by partially sequencing\\u000a randomly isolated gene transcripts and have proved valuable in molecular biology. Starting from the database with

Jing Zhuang; Ai-Sheng Xiong; Ri-He Peng; Feng Gao; Bo Zhu; Jian Zhang; Xiao-Yan Fu; Xiao-Feng Jin; Jian-Min Chen; Zhen Zhang; Yu-Shan Qiao; Quan-Hong Yao

2010-01-01

89

Evolutionary History of the Cancer Immunity Antigen MAGE Gene Family  

Microsoft Academic Search

The evolutionary mode of a multi-gene family can change over time, depending on the functional differentiation and local genomic environment of family members. In this study, we demonstrate such a change in the melanoma antigen (MAGE) gene family on the mammalian X chromosome. The MAGE gene family is composed of ten subfamilies that can be categorized into two types. Type

Yukako Katsura; Yoko Satta

2011-01-01

90

CLONING, CHARACTERIZATION, AND EVOLUTION OF THE NBS-LRR-ENCODING RESISTANCE GENE ANALOGUE FAMILY IN POLYPLOID COTTON (GOSSYPIUM HIRSUTUM L.)  

Technology Transfer Automated Retrieval System (TEKTRAN)

The NBS-LRR-encoding gene family has attracted research interests of many scientists because approximately 3/4 of the plant disease resistance (R) genes cloned to date are from this gene family. We cloned the NBS-LRR-encoding genes from polyploid cotton by a PCR-based approach using degenerate prim...

91

PIECE: a database for plant gene structure comparison and evolution.  

PubMed

Gene families often show degrees of differences in terms of exon-intron structures depending on their distinct evolutionary histories. Comparative analysis of gene structures is important for understanding their evolutionary and functional relationships within plant species. Here, we present a comparative genomics database named PIECE (http://wheat.pw.usda.gov/piece) for Plant Intron and Exon Comparison and Evolution studies. The database contains all the annotated genes extracted from 25 sequenced plant genomes. These genes were classified based on Pfam motifs. Phylogenetic trees were pre-constructed for each gene category. PIECE provides a user-friendly interface for different types of searches and a graphical viewer for displaying a gene structure pattern diagram linked to the resulting bootstrapped dendrogram for each gene family. The gene structure evolution of orthologous gene groups was determined using the GLOOME, Exalign and GECA software programs that can be accessed within the database. PIECE also provides a web server version of the software, GSDraw, for drawing schematic diagrams of gene structures. PIECE is a powerful tool for comparing gene sequences and provides valuable insights into the evolution of gene structure in plant genomes. PMID:23180792

Wang, Yi; You, Frank M; Lazo, Gerard R; Luo, Ming-Cheng; Thilmony, Roger; Gordon, Sean; Kianian, Shahryar F; Gu, Yong Q

2012-11-24

92

Structure and Evolution of the Actin Gene Family in Arabidopsis Thaliana  

PubMed Central

Higher plants contain families of actin-encoding genes that are divergent and differentially expressed. Progress in understanding the functions and evolution of plant actins has been hindered by the large size of the actin gene families. In this study, we characterized the structure and evolution of the actin gene family in Arabidopsis thaliana. DNA blot analyses with gene-specific probes suggested that all 10 of the Arabidopsis actin gene family members have been isolated and established that Arabidopsis has a much simpler actin gene family than other plants that have been examined. Phylogenetic analyses suggested that the Arabidopsis gene family contains at least two ancient classes of genes that diverged early in land plant evolution and may have separated vegetative from reproductive actins. Subsequent divergence produced a total of six distinct subclasses of actin, and five showed a distinct pattern of tissue specific expression. The concordance of expression patterns with the phylogenetic structure is discussed. These subclasses appear to be evolving independently, as no evidence of gene conversion was found. The Arabidopsis actin proteins have an unusually large number of nonconservative amino acid substitutions, which mapped to the surface of the actin molecule, and should effect protein-protein interactions.

McDowell, J. M.; Huang, S.; McKinney, E. C.; An, Y. Q.; Meagher, R. B.

1996-01-01

93

Codon usage in plant genes.  

PubMed Central

We have examined codon bias in 207 plant gene sequences collected from Genbank and the literature. When this sample was further divided into 53 monocot and 154 dicot genes, the pattern of relative use of synonymous codons was shown to differ between these taxonomic groups, primarily in the use of G + C in the degenerate third base. Maize and soybean codon bias were examined separately and followed the monocot and dicot codon usage patterns respectively. Codon preference in ribulose 1,5 bisphosphate and chlorophyll a/b binding protein, two of the most abundant proteins in leaves was investigated. These highly expressed are more restricted in their codon usage than plant genes in general.

Murray, E E; Lotzer, J; Eberle, M

1989-01-01

94

Functions of rol genes in plant secondary metabolism  

Microsoft Academic Search

For a long time, the Agrobacterium rhizogenes rolA, rolB and rolC oncogenes have been considered to be modulators of plant growth and cell differentiation. A new function of the rol genes in plant–Agrobacterium interaction became apparent with the discovery that these genes are potential activators of secondary metabolism in transformed cells from the Solanaceae, Araliaceae, Rubiaceae, Vitaceae and Rosaceae families.

Victor P. Bulgakov

2008-01-01

95

Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family.  

PubMed

The wall-associated kinase (WAK) gene family, one of the receptor-like kinase (RLK) gene families in plants, plays important roles in cell expansion, pathogen resistance, and heavy-metal stress tolerance in Arabidopsis (Arabidopsis thaliana). Through a reiterative database search and manual reannotation, we identified 125 OsWAK gene family members from rice (Oryza sativa) japonica cv Nipponbare; 37 (approximately 30%) OsWAKs were corrected/reannotated from earlier automated annotations. Of the 125 OsWAKs, 67 are receptor-like kinases, 28 receptor-like cytoplasmic kinases, 13 receptor-like proteins, 12 short genes, and five pseudogenes. The two-intron gene structure of the Arabidopsis WAK/WAK-Likes is generally conserved in OsWAKs; however, extra/missed introns were observed in some OsWAKs either in extracellular regions or in protein kinase domains. In addition to the 38 OsWAKs with full-length cDNA sequences and the 11 with rice expressed sequence tag sequences, gene expression analyses, using tiling-microarray analysis of the 20 OsWAKs on chromosome 10 and reverse transcription-PCR analysis for five OsWAKs, indicate that the majority of identified OsWAKs are likely expressed in rice. Phylogenetic analyses of OsWAKs, Arabidopsis WAK/WAK-Likes, and barley (Hordeum vulgare) HvWAKs show that the OsWAK gene family expanded in the rice genome due to lineage-specific expansion of the family in monocots. Localized gene duplications appear to be the primary genetic event in OsWAK gene family expansion and the 125 OsWAKs, present on all 12 chromosomes, are mostly clustered. PMID:16286450

Zhang, Shibo; Chen, Calvin; Li, Lei; Meng, Ling; Singh, Jaswinder; Jiang, Ning; Deng, Xing-Wang; He, Zheng-Hui; Lemaux, Peggy G

2005-11-01

96

Protease gene families in Populus and Arabidopsis  

Microsoft Academic Search

BACKGROUND: Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution. RESULTS: We have performed a comparative analysis of protease genes in the two sequenced

Maribel García-Lorenzo; Andreas Sjödin; Stefan Jansson; Christiane Funk

2006-01-01

97

The Maize PIN Gene Family of Auxin Transporters  

PubMed Central

Auxin is a key regulator of plant development and its differential distribution in plant tissues, established by a polar cell to cell transport, can trigger a wide range of developmental processes. A few members of the two families of auxin efflux transport proteins, PIN-formed (PIN) and P-glycoprotein (ABCB/PGP), have so far been characterized in maize. Nine new Zea mays auxin efflux carriers PIN family members and two maize PIN-like genes have now been identified. Four members of PIN1 (named ZmPIN1a–d) cluster, one gene homologous to AtPIN2 (ZmPIN2), three orthologs of PIN5 (ZmPIN5a–c), one gene paired with AtPIN8 (ZmPIN8), and three monocot-specific PINs (ZmPIN9, ZmPIN10a, and ZmPIN10b) were cloned and the phylogenetic relationships between early-land plants, monocots, and eudicots PIN proteins investigated, including the new maize PIN proteins. Tissue-specific expression patterns of the 12 maize PIN genes, 2 PIN-like genes and ZmABCB1, an ABCB auxin efflux carrier, were analyzed together with protein localization and auxin accumulation patterns in normal conditions and in response to drug applications. ZmPIN gene transcripts have overlapping expression domains in the root apex, during male and female inflorescence differentiation and kernel development. However, some PIN family members have specific tissue localization: ZmPIN1d transcript marks the L1 layer of the shoot apical meristem and inflorescence meristem during the flowering transition and the monocot-specific ZmPIN9 is expressed in the root endodermis and pericycle. The phylogenetic and gene structure analyses together with the expression pattern of the ZmPIN gene family indicate that subfunctionalization of some maize PINs can be associated to the differentiation and development of monocot-specific organs and tissues and might have occurred after the divergence between dicots and monocots.

Forestan, Cristian; Farinati, Silvia; Varotto, Serena

2012-01-01

98

Massive expansion of the calpain gene family in unicellular eukaryotes  

PubMed Central

Background Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex determination in nematodes and embryo lethality in plants. Although the calpain family is well characterized in animal and plant model organisms, there is a great lack of knowledge about these genes in unicellular eukaryote species (i.e. protists). Here, we study the distribution and evolution of calpain genes in a wide range of eukaryote genomes from major branches in the tree of life. Results Our investigations reveal 24 types of protein domains that are combined with the calpain-specific catalytic domain CysPc. In total we identify 41 different calpain domain architectures, 28 of these domain combinations have not been previously described. Based on our phylogenetic inferences, we propose that at least four calpain variants were established in the early evolution of eukaryotes, most likely before the radiation of all the major supergroups of eukaryotes. Many domains associated with eukaryotic calpain genes can be found among eubacteria or archaebacteria but never in combination with the CysPc domain. Conclusions The analyses presented here show that ancient modules present in prokaryotes, and a few de novo eukaryote domains, have been assembled into many novel domain combinations along the evolutionary history of eukaryotes. Some of the new calpain genes show a narrow distribution in a few branches in the tree of life, likely representing lineage-specific innovations. Hence, the functionally important classical calpain genes found among humans and vertebrates make up only a tiny fraction of the calpain family. In fact, a massive expansion of the calpain family occurred by domain shuffling among unicellular eukaryotes and contributed to a wealth of functionally different genes.

2012-01-01

99

Molecular biology and application of plant peroxidase genes.  

PubMed

Peroxidases are a family of isozymes found in all plants; they are heme-containing monomeric glycoproteins that utilize either H(2)O(2) or O(2) to oxidize a wide variety of molecules. These important enzymes are used in enzyme immunoassays, diagnostic assays and industrial enzymatic reactions. Peroxidase genes and their promoters can be used for molecular breeding of useful plants. Transgenic techniques have also been used to investigate the physiological and molecular functions of peroxidase genes in plants. Here, we review transgenic studies of peroxidase genes, including the functional analyses of the enzymes and their promoters. Regarding application of peroxidase genes, it has been reported that overexpression of the tomato TPX2 gene or the sweet potato swpa1 gene conferred increased salt-tolerance or oxidative-stress tolerance, respectively. The growth stimulation effect in transgenic tobacco and hybrid aspen upon overexpression of horseradish peroxidase gene is also discussed. PMID:12664144

Yoshida, K; Kaothien, P; Matsui, T; Kawaoka, A; Shinmyo, A

2002-12-18

100

Expression and genome-wide analysis of the xylogen-type gene family.  

PubMed

In higher plants, many extracellular proteins are involved in developmental processes, including cell-cell signaling and cell wall construction. Xylogen is an extracellular arabinogalactan protein (AGP) isolated from Zinnia elegans xylogenic culture medium, which promotes xylem cell differentiation. Xylogen has a unique structure, containing a non-specific lipid transfer protein (nsLTP) domain and AGP domains. We searched for xylogen-type genes in the genomes of land plants, including Arabidopsis thaliana, to further our knowledge of xylogen-type genes as functional extracellular proteins in plants. We found that many xylogen-type genes, including 13 Arabidopsis genes, comprise a gene family in land plants, including Populus trichocarpa, Vitis vinifera, Lotus japonicus, Oryza sativa, Selaginella moellendorffii and Physcomitrella patens. The genes shared an N-terminal signal peptide sequence, a distinct nsLTP domain, one or more AGP domains and a glycosylphosphatidylinositol (GPI)-anchored sequence. We analyzed transgenic plants harboring promoter::GUS (?-glucuronidase) constructs to test expression of the 13 Arabidopsis xylogen-type genes, and detected a diversity of gene family members with related expression patterns. AtXYP2 was the best candidate as the Arabidopsis counterpart of the Zinnia xylogen gene. We observed two distinct expression patterns for several genes, with some anther specific and others preferentially expressed in the endodermis/pericycle. We conclude that xylogen-type genes, which may have diverse functions, form a novel chimeric AGP gene family with a distinct nsLTP domain. PMID:21558309

Kobayashi, Yuuki; Motose, Hiroyasu; Iwamoto, Kuninori; Fukuda, Hiroo

2011-05-10

101

The Olfactory Receptor Gene Family of Marsupials  

Microsoft Academic Search

\\u000a Olfaction in vertebrates is mediated mainly by a large family of olfactory receptors in the olfactory epithelium that belong\\u000a to the superfamily of G protein-coupled receptors. Olfactory systems are well conserved among vertebrates, including marsupials,\\u000a but there is a large variation in the numbers of olfactory genes in different animals. Most marsupials are nocturnal so depend\\u000a on their sense of

Margaret L. Delbridge; Amir Mohammadi; Jennifer A. Marshall Graves

102

MICA gene polymorphism in HBDI multiplex families.  

PubMed

T1DM is a disease that affects pancreatic beta cells and results in severe insulin depletion. T1DM is a multigenic disease, and the strongest genetic association with this disease is shown by the genes in MHC class II, namely, DQA1 and DQB1. The other gene that has been implicated in susceptibility to T1DM is the MICA gene that lies within the MHC class I region. This gene has been investigated in many autoimmune diseases, including T1DM, in case-control as well as in family studies. The aim of our study was to test the transmission of MICA microsatellite alleles from unaffected parents to T1DM- affected offspring in HBDI multiplex nuclear families. We also looked at the transmission of MICA alleles together with high-risk DQA1-DQB1 haplotypes to determine the independent transmission of MICA alleles. We observed that MICA6 and MICA9 are transmitted to affected offspring less frequently than expected, and MICA5.1 was more frequently transmitted. DQA1 and DQB1 high-risk haplotypes were transmitted more frequently than expected and DQ6, which is a protective haplotype, was less frequently transmitted to affected offspring. Analysis of MICA-DQA1-DQB1 transmission showed that certain MICA alleles are preferably transmitted as a part of high-risk haplotypes, which might indicate that MICA together with high-risk HLA is associated with T1DM in this family material. However, this latter analysis should be repeated on a larger family sample. PMID:15699510

Nikitina-Zake, Liene; Ghaderi, Mehran; Park, Yongsoo; Babu, Sunanda; Eisenbarth, George; Sanjeevi, Carani B

2004-12-01

103

Transgenic plants with cyanobacterial genes  

Microsoft Academic Search

Over the years, cyanobacteria have been regarded as ideal model systems for studying fundamental biochemical processes like\\u000a oxygenic photosynthesis and carbon and nitrogen assimilation. Additionally, they have been used as human foods, sources for\\u000a vitamins, proteins, fine chemicals, and bioactive compounds. Aiming to increase plant productivity as well as nutritional\\u000a values, cyanobacterial genes involved in carbon metabolism, fatty acid biosynthesis,

Youn-Il Park; Sang-Bong Choi; Jang R. Liu

2009-01-01

104

The DMRT gene family in amphioxus.  

PubMed

Doublesex and Mab-3-related transcription factor (DMRT) gene family is widely known for its involvement in sex determination and/or differentiation among different phyla. In this study, we identify eight DMRT genes in the cephalochordate amphioxus, a protochordate holding a key phylogenetic position. The eight DMRTs can be divided into two groups based on the conserved domain: BfDM044, BfDM045, BfDM55.1, BfDM115.1, and BfDM17.1 belong to the first group which have both DM and DMA domains, while BfDM246.1, BfDM084, and BfDM175 belong to the second group which have only DM domain. Most of the first group members have same genomic structure except BfDM17.1, while no regular pattern exists in the second group. Phylogenetic analysis of the DM domain sequences shows that DMRT genes in vertebrates form seven different independent clusters, and some even contain genes from invertebrates with high bootstrap. Notably, the first group members of amphioxus cluster with vertebrate DMRTs; while the second group members cluster into a single branch, which diverge from the vertebrate classes. The results suggest that several DMRT genes in vertebrates may evolve from homologous genes in invertebrates. As in nematode, drosophila, fish, and vertebrates, DMRT genes cluster is also found in amphioxus, which may be the result of gene duplication. Interspecific differences in the amphioxus DMRTs and sea squirt DMRTs may suggest post-speciation duplication of some DMRT genes. PMID:22702730

Wang, Fei; Yu, Yang; Ji, Dongrui; Li, Hongyan

2012-01-01

105

Plant DNA viruses and gene silencing  

Microsoft Academic Search

Gene silencing is a multifaceted phenomenon leading to propagative down-regulation of gene expression. Gene silencing, first observed in plants containing transgenes, can operate both at the transcriptional and post-transcriptional levels. Silencing effects can be triggered by nuclear transgenes and by cytoplasmic RNA viruses, and it can be propagated between these elements and endogenous plant genes that share sequence homology. Although

Simon N. Covey; Nadia S. Al-Kaff

2000-01-01

106

The Tomato Terpene Synthase Gene Family1[W][OA  

PubMed Central

Compounds of the terpenoid class play numerous roles in the interactions of plants with their environment, such as attracting pollinators and defending the plant against pests. We show here that the genome of cultivated tomato (Solanum lycopersicum) contains 44 terpene synthase (TPS) genes, including 29 that are functional or potentially functional. Of these 29 TPS genes, 26 were expressed in at least some organs or tissues of the plant. The enzymatic functions of eight of the TPS proteins were previously reported, and here we report the specific in vitro catalytic activity of 10 additional tomato terpene synthases. Many of the tomato TPS genes are found in clusters, notably on chromosomes 1, 2, 6, 8, and 10. All TPS family clades previously identified in angiosperms are also present in tomato. The largest clade of functional TPS genes found in tomato, with 12 members, is the TPS-a clade, and it appears to encode only sesquiterpene synthases, one of which is localized to the mitochondria, while the rest are likely cytosolic. A few additional sesquiterpene synthases are encoded by TPS-b clade genes. Some of the tomato sesquiterpene synthases use z,z-farnesyl diphosphate in vitro as well, or more efficiently than, the e,e-farnesyl diphosphate substrate. Genes encoding monoterpene synthases are also prevalent, and they fall into three clades: TPS-b, TPS-g, and TPS-e/f. With the exception of two enzymes involved in the synthesis of ent-kaurene, the precursor of gibberellins, no other tomato TPS genes could be demonstrated to encode diterpene synthases so far.

Falara, Vasiliki; Akhtar, Tariq A.; Nguyen, Thuong T.H.; Spyropoulou, Eleni A.; Bleeker, Petra M.; Schauvinhold, Ines; Matsuba, Yuki; Bonini, Megan E.; Schilmiller, Anthony L.; Last, Robert L.; Schuurink, Robert C.; Pichersky, Eran

2011-01-01

107

Evolution of the glycophorin gene family in the hominoid primates  

Microsoft Academic Search

Analysis of nucleotide sequences of the human glycophorin A (GPA) and glycophorin B (GPB) genes has indicated that the GPA gene most closely resembles the ancestral gene, whereas the GPB gene likely arose from the GPA gene by homologous recombination. To study the evolution of the glycophorin gene family in the hominoid primates, restricted DNA on Southern blots from man,

Ann Rearden; Huan Phan; Shinichi Kudo; Minoru Fukuda

1990-01-01

108

Identification and characterization of the maize arogenate dehydrogenase gene family.  

PubMed

In plants, the amino acids tyrosine and phenylalanine are synthesized from arogenate by arogenate dehydrogenase and arogenate dehydratase, respectively, with the relative flux to each being tightly controlled. Here the characterization of a maize opaque endosperm mutant (mto140), which also shows retarded vegetative growth, is described The opaque phenotype co-segregates with a Mutator transposon insertion in an arogenate dehydrogenase gene (zmAroDH-1) and this led to the characterization of the four-member family of maize arogenate dehydrogenase genes (zmAroDH-1-zmAroDH-4) which share highly similar sequences. A Mutator insertion at an equivalent position in AroDH-3, the most closely related family member to AroDH-1, is also associated with opaque endosperm and stunted vegetative growth phenotypes. Overlapping but differential expression patterns as well as subtle mutant effects on the accumulation of tyrosine and phenylalanine in endosperm, embryo, and leaf tissues suggest that the functional redundancy of this gene family provides metabolic plasticity for the synthesis of these important amino acids. mto140/arodh-1 seeds shows a general reduction in zein storage protein accumulation and an elevated lysine phenotype typical of other opaque endosperm mutants, but it is distinct because it does not result from quantitative or qualitative defects in the accumulation of specific zeins but rather from a disruption in amino acid biosynthesis. PMID:20558569

Holding, David R; Meeley, Robert B; Hazebroek, Jan; Selinger, David; Gruis, Fred; Jung, Rudolf; Larkins, Brian A

2010-06-17

109

Estimating gene penetrance from family data.  

PubMed

Family data are useful for estimating disease risk in carriers of specific genotypes of a given gene (penetrance). Penetrance is frequently estimated assuming that relatives' phenotypes are independent, given their genotypes for the gene of interest. This assumption is unrealistic when multiple shared risk factors contribute to disease risk. In this setting, the phenotypes of relatives are correlated even after adjustment for the genotypes of any one gene (residual correlation). Many methods have been proposed to address this problem, but their performance has not been evaluated systematically. In simulations we generated genotypes for a rare (frequency 0.35%) allele of moderate penetrance, and a common (frequency 15%) allele of low penetrance, and then generated correlated disease survival times using the Clayton-Oakes copula model. We ascertained families using both population and clinic designs. We then compared the estimates of several methods to the optimal ones obtained from the model used to generate the data. We found that penetrance estimates for common low-risk genotypes were more robust to model misspecification than those for rare, moderate-risk genotypes. For the latter, penetrance estimates obtained ignoring residual disease correlation had large biases. Also biased were estimates based only on families that segregate the risk allele. In contrast, a method for accommodating phenotype correlation by assuming the presence of genetic heterogeneity performed nearly optimally, even when the survival data were coded as binary outcomes. We conclude that penetrance estimates that accommodate residual phenotype correlation (even only approximately) outperform those that ignore it, and that coding censored survival outcomes as binary does not substantially increase the mean-square error of the estimates, provided the censoring is not extensive. PMID:20397150

Gong, Gail; Hannon, Nathan; Whittemore, Alice S

2010-05-01

110

Orgenic plants: gene-manipulated plants compatible with organic farming.  

PubMed

Based on recent advances in plant gene technology, I propose to develop a new category of GM plants, orgenic plants, that are compatible with organic farming. These orgenic plants do not contain herbicide resistance genes to avoid herbicide application in agriculture. Furthermore, they either contain genes that are naturally exchanged between species, or are sterile to avoid outcrossing if they received a transgene from a different species. These GM plants are likely to be acceptable to most skeptics of GM plants and facilitate the use of innovative new crops. PMID:22893621

Ryffel, Gerhart U

2012-08-15

111

Genomic analysis of the terpenoid synthase ( AtTPS ) gene family of Arabidopsis thaliana  

Microsoft Academic Search

A family of 40 terpenoid synthase genes (AtTPS) was discovered by genome sequence analysis in Arabidopsis thaliana. This is the largest and most diverse group of TPS genes currently known for any species. AtTPS genes cluster into five phylogenetic subfamilies of the plant TPS superfamily. Surprisingly, thirty AtTPS closely resemble, in all aspects of gene architecture, sequence relatedness and phylogenetic

S. Aubourg; A. Lecharny; J. Bohlmann

2002-01-01

112

Widespread impact of horizontal gene transfer on plant colonization of land  

PubMed Central

In complex multicellular eukaryotes such as animals and plants, horizontal gene transfer is commonly considered rare with very limited evolutionary significance. Here we show that horizontal gene transfer is a dynamic process occurring frequently in the early evolution of land plants. Our genome analyses of the moss Physcomitrella patens identified 57 families of nuclear genes that were acquired from prokaryotes, fungi or viruses. Many of these gene families were transferred to the ancestors of green or land plants. Available experimental evidence shows that these anciently acquired genes are involved in some essential or plant-specific activities such as xylem formation, plant defence, nitrogen recycling as well as the biosynthesis of starch, polyamines, hormones and glutathione. These findings suggest that horizontal gene transfer had a critical role in the transition of plants from aquatic to terrestrial environments. On the basis of these findings, we propose a model of horizontal gene transfer mechanism in nonvascular and seedless vascular plants.

Yue, Jipei; Hu, Xiangyang; Sun, Hang; Yang, Yongping; Huang, Jinling

2012-01-01

113

Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.)  

PubMed Central

Members of the ERF transcription factor family play important roles in regulating gene expression in response to biotic and abiotic stresses. In soybean (Glycine max L.), however, only a few ERF genes have been studied so far. In this study, 98 unigenes that contained a complete AP2/ERF domain were identified from 63?676 unique sequences in the DFCI Soybean Gene Index database. The phylogeny, gene structures, and putative conserved motifs in soybean ERF proteins were analysed, and compared with those of Arabidopsis and rice. The members of the soybean ERF family were divided into 12 subgroups, similar to the case for Arabidopsis. AP2/ERF domains were conserved among soybean, Arabidopsis, and rice. Outside the AP2/ERF domain, many soybean-specific conserved motifs were detected. Expression analysis showed that nine unigenes belonging to six ERF family subgroups were induced by both biotic/abiotic stresses and hormone treatment, suggesting that they were involved in cross-talk between biotic and abiotic stress-responsive signalling pathways. Overexpression of two full-length genes from two different subgroups enhanced the tolerances to drought, salt stresses, and/or pathogen infection of the tobacco plants. These results will be useful for elucidating ERF gene-associated stress response signalling pathways in soybean.

Zhang, Gaiyun; Chen, Ming; Chen, Xueping; Xu, Zhaoshi; Guan, Shan; Li, Lian-Cheng; Li, Aili; Guo, Jiaming; Mao, Long; Ma, Youzhi

2008-01-01

114

Combining Expression and Comparative Evolutionary Analysis. The COBRA Gene Family[W][OA  

PubMed Central

Plant cell shape is achieved through a combination of oriented cell division and cell expansion and is defined by the cell wall. One of the genes identified to influence cell expansion in the Arabidopsis (Arabidopsis thaliana) root is the COBRA (COB) gene that belongs to a multigene family. Three members of the AtCOB gene family have been shown to play a role in specific types of cell expansion or cell wall biosynthesis. Functional orthologs of one of these genes have been identified in maize (Zea mays) and rice (Oryza sativa; Schindelman et al., 2001; Li et al., 2003; Brown et al., 2005; Persson et al., 2005; Ching et al., 2006; Jones et al., 2006). We present the maize counterpart of the COB gene family and the COB gene superfamily phylogeny. Most of the genes belong to a family with two main clades as previously identified by analysis of the Arabidopsis family alone. Within these clades, however, clear differences between monocot and eudicot family members exist, and these are analyzed in the context of Type I and Type II cell walls in eudicots and monocots. In addition to changes at the sequence level, gene regulation of this family in a eudicot, Arabidopsis, and a monocot, maize, is also characterized. Gene expression is analyzed in a multivariate approach, using data from a number of sources, including massively parallel signature sequencing libraries, transcriptional reporter fusions, and microarray data. This analysis has revealed that the expression of Arabidopsis and maize COB gene family members is highly developmentally and spatially regulated at the tissue and cell type-specific level, that gene superfamily members show overlapping and unique expression patterns, and that only a subset of gene superfamily members act in response to environmental stimuli. Regulation of expression of the Arabidopsis COB gene family members has highly diversified in comparison to that of the maize COB gene superfamily members. We also identify BRITTLE STALK 2-LIKE 3 as a putative ortholog of AtCOB.

Brady, Siobhan M.; Song, Shuang; Dhugga, Kanwarpal S.; Rafalski, J. Antoni; Benfey, Philip N.

2007-01-01

115

The SLEEPER genes: a transposase-derived angiosperm-specific gene family  

PubMed Central

Background DAYSLEEPER encodes a domesticated transposase from the hAT-superfamily, which is essential for development in Arabidopsis thaliana. Little is known about the presence of DAYSLEEPER orthologs in other species, or how and when it was domesticated. We studied the presence of DAYSLEEPER orthologs in plants and propose a model for the domestication of the ancestral DAYSLEEPER gene in angiosperms. Results Using specific BLAST searches in genomic and EST libraries, we found that DAYSLEEPER-like genes (hereafter called SLEEPER genes) are unique to angiosperms. Basal angiosperms as well as grasses (Poaceae) and dicotyledonous plants possess such putative orthologous genes, but SLEEPER-family genes were not found in gymnosperms, mosses and algae. Most species contain more than one SLEEPER gene. All SLEEPERs contain a C2H2 type BED-zinc finger domain and a hATC dimerization domain. We designated 3 motifs, partly overlapping the BED-zinc finger and dimerization domain, which are hallmark features in the SLEEPER family. Although SLEEPER genes are structurally conserved between species, constructs with SLEEPER genes from grapevine and rice did not complement the daysleeper phenotype in Arabidopsis, when expressed under control of the DAYSLEEPER promoter. However these constructs did cause a dominant phenotype when expressed in Arabidopsis. Rice plant lines with an insertion in the RICESLEEPER1 or 2 locus displayed phenotypic abnormalities, indicating that these genes are functional and important for normal development in rice. We suggest a model in which we hypothesize that an ancestral hAT transposase was retrocopied and stably integrated in the genome during early angiosperm evolution. Evidence is also presented for more recent retroposition events of SLEEPER genes, such as an event in the rice genome, which gave rise to the RICESLEEPER1 and 2 genes. Conclusions We propose the ancestral SLEEPER gene was formed after a process of retro-transposition during the evolution of the first angiosperms. It may have acquired an important function early on, as mutation of two SLEEPER genes in rice, like the daysleeper mutant in A. thaliana gave a developmental phenotype indicative of their importance for normal plant development.

2012-01-01

116

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

117

OrthoRBH: A streamlined pipeline for mining large gene family sequences in related species  

PubMed Central

Plant and animal genomes are replete with large gene families, making the task of ortholog identification difficult and labor intensive. OrthoRBH is an automated reciprocal blast pipeline tool enabling the rapid identification of specific gene families of interest in related species, streamlining the collection of homologs prior to downstream molecular evolutionary analysis. The efficacy of OrthoRBH is demonstrated with the identification of the 13-member PYR/PYL/RCAR gene family in Hordeum vulgare using Oryza sativa query sequences. OrthoRBH runs on the Linux command line and is freely available at SourceForge. Availability http://sourceforge.net/projects/ orthorbh/

Ziemann, Mark; Kamboj, Atul; Bhave, Mrinal

2013-01-01

118

The potential of the WRKY gene family for phylogenetic reconstruction: an example from the Malvaceae.  

Technology Transfer Automated Retrieval System (TEKTRAN)

The WRKY gene family of transcription factors is involved in several diverse pathways and includes components of plant-specific, ancient regulatory networks. WRKY genes contain one or two highly conserve DNA binding domains interrupted by an intron. We used partial sequences of five independent WRKY...

119

Molecular biology and application of plant peroxidase genes  

Microsoft Academic Search

Peroxidases are a family of isozymes found in all plants; they are heme-containing monomeric glycoproteins that utilize either H2O2 or O2 to oxidize a wide variety of molecules. These important enzymes are used in enzyme immunoassays, diagnostic assays and industrial enzymatic reactions. Peroxidase genes and their promoters can be used for molecular breeding of useful plants. Transgenic techniques have also

K. Yoshida; P. Kaothien; T. Matsui; A. Kawaoka; A. Shinmyo

2003-01-01

120

Silencing of the pollen-specific gene NTP303 and its family members in tobacco affects in vivo pollen tube growth and results in male sterile plants  

Microsoft Academic Search

In seed plants, successful fertilization requires correct regulation of pollen tube growth. At germination and during growth, the pollen tube interacts with tissues from the pistil while the pollen tube extends via tip growth. Despite the fact that much research has been devoted to the mechanisms regulating pollen tube growth, many aspects are currently unknown. Previously, we have isolated a

Peter de Groot; Koen Weterings; M. W. H. J. de Been; Floyd Wittink; Raymond Hulzink; J. B. M. Custers; Marinus van Herpen; George Wullems

2004-01-01

121

The tomato cis-prenyltransferase gene family.  

PubMed

cis-prenyltransferases (CPTs) are predicted to be involved in the synthesis of long-chain polyisoprenoids, all with five or more isoprene (C5) units. Recently, we identified a short-chain CPT, neryl diphosphate synthase (NDPS1), in tomato (Solanum lycopersicum). Here, we searched the tomato genome and identified and characterized its entire CPT gene family, which comprises seven members (SlCPT1-7, with NDPS1 designated as SlCPT1). Six of the SlCPT genes encode proteins with N-terminal targeting sequences, which, when fused to GFP, mediated GFP transport to the plastids of Arabidopsis protoplasts. The SlCPT3-GFP fusion protein was localized to the cytosol. Enzymatic characterization of recombinant SlCPT proteins demonstrated that SlCPT6 produces Z,Z-FPP, and SlCPT2 catalyzes the formation of nerylneryl diphosphate while SlCPT4, SlCPT5 and SlCPT7 synthesize longer-chain products (C25-C55). Although no in vitro activity was demonstrated for SlCPT3, its expression in the Saccharomyces cerevisiae dolichol biosynthesis mutant (rer2) complemented the temperature-sensitive growth defect. Transcripts of SlCPT2, SlCPT4, SlCPT5 and SlCPT7 are present at low levels in multiple tissues, SlCPT6 is exclusively expressed in red fruit and roots, and SlCPT1, SlCPT3 and SlCPT7 are highly expressed in trichomes. RNAi-mediated suppression of NDPS1 led to a large decrease in ?-phellandrene (which is produced from neryl diphosphate), with greater reductions achieved with the general 35S promoter compared to the trichome-specific MKS1 promoter. Phylogenetic analysis revealed CPT gene families in both eudicots and monocots, and showed that all the short-chain CPT genes from tomato (SlCPT1, SlCPT2 and SlCPT6) are closely linked to terpene synthase gene clusters. PMID:23134568

Akhtar, Tariq A; Matsuba, Yuki; Schauvinhold, Ines; Yu, Geng; Lees, Hazel A; Klein, Samuel E; Pichersky, Eran

2012-12-31

122

The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family  

PubMed Central

Background Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp) gene families that occurred independently in the mouse and rat genomes. Results Using dot plot analysis, we found that the most recent duplication in the Abp region of the mouse genome is flanked by L1Md_T elements. Analysis of the sequence of these elements revealed breakpoints that are the relicts of the recombination that caused the duplication, confirming that the duplication arose as a result of NAHR using L1 elements as substrates. L1 and ERVII retrotransposons are considerably denser in the Abp regions than in one Mb flanking regions, while other repeat types are depleted in the Abp regions compared to flanking regions. L1 retrotransposons preferentially accumulated in the Abp gene regions after lineage separation and roughly followed the pattern of Abp gene expansion. By contrast, the proportion of shared vs. lineage-specific ERVII repeats in the Abp region resembles the rest of the genome. Conclusions We confirmed the role of L1 repeats in Abp gene duplication with the identification of recombinant L1Md_T elements at the edges of the most recent mouse Abp gene duplication. High densities of L1 and ERVII repeats were found in the Abp gene region with abrupt transitions at the region boundaries, suggesting that their higher densities are tightly associated with Abp gene duplication. We observed that the major accumulation of L1 elements occurred after the split of the mouse and rat lineages and that there is a striking overlap between the timing of L1 accumulation and expansion of the Abp gene family in the mouse genome. Establishing a link between the accumulation of L1 elements and the expansion of the Abp gene family and identification of an NAHR-related breakpoint in the most recent duplication are the main contributions of our study.

2013-01-01

123

The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression  

PubMed Central

Background Lignin is a phenolic heteropolymer in secondary cell walls that plays a major role in the development of plants and their defense against pathogens. The biosynthesis of monolignols, which represent the main component of lignin involves many enzymes. The cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis as it catalyzes the final step in the synthesis of monolignols. The CAD gene family has been studied in Arabidopsis thaliana, Oryza sativa and partially in Populus. This is the first comprehensive study on the CAD gene family in woody plants including genome organization, gene structure, phylogeny across land plant lineages, and expression profiling in Populus. Results The phylogenetic analyses showed that CAD genes fall into three main classes (clades), one of which is represented by CAD sequences from gymnosperms and angiosperms. The other two clades are represented by sequences only from angiosperms. All Populus CAD genes, except PoptrCAD 4 are distributed in Class II and Class III. CAD genes associated with xylem development (PoptrCAD 4 and PoptrCAD 10) belong to Class I and Class II. Most of the CAD genes are physically distributed on duplicated blocks and are still in conserved locations on the homeologous duplicated blocks. Promoter analysis of CAD genes revealed several motifs involved in gene expression modulation under various biological and physiological processes. The CAD genes showed different expression patterns in poplar with only two genes preferentially expressed in xylem tissues during lignin biosynthesis. Conclusion The phylogeny of CAD genes suggests that the radiation of this gene family may have occurred in the early ancestry of angiosperms. Gene distribution on the chromosomes of Populus showed that both large scale and tandem duplications contributed significantly to the CAD gene family expansion. The duplication of several CAD genes seems to be associated with a genome duplication event that happened in the ancestor of Salicaceae. Phylogenetic analyses associated with expression profiling and results from previous studies suggest that CAD genes involved in wood development belong to Class I and Class II. The other CAD genes from Class II and Class III may function in plant tissues under biotic stresses. The conservation of most duplicated CAD genes, the differential distribution of motifs in their promoter regions, and the divergence of their expression profiles in various tissues of Populus plants indicate that genes in the CAD family have evolved tissue-specialized expression profiles and may have divergent functions.

Barakat, Abdelali; Bagniewska-Zadworna, Agnieszka; Choi, Alex; Plakkat, Urmila; DiLoreto, Denis S; Yellanki, Priyadarshini; Carlson, John E

2009-01-01

124

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

125

The gene encoding polyneuridine aldehyde esterase of monoterpenoid indole alkaloid biosynthesis in plants is an ortholog of the alpha/betahydrolase super family.  

PubMed

The biosynthesis of the anti-arrhythmic alkaloid ajmaline is catalysed by more than 10 specific enzymes. In this multistep process polyneuridine aldehyde esterase (PNAE) catalyses a central reaction by transforming polyneuridine aldehyde into epi-vellosimine, which is the immediate precursor for the synthesis of the ajmalane skeleton. PNAE was purified from cell suspension cultures of Rauvolfia serpentina. The N-terminal sequence and endoproteinase LysC fragments of the purified protein were used for primer design and for the amplification of specific PCR products leading to the isolation of PNAE-encoding cDNA from a R. serpentina library. The PNAE cDNA was fused with a C-terminal His-tag, expressed in Escherichia coli and purified to homogeneity using Ni-affinity chromatography. The pure enzyme shows extraordinary substrate specificity, completely different to other esterases. Sequence alignments indicate that PNAE is a new member of the alpha/beta hydrolase super family. PMID:10691977

Dogru, E; Warzecha, H; Seibel, F; Haebel, S; Lottspeich, F; Stöckigt, J

2000-03-01

126

Neutrality and Selection in the Evolution of Gene Families  

Microsoft Academic Search

Evolutionary relationships among genes, as revealed by sequence similarity, are used to characterize gene families. Surprisingly,\\u000a a power-law can reasonably describe the distribution of sizes of a genomes gene families. Evolutionary models are able to\\u000a reproduce the size distribution with simulations of a set of genes growing through duplications and modifications. Most conspicuously,\\u000a positive selection is not included in the

Itai Yanai

127

Genome-wide analysis of Aux\\/IAA and ARF gene families in Populus trichocarpa  

Microsoft Academic Search

BACKGROUND: Auxin\\/Indole-3-Acetic Acid (Aux\\/IAA) and Auxin Response Factor (ARF) transcription factors are key regulators of auxin responses in plants. We identified the suites of genes in the two gene families in Populus and performed comparative genomic analysis with Arabidopsis and rice. RESULTS: A total of 35 Aux\\/IAA and 39 ARF genes were identified in the Populus genome. Comparative phylogenetic analysis

Udaya C Kalluri; Stephen P DiFazio; Amy M Brunner; Gerald A Tuskan

2007-01-01

128

Molecular Evolution of Trehalose-6-Phosphate Synthase (TPS) Gene Family in Populus, Arabidopsis and Rice  

PubMed Central

Trehalose-6-phosphate synthase (TPS) plays important roles in trehalose metabolism and signaling. Plant TPS proteins contain both a TPS and a trehalose-6-phosphate phosphatase (TPP) domain, which are coded by a multi-gene family. The plant TPS gene family has been divided into class I and class II. A previous study showed that the Populus, Arabidopsis, and rice genomes have seven class I and 27 class II TPS genes. In this study, we found that all class I TPS genes had 16 introns within the protein-coding region, whereas class II TPS genes had two introns. A significant sequence difference between the two classes of TPS proteins was observed by pairwise sequence comparisons of the 34 TPS proteins. A phylogenetic analysis revealed that at least seven TPS genes were present in the monocot–dicot common ancestor. Segmental duplications contributed significantly to the expansion of this gene family. At least five and three TPS genes were created by segmental duplication events in the Populus and rice genomes, respectively. Both the TPS and TPP domains of 34 TPS genes have evolved under purifying selection, but the selective constraint on the TPP domain was more relaxed than that on the TPS domain. Among 34 TPS genes from Populus, Arabidopsis, and rice, four class I TPS genes (AtTPS1, OsTPS1, PtTPS1, and PtTPS2) were under stronger purifying selection, whereas three Arabidopsis class I TPS genes (AtTPS2, 3, and 4) apparently evolved under relaxed selective constraint. Additionally, a reverse transcription polymerase chain reaction analysis showed the expression divergence of the TPS gene family in Populus, Arabidopsis, and rice under normal growth conditions and in response to stressors. Our findings provide new insights into the mechanisms of gene family expansion and functional evolution.

