An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development.

Ai Oikawa,Chithra Manisseri,Emilie A Rennie,Hiren J Joshi,Berit Ebert,Henrik Vibe Scheller,Joshua L Heazlewood,Samuel P Hazen

doi:10.1371/journal.pone.0015481

Abstract

Xylans constitute the major non-cellulosic component of plant biomass. Xylan biosynthesis is particularly pronounced in cells with secondary walls, implying that the synthesis network consists of a set of highly expressed genes in such cells. To improve the understanding of xylan biosynthesis, we performed a comparative analysis of co-expression networks between Arabidopsis and rice as reference species with different wall types. Many co-expressed genes were represented by orthologs in both species, which implies common biological features, while some gene families were only found in one of the species, and therefore likely to be related to differences in their cell walls. To predict the subcellular location of the identified proteins, we developed a new method, PFANTOM (plant protein family information-based predictor for endomembrane), which was shown to perform better for proteins in the endomembrane system than other available prediction methods. Based on the combined approach of co-expression and predicted cellular localization, we propose a model for Arabidopsis and rice xylan synthesis in the Golgi apparatus and signaling from plasma membrane to nucleus for secondary cell wall differentiation. As an experimental validation of the model, we show that an Arabidopsis mutant in the PGSIP1 gene encoding one of the Golgi localized candidate proteins has a highly decreased content of glucuronic acid in secondary cell walls and substantially reduced xylan glucuronosyltransferase activity.

Highlights

Plant cell walls are complex structures, predominantly composed of polysaccharides
From a list comprising 1146 co-expressed genes from Arabidopsis and rice using the ATTED-II database, we identified novel candidates involved in signal transduction, regulation and substrate transport, as well as enzymes directly involved in secondary wall biosynthesis
Based on the co-expression analysis and the predictions of subcellular locations, we propose a model of Arabidopsis and rice xylan synthesis and conserved signaling components for secondary cell wall development

Summary

Introduction

Plant cell walls are complex structures, predominantly composed of polysaccharides. The polysaccharides in secondary walls are largely represented by cellulose and hemicelluloses, xylans. E.g. mannans and xyloglucans are much less abundant in secondary walls. Secondary walls in angiosperms contain xylan as the major hemicellulose, and this xylan generally has little or no arabinose and a high acetate content. Xylans from different dicot and gymnosperm species, including Arabidopsis, have been shown to contain the complex structure b-D-Xyl-(1R4)-b-D-Xyl-(1R3)-a-L-Rha-(1R2)-a-D-GalA -(1R4)-D-Xyl at the reducing end [2,3,4]. Such structures are yet to be reported in grasses

Methods

Results

Discussion

Conclusion