Survey of Genes Involved in Rice Secondary Cell Wall Formation Through a Co-Expression Network

Abstract

The plant secondary cell wall is the major source of lignocellulosic biomass, a renewable energy resource that can be used for bioethanol production. To comprehensively identify transcription factors (TFs), glycosyltransferase (GT) and glycosyl hydrolase (GH) involved in secondary cell wall formation in rice (Oryza sativa), co-expression network analysis was performed using 68 microarray data points for different rice tissues and stages. In addition to rice genes encoding orthologs of Arabidopsis thaliana TFs known to regulate secondary cell wall formation, the network analysis suggested many novel TF genes likely to be involved in cell wall formation. In the accompanying paper (Hirano et al.), several of these TFs are shown to be involved in rice secondary cell wall formation. Based on a comparison of the rice and Arabidopsis networks, TFs were classified as common to both species or specific to each plant species, suggesting that in addition to a common transcriptional regulatory mechanism of cell wall formation, the two plants may also use species-specific groups of TFs during secondary wall formation. Similarly, genes encoding GT and GH were also classified as genes showing species-common or species-specific expression patterns. In addition, genes for primary or secondary cell wall formation were also suggested. The list of rice TF, GT and GH genes provides an opportunity to unveil the regulation of secondary cell wall formation in grasses, leading to optimization of the cell wall for biofuel production.

The expression of a rice secondary wall-specific cellulose synthase gene, OsCesA7, is directly regulated by a rice transcription factor, OsMYB58/63

“…Ten genes encoding MYB TFs were found to be highly co-expressed (CORs C0.6) with genes encoding lignocellulose biosynthetic enzymes (Table 1). Except for OsMYB86-L1 and OsMYB86-L2, these genes were identical to the SCW-related genes reported by Hirano et al (2013a). The OsMYB55/61, OsMYB55/61-L, OsMYB58/63, and OsMYB42/85 genes (Fig.…”

Breeding maize for silage and biofuel production, an illustration of a step forward with the genome sequence

“…A colocalization was also shown with the two maize orthologs of the Arabidopsis AtXND1 (Xylem NAC Domain 1) gene, which encodes a negative regulator of secondary cell wall synthesis [54,57]. Finally, colocalizations were also found with four out of 11 NAC genes orthologs of rice genes expressed during stem lignification [49].…”

“…Maize MYB genes of G1 and G2 "defense" groups, and of the G14 "development" group were considered as possible candidates because MYB ortholog genes of these families were indeed shown significantly more expressed in Arabidopsis and rice lignifying stems than in other tissues [47][48][49]. Six ZmMYB of these three groups comprising nine genes colocalized with IVNDFD QTLs, thus substantiating the probable involvement of several members of these three MYB groups in constitutive secondary wall assembly in grasses.…”

MYB-mediated upregulation of lignin biosynthesis in <i>Oryza sativa</i> towards biomass refinery

“…Full-length Arabidopsis and rice R2R3-MYB protein sequences (Hirano et al 2013a;Zhao and Bartley 2014) were downloaded from The Arabidopsis Information Resource (TAIR; http:// www.arabidopsis.org), the Rice Annotation Project (RAP-DB, http://rapdb.dna.affrc.go.jp/), and the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/) databases. Multiple alignments were generated from the conserved R2R3 domain (Stracke et al 2001) with ClustalX (Thompson et al 1997) under default parameters.…”

“…In the present study, as the first preliminary experiment to represent the concept of lignin upregulation for biomass refinery, we selected three of these activator-type MYB genes, AtMYB61, AtMYB63, and AtMYB103. In addition, because Arabidopsis transcription factors may function differently when heterologously expressed in rice, we also included one close rice homolog of AtMYB61, OsMYB55/61 (BAF04687) (Hirano et al 2013a) (Figure 1), and two Arabidopsis homologs of AtMYB61, namely AtMYB55 and AtMYB86 (Figure 1). The selected genes were then overexpressed in rice plants under the control of the CaMV 35S promoter.…”