Yang, Hai-Ling; Liu, Yan-Jing; Wang, Cai-Ling; Zeng, Qing-Yin

2012-01-01

129

Molecular evolution of trehalose-6-phosphate synthase (TPS) gene family in Populus, Arabidopsis and rice.  

PubMed

Trehalose-6-phosphate synthase (TPS) plays important roles in trehalose metabolism and signaling. Plant TPS proteins contain both a TPS and a trehalose-6-phosphate phosphatase (TPP) domain, which are coded by a multi-gene family. The plant TPS gene family has been divided into class I and class II. A previous study showed that the Populus, Arabidopsis, and rice genomes have seven class I and 27 class II TPS genes. In this study, we found that all class I TPS genes had 16 introns within the protein-coding region, whereas class II TPS genes had two introns. A significant sequence difference between the two classes of TPS proteins was observed by pairwise sequence comparisons of the 34 TPS proteins. A phylogenetic analysis revealed that at least seven TPS genes were present in the monocot-dicot common ancestor. Segmental duplications contributed significantly to the expansion of this gene family. At least five and three TPS genes were created by segmental duplication events in the Populus and rice genomes, respectively. Both the TPS and TPP domains of 34 TPS genes have evolved under purifying selection, but the selective constraint on the TPP domain was more relaxed than that on the TPS domain. Among 34 TPS genes from Populus, Arabidopsis, and rice, four class I TPS genes (AtTPS1, OsTPS1, PtTPS1, and PtTPS2) were under stronger purifying selection, whereas three Arabidopsis class I TPS genes (AtTPS2, 3, and 4) apparently evolved under relaxed selective constraint. Additionally, a reverse transcription polymerase chain reaction analysis showed the expression divergence of the TPS gene family in Populus, Arabidopsis, and rice under normal growth conditions and in response to stressors. Our findings provide new insights into the mechanisms of gene family expansion and functional evolution. PMID:22905132

Yang, Hai-Ling; Liu, Yan-Jing; Wang, Cai-Ling; Zeng, Qing-Yin

2012-08-08

130

Application of gene silencing in plants  

Microsoft Academic Search

Recent studies of gene silencing in plants have revealed two RNA-mediated epigenetic processes, RNA-directed RNA degradation and RNA-directed DNA methylation. These natural processes have provided new avenues for developing high-efficiency, high-throughput technology for gene suppression in plants.

Ming-Bo Wang; Peter M Waterhouse

2002-01-01

131

Genome-Wide Identification and Analysis of the TIFY Gene Family in Grape  

PubMed Central

Background The TIFY gene family constitutes a plant-specific group of genes with a broad range of functions. This family encodes four subfamilies of proteins, including ZML, TIFY, PPD and JASMONATE ZIM-Domain (JAZ) proteins. JAZ proteins are targets of the SCFCOI1 complex, and function as negative regulators in the JA signaling pathway. Recently, it has been reported in both Arabidopsis and rice that TIFY genes, and especially JAZ genes, may be involved in plant defense against insect feeding, wounding, pathogens and abiotic stresses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of plant TIFY family members is limited, especially in a woody species such as grape. Methodology/Principal Findings A total of two TIFY, four ZML, two PPD and 11 JAZ genes were identified in the Vitis vinifera genome. Phylogenetic analysis of TIFY protein sequences from grape, Arabidopsis and rice indicated that the grape TIFY proteins are more closely related to those of Arabidopsis than those of rice. Both segmental and tandem duplication events have been major contributors to the expansion of the grape TIFY family. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologues of several grape TIFY genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of lineages that led to grape and Arabidopsis. Analyses of microarray and quantitative real-time RT-PCR expression data revealed that grape TIFY genes are not a major player in the defense against biotrophic pathogens or viruses. However, many of these genes were responsive to JA and ABA, but not SA or ET. Conclusion The genome-wide identification, evolutionary and expression analyses of grape TIFY genes should facilitate further research of this gene family and provide new insights regarding their evolutionary history and regulatory control.

Zhang, Yucheng; Gao, Min; Singer, Stacy D.; Fei, Zhangjun; Wang, Hua; Wang, Xiping

2012-01-01

132

An anaerobically inducible early (aie) gene family from rice  

Microsoft Academic Search

One of the major abiotic stresses that affect plant growth and development is anoxia or hypoxia. Plants respond to anoxia by regulation of gene expression at both the transcriptional and translational levels. Genes involved in such regulation are expected to be expressed soon after onset of anoxia. To date, however, anaerobically regulated genes that have been characterized predominantly encode enzymes

Enamul Huq; Thomas K. Hodges

1999-01-01

133

The Protein Disulfide Isomerase gene family in bread wheat (T. aestivum L.)  

PubMed Central

Background The Protein Disulfide Isomerase (PDI) gene family encodes several PDI and PDI-like proteins containing thioredoxin domains and controlling diversified metabolic functions, including disulfide bond formation and isomerisation during protein folding. Genomic, cDNA and promoter sequences of the three homoeologous wheat genes encoding the "typical" PDI had been cloned and characterized in a previous work. The purpose of present research was the cloning and characterization of the complete set of genes encoding PDI and PDI like proteins in bread wheat (Triticum aestivum cv Chinese Spring) and the comparison of their sequence, structure and expression with homologous genes from other plant species. Results Eight new non-homoeologous wheat genes were cloned and characterized. The nine PDI and PDI-like sequences of wheat were located in chromosome regions syntenic to those in rice and assigned to eight plant phylogenetic groups. The nine wheat genes differed in their sequences, genomic organization as well as in the domain composition and architecture of their deduced proteins; conversely each of them showed high structural conservation with genes from other plant species in the same phylogenetic group. The extensive quantitative RT-PCR analysis of the nine genes in a set of 23 wheat samples, including tissues and developmental stages, showed their constitutive, even though highly variable expression. Conclusions The nine wheat genes showed high diversity, while the members of each phylogenetic group were highly conserved even between taxonomically distant plant species like the moss Physcomitrella patens. Although constitutively expressed the nine wheat genes were characterized by different expression profiles reflecting their different genomic organization, protein domain architecture and probably promoter sequences; the high conservation among species indicated the ancient origin and diversification of the still evolving gene family. The comprehensive structural and expression characterization of the complete set of PDI and PDI-like wheat genes represents a basis for the functional characterization of this gene family in the hexaploid context of bread wheat.

2010-01-01

134

Gene duplication and evolutionary novelty in plants  

Microsoft Academic Search

Summary Duplication is a prominent feature of plant genomic architecture. This has led many researchers to speculate that gene duplication may have played an important role in the evolution of phenotypic novelty within plants. Until recently, however, it was difficult to make this connection. We are now beginning to understand how dupli- cation has contributed to adaptive evolution in plants.

Lex E. Flagel; Jonathan F. Wendel

2009-01-01

135

Factors affecting gene expression of patatin and proteinase-inhibitor-II gene families in detached potato leaves  

Microsoft Academic Search

In whole intact potato (Solanum tuberosum L.) plants, the gene families of class-I patatin and proteinase inhibitor II (Pin 2) are constitutively expressed in the tubers. However, they are also induced in detached potato leaves in the presence of light. To further characterize this light action, the detached leaves were subjected to monochromatic light of different wavelengths and to darkness

Hugo Peña-Cortés; Xiangjun Liu; José Sanchez Serrano; Rainer Schmid; Lothar Willmitzer

1992-01-01

136

Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees  

Microsoft Academic Search

BACKGROUND: Class III Homeodomain Leucine Zipper (HD-Zip III) proteins have been implicated in the regulation of cambium identity, as well as primary and secondary vascular differentiation and patterning in herbaceous plants. They have been proposed to regulate wood formation but relatively little evidence is available to validate such a role. We characterised and compared HD-Zip III gene family in an

Caroline L Côté; Francis Boileau; Vicky Roy; Mario Ouellet; Caroline Levasseur; Marie-Josée Morency; Janice EK Cooke; Armand Séguin; John J MacKay

2010-01-01

137

Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae  

PubMed Central

Numerous CCT domain genes are known to control flowering in plants. They belong to the CONSTANS-like (COL) and PREUDORESPONSE REGULATOR (PRR) gene families, which in addition to a CCT domain possess B-box or response-regulator domains, respectively. Ghd7 is the most recently identified COL gene to have a proven role in the control of flowering time in the Poaceae. However, as it lacks B-box domains, its inclusion within the COL gene family, technically, is incorrect. Here, we show Ghd7 belongs to a larger family of previously uncharacterized Poaceae genes which possess just a single CCT domain, termed here CCT MOTIF FAMILY (CMF) genes. We molecularly describe the CMF (and related COL and PRR) gene families in four sequenced Poaceae species, as well as in the draft genome assembly of barley (Hordeum vulgare). Genetic mapping of the ten barley CMF genes identified, as well as twelve previously unmapped HvCOL and HvPRR genes, finds the majority map to colinear positions relative to their Poaceae orthologues. Combined inter-/intra-species comparative and phylogenetic analysis of CMF, COL and PRR gene families indicates they evolved prior to the monocot/dicot divergence ?200 mya, with Poaceae CMF evolution described as the interplay between whole genome duplication in the ancestral cereal, and subsequent clade-specific mutation, deletion and duplication events. Given the proven role of CMF genes in the modulation of cereals flowering, the molecular, phylogenetic and comparative analysis of the Poaceae CMF, COL and PRR gene families presented here provides the foundation from which functional investigation can be undertaken.

Cockram, James; Thiel, Thomas; Steuernagel, Burkhard; Stein, Nils; Taudien, Stefan; Bailey, Paul C.; O'Sullivan, Donal M.

2012-01-01

138

Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa  

SciTech Connect

Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) transcription factors are key regulators of auxin responses in plants. A total of 35 Aux/IAA and 39 ARF genes were identified in the Populus genome. Comparative phylogenetic analysis revealed that the subgroups PoptrARF2, 6, 9 and 16 and PoptrIAA3, 16, 27 and 29 have differentially expanded in Populus relative to Arabidopsis. Activator ARFs were found to be two fold-overrepresented in the Populus genome. PoptrIAA and PoptrARF gene families appear to have expanded due to high segmental and low tandem duplication events. Furthermore, expression studies showed that genes in the expanded PoptrIAA3 subgroup display differential expression. The gene-family analysis reported here will be useful in conducting future functional genomics studies to understand how the molecular roles of these large gene families translate into a diversity of biologically meaningful auxin effects.

Kalluri, Udaya C [ORNL; DiFazio, Stephen P [West Virginia University; Brunner, A. [Virginia Polytechnic Institute and State University (Virginia Tech); Tuskan, Gerald A [ORNL

2007-01-01

139

BOTANY: A Plant Receptor with a Big Family  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. A hormone that controls plant development and survival acts through a member of a receptor family whose other members are pervasive in animal cells.

Erwin Grill (Technical University Munich;Department of Plant Science); Alexander Christmann (Technical University Munich;Department of Plant Science)

2007-03-23

140

SLC9/NHE gene family, a plasma membrane and organellar family of Na?/H? exchangers.  

PubMed

This brief review of the human Na/H exchanger gene family introduces a new classification with three subgroups to the SLC9 gene family. Progress in the structure and function of this gene family is reviewed with structure based on homology to the bacterial Na/H exchanger NhaA. Human diseases which result from genetic abnormalities of the SLC9 family are discussed although the exact role of these transporters in causing any disease is not established, other than poorly functioning NHE3 in congenital Na diarrhea. PMID:23506868

Donowitz, Mark; Ming Tse, C; Fuster, Daniel

141

Gene for Identifying Individuals with Familial Dysautonomia.  

National Technical Information Service (NTIS)

This invention relates to methods and compositions useful for detecting mutations which cause Familial Dysautonomia. Familial dysautonomia (FD; Riley-Day syndrome), an Ashkenazi Jewish disorder, is the best known and most frequent of a group of congenital...

S. Slaugenhaupt J. F. Gusella

2005-01-01

142

A Comparative Genome Analysis of PME and PMEI Families Reveals the Evolution of Pectin Metabolism in Plant Cell Walls.  

PubMed

Pectins are fundamental polysaccharides in the plant primary cell wall. Pectins are synthesized and secreted to cell walls as highly methyl-esterified polymers and then demethyl-esterified by pectin methylesterases (PMEs), which are spatially regulated by pectin methylesterase inhibitors (PMEIs). Although PME and PMEI genes are pivotal in plant cell wall formation, few studies have focused on the evolutionary patterns of the PME and PMEI gene families. In this study, the gene origin, evolution, and expression diversity of these two families were systematically analyzed using 11 representative species, including algae, bryophytes, lycophytes and flowering land plants. The results show that 1) for the two subfamilies (PME and proPME) of PME, the origin of the PME subfamily is consistent with the appearance of pectins in early charophyte cell walls, 2) Whole genome duplication (WGD) and tandem duplication contribute to the expansion of proPME and PMEI families in land plants, 3) Evidence of selection pressure shows that the proPME and PMEI families have rapidly evolved, particularly the PMEI family in vascular plants, and 4) Comparative expression profile analysis of the two families indicates that the eudicot Arabidopsis and monocot rice have different expression patterns. In addition, the gene structure and sequence analyses show that the origin of the PMEI domain may be derived from the neofunctionalization of the pro domain after WGD. This study will advance the evolutionary understanding of the PME and PMEI families and plant cell wall development. PMID:23951288

Wang, Maojun; Yuan, Daojun; Gao, Wenhui; Li, Yang; Tan, Jiafu; Zhang, Xianlong

2013-08-12

143

KT\\/HAK\\/KUP potassium transporters gene family and their whole-life cycle expression profile in rice ( Oryza sativa )  

Microsoft Academic Search

KT\\/HAK\\/KUP potassium transporter protein-encoding genes constitute a large family in the plant kingdom. The KT\\/HAK\\/KUP family\\u000a is important for various physiological processes of plant life. In this study, we identified 27 potential KT\\/HAK\\/KUP family\\u000a genes in rice (Oryza sativa) by database searching. Analysis of these KT\\/HAK\\/KUP family members identified three conserved motifs with unknown functions,\\u000a and 11–15 trans-membrane segments, most

Madhur Gupta; Xuhua Qiu; Lei Wang; Weibo Xie; Chengjun Zhang; Lizhong Xiong; Xingming Lian; Qifa Zhang

2008-01-01

144

Cloning and Characterization of Novel CIS Family Genes  

Microsoft Academic Search

We have reported two JAK-signaling modulators, CIS (cytokine-inducible SH2 protein) and JAB (JAK2 binding protein), which are structurally related. Here we cloned three additional CIS family genes (CIS2, CIS3, and CIS4) on the basis of an expression sequence tag (EST) database search. We also found at least two additional candidates of this gene family in the database. These genes were

Masaaki Masuhara; Hiroshi Sakamoto; Akira Matsumoto; Ritsu Suzuki; Hideo Yasukawa; Kaoru Mitsui; Toru Wakioka; Shyu Tanimura; Atsuo Sasaki; Hiroyuki Misawa; Masahiro Yokouchi; Motoaki Ohtsubo; Akihiko Yoshimura

1997-01-01

145

Plant KT/KUP/HAK Potassium Transporters: Single Family - Multiple Functions  

PubMed Central

Background and Aims Potassium transporters belonging to the KT/KUP/HAK family are important for various aspects of plant life including mineral nutrition and the regulation of development. Genes encoding these transporters are present in the genomes of all plants, but have not been found in the genomes of Protista or Animalia. The aim of this Botanical Briefing is to analyse the function of KT/KUP/HAK transporters from evolutionary, molecular and physiological perspectives. Scope This Briefing covers the phylogeny and evolution of KT/KUP/HAK transporters, the role of transporters in plant mineral nutrition and potassium homeostasis, and the role of KT/KUP/HAK transporters in plant development.

Grabov, Alexander

2007-01-01

146

3. LOOKING EAST OVER GENE PUMP PLANT AND CAMP; PARKER ...  

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

3. LOOKING EAST OVER GENE PUMP PLANT AND CAMP; PARKER DAM VILLAGE IN BACKGROUND. - Gene Pump Plant, South of Gene Wash Reservoir, 2 miles west of Whitsett Pump Plant, Parker Dam, San Bernardino County, CA

147

The SLC26 gene family of anion transporters and channels.  

PubMed

The phylogenetically ancient SLC26 gene family encodes multifunctional anion exchangers and anion channels transporting a broad range of substrates, including Cl(-), HCO3(-), sulfate, oxalate, I(-), and formate. SLC26 polypeptides are characterized by N-terminal cytoplasmic domains, 10-14 hydrophobic transmembrane spans, and C-terminal cytoplasmic STAS domains, and appear to be homo-oligomeric. SLC26-related SulP proteins of marine bacteria likely transport HCO3(-) as part of oceanic carbon fixation. SulP genes present in antibiotic operons may provide sulfate for antibiotic biosynthetic pathways. SLC26-related Sultr proteins transport sulfate in unicellular eukaryotes and in plants. Mutations in three human SLC26 genes are associated with congenital or early onset Mendelian diseases: chondrodysplasias for SLC26A2, chloride diarrhea for SLC26A3, and deafness with enlargement of the vestibular aqueduct for SLC26A4. Additional disease phenotypes evident only in mouse knockout models include oxalate urolithiasis for Slc26a6 and Slc26a1, non-syndromic deafness for Slc26a5, gastric hypochlorhydria for Slc26a7 and Slc26a9, distal renal tubular acidosis for Slc26a7, and male infertility for Slc26a8. STAS domains are required for cell surface expression of SLC26 proteins, and contribute to regulation of the cystic fibrosis transmembrane regulator in complex, cell- and tissue-specific ways. The protein interactomes of SLC26 polypeptides are under active investigation. PMID:23506885

Alper, Seth L; Sharma, Alok K

148

Characterization of TrcMADS1 gene of Trillium camtschatcense (Trilliaceae) reveals functional evolution of the SOC1 \\/ TM3 -like gene family  

Microsoft Academic Search

Plant MADS-box genes encode transcriptional regulators that are critical for a number of developmental processes, such as the establishment of floral organ identity, flowering time, and fruit development. It appears that the MADS-box gene family has undergone considerable gene duplication and divergence within various angiosperm lineages. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1)\\/Tomato MADS-box gene 3 (TM3)-like genes are members

Toru NakamuraIn-Ja; In-Ja Song; Tatsuya Fukuda; Jun Yokoyama; Masayuki Maki; Toshinori Ochiai; Toshiaki Kameya; Akira Kanno

2005-01-01

149

Expression analysis of LIM gene family in poplar, toward an updated phylogenetic classification  

PubMed Central

Background Plant LIM domain proteins may act as transcriptional activators of lignin biosynthesis and/or as actin binding and bundling proteins. Plant LIM genes have evolved in phylogenetic subgroups differing in their expression profiles: in the whole plant or specifically in pollen. However, several poplar PtLIM genes belong to uncharacterized monophyletic subgroups and the expression patterns of the LIM gene family in a woody plant have not been studied. Findings In this work, the expression pattern of the twelve duplicated poplar PtLIM genes has been investigated by semi quantitative RT-PCR in different vegetative and reproductive tissues. As in other plant species, poplar PtLIM genes were widely expressed in the tree or in particular tissues. Especially, PtXLIM1a, PtXLIM1b and PtWLIM1b genes were preferentially expressed in the secondary xylem, suggesting a specific function in wood formation. Moreover, the expression of these genes and of the PtPLIM2a gene was increased in tension wood. Western-blot analysis confirmed the preferential expression of PtXLIM1a protein during xylem differentiation and tension wood formation. Genes classified within the pollen specific PLIM2 and PLIM2-like subgroups were all strongly expressed in pollen but also in cottony hairs. Interestingly, pairs of duplicated PtLIM genes exhibited different expression patterns indicating subfunctionalisations in specific tissues. Conclusions The strong expression of several LIM genes in cottony hairs and germinating pollen, as well as in xylem fibers suggests an involvement of plant LIM domain proteins in the control of cell expansion. Comparisons of expression profiles of poplar LIM genes with the published functions of closely related plant LIM genes suggest conserved functions in the areas of lignin biosynthesis, pollen tube growth and mechanical stress response. Based on these results, we propose a novel nomenclature of poplar LIM domain proteins.

2012-01-01

150

Hormonal regulation in green plant lineage families.  

PubMed

The patterns of phytohormones distribution, their native function and possible origin of hormonal regulation across the green plant lineages (chlorophytes, charophytes, bryophytes and tracheophytes) are discussed. The five classical phytohormones - auxins, cytokinins, gibberellins (GA), abscisic acid (ABA) and ethylene occur ubiquitously in green plants. They are produced as secondary metabolites by microorganisms. Some of the bacterial species use phytohormones to interact with the plant as a part of their colonization strategy. Phytohormone biosynthetic pathways in plants seem to be of microbial origin and furthermore, the origin of high affinity perception mechanism could have preceded the recruitment of a metabolite as a hormone. The bryophytes represent the earliest land plants which respond to the phytohormones with the exception of gibberellins. The regulation by auxin and ABA may have evolved before the separation of green algal lineage. Auxin enhances rhizoid and caulonemal differentiation while cytokinins enhance shoot bud formation in mosses. Ethylene retards cell division but seems to promote cell elongation. The presence of responses specific to cytokinins and ethylene strongly suggest the origin of their regulation in bryophytes. The hormonal role of GAs could have evolved in some of the ferns where antheridiogens (compounds related to GAs) and GAs themselves regulate the formation of antheridia. During migration of life forms to land, the tolerance to desiccation may have evolved and is now observed in some of the microorganisms, animals and plants. Besides plants, sequences coding for late embryogenesis abundant-like proteins occur in the genomes of other anhydrobiotic species of microorganisms and nematodes. ABA acts as a stress signal and increases rapidly upon desiccation or in response to some of the abiotic stresses in green plants. As the salt stress also increases ABA release in the culture medium of cyanobacterium Trichormus variabilis, the recruitment of ABA in the regulation of stress responses could have been derived from prokaryotes and present at the level of common ancestor of green plants. The overall hormonal action mechanisms in mosses are remarkably similar to that of the higher plants. As plants are thought to be monophyletic in origin, the existence of remarkably similar hormonal mechanisms in the mosses and higher plants, suggests that some of the basic elements of regulation cascade could have also evolved at the level of common ancestor of plants. The networking of various steps in a cascade or the crosstalk between different cascades is variable and reflects the dynamic interaction between a species and its specific environment. PMID:23572871

Johri, M M

2008-06-15

151

The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana  

Microsoft Academic Search

BACKGROUND: Most genes in Arabidopsis thaliana are members of gene families. How do the members of gene families arise, and how are gene family copy numbers maintained? Some gene families may evolve primarily through tandem duplication and high rates of birth and death in clusters, and others through infrequent polyploidy or large-scale segmental duplications and subsequent losses. RESULTS: Our approach

Steven B Cannon; Arvind Mitra; Andrew Baumgarten; Nevin D Young; Georgiana May

2004-01-01

152

Evolution of the Class IV HD-Zip Gene Family in Streptophytes  

PubMed Central

Class IV homeodomain leucine zipper (C4HDZ) genes are plant-specific transcription factors that, based on phenotypes in Arabidopsis thaliana, play an important role in epidermal development. In this study, we sampled all major extant lineages and their closest algal relatives for C4HDZ homologs and phylogenetic analyses result in a gene tree that mirrors land plant evolution with evidence for gene duplications in many lineages, but minimal evidence for gene losses. Our analysis suggests an ancestral C4HDZ gene originated in an algal ancestor of land plants and a single ancestral gene was present in the last common ancestor of land plants. Independent gene duplications are evident within several lineages including mosses, lycophytes, euphyllophytes, seed plants, and, most notably, angiosperms. In recently evolved angiosperm paralogs, we find evidence of pseudogenization via mutations in both coding and regulatory sequences. The increasing complexity of the C4HDZ gene family through the diversification of land plants correlates to increasing complexity in epidermal characters.

Zalewski, Christopher S.; Floyd, Sandra K.; Furumizu, Chihiro; Sakakibara, Keiko; Stevenson, Dennis W.; Bowman, John L.

2013-01-01

153

Karrikins: A new family of plant growth regulators in smoke  

Microsoft Academic Search

Karrikins are a chemically defined family of plant growth regulators discovered in smoke from burning plant material. Karrikins are potent in breaking dormancy of seeds of many species adapted to environments that regularly experience fire and smoke. The recent discovery that karrikins trigger seed germination and control seedling growth in taxa that would rarely experience fire indicates that their significance

Sheila D. S. Chiwocha; Kingsley W. Dixon; Gavin R. Flematti; Emilio L. Ghisalberti; David J. Merritt; David C. Nelson; Julie-Anne M. Riseborough; Steven M. Smith; Jason C. Stevens

2009-01-01

154

Virus-mediated reprogramming of gene expression in plants  

Microsoft Academic Search

Plant viruses have made many significant contributions to plant biology over the years: they have provided plant researchers with functional promoters, transient expression systems and, most recently, with critical insights into the phenomenon of posttranscriptional gene silencing. Plant virus expression vectors have the ability to either overexpress genes or suppress gene expression in plants. Whereas the ‘rules’ for gene expression

John A Lindbo; Wayne P Fitzmaurice; Guy della-Cioppa

2001-01-01

155

Sub-genomic level sequence analysis of the aquaporin multi-gene family in cotton  

Technology Transfer Automated Retrieval System (TEKTRAN)

Aquaporins function mainly as water transport channel proteins that facilitate water movement across intracellular and intercellular membranes in most living organisms. Plant aquaporins belong to a multi-gene family and are commonly categorized into 5 subfamilies according to sequence similarity. Re...

156

Functional Diversity, Conservation, and Convergence in the Evolution of the ?-, ?-, and ?-Carbonic Anhydrase Gene Families  

Microsoft Academic Search

The carbonic anhydrases (CA) catalyze with high efficiency the reversible hydration of carbon dioxide, a reaction underlying many diverse physiological processes in animals, plants, archaebacteria, and eubacteria. We examined the evolutionary history and functional convergence of the CAs encoded by members of three independent CA gene families (?-CA, ?-CA and ?CA). Surprisingly, the six mammalian ?-CA isozymes of defined function

David Hewett-Emmett; Richard E. Tashian

1996-01-01

157

Reprogramming plant gene expression: a prerequisite to geminivirus DNA replication.  

PubMed

SUMMARY Geminiviruses constitute a large family of plant-infecting viruses with small, single-stranded DNA genomes that replicate through double-stranded intermediates. Because of their limited coding capacity, geminiviruses supply only the factors required to initiate their replication and use plant nuclear DNA polymerases to amplify their genomes. Many geminiviruses replicate in differentiated cells that no longer contain detectable levels of host DNA polymerases and associated factors. To overcome this barrier, geminiviruses induce the accumulation of DNA replication machinery in mature plant cells by reprogramming host gene expression. The mammalian DNA tumour viruses activate host genes required for DNA replication by binding to the retinoblastoma protein, a negative regulator of cell cycle progression, and relieving repression through the E2F family of transcription factors. In this review, we discuss recent experiments showing that geminiviruses also modulate components of the retinoblastoma/E2F transcription regulatory network to induce quiescent plant cells to re-enter the cell cycle and regain the capacity to support high levels of DNA replication. Regulation of the cell division cycle and its integration with developmental pathways is complex, with many factors, including hormones, sucrose and environmental signals, controlling re-entry into the plant cell cycle. Geminivirus interactions with these regulatory networks are likely to determine if and where they can replicate their genomes in different plant tissues and hosts. PMID:20565592

Hanley-Bowdoin, Linda; Settlage, Sharon B; Robertson, Dominique

2004-03-01

158

Members of the Arabidopsis actin gene family are widely dispersed in the genome.  

PubMed Central

Plant genomes are subjected to a variety of DNA turnover mechanisms that are thought to result in rapid expansion and presumable contraction of gene copy number. The evolutionary history of the 10 actin genes in Arabidopsis thaliana is well characterized and can be traced to the origin of vascular plant genomes. Knowledge about the genomic position of each actin gene may be the key to tracing landmark genomic duplication events that define plant families or genera and facilitate further mutant isolation. All 10 actin genes were mapped by following the segregation of cleaved amplified polymorphisms between two ecotypes and identifying actin gene locations among yeast artificial chromosomes. The Arabidopsis actin genes are widely dispersed on four different chromosomes (1, 2, 3, and 5). Even the members of three closely related and recently duplicated pairs of actin genes are unlinked. Several other cytoskeletal genes (profilins, tubulins) that might have evolved in concert with actins were also mapped, but showed few patterns consistent with that evolutionary history. Thus, the events that gave rise to the actin gene family have been obscured either by the duplication of very small genic fragments or by extensive rearrangement of the genome.

McKinney, E C; Meagher, R B

1998-01-01

159

Hormonal regulation in green plant lineage families  

Microsoft Academic Search

The patterns of phytohormones distribution, their native function and possible origin of hormonal regulation across the green\\u000a plant lineages (chlorophytes, charophytes, bryophytes and tracheophytes) are discussed. The five classical phytohormones —\\u000a auxins, cytokinins, gibberellins (GA), abscisic acid (ABA) and ethylene occur ubiquitously in green plants. They are produced\\u000a as secondary metabolites by microorganisms. Some of the bacterial species use phytohormones

M. M. Johri

2008-01-01

160

Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families  

PubMed Central

The carbohydrate active enzyme (CAZy) database is an invaluable resource for glycobiology and currently contains 45 glycosyltransferase families that are represented in plants. Glycosyltransferases (GTs) have many functions in plants, but the majority are likely to be involved in biosynthesis of polysaccharides and glycoproteins in the plant cell wall. Bioinformatic approaches and structural modeling suggest that a number of protein families in plants include GTs that have not yet been identified as such and are therefore not included in CAZy. These families include proteins with domain of unknown function (DUF) DUF23, DUF246, and DUF266. The evidence for these proteins being GTs and their possible roles in cell wall biosynthesis is discussed.

Hansen, Sara Fasmer; Harholt, Jesper; Oikawa, Ai; Scheller, Henrik V.

2012-01-01

161

Interferon Induced IFIT Family Genes in Host Antiviral Defense  

PubMed Central

Secretion of interferons (IFNs) from virus-infected cells is a hallmark of host antiviral immunity and in fact, IFNs exert their antiviral activities through the induction of antiviral proteins. The IFN-induced protein with tetratricopeptide repeats (IFITs) family is among hundreds of IFN-stimulated genes. This family contains a cluster of duplicated loci. Most mammals have IFIT1, IFIT2, IFIT3 and IFIT5; however, bird, marsupial, frog and fish have only IFIT5. Regardless of species, IFIT5 is always adjacent to SLC16A12. IFIT family genes are predominantly induced by type I and type III interferons and are regulated by the pattern recognition and the JAK-STAT signaling pathway. IFIT family proteins are involved in many processes in response to viral infection. However, some viruses can escape the antiviral functions of the IFIT family by suppressing IFIT family genes expression or methylation of 5' cap of viral molecules. In addition, the variants of IFIT family genes could significantly influence the outcome of hepatitis C virus (HCV) therapy. We believe that our current review provides a comprehensive picture for the community to understand the structure and function of IFIT family genes in response to pathogens in human, as well as in animals.

Zhou, Xiang; Michal, Jennifer J.; Zhang, Lifan; Ding, Bo; Lunney, Joan K.; Liu, Bang; Jiang, Zhihua

2013-01-01

162

Classification and evolution of alpha-amylase genes in plants.  

PubMed

The DNA sequences for 17 plant genes for alpha-amylase (EC 3.2.1.1) were analyzed to determine their phylogenetic relationship. A phylogeny for these genes was obtained using two separate approaches, one based on molecular clock assumptions and the other based on a comparison of sequence polymorphisms (i.e., small and localized insertions) in the alpha-amylase genes. These polymorphisms are called "alpha-amylase signatures" because they are diagnostic of the gene subfamily to which a particular alpha-amylase gene belongs. Results indicate that the cereal alpha-amylase genes fall into two major classes: AmyA and AmyB. The AmyA class is subdivided into the Amy1 and Amy2 subfamilies previously used to classify alpha-amylase genes in barley and wheat. The AmyB class includes the Amy3 subfamily to which most of the alpha-amylase genes of rice belong. Using polymerase chain reaction and oligonucleotide primers that flank one of the two signature regions, we show that the AmyA and AmyB gene classes are present in approximately equal amounts in all grass species examined except barley. The AmyB (Amy3 subfamily) genes in the latter case are comparatively underrepresented. Additional evidence suggests that the AmyA genes appeared recently and may be confined to the grass family. PMID:1502164

Huang, N; Stebbins, G L; Rodriguez, R L

1992-08-15

163

New Insights into the Evolution of Metazoan Tyrosinase Gene Family  

PubMed Central

Tyrosinases, widely distributed among animals, plants and fungi, are involved in the biosynthesis of melanin, a pigment that has been exploited, in the course of evolution, to serve different functions. We conducted a deep evolutionary analysis of tyrosinase family amongst metazoa, thanks to the availability of new sequenced genomes, assessing that tyrosinases (tyr) represent a distinctive feature of all the organisms included in our study and, interestingly, they show an independent expansion in most of the analyzed phyla. Tyrosinase-related proteins (tyrp), which derive from tyr but show distinct key residues in the catalytic domain, constitute an invention of chordate lineage. In addition we here reported a detailed study of the expression territories of the ascidian Ciona intestinalis tyr and tyrps. Furthermore, we put efforts in the identification of the regulatory sequences responsible for their expression in pigment cell lineage. Collectively, the results reported here enlarge our knowledge about the tyrosinase gene family as valuable resource for understanding the genetic components involved in pigment cells evolution and development.

Squarzoni, Paola; Pezzotti, Maria Rosa; Ristoratore, Filomena; Spagnuolo, Antonietta

2012-01-01

164

Analysis of the glutathione S-transferase (GST) gene family  

PubMed Central

The glutathione S-transferase (GST) gene family encodes genes that are critical for certain life processes, as well as for detoxication and toxification mechanisms, via conjugation of reduced glutathione (GSH) with numerous substrates such as pharmaceuticals and environmental pollutants. The GST genes are upregulated in response to oxidative stress and are inexplicably overexpressed in many tumours, leading to problems during cancer chemotherapy. An analysis of the GST gene family in the Human Genome Organization-sponsored Human Gene Nomenclature Committee database showed 21 putatively functional genes. Upon closer examination, however, GST-kappa 1 (GSTK1), prostaglandin E synthase (PTGES) and three microsomal GSTs (MGST1, MGST2, MGST3) were determined as encoding membrane-bound enzymes having GST-like activity, but these genes are not evolutionarily related to the GST gene family. It is concluded that the complete GST gene family comprises 16 genes in six subfamilies -- alpha (GSTA), mu (GSTM), omega (GSTO), pi (GSTP), theta (GSTT) and zeta (GSTZ).

2004-01-01

165

Considering Plants.  

ERIC Educational Resources Information Center

|Examples from research that incorporate plants to illustrate biological principles are presented. Topics include dried pea shape, homeotic genes, gene transcription in plants that are touched or wounded, production of grasslands, seaweed defenses, migrating plants, camouflage, and family rivalry. (KR)|

Flannery, Maura C.

1991-01-01

166

Arabidopsis Ovate Family Proteins, a Novel Transcriptional Repressor Family, Control Multiple Aspects of Plant Growth and Development  

SciTech Connect

BACKGROUND: The Arabidopsis genome contains 18 genes that are predicted to encode Ovate Family Proteins (AtOFPs), a protein family characterized by a conserved OVATE domain, an approximately 70-amino acid domain that was originally found in tomato OVATE protein. Among AtOFP family members, AtOFP1 has been shown to suppress cell elongation, in part, by suppressing the expression of AtGA20ox1, AtOFP4 has been shown to regulate secondary cell wall formation by interact with KNOTTED1-LIKE HOMEODOMAIN PROTEIN 7 (KNAT7), and AtOFP5 has been shown to regulate the activity of a BEL1-LIKEHOMEODOMAIN 1(BLH1)-KNAT3 complex during early embryo sac development, but little is known about the function of other AtOFPs. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrated here that AtOFP proteins could function as effective transcriptional repressors in the Arabidopsis protoplast transient expression system. The analysis of loss-of-function alleles of AtOFPs suggested AtOFP genes may have overlapping function in regulating plant growth and development, because none of the single mutants identified, including T-DNA insertion mutants in AtOFP1, AtOFP4, AtOFP8, AtOFP10, AtOFP15 and AtOFP16, displayed any apparent morphological defects. Further, Atofp1 Atofp4 and Atofp15 Atofp16 double mutants still did not differ significantly from wild-type. On the other hand, plants overexpressing AtOFP genes displayed a number of abnormal phenotypes, which could be categorized into three distinct classes, suggesting that AtOFP genes may also have diverse functions in regulating plant growth and development. Further analysis suggested that AtOFP1 regulates cotyledon development in a postembryonic manner, and global transcript profiling revealed that it suppress the expression of many other genes. CONCLUSIONS/SIGNIFICANCE: Our results showed that AtOFPs function as transcriptional repressors and they regulate multiple aspects of plant growth and development. These results provided the first overview of a previously unknown transcriptional repressor family, and revealed their possible roles in plant growth and development.

Wang, Shucai [University of British Columbia, Vancouver; Chang, Ying [Northeast Agricultural University; Guo, Jianjun [Harvard University; Zeng, Qingning [University of British Columbia, Vancouver; Ellis, Brian [University of British Columbia, Vancouver; Chen, Jay [ORNL

2011-01-01

167

Arabidopsis Ovate Family Proteins, a Novel Transcriptional Repressor Family, Control Multiple Aspects of Plant Growth and Development  

PubMed Central

Background The Arabidopsis genome contains 18 genes that are predicted to encode Ovate Family Proteins (AtOFPs), a protein family characterized by a conserved OVATE domain, an approximately 70-amino acid domain that was originally found in tomato OVATE protein. Among AtOFP family members, AtOFP1 has been shown to suppress cell elongation, in part, by suppressing the expression of AtGA20ox1, AtOFP4 has been shown to regulate secondary cell wall formation by interact with KNOTTED1-LIKE HOMEODOMAIN PROTEIN 7 (KNAT7), and AtOFP5 has been shown to regulate the activity of a BEL1-LIKEHOMEODOMAIN 1(BLH1)-KNAT3 complex during early embryo sac development, but little is known about the function of other AtOFPs. Methodology/Principal Findings We demonstrated here that AtOFP proteins could function as effective transcriptional repressors in the Arabidopsis protoplast transient expression system. The analysis of loss-of-function alleles of AtOFPs suggested AtOFP genes may have overlapping function in regulating plant growth and development, because none of the single mutants identified, including T-DNA insertion mutants in AtOFP1, AtOFP4, AtOFP8, AtOFP10, AtOFP15 and AtOFP16, displayed any apparent morphological defects. Further, Atofp1 Atofp4 and Atofp15 Atofp16 double mutants still did not differ significantly from wild-type. On the other hand, plants overexpressing AtOFP genes displayed a number of abnormal phenotypes, which could be categorized into three distinct classes, suggesting that AtOFP genes may also have diverse functions in regulating plant growth and development. Further analysis suggested that AtOFP1 regulates cotyledon development in a postembryonic manner, and global transcript profiling revealed that it suppress the expression of many other genes. Conclusions/Significance Our results showed that AtOFPs function as transcriptional repressors and they regulate multiple aspects of plant growth and development. These results provided the first overview of a previously unknown transcriptional repressor family, and revealed their possible roles in plant growth and development.

