Abstract
Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.
Highlights
Plant cell walls are the most abundant source of biomass and stored solar energy on Earth
CLASSIFICATION OF 437 GLYCOSIDE HYDROLASE GENES IN RICE INTO 34 FAMILIES When accessed for this study, the Carbohydrate-Active EnZymes (CAZy) database contained 430 genes annotated as coding for glycoside hydrolases in rice
Using homology and domain searches, we identified an additional seven family members resulting in 437 Glycoside hydrolases (GHs) genes in rice
Summary
Plant cell walls are the most abundant source of biomass and stored solar energy on Earth. The identification and characterization of genes encoding enzymes that catalyze the synthesis and degradation of plant cell wall polysaccharides is needed to advance the knowledge required for production of genetically improved biofuel feedstocks (Mansfield, 2009; Lionetti et al, 2010; Yang et al, 2013). GHs catalyze the hydrolysis of O- or S- glycosidic linkages to release sugars and, can make major contributions to degrading biomass for biofuel production. The meta-analysis tool of Rice Oligonucleotide Array Database (ROAD; http://www.ricearray.org/), designed to allow easy extraction of gene expression profiles across 1867 publicly available microarray datasets (Cao et al, 2012), allowed us to analyze the expression patterns of all GH genes in twenty different anatomic tissues of rice. The short list of genes identified provides a good starting point for functional studies that will increase our understanding of and ability to manipulate grass cell wall qualities
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.