Construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases
Construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases
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DOI：
10.1093/mp/ssn052
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发表时间：
2008-09-01
期刊：
影响因子：
27.5
通讯作者：
Ronald, Pamela C.
中科院分区：
文献类型：
--
作者：
Cao, Pei-Jian;Bartley, Laura E.;Ronald, Pamela C.
糖基转移酶（GT; EC 2.4. X. y）构成通过将糖从活化的供体分子转移到受体分子而形成糖苷键的一大组酶。GT对植物细胞壁的生物合成以及其他多种功能至关重要。基于碳水化合物活性酶（CAZy）数据库和序列相似性搜索，我们已经确定了609个潜在的GT基因（位点）对应于769个转录本（基因模型）在水稻（水稻），参考单子叶植物物种。使用结构域组成和序列相似性，这些水稻GT被分为40个CAZy家族加上一个额外的未知类。我们发现两个功能未知的Pfam结构域PF 04577和PF 04646分别与GT家族GT 61和GT31相关。为了便于对这个重要的大基因家族进行功能分析，我们创建了一个水稻基因组GT数据库（http：//riceobservinggenomics. ucdavis。edu/cellwalls/gt/）。通过该数据库，几类功能基因组数据，包括突变株系和基因表达数据，可以显示每个水稻GT的系统发育树的背景下，允许GT家族内和之间的比较分析。对公开基因表达数据的综合数字表达分析显示，大多数（接近80%）水稻GT都有表达。基于与Inparanoid的分析，我们确定了282个“水稻分歧”GT，在测序的双子叶植物（拟南芥，杨树，蒺藜苜蓿，蓖麻）中缺乏直系同源物。结合这些分析，我们确定了33个水稻分化的GT基因（45个基因模型），在地上部，营养组织中高度表达。从文献和这项分析中，这些位点中的21个是理解和操纵草细胞壁质量的功能检查的极好目标。对其余部分的研究可能揭示对水稻生物学至关重要的激素和蛋白质代谢方面。这33个基因的列表和水稻GT数据库将促进水稻和其他植物中GT和细胞壁合成的研究。
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 (similar to 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.