Guo, Jianjun; Zeng, Qingning; Ellis, Brian E.; Chen, Jin-Gui

2011-01-01

168

How Many Processed Pseudogenes Are Accumulated in a Gene Family?  

PubMed Central

A simple kinetic model is developed that describes the accumulation of processed pseudogenes in a functional gene family. Insertion of new pseudogenes occurs at rate ? per gene and is countered by spontaneous deletion (at rate ? per DNA segment) of segments containing processed pseudogenes. If there are k functional genes in a gene family, the equilibrium number of processed pseudogenes is k(?/?), and the percentage of functional genes in the gene family at equilibrium is 1/[1 + (?/?)]. ?/? values estimated for five gene families ranged from 1.7 to 15. This fairly narrow range suggests that the rates of formation and deletion of processed pseudogenes may be positively correlated for these families. If ? is sufficiently large relative to the per nucleotide mutation rate µ (? > 20µ), processed pseudogenes will show high homology with each other, even in the absence of gene conversion between pseudogenes. We argue that formation of processed pseudogenes may share common pathways with transposable elements and retroviruses, creating the potential for correlated responses in the evolution of processed pseudogenes due to direct selection for control of transposable elements and/or retroviruses. Finally, we discuss the nature of the selective forces that may act directly or indirectly to influence the evolution of processed pseudogenes. Anything produced by evolution is bound to be a bit of a mess—S. Brenner

Walsh, James Bruce

1985-01-01

169

The SLC26 gene family of multifunctional anion exchangers  

Microsoft Academic Search

The ten-member SLC26 gene family encodes anion exchangers capable of transporting a wide variety of monovalent and divalent anions. The physiological role(s) of individual paralogs is evidently due to variation in both anion specificity and expression pattern. Three members of the gene family are involved in genetic disease; SLC26A2 in chondrodysplasias, SLC26A3 in chloride-losing diarrhea, and SLC26A4 in Pendred syndrome

David B. Mount; Michael F. Romero

2004-01-01

170

Sequence, Regulation, and Evolution of the Maize 22-kD ? Zein Gene Family  

PubMed Central

We have isolated and sequenced all 23 members of the 22-kD ? zein (z1C) gene family of maize. This is one of the largest plant gene families that has been sequenced from a single genetic background and includes the largest contiguous genomic DNA from maize with 346,292 bp to date. Twenty-two of the z1C members are found in a roughly tandem array on chromosome 4S forming a dense gene cluster 168,489-bp long. The twenty-third copy of the gene family is also located on chromosome 4S at a site ?20 cM closer to the centromere and appears to be the wild-type allele of the floury-2 (fl2) mutation. On the basis of an analysis of maize cDNA databases, only seven of these genes appear to be expressed including the fl2 allele. The expressed genes in the cluster are interspersed with nonexpressed genes. Interestingly, some of the expressed genes differ in their transcriptional regulation. Gene amplification appears to be in blocks of genes explaining the rapid and compact expansion of the cluster during the evolution of maize. [The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF090447, AF031569, and AF090446

Song, Rentao; Llaca, Victor; Linton, Eric; Messing, Joachim

2001-01-01

171

Porcine KLF gene family: Structure, mapping, and phylogenetic analysis  

Microsoft Academic Search

The Kruppel-like factors (KLFs) belong to the family of zinc finger-containing transcription factors that regulates a diverse array of cellular processes, including cell proliferation, differentiation, and apoptosis. Here we reported the structure, mapping and phylogenetic analysis of KLF gene family in pigs. Comparative analyses revealed strong conservation between pig and human KLFs at the genomic and protein structure levels. Porcine

Zhilong Chen; Ting Lei; Xiaodong Chen; Jian Zhang; An Yu; Qinqiang Long; Huan Long; Dan Jin; Li Gan; Zaiqing Yang

2010-01-01

172

Heterelogous Expression of Plant Genes  

PubMed Central

Heterologous expression allows the production of plant proteins in an organism which is simpler than the natural source. This technology is widely used for large-scale purification of plant proteins from microorganisms for biochemical and biophysical analyses. Additionally expression in well-defined model organisms provides insights into the functions of proteins in complex pathways. The present review gives an overview of recombinant plant protein production methods using bacteria, yeast, insect cells, and Xenopus laevis oocytes and discusses the advantages of each system for functional studies and protein characterization.

Yesilirmak, Filiz; Sayers, Zehra

2009-01-01

173

Heterelogous expression of plant genes.  

PubMed

Heterologous expression allows the production of plant proteins in an organism which is simpler than the natural source. This technology is widely used for large-scale purification of plant proteins from microorganisms for biochemical and biophysical analyses. Additionally expression in well-defined model organisms provides insights into the functions of proteins in complex pathways. The present review gives an overview of recombinant plant protein production methods using bacteria, yeast, insect cells, and Xenopus laevis oocytes and discusses the advantages of each system for functional studies and protein characterization. PMID:19672459

Yesilirmak, Filiz; Sayers, Zehra

2009-08-06

174

Gene duplications in evolution of archaeal family B DNA polymerases.  

PubMed Central

All archaeal DNA-dependent DNA polymerases sequenced to date are homologous to family B DNA polymerases from eukaryotes and eubacteria. Presently, representatives of the euryarchaeote division of archaea appear to have a single family B DNA polymerase, whereas two crenarchaeotes, Pyrodictium occultum and Sulfolobus solfataricus, each possess two family B DNA polymerases. We have found the gene for yet a third family B DNA polymerase, designated B3, in the crenarchaeote S. solfataricus P2. The encoded protein is highly divergent at the amino acid level from the previously characterized family B polymerases in S. solfataricus P2 and contains a number of nonconserved amino acid substitutions in catalytic domains. We have cloned and sequenced the ortholog of this gene from the closely related Sulfolobus shibatae. It is also highly divergent from other archaeal family B DNA polymerases and, surprisingly, from the S. solfataricus B3 ortholog. Phylogenetic analysis using all available archaeal family B DNA polymerases suggests that the S. solfataricus P2 B3 and S. shibatae B3 paralogs are related to one of the two DNA polymerases of P. occultum. These sequences are members of a group which includes all euryarchaeote family B homologs, while the remaining crenarchaeote sequences form another distinct group. Archaeal family B DNA polymerases together constitute a monophyletic subfamily whose evolution has been characterized by a number of gene duplication events.

Edgell, D R; Klenk, H P; Doolittle, W F

1997-01-01

175

MICA Gene Polymorphism in HBDI Multiplex Families  

Microsoft Academic Search

T1DM is a disease that affects pancreatic beta cells and results in severe insulin depletion. T1DM is a multigenic disease, and the strongest genet- ic association with this disease is shown by the genes in MHC class II, namely, DQA1 and DQB1. The other gene that has been implicated in susceptibility to T1DM is the MICA gene that lies within

LIENE NIKITINA-ZAKE; MEHRAN GHADERI; SUNANDA BABU; GEORGE EISENBARTH; CARANI B. SANJEEVI

2004-01-01

176

UBR5 Gene Mutation Is Associated with Familial Adult Myoclonic Epilepsy in a Japanese Family  

PubMed Central

The causal gene(s) for familial adult myoclonic epilepsy (FAME) remains undetermined. To identify it, an exome analysis was performed for the proband in a Japanese FAME family. Of the 383 missense/nonsense variants examined, only c.5720G>A mutation (p.Arg1907His) in the UBR5 gene was found in all of the affected individuals in the family, but not in the nonaffected members. Such mutation was not found in any of the 85 healthy individuals in the same community nor in any of the 24 individuals of various ethnicities. The present study demonstrated an FAME-associated mutation in the UBR5 gene, which is located close to the reported locus linked to Japanese FAME families.

Kato, Takeo; Tamiya, Gen; Koyama, Shingo; Nakamura, Tomohiro; Makino, Satoshi; Arawaka, Shigeki; Kawanami, Toru; Tooyama, Ikuo

2012-01-01

177

The aquaporin gene family of cotton  

Technology Transfer Automated Retrieval System (TEKTRAN)

Aquaporin proteins are found in most living organisms and are quite diverse in plants where they function as transport systems for water and other small molecules. Plant aquaporins have been shown to be differentially regulated under environmental stress such as drought, salt and cold treatment. The...

178

A Novel Family of Bromodomain Genes  

Microsoft Academic Search

The bromodomain is a structural motif characteristic of proteins involved in chromatin-dependent regulation of transcription. Bromodomain proteins have been identified as integral components of chromatin remodeling complexes and frequently possess histone acetyltransferase activity. Their encoding genes have been identified at translocation breakpoints, and at least one, CBP, is a tumor suppressor gene. We have identified a series of novel bromodomain

Michael H. Jones; Naeko Hamana; Jun-ichi Nezu; Miyuki Shimane

2000-01-01

179

Characterization of the GGPP synthase gene family in Arabidopsis thaliana.  

PubMed

Geranylgeranyl diphosphate (GGPP) is a key precursor of various isoprenoids that have diverse functions in plant metabolism and development. The annotation of the Arabidopsis thaliana genome predicts 12 genes to encode geranylgeranyl diphosphate synthases (GGPPS). In this study we analyzed GGPPS activity as well as the subcellular localization and tissue-specific expression of the entire protein family in A. thaliana. GGPPS2 (At2g18620), GGPPS3 (At2g18640), GGPPS6 (At3g14530), GGPPS7 (At3g14550), GGPPS8 (At3g20160), GGPPS9 (At3g29430), GGPPS10 (At3g32040) and GGPPS11 (At4g36810) showed GGPPS activity in Escherichia coli, similar to activities reported earlier for GGPPS1 (At1g49530) and GGPPS4 (At2g23800) (Zhu et al. in Plant Cell Physiol 38(3):357-361, 1997a; Plant Mol Biol 35(3):331-341, b). GGPPS12 (At4g38460) did not produce GGPP in E. coli. Based on DNA sequence analysis we propose that GGPPS5 (At3g14510) is a pseudogene. GGPPS-GFP (green fluorescent protein) fusion proteins of the ten functional GGPP synthases localized to plastids, mitochondria and the endoplasmic reticulum, with the majority of the enzymes located in plastids. Gene expression analysis using quantitative real time-PCR, GGPPS promoter-GUS (?-glucuronidase) assays and publicly available microarray data revealed a differential spatio-temporal expression of GGPPS genes. The results suggest that plastids and mitochondria are key subcellular compartments for the synthesis of ubiquitous GGPP-derived isoprenoid species. GGPPS11 and GGPPS1 are the major isozymes responsible for their biosynthesis. All remaining paralogs, encoding six plastidial isozymes and two cytosolic isozymes, were expressed in specific tissues and/or at specific developmental stages, suggesting their role in developmentally regulated isoprenoid biosynthesis. Our results show that of the 12 predicted GGPPS encoded in the A. thaliana genome 10 are functional proteins that can synthesize GGPP. Their specific subcellular location and differential expression pattern suggest subfunctionalization in providing GGPP to specific tissues, developmental stages, or metabolic pathways. PMID:23729351

Beck, Gilles; Coman, Diana; Herren, Edgar; Ruiz-Sola, M Aguila; Rodríguez-Concepción, Manuel; Gruissem, Wilhelm; Vranová, Eva

2013-06-01

180

Evolutionary History of the Cancer Immunity Antigen MAGE Gene Family  

PubMed Central

The evolutionary mode of a multi-gene family can change over time, depending on the functional differentiation and local genomic environment of family members. In this study, we demonstrate such a change in the melanoma antigen (MAGE) gene family on the mammalian X chromosome. The MAGE gene family is composed of ten subfamilies that can be categorized into two types. Type I genes are of relatively recent origin, and they encode epitopes for human leukocyte antigen (HLA) in cancer cells. Type II genes are relatively ancient and some of their products are known to be involved in apoptosis or cell proliferation. The evolutionary history of the MAGE gene family can be divided into four phases. In phase I, a single-copy state of an ancestral gene and the evolutionarily conserved mode had lasted until the emergence of eutherian mammals. In phase II, eight subfamily ancestors, with the exception for MAGE-C and MAGE-D subfamilies, were formed via retrotransposition independently. This would coincide with a transposition burst of LINE elements at the eutherian radiation. However, MAGE-C was generated by gene duplication of MAGE-A. Phase III is characterized by extensive gene duplication within each subfamily and in particular the formation of palindromes in the MAGE-A subfamily, which occurred in an ancestor of the Catarrhini. Phase IV is characterized by the decay of a palindrome in most Catarrhini, with the exception of humans. Although the palindrome is truncated by frequent deletions in apes and Old World monkeys, it is retained in humans. Here, we argue that this human-specific retention stems from negative selection acting on MAGE-A genes encoding epitopes of cancer cells, which preserves their ability to bind to highly divergent HLA molecules. These findings are interpreted with consideration of the biological factors shaping recent human MAGE-A genes.

Katsura, Yukako; Satta, Yoko

2011-01-01

181

Recommended nomenclature for the vertebrate alcohol dehydrogenase gene family  

Microsoft Academic Search

The alcohol dehydrogenase (ADH) gene family encodes enzymes that metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. Studies on 19 vertebrate animals have identified ADH orthologs across several species, and this has now led to questions of how best to name ADH proteins and genes. Seven distinct classes of vertebrate ADH

Gregg Duester; Jaume Farrés; Michael R Felder; Roger S Holmes; Jan-Olov Höög; Xavier Parés; Bryce V Plapp; Shih-Jiun Yin; Hans Jörnvall

1999-01-01

182

Recommended nomenclature for five mammalian carboxylesterase gene families: human, mouse, and rat genes and proteins  

PubMed Central

Mammalian carboxylesterase (CES or Ces) genes encode enzymes that participate in xenobiotic, drug, and lipid metabolism in the body and are members of at least five gene families. Tandem duplications have added more genes for some families, particularly for mouse and rat genomes, which has caused confusion in naming rodent Ces genes. This article describes a new nomenclature system for human, mouse, and rat carboxylesterase genes that identifies homolog gene families and allocates a unique name for each gene. The guidelines of human, mouse, and rat gene nomenclature committees were followed and “CES” (human) and “Ces” (mouse and rat) root symbols were used followed by the family number (e.g., human CES1). Where multiple genes were identified for a family or where a clash occurred with an existing gene name, a letter was added (e.g., human CES4A; mouse and rat Ces1a) that reflected gene relatedness among rodent species (e.g., mouse and rat Ces1a). Pseudogenes were named by adding “P” and a number to the human gene name (e.g., human CES1P1) or by using a new letter followed by ps for mouse and rat Ces pseudogenes (e.g., Ces2d-ps). Gene transcript isoforms were named by adding the GenBank accession ID to the gene symbol (e.g., human CES1_AB119995 or mouse Ces1e_BC019208). This nomenclature improves our understanding of human, mouse, and rat CES/Ces gene families and facilitates research into the structure, function, and evolution of these gene families. It also serves as a model for naming CES genes from other mammalian species.

Holmes, Roger S.; Wright, Matthew W.; Laulederkind, Stanley J. F.; Cox, Laura A.; Hosokawa, Masakiyo; Imai, Teruko; Ishibashi, Shun; Lehner, Richard; Miyazaki, Masao; Perkins, Everett J.; Potter, Phillip M.; Redinbo, Matthew R.; Robert, Jacques; Satoh, Tetsuo; Yamashita, Tetsuro; Yan, Bingfan; Yokoi, Tsuyoshi; Zechner, Rudolf; Maltais, Lois J.

2011-01-01

183

Gene - Environment Interplay, Family Relationships, and Child Adjustment.  

PubMed

This paper reviews behavioral genetic research from the past decade that has moved beyond simply studying the independent influences of genes and environments. The studies considered in this review have instead focused on understanding gene - environment interplay, including genotype - environment correlation ( rGE) and genotype × environment interaction (G × E). Studies have suggested that rGE is an important pathway through which family relationships are associated with child adjustment. Also important are direct causal influences of family relationships on child adjustment, independent of genetic confounds. Other studies have indicated that genetic and environmental influences on child adjustment are moderated by different levels of family relationships in G × E interactions. Genetically informed studies that have examined family relations have been critical to advancing our understanding of gene - environment interplay. PMID:22162877

Horwitz, Briana N; Neiderhiser, Jenae M

2011-08-01

184

Gene - Environment Interplay, Family Relationships, and Child Adjustment  

PubMed Central

This paper reviews behavioral genetic research from the past decade that has moved beyond simply studying the independent influences of genes and environments. The studies considered in this review have instead focused on understanding gene – environment interplay, including genotype – environment correlation ( rGE) and genotype × environment interaction (G × E). Studies have suggested that rGE is an important pathway through which family relationships are associated with child adjustment. Also important are direct causal influences of family relationships on child adjustment, independent of genetic confounds. Other studies have indicated that genetic and environmental influences on child adjustment are moderated by different levels of family relationships in G × E interactions. Genetically informed studies that have examined family relations have been critical to advancing our understanding of gene – environment interplay.

Horwitz, Briana N.; Neiderhiser, Jenae M.

2011-01-01

185

The Bacillus thuringiensis cyt Genes for Hemolytic Endotoxins Constitute a Gene Family  

Microsoft Academic Search

In the same way that cry genes, coding for larvicidal delta endotoxins, constitute a large and diverse gene family, the cyt genes for hemolytic toxins seem to compose another set of highly related genes in Bacillus thuringiensis. Although the occurrence of Cyt hemolytic factors in B. thuringiensis has been typically associated with mosquitocidal strains, we have recently shown that cyt

ALEJANDRA GUERCHICOFF; ARMELLE DELECLUSE; CLARA P. RUBINSTEIN

2001-01-01

186

Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice  

Microsoft Academic Search

NAM, ATAF, and CUC (NAC) transcription factors comprise a large plant-specific gene family and a few members of this family\\u000a have been characterized for their roles in plant growth, development, and stress tolerance. In this study, systematic sequence\\u000a analysis revealed 140 putative NAC or NAC-like genes (ONAC) in rice. Phylogenetic analysis suggested that NAC family can be divided into five

Yujie Fang; Jun You; Kabin Xie; Weibo Xie; Lizhong Xiong

2008-01-01

187

Phylogeny and Biogeography of the Carnivorous Plant Family Sarraceniaceae  

Microsoft Academic Search

The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich

Aaron M. Ellison; Elena D. Butler; Emily Jean Hicks; Robert F. C. Naczi; Patrick J. Calie; Charles D. Bell; Charles C. Davis

2012-01-01

188

The ZIC gene family in development and disease.  

PubMed

The human ZIC gene family is comprised of five members encoding zinc-finger transcription factors, which are the vertebrate homologs of the Drosophila odd-paired gene. Mutations in ZIC genes in humans have recently been implicated in a wide variety of congenital malformations, including Dandy-Walker malformation, holoprosencephaly, neural tube defects, and heterotaxy. Mutant analysis of these genes in mice has underscored the conserved developmental roles of these genes. Further, this analysis has begun to elucidate the molecular and developmental mechanisms underlying these important birth defects. PMID:15733262

Grinberg, I; Millen, K J

2005-04-01

189

Identification of a family of muscarinic acetylcholine receptor genes  

SciTech Connect

Complementary DNAs for three different muscarinic acetylcholine receptors were isolated from a rat cerebral cortex library, and the cloned receptors were expressed in mammalian cells. Analysis of human and rat genomic clones indicates that there are at least four functional muscarinic receptor genes and that these genes lack introns in the coding sequence. This gene family provides a new basis for evaluating the diversity of muscarinic mechanisms in the nervous system.

Bonner, T.I.; Buckley, N.J.; Young, A.C.; Brann, M.R.

1987-07-31

190

Sleep, genes and death: fatal familial insomnia  

Microsoft Academic Search

Over the past 30 years, significant progress has been made in understanding the physiologic mechanisms of sleep. Insomnia, a common complaint in general medical practice, and other sleep disorders have become increasingly recognized. In 1986, a heritable total insomnia was described and termed fatal familial insomnia; since then, the pathology of this disease has been shown to involve an accumulation

Anthony S. Fiorino

1996-01-01

191

The peroxiredoxin gene family in drosophila melanogaster  

Microsoft Academic Search

Five peroxiredoxin genes have been identified in Drosophila melanogaster on the basis of a genome-wide search. Three of the genes (DPx-4156, DPx-4783, and DPx-5037) fall into the 2-Cys subgroup, while the other two (DPx-2540 and DPx-6005) belong to the 1-Cys subgroup. Using cDNAs, all five were expressed in E. coli and the purified recombinant proteins were shown to reduce H2O2

Svetlana N. Radyuk; Vladimir I. Klichko; Benedetta Spinola; Rajindar S. Sohal; William C. Orr

2001-01-01

192

Genomic Organization, Phylogenetic Comparison and Differential Expression of the SBP-Box Family Genes in Grape  

PubMed Central

Background The SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants including green algae, moss, silver birch, snapdragon, Arabidopsis, rice and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157, function in grapevine. Methodology/Principal Findings Eighteen SBP-box gene family members were identified in Vitis vinifera, twelve of which bore sequences that were complementary to miRNA156/157. Phylogenetic reconstruction demonstrated that plant SBP-domain proteins could be classified into seven subgroups, with the V. vinifera SBP-domain proteins being more closely related to SBP-domain proteins from dicotyledonous angiosperms than those from monocotyledonous angiosperms. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologs of several grape SBP genes were found in corresponding syntenic blocks of Arabidopsis. Expression analysis of the grape SBP-box genes in various organs and at different stages of fruit development in V. quinquangularis ‘Shang-24’ revealed distinct spatiotemporal patterns. While the majority of the grape SBP-box genes lacking a miR156/157 target site were expressed ubiquitously and constitutively, most genes bearing a miR156/157 target site exhibited distinct expression patterns, possibly due to the inhibitory role of the microRNA. Furthermore, microarray data mining and quantitative real-time RT-PCR analysis identified several grape SBP-box genes that are potentially involved in the defense against biotic and abiotic stresses. Conclusion The results presented here provide a further understanding of SBP-box gene function in plants, and yields additional insights into the mechanism of stress management in grape, which may have important implications for the future success of this crop.

Hou, Hongmin; Li, Jun; Gao, Min; Singer, Stacy D.; Wang, Hao; Mao, Linyong; Fei, Zhangjun; Wang, Xiping

2013-01-01

193

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

194

MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress  

Microsoft Academic Search

BACKGROUND: MADS-box transcription factors, besides being involved in floral organ specification, have also been implicated in several aspects of plant growth and development. In recent years, there have been reports on genomic localization, protein motif structure, phylogenetic relationships, gene structure and expression of the entire MADS-box family in the model plant system, Arabidopsis. Though there have been some studies in

Rita Arora; Pinky Agarwal; Swatismita Ray; Ashok Kumar Singh; Vijay Pal Singh; Akhilesh K Tyagi; Sanjay Kapoor

2007-01-01

195

The diageotropica mutation alters auxin induction of a subset of the Aux\\/IAA gene family in tomato  

Microsoft Academic Search

The diageotropica (dgt) mutation has been proposed to affect either auxin perception or responsiveness in tomato plants. It has previously been demonstrated that the expression of one member of the Aux\\/IAA family of auxin-regulated genes is reduced in dgt plants. Here, we report the cloning of ten new members of the tomato Aux\\/IAA family by PCR amplification based on conserved

Andreas Nebenführ; TJ White; Terri L. Lomax

2000-01-01

196

Molecular evolution of the polyamine oxidase gene family in Metazoa  

PubMed Central

Background Polyamine oxidase enzymes catalyze the oxidation of polyamines and acetylpolyamines. Since polyamines are basic regulators of cell growth and proliferation, their homeostasis is crucial for cell life. Members of the polyamine oxidase gene family have been identified in a wide variety of animals, including vertebrates, arthropodes, nematodes, placozoa, as well as in plants and fungi. Polyamine oxidases (PAOs) from yeast can oxidize spermine, N1-acetylspermine, and N1-acetylspermidine, however, in vertebrates two different enzymes, namely spermine oxidase (SMO) and acetylpolyamine oxidase (APAO), specifically catalyze the oxidation of spermine, and N1-acetylspermine/N1-acetylspermidine, respectively. Little is known about the molecular evolutionary history of these enzymes. However, since the yeast PAO is able to catalyze the oxidation of both acetylated and non acetylated polyamines, and in vertebrates these functions are addressed by two specialized polyamine oxidase subfamilies (APAO and SMO), it can be hypothesized an ancestral reference for the former enzyme from which the latter would have been derived. Results We analysed 36 SMO, 26 APAO, and 14 PAO homologue protein sequences from 54 taxa including various vertebrates and invertebrates. The analysis of the full-length sequences and the principal domains of vertebrate and invertebrate PAOs yielded consensus primary protein sequences for vertebrate SMOs and APAOs, and invertebrate PAOs. This analysis, coupled to molecular modeling techniques, also unveiled sequence regions that confer specific structural and functional properties, including substrate specificity, by the different PAO subfamilies. Molecular phylogenetic trees revealed a basal position of all the invertebrates PAO enzymes relative to vertebrate SMOs and APAOs. PAOs from insects constitute a monophyletic clade. Two PAO variants sampled in the amphioxus are basal to the dichotomy between two well supported monophyletic clades including, respectively, all the SMOs and APAOs from vertebrates. The two vertebrate monophyletic clades clustered strictly mirroring the organismal phylogeny of fishes, amphibians, reptiles, birds, and mammals. Evidences from comparative genomic analysis, structural evolution and functional divergence in a phylogenetic framework across Metazoa suggested an evolutionary scenario where the ancestor PAO coding sequence, present in invertebrates as an orthologous gene, has been duplicated in the vertebrate branch to originate the paralogous SMO and APAO genes. A further genome evolution event concerns the SMO gene of placental, but not marsupial and monotremate, mammals which increased its functional variation following an alternative splicing (AS) mechanism. Conclusions In this study the explicit integration in a phylogenomic framework of phylogenetic tree construction, structure prediction, and biochemical function data/prediction, allowed inferring the molecular evolutionary history of the PAO gene family and to disambiguate paralogous genes related by duplication event (SMO and APAO) and orthologous genes related by speciation events (PAOs, SMOs/APAOs). Further, while in vertebrates experimental data corroborate SMO and APAO molecular function predictions, in invertebrates the finding of a supported phylogenetic clusters of insect PAOs and the co-occurrence of two PAO variants in the amphioxus urgently claim the need for future structure-function studies.

2012-01-01

197

Evolution of the multifaceted eukaryotic akirin gene family  

PubMed Central

Background Akirins are nuclear proteins that form part of an innate immune response pathway conserved in Drosophila and mice. This studies aim was to characterise the evolution of akirin gene structure and protein function in the eukaryotes. Results akirin genes are present throughout the metazoa and arose before the separation of animal, plant and fungi lineages. Using comprehensive phylogenetic analysis, coupled with comparisons of conserved synteny and genomic organisation, we show that the intron-exon structure of metazoan akirin genes was established prior to the bilateria and that a single proto-orthologue duplicated in the vertebrates, before the gnathostome-agnathan separation, producing akirin1 and akirin2. Phylogenetic analyses of seven vertebrate gene families with members in chromosomal proximity to both akirin1 and akirin2 were compatible with a common duplication event affecting the genomic neighbourhood of the akirin proto-orthologue. A further duplication of akirins occurred in the teleost lineage and was followed by lineage-specific patterns of paralogue loss. Remarkably, akirins have been independently characterised by five research groups under different aliases and a comparison of the available literature revealed diverse functions, generally in regulating gene expression. For example, akirin was characterised in arthropods as subolesin, an important growth factor and in Drosophila as bhringi, which has an essential myogenic role. In vertebrates, akirin1 was named mighty in mice and was shown to regulate myogenesis, whereas akirin2 was characterised as FBI1 in rats and promoted carcinogenesis, acting as a transcriptional repressor when bound to a 14-3-3 protein. Both vertebrate Akirins have evolved under comparably strict constraints of purifying selection, although a likelihood ratio test predicted that functional divergence has occurred between paralogues. Bayesian and maximum likelihood tests identified amino-acid positions where the rate of evolution had shifted significantly between paralogues. Interestingly, the highest scoring position was within a conserved, validated binding-site for 14-3-3 proteins. Conclusion This work offers an evolutionary framework to facilitate future studies of eukaryotic akirins and provides insight into their multifaceted and conserved biochemical functions.

Macqueen, Daniel J; Johnston, Ian A

2009-01-01

198

Plant defense genes are regulated by ethylene  

SciTech Connect

One of the earliest detectable events during plant-pathogen interaction is a rapid increase in ethylene biosynthesis. This gaseous plant stress hormone may be a signal for plants to activate defense mechanisms against invading pathogens such as bacteria, fungi, and viruses. The effect of ethylene on four plant genes involved in three separate plant defense response pathways was examined; these included (i and ii) genes that encode L-phenylalanine ammonia-lyase (EC 4.3.1.5) and 4-coumarate:CoA ligase (4-coumarate:CoA ligase (AMP-forming), EC 6.2.1.12), enzymes of the phenylpropanoid pathway, (iii) the gene encoding chalcone synthase, an enzyme of the flavonoid glycoside pathway, and (iv) the genes encoding hydroxyproline-rich glycoprotein, a major protein component(s) of plant cell walls. Blot hybridization analysis of mRNA from ethylene-treated carrot roots reveals marked increases in the levels of phenylalanine ammonia-lyase mRNA, 4-coumarate CoA ligase mRNA, chalcone synthase mRNA, and certain hydroxyproline-rich glycoprotein transcripts. The effect of ethylene on hydroxyproline-rich glycoprotein mRNA accumulation was different from that of wounding. Ethylene induces two hydroxyproline-rich glycoprotein mRNAs (1.8 and 4.0 kilobases), whereas wounding of carrot root leads to accumulation of an additional hydroxyproline-rich mRNA (1.5 kilobases). These results indicate that at least two distinct signals, ethylene and a wound signal, can affect the expression of plant defense-response genes.

Ecker, J.R.; Davis, R.W.

1987-08-01

199

Two mutations in LDLR gene were found in two Chinese families with familial hypercholesterolemia  

Microsoft Academic Search

Familial hypercholesterolemia (FH) (OMIM 143890) is an autosomal dominantly inherited disease mainly caused by mutations of\\u000a the gene encoding the low density lipoprotein receptor (LDLR) and Apolipoprotein (Apo) B. First the common mutation R3500Q\\u000a in ApoB gene was determined using PCR\\/RFLP method. Then the LDLR gene was screened for mutations using Touch-down PCR, SSCP\\u000a and sequencing techniques. Furthermore, the secondary

Xiaohuan Cheng; Junfa Ding; Fang Zheng; Xin Zhou; Chenling Xiong

2009-01-01

200

TAMARICACEAE IN THE FAMILIES AND GENERA OF VASCULAR PLANTS  

Technology Transfer Automated Retrieval System (TEKTRAN)

The plant family Tamaricaceae contains 3-4 genera and some 80 species of shrubs and small trees, usually halophytic. They are native to Europe, Asia, and Africa, but species of Tamarix have become naturalized in Australia and the Americas. This treatment reviews the latest knowledge of vegetative mo...

201

Comprehensive analysis of NAC domain transcription factor gene family in Vitis vinifera.  

PubMed

KEY MESSAGE : Genome-wide identification of grapevine NAC domain genes and investigation of their chromosome locations, gene structures, duplication, evolution, phylogeny and expression profiles. Grapevine is a widely used fruit crop. NAC (NAM, ATAF1/2 and CUC2) domain genes are plant-specific transcription factors (TFs) that comprise a conserved NAM domain in the N-terminus. Members of this gene family have been reported to contribute to plant development. During this study, 74 NAC genes were identified from 12× assembled grapevine genomic sequences. The duplication patterns, genomic structures and phylogeny of these 74 grapevine NAC genes were investigated. To understand the roles of VvNAC during grapevine development, their expression profiles in different tissues including leaf, tendril, inflorescence, stem, root and veraison berry skin were tested using quantitative real-time PCR. Analysis revealed expression diversity of various VvNAC genes among different grapevine tissues. To identify candidate grapevine NAC genes with a role in response to stress, publicly available microarray data were obtained to calculate their expression change under abiotic and biotic treatments, with a number of VvNAC genes displaying up-regulation after stress induction. Therefore, this study has uncovered more knowledge relating to the gene structures, chromosome organizations, evolution, expression profiles and functions of VvNAC genes. PMID:22983198

Wang, Nian; Zheng, Yu; Xin, Haiping; Fang, Linchuan; Li, Shaohua

2012-09-15

202

Developmental regulation of embryonic genes in plants  

SciTech Connect

Somatic embryogenesis from cultured carrot cells progresses through successive morphogenetic stages termed globular, heart, and torpedo. To understand the molecular mechanisms underlying plant embryogenesis, the authors isolated two genes differentially expressed during embryo development. The expression of these two genes is associated with heart-stage embryogenesis. By altering the culture conditions and examining their expressions in a developmental variant cell line, they found that these genes were controlled by the developmental program of embryogenesis and were not directly regulated by 2,4-dichlorophenoxyacetic acid, the growth regulator that promotes unorganized growth of cultured cells and suppresses embryo morphogenesis. These genes are also expressed in carrot zygotic embryos but not in seedlings or mature plants.

Borkird, C.; Choi, Jung, H.; Jin, Zhenghua; Franz, G.; Hatzopoulos, P.; Chorneaus, R.; Bonas, U.; Pelegri, F.; Sung, Z.R.

1988-09-01

203

Genome-wide analysis of SAUR gene family in Solanaceae species.  

PubMed

The plant hormone auxin plays a vital role in regulating many aspects of plant growth and development. Small auxin up-regulated RNAs (SAURs) are primary auxin response genes hypothesized to be involved in auxin signaling pathway, but their functions remain unclear. Here, a genome-wide search for SAUR gene homologues in Solanaceae species identified 99 and 134 members of SAUR gene family from tomato and potato, respectively. Phylogenetic analysis indicated that the SAUR proteins from Arabidopsis, rice, sorghum, tomato and potato were divided into four major groups with 16 subgroups. Among them, 25 histidine-rich SAURs genes with metal-binding characteristics were found in Arabidopsis, sorghum and Solanaceae species, but not in rice. Using tomato as a model, a comprehensive overview of SAUR gene family is presented, including the gene structures, phylogeny and chromosome locations. Quantitative real-time PCR analysis indicated that 11 randomly selected SlSAUR genes in tomato could be expressed at least in one of the tomato organs/tissues tested. However, different SlSAUR genes displayed distinctive expression levels. SlSAUR16 and SlSAUR71 exhibited highly tissue-specific expression patterns. Almost all of the detected SlSAURs showed an accumulating pattern of mRNA along tomato flower and fruit development. Some of them displayed differential response to exogenous IAA treatment. The abiotic (cold, salt and drought) stresses significantly modified transcript levels of SlSAURs genes. Most of them were down-regulated in response to abiotic stresses (drought, heat and salinity), but SlSAUR58, as a histidine-rich SAUR gene, was up-regulated after salt treatment, indicating that it may play a specific role in the salt signaling transduction pathway. Our comparative analysis provides some basic genomic information for the SAUR genes in the Solanaceae species and will pave the way for deciphering their function during plant development. PMID:22903030

Wu, Jian; Liu, Songyu; He, Yanjun; Guan, Xiaoyan; Zhu, Xiangfei; Cheng, Lin; Wang, Jie; Lu, Gang

2012-08-11

204

Cystatins, serpins and other families of protease inhibitors in plants.  

PubMed

Plant protease inhibitors (PIs) are generally small proteins present in high concentrations in storage tissues (tubers and seeds), and to a lower level in leaves. Even if most of them are active against serine and cysteine proteases, PIs active against aspartic proteases and carboxypeptidases have also been identified. Inhibitors of serine proteases are further classifiable in several families on the basis of their structural features. They comprise the families known as Bowman-Birk, Kunitz, Potato I and Potato II, which are the subject of review articles included in this special issue. In the present article we aim to give an overview of other families of plant PIs, active either against serine proteases or other class of proteases, describing their distribution, activity and main structural characteristics. PMID:21418017

Volpicella, Mariateresa; Leoni, Claudia; Costanza, Alessandra; De Leo, Francesca; Gallerani, Raffaele; Ceci, Luigi R

2011-08-01

205

Gene turnover and differential retention in the relaxin/insulin-like gene family in primates.  

PubMed

The relaxin/insulin-like gene family is related to the insulin gene family, and includes two separate types of peptides: relaxins (RLNs) and insulin-like peptides (INSLs) that perform a variety of physiological roles including testicular descent, growth and differentiation of the mammary glands, trophoblast development, and cell differentiation. In vertebrates, these genes are found on three separate genomic loci, and in mammals, variation in the number and nature of genes in this family is mostly restricted to the Relaxin Family Locus B. For example, this locus contains a single copy of RLN in platypus and opossum, whereas it contains copies of the INSL6, INSL4, RLN2 and RLN1 genes in human and chimp. The main objective of this research is to characterize changes in the size and membership composition of the RLN/INSL gene family in primates, reconstruct the history of the RLN/INSL genes of primates, and test competing evolutionary scenarios regarding the origin of INSL4 and of the duplicated copies of the RLN gene of apes. Our results show that the relaxin/INSL-like gene family of primates has had a more dynamic evolutionary history than previously thought, including several examples of gene duplications and losses which are consistent with the predictions of the birth-and-death model of gene family evolution. In particular, we found that the differential retention of relatively old paralogs played a key role in shaping the gene complement of this family in primates. Two examples of this phenomenon are the origin of the INSL4 gene of catarrhines (the group that includes Old World monkeys and apes), and of the duplicate RLN1 and RLN2 paralogs of apes. In the case of INSL4, comparative genomics and phylogenetic analyses indicate that the origin of this gene, which was thought to represent a catarrhine-specific evolutionary innovation, is as old as the split between carnivores and primates, which took place approximately 97 million years ago. In addition, in the case of the RLN1 and RLN2 genes of apes our phylogenetic trees and topology tests indicate that the duplication that gave rise to these two genes maps to the last common ancestor of anthropoid primates. All these genomic changes in gene complement, which are particularly prevalent among anthropoid primates, might be linked to the many physiological and anatomical changes found in this group. Given the various roles of members of the RLN/INSL-like gene family in reproductive biology, it might be that changes in this gene family are associated to changes in reproductive traits. PMID:22405815

Arroyo, José Ignacio; Hoffmann, Federico G; Opazo, Juan C

2012-03-01

206

Evolutionary Relationship and Structural Characterization of the EPF/EPFL Gene Family  

PubMed Central

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

2013-01-01

207

GenPhyloData: realistic simulation of gene family evolution  

PubMed Central

Background PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and—perhaps more interestingly—also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock. Result Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data. Conclusion The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.

2013-01-01

208

Characterization of the Class IV Homeodomain-Leucine Zipper Gene Family in Arabidopsis1[W  

PubMed Central

The Arabidopsis (Arabidopsis thaliana) genome contains 16 genes belonging to the class IV homeodomain-Leucine zipper gene family. These include GLABRA2, ANTHOCYANINLESS2, FWA, ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1), and PROTODERMAL FACTOR2 (PDF2). Our previous study revealed that atml1 pdf2 double mutants have severe defects in the shoot epidermal cell differentiation. Here, we have characterized additional members of this gene family, which we designated HOMEODOMAIN GLABROUS1 (HDG1) through HDG12. Analyses of transgenic Arabidopsis plants carrying the gene-specific promoter fused to the bacterial ?-glucuronidase reporter gene revealed that some of the promoters have high activities in the epidermal layer of the shoot apical meristem and developing shoot organs, while others are temporarily active during reproductive organ development. Expression profiles of highly conserved paralogous gene pairs within the family were found to be not necessarily overlapping. Analyses of T-DNA insertion mutants of these HDG genes revealed that all mutants except hdg11 alleles exhibit no abnormal phenotypes. hdg11 mutants show excess branching of the trichome. This phenotype is enhanced in hdg11 hdg12 double mutants. Double mutants were constructed for other paralogous gene pairs and genes within the same subfamily. However, novel phenotypes were observed only for hdg3 atml1 and hdg3 pdf2 mutants that both exhibited defects in cotyledon development. These observations suggest that some of the class IV homeodomain-Leucine zipper members act redundantly with other members of the family during various aspects of cell differentiation. DNA-binding sites were determined for two of the family members using polymerase chain reaction-assisted DNA selection from random oligonucleotides with their recombinant proteins. The binding sites were found to be similar to those previously identified for ATML1 and PDF2, which correspond to the pseudopalindromic sequence 5?-GCATTAAATGC-3? as the preferential binding site.

