An Arabidopsis gene regulatory network for secondary cell wall synthesis

Abstract

SummaryThe plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here, we present a protein-DNA network between Arabidopsis transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism

“…Several genes belonging to these same transcription factor families had similar expression patterns to the shikimate and monolignol pathway genes (Table III) and also were differentially expressed (P adj , 0.001). In the present study, enrichment analysis (Taylor-Teeples et al, 2015) showed statistically significant overrepresentation of the members of AUX-IAA, homeobox, MYB, and WRKY transcription factor families within the differentially expressed genes (hypergeometric probability; Supplemental Table S9). Members of the MYB, Tify, and ABSCISIC STRESS-RIPENING PROTEIN (ASR) transcription factor families also were present in the subnetwork (Tables II and III; Supplemental Table S11), some of which have expression in developing xylem (Nystedt et al, 2013).…”

“…In recent years, secondary cell wall and lignin biosynthesis studies have revealed new members of the transcriptional gene regulatory network (Cassan-Wang et al, 2013;Taylor-Teeples et al, 2015;Shi et al, 2017). Using a yeast one-hybrid approach on Arabidopsis root xylem-expressed transcription factors, TaylorTeeples and colleagues (2015) revealed a highly interconnected gene regulatory network enabling subtle and highly focused regulation of cell wall biosynthesis.…”

“…Gene family enrichment in the differentially expressed genes was determined using the hypergeometric distribution online tool (www.geneprof.org; Taylor-Teeples et al, 2015). Success is a number of genes differentially expressed in ligninforming versus non-lignin-forming comparison (P adj , 0.001) from the population of genes in the spruce genome.…”

Changes in cell wall polysaccharide composition, gene transcription and alternative splicing in germinating barley embryos

“…A cascade TF regulations exist with NAC domain TFs acting as master switches and MYB TFs servicing as second-level regulators (Taylor-Teeples et al , 2015, Zhong et al , 2010, Zhong et al , 2008. Barley genome contains at least 52 NAC and 119 MYB domain TF genes (Supplemental Table S10).…”

Transcription Factor MYB26 Is Key to Spatial Specificity in Anther Secondary Thickening Formation

“…Studies of the NST2-NST3/SND1 and VND1-VND7 genes suggest that secondary cell wall regulating NACdomain genes are all able to directly bind targets associated with cellulose, lignin, and hemicellulose biosynthesis, through a 19-bp consensus sequence secondary wall NAC-binding element (Zhong et al, 2010;Yamaguchi et al, 2011;Taylor-Teeples et al, 2015). Complementation studies have shown that by misexpression of one NAC-domain gene is able to rescue the mutant phenotype, indicating that these genes are functional Figure 9.…”