Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum).

Xiaolan Rao,Yuhong Tang,Qin Ma,Scott Lenaghan,Guifen Li,Taylor P Frazier,Maria Pena,Fang Chen,Hui Shen,Richard A Dixon,Xirong Xiao,William York,Xin Chen

doi:10.1111/pbi.13000

Abstract

SummaryCell wall recalcitrance is the major challenge to improving saccharification efficiency in converting lignocellulose into biofuels. However, information regarding the transcriptional regulation of secondary cell wall biogenesis remains poor in switchgrass (Panicum virgatum), which has been selected as a biofuel crop in the United States. In this study, we present a combination of computational and experimental approaches to develop gene regulatory networks for lignin formation in switchgrass. To screen transcription factors (TFs) involved in lignin biosynthesis, we developed a modified method to perform co‐expression network analysis using 14 lignin biosynthesis genes as bait (target) genes. The switchgrass lignin co‐expression network was further extended by adding 14 TFs identified in this study, and seven TFs identified in previous studies, as bait genes. Six TFs (PvMYB58/63, PvMYB42/85, PvMYB4, PvWRKY12, PvSND2 and PvSWN2) were targeted to generate overexpressing and/or down‐regulated transgenic switchgrass lines. The alteration of lignin content, cell wall composition and/or plant growth in the transgenic plants supported the role of the TFs in controlling secondary wall formation. RNA‐seq analysis of four of the transgenic switchgrass lines revealed downstream target genes of the secondary wall‐related TFs and crosstalk with other biological pathways. In vitro transactivation assays further confirmed the regulation of specific lignin pathway genes by four of the TFs. Our meta‐analysis provides a hierarchical network of TFs and their potential target genes for future manipulation of secondary cell wall formation for lignin modification in switchgrass.

Highlights

The cell wall is deposited outside the plant cell membrane as a cellular exoskeleton that can be classified as primary or secondary depending on function and composition (Vogel, 2008)
We developed a new method based on a bi-clustering algorithm to detect transcription factors (TFs) that are strongly co-expressed with previously validated lignin biosynthesis genes in switchgrass, and extended the switchgrass coexpression network by adding 21 switchgrass TF genes identified as secondary wall regulators as seed genes
To detect genes with similar expression patterns in large data sets, we developed a modified method for co-expression analysis based on QUBIC, a previously reported bi-clustering algorithm (Li et al, 2009; Zhang et al, 2017)

Summary

Introduction

The cell wall is deposited outside the plant cell membrane as a cellular exoskeleton that can be classified as primary or secondary depending on function and composition (Vogel, 2008). The secondary cell wall polymers cellulose, hemicellulose and lignin constitute the most abundant source of plant biomass that provides raw materials for generating renewable biofuels (Bouton, 2007; Pauly and Keegstra, 2010). Covalently incorporated into the cross-linked matrix of polysaccharides, prevents access of hydrolytic enzymes for degrading the lignocellulosic components to monosaccharides for subsequent biofuel production (Pauly and Keegstra, 2010). Lignin has potential to be developed as a high value co-product of bioprocessing (Ragauskas et al, 2014). For both applications, knowledge of the gene regulatory networks underlying lignin and secondary cell wall biosynthesis is necessary to facilitate targeted genetic interventions

Results

Discussion

Conclusion