Nakamura, Miyuki; Katsumata, Hiroshi; Abe, Mitsutomo; Yabe, Naoto; Komeda, Yoshibumi; Yamamoto, Kotaro T.; Takahashi, Taku

2006-01-01

209

Phylogenetic diversification of glycogen synthase kinase 3\\/SHAGGY-like kinase genes in plants  

Microsoft Academic Search

BACKGROUND: The glycogen synthase kinase 3 (GSK3)\\/SHAGGY-like kinases (GSKs) are non-receptor serine\\/threonine protein kinases that are involved in a variety of biological processes. In contrast to the two members of the GSK3 family in mammals, plants appear to have a much larger set of divergent GSK genes. Plant GSKs are encoded by a multigene family; analysis of the Arabidopsis genome

Mi-Jeong Yoo; Victor A Albert; Pamela S Soltis; Douglas E Soltis

2006-01-01

210

Argonaute catapults new gene family to prominence  

Microsoft Academic Search

AGO1 defines a novel locus of Arabidopsis controlling leaf development Bohmert, K. et al. EMBO J. 17, 170–180Role of the ZWILLE gene in the regulation of central shoot meristem cell fate during Arabidopsis embryogenesis Moussian, B. et al. EMBO J. 7, 1799–1809

Catherine Kidner

1998-01-01

211

Endo-(1,4)-?-Glucanase gene families in the grasses: temporal and spatial Co-transcription of orthologous genes1  

PubMed Central

Background Endo-(1,4)-?-glucanase (cellulase) glycosyl hydrolase GH9 enzymes have been implicated in several aspects of cell wall metabolism in higher plants, including cellulose biosynthesis and degradation, modification of other wall polysaccharides that contain contiguous (1,4)-?-glucosyl residues, and wall loosening during cell elongation. Results The endo-(1,4)-?-glucanase gene families from barley (Hordeum vulgare), maize (Zea mays), sorghum (Sorghum bicolor), rice (Oryza sativa) and Brachypodium (Brachypodium distachyon) range in size from 23 to 29 members. Phylogenetic analyses show variations in clade structure between the grasses and Arabidopsis, and indicate differential gene loss and gain during evolution. Map positions and comparative studies of gene structures allow orthologous genes in the five species to be identified and synteny between the grasses is found to be high. It is also possible to differentiate between homoeologues resulting from ancient polyploidizations of the maize genome. Transcript analyses using microarray, massively parallel signature sequencing and quantitative PCR data for barley, rice and maize indicate that certain members of the endo-(1,4)-?-glucanase gene family are transcribed across a wide range of tissues, while others are specifically transcribed in particular tissues. There are strong correlations between transcript levels of several members of the endo-(1,4)-?-glucanase family and the data suggest that evolutionary conservation of transcription exists between orthologues across the grass family. There are also strong correlations between certain members of the endo-(1,4)-?-glucanase family and other genes known to be involved in cell wall loosening and cell expansion, such as expansins and xyloglucan endotransglycosylases. Conclusions The identification of these groups of genes will now allow us to test hypotheses regarding their functions and joint participation in wall synthesis, re-modelling and degradation, together with their potential role in lignocellulose conversion during biofuel production from grasses and cereal crop residues.

2012-01-01

212

Review: the dominant flocculation genes of Saccharomyces cerevisiae constitute a new subtelomeric gene family.  

PubMed

The quality of brewing strains is, in large part, determined by their flocculation properties. By classical genetics, several dominant, semidominant and recessive flocculation genes have been recognized. Recent results of experiments to localize the flocculation genes FLO5 and FLO8, combined with the in silicio analysis of the available sequence data of the yeast genome, have revealed that the flocculation genes belong to a family which comprises at least four genes and three pseudogenes. All members of this gene family are located near the end of chromosomes, just like the SUC, MEL and MAL genes, which are also important for good quality baking or brewing strains. Transcription of the flocculation genes is repressed by several regulatory genes. In addition, a number of genes have been found which cause cell aggregation upon disruption or overexpression in an as yet unknown manner. In total, 33 genes have been reported that are involved in flocculation or cell aggregation. PMID:7502576

Teunissen, A W; Steensma, H Y

1995-09-15

213

Genome-wide characterization of the CBF/DREB1 gene family in Brassica rapa.  

PubMed

The C-repeat/dehydration-responsive element binding transcription factors (CBF/DREBs) are important proteins in involved in responses to abiotic stress in plants. We identified ten BrDREB1 genes belonging to the CBF/DREB1 gene family in the Brassica rapa whole genome sequence, whereas six genes are found in the Arabidopsis thaliana genome. The deduced amino acid sequences of the B. rapa genes showed conserved motifs shared with other known plant CBF/DREB1s. Comparative analysis revealed that nine of the BrDREB1 genes were derived from the recent genome triplication in the tribe Brassiceae and the other one was translocated. The nine genes were located in seven of the 12 macrosyntenic blocks that are triplicated counterparts of four Arabidopsis macrosyntenic blocks harboring six CBF/DREB1 genes: one gene on each of three blocks and three tandemly arrayed genes on another block. We inspected the expression patterns of eight BrDREB1 genes by RT-PCR and microarray database searches. All eight genes were highly up-regulated during cold (4 °C) treatment, and some of them were also responsive to salt (250 mM NaCl), drought (air drying), and ABA (100 ?M) treatment. Microarray data for plant developmental stages revealed that BrDREB1C2 was highly expressed during a period of cold treatment for vernalization, similar to abiotic stress-inducible genes homologous to Bn28a, Bn47, Bn115, and BoRS1, but almost opposite of BrFLC genes. Taken together, the number of BrDREB1 genes increased to 10 by genome triplication and reorganization, providing additional functions in B. rapa abiotic stress responses and development, as distinct from their Arabidopsis homologs. PMID:23148914

Lee, Sang-Choon; Lim, Myung-Ho; Yu, Jae-Gyeong; Park, Beom-Seok; Yang, Tae-Jin

2012-11-01

214

Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis  

PubMed Central

Fungi and oomycetes are the causal agents of many of the most serious diseases of plants. Here we report a detailed comparative analysis of the genome sequences of thirty-six species of fungi and oomycetes, including seven plant pathogenic species, that aims to explore the common genetic features associated with plant disease-causing species. The predicted translational products of each genome have been clustered into groups of potential orthologues using Markov Chain Clustering and the data integrated into the e-Fungi object-oriented data warehouse (http://www.e-fungi.org.uk/). Analysis of the species distribution of members of these clusters has identified proteins that are specific to filamentous fungal species and a group of proteins found only in plant pathogens. By comparing the gene inventories of filamentous, ascomycetous phytopathogenic and free-living species of fungi, we have identified a set of gene families that appear to have expanded during the evolution of phytopathogens and may therefore serve important roles in plant disease. We have also characterised the predicted set of secreted proteins encoded by each genome and identified a set of protein families which are significantly over-represented in the secretomes of plant pathogenic fungi, including putative effector proteins that might perturb host cell biology during plant infection. The results demonstrate the potential of comparative genome analysis for exploring the evolution of eukaryotic microbial pathogenesis.

Soanes, Darren M.; Alam, Intikhab; Cornell, Mike; Wong, Han Min; Hedeler, Cornelia; Paton, Norman W.; Rattray, Magnus; Hubbard, Simon J.; Oliver, Stephen G.; Talbot, Nicholas J.

2008-01-01

215

Evolution of the multifaceted eukaryotic akirin gene family  

Microsoft Academic Search

BACKGROUND: Akirins are nuclear proteins that form part of an innate immune response pathway conserved in Drosophila and mice. This studies aim was to characterise the evolution of akirin gene structure and protein function in the eukaryotes. RESULTS: akirin genes are present throughout the metazoa and arose before the separation of animal, plant and fungi lineages. Using comprehensive phylogenetic analysis,

Daniel J Macqueen; Ian A Johnston

2009-01-01

216

Eleven Candidate Susceptibility Genes for Common Familial Colorectal Cancer  

PubMed Central

Hereditary factors are presumed to play a role in one third of colorectal cancer (CRC) cases. However, in the majority of familial CRC cases the genetic basis of predisposition remains unexplained. This is particularly true for families with few affected individuals. To identify susceptibility genes for this common phenotype, we examined familial cases derived from a consecutive series of 1514 Finnish CRC patients. Ninety-six familial CRC patients with no previous diagnosis of a hereditary CRC syndrome were included in the analysis. Eighty-six patients had one affected first-degree relative, and ten patients had two or more. Exome sequencing was utilized to search for genes harboring putative loss-of-function variants, because such alterations are likely candidates for disease-causing mutations. Eleven genes with rare truncating variants in two or three familial CRC cases were identified: UACA, SFXN4, TWSG1, PSPH, NUDT7, ZNF490, PRSS37, CCDC18, PRADC1, MRPL3, and AKR1C4. Loss of heterozygosity was examined in all respective cancer samples, and was detected in seven occasions involving four of the candidate genes. In all seven occasions the wild-type allele was lost (P?=?0.0078) providing additional evidence that these eleven genes are likely to include true culprits. The study provides a set of candidate predisposition genes which may explain a subset of common familial CRC. Additional genetic validation in other populations is required to provide firm evidence for causality, as well as to characterize the natural history of the respective phenotypes.

Gylfe, Alexandra E.; Katainen, Riku; Kondelin, Johanna; Tanskanen, Tomas; Cajuso, Tatiana; Hanninen, Ulrika; Taipale, Jussi; Taipale, Minna; Renkonen-Sinisalo, Laura; Jarvinen, Heikki; Mecklin, Jukka-Pekka; Kilpivaara, Outi; Pitkanen, Esa; Vahteristo, Pia; Tuupanen, Sari; Karhu, Auli; Aaltonen, Lauri A.

2013-01-01

217

Exploiting Gene Families for Phylogenomic Analysis of Myzostomid Transcriptome Data  

PubMed Central

Background In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic (or parasitic) protostomes that are either placed with annelids or flatworms. Methodology Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony. Conclusions Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic.

Hartmann, Stefanie; Helm, Conrad; Nickel, Birgit; Meyer, Matthias; Struck, Torsten H.; Tiedemann, Ralph; Selbig, Joachim; Bleidorn, Christoph

2012-01-01

218

Genetic Variance in the Adiponutrin Gene Family and Childhood Obesity  

PubMed Central

Aim The adiponutrin gene family consists of five genes (PNPLA1-5) coding for proteins with both lipolytic and lipogenic properties. PNPLA3 has previously been associated with adult obesity. Here we investigated the possible association between genetic variants in these genes and childhood and adolescent obesity. Methods/Results Polymorphisms in the five genes of the adiponutrin gene family were selected and genotyped using the Sequenom platform in a childhood and adolescent obesity case-control study. Six variants in PNPLA1 showed association with obesity (rs9380559, rs12212459, rs1467912, rs4713951, rs10947600, and rs12199580, p<0.05 after adjustment for age and gender). Three variants in PNPLA3 showed association with obesity before, but not after, adjustment for age and gender (rs139051, rs12483959, and rs2072907, p>0.05). When analyzing these SNPs in relation to phenotypes, two SNPs in the PNPLA3 gene showed association with insulin sensitivity (rs12483959: ??=??0.053, p?=?0.016, and rs2072907: ??=??0.049, p?=?0.024). No associations were seen for PNPLA2, PNPLA4, and PNPLA5. Conclusions Genetic variation in the adiponutrin gene family does not seem to contribute strongly to obesity in children and adolescents. PNPLA1 exhibited a modest effect on obesity and PNPLA3 on insulin sensitivity. These data, however, require confirmation in other cohorts and ethnic groups.

Johansson, Lovisa E.; Johansson, Lina M.; Danielsson, Pernilla; Norgren, Svante; Johansson, Stina; Marcus, Claude; Ridderstrale, Martin

2009-01-01

219

Plant gene expression response to Agrobacterium tumefaciens  

PubMed Central

To elucidate the nature of plant response to infection and transformation by Agrobacterium tumefaciens, we compared the cDNA-amplified fragment length polymorphism (AFLP) pattern of Agrobacterium- and mock-inoculated Ageratum conyzoides plant cell cultures. From 16,000 cDNA fragments analyzed, 251 (1.6%) were differentially regulated (0.5% down-regulated) 48 h after cocultivation with Agrobacterium. From 75 strongly regulated fragments, 56 were already regulated 24 h after cocultivation. Sequence similarities were obtained for 20 of these fragments, and reverse transcription–PCR analysis was carried out with seven to confirm their cDNA-AFLP differential pattern. Their sequence similarities suggest a role for these genes in signal perception, transduction, and plant defense. Reverse transcription–PCR analysis indicated that four genes involved in defense response are regulated in a similar manner by nonpathogenic bacteria, whereas one gene putatively involved in signal transduction appeared to respond more strongly to Agrobacterium. A nodulin-like gene was regulated only by Agrobacterium. These results demonstrate a rapid plant cell response to Agrobacterium infection, which overlaps a general response to bacteria but also has Agrobacterium-specific features.

Ditt, Renata F.; Nester, Eugene W.; Comai, Luca

2001-01-01

220

Inducible gene expression systems and plant biotechnology  

Microsoft Academic Search

Plant biotechnology relies heavily on the genetic manipulation of crops. Almost invariantly, the gene of interest is expressed in a constitutive fashion, although this may not be strictly necessary for several applications. Currently, there are several regulatable expression systems for the temporal, spatial and quantitative control of transgene activity. These molecular switches are based on components derived from different organisms,

Giandomenico Corrado; Marianthi Karali

2009-01-01

221

The FKBP families of higher plants: Exploring the structures and functions of protein interaction specialists.  

PubMed

The FK506-binding proteins (FKBPs) are known both as the receptors for immunosuppressant drugs and as prolyl isomerase (PPIase) enzymes that catalyse rotation of prolyl bonds. FKBPs are characterised by the inclusion of at least one FK506-binding domain (FKBd), the receptor site for proline and the active site for PPIase catalysis. The FKBPs form large and diverse families in most organisms, with the largest FKBP families occurring in higher plants. Plant FKBPs are molecular chaperones that interact with specific protein partners to regulate a diversity of cellular processes. Recent studies have found that plant FKBPs operate in intricate and coordinated mechanisms for regulating stress response and development processes, and discoveries of new interaction partners expand their cellular influences to gene expression and photosynthetic adaptations. This review presents an examination of the molecular and structural features and functional roles of the higher plant FKBP family within the context of these recent findings, and discusses the significance of domain conservation and variation for the development of a diverse, versatile and complex chaperone family. PMID:22982859

Gollan, Peter J; Bhave, Mrinal; Aro, Eva-Mari

2012-09-13

222

Normal CAG repeats in the Huntington gene in a family with benign familial chorea.  

PubMed

Benign familial chorea (BFC) is a rare neurological disease with an autosomal dominant transmission. The disorder is characterized by its early onset in childhood, a non-progressive course of choreatic movements and the absence of intellectual impairment. There is one study describing an expanded (CAG)n repeat in the gene IT15 (Huntington) on chromosome 4p (causative for Huntington's chorea) in a family reported to have BFC that was diagnosed on the basis of onset and non-progressive course. We failed to find an expansion of the (CAG)n repeats in an Austrian family having BFC. The three affected individuals of the family had 18-25 CAG repeats. These results indicate that the diagnostic criteria for BFC should include a normal result in the analysis of the (CAG)n repeat region of the Huntington gene. PMID:8840396

Meszaros, K; Brücke, T; Fuchs, K; Gerhard, E; Sieghart, W; vanDer Meer, C H; Aschauer, H N

1996-01-01

223

Genome-wide analysis of WRKY gene family in Cucumis sativus  

PubMed Central

Background WRKY proteins are a large family of transcriptional regulators in higher plant. They are involved in many biological processes, such as plant development, metabolism, and responses to biotic and abiotic stresses. Prior to the present study, only one full-length cucumber WRKY protein had been reported. The recent publication of the draft genome sequence of cucumber allowed us to conduct a genome-wide search for cucumber WRKY proteins, and to compare these positively identified proteins with their homologs in model plants, such as Arabidopsis. Results We identified a total of 55 WRKY genes in the cucumber genome. According to structural features of their encoded proteins, the cucumber WRKY (CsWRKY) genes were classified into three groups (group 1-3). Analysis of expression profiles of CsWRKY genes indicated that 48 WRKY genes display differential expression either in their transcript abundance or in their expression patterns under normal growth conditions, and 23 WRKY genes were differentially expressed in response to at least one abiotic stresses (cold, drought or salinity). The expression profile of stress-inducible CsWRKY genes were correlated with those of their putative Arabidopsis WRKY (AtWRKY) orthologs, except for the group 3 WRKY genes. Interestingly, duplicated group 3 AtWRKY genes appear to have been under positive selection pressure during evolution. In contrast, there was no evidence of recent gene duplication or positive selection pressure among CsWRKY group 3 genes, which may have led to the expressional divergence of group 3 orthologs. Conclusions Fifty-five WRKY genes were identified in cucumber and the structure of their encoded proteins, their expression, and their evolution were examined. Considering that there has been extensive expansion of group 3 WRKY genes in angiosperms, the occurrence of different evolutionary events could explain the functional divergence of these genes.

2011-01-01

224

Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family  

PubMed Central

The gene family of subtilisin-like serine proteases (subtilases) in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens confirmed 144 T-DNA insertion lines with knockouts for 55 out of the 56 subtilases. Apart from SDD1, none of the confirmed homozygous mutants revealed any obvious visible phenotypic alteration during growth under standard conditions. Apart from this specific case, forward genetics gave us no hints about the function of the individual 54 non-characterized subtilase genes. Therefore, the main objective of our work was to overcome the shortcomings of the forward genetic approach and to infer alternative experimental approaches by using an integrative bioinformatics and biological approach. Computational analyses based on transcriptional co-expression and co-response pattern revealed at least two expression networks, suggesting that functional redundancy may exist among subtilases with limited similarity. Furthermore, two hubs were identified, which may be involved in signalling or may represent higher-order regulatory factors involved in responses to environmental cues. A particular enrichment of co-regulated genes with metabolic functions was observed for four subtilases possibly representing late responsive elements of environmental stress. The kexin homologs show stronger associations with genes of transcriptional regulation context. Based on the analyses presented here and in accordance with previously characterized subtilases, we propose three main functions of subtilases: involvement in (i) control of development, (ii) protein turnover, and (iii) action as downstream components of signalling cascades. Supplemental material is available in the Plant Subtilase Database (PSDB) (http://csbdb.mpimp-golm.mpg.de/psdb.html) , as well as from the CSB.DB (http://csbdb.mpimp-golm.mpg.de).

Bussis, Dirk; Stintzi, Annick; Schaller, Andreas; Kopka, Joachim; Altmann, Thomas

2005-01-01

225

Poplar and Pathogen Interactions: Insights from Populus Genome-Wide Analyses of Resistance and Defense Gene Families and Gene Expression Profiling  

Microsoft Academic Search

Our understanding of the molecular basis of plant-pathogen interactions is derived mostly from studies of model annual plant species, and until recently, few addressed disease resistance and defense responses in long-lived species such as trees. The release of the Populus genome sequence has permitted extensive genome-wide surveys of gene families and comparative analyses of other sequenced plant genomes. These have

Sébastien Duplessis; Ian Major; Francis Martin; Armand Séguin

2009-01-01

226

The EGF-CFC gene family in vertebrate development  

Microsoft Academic Search

EGF-CFC genes encode extracellular proteins that play key roles in intercellular signaling pathways during vertebrate embryogenesis. Mutations in zebrafish and mouse EGF-CFC genes lead to defects in germ-layer formation, anterior–posterior axis orientation and left–right axis specification. In addition, members of the EGF-CFC family have been implicated in carcinogenesis. Although formerly regarded as signaling molecules that are distant relatives of epidermal

Michael M Shen; Alexander F Schier

2000-01-01

227

Expression of a subset of the Arabidopsis Cys 2\\/His 2-type zinc-finger protein gene family under water stress  

Microsoft Academic Search

The genes encoding Cys2\\/His2-type zinc-finger proteins constitute a large family in higher plants. To elucidate the functional roles of these types of protein, four different members of the gene family were cloned from Arabidopsis by PCR-aided methods. One was identical to the already reported gene STZ\\/ZAT10 and three were as yet unidentified genes, then designated AZF1 (Arabidopsis zinc-finger protein 1),

Hideki Sakamoto; Takashi Araki; Tetsuo Meshi; Masaki Iwabuchi

2000-01-01

228

Genome-wide identification and analysis of the SBP-box family genes in apple (Malus × domestica Borkh.).  

PubMed

SQUAMOSA promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors and play many crucial roles in plant development. In this study, 27 SBP-box gene family members were identified in the apple (Malus × domestica Borkh.) genome, 15 of which were suggested to be putative targets of MdmiR156. Plant SBPs were classified into eight groups according to the phylogenetic analysis of SBP-domain proteins. Gene structure, gene chromosomal location and synteny analyses of MdSBP genes within the apple genome demonstrated that tandem and segmental duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of the SBP-box gene family in apple. Additionally, synteny analysis between apple and Arabidopsis indicated that several paired homologs of MdSBP and AtSPL genes were located in syntenic genomic regions. Tissue-specific expression analysis of MdSBP genes in apple demonstrated their diversified spatiotemporal expression patterns. Most MdmiR156-targeted MdSBP genes, which had relatively high transcript levels in stems, leaves, apical buds and some floral organs, exhibited a more differential expression pattern than most MdmiR156-nontargeted MdSBP genes. Finally, expression analysis of MdSBP genes in leaves upon various plant hormone treatments showed that many MdSBP genes were responsive to different plant hormones, indicating that MdSBP genes may be involved in responses to hormone signaling during stress or in apple development. PMID:23771035

Li, Jun; Hou, Hongmin; Li, Xiaoqin; Xiang, Jiang; Yin, Xiangjing; Gao, Hua; Zheng, Yi; Bassett, Carole L; Wang, Xiping

2013-05-25

229

Extreme variability among mammalian V1R gene families.  

PubMed

We report an evolutionary analysis of the V1R gene family across 37 mammalian genomes. V1Rs comprise one of three chemosensory receptor families expressed in the vomeronasal organ, and contribute to pheromone detection. We first demonstrate that Trace Archive data can be used effectively to determine V1R family sizes and to obtain sequences of most V1R family members. Analyses of V1R sequences from trace data and genome assemblies show that species-specific expansions previously observed in only eight species were prevalent throughout mammalian evolution, resulting in "semi-private" V1R repertoires for most mammals. The largest families are found in mouse and platypus, whose V1R repertoires have been published previously, followed by mouse lemur and rabbit (approximately 215 and approximately 160 intact V1Rs, respectively). In contrast, two bat species and dolphin possess no functional V1Rs, only pseudogenes, and suffered inactivating mutations in the vomeronasal signal transduction gene Trpc2. We show that primate V1R decline happened prior to acquisition of trichromatic vision, earlier during evolution than was previously thought. We also show that it is extremely unlikely that decline of the dog V1R repertoire occurred in response to selective pressures imposed by humans during domestication. Functional repertoire sizes in each species correlate roughly with anatomical observations of vomeronasal organ size and quality; however, no single ecological correlate explains the very diverse fates of this gene family in different mammalian genomes. V1Rs provide one of the most extreme examples observed to date of massive gene duplication in some genomes, with loss of all functional genes in other species. PMID:19952141

Young, Janet M; Massa, Hillary F; Hsu, Li; Trask, Barbara J

2009-12-01

230

Combined transcriptome profiling reveals a novel family of arbuscular mycorrhizal-specific Medicago truncatula lectin genes.  

PubMed

The large majority of plants are capable of undergoing a tight symbiosis with arbuscular mycorrhizal (AM) fungi. During this symbiosis, highly specialized new structures called arbuscules are formed within the host cells, indicating that, during interaction with AM fungi, plants express AM-specific genetic programs. Despite increasing efforts, the number of genes known to be induced in the AM symbiosis is still low. In order to identify novel AM-induced genes which have not been listed before, 5,646 expressed sequence tags (ESTs) were generated from two Medicago truncatula cDNA libraries: a random cDNA library (MtAmp) and a suppression subtractive hybridization (SSH) library (MtGim), the latter being designed to enhance the cloning of mycorrhiza-upregulated genes. In silico expression analysis was applied to identify those tentative consensus sequences (TCs) of The Institute for Genomic Research M. truncatula gene index (MtGI) that are composed exclusively of ESTs deriving from the MtGim or MtAmp library, but not from any other cDNA library of the MtGI. This search revealed 115 MtAmp- or MTGim-specific TCs. For the majority of these TCs with sequence similarities to plant genes, the AM-specific expression was verified by quantitative reverse-transcription polymerase chain reaction. Annotation of the novel genes induced in mycorrhizal roots suggested their involvement in different transport as well as signaling processes and revealed a novel family of AM-specific lectin genes. The expression of reporter gene fusions in transgenic roots revealed an arbuscule-related expression of two members of the lectin gene family, indicating a role for AM-specific lectins during arbuscule formation or functioning. PMID:16134889

Frenzel, André; Manthey, Katja; Perlick, Andreas M; Meyer, Folker; Pühler, Alfred; Küster, Helge; Krajinski, Franziska

2005-08-01

231

The d4 gene family in the human genome  

SciTech Connect

The d4 domain, a novel zinc finger-like structural motif, was first revealed in the rat neuro-d4 protein. Here we demonstrate that the d4 domain is conserved in evolution and that three related genes form a d4 family in the human genome. The human neuro-d4 is very similar to rat neuro-d4 at both the amino acid and the nucleotide levels. Moreover, the same splice variants have been detected among rat and human neuro-d4 transcripts. This gene has been localized on chromosome 19, and two other genes, members of the d4 family isolated by screening of the human genomic library at low stringency, have been mapped to chromosomes 11 and 14. The gene on chromosome 11 is the homolog of the ubiquitously expressed mouse gene ubi-d4/requiem, which is required for cell death after deprivation of trophic factors. A gene with a conserved d4 domain has been found in the genome of the nematode Caenorhabditis elegans. The conservation of d4 proteins from nematodes to vertebrates suggests that they have a general importance, but a diversity of d4 proteins expressed in vertebrate nervous systems suggests that some family members have special functions. 11 refs., 2 figs.

Chestkov, A.V.; Baka, I.D.; Kost, M.V. [Engelhardt Inst. of Molecular Biology, Moscow (Russian Federation)] [and others

1996-08-15

232

Multigenic families and proteomics: extended protein characterization as a tool for paralog gene identification.  

PubMed

In classical proteomic studies, the searches in protein databases lead mostly to the identification of protein functions by homology due to the non-exhaustiveness of the protein databases. The quality of the identification depends on the studied organism, its complexity and its representation in the protein databases. Nevertheless, this basic function identification is insufficient for certain applications namely for the development of RNA-based gene-silencing strategies, commonly termed RNA interference (RNAi) in animals and post-transcriptional gene silencing (PTGS) in plants, that require an unambiguous identification of the targeted gene sequence. A PTGS strategy was considered in the study of the infection of Oryza sativa by the Rice Yellow Mottle Virus (RYMV). It is suspected that the RYMV recruits host proteins after its entry into plant cells to form a complex facilitating virus multiplication and spreading. The protein partners of this complex were identified by a classical proteomic approach, nano liquid chromatography tandem mass spectrometry. Among the identified proteins, several were retained for a PTGS strategy. Nevertheless most of the protein candidates appear to be members of multigenic families for which all paralog genes are not present in protein databases. Thus the identification of the real expressed paralog gene with classical protein database searches is impossible. Consequently, as the genome contains all genes and thus all paralog genes, a whole genome search strategy was developed to determine the specific expressed paralog gene. With this approach, the identification of peptides matching only a single gene, called discriminant peptides, allows definitive proof of the expression of this identified gene. This strategy has several requirements: (i) a genome completely sequenced and accessible; (ii) high protein sequence coverage. In the present work, through three examples, we report and validate for the first time a genome database search strategy to specifically identify paralog genes belonging to multigenic families expressed under specific conditions. PMID:15627959

Delalande, François; Carapito, Christine; Brizard, Jean-Paul; Brugidou, Christophe; Van Dorsselaer, Alain

2005-02-01

233

Genome-wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa  

PubMed Central

Background Calcium signaling plays a prominent role in plants for coordinating a wide range of developmental processes and responses to environmental cues. Stimulus-specific generation of intracellular calcium transients, decoding of calcium signatures, and transformation of the signal into cellular responses are integral modules of the transduction process. Several hundred proteins with functions in calcium signaling circuits have been identified, and the number of downstream targets of calcium sensors is expected to increase. We previously identified a novel, calmodulin-binding nuclear protein, IQD1, which stimulates glucosinolate accumulation and plant defense in Arabidopsis thaliana. Here, we present a comparative genome-wide analysis of a new class of putative calmodulin target proteins in Arabidopsis and rice. Results We identified and analyzed 33 and 29 IQD1-like genes in Arabidopsis thaliana and Oryza sativa, respectively. The encoded IQD proteins contain a plant-specific domain of 67 conserved amino acid residues, referred to as the IQ67 domain, which is characterized by a unique and repetitive arrangement of three different calmodulin recruitment motifs, known as the IQ, 1-5-10, and 1-8-14 motifs. We demonstrated calmodulin binding for IQD20, the smallest IQD protein in Arabidopsis, which consists of a C-terminal IQ67 domain and a short N-terminal extension. A striking feature of IQD proteins is the high isoelectric point (~10.3) and frequency of serine residues (~11%). We compared the Arabidopsis and rice IQD gene families in terms of gene structure, chromosome location, predicted protein properties and motifs, phylogenetic relationships, and evolutionary history. The existence of an IQD-like gene in bryophytes suggests that IQD proteins are an ancient family of calmodulin-binding proteins and arose during the early evolution of land plants. Conclusion Comparative phylogenetic analyses indicate that the major IQD gene lineages originated before the monocot-eudicot divergence. The extant IQD loci in Arabidopsis primarily resulted from segmental duplication and reflect preferential retention of paralogous genes, which is characteristic for proteins with regulatory functions. Interaction of IQD1 and IQD20 with calmodulin and the presence of predicted calmodulin binding sites in all IQD family members suggest that IQD proteins are a new class of calmodulin targets. The basic isoelectric point of IQD proteins and their frequently predicted nuclear localization suggest that IQD proteins link calcium signaling pathways to the regulation of gene expression. Our comparative genomics analysis of IQD genes and encoded proteins in two model plant species provides the first step towards the functional dissection of this emerging family of putative calmodulin targets.

Abel, Steffen; Savchenko, Tatyana; Levy, Maggie

2005-01-01

234

Origin of plant glycerol transporters by horizontal gene transfer and functional recruitment  

PubMed Central

Gene-family evolution mostly relies on gene duplication coupled with functional diversification of gene products. However, other evolutionary mechanisms may also be important in generating protein diversity. The ubiquitous membrane intrinsic protein (MIP) gene family is an excellent model system to search for such alternative evolutionary mechanisms. MIPs are proteins that transport water, glycerol, and small solutes across cell membranes in all living organisms. We reconstructed the molecular phylogeny of MIPs based on amino acid sequence data by using neighbor-joining, maximum-likelihood, and Bayesian methods of phylogenetic inference. The recovered trees show an early and distinct separation of water and glycerol transporters, i.e., aquaporins (AQPs), and aquaglyceroporins. The latter are absent from plants. As expected, gene duplication and functional diversification account for most of the diversity of animal and plant members of the family. However, in contrast to this model, we find that the sister group of plant glycerol transporters are bacterial AQPs. This relationship suggests first that plant glycerol transporters may resulted from a single event of horizontal gene transfer from bacteria, which we have estimated to have occurred ?1,200 million years ago, at the origin of plants, and second that bacterial AQPs were likely recruited to transport glycerol in plants because of their absence of aquaglyceroporins. This striking example of adaptive evolution at the molecular level was demonstrated further by finding convergent or parallel replacements at particular amino acid positions related to water- and glycerol-transporting specificity.

Zardoya, Rafael; Ding, Xiaodong; Kitagawa, Yoshichika; Chrispeels, Maarten J.

2002-01-01

235

Characterization of a Family of Arabidopsis Genes Related to Xyloglucan Fucosyltransferase11  

PubMed Central

To understand primary cell wall assembly in Arabidopsis, we have focused on identifying and characterizing enzymes involved in xyloglucan biosynthesis. Nine genes (AtFUT2–10) were identified that share between 47% and 62% amino acid similarity with the xyloglucan-specific fucosyltransferase AtFUT1. Reverse transcriptase-PCR analysis indicates that all these genes are expressed. Bioinformatic analysis predicts that these family members are fucosyltransferases, and we first hypothesized that some may also be involved in xyloglucan biosynthesis. AtFUT3, AtFUT4, and AtFUT5 were expressed in tobacco (Nicotiana tabacum L. cv BY2) suspension culture cells, and the resulting proteins did not transfer fucose (Fuc) from GDP-Fuc to tamarind xyloglucan. AtFUT3, AtFUT4, and AtFUT5 were overexpressed in Arabidopsis plants. Leaves of plants overexpressing AtFUT4 or AtFUT5 contained more Fuc than wild-type plants. Stems of plants overexpressing AtFUT4 or AtFUT5 contained more xylose, less arabinose, and less galactose than wild-type plants. We suggest that the AtFUT family is likely to include fucosyltransferases important for the synthesis of wall carbohydrates. A targeted analysis of isolated cell wall matrix components from plants altered in expression of these proteins will help determine their specificity and biological function.

Sarria, Rodrigo; Wagner, Tanya A.; O'Neill, Malcolm A.; Faik, Ahmed; Wilkerson, Curtis G.; Keegstra, Kenneth; Raikhel, Natasha V.

2001-01-01

236

The Vein Patterning 1 (VEP1) Gene Family Laterally Spread through an Ecological Network  

PubMed Central

Lateral gene transfer (LGT) is a major evolutionary mechanism in prokaryotes. Knowledge about LGT— particularly, multicellular— eukaryotes has only recently started to accumulate. A widespread assumption sees the gene as the unit of LGT, largely because little is yet known about how LGT chances are affected by structural/functional features at the subgenic level. Here we trace the evolutionary trajectory of VEin Patterning 1, a novel gene family known to be essential for plant development and defense. At the subgenic level VEP1 encodes a dinucleotide-binding Rossmann-fold domain, in common with members of the short-chain dehydrogenase/reductase (SDR) protein family. We found: i) VEP1 likely originated in an aerobic, mesophilic and chemoorganotrophic ?-proteobacterium, and was laterally propagated through nets of ecological interactions, including multiple LGTs between phylogenetically distant green plant/fungi-associated bacteria, and five independent LGTs to eukaryotes. Of these latest five transfers, three are ancient LGTs, implicating an ancestral fungus, the last common ancestor of land plants and an ancestral trebouxiophyte green alga, and two are recent LGTs to modern embryophytes. ii) VEP1's rampant LGT behavior was enabled by the robustness and broad utility of the dinucleotide-binding Rossmann-fold, which provided a platform for the evolution of two unprecedented departures from the canonical SDR catalytic triad. iii) The fate of VEP1 in eukaryotes has been different in different lineages, being ubiquitous and highly conserved in land plants, whereas fungi underwent multiple losses. And iv) VEP1-harboring bacteria include non-phytopathogenic and phytopathogenic symbionts which are non-randomly distributed with respect to the type of harbored VEP1 gene. Our findings suggest that VEP1 may have been instrumental for the evolutionary transition of green plants to land, and point to a LGT-mediated ‘Trojan Horse’ mechanism for the evolution of bacterial pathogenesis against plants. VEP1 may serve as tool for revealing microbial interactions in plant/fungi-associated environments.

Tarrio, Rosa; Ayala, Francisco J.; Rodriguez-Trelles, Francisco

2011-01-01

237

Functional Characterization of the Plastidic Phosphate Translocator Gene Family from the Thermo-Acidophilic Red Alga Galdieria sulphuraria Reveals Specific Adaptations of Primary Carbon Partitioning in Green Plants and Red Algae1[W][OA  

PubMed Central

In chloroplasts of green plants and algae, CO2 is assimilated into triose-phosphates (TPs); a large part of these TPs is exported to the cytosol by a TP/phosphate translocator (TPT), whereas some is stored in the plastid as starch. Plastidial phosphate translocators have evolved from transport proteins of the host endomembrane system shortly after the origin of chloroplasts by endosymbiosis. The red microalga Galdieria sulphuraria shares three conserved putative orthologous transport proteins with the distantly related seed plants and green algae. However, red algae, in contrast to green plants, store starch in their cytosol, not inside plastids. Hence, due to the lack of a plastidic starch pool, a larger share of recently assimilated CO2 needs to be exported to the cytosol. We thus hypothesized that red algal transporters have distinct substrate specificity in comparison to their green orthologs. This hypothesis was tested by expression of the red algal genes in yeast (Saccharomyces cerevisiae) and assessment of their substrate specificities and kinetic constants. Indeed, two of the three red algal phosphate translocator candidate orthologs have clearly distinct substrate specificities when compared to their green homologs. GsTPT (for G. sulphuraria TPT) displays very narrow substrate specificity and high affinity; in contrast to green plant TPTs, 3-phosphoglyceric acid is poorly transported and thus not able to serve as a TP/3-phosphoglyceric acid redox shuttle in vivo. Apparently, the specific features of red algal primary carbon metabolism promoted the evolution of a highly efficient export system with high affinities for its substrates. The low-affinity TPT of plants maintains TP levels sufficient for starch biosynthesis inside of chloroplasts, whereas the red algal TPT is optimized for efficient export of TP from the chloroplast.

Linka, Marc; Jamai, Aziz; Weber, Andreas P.M.

2008-01-01

238

Expansive evolution of the trehalose-6-phosphate phosphatase gene family in Arabidopsis.  

PubMed

Trehalose is a nonreducing sugar used as a reserve carbohydrate and stress protectant in a variety of organisms. While higher plants typically do not accumulate high levels of trehalose, they encode large families of putative trehalose biosynthesis genes. Trehalose biosynthesis in plants involves a two-step reaction in which trehalose-6-phosphate (T6P) is synthesized from UDP-glucose and glucose-6-phosphate (catalyzed by T6P synthase [TPS]), and subsequently dephosphorylated to produce the disaccharide trehalose (catalyzed by T6P phosphatase [TPP]). In Arabidopsis (Arabidopsis thaliana), 11 genes encode proteins with both TPS- and TPP-like domains but only one of these (AtTPS1) appears to be an active (TPS) enzyme. In addition, plants contain a large family of smaller proteins with a conserved TPP domain. Here, we present an in-depth analysis of the 10 TPP genes and gene products in Arabidopsis (TPPA-TPPJ). Collinearity analysis revealed that all of these genes originate from whole-genome duplication events. Heterologous expression in yeast (Saccharomyces cerevisiae) showed that all encode active TPP enzymes with an essential role for some conserved residues in the catalytic domain. These results suggest that the TPP genes function in the regulation of T6P levels, with T6P emerging as a novel key regulator of growth and development in higher plants. Extensive gene expression analyses using a complete set of promoter-?-glucuronidase/green fluorescent protein reporter lines further uncovered cell- and tissue-specific expression patterns, conferring spatiotemporal control of trehalose metabolism. Consistently, phenotypic characterization of knockdown and overexpression lines of a single TPP, AtTPPG, points to unique properties of individual TPPs in Arabidopsis, and underlines the intimate connection between trehalose metabolism and abscisic acid signaling. PMID:22855938

Vandesteene, Lies; López-Galvis, Lorena; Vanneste, Kevin; Feil, Regina; Maere, Steven; Lammens, Willem; Rolland, Filip; Lunn, John E; Avonce, Nelson; Beeckman, Tom; Van Dijck, Patrick

2012-08-01

239

Expansive Evolution of the TREHALOSE-6-PHOSPHATE PHOSPHATASE Gene Family in Arabidopsis1[W  

PubMed Central

Trehalose is a nonreducing sugar used as a reserve carbohydrate and stress protectant in a variety of organisms. While higher plants typically do not accumulate high levels of trehalose, they encode large families of putative trehalose biosynthesis genes. Trehalose biosynthesis in plants involves a two-step reaction in which trehalose-6-phosphate (T6P) is synthesized from UDP-glucose and glucose-6-phosphate (catalyzed by T6P synthase [TPS]), and subsequently dephosphorylated to produce the disaccharide trehalose (catalyzed by T6P phosphatase [TPP]). In Arabidopsis (Arabidopsis thaliana), 11 genes encode proteins with both TPS- and TPP-like domains but only one of these (AtTPS1) appears to be an active (TPS) enzyme. In addition, plants contain a large family of smaller proteins with a conserved TPP domain. Here, we present an in-depth analysis of the 10 TPP genes and gene products in Arabidopsis (TPPA-TPPJ). Collinearity analysis revealed that all of these genes originate from whole-genome duplication events. Heterologous expression in yeast (Saccharomyces cerevisiae) showed that all encode active TPP enzymes with an essential role for some conserved residues in the catalytic domain. These results suggest that the TPP genes function in the regulation of T6P levels, with T6P emerging as a novel key regulator of growth and development in higher plants. Extensive gene expression analyses using a complete set of promoter-?-glucuronidase/green fluorescent protein reporter lines further uncovered cell- and tissue-specific expression patterns, conferring spatiotemporal control of trehalose metabolism. Consistently, phenotypic characterization of knockdown and overexpression lines of a single TPP, AtTPPG, points to unique properties of individual TPPs in Arabidopsis, and underlines the intimate connection between trehalose metabolism and abscisic acid signaling.

