Construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases.
Glycosyltransferases (GTs; EC 2.4.x.y) constitute a large group of enzymes that form glycosidic bonds through transfer of sugars from activated donor molecules to acceptor molecules. GTs are critical to the biosynthesis of plant cell walls, among other diverse functions. Based on the Carbohydrate-Active enZymes (CAZy) database and sequence similarity searches, we have identified 609 potential GT genes (loci) corresponding to 769 transcripts (gene models) in rice (Oryza sativa), the reference monocotyledonous species. Using domain composition and sequence similarity, these rice GTs were classified into 40 CAZy families plus an additional unknown class. We found that two Pfam domains of unknown function, PF04577 and PF04646, are associated with GT families GT61 and GT31, respectively. To facilitate functional analysis of this important and large gene family, we created a phylogenomic Rice GT Database (http://ricephylogenomics.ucdavis.edu/cellwalls/gt/). Through the database, several classes of functional genomic data, including mutant lines and gene expression data, can be displayed for each rice GT in the context of a phylogenetic tree, allowing for comparative analysis both within and between GT families. Comprehensive digital expression analysis of public gene expression data revealed that most ( approximately 80%) rice GTs are expressed. Based on analysis with Inparanoid, we identified 282 'rice-diverged' GTs that lack orthologs in sequenced dicots (Arabidopsis thaliana, Populus tricocarpa, Medicago truncatula, and Ricinus communis). Combining these analyses, we identified 33 rice-diverged GT genes (45 gene models) that are highly expressed in above-ground, vegetative tissues. From the literature and this analysis, 21 of these loci are excellent targets for functional examination toward understanding and manipulating grass cell wall qualities. Study of the remainder may reveal aspects of hormone and protein metabolism that are critical for rice biology. This list of 33 genes and the Rice GT Database will facilitate the study of GTs and cell wall synthesis in rice and other plants.
Cao
Pei-Jian
PJ
Department of Plant Pathology, University of California, Davis, CA 95616, USA.
Bartley
Laura E
LE
Jung
Ki-Hong
KH
Ronald
Pamela C
PC
D016000:Cluster Analysis; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D016695:Glycosyltransferases / Q000235:genetics* / Q000378:metabolism; D020407:Internet; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000201:enzymology* / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013045:Species Specificity
D010940:Plant Proteins; D016695:Glycosyltransferases