PlantCAZyme: a database for plant carbohydrate-active enzymes

Ekström, Alexander; Taujale, Rahil; McGinn, Nathan; Yin, Yanbin

doi:10.1093/database/bau079

Cited by 29 publications

(20 citation statements)

References 38 publications

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“…org/; Coutinho et al, 2003) includes members from a diverse range of species including humans and Drosophila melanogaster, Selaginella moellendorffii, Arabidopsis, and rice (Oryza sativa). However, while most animal proteins contain both a GT64 and GT47 domain, the 143 genes currently annotated as GT64 in the plant CAZyme database have only a GT64 domain (Edvardsson et al, 2010;Ekstrom et al, 2014).…”

Section: Resultsmentioning

confidence: 99%

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Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis

et al. 2016

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Glycosylinositol phosphorylceramides (GIPCs) are a class of glycosylated sphingolipids found in plants, fungi, and protozoa. These lipids are abundant in the plant plasma membrane, forming ;25% of total plasma membrane lipids. Little is known about the function of the glycosylated headgroup, but two recent studies have indicated that they play a key role in plant signaling and defense. Here, we show that a member of glycosyltransferase family 64, previously named ECTOPICALLY PARTING CELLS1, is likely a Golgi-localized GIPC-specific mannosyl-transferase, which we renamed GIPC MANNOSYL-TRANSFERASE1 (GMT1). Sphingolipid analysis revealed that the Arabidopsis thaliana gmt1 mutant almost completely lacks mannose-carrying GIPCs. Heterologous expression of GMT1 in Saccharomyces cerevisiae and tobacco (Nicotiana tabacum) cv Bright Yellow 2 resulted in the production of non-native mannosylated GIPCs. gmt1 displays a severe dwarfed phenotype and a constitutive hypersensitive response characterized by elevated salicylic acid and hydrogen peroxide levels, similar to that we previously reported for the Golgi-localized, GIPC-specific, GDP-Man transporter GONST1 (Mortimer et al., 2013). Unexpectedly, we show that gmt1 cell walls have a reduction in cellulose content, although other matrix polysaccharides are unchanged.

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Section: Resultsmentioning

confidence: 99%

“…GT64 protein sequences were downloaded from PlantCAZyme (Ekstrom et al, 2014) on February 10, 2015. Sequences were aligned using ClustalOmega using default settings (www.ebi.ac.uk; McWilliam et al, 2013) and exported in PHYLIP format.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis

et al. 2016

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“…Carbohydrate-active enzymes (CAZymes) are essential and abundant in plant proteomes (Ekstrom et al, 2014). CAZymes perform the synthesis and modification of the diverse polysaccharides that constitute the plant cell wall, and are also involved in pathways related to signaling, defense and energy storage.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive cross‐genome survey and phylogeny of glycoside hydrolase family 16 members reveals the evolutionary origin of EG16 and XTH proteins in plant lineages

2018

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Carbohydrate-active enzymes (CAZymes) are central to the biosynthesis and modification of the plant cell wall. An ancient clade of bifunctional plant endo-glucanases (EG16 members) was recently revealed and proposed to represent a transitional group uniting plant xyloglucan endo-transglycosylase/hydrolase (XTH) gene products and bacterial mixed-linkage endo-glucanases in the phylogeny of glycoside hydrolase family 16 (GH16). To gain broader insights into the distribution and frequency of EG16 and other GH16 members in plants, the PHYTOZOME, PLAZA, NCBI and 1000 PLANTS databases were mined to build a comprehensive census among 1289 species, spanning the broad phylogenetic diversity of multiple algae through recent plant lineages. EG16, newly identified EG16-2 and XTH members appeared first in the green algae. Extant EG16 members represent the early adoption of the β-jellyroll protein scaffold from a bacterial or early-lineage eukaryotic GH16 gene, which is characterized by loop deletion and extension of the N terminus (in EG16-2 members) or C terminus (in XTH members). Maximum-likelihood phylogenetic analysis of EG16 and EG16-2 sequences are directly concordant with contemporary estimates of plant evolution. The lack of expansion of EG16 members into multi-gene families across green plants may point to a core metabolic role under tight control, in contrast to XTH genes that have undergone the extensive duplications typical of cell-wall CAZymes. The present census will underpin future studies to elucidate the physiological role of EG16 members across plant species, and serve as roadmap for delineating the closely related EG16 and XTH gene products in bioinformatic analyses of emerging genomes and transcriptomes.

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“…However, some unicellular green algal species, such as C. reinhardtii , have a glycoprotein-layer structure similar in composition to those of land plant species [ 33 ]. Additionally, quite a few members of cell wall gene families have been found in unicellular green algae genome sequences [ 34 , 35 ]. For example, the C. subellipsoidea C-169 genome reveals cellulose synthase-like domains, although not orthologous to the cellulose synthases and hemicellulose synthases of land plant species [ 36 ].…”

Section: Cell Wall Diversity and Plant Evolutionmentioning

confidence: 99%

A Genomic Perspective on the Evolutionary Diversity of the Plant Cell Wall

Yokoyama

2020

Plants

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The plant cell wall is a complex and dynamic structure composed of numerous different molecules that play multiple roles in all aspects of plant life. Currently, a new frontier in biotechnology is opening up, which is providing new insights into the structural and functional diversity of cell walls, and is thus serving to re-emphasize the significance of cell wall divergence in the evolutionary history of plant species. The ever-increasing availability of plant genome datasets will thus provide an invaluable basis for enhancing our knowledge regarding the diversity of cell walls among different plant species. In this review, as an example of a comparative genomics approach, I examine the diverse patterns of cell wall gene families among 100 species of green plants, and illustrate the evident benefits of using genome databases for studying cell wall divergence. Given that the growth and development of all types of plant cells are intimately associated with cell wall dynamics, gaining a further understanding of the functional diversity of cell walls in relation to diverse biological events will make significant contributions to a broad range of plant sciences.

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PlantCAZyme: a database for plant carbohydrate-active enzymes

Cited by 29 publications

References 38 publications

Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis

Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis

Comprehensive cross‐genome survey and phylogeny of glycoside hydrolase family 16 members reveals the evolutionary origin of EG16 and XTH proteins in plant lineages

A Genomic Perspective on the Evolutionary Diversity of the Plant Cell Wall

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