Vandesteene, Lies; Lopez-Galvis, Lorena; Vanneste, Kevin; Feil, Regina; Maere, Steven; Lammens, Willem; Rolland, Filip; Lunn, John E.; Avonce, Nelson; Beeckman, Tom; Van Dijck, Patrick

2012-01-01

240

Estimating the tempo and mode of gene family evolution from comparative genomic data  

Microsoft Academic Search

Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible to estimate ancestral states or to infer upon which lineages gene families have contracted or expanded. In addition, large differences in family size have generally been

Matthew W. Hahn; Tijl De Bie; Jason E. Stajich; Chi Nguyen; Nello Cristianini

2005-01-01

241

Update on the Kelch-like (KLHL) gene family.  

PubMed

The Kelch-like (KLHL) gene family encodes a group of proteins that generally possess a BTB/POZ domain, a BACK domain, and five to six Kelch motifs. BTB domains facilitate protein binding and dimerization. The BACK domain has no known function yet is of functional importance since mutations in this domain are associated with disease. Kelch domains form a tertiary structure of ?-propellers that have a role in extracellular functions, morphology, and binding to other proteins. Presently, 42 KLHL genes have been classified by the HUGO Gene Nomenclature Committee (HGNC), and they are found across multiple human chromosomes. The KLHL family is conserved throughout evolution. Phylogenetic analysis of KLHL family members suggests that it can be subdivided into three subgroups with KLHL11 as the oldest member and KLHL9 as the youngest. Several KLHL proteins bind to the E3 ligase cullin 3 and are known to be involved in ubiquitination. KLHL genes are responsible for several Mendelian diseases and have been associated with cancer. Further investigation of this family of proteins will likely provide valuable insights into basic biology and human disease. PMID:23676014

Dhanoa, Bajinder S; Cogliati, Tiziana; Satish, Akhila G; Bruford, Elspeth A; Friedman, James S

2013-05-15

242

Evolutionary Dynamics of the wnt Gene Family: A Lophotrochozoan Perspective  

PubMed Central

The wnt gene family encodes a set of secreted glycoproteins involved in key developmental processes, including cell fate specification and regulation of posterior growth (Cadigan KM, Nusse R. 1997. Wnt signaling: a common theme in animal development. Genes Dev. 11:3286–3305.; Martin BL, Kimelman D. 2009. Wnt signaling and the evolution of embryonic posterior development. Curr Biol. 19:R215–R219.). As for many other gene families, evidence for expansion and/or contraction of the wnt family is available from deuterostomes (e.g., echinoderms and vertebrates [Nusse R, Varmus HE. 1992. Wnt genes. Cell. 69:1073–1087.; Schubert M, Holland LZ, Holland ND, Jacobs DK. 2000. A phylogenetic tree of the Wnt genes based on all available full-length sequences, including five from the cephalochordate amphioxus. Mol Biol Evol. 17:1896–1903.; Croce JC, Wu SY, Byrum C, Xu R, Duloquin L, Wikramanayake AH, Gache C, McClay DR. 2006. A genome-wide survey of the evolutionarily conserved Wnt pathways in the sea urchin Strongylocentrotus purpuratus. Dev Biol. 300:121–131.]) and ecdysozoans (e.g., arthropods and nematodes [Eisenmann DM. 2005. Wnt signaling. WormBook. 1–17.; Bolognesi R, Farzana L, Fischer TD, Brown SJ. 2008. Multiple Wnt genes are required for segmentation in the short-germ embryo of Tribolium castaneum. Curr Biol. 18:1624–1629.]), but little is known from the third major bilaterian group, the lophotrochozoans (e.g., mollusks and annelids [Prud'homme B, Lartillot N, Balavoine G, Adoutte A, Vervoort M. 2002. Phylogenetic analysis of the Wnt gene family. Insights from lophotrochozoan members. Curr Biol. 12:1395.]). To obtain a more comprehensive scenario of the evolutionary dynamics of this gene family, we exhaustively mined wnt gene sequences from the whole genome assemblies of a mollusk (Lottia gigantea) and two annelids (Capitella teleta and Helobdella robusta) and examined them by phylogenetic, genetic linkage, intron–exon structure, and embryonic expression analyses. The 36 wnt genes obtained represent 11, 12, and 9 distinct wnt subfamilies in Lottia, Capitella, and Helobdella, respectively. Thus, two of the three analyzed lophotrochozoan genomes retained an almost complete ancestral complement of wnt genes emphasizing the importance and complexity of this gene family across metazoans. The genome of the leech Helobdella reflects significantly more dynamism than those of Lottia and Capitella, as judged by gene duplications and losses, branch length, and changes in genetic linkage. Finally, we performed a detailed expression analysis for all the Helobdella wnt genes during embryonic development. We find that, although the patterns show substantial overlap during early cleavage stages, each wnt gene has a unique expression pattern in the germinal plate and during tissue morphogenesis. Comparisons of the embryonic expression patterns of the duplicated wnt genes in Helobdella with their orthologs in Capitella reveal extensive regulatory diversification of the duplicated leech wnt genes.

Cho, Sung-Jin; Valles, Yvonne; Giani, Vincent C.; Seaver, Elaine C.; Weisblat, David A.

2010-01-01

243

Contribution of gene conversion in the evolution of the human ?-like globin gene family  

Microsoft Academic Search

Gene conversion is referred to as one of two types of mechanisms known to act on gene families, mainly to maintain their\\u000a sequence homogeneity or, in certain cases, to produce sequence diversity. The concept of gene conversion was established 20\\u000a years ago by researchers working with fungi. A few years later, gene conversion was also observed in the human genome,

Manoussos N. Papadakis; George P. Patrinos

1999-01-01

244

The myrosinase gene family in Arabidopsis thaliana: gene organization, expression and evolution  

Microsoft Academic Search

Myrosinase (thioglucoside glucohydrolase, EC 3.2.3.1.) is in Brassicaceae species such as Brassica napus and Sinapis alba encoded by two differentially expressed gene families, MA and MB, consisting of about 4 and 10 genes, respectively. Southern blot analysis showed that Arabidopsis thaliana contains three myrosinase genes. These genes were isolated from a genomic library and two of them, TGG1 and TGG2,

Jiaping Xue; Mette Jørgensen; Ulla Pihlgren; Lars Rask

1995-01-01

245

Chromosome assignment of eight SOX family genes in chicken  

Microsoft Academic Search

Chromosome locations of the eight SOX family genes, SOX1, SOX2, SOX3, SOX5, SOX9, SOX10, SOX14 and SOX21, were determined in the chicken by fluorescence in situ hybridization. The SOX1 and SOX21 genes were localized to chicken chromosome 1q3.1?q3.2, SOX5 to chromosome 1p1.6?p1.4, SOX10 to chromosome 1p1.6, and SOX3 to chromosome 4p1.2?p1.1. The SOX2 and SOX14 genes were shown to be

A. Kuroiwa; M. Uchikawa; Y. Kamachi; H. Kondoh; C. Nishida-Umehara; J. Masabanda; D. K. Griffin; Y. Matsuda

2002-01-01

246

Chromosome assignment of eight SOX family genes in chicken.  

PubMed

Chromosome locations of the eight SOX family genes, SOX1, SOX2, SOX3, SOX5, SOX9, SOX10, SOX14 and SOX21, were determined in the chicken by fluorescence in situ hybridization. The SOX1 and SOX21 genes were localized to chicken chromosome 1q3.1-->q3.2, SOX5 to chromosome 1p1.6-->p1.4, SOX10 to chromosome 1p1.6, and SOX3 to chromosome 4p1.2-->p1.1. The SOX2 and SOX14 genes were shown to be linked to chromosome 9 using two-colored FISH and chromosome painting, and the SOX9 gene was assigned to a pair of microchromosomes. These results suggest that these SOX genes form at least three clusters on chicken chromosomes. The seven SOX genes, SOX1, SOX2, SOX3, SOX5, SOX10, SOX14 and SOX21 were localized to chromosome segments with homologies to human chromosomes, indicating that the chromosome locations of SOX family genes are highly conserved between chicken and human. PMID:12698002

Kuroiwa, A; Uchikawa, M; Kamachi, Y; Kondoh, H; Nishida-Umehara, C; Masabanda, J; Griffin, D K; Matsuda, Y

2002-01-01

247

Crystallin gene mutations in Indian families with inherited pediatric cataract  

PubMed Central

Purpose Pediatric cataract is the most common form of treatable childhood blindness and is both clinically and genetically heterogeneous. Autosomal dominant and recessive forms of cataract have been reported to be caused by mutations in 22 different genes so far. Of the cataract mutations reported to date, about half the mutations occur in crystallins, a quarter of the mutations in connexins, and the remainder is evenly divided between intrinsic membrane proteins, intermediate filament proteins, and transcription factors. This study is aimed at identification of the spectrum and frequency of crystallin gene mutations in cataractous patients in an Indian population. Methods Genetic analysis was extended to screen the entire coding region of the CRYAA, CRYAB, CRYBA1, CRYBA4, CRYBB1, CRYBB2, CRYBB3, CRYGC, CRYGD, and CRYGS genes using single stranded conformational polymorphism (SSCP) analysis as a screening technique followed by direct sequencing of all subjects that displayed an electrophoretic shift. Results This report describes the first simultaneous mutation analysis of 10 crystallin genes in the same population, represented by 60 south Indian families. The analysis allowed the identification of causative mutations in 10 of the families (three novel and six reported). This includes six missense mutations (CRYAA-R12C, R21W, R54C, CRYAB- A171T, CRYGC-R168W, CRYGS- S39C), two nonsense mutations (CRYBB2- Q155X, CRYGD- R140X), and one splice mutation, which was identified in two families (CRYBA1-IVS3+1G>A). Conclusions Crystallin mutations are responsible for 16.6% of the inherited pediatric cataract in this population. As causative mutations have not been found in many of the families analyzed, this study suggests the presence of further novel genes or sequence elements involved in the pathogenesis of cataract in these families.

Devi, Ramachandran Ramya; Yao, Wenliang; Vijayalakshmi, Perumalsamy; Sergeev, Yuri V.; Sundaresan, Periasamy

2008-01-01

248

Hepatoblastoma and APC gene mutation in familial adenomatous polyposis.  

PubMed Central

BACKGROUND: Hepatoblastoma is a rare, rapidly progressive, usually fatal childhood malignancy, which if confined to the liver can be cured by radical surgical resection. An association between hepatoblastoma and familial adenomatous polyposis (FAP), which is due to germline mutation of the APC (adenomatous polyposis coli) gene, has been confirmed, but correlation with site of APC mutation has not been studied. AIM: To analyse the APC mutational spectrum in FAP families with hepatoblastoma as a possible basis to select kindreds for surveillance. PATIENTS: Eight patients with hepatoblastoma in seven FAP kindreds were compared with 97 families with identified APC gene mutation in a large Registry. METHODS: APC gene mutation was evaluated by RNase protection assay or in vitro synthesis protein assay. The chi 2 test and correlation were used for data analysis. RESULTS: APC gene mutation was identified in all seven FAP kindreds in which an at risk member developed hepatoblastoma. A male predominance was noted (six of eight), similar to literature cases (18 of 25, p < 0.01. Mutations were restricted to codons 141 to 1230, but no significant difference in site of mutation between pedigrees with and without hepatoblastoma was identified. CONCLUSIONS: Hepatoblastoma occurs primarily in boys in FAP kindreds and is associated with germline APC mutation in the 5' end of the gene. However, the site of APC mutation cannot be used to predict occurrence of this extracolonic cancer in FAP pedigrees.

Giardiello, F M; Petersen, G M; Brensinger, J D; Luce, M C; Cayouette, M C; Bacon, J; Booker, S V; Hamilton, S R

1996-01-01

249

Genome-wide characterization of phenylalanine ammonia-lyase gene family in watermelon (Citrullus lanatus).  

PubMed

Phenylalanine ammonia-lyase (PAL), the first enzyme in the phenylpropanoid pathway, plays a critical role in plant growth, development, and adaptation. PAL enzymes are encoded by a gene family in plants. Here, we report a genome-wide search for PAL genes in watermelon. A total of 12 PAL genes, designated ClPAL1-12, are identified . Nine are arranged in tandem in two duplication blocks located on chromosomes 4 and 7, and the other three ClPAL genes are distributed as single copies on chromosomes 2, 3, and 8. Both the cDNA and protein sequences of ClPALs share an overall high identity with each other. A phylogenetic analysis places 11 of the ClPALs into a separate cucurbit subclade, whereas ClPAL2, which belongs to neither monocots nor dicots, may serve as an ancestral PAL in plants. In the cucurbit subclade, seven ClPALs form homologous pairs with their counterparts from cucumber. Expression profiling reveals that 11 of the ClPAL genes are expressed and show preferential expression in the stems and male and female flowers. Six of the 12 ClPALs are moderately or strongly expressed in the fruits, particularly in the pulp, suggesting the potential roles of PAL in the development of fruit color and flavor. A promoter motif analysis of the ClPAL genes implies redundant but distinctive cis-regulatory structures for stress responsiveness. Finally, duplication events during the evolution and expansion of the ClPAL gene family are discussed, and the relationships between the ClPAL genes and their cucumber orthologs are estimated. PMID:23546528

Dong, Chun-Juan; Shang, Qing-Mao

2013-04-02

250

Molecular and functional analysis of new members of the wheat PR4 gene family.  

PubMed

Five new genes belonging to the pathogenesis-related (PR) 4 family have been cloned and characterised in Triticum aestivum. Two full-length genes, named wPR4e and wPR4f-b, were isolated by library screening, demonstrating the presence of a small intron only in wPR4f-b. Two other PR4 genes (wPR4f-a and wPR4f-c) were isolated by PCR, showing very high sequence identity with wPR4f-b and constituting a new sub-family. Transcription start analysis was performed by RLM-RACE, leading to the isolation of a fifth gene, named wPR4g, that is highly homologous to wPR4e; both encode putative vacuolar PR4 proteins (Wheatwin7 and Wheatwin5, respectively). wPR4e and wPR4f sub-family genes are induced by F. culmorum infection, by chemicals that lead to systemic acquired resistance and by wounding, showing different spatial and temporal induction pathways. In silico analysis of the 5' untranslated regions of wPR4e and wPR4f-b revealed the presence of several abiotic and biotic stress-responsive elements. wPR4e and wPR4f-b putative promoters were fused to the beta-glucuronidase (GUS) reporter gene, and transient and stable expression assays demonstrated that both are able to drive expression of GUS. Characterisation of these new PR4 genes and particularly of their 5' untranslated regions, as well as the determination of their expression patterns, will contribute to our understanding of the responsiveness of this gene family to various stress conditions and of its role in plant defence. PMID:16895481

Bertini, Laura; Cascone, Annunziata; Tucci, Marina; D'Amore, Rosalinda; Di Berardino, Iris; Buonocore, Vincenzo; Caporale, Carlo; Caruso, Carla

2006-08-01

251

Genomic Organization and Control of the Grb7 Gene Family  

PubMed Central

Grb7 and their related family members Grb10 and Grb14 are adaptor proteins, which participate in the functionality of multiple signal transduction pathways under the control of a variety of activated tyrosine kinase receptors and other tyrosine-phosphorylated proteins. They are involved in the modulation of important cellular and organismal functions such as cell migration, cell proliferation, apoptosis, gene expression, protein degradation, protein phosphorylation, angiogenesis, embryonic development and metabolic control. In this short review we shall describe the organization of the genes encoding the Grb7 protein family, their transcriptional products and the regulatory mechanisms implicated in the control of their expression. Finally, the alterations found in these genes and the mechanisms affecting their expression under pathological conditions such as cancer, diabetes and some congenital disorders will be highlighted.

Lucas-Fernandez, E; Garcia-Palmero, I; Villalobo, A

2008-01-01

252

Genome-Wide Analysis of LIM Gene Family in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa  

PubMed Central

Abstract In Eukaryotes, LIM proteins act as developmental regulators in basic cellular processes such as regulating the transcription or organizing the cytoskeleton. The LIM domain protein family in plants has mainly been studied in sunflower and tobacco plants, where several of its members exhibit a specific pattern of expression in pollen. In this paper, we finely characterized in poplar six transcripts encoding these proteins. In Populus trichocarpa genome, the 12 LIM gene models identified all appear to be duplicated genes. In addition, we describe several new LIM domain proteins deduced from Arabidopsis and rice genomes, raising the number of LIM gene models to six for both species. Plant LIM genes have a core structure of four introns with highly conserved coding regions. We also identified new LIM domain proteins in several other species, and a phylogenetic analysis of plant LIM proteins reveals that they have undergone one or several duplication events during the evolution. We gathered several LIM protein members within new monophyletic groups. We propose to classify the plant LIM proteins into four groups: ?LIM1, ?LIM1, ?LIM2, and ?LIM2, subdivided according to their specificity to a taxonomic class and/or to their tissue-specific expression. Our investigation of the structure of the LIM domain proteins revealed that they contain many conserved motifs potentially involved in their function.

Arnaud, Dominique; Dejardin, Annabelle; Leple, Jean-Charles; Lesage-Descauses, Marie-Claude; Pilate, Gilles

2007-01-01

253

Population- and Family-Based Studies Associate the "MTHFR" Gene with Idiopathic Autism in Simplex Families  

ERIC Educational Resources Information Center

|Two methylenetetrahydrofolate reductase gene ("MTHFR") functional polymorphisms were studied in 205 North American simplex (SPX) and 307 multiplex (MPX) families having one or more children with an autism spectrum disorder. Case-control comparisons revealed a significantly higher frequency of the low-activity 677T allele, higher prevalence of the…

Liu, Xudong; Solehdin, Fatima; Cohen, Ira L.; Gonzalez, Maripaz G.; Jenkins, Edmund C.; Lewis, M. E. Suzanne; Holden, Jeanette J. A.

2011-01-01

254

A large and functionally diverse family of Fad2 genes in safflower (Carthamus tinctorius L.)  

PubMed Central

Background The application and nutritional value of vegetable oil is highly dependent on its fatty acid composition, especially the relative proportion of its two major fatty acids, i.e oleic acid and linoleic acid. Microsomal oleoyl phosphatidylcholine desaturase encoded by FAD2 gene is known to introduce a double bond at the ?12 position of an oleic acid on phosphatidylcholine and convert it to linoleic acid. The known plant FAD2 enzymes are encoded by small gene families consisting of 1-4 members. In addition to the classic oleate ?12-desaturation activity, functional variants of FAD2 that are capable of undertaking additional or alternative acyl modifications have also been reported in a limited number of plant species. In this study, our objective was to identify FAD2 genes from safflower and analyse their differential expression profile and potentially diversified functionality. Results We report here the characterization and functional expression of an exceptionally large FAD2 gene family from safflower, and the temporal and spatial expression profiles of these genes as revealed through Real-Time quantitative PCR. The diversified functionalities of some of the safflower FAD2 gene family members were demonstrated by ectopic expression in yeast and transient expression in Nicotiana benthamiana leaves. CtFAD2-1 and CtFAD2-10 were demonstrated to be oleate desaturases specifically expressed in developing seeds and flower head, respectively, while CtFAD2-2 appears to have relatively low oleate desaturation activity throughout the plant. CtFAD2-5 and CtFAD2-8 are specifically expressed in root tissues, while CtFAD2-3, 4, 6, 7 are mostly expressed in the cotyledons and hypocotyls in young safflower seedlings. CtFAD2-9 was found to encode a novel desaturase operating on C16:1 substrate. CtFAD2-11 is a tri-functional enzyme able to introduce a carbon double bond in either cis or trans configuration, or a carbon triple (acetylenic) bond at the ?12 position. Conclusions In this study, we isolated an unusually large FAD2 gene family with 11 members from safflower. The seed expressed FAD2 oleate ?12 desaturase genes identified in this study will provide candidate targets to manipulate the oleic acid level in safflower seed oil. Further, the divergent FAD2 enzymes with novel functionality could be used to produce rare fatty acids, such as crepenynic acid, in genetically engineered crop plants that are precursors for economically important phytoalexins and oleochemical products.

2013-01-01

255

Effects of the Family Environment: Gene-Environment Interaction and Passive Gene-Environment Correlation  

ERIC Educational Resources Information Center

|The classical twin study provides a useful resource for testing hypotheses about how the family environment influences children's development, including how genes can influence sensitivity to environmental effects. However, existing statistical models do not account for the possibility that children can inherit exposure to family environments…

Price, Thomas S.; Jaffee, Sara R.

2008-01-01

256

Reproduction on orbit by plants in the Brassicaceae family  

NASA Astrophysics Data System (ADS)

Previous studies on growth and development during spaceflight had indicated that the transition from vegetative to reproductive growth was particularly difficult for plants. Our objective has been to study how the spaceflight environment impacts the different steps in plant reproduction. This goal has been pursued in two general ways: by using plants that had been pre-grown to the flowering stage on earth, and by using plants that developed completely on orbit. Our objectives have been met by a combination of experiments that required essentially no crew time on orbit, and those that required an extensive commitment of crew time. The plants chosen for the studies were closely related members of the family Brassicaceae: Arabidopsis thaliana and Brassica rapa. In a series of short-duration experiments with Arabidopsis on the space shuttle we found that depletion of carbon dioxide in closed chambers resulted in aborted development of both the male and female reproductive apparatus in microgravity. Normal development was restored by addition of carbon dioxide or by providing air flow. A subsequent shuttle experiment with Brassica utilizing hardware that provides a vigorous air flow confirmed embryo development following pollination on orbit. Brassica plants grown from seed on the Mir space station produced seed that germinated and grew when replanted on orbit. Future experiments will determine effects of multiple generations in space.

Musgrave, Mary E.; Kuang, Anxiu; Xiao, Ying; Matthews, Sharon W.

1999-01-01

257

7 CFR 201.56-12 - Miscellaneous plant families.  

Code of Federal Regulations, 2010 CFR

... Carrot family, Apiaceae (Umbelliferae)âcarrot, celery, celeriac, dill, parsley, parsnip; Hemp family, Cannabaceaeâhemp; Dichondra family, Dichondraceaeâdichondra; Geranium family, Geraniaceaeâalfilaria; Mint...

2009-01-01

258

7 CFR 201.56-12 - Miscellaneous plant families.  

Code of Federal Regulations, 2010 CFR

... Carrot family, Apiaceae (Umbelliferae)âcarrot, celery, celeriac, dill, parsley, parsnip; Hemp family, Cannabaceaeâhemp; Dichondra family, Dichondraceaeâdichondra; Geranium family, Geraniaceaeâalfilaria; Mint...

2010-01-01

259

Building blocks for plant gene assembly.  

PubMed

The MultiSite Gateway cloning system, based on site-specific recombination, enables the assembly of multiple DNA fragments in predefined order, orientation, and frame register. To streamline the construction of recombinant genes for functional analysis in plants, we have built a collection of 36 reference Gateway entry clones carrying promoters, terminators, and reporter genes, as well as elements of the LhG4/LhGR two-component system. This collection obeys simple engineering rules. The genetic elements (parts) are designed in a standard format. They are interchangeable, fully documented, and can be combined at will according to the desired output. We also took advantage of the MultiSite Gateway recombination sites to create vectors in which two or three genes can be cloned simultaneously in separate expression cassettes. To illustrate the flexibility of these core resources for the construction of a wide variety of plant transformation vectors, we generated various transgenes encoding fluorescent proteins and tested their activity in plant cells. The structure and sequence of all described plasmids are accessible online at http://www.psb.ugent.be/gateway/. All accessions can be requested via the same Web site. PMID:17965171

Karimi, Mansour; Bleys, Annick; Vanderhaeghen, Rudy; Hilson, Pierre

2007-10-26

260

Systematic Analysis of Sequences and Expression Patterns of Drought-Responsive Members of the HD-Zip Gene Family in Maize  

Microsoft Academic Search

BackgroundMembers of the homeodomain-leucine zipper (HD-Zip) gene family encode transcription factors that are unique to plants and have diverse functions in plant growth and development such as various stress responses, organ formation and vascular development. Although systematic characterization of this family has been carried out in Arabidopsis and rice, little is known about HD-Zip genes in maize (Zea mays L.).Methods

Yang Zhao; Yuqiong Zhou; Haiyang Jiang; Xiaoyu Li; Defang Gan; Xiaojian Peng; Suwen Zhu; Beijiu Cheng

2011-01-01

261

Plant introductions, hybridization and gene flow.  

PubMed Central

Many regional floras contain a high proportion of recently introduced plant species. Occasionally, hybridization between an introduced species and another species (introduced or native) can result in interspecific gene flow. This may occur even in instances where the F(1) hybrid shows very high sterility, but occasionally produces a few viable gametes. We provide examples of gene flow occurring between some rhododendrons recently introduced to the British flora, and between an introduced and native Senecio species. Neutral molecular markers have normally been employed to obtain evidence of interspecific gene flow, but the challenge now is to isolate and characterize functional introgressed genes and to determine how they affect the fitness of introgressants and whether they improve adaptation to novel habitats allowing introgressants to expand the range of a species. We outline a candidate gene approach for isolating and characterizing an allele of the RAY gene in Senecio vulgaris, which is believed to have introgressed from S. squalidus, and which causes the production of ray florets in flower heads. We discuss the effects of this introgressed allele on individual fitness, including those that originate directly from the production of ray florets plus those that may arise from pleiotropy and/or linkage.

Abbott, Richard J; James, Juliet K; Milne, Richard I; Gillies, Amanda C M

2003-01-01

262

Putting knowledge of plant disease resistance genes to work  

Microsoft Academic Search

Plant disease resistance genes trigger defence mechanisms upon recognition of pathogen compatibility factors, which are encoded by avirulence genes. Isolation of the barley powdery mildew resistance gene Mla opens the door to understanding the extensive allelic diversity of this locus. Completion of the Arabidopsis genome sequence enables the analysis of the complete set of R-gene homologues in a flowering plant.

Jonathan D. G Jones

2001-01-01

263

Plant cells contain a novel member of the retinoblastoma family of growth regulatory proteins.  

PubMed Central

The product of the retinoblastoma susceptibility gene (Rb) controls the passage of mammalian cells through G1 phase. Animal virus oncoproteins interact with the Rb protein via an LXCXE motif and disrupt Rb-E2F complexes, driving cells into S-phase. Recently, we found that the RepA protein of a plant geminivirus contains an LXCXE motif that is essential for its function, a finding that predicts the existence of Rb-related proteins in plant cells. Here we report the isolation of a maize cDNA clone encoding a protein (ZmRb1) which, based on structural and functional studies, is closely related to the mammalian Rb family of growth regulatory proteins. ZmRb1 shows a high degree of amino acid conservation when compared with animal Rb members, particularly in the A/B 'pocket' domain, but ZmRb1 has a shorter N-terminal domain. ZmRb1 forms stable complexes with plant LXCXE-containing proteins, e.g. geminivirus RepA protein. Geminivirus DNA replication is reduced in plant cells transfected with plasmids encoding either ZmRb1 or human p130, a member of the Rb family. This suggests that ZmRb1 controls the G1/S transit in plant cells and is consistent with the fact that geminiviruses need an S-phase environment for DNA replication, as animal DNA tumor viruses do. Our results allow the extension of the Rb family of tumor suppressor proteins to plants and have implications on animal and plant strategies for cell growth control. Images

Xie, Q; Sanz-Burgos, A P; Hannon, G J; Gutierrez, C

1996-01-01

264

A small family of LLS1-related non-heme oxygenases in plants with an origin amongst oxygenic photosynthesizers  

Microsoft Academic Search

Conservation of Lethal-leaf spot 1 (Lls1) lesion mimic gene in land plants including moss is consistent with its recently reported function as pheophorbide a oxygenase (Pao) which catalyzes a key step in chlorophyll degradation (Pruzinska et al., 2003). A bioinformatics survey of complete plant genomes reveals that LLS1(PAO) belongs to a small 5-member family of non-heme oxygenases defined by the

John Gray; Ellen Wardzala; Manli Yang; Steffen Reinbothe; Steve Haller; Florencia Pauli

2004-01-01

265

Genome-wide and molecular evolution analysis of the Poplar KT/HAK/KUP potassium transporter gene family  

PubMed Central

As the largest K+ transport gene family, KT/HAK/KUP family plays an important role in plant growth, development, and stress adaptation. However, there is limited information about this family in woody plant species. In this study, with genome-wide in-depth investigation, 31 Poplar KT/HAK/KUP transporter genes including six pairs of tandem duplicated and eight pairs of segmental duplicated paralogs have been identified, suggesting segmental and tandem duplication events contributed to the expansion of this family in Poplar. The combination of phylogenetic, exon structure and splice site, and paragon analysis revealed 11 pairs of Poplar KT/HAK/KUP duplicates. For these 11 pairs, all pairs are subject to purify selection, and asymmetric evolutionary rates have been found to occur in three pairs. This study might provide more insights into the underlying evolution mechanisms of trees acclimating to their natural habitat.

He, Caiyun; Cui, Kai; Duan, Aiguo; Zeng, Yanfei; Zhang, Jianguo

2012-01-01

266

Early evolution of the LIM homeobox gene family  

SciTech Connect

LIM homeobox (Lhx) transcription factors are unique to the animal lineage and have patterning roles during embryonic development in flies, nematodes and vertebrates, with a conserved role in specifying neuronal identity. Though genes of this family have been reported in a sponge and a cnidarian, the expression patterns and functions of the Lhx family during development in non-bilaterian phyla are not known. We identified Lhx genes in two cnidarians and a placozoan and report the expression of Lhx genes during embryonic development in Nematostella and the demosponge Amphimedon. Members of the six major LIM homeobox subfamilies are represented in the genomes of the starlet sea anemone, Nematostella vectensis, and the placozoan Trichoplax adhaerens. The hydrozoan cnidarian, Hydra magnipapillata, has retained four of the six Lhx subfamilies, but apparently lost two others. Only three subfamilies are represented in the haplosclerid demosponge Amphimedon queenslandica. A tandem cluster of three Lhx genes of different subfamilies and a gene containing two LIM domains in the genome of T. adhaerens (an animal without any neurons) indicates that Lhx subfamilies were generated by tandem duplication. This tandem cluster in Trichoplax is likely a remnant of the original chromosomal context in which Lhx subfamilies first appeared. Three of the six Trichoplax Lhx genes are expressed in animals in laboratory culture, as are all Lhx genes in Hydra. Expression patterns of Nematostella Lhx genes correlate with neural territories in larval and juvenile polyp stages. In the aneural demosponge, A. queenslandica, the three Lhx genes are expressed widely during development, including in cells that are associated with the larval photosensory ring. The Lhx family expanded and diversified early in animal evolution, with all six subfamilies already diverged prior to the cnidarian-placozoan-bilaterian last common ancestor. In Nematostella, Lhx gene expression is correlated with neural territories in larval and juvenile polyp stages. This pattern is consistent with a possible role in patterning the Nematostella nervous system. We propose a scenario in which Lhx genes play a homologous role in neural patterning across eumetazoans.

Srivastava, Mansi; Larroux, Claire; Lu, Daniel R; Mohanty, Kareshma; Chapman, Jarrod; Degnan, Bernard M; Rokhsar, Daniel S

2010-01-01

267

Gene conversions are under purifying selection in the carcinoembryonic antigen immunoglobulin gene families of primates.  

PubMed

The carcinoembryonic antigen (CEA) family contains a large number of glycoproteins belonging to the immunoglobulin superfamily. Here, we investigate whether the gene conversions occurring between primate CEA-related genes are adaptive. Our results show that primate CEA-related genes are subject to frequent and repeated gene conversion events. Furthermore, gene conversions occur most frequently between nearby genes sharing similar sequences, are not more frequent in Ig-like V-type 1 domains than in the Ig-like C2-type 1 domains and dN/dS ratio tests shown that both these domains evolve either neutrally or under purifying selection. Our results therefore suggest that CEA-related genes evolve under purifying selection and the frequent gene conversion events we observed likely represent selectively neutral events between genes having similar sequences and functions. PMID:23867109

Zid, Mouldi; Drouin, Guy

2013-07-15

268

The mammalian PYHIN gene family: Phylogeny, evolution and expression  

PubMed Central

Background Proteins of the mammalian PYHIN (IFI200/HIN-200) family are involved in defence against infection through recognition of foreign DNA. The family member absent in melanoma 2 (AIM2) binds cytosolic DNA via its HIN domain and initiates inflammasome formation via its pyrin domain. AIM2 lies within a cluster of related genes, many of which are uncharacterised in mouse. To better understand the evolution, orthology and function of these genes, we have documented the range of PYHIN genes present in representative mammalian species, and undertaken phylogenetic and expression analyses. Results No PYHIN genes are evident in non-mammals or monotremes, with a single member found in each of three marsupial genomes. Placental mammals show variable family expansions, from one gene in cow to four in human and 14 in mouse. A single HIN domain appears to have evolved in the common ancestor of marsupials and placental mammals, and duplicated to give rise to three distinct forms (HIN-A, -B and -C) in the placental mammal ancestor. Phylogenetic analyses showed that AIM2 HIN-C and pyrin domains clearly diverge from the rest of the family, and it is the only PYHIN protein with orthology across many species. Interestingly, although AIM2 is important in defence against some bacteria and viruses in mice, AIM2 is a pseudogene in cow, sheep, llama, dolphin, dog and elephant. The other 13 mouse genes have arisen by duplication and rearrangement within the lineage, which has allowed some diversification in expression patterns. Conclusions The role of AIM2 in forming the inflammasome is relatively well understood, but molecular interactions of other PYHIN proteins involved in defence against foreign DNA remain to be defined. The non-AIM2 PYHIN protein sequences are very distinct from AIM2, suggesting they vary in effector mechanism in response to foreign DNA, and may bind different DNA structures. The PYHIN family has highly varied gene composition between mammalian species due to lineage-specific duplication and loss, which probably indicates different adaptations for fighting infectious disease. Non-genomic DNA can indicate infection, or a mutagenic threat. We hypothesise that defence of the genome against endogenous retroelements has been an additional evolutionary driver for PYHIN proteins.

2012-01-01

269

The map-1 Gene Family in Root-Knot Nematodes, Meloidogyne spp.: A Set of Taxonomically Restricted Genes Specific to Clonal Species  

PubMed Central

Taxonomically restricted genes (TRGs), i.e., genes that are restricted to a limited subset of phylogenetically related organisms, may be important in adaptation. In parasitic organisms, TRG-encoded proteins are possible determinants of the specificity of host-parasite interactions. In the root-knot nematode (RKN) Meloidogyne incognita, the map-1 gene family encodes expansin-like proteins that are secreted into plant tissues during parasitism, thought to act as effectors to promote successful root infection. MAP-1 proteins exhibit a modular architecture, with variable number and arrangement of 58 and 13-aa domains in their central part. Here, we address the evolutionary origins of this gene family using a combination of bioinformatics and molecular biology approaches. Map-1 genes were solely identified in one single member of the phylum Nematoda, i.e., the genus Meloidogyne, and not detected in any other nematode, thus indicating that the map-1 gene family is indeed a TRG family. A phylogenetic analysis of the distribution of map-1 genes in RKNs further showed that these genes are specifically present in species that reproduce by mitotic parthenogenesis, with the exception of M. floridensis, and could not be detected in RKNs reproducing by either meiotic parthenogenesis or amphimixis. These results highlight the divergence between mitotic and meiotic RKN species as a critical transition in the evolutionary history of these parasites. Analysis of the sequence conservation and organization of repeated domains in map-1 genes suggests that gene duplication(s) together with domain loss/duplication have contributed to the evolution of the map-1 family, and that some strong selection mechanism may be acting upon these genes to maintain their functional role(s) in the specificity of the plant-RKN interactions.

Tomalova, Iva; Iachia, Cathy; Mulet, Karine; Castagnone-Sereno, Philippe

2012-01-01

270

The map-1 gene family in root-knot nematodes, Meloidogyne spp.: a set of taxonomically restricted genes specific to clonal species.  

PubMed

Taxonomically restricted genes (TRGs), i.e., genes that are restricted to a limited subset of phylogenetically related organisms, may be important in adaptation. In parasitic organisms, TRG-encoded proteins are possible determinants of the specificity of host-parasite interactions. In the root-knot nematode (RKN) Meloidogyne incognita, the map-1 gene family encodes expansin-like proteins that are secreted into plant tissues during parasitism, thought to act as effectors to promote successful root infection. MAP-1 proteins exhibit a modular architecture, with variable number and arrangement of 58 and 13-aa domains in their central part. Here, we address the evolutionary origins of this gene family using a combination of bioinformatics and molecular biology approaches. Map-1 genes were solely identified in one single member of the phylum Nematoda, i.e., the genus Meloidogyne, and not detected in any other nematode, thus indicating that the map-1 gene family is indeed a TRG family. A phylogenetic analysis of the distribution of map-1 genes in RKNs further showed that these genes are specifically present in species that reproduce by mitotic parthenogenesis, with the exception of M. floridensis, and could not be detected in RKNs reproducing by either meiotic parthenogenesis or amphimixis. These results highlight the divergence between mitotic and meiotic RKN species as a critical transition in the evolutionary history of these parasites. Analysis of the sequence conservation and organization of repeated domains in map-1 genes suggests that gene duplication(s) together with domain loss/duplication have contributed to the evolution of the map-1 family, and that some strong selection mechanism may be acting upon these genes to maintain their functional role(s) in the specificity of the plant-RKN interactions. PMID:22719916

Tomalova, Iva; Iachia, Cathy; Mulet, Karine; Castagnone-Sereno, Philippe

2012-06-18

271

MORC family ATPases required for heterochromatin condensation and gene silencing.  

PubMed

Transposable elements (TEs) and DNA repeats are commonly targeted by DNA and histone methylation to achieve epigenetic gene silencing. We isolated mutations in two Arabidopsis genes, AtMORC1 and AtMORC6, which cause derepression of DNA-methylated genes and TEs but no losses of DNA or histone methylation. AtMORC1 and AtMORC6 are members of the conserved Microrchidia (MORC) adenosine triphosphatase (ATPase) family, which are predicted to catalyze alterations in chromosome superstructure. The atmorc1 and atmorc6 mutants show decondensation of pericentromeric heterochromatin, increased interaction of pericentromeric regions with the rest of the genome, and transcriptional defects that are largely restricted to loci residing in pericentromeric regions. Knockdown of the single MORC homolog in Caenorhabditis elegans also impairs transgene silencing. We propose that the MORC ATPases are conserved regulators of gene silencing in eukaryotes. PMID:22555433

Moissiard, Guillaume; Cokus, Shawn J; Cary, Joshua; Feng, Suhua; Billi, Allison C; Stroud, Hume; Husmann, Dylan; Zhan, Ye; Lajoie, Bryan R; McCord, Rachel Patton; Hale, Christopher J; Feng, Wei; Michaels, Scott D; Frand, Alison R; Pellegrini, Matteo; Dekker, Job; Kim, John K; Jacobsen, Steven E

2012-05-03

272

A family of genes related to a new expression site-associated gene in Trypanosoma equiperdum.  

PubMed Central

Two genes, belonging to a new expression site-associated gene family of six to eight members in Trypanosoma equiperdum and Trypanosoma brucei, have been cloned from a T. equiperdum variant. One of them, called ESAG-9c, is contained in the 1.78-C expression site and is found just upstream of the 5' barren region. The other one, called ESAG-9u, is unique in the family, is not telomere linked, and apparently is not expression site related. A 2-kb poly(A)+ mRNA is detected with probes for this ESAG-9 family in all T. equiperdum variants examined. By using polymerase chain reaction and restriction fragment length polymorphism techniques, it has been possible to distinguish between ESAG-9c and ESAG-9u and to show that ESAG-9c is transcribed in an expression site-specific manner. However, ESAG-9u (or another gene in the family having identical characteristics) is transcribed in all variants, regardless of the expression site used by these variants. Thus, this ESAG-9 family contains at least one gene that is under expression site control but might have other genes that are not. The function of these ESAG-9 genes is unknown. Transcripts homologous to ESAG-9 were detected in T. brucei bloodstream forms but not in procyclics. Images

Florent, I C; Raibaud, A; Eisen, H

1991-01-01

273

Runx family genes, niche, and stem cell quiescence.  

