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Evolution of xyloglucan-related genes in green plants.

ABSTRACT: BACKGROUND: The cell shape and morphology of plant tissues are intimately related to structural modifications in the primary cell wall that are associated with key processes in the regulation of cell growth and differentiation. The primary cell wall is composed mainly of cellulose immersed in a matrix of hemicellulose, pectin, lignin and some structural proteins. Xyloglucan is a hemicellulose polysaccharide present in the cell walls of all land plants (Embryophyta) and is the main hemicellulose in non-graminaceous angiosperms. RESULTS: In this work, we used a comparative genomic approach to obtain new insights into the evolution of the xyloglucan-related enzymatic machinery in green plants. Detailed phylogenetic analyses were done for enzymes involved in xyloglucan synthesis (xyloglucan transglycosylase/hydrolase, ?-xylosidase, ?-galactosidase, ?-glucosidase and ?-fucosidase) and mobilization/degradation (?-(1?4)-glucan synthase, ?-fucosyltransferases, ?-galactosyltransferases and ?-xylosyl transferase) based on 12 fully sequenced genomes and expressed sequence tags from 29 species of green plants. Evidence from Chlorophyta and Streptophyta green algae indicated that part of the Embryophyta xyloglucan-related machinery evolved in an aquatic environment, before land colonization. Streptophyte algae have at least three enzymes of the xyloglucan machinery: xyloglucan transglycosylase/hydrolase, ?-(1?4)-glucan synthase from the cellulose synthase-like C family and ?-xylosidase that is also present in chlorophytes. Interestingly, gymnosperm sequences orthologs to xyloglucan transglycosylase/hydrolases with exclusively hydrolytic activity were also detected, suggesting that such activity must have emerged within the last common ancestor of spermatophytes. There was a positive correlation between the numbers of founder genes within each gene family and the complexity of the plant cell wall. CONCLUSIONS: Our data support the idea that a primordial xyloglucan-like polymer emerged in streptophyte algae as a pre-adaptation that allowed plants to subsequently colonize terrestrial habitats. Our results also provide additional evidence that charophycean algae and land plants are sister groups.

SUBMITTER: Del Bem LE

PROVIDER: S-EPMC3087550 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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Evolution of xyloglucan-related genes in green plants.

Del Bem Luiz Eduardo V LE Vincentz Michel G A MG

BMC evolutionary biology 20101105

<h4>Background</h4>The cell shape and morphology of plant tissues are intimately related to structural modifications in the primary cell wall that are associated with key processes in the regulation of cell growth and differentiation. The primary cell wall is composed mainly of cellulose immersed in a matrix of hemicellulose, pectin, lignin and some structural proteins. Xyloglucan is a hemicellulose polysaccharide present in the cell walls of all land plants (Embryophyta) and is the main hemicel ...[more]

PMID: 21054875

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Project description:BACKGROUND:DNA methylation is a crucial epigenetic modification, which is involved in many biological processes, including gene expression regulation, embryonic development, cell differentiation and genomic imprinting etc. And it also involves many key regulatory genes in eukaryotes. By tracing the evolutionary history of methylation-related genes, we can understand the origin and expansion time of these genes, which helps to understand the evolutionary history of plants, and we can also understand the changes of DNA methylation patterns in different species. However, most studies on the evolution of methylation-related genes failed to be carried out for the whole DNA methylation pathway. RESULTS:In this study, we conducted a comprehensive identification of 33 methylation-related genes in 77 species, and investigated gene origin and evolution throughout the plant kingdom. We found that the origin of genes responsible for methylation maintenance and demethylation evolved early, while most de novo methylation-related genes appeared late. The methylation-related genes were expanded by whole genome duplication and tandem replication, but were also accompanied by a large number of gene absence events in different species. The gene length and intron length varied a lot in different species, but exon structure and functional domains were relatively conserved. The phylogenetic relationships of methylation-related genes were traced to reveal the evolution history of DNA methylation in different species. The expression patterns of methylation-related genes have changed during the evolution of species, and the expression patterns of these genes in different species can be clustered into four categories. CONCLUSIONS:The study describes a global characterization of DNA methylation-related genes in the plant kingdom. The similarities and differences in origin time, gene structure and phylogenetic relationship of these genes lead us to understand the evolutionary conservation and dynamics of DNA methylation in plants.

