Rice Genome-Scale Network Integration Reveals Transcriptional Regulators of Grass Cell Wall Synthesis.

Kangmei Zhao,Ki-Hong Jung,Fan Lin,Gynheung An,Hyung-Jung Goh,Samuel P Hazen,Prasenjit Saha,Laura E Bartley,Sandra P Romero-Gamboa

doi:10.3389/fpls.2019.01275

Kangmei Zhao, Ki-Hong Jung + Show 7 more

Open Access

https://doi.org/10.3389/fpls.2019.01275

Copy DOI

Abstract

Grasses have evolved distinct cell wall composition and patterning relative to dicotyledonous plants. However, despite the importance of this plant family, transcriptional regulation of its cell wall biosynthesis is poorly understood. To identify grass cell wall-associated transcription factors, we constructed the Rice Combined mutual Ranked Network (RCRN). The RCRN covers >90% of annotated rice (Oryza sativa) genes, is high quality, and includes most grass-specific cell wall genes, such as mixed-linkage glucan synthases and hydroxycinnamoyl acyltransferases. Comparing the RCRN and an equivalent Arabidopsis network suggests that grass orthologs of most genetically verified eudicot cell wall regulators also control this process in grasses, but some transcription factors vary significantly in network connectivity between these divergent species. Reverse genetics, yeast-one-hybrid, and protoplast-based assays reveal that OsMYB61a activates a grass-specific acyltransferase promoter, which confirms network predictions and supports grass-specific cell wall synthesis genes being incorporated into conserved regulatory circuits. In addition, 10 of 15 tested transcription factors, including six novel Wall-Associated regulators (WAP1, WACH1, WAHL1, WADH1, OsMYB13a, and OsMYB13b), alter abundance of cell wall-related transcripts when transiently expressed. The results highlight the quality of the RCRN for examining rice biology, provide insight into the evolution of cell wall regulation, and identify network nodes and edges that are possible leads for improving cell wall composition.

Highlights

Cultivated grasses are the most abundant sustainable biomass source produced worldwide (Lal, 2005), and cell walls constitute the bulk of plant dry mass available for conversion to biofuels and other bioproducts
Our goal was to utilize rice genome-scale networks to understand grass cell wall biosynthesis and regulation especially related to grass-specific aspects of the process
The Bayesian functional network, RiceNet v2 lacks approximately one quarter of these genes. This high-quality functional network may be incomplete with respect to grass-diverged cell wall synthesis

Summary

Introduction

Cultivated grasses are the most abundant sustainable biomass source produced worldwide (Lal, 2005), and cell walls constitute the bulk of plant dry mass available for conversion to biofuels and other bioproducts. Primary walls surround growing cells; whereas, after cessation of growth, secondary walls form around cells such as tracheids, vessels, and fibers. Primary and secondary cell walls consist of both conserved components and those that vary across plant diversity (Liepman et al, 2010; Popper et al, 2011; Fangel et al, 2012). Lignin is characteristic of secondary cell walls and forms a barrier for breakdown of cellulose and other wall polysaccharides, including during biofuel production (Bonawitz and Chapple, 2010; Vanholme et al, 2010). Phylogenetic analyses have revealed orthologs of lignin biosynthesis genes and CESAs across eudicots and monocots (Hazen et al, 2002; Penning et al, 2009; Popper et al, 2011; Carpita, 2012)

Objectives

Methods

Results

Conclusion