PubMed

In multicellular organisms, terminally differentiated cells of most tissues are short-lived and therefore require constant replenishment from rapidly dividing stem cells for homeostasis and tissue repair. For the stem cells to last throughout the lifetime of the organism, however, a small subset of stem cells, which are maintained in a hibernation-like state known as stem cell quiescence, is required. Such dormant stem cells reside in the niche and are activated into proliferation only when necessary. A multitude of factors are required for the maintenance of stem cell quiescence and niche. In particular, the Runx family genes have been implicated in stem cell quiescence in various organisms and tissues. In this review, we discuss the maintenance of stem cell quiescence in various tissues, mainly in the context of the Runx family genes, and with special focus on the hematopoietic system. PMID:20144877

Wang, Chelsia Qiuxia; Jacob, Bindya; Nah, Giselle Sek Suan; Osato, Motomi

2010-02-09

274

Evolutionarily conserved gene family important for fat storage.  

PubMed

The ability to store fat in the form of cytoplasmic triglyceride droplets is conserved from Saccharomyces cerevisiae to humans. Although much is known regarding the composition and catabolism of lipid droplets, the molecular components necessary for the biogenesis of lipid droplets have remained obscure. Here we report the characterization of a conserved gene family important for lipid droplet formation named fat-inducing transcript (FIT). FIT1 and FIT2 are endoplasmic reticulum resident membrane proteins that induce lipid droplet accumulation in cell culture and when expressed in mouse liver. shRNA silencing of FIT2 in 3T3-LI adipocytes prevents accumulation of lipid droplets, and depletion of FIT2 in zebrafish blocks diet-induced accumulation of lipid droplets in the intestine and liver, highlighting an important role for FIT2 in lipid droplet formation in vivo. Together these studies identify and characterize a conserved gene family that is important in the fundamental process of storing fat. PMID:18160536

Kadereit, Bert; Kumar, Pradeep; Wang, Wen-Jun; Miranda, Diego; Snapp, Erik L; Severina, Nadia; Torregroza, Ingrid; Evans, Todd; Silver, David L

2007-12-26

275

Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families  

PubMed Central

The taxonomic class of oomycetes contains numerous pathogens of plants and animals but is related to nonpathogenic diatoms and brown algae. Oomycetes have flexible genomes comprising large gene families that play roles in pathogenicity. The evolutionary processes that shaped the gene content have not yet been studied by applying systematic tree reconciliation of the phylome of these species. We analyzed evolutionary dynamics of ten Stramenopiles. Gene gains, duplications, and losses were inferred by tree reconciliation of 18,459 gene trees constituting the phylome with a highly supported species phylogeny. We reconstructed a strikingly large last common ancestor of the Stramenopiles that contained ?10,000 genes. Throughout evolution, the genomes of pathogenic oomycetes have constantly gained and lost genes, though gene gains through duplications outnumber the losses. The branch leading to the plant pathogenic Phytophthora genus was identified as a major transition point characterized by increased frequency of duplication events that has likely driven the speciation within this genus. Large gene families encoding different classes of enzymes associated with pathogenicity such as glycoside hydrolases are formed by complex and distinct patterns of duplications and losses leading to their expansion in extant oomycetes. This study unveils the large-scale evolutionary dynamics that shaped the genomes of pathogenic oomycetes. By the application of phylogenetic based analyses methods, it provides additional insights that shed light on the complex history of oomycete genome evolution and the emergence of large gene families characteristic for this important class of pathogens.

Seidl, Michael F.; Van den Ackerveken, Guido; Govers, Francine; Snel, Berend

2012-01-01

276

Phylogeny and Biogeography of the Carnivorous Plant Family Sarraceniaceae  

PubMed Central

The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniaceae based on seven mitochondrial, nuclear, and plastid loci, which we use to illuminate this family's phylogenetic and biogeographic history. The family and genera are monophyletic: Darlingtonia is sister to a clade consisting of Heliamphora+Sarracenia. Within Sarracenia, two clades were strongly supported: one consisting of S. purpurea, its subspecies, and S. rosea; the other consisting of nine species endemic to the southeastern United States. Divergence time estimates revealed that stem group Sarraceniaceae likely originated in South America 44–53 million years ago (Mya) (highest posterior density [HPD] estimate?=?47 Mya). By 25–44 (HPD?=?35) Mya, crown-group Sarraceniaceae appears to have been widespread across North and South America, and Darlingtonia (western North America) had diverged from Heliamphora+Sarracenia (eastern North America+South America). This disjunction and apparent range contraction is consistent with late Eocene cooling and aridification, which may have severed the continuity of Sarraceniaceae across much of North America. Sarracenia and Heliamphora subsequently diverged in the late Oligocene, 14–32 (HPD?=?23) Mya, perhaps when direct overland continuity between North and South America became reduced. Initial diversification of South American Heliamphora began at least 8 Mya, but diversification of Sarracenia was more recent (2–7, HPD?=?4 Mya); the bulk of southeastern United States Sarracenia originated co-incident with Pleistocene glaciation, <3 Mya. Overall, these results suggest climatic change at different temporal and spatial scales in part shaped the distribution and diversity of this carnivorous plant clade.

Ellison, Aaron M.; Butler, Elena D.; Hicks, Emily Jean; Naczi, Robert F. C.; Calie, Patrick J.; Bell, Charles D.; Davis, Charles C.

2012-01-01

277

The defensin gene family expansion in the tick Ixodes scapularis.  

PubMed

Ixodid ticks transmit a variety of pathogens by blood feeding. Here, we report computational identification of two multigene families of defensin-like peptides (DLPs) in the Ixodes scapularis genome, one corresponding to scapularisin and the other named scasin. Members in the scapularisin family share high sequence similarity to some antibacterial ancient invertebrate-type defensins (AITDs) isolated from primitive insects, arachnids, bivalvia, and fungi whereas scasins represent a novel family of DLPs identified by their overall acidic molecular surface and low sequence similarity to any known defensins. Codon-substitution models support neutral evolution in scapularisins but strong positive selection signal was found throughout the molecules of scasins. The synthetic ?-core region of scapularisin-20 exhibits a wide-spectrum of antimicrobial activity at micromolar concentrations. The finding of extensive gene expansion of DLPs in a vector arachnida may be valuable in the understanding of its role in pathogen transmission. PMID:21540051

Wang, Yanbing; Zhu, Shunyi

2011-04-20

278

Tau gene mutation in familial progressive subcortical gliosis  

Microsoft Academic Search

Familial forms of frontotemporal dementias are associated with mutations in the tau gene. A kindred affected by progressive subcortical gliosis (PSG), a rare form of presenile dementia, has genetic linkage to chromosome 17q21-22 (refs. 1,2, 3). This kindred (PSG-1) is included in the 'frontotemporal dementias and Parkinsonism linked to chromosome 17' group along with kindreds affected by apparently different forms

M. G. Spillantini; R. A. Crowther; S. G. Chen; P. Parchi; M. Tabaton; D. J. Lanska; W. R. Markesbery; K. C. Wilhelmsen; D. W. Dickson; R. B. Petersen; M. Goedert; P. Gambetti

1999-01-01

279

Mutations in RNA Binding Protein Gene Cause Familial Dilated Cardiomyopathy  

PubMed Central

Objectives We sought to identify a novel gene for dilated cardiomyopathy (DCM). Background DCM is a heritable, genetically heterogeneous disorder that remains idiopathic in a majority of patients. Familial cases provide an opportunity to discover unsuspected molecular bases of DCM, enabling preclinical risk detection. Methods Two large families with autosomal dominant DCM were studied. Genome-wide linkage analysis was used to identify a disease locus, followed by fine mapping and positional candidate gene sequencing. Mutation scanning was then performed in 278 unrelated subjects with idiopathic DCM, prospectively identified at the Mayo Clinic. Results Overlapping loci for DCM were independently mapped to chromosome 10q25-q26. DNA sequencing of affected individuals in each family revealed distinct heterozygous missense mutations in exon 9 of RBM20, encoding RNA binding motif protein 20. Comprehensive coding sequence analyses identified missense mutations clustered within this same exon in six additional DCM families. Mutations segregated with DCM (composite logarithm of the odds score >11.49), were absent in 480 control samples, and altered residues within a highly conserved arginine/serine (RS)-rich region. Expression of RBM20 messenger RNA was confirmed in human heart tissue. Conclusions Our findings establish RBM20 as a DCM gene and reveal a mutation hotspot in the RS domain. RBM20 is preferentially expressed in the heart and encodes motifs prototypical of spliceosome proteins that regulate alternative pre-mRNA splicing, thus implicating a functionally distinct gene in human cardiomyopathy. RBM20 mutations are associated with young age at diagnosis, end-stage heart failure, and high mortality.

Brauch, Katharine M.; Karst, Margaret L.; Herron, Kathleen J.; de Andrade, Mariza; Pellikka, Patricia A.; Rodeheffer, Richard J.; Michels, Virginia V.; Olson, Timothy M.

2009-01-01

280

Oncogenic potential of the RUNX gene family: ‘Overview’  

Microsoft Academic Search

Runt-related (RUNX) gene family is composed of three members, RUNX1\\/AML1, RUNX2 and RUNX3, and encodes the DNA-binding (?) subunits of the Runt domain transcription factor polyomavirus enhancer-binding protein 2 (PEBP2)\\/core-binding factor (CBF), which is a heterodimeric transcription factor. RUNX1 is most frequently involved in human acute leukemia. RUNX2 shows oncogenic potential in mouse experimental system. RUNX3 is a strong candidate

Yoshiaki Ito

2004-01-01

281

Familial Dysautonomia Is Caused by Mutations of the IKAP Gene  

Microsoft Academic Search

The defective gene DYS, which is responsible for familial dysautonomia (FD) and has been mapped to a 0.5-cM region on chromosome 9q31, has eluded identification. We identified and characterized the RNAs encoded by this region of chromosome 9 in cell lines derived from individuals homozygous for the major FD haplotype, and we observed that the RNA encoding the IkB kinase

Sylvia L. Anderson; Rocco Coli; Ira W. Daly; Elizabeth A. Kichula; Matthew J. Rork; Sabrina A. Volpi; Josef Ekstein; Berish Y. Rubin

2001-01-01

282

Evolution of the MAGUK protein gene family in premetazoan lineages  

Microsoft Academic Search

BACKGROUND: Cell-to-cell communication is a key process in multicellular organisms. In multicellular animals, scaffolding proteins belonging to the family of membrane-associated guanylate kinases (MAGUK) are involved in the regulation and formation of cell junctions. These MAGUK proteins were believed to be exclusive to Metazoa. However, a MAGUK gene was recently identified in an EST survey of Capsaspora owczarzaki, an unicellular

Alex de Mendoza; Hiroshi Suga; Iñaki Ruiz-Trillo

2010-01-01

283

Four members of the HSP101 gene family are differently regulated in Triticum durum Desf.  

PubMed

Heat shock proteins play an essential role in preventing deleterious effects of high temperatures. In many plants, HSP101 has a central role in heat stress survival. We report the isolation and characterization of four cDNAs corresponding to different members of the durum wheat HSP101 gene family. Expression analysis revealed differences in their induction. Accordingly, durum wheat HSP101 genes are differently regulated, therefore having distinct roles in stress response and thermotolerance acquisition. These findings are important for further dissection of the molecular mechanisms underlying the stress response and for understanding the functions of the HSP101 family members. This information could be important for the exploitation of specific alleles in marker assisted selection for abiotic stress resistance. PMID:17888913

Gullì, Mariolina; Corradi, Massimiliano; Rampino, Patrizia; Marmiroli, Nelson; Perrotta, Carla

2007-09-14

284

Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers  

PubMed Central

Members of the ERF transcription-factor family participate in a number of biological processes, viz., responses to hormones, adaptation to biotic and abiotic stress, metabolism regulation, beneficial symbiotic interactions, cell differentiation and developmental processes. So far, no tissue-expression profile of any cucumber ERF protein has been reported in detail. Recent completion of the cucumber full-genome sequence has come to facilitate, not only genome-wide analysis of ERF family members in cucumbers themselves, but also a comparative analysis with those in Arabidopsis and rice. In this study, 103 hypothetical ERF family genes in the cucumber genome were identified, phylogenetic analysis indicating their classification into 10 groups, designated I to X. Motif analysis further indicated that most of the conserved motifs outside the AP2/ERF domain, are selectively distributed among the specific clades in the phylogenetic tree. From chromosomal localization and genome distribution analysis, it appears that tandem-duplication may have contributed to CsERF gene expansion. Intron/exon structure analysis indicated that a few CsERFs still conserved the former intron-position patterns existent in the common ancestor of monocots and eudicots. Expression analysis revealed the widespread distribution of the cucumber ERF gene family within plant tissues, thereby implying the probability of their performing various roles therein. Furthermore, members of some groups presented mutually similar expression patterns that might be related to their phylogenetic groups.

Hu, Lifang; Liu, Shiqiang

2011-01-01

285

The Phenylalanine Ammonia-Lyase Gene Family in Raspberry. Structure, Expression, and Evolution1  

PubMed Central

In raspberry (Rubus idaeus), development of fruit color and flavor are critically dependent on products of the phenylpropanoid pathway. To determine how these metabolic functions are integrated with the fruit ripening program, we are examining the properties and expression of key genes in the pathway. Here, we report that l- phenylalanine ammonia-lyase (PAL) is encoded in raspberry by a family of two genes (RiPAL1 and RiPAL2). RiPAL1 shares 88% amino acid sequence similarity to RiPAL2, but phylogenetic analysis places RiPAL1 and RiPAL2 in different clusters within the plant PAL gene family. The spatial and temporal expression patterns of the two genes were investigated in various vegetative and floral tissues using the reverse transcriptase competitor polymerase chain reaction assay. Although expression of both genes was detected in all tissues examined, RiPAL1 was associated with early fruit ripening events, whereas expression of RiPAL2 correlated more with later stages of flower and fruit development. Determination of the absolute levels of the two transcripts in various tissues showed that RiPAL1 transcripts were 3- to 10-fold more abundant than those of RiPAL2 in leaves, shoots, roots, young fruits, and ripe fruits. The two RiPAL genes therefore appear to be controlled by different regulatory mechanisms.

Kumar, Amrita; Ellis, Brian E.

2001-01-01

286

The potential of the WRKY gene family for phylogenetic reconstruction: an example from the Malvaceae.  

PubMed

The WRKY gene family of transcription factors is involved in several diverse pathways and includes components of plant-specific, ancient regulatory networks. WRKY genes contain one or two highly conserved DNA binding domains interrupted by an intron. We used partial sequences of five independent WRKY loci to assess their potential for phylogeny reconstruction. Loci were originally isolated from Theobroma cacao L. by PCR with a single pair of degenerate primers; loci-specific primers were subsequently designed. We tested those loci across the sister genera Herrania Goudot and Theobroma L., with Guazuma ulmifolia Lam. as the outgroup. Overall, the combined WRKY matrices performed as well or better than other genes in resolving the intrageneric phylogeny of Herrania and Theobroma. The ease of isolating numerous, independent WRKY loci from diverse plant species with a single pair of degenerate primers designed to the highly conserved WRKY domain, renders them extremely useful tools for generating multiple, single or low copy nuclear loci for molecular phylogenetic studies at lower taxonomic levels. This is the first demonstration of the potential for members of the WRKY gene family for phylogenetic reconstruction. PMID:17681475

Borrone, James W; Meerow, Alan W; Kuhn, David N; Whitlock, Barbara A; Schnell, Raymond J

2007-06-30

287

Phytochrome-mediated differential gene expression of plant Ran\\/TC4 small G-proteins  

Microsoft Academic Search

Ran\\/TC4 is the only known member of the family of small GTP-binding proteins primarily localized inside the nucleus. We cloned\\u000a a pea Ran gene (PsRan1) and characterized its expression in tissues, and under different light sources. PsRan1 is a member of a highly homologous multigene family, and it encodes a protein containing plant-specific amino acids in its\\u000a sequence. It is

Yew Lee; Min-Hee Kim; Seong-Ki Kim; Soo-Hwan Kim

2008-01-01

288

High frequency of the Lebanese allele of the LDLr gene among Brazilian patients with familial hypercholesterolaemia  

Microsoft Academic Search

We analysed the LDL receptor (LDLr) gene in 18 Brazilian patients with familial hypercholesterolaemia (FH) from 10 unrelated families. The combination of a direct search for the Lebanese allele of the LDLr gene by a PCR method and Southern blotting using cDNA probes allowed the identification of the gene defect in six out of 10 families. The Lebanese allele was

M S Figueiredo; J E Dos Santos; F L Alberto; M A Zago

1992-01-01

289

Organization of the human lipoprotein lipase gene and evolution of the lipase gene family  

SciTech Connect

The human lipoprotein lipase gene was cloned and characterized. It is composed of 10 exons spanning {approx} 30 kilobase. The first exon encodes the 5{prime}-untranslated region, the signal peptide plus the first two amino acids of the mature protein. The next eight exons encode the remaining 446 amino acids, and the tenth exon encodes the long 3{prime}-untranslated region of 1948 nucleotides. The lipoprotein lipase transcription start site and the sequence of the 5{prime}-flanking region were also determined. The authors compared the organization of genes for lipoprotein lipase, hepatic lipase, pancreatic lipase, and Drosophila yolk protein 1, which are members of a family of related genes. A model for the evolution of the lipase gene family is presented that involves multiple rounds of gene duplication plus exon-shuffling and intron-loss events.

Kirchgessner, T.G.; Heinzmann, C.; Svenson, K.; Ameis, D.; Lusis, A.J. (Univ. of California, Los Angeles (USA)); Chuat, J.C.; Etienne, J.; Guilhot, S.; Pilon, C.; D'Auriol, L.; Galibert, F. (Laboratoire d'Hematologie Experimentale, Paris (France)); Schotz, M.C. (Univ. of California, Los Angeles (USA) Wadsworth Medical Center, Los Angeles, CA (USA))

1989-12-01

290

Genome-wide and molecular evolution analyses of the phospholipase D gene family in Poplar and Grape  

PubMed Central

Background The Phospholipase D (PLD) family plays an important role in the regulation of cellular processes in plants, including abscisic acid signaling, programmed cell death, root hair patterning, root growth, freezing tolerance and other stress responses. PLD genes constitute an important gene family in higher plants. However, until now our knowledge concerning the PLD gene family members and their evolutionary relationship in woody plants such as Poplar and Grape has been limited. Results In this study, we have provided a genome-wide analysis of the PLD gene family in Poplar and Grape. Eighteen and eleven members of the PLD gene family were identified in Poplar and Grape respectively. Phylogenetic and gene structure analyses showed that the PLD gene family can be divided into 6 subgroups: ?, ?/?, ?, ?, ?, and ?, and that the 6 PLD subgroups originated from 4 original ancestors through a series of gene duplications. Interestingly, the majority of the PLD genes from both Poplar (76.5%, 13/17) and Grape (90.9%, 10/11) clustered closely together in the phylogenetic tree to the extent that their evolutionary relationship appears more tightly linked to each other, at least in terms of the PLD gene family, than it does to either Arabidopsis or rice. Five pairs of duplicated PLD genes were identified in Poplar, more than those in Grape, suggesting that frequent gene duplications occurred after these species diverged, resulting in a rapid expansion of the PLD gene family in Poplar. The majority of the gene duplications in Poplar were caused by segmental duplication and were distinct from those in Arabidopsis, rice and Grape. Additionally, the gene duplications in Poplar were estimated to have occurred from 11.31 to 13.76 million years ago, which are later than those that occurred in the other three plant species. Adaptive evolution analysis showed that positive selection contributed to the evolution of the PXPH- and SP-PLDs, whereas purifying selection has driven the evolution of C2-PLDs that contain a C2 domain in their N-terminal. Analyses have shown that the C2-PLDs generally contain 23 motifs, more than 17 motifs in PXPH-PLDs that contain PX and PH domains in N-terminal. Among these identified motifs, eight, (6, 8, 5, 4, 3, 14, 1 and 19) were shared by both the C2- and PXPH-PLD subfamilies, implying that they may be necessary for PLD function. Five of these shared motifs are located in the central region of the proteins, thus strongly suggesting that this region containing a HKD domain (named after three conserved H, K and D residues) plays a key role in the lipase activity of the PLDs. Conclusion As a first step towards genome wide analyses of the PLD genes in woody plants, our results provide valuable information for increasing our understanding of the function and evolution of the PLD gene family in higher plants.

2010-01-01

291

Plant cytochrome CYP74 family: biochemical features, endocellular localisation, activation mechanism in plant defence and improvements for industrial applications.  

PubMed

Not just another P450: Shown here is a model of the overall structure of CYP74C3 with the putative membrane-binding region that is required for enzyme activation. Members of the CYP74 family of cytochrome P450 enzymes are specialised in the metabolism of hydroperoxides and play an important role in oxylipin metabolism, which is one of the main defence mechanisms employed by plants. In order to respond to their rapidly changing environments, plants have evolved complex signalling pathways, which enable tight control over stress responses. Recent work has shed new light on one of these pathways that involves the different classes of plant oxylipins that are produced through the CYP74 pathway. These phytochemicals play an important role in plant defence, and can act as direct antimicrobials or as signalling molecules that inducing the expression of defence genes. The fine-tuning regulation of defence responses, which depends on the precise cross-talk among different signalling pathways, has important consequences for plant fitness and is a new, challenging area of research. In this review we focus on new data relating to the physiological significance of different phyto-oxylipins and related enzymes. Moreover, recent advances in the biotechnological production of oxylipins are also discussed. PMID:19322850

Hughes, Richard K; De Domenico, Stefania; Santino, Angelo

2009-05-01

292

The Phytocyanin Gene Family in Rice (Oryza sativa L.): Genome-Wide Identification, Classification and Transcriptional Analysis  

PubMed Central

Background Phytocyanins (PCs) are plant-specific blue copper proteins involved in electron transport, and a large number of known PCs are considered to be chimeric arabinogalactan proteins (AGPs). To date there has not been a genome-wide overview of the OsPC gene family. Therefore, as the first step and a useful strategy to elucidate the functions of OsPCs, there is an urgent need for a thorough genome-wide analysis of this gene family. Methodology/Principal Findings In this study, a total of 62 OsPC genes were identified through a comprehensive bioinformatics analysis of the rice (Oryza sativa L.) genome. Based on phylogeny and motif constitution, the family of OsPCs was classified into three subclasses: uclacyanin-like proteins (OsUCLs), stellacyanin-like proteins (OsSCLs) and early nodulin-like proteins (OsENODLs). Structure and glycosylation prediction indicated that 46 OsPCs were glycosylphosphatigylinositol-anchored proteins and 38 OsPCs were chimeric AGPs. Gene duplication analysis revealed that chromosomal segment and tandem duplications contributed almost equally to the expansion of this gene family, and duplication events were mostly happened in the OsUCL subfamily. The expression profiles of OsPC genes were analyzed at different stages of vegetative and reproductive development and under abiotic stresses. It revealed that a large number of OsPC genes were abundantly expressed in the various stages of development. Moreover, 17 genes were regulated under the treatments of abiotic stresses. Conclusions/Significance The genome-wide identification and expression analysis of OsPC genes should facilitate research in this gene family and give new insights toward elucidating their functions in higher plants.

Ma, Haoli; Zhao, Heming; Liu, Zhi; Zhao, Jie

2011-01-01

293

The Classical Arabinogalactan Protein Gene Family of Arabidopsis  

PubMed Central

Arabinogalactan proteins (AGPs) are extracellular proteoglycans implicated in plant growth and development. We searched for classical AGPs in Arabidopsis by identifying expressed sequence tags based on the conserved domain structure of the predicted protein backbone. To confirm that these genes encoded bona fide AGPs, we purified native AGPs and then deglycosylated and deblocked them for N-terminal protein sequencing. In total, we identified 15 genes encoding the protein backbones of classical AGPs, including genes for AG peptides—AGPs with very short backbones (10 to 13 amino acid residues). Seven of the AGPs were verified as AGPs by protein sequencing. A gene encoding a putative cell adhesion molecule with AGP-like domains was also identified. This work provides a firm foundation for beginning functional analysis by using a genetic approach.

Schultz, Carolyn J.; Johnson, Kim L.; Currie, Graeme; Bacic, Antony

2000-01-01

294

The Evolution of Novelty in Conserved Gene Families  

PubMed Central

One of the major aims of contemporary evolutionary biology is the understanding of the current pattern of biological diversity. This involves, first, the description of character distribution at various nodes of the phylogenetic tree of life and, second, the functional explanation of such changes. The analysis of character distribution is a powerful tool at both the morphological and molecular levels. Recent high-throughput sequencing approaches provide new opportunities to study the genetic architecture of organisms at the genome-wide level. In eukaryotes, one overarching finding is the absence of simple correlations of gene count and biological complexity. Instead, the domain architecture of proteins is becoming a central focus for large-scale evolutionary innovations. Here, we review examples of the evolution of novelty in conserved gene families in insects and nematodes. We highlight how in the absence of whole-genome duplications molecular novelty can arise, how members of gene families have diversified at distinct mechanistic levels, and how gene expression can be maintained in the context of multiple innovations in regulatory mechanisms.

Markov, Gabriel V.; Sommer, Ralf J.

2012-01-01

295

Evolutionary dynamism of the primate LRRC37 gene family  

PubMed Central

Core duplicons in the human genome represent ancestral duplication modules shared by the majority of intrachromosomal duplication blocks within a given chromosome. These cores are associated with the emergence of novel gene families in the hominoid lineage, but their genomic organization and gene characterization among other primates are largely unknown. Here, we investigate the genomic organization and expression of the core duplicon on chromosome 17 that led to the expansion of LRRC37 during primate evolution. A comparison of the LRRC37 gene family organization in human, orangutan, macaque, marmoset, and lemur genomes shows the presence of both orthologous and species-specific gene copies in all primate lineages. Expression profiling in mouse, macaque, and human tissues reveals that the ancestral expression of LRRC37 was restricted to the testis. In the hominid lineage, the pattern of LRRC37 became increasingly ubiquitous, with significantly higher levels of expression in the cerebellum and thymus, and showed a remarkable diversity of alternative splice forms. Transfection studies in HeLa cells indicate that the human FLAG-tagged recombinant LRRC37 protein is secreted after cleavage of a transmembrane precursor and its overexpression can induce filipodia formation.

Giannuzzi, Giuliana; Siswara, Priscillia; Malig, Maika; Marques-Bonet, Tomas; Mullikin, James C.; Ventura, Mario; Eichler, Evan E.

2013-01-01

296

A Blumeria graminis gene family encoding proteins with a C-terminal variable region with homologues in pathogenic fungi.  

PubMed

In a study aimed at characterising, at the molecular level, the obligate biotrophic fungus Blumeria graminis f. sp. hordei (Bgh), we have identified a novel group of genes, the Egh16H genes, and shown that two of these are up-regulated during primary infection of barley leaves. The genes have partial homology to a previously characterised Bgh gene family, Egh16. Egh16 and Egh16H are subfamilies of a larger multigene family with presently about 15 members identified in Bgh. Egh16H has about ten members, and we show that five of these are expressed as highly conserved mRNAs that are predicted to encode proteins with a C-terminal variable region. Egh16H has high homology to sequences in Magnaporthe grisea and other plant pathogenic fungi, as well as sequences of both the insect pathogen Metarhizium anisopliae and the human pathogen Aspergillus fumigatus. No close homologues of Egh16H were found in the non-pathogenic fungi Neurospora crassa and Aspergillus nidulans. We predict that Egh16H plays a general role in the interaction between pathogenic fungi and their hosts. At present, the large number of gene family members with C-terminal variation appears to be unique for Bgh, and the Egh16/Egh16H gene family is to our knowledge the largest gene family so far characterised in this fungus. PMID:12853153

Grell, Morten N; Mouritzen, Peter; Giese, Henriette

2003-06-01

297

The evolutionarily conserved porcupine gene family is involved in the processing of the Wnt family.  

PubMed

The Drosophila segment polarity gene product Porcupine (Porc) was first identified as being necessary for processing Wingless (Wg), a Drosophila Wnt (Wnt) family member. Mouse and Xenopus homologs of porc (Mporc and Xporc) were identified and found to encode endoplasmic reticulum (ER) proteins with multiple transmembrane domains. In contrast with porc, four different types of Mporc and Xporc mRNA (A-D) are generated from a single gene by alternative splicing. Mporc mRNA is differentially expressed during embryogenesis and in various adult tissues, demonstrating that the alternative splicing is regulated to synthesize the specific types of Mporc. In transfected mammalian cells, all Mporc types affect the processing of mouse Wnt 1, 3A, 4, 6, and 7B but not 5A. Furthermore, all Mporc types are co-immunoprecipitated with various Wnt proteins. These results suggest that Mporc may function as a chaperone-like molecule for Wnt. Interestingly, all Mporc types can substitute for Porc, as they are able to rescue the phenotypes of Drosophila porc embryos. Consistent with this observation, Mporc, like Porc, modifies the processing of Wg expressed in mammalian cells. These results demonstrate that the porc gene family encodes the multitransmembrane ER proteins, which are evolutionarily well conserved and involved in processing the Wnt family. PMID:10866835

Tanaka, K; Okabayashi, K; Asashima, M; Perrimon, N; Kadowaki, T

2000-07-01

298

Euteleost Fish Genomes are Characterized by Expansion of Gene Families  

PubMed Central

The presence of additional hox clusters in the zebrafish has led to the hypothesis that there was a whole genome duplication at the origin of modern fish. To investigate the generality of this assumption, we analyzed all available actinopterygian fish gene families, and sequenced nuclear receptors from diverse teleost fish. The origin and timing of duplications was systematically determined by phylogenetic analysis. More genes are indeed found in zebrafish than in mouse. This abundance is shared by all major groups of euteleost fish, but not by eels. Phylogenetic analysis shows that it may result from frequent independent duplications, rather than from an ancestral genome duplication. We predict two zebrafish paralogs for most mouse or human genes, thus expressing a note of caution in functional comparison of fish and mammalian genomes. Redundancy appears to be the rule in fish developmental genetics. Finally, our results imply that the outcome of genome projects cannot be extrapolated easily between fish species.

Robinson-Rechavi, Marc; Marchand, Oriane; Escriva, Hector; Bardet, Pierre-Luc; Zelus, Dominique; Hughes, Sandrine; Laudet, Vincent

2001-01-01

299

Genome-wide identification, classification, and expression analysis of CDPK and its closely related gene families in poplar (Populus trichocarpa).  

PubMed

Calcium-dependent protein kinases (CDPKs) are Ca(2+)-binding proteins known to play crucial roles in Ca(2+) signal transduction pathways which have been identified throughout plant kingdom and in certain types of protists. Genome-wide analysis of CDPKs have been carried out in Arabidopsis, rice and wheat, and quite a few of CDPKs were proved to play crucial roles in plant stress responsive signature pathways. In this study, a comprehensive analysis of Populus CDPK and its closely related gene families was performed, including phylogeny, chromosome locations, gene structures, and expression profiles. Thirty Populus CDPK genes and twenty closely related kinase genes were identified, which were phylogenetically clustered into eight distinct subfamilies and predominately distributed across fifteen linkage groups (LG). Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus CDPK gene family. Furthermore, microarray analysis showed that a number of Populus CDPK and its closely related genes differentially expressed across disparate tissues and under various stresses. The expression profiles of paralogous pairs were also investigated to reveal their evolution fates. In addition, quantitative real-time RT-PCR was performed on nine selected CDPK genes to confirm their responses to drought stress treatment. These observations may lay the foundation for future functional analysis of Populus CDPK and its closely related gene families to unravel their biological roles. PMID:23242656

Zuo, Ran; Hu, Ruibo; Chai, Guohua; Xu, Meiling; Qi, Guang; Kong, Yingzhen; Zhou, Gongke

2012-12-15

300

ALCOHOL DEHYDROGENASE IN THE DIPLOID PLANT STEPHANOMERZA EXZGUA (COMPOSITAE) : GENE DUPLICATION. MODE OF INHERITANCE AND LINKAGE  

Microsoft Academic Search

Study of the biochemical genetics of alcohol dehydrogenase (ADH) in the annual plant Stephanameria exigua (Compositae) revealed that the isozymes are specified by a small family of tightly linked structural genes. One set of ADH isozymes (ADH-1) was induced in roots by flooding, and was also ex- pressed in thickened unflooded tap roots, stems, ovaries and seeds. As in other

M. L. ROOSEI; L. D. GOTTLIEB

301

How and Why Do Plants lnactivate Homologous (Trans)genes?  

Microsoft Academic Search

Gene silencing in transgenic plants has emerged in the last 5 years as a topic of intense interest for both applied and basic plant scientists. From the applied side, gene silencing has come as an unwelcome surprise. Early re- views of the prospects for plant genetic engineering did not pinpoint this as a potential obstacle. Rather, the anticipated challenge was

Marjori A. Matzke; Antonius J. M. Matzke

302

Genome-wide analysis of the dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.  

PubMed

The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max). In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs) were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling. PMID:24098807

Guo, Yong; Qiu, Li-Juan

2013-09-30

303

Genome-Wide Analysis of the Dof Transcription Factor Gene Family Reveals Soybean-Specific Duplicable and Functional Characteristics  

PubMed Central

The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max). In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs) were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.

Guo, Yong; Qiu, Li-Juan

2013-01-01

304

An Evolutionarily Conserved Mediator of Plant Disease Resistance Gene Function Is Required for Normal Arabidopsis Development  

Microsoft Academic Search

Plants recognize many pathogens through the action of a diverse family of proteins called disease resistance (R) genes. The Arabidopsis R gene RPM1 encodes resistance to specific Pseudomonas syringae strains. We describe an RPM1-interacting protein that is an ortholog of TIP49a, previously shown to interact with the TATA binding protein (TBP) complex and to modulate c-myc- and ?-catenin-mediated signaling in

Ben F. Holt III; Douglas C. Boyes; Mats Ellerström; Nicholas Siefers; Aaron Wiig; Scott Kauffman; Murray R. Grant; Jeffery L. Dangl

2002-01-01

305

Identification and characterization of TMEM24 family genes in silico.  

PubMed

MLL gene at human chromosome 11q23.3 is frequently rearranged or amplified in hematological malignancies, while PHLDB1, BCL9L, FOXN5 (FOXR1), RNF26, and MFRP genes linked to MLL gene are deleted in neuroblastoma. Here, we characterized the TMEM24 gene family by using bioinformatics. KIAA0285 gene within the 11q23.3 commonly deleted region of neuroblastoma was designated TMEM24, because KIAA0285 gene product was a 707-aa (or 706-aa) protein with N-terminal short cytoplasmic region, single transmembrane domain, and C-terminal large extracellular region. C21orf25 (NM_199050.1) encoded an N-terminally truncated 541-aa protein homologous to TMEM24. Complete coding sequence of C21orf25 was determined by assembling exons 1 and 2 within human genome sequence AP001745 and NM_199050.1 cDNA. Full-length C21orf25 encoded a 696-aa TMEM24-related protein with similar membrane topology. Exon-intron structure was conserved between TMEM24 and C21orf25 genes. TMEM24-ABCG4 locus at human chromosome 11q23.3 and C21orf25-ABCG1 locus at human chromosome 21q22.3 were paralogous regions (paralogons) with insertions of other genes due to recombination during evolution. Mouse 1300006O23 (BC060156.1) and 5830404H04 (NM_174847.1) cDNAs were derived from orthologs of human TMEM24 and C21orf25 genes, respectively. TMEM24 homologous domains (TM24H1 and TM24H2) were identified as novel domains conserved among TMEM24, C21orf25, 1300006O23, and 5830404H04. Human TMEM24, C21orf25 and their mouse homologs were type II transmembrane proteins with extracellular TM24H1 and TM24H2 domains. This is the first report on identification and characterization of the TMEM24 family. PMID:15289880

Katoh, Masuko; Katoh, Masaru

2004-09-01

306

Cancer genetics and genomics of human FOX family genes.  

PubMed

Forkhead-box (FOX) family proteins, involved in cell growth and differentiation as well as embryogenesis and longevity, are DNA-binding proteins regulating transcription and DNA repair. The focus of this review is on the mechanisms of FOX-related human carcinogenesis. FOXA1 is overexpressed as a result of gene amplification in lung cancer, esophageal cancer, ER-positive breast cancer and anaplastic thyroid cancer and is point-mutated in prostate cancer. FOXA1 overexpression in breast cancer and prostate cancer is associated with good or poor prognosis, respectively. Single nucleotide polymorphism (SNP) within the 5'-UTR of the FOXE1 (TTF2) gene is associated with thyroid cancer risk. FOXF1 overexpression in breast cancer is associated with epithelial-to-mesenchymal transition (EMT). FOXM1 is overexpressed owing to gene amplification in basal-type breast cancer and diffuse large B-cell lymphoma (DLBCL), and it is transcriptionally upregulated owing to Hedgehog-GLI, hypoxia-HIF1? or YAP-TEAD signaling activation. FOXM1 overexpression leads to malignant phenotypes by directly upregulating CCNB1, AURKB, MYC and SKP2 and indirectly upregulating ZEB1 and ZEB2 via miR-200b downregulation. Tumor suppressor functions of FOXO transcription factors are lost in cancer cells as a result of chromosomal translocation, deletion, miRNA-mediated repression, AKT-mediated cytoplasmic sequestration or ubiquitination-mediated proteasomal degradation. FOXP1 is upregulated as a result of gene fusion or amplification in DLBCL and MALT lymphoma and also repression of miRNAs, such as miR-1, miR-34a and miR-504. FOXP1 overexpression is associated with poor prognosis in DLBCL, gastric MALT lymphoma and hepatocellular carcinoma but with good prognosis in breast cancer. In neuroblastoma, the entire coding region of the FOXR1 (FOXN5) gene is fused to the MLL or the PAFAH1B gene owing to interstitial deletions. FOXR1 fusion genes function as oncogenes that repress transcription of FOXO target genes. Whole-genome sequencing data from tens of thousands of human cancers will uncover the mutational landscape of FOX family genes themselves as well as FOX-binding sites, which will be ultimately applied for cancer diagnostics, prognostics, and therapeutics. PMID:23022474

Katoh, Masuko; Igarashi, Maki; Fukuda, Hirokazu; Nakagama, Hitoshi; Katoh, Masaru

2012-09-27

307

The New Human Tissue Kallikrein Gene Family: Structure, Function, and Association to Disease  

Microsoft Academic Search

The human tissue kallikrein gene family was, until recently, thought to consist of only three genes. Two of these human kallikreins, prostate-specific antigen and human glandular kallikrein 2, are cur- rently used as valuable biomarkers of prostatic carcinoma. More re- cently, new kallikrein-like genes have been discovered. It is now clear that the human tissue kallikrein gene family contains at

GEORGE M. YOUSEF; ELEFTHERIOS P. DIAMANDIS

2001-01-01

308

Expression of a truncated tomato polygalacturonase gene inhibits expression of the endogenous gene in transgenic plants  

Microsoft Academic Search

Tomato plants were transformed with a chimaeric polygalacturonase (PG) gene, designed to produce a truncated PG transcript constitutively. In these plants expression of the endogenous PG gene was inhibited during ripening, resulting in a substantial reduction in PG mRNA and enzyme accumulation. This inhibition was comparable to that achieved previously using antisense genes. The expression of the truncated gene in

C. J. S. Smith; C. F. Watson; C. R. Bird; J. Ray; W. Schuch; D. Grierson

1990-01-01

309

Evolution and Function of the Plant Cell Wall Synthesis-Related Glycosyltransferase Family 81[W][OA  

PubMed Central

Carbohydrate-active enzyme glycosyltransferase family 8 (GT8) includes the plant galacturonosyltransferase1-related gene family of proven and putative ?-galacturonosyltransferase (GAUT) and GAUT-like (GATL) genes. We computationally identified and investigated this family in 15 fully sequenced plant and green algal genomes and in the National Center for Biotechnology Information nonredundant protein database to determine the phylogenetic relatedness of the GAUTs and GATLs to other GT8 family members. The GT8 proteins fall into three well-delineated major classes. In addition to GAUTs and GATLs, known or predicted to be involved in plant cell wall biosynthesis, class I also includes a lower plant-specific GAUT and GATL-related (GATR) subfamily, two metazoan subfamilies, and proteins from other eukaryotes and cyanobacteria. Class II includes galactinol synthases and plant glycogenin-like starch initiation proteins that are not known to be directly involved in cell wall synthesis, as well as proteins from fungi, metazoans, viruses, and bacteria. Class III consists almost entirely of bacterial proteins that are lipooligo/polysaccharide ?-galactosyltransferases and ?-glucosyltransferases. Sequence motifs conserved across all GT8 subfamilies and those specific to plant cell wall-related GT8 subfamilies were identified and mapped onto a predicted GAUT1 protein structure. The tertiary structure prediction identified sequence motifs likely to represent key amino acids involved in catalysis, substrate binding, protein-protein interactions, and structural elements required for GAUT1 function. The results show that the GAUTs, GATLs, and GATRs have a different evolutionary origin than other plant GT8 genes, were likely acquired from an ancient cyanobacterium (Synechococcus) progenitor, and separate into unique subclades that may indicate functional specialization.