Project description:BACKGROUND: The Viridiplantae (land plants and green algae) consist of two monophyletic lineages, the Chlorophyta and the Streptophyta. The Streptophyta include all embryophytes and a small but diverse group of freshwater algae traditionally known as the Charophyceae (e.g. Charales, Coleochaete and the Zygnematales). The only flagellate currently included in the Streptophyta is Mesostigma viride Lauterborn. To gain insight into the genome evolution in streptophytes, we have sequenced 10,395 ESTs from Mesostigma representing 3,300 independent contigs and compared the ESTs of Mesostigma with available plant genomes (Arabidopsis, Oryza, Chlamydomonas), with ESTs from the bryophyte Physcomitrella, the genome of the rhodophyte Cyanidioschyzon, the ESTs from the rhodophyte Porphyra, and the genome of the diatom Thalassiosira. RESULTS: The number of expressed genes shared by Mesostigma with the embryophytes (90.3 % of the expressed genes showing similarity to known proteins) is higher than with Chlamydomonas (76.1 %). In general, cytosolic metabolic pathways, and proteins involved in vesicular transport, transcription, regulation, DNA-structure and replication, cell cycle control, and RNA-metabolism are more conserved between Mesostigma and the embryophytes than between Mesostigma and Chlamydomonas. However, plastidic and mitochondrial metabolic pathways, cytoskeletal proteins and proteins involved in protein folding are more conserved between Mesostigma and Chlamydomonas than between Mesostigma and the embryophytes. CONCLUSION: Our EST-analysis of Mesostigma supports the notion that this organism should be a suitable unicellular model for the last flagellate common ancestor of the streptophytes. Mesostigma shares more genes with the embryophytes than with the chlorophyte Chlamydomonas reinhardtii, although both organisms are flagellate unicells. Thus, it seems likely that several major physiological changes (e.g. in the regulation of photosynthesis and photorespiration) took place early during the evolution of streptophytes, i.e. before the transition to land.

Project description:1. Cell-free extracts of all plants tested contained a novel enzyme activity (xyloglucan endotransglycosylase, XET) able to transfer a high-Mr portion from a donor xyloglucan to a suitable acceptor such as a xyloglucan-derived nonasaccharide (Glc4Xyl3GalFuc; XG9). 2. A simple assay for the enzyme, using [3H]XG9 and based on the ability of the [3H]polysaccharide product to bind to filter paper, is described. 3. The enzyme was highly specific for xyloglucan as the glycosyl donor, and showed negligible transglycosylation of other polysaccharides, including CM-cellulose. 4. The Km for XG9 was 50 microM; certain other 3H-labelled xyloglucan oligosaccharides also acted as acceptors, and certain non-radioactive xyloglucan oligosaccharides competed with [3H]XG9 as acceptor; the minimum acceptor structure was deduced to be: [formula: see text] 5. The pH optimum was approx. 5.5 and the enzyme was less than half as active at pH 7.0. The enzyme was slightly activated by Ca2+, Mg2+, Mn2+, spermidine, ascorbate and 2-mercaptoethanol, and inhibited by Ag+, Hg2+, Zn2+ and La3+. 6. XET activity was essentially completely extracted by aqueous solutions of low ionic strength; Triton X-100, Ca2+, La3+, and Li+ did not enhance extraction. Negligible activity was left in the unextractable (cell-wall-rich) residue. 7. The enzyme differed from the major cellulases (EC 3.2.1.4) of pea in: (a) susceptibility to inhibition by cello-oligosaccharides, (b) polysaccharide substrate specificity, (c) inducibility by auxin, (d) requirement for salt in the extraction buffer and (e) activation by 2-mercaptoethanol. XET is therefore concluded to be a new enzyme activity (xyloglucan: xyloglucan xyloglucanotransferase; EC 2.4.1.-). 8. XET was detected in extracts of the growing portions of dicotyledons, monocotyledons (graminaceous and liliaceous) and bryophytes. 9. The activity was positively correlated with growth rate in different zones of the pea stem. 10. We propose that XET is responsible for cutting and rejoining intermicrofibrillar xyloglucan chains and that it thus causes the wall-loosening required for plant cell expansion.

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Evolution of xyloglucan-related genes in green plants.

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Evolution of xyloglucan-related genes in green plants.

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