An integrated genomic and metabolomic framework for cell wall biology in rice

Abstract

BackgroundPlant cell walls are complex structures that full-fill many diverse functions during plant growth and development. It is therefore not surprising that thousands of gene products are involved in cell wall synthesis and maintenance. However, functional association for the majority of these gene products remains obscure. One useful approach to infer biological associations is via transcriptional coordination, or co-expression of genes. This approach has proved useful for several biological processes. Nevertheless, combining co-expression with other large-scale measurements may improve the biological inferences.ResultsIn this study, we used a combined approach of co-expression and cell wall metabolomics to obtain new insight into cell wall synthesis in rice. We initially created a weighted gene co-expression network from publicly available datasets, and then established a comprehensive cell wall dataset by determining cell wall compositions from 29 tissues that almost cover the whole life cycle of rice. We subsequently combined the datasets through the conversion of co-expressed gene modules into eigen-vectors, representing expression profiles for the genes in the modules, and performed comparative analyses against the cell wall contents. Here, we made three major discoveries. First, we confirmed our approach by finding primary and secondary wall cellulose biosynthesis modules, respectively. Second, we found co-expressed modules that strongly correlated with re-organization of the secondary cell walls and with modifications and degradation of hemicellulosic structures. Third, we inferred that at least one module is likely to play a regulatory role in the production of G-rich lignification.ConclusionsHere, we integrated transcriptomic associations and cell wall metabolism and found that certain co-expressed gene modules are positively correlated with distinct cell wall characteristics. We propose that combining multiple data-types, such as coordinated transcription and cell wall analyses, may be a useful approach to glean new insight into biological processes. The combination of multiple datasets, as illustrated here, can further improve the functional inferences that typically are generated via a single type of datasets. In addition, our data extend the typical co-expression approach to allow deeper insight into cell wall biology in rice.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-596) contains supplementary material, which is available to authorized users.

Silica distinctively affects cell wall features and lignocellulosic saccharification with large enhancement on biomass production in rice

“…Although silica is a reported plant cell wall component [22][23][24]48], little is known about its effects on cell wall networks. Systems biology analysis based on correlations of large sample populations is a powerful approach to address these issues [44,45]. In this study, we have observed a significant positive correlation between silica and three major wall polymers (cellulose, hemicelluloses and lignin) using 42 distinct cell wall mutants.…”

CmMYB19 Over-Expression Improves Aphid Tolerance in Chrysanthemum by Promoting Lignin Synthesis

“…Both AtMYB15 and AtMYB38 interact with a harpin protein to modulate the plant’s tolerance to infestation by the green peach aphid [16]. The phylogenetic analysis indicated that CmMYB19 was included in the group of lignin biosynthesis or wall deposition [11], of which AtMYB103 , AtMYB61 , AtMYB55 [17] AtMYB83 , AtMYB46 [18], AtMYB86 [19], AtMYB26 [20], and AtMYB50 [21] have been proved to be involved in the biosynthesis of lignin; however, the roles of AtMYB18 , AtMYB 19, AtMYB 45 and AtMYB 67 in lignin biosynthesis have not been described yet. Here, CmMYB19 overexpression enhanced the accumulation of lignin.…”

Advances in Genetic Manipulation of Lignocellulose to Reduce Biomass Recalcitrance and Enhance Biofuel Production in Bioenergy Crops

“…KORRIGAN protein, a GH 9 A family member, can play a role in cellulose biosynthesis by either cleaving a sterol-cellodextrin substrate or removing glucan chains incorrectly assembled in the growing microfibrils. KORRIGAN (kor) mutants show reduced cellulose levels and imperfect plant growth, while overexpression of PtCel 9 A 1 (GH 9 A) leads to reduced cellulose CrI and increased biomass yield [83]. In rice mutants, the expression levels of OsGH 9 B family genes are meaningfully associated with cellulase activity and cellulose CrI, recommending that GH9B family should play a role in cellulose degradation.…”

“…In rice mutants, the expression levels of OsGH 9 B family genes are meaningfully associated with cellulase activity and cellulose CrI, recommending that GH9B family should play a role in cellulose degradation. It have reported that the overexpression of PtGH 9 B 5 /C 2 genes redound to low plant growth and biomass yield, but RNAi silencing of the AtGH 9 C 2 gene could reduce cellulose CrI and improve biomass yield [83].…”