Yin, Yanbin; Chen, Huiling; Hahn, Michael G.; Mohnen, Debra; Xu, Ying

2010-01-01

310

Validation of an NSP-based (negative selection pattern) gene family identification strategy  

PubMed Central

Background Gene family identification from ESTs can be a valuable resource for analysis of genome evolution but presents unique challenges in organisms for which the entire genome is not yet sequenced. We have developed a novel gene family identification method based on negative selection patterns (NSP) between family members to screen EST-generated contigs. This strategy was tested on five known gene families in Arabidopsis to see if individual paralogs could be identified with accuracy from EST data alone when compared to the actual gene sequences in this fully sequenced genome. Results The NSP method uniquely identified family members in all the gene families tested. Two members of the FtsH gene family, three members each of the PAL, RF1, and ribosomal L6 gene families, and four members of the CAD gene family were correctly identified. Additionally all ESTs from the representative contigs when checked against MapViewer data successfully identify the gene locus predicted. Conclusion We demonstrate the effectiveness of the NSP strategy in identifying specific gene family members in Arabidopsis using only EST data and we describe how this strategy can be used to identify many gene families in agronomically important crop species where they are as yet undiscovered.

Frank, Ronald L; Kandoth, Cyriac; Ercal, Fikret

2008-01-01

311

PEN-2 gene mutation in a familial Alzheimer's disease case.  

PubMed

Genetic evidence indicates a central role of cerebral accumulation of beta-amyloid (Abeta) in the pathogenesis of Alzheimer's disease (AD). Beside presenilin 1 and 2, three other recently discovered proteins (Aph 1, PEN 2 and nicastrin) are associated with gamma-secretase activity, the enzymatic complex generating Abeta. Alterations in genes encoding these proteins were candidates for a role in AD. The PEN 2 gene was examined for unknown mutations and polymorphisms in sporadic and familial Alzheimer patients. Samples from age-matched controls (n=253), sporadic AD (SAD, n=256) and familial AD (FAD, n=140) were screened with DHPLC methodology followed by sequencing. Scanning the gene identified for the first time a missense mutation (D90N) in a patient with FAD. Three intronic polymorphisms were also identified, one of which had a higher presence of the mutated allele in AD subjects carrying the allele epsilon4 of apolipoprotein E than controls. The pathogenic role of the PEN-2 D90N mutation in AD is not clear, but the findings might lead to new studies on its functional and genetic role. PMID:16170650

Sala Frigerio, C; Piscopo, P; Calabrese, E; Crestini, A; Malvezzi Campeggi, L; Civita di Fava, R; Fogliarino, S; Albani, D; Marcon, G; Cherchi, R; Piras, R; Forloni, G; Confaloni, A

2005-03-16

312

A Family of MicroRNAs Present in Plants and Animals[W][OA  

PubMed Central

Although many miRNAs are deeply conserved within each kingdom, none are known to be conserved between plants and animals. We identified Arabidopsis thaliana miR854 and miR855, two microRNAs (miRNAs) with multiple binding sites in the 3? untranslated region (3?UTR) of OLIGOURIDYLATE binding PROTEIN1b (At UBP1b), forming miRNA:mRNA interactions similar to those that cause translational repression/mRNA cleavage in animals. At UBP1b encodes a member of a heterogeneous nuclear RNA binding protein (hnRNP) family. The 3?UTR of At UBP1b is sufficient to repress reporter protein expression in tissues expressing miR854 or miR855 (rosette leaves and flowers, respectively) but not where both miRNAs are absent (cauline leaves). Intergenic regions containing sequences closely resembling miR854 are predicted to fold into stable miRNA precursors in animals, and members of the miR854 family are expressed in Caenorhabditis elegans, Mus musculus, and Homo sapiens, all with imperfect binding sites in the 3?UTR of genes encoding the T cell Intracellular Antigen-Related protein, an hnRNP of the UBP1 family. Potential binding sites for miR854 are absent from UBP1-like genes in fungi lacking the miRNA biogenetic machinery. Our results indicate that plants and animals share miRNAs of the miR854 family, suggesting a common origin of these miRNAs as regulators of basal transcriptional mechanisms.

Arteaga-Vazquez, Mario; Caballero-Perez, Juan; Vielle-Calzada, Jean-Philippe

2006-01-01

313

Evolution of multigene families under interchromosomal gene conversion.  

PubMed Central

A model for the evolution of the probabilities of genetic identity within and between loci of a multigene family in a finite population is formulated and investigated. Unbiased interchromosomal gene conversion, equal crossing-over between tandemly repeated genes, random genetic drift, and mutation to new alleles are incorporated. Generations are discrete and nonoverlapping; the diploid, monoecious population mates at random. Formulae for the equilibrium values of the probabilities of identity and for the rate of convergence are deduced. At equilibrium, the amount of intralocus homology, f, always exceeds the amount of interlocus homology, ?. The equilibrium homologies f and ? and the characteristic convergence time T are independent of the crossover rate. As the population size and the number of repeats increase, f and ? decrease and T increases; as the rate of gene conversion increases, f and T decrease whereas ? increases. The time T can be sufficiently short to imply that interchromosomal gene conversion may be an important mechanism for maintaining sequence homogeneity among repeated genes.

Nagylaki, T

1984-01-01

314

Novel alleles among soybean Bowman-Birk proteinase inhibitor gene families.  

PubMed

Trypsin inhibitors have been found in various animals, plants and microorganisms. There were two types of trypsin inhibitors in soybean including Bowman-Birk protease inhibitors (BBI) and Kunitz inhibitors (KTI). The different BBI genes from wild soybean (G. soja) and cultivated soybean (G. max) formed a multigene family. We constructed a cDNA library of cultivar 'SuiNong 14' seed at the R7 growth stage using the SMART Kit. Seventeen contigs or singletons were highly homologous to soybean protease inhibitors. Contigs of 5, 35, 8 and 9 were highly homologous to BBI family members BBI-A1, BBI-A2, BBI-C and BBI-D, respectively. Sequence analyses showed there were novel allelic variations among the 4 BBI members in SuiNong 14. Based on the comparison of soybean seed cDNA libraries from different developmental stages, it was apparent that the expression of trypsin inhibitors increased during seed development in soybean. Phylogenetic analysis of BBI gene sequences among dicotyledonous and monocotyledonous plants demonstrated that these genes shared a common progenitor. PMID:18677596

Wang, Yueping; Chen, Xiongting; Qiu, Lijuan

2008-08-03

315

Overrepresentation of a Gene Family Encoding Extracytoplasmic Solute Receptors in Bordetella  

PubMed Central

A family of genes that are likely to encode extracytoplasmic solute receptors is strongly overrepresented in several ?-proteobacteria, including Bordetella pertussis. This gene family, of which members have been called bug genes, contains some examples that are contained within polycistronic operons coding for tripartite uptake transporters of the TTT family, while the vast majority are “orphan” genes. Proteomic and functional analyses demonstrated that several of these genes are expressed in B. pertussis, and one is involved in citrate uptake. The bug genes probably form an ancient family that has been subjected to a large expansion in a restricted phylogenic group.

Antoine, Rudy; Jacob-Dubuisson, Francoise; Drobecq, Herve; Willery, Eve; Lesjean, Sarah; Locht, Camille

2003-01-01

316

Living With Her Genes Early Onset Familial Alzheimer's Disease  

NSDL National Science Digital Library

When a 30-year-old genetic counselor learns that her 38-year-old sister has developed early onset familial Alzheimer’s disease (EOFAD), a dominantly inherited disorder that led to their father's death at age 42, she struggles with whether to undergo genetic testing and whether to have children. This interrupted case study examines the impact of genetic testing on people and their families when there is no treatment or cure for a disease. It covers principles of Mendelian inheritance as well as genetic and reproductive technologies ,such as gene tests, pre-implantation genetic diagnosis, and in vitro fertilization. It can be used in introductory biology courses for both majors and non-majors or adapted for more advanced courses in genetics and molecular biology.

Gildensoph, Lynne H.; Stanford, Alice M.; Wygal, Deborah D.

2008-01-01

317

Comparative genomics of gene-family size in closely related bacteria  

PubMed Central

Background The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. Results The relative content of paralogous genes in bacterial genomes increases with genome size, largely due to the expansion of gene family size in large genomes. Bacteria undergoing genome reduction display a parallel process of redundancy elimination, by which gene families are reduced to one or a few members. Gene family size is also influenced by sequence divergence and physiological function. Large gene families show wider sequence divergence, suggesting they are probably older, and certain functions (such as metabolite transport mechanisms) are overrepresented in large families. The size of a given gene family is remarkably similar in strains of the same species and in closely related species, suggesting that homologous gene families are vertically transmitted and depend little on horizontal gene transfer (HGT). Conclusions The remarkable preservation of copy numbers in widely different ecotypes indicates a functional role for the different copies rather than simply a back-up role. When different genera are compared, the increase in phylogenetic distance and/or ecological specialization disrupts this preservation, albeit in a gradual manner and maintaining an overall similarity, which also supports this view. HGT can have an important role, however, in nonhomologous gene families, as exemplified by a comparison between saprophytic and enterohemorrhagic strains of Escherichia coli.

Pushker, Ravindra; Mira, Alex; Rodriguez-Valera, Francisco

2004-01-01

318

11. PUMP ROOM FLOOR OF GENE PLANT FROM NORTH END, ...  

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

11. PUMP ROOM FLOOR OF GENE PLANT FROM NORTH END, CENTRIFUGAL PUMPS DESIGNED BY BYRON JACKSON CO., MANUFACTURED BY PELTON WATER WHEEL CO. OF SAN FRANCISCO. POWERED BY G.E. SYNCHRONOUS MOTOR 9000 HP, 6900 VOLTS, 612 AMPS, 7320 KVA, 3 PHASE, 60 CYCLES, 400 RPM, EXCITATION AT 125 VOLTS, 540 AMPS. - Gene Pump Plant, South of Gene Wash Reservoir, 2 miles west of Whitsett Pump Plant, Parker Dam, San Bernardino County, CA

319

Evolution of the Vertebrate Paralemmin Gene Family: Ancient Origin of Gene Duplicates Suggests Distinct Functions  

PubMed Central

Paralemmin-1 is a protein implicated in plasma membrane dynamics, the development of filopodia, neurites and dendritic spines, as well as the invasiveness and metastatic potential of cancer cells. However, little is known about its mode of action, or about the biological functions of the other paralemmin isoforms: paralemmin-2, paralemmin-3 and palmdelphin. We describe here evolutionary analyses of the paralemmin gene family in a broad range of vertebrate species. Our results suggest that the four paralemmin isoform genes (PALM1, PALM2, PALM3 and PALMD) arose by quadruplication of an ancestral gene in the two early vertebrate genome duplications. Paralemmin-1 and palmdelphin were further duplicated in the teleost fish specific genome duplication. We identified a unique sequence motif common to all paralemmins, consisting of 11 highly conserved residues of which four are invariant. A single full-length paralemmin homolog with this motif was identified in the genome of the sea lamprey Petromyzon marinus and an isolated putative paralemmin motif could be detected in the genome of the lancelet Branchiostoma floridae. This allows us to conclude that the paralemmin gene family arose early and has been maintained throughout vertebrate evolution, suggesting functional diversification and specific biological roles of the paralemmin isoforms. The paralemmin genes have also maintained specific features of gene organisation and sequence. This includes the occurrence of closely linked downstream genes, initially identified as a readthrough fusion protein with mammalian paralemmin-2 (Palm2-AKAP2). We have found evidence for such an arrangement for paralemmin-1 and -2 in several vertebrate genomes, as well as for palmdelphin and paralemmin-3 in teleost fish genomes, and suggest the name paralemmin downstream genes (PDG) for this new gene family. Thus, our findings point to ancient roles for paralemmins and distinct biological functions of the gene duplicates.

Hultqvist, Greta; Ocampo Daza, Daniel; Larhammar, Dan; Kilimann, Manfred W.

2012-01-01

320

The MAPKKK Gene Family in Gossypium raimondii: Genome-Wide Identification, Classification and Expression Analysis  

PubMed Central

Mitogen-activated protein kinase (MAPK) cascades are conserved signal transduction pathways in all eukaryotic organisms. MAPKKKs (MAPK kinase kinases) operate at the top levels of these cascades. Recently, this family of genes has been systematically investigated in Arabidopsis, rice and maize, but has not yet been characterized in cotton. In this study, we identified 78 putative MAPKKK genes in the genome of the diploid cotton, Gossypium raimondii. They were classified into three subfamilies, of which 12 were ZIK, 22 were MEKK and 44 were Raf. The ZIK and MEKK genes displayed a scattered genomic distribution across 11 of the 13 chromosomes, whereas Raf genes were distributed across the entire genome. Their conserved patterns observed for introns and additional domains were consistent with the evolutionary relationships inferred from the phylogenetic analysis within subfamily. Transcriptome sequencing data were used to investigate their transcript profiles in mature leaves, 0 day and 3 days post-anthesis (DPA) ovules. Sixty MAPKKK genes were expressed, of which 41 were strongly expressed in mature leaves. Twelve MAPKKK genes were more highly expressed in 3-DPA ovules than in 0-DPA ovules. Our results provide a foundation for future evolutionary and functional characterizations of MAPKKK genes in cotton and probably other Gossypium plants.

Yin, Zujun; Wang, Junjuan; Wang, Delong; Fan, Weili; Wang, Shuai; Ye, Wuwei

2013-01-01

321

Genome-wide identification and expression profile of homeodomain-leucine zipper Class I gene family in Cucumis sativus.  

PubMed

The HD-Zip proteins comprise one of the largest families of transcription factors in plants. HD-Zip genes have been grouped into four different classes: HD-Zip I to IV. In this study, we described the identification and structural characterization of Class I HD-Zip genes in cucumber. A complete set of 13 HD-Zip I genes were identified in the cucumber genome using Blast search tools and phylogeny. The cucumber HD-Zip I family contained a smaller number of identified genes compared to other higher plants such as Arabidopsis and maize due to the absence of recent gene duplication events. Chromosomal location of these genes revealed that they are distributed unevenly across 5 of 7 chromosomes. Tissue-specific expression profiles showed that 13 cucumber HD-Zip I genes were expressed in at least one of the tissues, which suggested that cucumber HD-Zip I genes took part in many cellular processes. The transcript abundance level analysis during abiotic stress conditions (NaCl, ABA and low temperature treatments) identified a group of HD-Zip I genes that responded to one or more treatments. PMID:24013079

Liu, Wei; Fu, Rao; Li, Qiang; Li, Jing; Wang, Lina; Ren, Zhonghai

2013-09-05

322

Analysis of genetically modified plant gene expression using GUS fluorimetry  

Microsoft Academic Search

A fluorimetric assay method for the analysis of beta-glucuronidase (GUS) reporter gene expression in genetically modified\\u000a plants is described. Optimization of this method for woody plants and a statistical approach suitable for comparisons of gene\\u000a expression in different transformants or tissues of the same plant is described. Example data from elm (Ulmus procera) SR4 regenerant plants, shown to be genetically

Kevan M. A. Gartland; Angela T. McHugh; Stanislav Vitha; Karel Benes; Richard J. Irvine; Jill S. Gartland

2000-01-01

323

The multi-protein family of Arabidopsis sulphotransferases and their relatives in other plant species.  

PubMed

All members of the sulphotransferase (SOT, EC 2.8.2.-) protein family use 3'-phosphoadenosine 5'-phosphosulphate (PAPS) as the sulphuryl donor and transfer the sulphonate group to an appropriate hydroxyl group of several classes of substrates. These enzymes have highly conserved domains and can be found in eubacteria and eukaryotes. In mammals, sulphate conjugation catalysed by SOTs constitutes an important reaction in the transformation of xenobiotics, and in the modulation of the biological activity of steroid hormones and neurotransmitters. In plants, sulphate-conjugation reactions seem to play an important role in plant growth, development, and adaptation to stress. To date only a few plant SOTs have been characterized in detail. The flavonol 3- and 4'-SOTs from Flaveria species (Asteraceae), which catalyse the sulphonation of flavonol aglycones and flavonol 3-sulphates, respectively, were the first plant SOTs for which cDNA clones were isolated. The plasma membrane associated gallic acid SOT of Mimosa pudica L. pulvini cells may be intrinsic to signalling events that modify the seismonastic response. In Brassica napus L. a SOT catalyses the O-sulphonation of brassinosteroids and thereby abolishes specifically the biological activity of 24-epibrassinolide. The fully sequenced genome of Arabidopsis thaliana Heynh. contains in total 18 genes that are likely to encode SOT proteins based on sequence similarities of the translated products with an average identity of 51.1%. So far only one SOT from A. thaliana (At5g07000) was functionally characterized: the protein was shown to catalyse the sulphonation of 12-hydroxyjasmonate and thereby inactivate excess jasmonic acid in plants. The substrates and, therefore, the physiological roles of SOTs are very diverse. By using the numerous informative databases and methods available for the model plant A. thaliana, the elucidation of the functional role of the SOT protein family will be accelerated. PMID:15234990

Klein, Marion; Papenbrock, Jutta

2004-07-02

324

Plant disease resistance genes: recent insights and potential applications  

Microsoft Academic Search

Plant disease resistance genes (R genes) encode proteins that detect pathogens. R genes have been used in resistance breeding programs for decades, with varying degrees of success. Recent molecular research on R proteins and downstream signal transduction networks has provided exciting insights, which will enhance the use of R genes for disease control. Definition of conserved structural motifs in R

John M. McDowell; Bonnie J. Woffenden

2003-01-01

325

IDENTIFICATION AND CHARACTERIZATION OF THERMOBIFIDA FUSCA GENES INVOLVED IN PLANT CELL WALL DEGRADATION.  

SciTech Connect

Micro-array experiments identified a number of Thermobifida fusca genes which were upregulated by growth on cellulose or plant biomass. Five of these genes were cloned, overexpressed in E. coli and the expressed proteins were purified and characterized. These were a xyloglucanase,a 1-3,beta glucanase, a family 18 hydrolase and twocellulose binding proteins that contained no catalytic domains. The catalyic domain of the family 74 endoxyloglucanase with a C-terminal, cellulose binding module was crystalized and its 3-dimensional structure was determined by X-ray crystallography.

David B. Wilson

2006-01-23

326

A Gene Family Derived from Transposable Elements during Early Angiosperm Evolution Has Reproductive Fitness Benefits in Arabidopsis thaliana  

PubMed Central

The benefits of ever-growing numbers of sequenced eukaryotic genomes will not be fully realized until we learn to decipher vast stretches of noncoding DNA, largely composed of transposable elements. Transposable elements persist through self-replication, but some genes once encoded by transposable elements have, through a process called molecular domestication, evolved new functions that increase fitness. Although they have conferred numerous adaptations, the number of such domesticated transposable element genes remains unknown, so their evolutionary and functional impact cannot be fully assessed. Systematic searches that exploit genomic signatures of natural selection have been employed to identify potential domesticated genes, but their predictions have yet to be experimentally verified. To this end, we investigated a family of domesticated genes called MUSTANG (MUG), identified in a previous bioinformatic search of plant genomes. We show that MUG genes are functional. Mutants of Arabidopsis thaliana MUG genes yield phenotypes with severely reduced plant fitness through decreased plant size, delayed flowering, abnormal development of floral organs, and markedly reduced fertility. MUG genes are present in all flowering plants, but not in any non-flowering plant lineages, such as gymnosperms, suggesting that the molecular domestication of MUG may have been an integral part of early angiosperm evolution. This study shows that systematic searches can be successful at identifying functional genetic elements in noncoding regions and demonstrates how to combine systematic searches with reverse genetics in a fruitful way to decipher eukaryotic genomes.

Juretic, Nikoleta; Bureau, Thomas E.

2012-01-01

327

[Recent advances in natriuretic peptide family genes and cardiovascular diseases].  

PubMed

Natriuretic peptide family consists of several hormones produced by cardiomyocyte, including atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP) and C-type natriuretic peptide (CNP). They possess similar gene structures and protective effects of cardiovascular physiology, such as anti-hypertrophy, anti-fibrosis, myocardial relaxation and blood pressure regulation. The corresponding natriuretic peptide receptor A, B and C mediate multiple effects of natriuretic peptides to maintain cardiovascular homeostasis. Specially, natriuretic peptide receptor-A preferentially binds ANP and BNP, while natriuretic peptide receptor-B is more selective for C-type natriuretic peptides. Natriuretic peptide receptor-C(NPR-C), binding all kinds of natriuretic peptides, clears natriuretic peptides from the circulation through receptor-mediated internalization and degradation. BNP levels were reported to be a good predictor of left ventricular dysfunction and decompensated heart failure from a clinical standpoint. BNP infusion is an effective treatment for acute heart failure. Investigations on natriuretic peptides' single nucleotide polymorphisms and biological function suggested that they could be associated with several cardiovascular diseases, such as atrial fibrillation, cardiomyopathy, heart failure and so on. Transgenic mice with natriuretic peptides and their receptors gene deletion display myocardial hypertrophy and fibrosis, which are associated with the development of hypertension, cardiomyopathy and heart failure. Certain stimuli triggering cardiac hypertrophy and ischemic injuries may be involved in regulating gene expression of natriuretic peptides and their receptors. Therefore, advances in understanding of natriuretic peptide family genes and their regulatory mechanisms will lead to greater insight into the pathogenesis of cardiovascular diseases and blaze a new trail in clinical treatment. PMID:22382054

Wu, Zhi-Jun; Jin, Wei; Zhang, Feng-Ru; Liu, Yan

2012-02-01

328

The gamma-tubulin gene family in humans.  

PubMed

Despite the central role of gamma-tubulin in the organization of the microtubule cytoskeleton, the gamma-tubulin gene family in humans has not been characterized. We now report the identification of a second expressed human gamma-tubulin gene (TUBG2) and a gamma-tubulin pseudogene (TUBG1P) in addition to the previously identified gamma-tubulin gene (TUBG1). Evidence from Southern hybridizations suggests that there are probably no additional gamma-tubulin sequences in the human genome. TUBG1 and TUBG2 are within 20 kb of each other in region q21 of chromosome 17, and TUBG1P is on chromosome 7. The proteins encoded by TUBG1 and TUBG2 share 97.3% amino acid identity, and the two genes are coexpressed in a variety of tissues. Previous studies of gamma-tubulin in human tissues and cell lines have been based on the tacit assumption that a single gamma-tubulin (the gamma-tubulin encoded by TUBG1) was present. While this assumption is not correct, the similarity of the products of TUBG1 and TUBG2 suggests that results of previous immunolocalization and immunoprecipitation studies in human cells and tissues are likely to be valid. In addition, any pharmacological agents that target one human gamma-tubulin are likely to target both. PMID:10903841

Wise, D O; Krahe, R; Oakley, B R

2000-07-15

329

Common Familial Mediterranean Fever gene mutations in a Turkish cohort.  

PubMed

Familial Mediterranean Fever (FMF) is an autosomal recessive autoinflammatory disorder with the responsible gene of MEFV which primarily affects Jewish, Armenian, Turkish and Arab populations. The FMF gene (MEFV) has recently been cloned to chromosome 16 p, which encodes pyrin. In the present study, we enrolled 2,067 unrelated patients with the suspicion of FMF in Middle Anatolia between the years 2006-2009 and identified the 12 MEFV mutations. DNA was amplified by PCR and subjected to reverse hybridization for the detection of MEFV gene mutations. Among the 2,067 patients, 866 (41.9%) were males and 1,201 (58.1%) were females. The mutations were homozygous in 176 (16.85%) patients, compound heterozygous in 314 (30.1%) patients, heterozygous in 546 (52.25%) patients and the other forms of mutations were found in 8 patients (0.76%). No mutation was detected in 1,023 (49.5%) patients. The most frequent mutations were M694V, M680I (G/C), E148Q and V726A. We could not find any significant differences between the two common mutations according to the gender. The high incidence of MEFV gene mutations in the Turkish population indicated that newborn screening may be discussed in the future. Because of the ethnic origin of Anatolia, larger serial analyses are necessary to investigate the rate and coexistence of these mutations. PMID:21153919

Dundar, Munis; Emirogullari, Elif Funda; Kiraz, Aslihan; Taheri, Serpil; Baskol, Mevlut

2010-12-14

330

Population and Family-Based Studies Associate the MTHFR Gene with Idiopathic Autism in Simplex Families  

Microsoft Academic Search

Two methylenetetrahydrofolate reductase gene (MTHFR) functional polymorphisms were studied in 205 North American simplex (SPX) and 307 multiplex (MPX) families having one or\\u000a more children with an autism spectrum disorder. Case–control comparisons revealed a significantly higher frequency of the\\u000a low-activity 677T allele, higher prevalence of the 677TT genotype and higher frequencies of the 677T-1298A haplotype and double\\u000a homozygous 677TT\\/1298AA genotype

Xudong Liu; Fatima Solehdin; Ira L. Cohen; Maripaz G. Gonzalez; Edmund C. Jenkins; M. E. Suzanne Lewis; Jeanette J. A. Holden

2011-01-01

331

TreeFam: a curated database of phylogenetic trees of animal gene families  

Microsoft Academic Search

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary his- 20 tory of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed align- ments and trees in a similar fashion to Pfam.

Heng Li; Avril Coghlan; Jue Ruan; Lachlan James M. Coin; Jean-karim Hériché; Lara Osmotherly; Ruiqiang Li; Tao Liu; Zhang Zhang; Lars Bolund; Gane Ka-shu Wong; Wei-mou Zheng; Paramvir Dehal; Jun Wang; Richard Durbin

2006-01-01

332

Genome-wide identification and expression analysis of MAPK and MAPKK gene family in Malus domestica.  

PubMed

MAPK signal transduction modules play crucial roles in regulating many biological processes in plants, which are composed of three classes of hierarchically organized protein kinases, namely MAPKKKs, MAPKKs, and MAPKs. Although genome-wide analysis of this family has been carried out in some species, little is known about MAPK and MAPKK genes in apple (Malus domestica). In this study, a total of 26 putative apple MAPK genes (MdMPKs) and 9 putative apple MAPKK genes (MdMKKs) have been identified and located within the apple genome. Phylogenetic analysis revealed that MdMAPKs and MdMAPKKs could be divided into 4 subfamilies (groups A, B, C and D), respectively. The predicted MdMAPKs and MdMAPKKs were distributed across 13 out of 17 chromosomes with different densities. In addition, analysis of exon-intron junctions and of intron phase inside the predicted coding region of each candidate gene has revealed high levels of conservation within and between phylogenetic groups. According to the microarray and expressed sequence tag (EST) analysis, the different expression patterns indicate that they may play different roles during fruit development and rootstock-scion interaction process. Moreover, MAPK and MAPKK genes were performed expression profile analyses in different tissues (root, stem, leaf, flower and fruit), and all of the selected genes were expressed in at least one of the tissues tested, indicating that the MAPKs and MAPKKs are involved in various aspects of physiological and developmental processes of apple. To our knowledge, this is the first report of a genome-wide analysis of the apple MAPK and MAPKK gene family. This study provides valuable information for understanding the classification and putative functions of the MAPK signal in apple. PMID:23939467

Zhang, Shizhong; Xu, Ruirui; Luo, Xiaocui; Jiang, Zesheng; Shu, Huairui

2013-08-09

333

Discovery of Gene Families and Alternatively Spliced Variants by RecA-Mediated Cloning  

Microsoft Academic Search

Probing the functional complexity of the human genome will require new gene cloning techniques, not only to discover intraspecies gene homologs and interspecies gene orthologs, but also to identify alternatively spliced gene variants. We report homologous cDNA cloning methods that allow cloning of gene family members, genes from different species, and alternatively spliced gene variants. We cloned human 14-3-3 gene

Hong Zeng; Elizabeth Allen; Chris W. Lehman; R. Geoffrey Sargent; Sushma Pati; David A. Zarling

2002-01-01

334

GFam: a platform for automatic annotation of gene families  

PubMed Central

We have developed GFam, a platform for automatic annotation of gene/protein families. GFam provides a framework for genome initiatives and model organism resources to build domain-based families, derive meaningful functional labels and offers a seamless approach to propagate functional annotation across periodic genome updates. GFam is a hybrid approach that uses a greedy algorithm to chain component domains from InterPro annotation provided by its 12 member resources followed by a sequence-based connected component analysis of un-annotated sequence regions to derive consensus domain architecture for each sequence and subsequently generate families based on common architectures. Our integrated approach increases sequence coverage by 7.2 percentage points and residue coverage by 14.6 percentage points higher than the coverage relative to the best single-constituent database within InterPro for the proteome of Arabidopsis. The true power of GFam lies in maximizing annotation provided by the different InterPro data sources that offer resource-specific coverage for different regions of a sequence. GFam’s capability to capture higher sequence and residue coverage can be useful for genome annotation, comparative genomics and functional studies. GFam is a general-purpose software and can be used for any collection of protein sequences. The software is open source and can be obtained from http://www.paccanarolab.org/software/gfam/.

Sasidharan, Rajkumar; Nepusz, Tamas; Swarbreck, David; Huala, Eva; Paccanaro, Alberto

2012-01-01

335

Analysis of promoter activity of members of the PECTATE LYASE-LIKE (PLL) gene family in cell separation in Arabidopsis  

PubMed Central

Background Pectate lyases depolymerize pectins by catalyzing the eliminative cleavage of ?-1,4-linked galacturonic acid. Pectate lyase-like (PLL) genes make up among the largest and most complex families in plants, but their cellular and organismal roles have not been well characterized, and the activity of these genes has been assessed only at the level of entire organs or plant parts, potentially obscuring important sub-organ or cell-type-specific activities. As a first step to understand the potential functional diversity of PLL genes in plants and specificity of individual genes, we utilized a reporter gene approach to document the spatial and temporal promoter activity for 23 of the 26 members of the Arabidopsis thaliana (Arabidopsis) PLL gene family throughout development, focusing on processes involving cell separation. Results Numerous PLL promoters directed activity in localized domains programmed for cell separation, such as the abscission zones of the sepal, petal, stamen, and seed, as well as the fruit dehiscence zone. Several drove activity in cell types expected to facilitate separation, including the style and root endodermal and cortical layers during lateral root emergence. However, PLL promoters were active in domains not obviously programmed for separation, including the stipule, hydathode and root axis. Nearly all PLL promoters showed extensive overlap of activity in most of the regions analyzed. Conclusions Our results document potential for involvement of PLL genes in numerous aspects of growth and development both dependent and independent of cell separation. Although the complexity of the PLL gene family allows for enormous potential for gene specialization through spatial or temporal regulation, the high degree of overlap of activity among the PLL promoters suggests extensive redundancy. Alternatively, functional specialization might be determined at the post-transcriptional or protein level.

2010-01-01

336

Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance genes  

Microsoft Academic Search

NBS-LRR genes are the major class of disease resistance genes in flowering plants, and are arranged as single genes and as clustered loci. The evolution of these genes has been investigated in Arabidopsis thaliana by combining data on their genomic organisation and position in phylogenetic trees. Tandem and segmental duplications distribute and separate NBS-LRR genes in the genome. It is,

Dario Leister

2004-01-01

337

The wheat low-molecular-weight glutenin genes: characterization of six new genes and progress in understanding gene family structure  

Microsoft Academic Search

Although the low-molecular-weight (LMW) glutenin subunits are important for aspects of wheat quality and dough processing,\\u000a a detailed description of the DNA structure and encoded polypeptides of this multigene family is still lacking. We report\\u000a progress in obtaining a more thorough description of the LMW-glutenin gene family from a single wheat cultivar (‘Cheyenne’).\\u000a Six new genomic sequences are reported and

B. G. Cassidy; J. Dvorak; O. D. Anderson

1998-01-01

338

Coordinations between gene modules control the operation of plant amino acid metabolic networks  

PubMed Central

Background Being sessile organisms, plants should adjust their metabolism to dynamic changes in their environment. Such adjustments need particular coordination in branched metabolic networks in which a given metabolite can be converted into multiple other metabolites via different enzymatic chains. In the present report, we developed a novel "Gene Coordination" bioinformatics approach and use it to elucidate adjustable transcriptional interactions of two branched amino acid metabolic networks in plants in response to environmental stresses, using publicly available microarray results. Results Using our "Gene Coordination" approach, we have identified in Arabidopsis plants two oppositely regulated groups of "highly coordinated" genes within the branched Asp-family network of Arabidopsis plants, which metabolizes the amino acids Lys, Met, Thr, Ile and Gly, as well as a single group of "highly coordinated" genes within the branched aromatic amino acid metabolic network, which metabolizes the amino acids Trp, Phe and Tyr. These genes possess highly coordinated adjustable negative and positive expression responses to various stress cues, which apparently regulate adjustable metabolic shifts between competing branches of these networks. We also provide evidence implying that these highly coordinated genes are central to impose intra- and inter-network interactions between the Asp-family and aromatic amino acid metabolic networks as well as differential system interactions with other growth promoting and stress-associated genome-wide genes. Conclusion Our novel Gene Coordination elucidates that branched amino acid metabolic networks in plants are regulated by specific groups of highly coordinated genes that possess adjustable intra-network, inter-network and genome-wide transcriptional interactions. We also hypothesize that such transcriptional interactions enable regulatory metabolic adjustments needed for adaptation to the stresses.

Less, Hadar; Galili, Gad

2009-01-01

339

Differential roles of TGIF family genes in mammalian reproduction  

PubMed Central

Background TG-interacting factors (TGIFs) belong to a family of TALE-homeodomain proteins including TGIF1, TGIF2 and TGIFLX/Y in human. Both TGIF1 and TGIF2 act as transcription factors repressing TGF-? signalling. Human TGIFLX and its orthologue, Tex1 in the mouse, are X-linked genes that are only expressed in the adult testis. TGIF2 arose from TGIF1 by duplication, whereas TGIFLX arose by retrotransposition to the X-chromosome. These genes have not been characterised in any non-eutherian mammals. We therefore studied the TGIF family in the tammar wallaby (a marsupial mammal) to investigate their roles in reproduction and how and when these genes may have evolved their functions and chromosomal locations. Results Both TGIF1 and TGIF2 were present in the tammar genome on autosomes but TGIFLX was absent. Tammar TGIF1 shared a similar expression pattern during embryogenesis, sexual differentiation and in adult tissues to that of TGIF1 in eutherian mammals, suggesting it has been functionally conserved. Tammar TGIF2 was ubiquitously expressed throughout early development as in the human and mouse, but in the adult, it was expressed only in the gonads and spleen, more like the expression pattern of human TGIFLX and mouse Tex1. Tammar TGIF2 mRNA was specifically detected in round and elongated spermatids. There was no mRNA detected in mature spermatozoa. TGIF2 protein was specifically located in the cytoplasm of spermatids, and in the residual body and the mid-piece of the mature sperm tail. These data suggest that tammar TGIF2 may participate in spermiogenesis, like TGIFLX does in eutherians. TGIF2 was detected for the first time in the ovary with mRNA produced in the granulosa and theca cells, suggesting it may also play a role in folliculogenesis. Conclusions The restricted and very similar expression of tammar TGIF2 to X-linked paralogues in eutherians suggests that the evolution of TGIF1, TGIF2 and TGIFLX in eutherians was accompanied by a change from ubiquitous to tissue-specific expression. The distribution and localization of TGIF2 in tammar adult gonads suggest that there has been an ultra-conserved function for the TGIF family in fertility and that TGIF2 already functioned in spermatogenesis and potentially folliculogenesis long before its retrotransposition to the X-chromosome of eutherian mammals. These results also provide further evidence that the eutherian X-chromosome has actively recruited sex and reproductive-related genes during mammalian evolution.

2011-01-01

340

Phylogenetic, Molecular, and Biochemical Characterization of Caffeic Acid o-Methyltransferase Gene Family in Brachypodium distachyon  

PubMed Central

Caffeic acid o-methyltransferase (COMT) is one of the important enzymes controlling lignin monomer production in plant cell wall synthesis. Analysis of the genome sequence of the new grass model Brachypodium distachyon identified four COMT gene homologs, designated as BdCOMT1, BdCOMT2, BdCOMT3, and BdCOMT4. Phylogenetic analysis suggested that they belong to the COMT gene family, whereas syntenic analysis through comparisons with rice and sorghum revealed that BdCOMT4 on Chromosome 3 is the orthologous copy of the COMT genes well characterized in other grass species. The other three COMT genes are unique to Brachypodium since orthologous copies are not found in the collinear regions of rice and sorghum genomes. Expression studies indicated that all four Brachypodium COMT genes are transcribed but with distinct patterns of tissue specificity. Full-length cDNAs were cloned in frame into the pQE-T7 expression vector for the purification of recombinant Brachypodium COMT proteins. Biochemical characterization of enzyme activity and substrate specificity showed that BdCOMT4 has significant effect on a broad range of substrates with the highest preference for caffeic acid. The other three COMTs had low or no effect on these substrates, suggesting that a diversified evolution occurred on these duplicate genes that not only impacted their pattern of expression, but also altered their biochemical properties.

Wu, Xianting; Wu, Jiajie; Luo, Yangfan; Bragg, Jennifer; Anderson, Olin; Vogel, John; Gu, Yong Q.

2013-01-01

341

Identification of wild soybean (Glycine soja) TIFY family genes and their expression profiling analysis under bicarbonate stress.  

PubMed

Wild soybean (Glycine soja L. G07256) exhibits a greater adaptability to soil bicarbonate stress than cultivated soybean, and recent discoveries show that TIFY family genes are involved in the response to several abiotic stresses. A genomic and transcriptomic analysis of all TIFY genes in G. soja, compared with G. max, will provide insight into the function of this gene family in plant bicarbonate stress response. This article identified and characterized 34 TIFY genes in G. soja. Sequence analyses indicated that most GsTIFY proteins had two conserved domains: TIFY and Jas. Phylogenetic analyses suggested that these GsTIFY genes could be classified into two groups. A clustering analysis of all GsTIFY transcript expression profiles from bicarbonate stress treated G. soja showed that there were five different transcript patterns in leaves and six different transcript patterns in roots when the GsTIFY family responds to bicarbonate stress. Moreover, the expression level changes of all TIFY genes in cultivated soybean, treated with bicarbonate stress, were also verified. The expression comparison analysis of TIFYs between wild and cultivated soybeans confirmed that, different from the cultivated soybean, GsTIFY (10a, 10b, 10c, 10d, 10e, 10f, 11a, and 11b) were dramatically up-regulated at the early stage of stress, while GsTIFY 1c and 2b were significantly up-regulated at the later period of stress. The frequently stress responsive and diverse expression profiles of the GsTIFY gene family suggests that this family may play important roles in plant environmental stress responses and adaptation. PMID:23090726

Zhu, Dan; Bai, Xi; Luo, Xiao; Chen, Qin; Cai, Hua; Ji, Wei; Zhu, Yanming

2012-10-23

342

Comprehensive Genomic Analysis and Expression Profiling of Phospholipase C Gene Family during Abiotic Stresses and Development in Rice  

PubMed Central

Background Phospholipase C (PLC) is one of the major lipid hydrolysing enzymes, implicated in lipid mediated signaling. PLCs have been found to play a significant role in abiotic stress triggered signaling and developmental processes in various plant species. Genome wide identification and expression analysis have been carried out for this gene family in Arabidopsis, yet not much has been accomplished in crop plant rice. Methodology/Principal Findings An exhaustive in-silico exploration of rice genome using various online databases and tools resulted in the identification of nine PLC encoding genes. Based on sequence, motif and phylogenetic analysis rice PLC gene family could be divided into phosphatidylinositol-specific PLCs (PI-PLCs) and phosphatidylcholine- PLCs (PC-PLC or NPC) classes with four and five members, respectively. A comparative analysis revealed that PLCs are conserved in Arabidopsis (dicots) and rice (monocot) at gene structure and protein level but they might have evolved through a separate evolutionary path. Transcript profiling using gene chip microarray and quantitative RT-PCR showed that most of the PLC members expressed significantly and differentially under abiotic stresses (salt, cold and drought) and during various developmental stages with condition/stage specific and overlapping expression. This finding suggested an important role of different rice PLC members in abiotic stress triggered signaling and plant development, which was also supported by the presence of relevant cis-regulatory elements in their promoters. Sub-cellular localization of few selected PLC members in Nicotiana benthamiana and onion epidermal cells has provided a clue about their site of action and functional behaviour. Conclusion/Significance The genome wide identification, structural and expression analysis and knowledge of sub-cellular localization of PLC gene family envisage the functional characterization of these genes in crop plants in near future.

Singh, Amarjeet; Kanwar, Poonam; Pandey, Amita; Tyagi, Akhilesh K.; Sopory, Sudhir K.; Kapoor, Sanjay; Pandey, Girdhar K.

2013-01-01

343

The UDP-glucuronate decarboxylase gene family in Populus: structure, expression, and association genetics.  

