Identification of Transcription Factors Involved in Rice Secondary Cell Wall Formation

Abstract

Using co-expression network analysis, we identified 123 transcription factors (TFs) as candidate secondary cell wall regulators in rice. To validate whether these TFs are associated with secondary cell wall formation, six TF genes belonging to the MYB, NAC or homeodomain-containing TF families were overexpressed or downregulated in rice. With the exception of OsMYB58/63-RNAi plants, all transgenic plants showed phenotypes possibly related to secondary cell wall alteration, such as dwarfism, narrow and dark green leaves, and also altered rice cinnamyl alcohol dehydrogenase 2 (OsCAD2) gene expression and lignin content. These results suggest that many of the 123 candidate secondary cell wall-regulating TFs are likely to function in secondary cell wall formation in rice. Further analyses were performed for the OsMYB55/61 and OsBLH6 TFs, the former being a TF in which the Arabidopsis ortholog is known to participate in lignin biosynthesis (AtMYB61) and the latter being one for which no previous involvement in cell wall formation has been reported even in Arabidopsis (BLH6). OsMYB55/61 and OsBLH6-GFP fusion proteins localized to the nucleus of onion epidermal cells. Moreover, expression of a reporter gene driven by the OsCAD2 promoter was enhanced in rice calli when OsMYB55/61 or OsBLH6 was transiently expressed, demonstrating that they function in secondary cell wall formation. These results show the validity of identifying potential secondary cell wall TFs in rice by the use of rice co-expression network analysis.

Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass

“…The switchgrass ortholog in this clade with gene expression data available, AP13ISTG56055 , shows high expression in E4 vascular bundles and internodes, consistent with the possibility that they regulate SCW biosynthesis (Figure 9). Overexpression of the two OsMYB58/63 genes was recently found to promote lignin deposition in rice stems, supporting their orthologous relationship with the AtMYB58 and 63 [75]. In the OrthoMCL analysis, AtMYB58 and AtMYB63 are paralogs and putative co-orthologs are found in the grasses.…”

“…Sequence identity between AtMYB103 and the putative grass orthologs is intermediate, ranging from 48% to 51%, and OrthoMCL mostly supports the phylogenetic analysis, further evidence that AP13ISTG58495 may be a SCW regulator in switchgrass (Table 4). In rice, a preliminary study reported that RNAi lines of OsMYB103 show a severe dwarf phenotype and did not grow to maturity [75]; whereas, only altered tapetum, pollen and trichome morphology were observed in Arabidopsis AtMYB103 silencing mutants [28,29]. This difference in phenotypes caused by expression disruption of apparently orthologous genes between rice and Arabidopsis suggests differences in the SCW regulatory network between grasses and dicots not obvious from the phylogenetic relationships of the Class I proteins.…”

“…Overexpression of AtMYB85, AtMYB52 , or AtMYB54 (but not of AtMYB42, AtMYB20 , or AtMYB43 ) leads to ectopic deposition of lignin in epidermal and cortical cells in stems [31]. Moreover, RNAi of OsMYB42/85 ( LOC_Os09g36250 ) causes a severe dwarf phenotype [75]. The maximum likelihood phylogenic trees of each of these Arabidopsis protein pairs contains one or two rice proteins, one to three maize proteins and two or more poplar proteins (Figure 4, Figure 5, Table 4).…”

“…We found that this clade is expanded in poplar and switchgrass; whereas, rice and maize possess two paralogs (Figure 4). RNAi of the two OsMYB61 s downregulates the expression of OsCAD2 , which encodes a lignin biosynthesis enzyme [75]. AtMYB61 is expressed in xylem, leaf and root.…”

A Gibberellin-Mediated DELLA-NAC Signaling Cascade Regulates Cellulose Synthesis in Rice

“…This discrepancy indicates that the secondary wall regulatory network in monocot plants may be distinct from the one in dicots in certain respects. In this study, although total lignin content was not changed in the transgenic plants, we cannot exclude the possibility that their lignin composition was altered, as Os-NAC31 and Os-MYB61 were reported to regulate Os-MYB46 and Os-CINNAMYL ALCOHOL DEHYDROGENASE2 expression (Zhong et al, 2011;Hirano et al, 2013). Moreover, cellulosic biofuel is a type of sustainable energy source that has gained popular support due to its potential benefit to the global environment.…”