PubMed

In woody crop plants, the oligosaccharide components of the cell wall are essential for important traits such as bioenergy content, growth, and structural wood properties. UDP-glucuronate decarboxylase (UXS) is a key enzyme in the synthesis of UDP-xylose for the formation of xylans during cell wall biosynthesis. Here, we isolated a multigene family of seven members (PtUXS1-7) encoding UXS from Populus tomentosa, the first investigation of UXSs in a tree species. Analysis of gene structure and phylogeny showed that the PtUXS family could be divided into three groups (PtUXS1/4, PtUXS2/5, and PtUXS3/6/7), consistent with the tissue-specific expression patterns of each PtUXS. We further evaluated the functional consequences of nucleotide polymorphisms in PtUXS1. In total, 243 single-nucleotide polymorphisms (SNPs) were identified, with a high frequency of SNPs (1/18 bp) and nucleotide diversity (?T?=?0.01033, ?w?=?0.01280). Linkage disequilibrium (LD) analysis showed that LD did not extend over the entire gene (r (2)<0.1, P<0.001, within 700 bp). SNP- and haplotype-based association analysis showed that nine SNPs (Q <0.10) and 12 haplotypes (P<0.05) were significantly associated with growth and wood property traits in the association population (426 individuals), with 2.70% to 12.37% of the phenotypic variation explained. Four significant single-marker associations (Q <0.10) were validated in a linkage mapping population of 1200 individuals. Also, RNA transcript accumulation varies among genotypic classes of SNP10 was further confirmed in the association population. This is the first comprehensive study of the UXS gene family in woody plants, and lays the foundation for genetic improvements of wood properties and growth in trees using genetic engineering or marker-assisted breeding. PMID:23613749

Du, Qingzhang; Pan, Wei; Tian, Jiaxing; Li, Bailian; Zhang, Deqiang

2013-04-16

344

Expression and evolution of functionally distinct haemoglobin genes in plants  

Microsoft Academic Search

Haemoglobin genes have been found in a number of plant species, but the number of genes known has been too small to allow effective evolutionary inferences. We present nine new non-symbiotic haemoglobin sequences from a range of plants, including class 1 haemoglobins from cotton, Citrus and tomato, class 2 haemoglobins from cotton, tomato, sugar beet and canola and two haemoglobins from the

P. W. Hunt; R. A. Watts; B. Trevaskis; D. J. Llewelyn; J. Burnell; E. S. Dennis; W. J. Peacock

2001-01-01

345

Intrastrain and interstrain genetic variation within a paralogous gene family in Chlamydia pneumoniae  

Microsoft Academic Search

BACKGROUND: Chlamydia pneumoniae causes human respiratory diseases and has recently been associated with atherosclerosis. Analysis of the three recently published C. pneumoniae genomes has led to the identification of a new gene family (the Cpn 1054 family) that consists of 11 predicted genes and gene fragments. Each member encodes a polypeptide with a hydrophobic domain characteristic of proteins localized to

Wasna Viratyosin; Lee Ann Campbell; Cho-Chou Kuo; Daniel D Rockey

2002-01-01

346

stevor and rif are Plasmodium falciparum multicopy gene families which potentially encode variant antigens  

Microsoft Academic Search

Several multicopy gene families have been described in Plasmodium falciparum, including the var genes that code for the variant surface antigen PfEMP1, the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. This report documents the chromosomal location of stevor genes, their transcription and characteristics of the deduced protein. On 14 chromosomes, 34 stevor copies were

Qin Cheng; Nicole Cloonan; Katja Fischer; Jenny Thompson; Gary Waine; Michael Lanzer; Allan Saul

1998-01-01

347

Characterisation of the phosphoenolpyruvate carboxylase gene family in sugarcane ( Saccharum spp.)  

Microsoft Academic Search

Phosphoenolpyruvate carboxylases (PEPCs) are encoded by a small multigenic family. In order to characterise this gene family in sugarcane, seven DNA fragments displaying a high homology with grass PEPC genes were isolated using polymerase chain reaction-based cloning. A phylogenetic study revealed the existence of four main PEPC gene lineages in grasses and particularly in sugarcane. Moreover, this analysis suggests that

G. Besnard; G. Pinçon; A. D'Hont; J.-Y. Hoarau; F. Cadet; B. Offmann

2003-01-01

348

The Heme-Oxygenase Family Required for Phytochrome Chromophore Biosynthesis Is Necessary for Proper Photomorphogenesis in Higher Plants1  

PubMed Central

The committed step in the biosynthesis of the phytochrome chromophore phytochromobilin involves the oxidative cleavage of heme by a heme oxygenase (HO) to form biliverdin IX?. Through positional cloning of the photomorphogenic mutant hy1, the Arabidopsis HO (designated AtHO1) responsible for much of phytochromobilin synthesis recently was identified. Using the AtHO1 sequence, we identified families of HO genes in a number of plants that cluster into two subfamilies (HO1- and HO2-like). The tomato (Lycopersicon esculentum) yg-2 and Nicotiana plumbaginifolia pew1 photomorphogenic mutants are defective in specific HO genes. Phenotypic analysis of a T-DNA insertion mutant of Arabidopsis HO2 revealed that the second HO subfamily also contributes to phytochromobilin synthesis. Homozygous ho2-1 plants show decreased chlorophyll accumulation, reduced growth rate, accelerated flowering time, and reduced de-etiolation. A mixture of apo- and holo-phyA was detected in etiolated ho2-1 seedlings, suggesting that phytochromobilin is limiting in this mutant, even in the presence of functional AtHO1. The patterns of Arabidopsis HO1 and HO2 expression suggest that the products of both genes overlap temporally and spatially. Taken together, the family of HOs is important for phytochrome-mediated development in a number of plants and that each family member may uniquely contribute to the phytochromobilin pool needed to assemble holo-phytochromes.

Davis, Seth J.; Bhoo, Seong Hee; Durski, Adam M.; Walker, Joseph M.; Vierstra, Richard D.

2001-01-01

349

Organization and function of the plant pleiotropic drug resistance ABC transporter family  

Microsoft Academic Search

Among the ABC transporters, the pleiotropic drug resistance (PDR) family is particular in that its members are found only in fungi and plants and have a reverse domain organization, i.e., the nucleotide binding domain precedes the transmembrane domain. In Arabidopsis and rice, for which the full genome has been sequenced, the family of plant ABC transporters contains 15 and 23

Jérôme Crouzet; Tomasz Trombik; Å. Staffan Fraysse; Marc Boutry

2006-01-01

350

Structure and evolution of plant disease resistance genes  

Microsoft Academic Search

This article reviews recent advances that shed light on plant disease resis- tance genes, beginning with a brief overview of their structure, followed by their genomic organization and evolution. Plant disease resistance genes have been exhaustively investigated in terms of their structural organization, sequence evolution and genome distribution. There are probably hundreds of NBS-LRR sequences and other types of R-gene-like

351

Genome-wide expression analysis of HSP70 family genes in rice and identification of a cytosolic HSP70 gene highly induced under heat stress.  

PubMed

The heat shock protein 70 (HSP70) gene family plays a key role in protecting plant cells or tissues from thermal or oxidative stress. Although many studies have elucidated the molecular functions of individual family members, genome-wide analysis of this family is still limited, especially for crop species. Our objective was to integrate various meta-profiling data into the context of a phylogenetic tree, which would enable us to perform fine evaluation of functional dominancy or redundancy within this family. Our data indicated that a loss-of-function mutant of a rice cytosolic HSP70 gene (OsctHSP70-1) did not show a clear defective phenotype in response to high temperature because of the existence of another gene family member that was closely clustered with OsctHSP70-1 and had similar expression patterns. Moreover, the second gene showed much stronger anatomical expression. We indirectly analyzed the function of OsctHSP70-1 by studying GUS activity under the control of the endogenous promoter. We also designed a probable interaction network mediated by OsctHSP70-1 and used co-expression analysis among its components to refine the network, suggesting more probable model to explain the function of OsctHSP70-1. PMID:23852542

Jung, Ki-Hong; Gho, Hyun-Jung; Nguyen, Minh Xuan; Kim, Sung-Ryul; An, Gynheung

2013-07-14

352

Defense mechanisms against herbivory in Picea: sequence evolution and expression regulation of gene family members in the phenylpropanoid pathway  

PubMed Central

Background In trees, a substantial amount of carbon is directed towards production of phenolics for development and defense. This metabolic pathway is also a major factor in resistance to insect pathogens in spruce. In such gene families, environmental stimuli may have an important effect on the evolutionary fate of duplicated genes, and different expression patterns may indicate functional diversification. Results Gene families in spruce (Picea) have expanded to superfamilies, including O-methyltransferases, cytochrome-P450, and dirigents/classIII-peroxidases. Neo-functionalization of superfamily members from different clades is reflected in expression diversification. Genetical genomics can provide new insights into the genetic basis and evolution of insect resistance in plants. Adopting this approach, we merged genotype data (252 SNPs in a segregating pedigree), gene expression levels (for 428 phenylpropanoid-related genes) and measures of susceptibility to Pissodes stobi, using a partial-diallel crossing-design with white spruce (Picea glauca). Thirty-eight expressed phenylpropanoid-related genes co-segregated with weevil susceptibility, indicating either causative or reactive effects of these genes to weevil resistance. We identified eight regulatory genomic regions with extensive overlap of quantitative trait loci from susceptibility and growth phenotypes (pQTLs) and expression QTL (eQTL) hotspots. In particular, SNPs within two different CCoAOMT loci regulate phenotypic variation from a common set of 24 genes and three resistance traits. Conclusions Pest resistance was associated with individual candidate genes as well as with trans-regulatory hotspots along the spruce genome. Our results showed that specific genes within the phenylpropanoid pathway have been duplicated and diversified in the conifer in a process fundamentally different from short-lived angiosperm species. These findings add to the information about the role of the phenylpropanoid pathway in the evolution of plant defense mechanisms against insect pests and provide substantial potential for the functional characterization of several not yet resolved alternative pathways in plant defenses.

2011-01-01

353

Control of mucin-type O-glycosylation: A classification of the polypeptide GalNAc-transferase gene family  

PubMed Central

Glycosylation of proteins is an essential process in all eukaryotes and a great diversity in types of protein glycosylation exists in animals, plants and microorganisms. Mucin-type O-glycosylation, consisting of glycans attached via O-linked N-acetylgalactosamine (GalNAc) to serine and threonine residues, is one of the most abundant forms of protein glycosylation in animals. Although most protein glycosylation is controlled by one or two genes encoding the enzymes responsible for the initiation of glycosylation, i.e. the step where the first glycan is attached to the relevant amino acid residue in the protein, mucin-type O-glycosylation is controlled by a large family of up to 20 homologous genes encoding UDP-GalNAc:polypeptide GalNAc-transferases (GalNAc-Ts) (EC 2.4.1.41). Therefore, mucin-type O-glycosylation has the greatest potential for differential regulation in cells and tissues. The GalNAc-T family is the largest glycosyltransferase enzyme family covering a single known glycosidic linkage and it is highly conserved throughout animal evolution, although absent in bacteria, yeast and plants. Emerging studies have shown that the large number of genes (GALNTs) in the GalNAc-T family do not provide full functional redundancy and single GalNAc-T genes have been shown to be important in both animals and human. Here, we present an overview of the GalNAc-T gene family in animals and propose a classification of the genes into subfamilies, which appear to be conserved in evolution structurally as well as functionally.

Bennett, Eric P; Mandel, Ulla; Clausen, Henrik; Gerken, Thomas A; Fritz, Timothy A; Tabak, Lawrence A

2012-01-01

354

Recent Advances of Flowering Locus T Gene in Higher Plants  

PubMed Central

Flowering Locus T (FT) can promote flowering in the plant photoperiod pathway and also facilitates vernalization flowering pathways and other ways to promote flowering. The expression of products of the FT gene is recognized as important parts of the flowering hormone and can induce flowering by long-distance transportation. In the present study, many FT-like genes were isolated, and the transgenic results show that FT gene can promote flowering in plants. This paper reviews the progress of the FT gene and its expression products to provide meaningful information for further studies of the functions of FT genes.

Xu, Feng; Rong, Xiaofeng; Huang, Xiaohua; Cheng, Shuiyuan

2012-01-01

355

Tubulin evolution in insects: gene duplication and subfunctionalization provide specialized isoforms in a functionally constrained gene family  

Microsoft Academic Search

BACKGROUND: The completion of 19 insect genome sequencing projects spanning six insect orders provides the opportunity to investigate the evolution of important gene families, here tubulins. Tubulins are a family of eukaryotic structural genes that form microtubules, fundamental components of the cytoskeleton that mediate cell division, shape, motility, and intracellular trafficking. Previous in vivo studies in Drosophila find a stringent

Mark G. Nielsen; Sudhindra R. Gadagkar; Lisa Gutzwiller

2010-01-01

356

Plant disease resistance genes: structure, function and evolution  

Microsoft Academic Search

Disease resistance genes enable plants to recognize specific races of pathogens and to mount an effective localized defence response. The DNA sequences of nine resistance genes have recently been reported. Most encode a leucine-rich repeat motif, which might provide a basis for recognitional specificities and their evolution. Resistance genes appear to fall into two classes, recognizing either extracellular or intracellular

Jonathan DG Jones

1996-01-01

357

A short history of MADS-box genes in plants  

Microsoft Academic Search

Evolutionary developmental genetics (evodevotics) is a novel scientific endeavor which assumes that changes in developmental control genes are a major aspect of evolutionary changes in morphology. Understanding the phylogeny of developmental control genes may thus help us to understand the evolution of plant and animal form. The principles of evodevotics are exemplified by outlining the role of MADS-box genes in

Günter Theissen; Annette Becker; Alexandra Di Rosa; Akira Kanno; Jan T. Kim; Thomas Münster; Kai-Uwe Winter; Heinz Saedler

2000-01-01

358

Exploring plant genomes by RNA-induced gene silencing  

Microsoft Academic Search

The nucleotide sequences of several animal, plant and bacterial genomes are now known, but the functions of many of the proteins that they are predicted to encode remain unclear. RNA interference is a gene-silencing technology that is being used successfully to investigate gene function in several organisms — for example, Caenorhabditis elegans. We discuss here that RNA-induced gene silencing approaches

Christopher A. Helliwell; Peter M. Waterhouse

2003-01-01

359

Molecular homology among members of the R gene family in maize.  

PubMed

The R gene family determines the timing, distribution and amount of anthocyanin pigmentation in maize. This family comprises a set of regulatory genes, consisting of a cluster of several elements at the R locus, on chromosome 10, the Lc and Sn gene lying about two units R distal and B on chromosome 2. Each gene determines a tissue-specific pigmentation of different parts of the seed and plant. The proposed duplicated function of R, Sn, Lc and B loci is reflected in cDNA sequence similarity. In this paper an extensive analysis of the predicted proteins of the R, Sn, Lc and B genes together with a search for putative sites of post-translational modification is reported. A comparison with the prosite database discloses several N-glycosylation and phosphorylation sites, as well as the basic Helix-Loop-Helix (HLH) domain of transcriptional activators. Sn, Lc, and R-S show a high conservation of these sites, while B is more divergent. Analysis of the 5' leader of mRNA sequences discloses the presence of five ATG triplets with two upstream open reading frames (uORFs) of 38 and 15 amino acids and a loop structure indicating a possible mechanism of control at the translational level. It is conceivable that possible mechanisms acting at the translational and post-translational level could modulate the expression and the activation of these transcription factors. Northern analysis of various tissues of different R alleles highlights a strict correlation between pigment accumulation in different tissues and the expression of the regulatory and structural genes suggesting that the pattern of pigmentation relies on a mechanism of differential expression of the members of the R family. Analysis of the Sn promoter discloses the presence of several sequences resembling binding sites of known transcription factors (as GAGA and GT) that might be responsible for the spatial and light-induced expression of this gene. Two regions include a short sequence homologous to the consensus binding site of the B-HLH domain suggesting a self-regulatory control of the Sn gene. PMID:8220447

Consonni, G; Geuna, F; Gavazzi, G; Tonelli, C

1993-02-01

360

Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes  

PubMed Central

Background Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the hybrid-cluster protein, A-type flavoprotein, glucosamine-6-phosphate isomerase, and alcohol dehydrogenase E. These four genes have a limited distribution among sequenced prokaryotic and eukaryotic genomes and were previously implicated in gene transfer events affecting eukaryotes. If our previous contention that these genes were introduced by LGT independently into the diplomonad and Entamoeba lineages were true, we expect that the number of putative transfers and the phylogenetic signal supporting LGT should be stable or increase, rather than decrease, when novel eukaryotic and prokaryotic homologs are added to the analyses. Results The addition of homologs from phagotrophic protists, including several Entamoeba species, the pelobiont Mastigamoeba balamuthi, and the parabasalid Trichomonas vaginalis, and a large quantity of sequences from genome projects resulted in an apparent increase in the number of putative transfer events affecting all three domains of life. Some of the eukaryotic transfers affect a wide range of protists, such as three divergent lineages of Amoebozoa, represented by Entamoeba, Mastigamoeba, and Dictyostelium, while other transfers only affect a limited diversity, for example only the Entamoeba lineage. These observations are consistent with a model where these genes have been introduced into protist genomes independently from various sources over a long evolutionary time. Conclusion Phylogenetic analyses of the updated datasets using more sophisticated phylogenetic methods, in combination with the gene distribution analyses, strengthened, rather than weakened, the support for LGT as an important mechanism affecting the evolution of these gene families. Thus, gene transfer seems to be an on-going evolutionary mechanism by which genes are spread between unrelated lineages of all three domains of life, further indicating the importance of LGT from non-organellar sources into eukaryotic genomes.

Andersson, Jan O; Hirt, Robert P; Foster, Peter G; Roger, Andrew J

2006-01-01

361

Analysis of the Arabidopsis MADS AFFECTING FLOWERING Gene Family  

PubMed Central

The Arabidopsis FLOWERING LOCUS C (FLC) gene is a key floral repressor in the maintenance of a vernalization response. In vernalization-sensitive genetic backgrounds, FLC levels are high, and they decline after exposure to long cold periods. Four FLC paralogs (MAF2 [MADS AFFECTING FLOWERING2] to MAF5) are arranged in a tandem array on the bottom of Arabidopsis chromosome V. We used a reverse genetics approach to analyze their functions. Loss-of-function and gain-of-function studies indicate that MAF2 acts as a floral repressor. In particular, maf2 mutant plants display a pronounced vernalization response when subjected to relatively short cold periods, which are insufficient to elicit a strong flowering response in the wild type, despite producing a large reduction in FLC levels. MAF2 expression is less sensitive to vernalization than that of FLC, and its repressor activity is exerted independently or downstream of FLC transcription. Thus, MAF2 can prevent premature vernalization in response to brief cold spells. Overexpression of MAF3 or MAF4 produces alterations in flowering time that suggest that these genes also act as floral repressors and might contribute to the maintenance of a vernalization requirement. However, the final gene in the cluster, MAF5, is upregulated by vernalization. Therefore, MAF5 could play an opposite role to FLC in the vernalization response.

Ratcliffe, Oliver J.; Kumimoto, Roderick W.; Wong, Becky J.; Riechmann, Jose Luis

2003-01-01

362

Genome-Wide Survey and Expression Analysis of Amino Acid Transporter Gene Family in Rice (Oryza sativa L.)  

PubMed Central

Background Amino acid transporters (AATs) that transport amino acids across cellular membranes are essential for plant growth and development. To date, a genome-wide overview of the AAT gene family in rice is not yet available. Methodology/Principal Findings In this study, a total of 85 AAT genes were identified in rice genome and were classified into eleven distinct subfamilies based upon their sequence composition and phylogenetic relationship. A large number of OsAAT genes were expanded via gene duplication, 23 and 24 OsAAT genes were tandemly and segmentally duplicated, respectively. Comprehensive analyses were performed to investigate the expression profiles of OsAAT genes in various stages of vegetative and reproductive development by using data from EST, Microarrays, MPSS and Real-time PCR. Many OsAAT genes exhibited abundant and tissue-specific expression patterns. Moreover, 21 OsAAT genes were found to be differentially expressed under the treatments of abiotic stresses. Comparative analysis indicates that 26 AAT genes with close evolutionary relationships between rice and Arabidopsis exhibited similar expression patterns. Conclusions/Significance This study will facilitate further studies on OsAAT family and provide useful clues for functional validation of OsAATs.

Zhao, Heming; Ma, Haoli; Yu, Li; Wang, Xin; Zhao, Jie

2012-01-01

363

A gene from the cellulose synthase-like C family encodes a ?-1,4 glucan synthase  

PubMed Central

Despite the central role of xyloglucan (XyG) in plant cell wall structure and function, important details of its biosynthesis are not understood. To identify the gene(s) responsible for synthesizing the ?-1,4 glucan backbone of XyG, we exploited a property of nasturtium (Tropaeolum majus) seed development. During the last stages of nasturtium seed maturation, a large amount of XyG is deposited as a reserve polysaccharide. A cDNA library was produced from mRNA isolated during the deposition of XyG, and partial sequences of 10,000 cDNA clones were determined. A single member of the C subfamily from the large family of cellulose synthase-like (CSL) genes was found to be overrepresented in the cDNA library. Heterologous expression of this gene in the yeast Pichia pastoris resulted in the production of a ?-1,4 glucan, confirming that the CSLC protein has glucan synthase activity. The Arabidopsis CSLC4 gene, which is the gene with the highest sequence similarity to the nasturtium CSL gene, is coordinately expressed with other genes involved in XyG biosynthesis. These and other observations provide a compelling case that the CSLC gene family encode proteins that synthesize the XyG backbone.

Cocuron, Jean-Christophe; Lerouxel, Olivier; Drakakaki, Georgia; Alonso, Ana P.; Liepman, Aaron H.; Keegstra, Kenneth; Raikhel, Natasha; Wilkerson, Curtis G.

2007-01-01

364

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts  

PubMed Central

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.

Aubourg, Sebastien; Brunaud, Veronique; Bruyere, Clemence; Cock, Mark; Cooke, Richard; Cottet, Annick; Couloux, Arnaud; Dehais, Patrice; Deleage, Gilbert; Duclert, Aymeric; Echeverria, Manuel; Eschbach, Aimee; Falconet, Denis; Filippi, Ghislain; Gaspin, Christine; Geourjon, Christophe; Grienenberger, Jean-Michel; Houlne, Guy; Jamet, Elisabeth; Lechauve, Frederic; Leleu, Olivier; Leroy, Philippe; Mache, Regis; Meyer, Christian; Nedjari, Hafed; Negrutiu, Ioan; Orsini, Valerie; Peyretaillade, Eric; Pommier, Cyril; Raes, Jeroen; Risler, Jean-Loup; Riviere, Stephane; Rombauts, Stephane; Rouze, Pierre; Schneider, Michel; Schwob, Philippe; Small, Ian; Soumayet-Kampetenga, Ghislain; Stankovski, Darko; Toffano, Claire; Tognolli, Michael; Caboche, Michel; Lecharny, Alain

2005-01-01

365

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.  

PubMed

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot. PMID:15608279

Aubourg, Sébastien; Brunaud, Véronique; Bruyère, Clémence; Cock, Mark; Cooke, Richard; Cottet, Annick; Couloux, Arnaud; Déhais, Patrice; Deléage, Gilbert; Duclert, Aymeric; Echeverria, Manuel; Eschbach, Aimée; Falconet, Denis; Filippi, Ghislain; Gaspin, Christine; Geourjon, Christophe; Grienenberger, Jean-Michel; Houlné, Guy; Jamet, Elisabeth; Lechauve, Frédéric; Leleu, Olivier; Leroy, Philippe; Mache, Régis; Meyer, Christian; Nedjari, Hafed; Negrutiu, Ioan; Orsini, Valérie; Peyretaillade, Eric; Pommier, Cyril; Raes, Jeroen; Risler, Jean-Loup; Rivière, Stéphane; Rombauts, Stéphane; Rouzé, Pierre; Schneider, Michel; Schwob, Philippe; Small, Ian; Soumayet-Kampetenga, Ghislain; Stankovski, Darko; Toffano, Claire; Tognolli, Michael; Caboche, Michel; Lecharny, Alain

2005-01-01

366

Comparison of gene expression in segregating families identifies genes and genomic regions involved in a novel adaptation, zinc hyperaccumulation.  

PubMed

One of the challenges of comparative genomics is to identify specific genetic changes associated with the evolution of a novel adaptation or trait. We need to be able to disassociate the genes involved with a particular character from all the other genetic changes that take place as lineages diverge. Here we show that by comparing the transcriptional profile of segregating families with that of parent species differing in a novel trait, it is possible to narrow down substantially the list of potential target genes. In addition, by assuming synteny with a related model organism for which the complete genome sequence is available, it is possible to use the cosegregation of markers differing in transcription level to identify regions of the genome which probably contain quantitative trait loci (QTLs) for the character. This novel combination of genomics and classical genetics provides a very powerful tool to identify candidate genes. We use this methodology to investigate zinc hyperaccumulation in Arabidopsis halleri, the sister species to the model plant, Arabidopsis thaliana. We compare the transcriptional profile of A. halleri with that of its sister nonaccumulator species, Arabidopsis petraea, and between accumulator and nonaccumulator F(3)s derived from the cross between the two species. We identify eight genes which consistently show greater expression in accumulator phenotypes in both roots and shoots, including two metal transporter genes (NRAMP3 and ZIP6), and cytoplasmic aconitase, a gene involved in iron homeostasis in mammals. We also show that there appear to be two QTLs for zinc accumulation, on chromosomes 3 and 7. PMID:16911220

Filatov, Victor; Dowdle, John; Smirnoff, Nicholas; Ford-Lloyd, Brian; Newbury, H John; Macnair, Mark R

2006-09-01

367

Gene family encoding the major toxins of lethal Amanita mushrooms  

PubMed Central

Amatoxins, the lethal constituents of poisonous mushrooms in the genus Amanita, are bicyclic octapeptides. Two genes in A. bisporigera, AMA1 and PHA1, directly encode ?-amanitin, an amatoxin, and the related bicyclic heptapeptide phallacidin, a phallotoxin, indicating that these compounds are synthesized on ribosomes and not by nonribosomal peptide synthetases. ?-Amanitin and phallacidin are synthesized as proproteins of 35 and 34 amino acids, respectively, from which they are predicted to be cleaved by a prolyl oligopeptidase. AMA1 and PHA1 are present in other toxic species of Amanita section Phalloidae but are absent from nontoxic species in other sections. The genomes of A. bisporigera and A. phalloides contain multiple sequences related to AMA1 and PHA1. The predicted protein products of this family of genes are characterized by a hypervariable “toxin” region capable of encoding a wide variety of peptides of 7–10 amino acids flanked by conserved sequences. Our results suggest that these fungi have a broad capacity to synthesize cyclic peptides on ribosomes.

Hallen, Heather E.; Luo, Hong; Scott-Craig, John S.; Walton, Jonathan D.

2007-01-01

368

Characterisation of the gene encoding the Merlot ripening-induced protein 1 ( mrip1): evidence that this putative protein is a distinct member of the plant proline-rich protein family  

Microsoft Academic Search

Proline-rich proteins (PRPs) are considered to be involved in cell wall composition and structure. Despite this proposed role and the fact that cell wall modification is one of the most important changes during fruit ripening, very little is known about PRPs involved in fruit ripening. In this study a gene encoding a PRP associated with ripening, Merlot ripening-induced protein 1

Anita L. Burger; Jacobus P. Zwiegelaar; Frederik C. Botha

2004-01-01

369

Differential Expansion and Expression of ?- and ?-Tubulin Gene Families in Populus1[W][OA  

PubMed Central

Microtubule organization is intimately associated with cellulose microfibril deposition, central to plant secondary cell wall development. We have determined that a relatively large suite of eight ?-TUBULIN (TUA) and 20 ?-TUBULIN (TUB) genes is expressed in the woody perennial Populus. A number of features, including gene number, ?:? gene representation, amino acid changes at the C terminus, and transcript abundance in wood-forming tissue, distinguish the Populus tubulin suite from that of Arabidopsis thaliana. Five of the eight Populus TUAs are unusual in that they contain a C-terminal methionine, glutamic acid, or glutamine, instead of the more typical, and potentially regulatory, C-terminal tyrosine. Both C-terminal Y-type (TUA1) and M-type (TUA5) TUAs were highly expressed in wood-forming tissues and pollen, while the Y-type TUA6 and TUA8 were abundant only in pollen. Transcripts of the disproportionately expanded TUB family were present at comparatively low levels, with phylogenetically distinct classes predominating in xylem and pollen. When tension wood induction was used as a model system to examine changes in tubulin gene expression under conditions of augmented cellulose deposition, xylem-abundant TUA and TUB genes were up-regulated. Immunolocalization of TUA and TUB in xylem and phloem fibers of stems further supported the notion of heavy microtubule involvement during cellulose microfibril deposition in secondary walls. The high degree of sequence diversity, differential expansion, and differential regulation of Populus TUA and TUB families may confer flexibility in cell wall formation that is of adaptive significance to the woody perennial growth habit.

Oakley, Rodney V.; Wang, Yuh-Shuh; Ramakrishna, Wusirika; Harding, Scott A.; Tsai, Chung-Jui

2007-01-01

370

Pollen tubes of Nicotiana alata express two genes from different beta-glucan synthase families.  

PubMed

The walls deposited by growing pollen tubes contain two types of beta-glucan, the (1,3)-beta-glucan callose and the (1,4)-beta-glucan cellulose, as well as various alpha-linked pectic polysaccharides. Pollen tubes of Nicotiana alata Link et Otto, an ornamental tobacco, were therefore used to identify genes potentially encoding catalytic subunits of the callose synthase and cellulose synthase enzymes. Reverse transcriptase-polymerase chain reactions (RT-PCR) with pollen-tube RNA and primers designed to conserved regions of bacterial and plant cellulose synthase (CesA) genes amplified a fragment that corresponded to an abundantly expressed cellulose-synthase-like gene named NaCslD1. A fragment from a true CesA gene (NaCesA1) was also amplified, but corresponding cDNAs could not be identified in a pollen-tube library, consistent with the very low level of expression of the NaCesA1 gene. RT-PCR with pollen-tube RNA and primers designed to regions conserved between the fungal FKS genes [that encode (1,3)-beta-glucan synthases] and their presumed plant homologs (the Gsl or glucan-synthase-like genes) amplified a fragment that corresponded to an abundantly expressed gene named NaGsl1. A second Gsl gene detected by RT-PCR (NaGsl2) was expressed at low levels in immature floral organs. The structure of full-length cDNAs of NaCslD1, NaCesA1, and NaGsl1 are presented. Both NaCslD1 and NaGsl1 are predominantly expressed in the male gametophyte (developing and mature pollen and growing pollen tubes), and we propose that they encode the catalytic subunits of two beta-glucan synthases involved in pollen-tube wall synthesis. Different beta-glucans deposited in one cell type may therefore be synthesized by enzymes from different gene families. PMID:11299383

Doblin, M S; De Melis, L; Newbigin, E; Bacic, A; Read, S M

2001-04-01

371

Characterization of the multicopper oxidase gene family in Anopheles gambiae  

PubMed Central

The multicopper oxidase (MCO) family of enzymes includes laccases, which oxidize a broad range of substrates including diphenols, and several oxidases with specific substrates such as iron, copper or ascorbic acid. We have identified five putative MCO genes in the genome of Anopheles gambiae and have cloned cDNAs encompassing the full coding region for each gene. MCO1 mRNA was detected in all developmental stages and in all of the larval and adult tissues tested. We observed an increase in MCO1 transcript abundance in the midguts and Malphighian tubules of adult females following a blood meal and in adult abdominal carcasses in response to an immune challenge. Two alternatively spliced isoforms of MCO2 mRNA were identified. The A isoform of MCO2 was previously detected in larval and pupal cuticle where it probably catalyzes sclerotization reactions (He et al., 2007). The B isoform was transcriptionally upregulated in ovaries in response to a blood meal. MCO3 mRNA was detected in the adult midgut, Malpighian tubules, and male reproductive tissues; like MCO1, it was upregulated in response to an immune challenge or a blood meal. MCO4 and MCO5 were observed primarily in eggs and in the abdominal carcass of larvae. A phylogenetic analysis of insect MCO genes identified putative orthologs of MCO1 and MCO2 in all of the insect genomes tested, whereas MCO3, MCO4 and MCO5 were found only in the two mosquito species analyzed. MCO2 orthologs have especially high sequence similarity, suggesting that they are under strong purifying selection; the A isoforms are more conserved than the B isoforms. The mosquito specific group shares a common ancestor with MCO2. This initial study of mosquito MCOs suggests that MCO2 may be required for egg development or eggshell tanning in addition to cuticle tanning, while MCO1 and MCO3 may be involved in metal metabolism or immunity.

Gorman, Maureen J.; Dittmer, Neal T.; Marshall, Jeremy L.; Kanost, Michael R.

2008-01-01

372

The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula  

PubMed Central

Background Soybean lipoxygenases (Lxs) play important roles in plant resistance and in conferring the distinct bean flavor. Lxs comprise a multi-gene family that includes GmLx1, GmLx2 and GmLx3, and many of these genes have been characterized. We were interested in investigating the relationship between the soybean lipoxygenase isozymes from an evolutionary perspective, since soybean has undergone two rounds of polyploidy. Here we report the tetrad genome structure of soybean Lx regions produced by ancient and recent polyploidy. Also, comparative genomics with Medicago truncatula was performed to estimate Lxs in the common ancestor of soybean and Medicago. Results Two Lx regions in Medicago truncatula showing synteny with soybean were analyzed. Differential evolutionary rates between soybean and Medicago were observed and the median Ks values of Mt-Mt, Gm-Mt, and Gm-Gm paralogs were determined to be 0.75, 0.62, and 0.46, respectively. Thus the comparison of Gm-Mt paralogs (Ks = 0.62) and Gm-Mt orthologs (Ks = 0.45) supports the ancient duplication of Lx regions in the common ancestor prior to the Medicago-Glycine split. After speciation, no Lx regions generated by another polyploidy were identified in Medicago. Instead tandem duplication of Lx genes was observed. On the other hand, a lineage-specific duplication occurred in soybean resulting in two pairs of Lx regions. Each pair of soybean regions was co-orthologous to one Lx region in Medicago. A total of 34 Lx genes (15 MtLxs and 19 GmLxs) were divided into two groups by phylogenetic analysis. Our study shows that the Lx gene family evolved from two distinct Lx genes in the most recent common ancestor. Conclusion This study analyzed two pairs of Lx regions generated by two rounds of polyploidy in soybean. Each pair of soybean homeologous regions is co-orthologous to one region of Medicago, demonstrating the quartet structure of the soybean genome. Differential evolutionary rates between soybean and Medicago were observed; thus optimized rates of Ks per year should be applied for accurate estimation of coalescence times to each case of comparison: soybean-soybean, soybean-Medicago, or Medicago-Medicago. In conclusion, the soybean Lx gene family expanded by ancient polyploidy prior to taxon divergence, followed by a soybean- specific duplication and tandem duplications, respectively.

Shin, Jin Hee; Van, Kyujung; Kim, Dong Hyun; Kim, Kyung Do; Jang, Young Eun; Choi, Beom-Soon; Kim, Moon Young; Lee, Suk-Ha

2008-01-01

373

Molecular analysis of two salt-responsive NAC-family genes and their expression analysis in tomato  

Microsoft Academic Search

The NAC family transcription factor has demonstrated its importance in plant development and environmental stress response.\\u000a Based on the microarray results under salt stress and EST information, the full-length cDNAs of two salt-inducible NAC-family\\u000a genes (SlNAC1, SlNAM1) were isolated from a salt tolerant tomato cultivar, Edkawi, using Rapid Amplification of cDNA Ends (RACE). SlNAC1 and SlNAM1 encoded 301 and 296

Rongchao Yang; Chunting Deng; Bo Ouyang; Zhibiao Ye

2011-01-01

374

Virus-induced gene silencing of the alkaloid-producing basal eudicot model plant Eschscholzia californica (California Poppy).  

PubMed

Eschscholzia californica (California poppy), a member of the basal eudicot family of the Papaveraceae, is an important species to study alkaloid biosynthesis and the effect of alkaloids on plant metabolism. More recently, it has also been developed as a model system to study the evolution of plant morphogenesis. While progress has been made towards establishing methods for generating genetically modified cell culture lines, transcriptome data and gene expression analysis, the stable transformation and subsequent regeneration of transgenic plants has proven extremely time consuming and difficult. Here, we describe in detail a method to transiently down regulate expression of a target gene by virus-induced gene silencing (VIGS) and the subsequent analysis of the VIGS treated plants. VIGS in E. californica allows for the study of gene function within 2 to 3 weeks after inoculation, and the method proves very efficient, enabling the rapid analysis of gene functions. PMID:23386297

Tekleyohans, Dawit G; Lange, Sabrina; Becker, Annette

2013-01-01

375

Plant Transformation by Gene Transfer into Pollen.  

National Technical Information Service (NTIS)

Plant germplasm is transformed with foreign DNA by introducing the DNA into pollen grains by a technique such as electroporation, mating ova of the desired plant line with the transformed pollen, and selecting for the transformed germplasm. The germinatin...

J. A. Saunders B. F. Matthews

1989-01-01

376

The Irx gene family in zebrafish: genomic structure, evolution and initial characterization of irx5b  

Microsoft Academic Search

Genes of the iroquois (Iro\\/Irx) family are highly conserved from Drosophila to mammals and they have been implicated in a number of developmental processes. In flies, the Iro genes participate in patterning events in the early larva and in imaginal disk specification. In vertebrates, the Irx genes regulate developmental events during gastrulation, nervous system regionalization, activation of proneural genes and

Carmen Gloria Feijóo; Miguel Manzanares; Elisa de la Calle-Mustienes; José Luis Gómez-Skarmeta; Miguel L. Allende

2004-01-01

377

ETS family-associated gene fusions in Japanese prostate cancer: analysis of 194 radical prostatectomy samples  

Microsoft Academic Search

The incidence and clinical significance of the TMPRSS2:ERG gene fusion in prostate cancer has been investigated with contradictory results. It is now common knowledge that significant variability in gene alterations exists according to ethnic background in various kinds of cancer. In this study, we evaluated gene fusions involving the ETS gene family in Japanese prostate cancer. Total RNA from 194

Yohei Miyagi; Takeshi Sasaki; Kiyoshi Fujinami; Jinyu Sano; Yutaka Senga; Takeshi Miura; Yoichi Kameda; Yuji Sakuma; Yoshiyasu Nakamura; Masaoki Harada; Eiju Tsuchiya

2010-01-01

378

The rice R gene family: two distinct subfamilies containing several miniature inverted-repeat transposable elements  

Microsoft Academic Search

The R and B genes of maize regulate the anthocyanin biosynthetic pathway and constitute a small gene family whose evolution has been shaped by polyploidization and transposable element activity. To compare the evolution of regulatory genes in the distinct but related genomes of rice and maize, we previously isolated two R homologues from rice (Oryza sativa). The Ra1 gene on

Jianping Hu; Vaka S. Reddy; Susan R. Wessler

2000-01-01

379

Gene duplication and transfer events in plant mitochondria genome  

SciTech Connect

Gene or genome duplication events increase the amount of genetic material available to increase the genomic, and thereby phenotypic, complexity of organisms during evolution. Gene duplication and transfer events have been important to molecular evolution in all three domains of life, and may be the first step in the emergence of new gene functions. Gene transfer events have been proposed as another accelerator of evolution. The duplicated gene or genome, mainly nuclear, has been the subject of several recent reviews. In addition to the nuclear genome, organisms have organelle genomes, including mitochondrial genome. In this review, we briefly summarize gene duplication and transfer events in the plant mitochondrial genome.

Xiong Aisheng [Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106 (China)], E-mail: aishengxiongcn@yahoo.com.cn; Peng Rihe; Zhuang Jing; Gao Feng; Zhu Bo; Fu Xiaoyan; Xue Yong; Jin Xiaofen; Tian Yongsheng; Zhao Wei [Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106 (China); Yao Quanhong [Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106 (China)], E-mail: yaoquanhong@saas.sh.cn

2008-11-07

380

Molecular cloning and characterization of one member of 3beta-hydroxy sterol glucosyltransferase gene family in Withania somnifera.  

PubMed

Sterol glycosides are constituents of plant cell membranes. Glucosylations of the sterols are catalyzed by sterol glucosyltransferases (SGTs), which are members of family 1 glycosyltransferases. We have identified the family of SGT genes expressed in the leaves of a medicinal plant Withania somnifera. One member (SGTL1) of this gene family was cloned. The full-length cDNA sequence of SGTL1 represents 2532 bp, comprising untranslated regions (UTRs) of 337 and 89 bp at the 5' and 3' ends, respectively. The amino acid sequence deduced from the 2103 bp open reading frame (ORF) showed homology (67-45%) to the reported plant SGTs. The presence of two putative transmembrane domains suggested the association of SGTL1 with membrane. The SGTL1 was expressed in Escherichi