Navigating the transcriptional roadmap regulating plant secondary cell wall deposition

Abstract

The current status of lignocellulosic biomass as an invaluable resource in industry, agriculture, and health has spurred increased interest in understanding the transcriptional regulation of secondary cell wall (SCW) biosynthesis. The last decade of research has revealed an extensive network of NAC, MYB and other families of transcription factors regulating Arabidopsis SCW biosynthesis, and numerous studies have explored SCW-related transcription factors in other dicots and monocots. Whilst the general structure of the Arabidopsis network has been a topic of several reviews, they have not comprehensively represented the detailed protein-DNA and protein-protein interactions described in the literature, and an understanding of network dynamics and functionality has not yet been achieved for SCW formation. Furthermore the methodologies employed in studies of SCW transcriptional regulation have not received much attention, especially in the case of non-model organisms. In this review, we have reconstructed the most exhaustive literature-based network representations to date of SCW transcriptional regulation in Arabidopsis. We include a manipulable Cytoscape representation of the Arabidopsis SCW transcriptional network to aid in future studies, along with a list of supporting literature for each documented interaction. Amongst other topics, we discuss the various components of the network, its evolutionary conservation in plants, putative modules and dynamic mechanisms that may influence network function, and the approaches that have been employed in network inference. Future research should aim to better understand network function and its response to dynamic perturbations, whilst the development and application of genome-wide approaches such as ChIP-seq and systems genetics are in progress for the study of SCW transcriptional regulation in non-model organisms.

Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis

“…site. To evaluate our network, we used an experimental GRN of 1092 confirmed interactions derived from AtRegNet (Davuluri et al, 2003) and a collection of regulatory interactions obtained from small-scale studies concerning secondary cell wall metabolism (Hussey et al, 2013). Overlap analysis between the predicted network and the experimental network revealed that edges present in the predicted network are significantly more likely to also be present in the experimental network than would be expected by chance (4.65-fold enrichment, P value < 0.001; see Methods).…”

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

“…A tree's amenability to bioprocessing for pulp, paper, cellulose, and other bioproducts is dependent on the aggregate of its wood properties, which are a function of cellular architecture and the chemistry and ultrastructure of the secondary cell walls (SCWs) of wood fiber cells that compose the bulk of woody biomass (9). These properties are determined by overlapping developmental programs and pathways that have to be coordinated during secondary xylem development (xylogenesis) (10). Some of these pathways, SCW polysaccharide and lignin biosynthesis in particular, represent a strong, irreversible carbon sink and directly or indirectly use core metabolites (glucose/ UDP-glucose and fructose) that are also used for growth and physiological/cellular homeostasis (energy metabolism, production of amino acids, etc.).…”

Primary Metabolism during Biosynthesis of Secondary Wall Polymers of Protoxylem Vessel Elements

“…], Rengel et al, 2009) and studies in the in vitro system (Demura et al, 2002;Ohashi-Ito et al, 2010;Zhong et al, 2010;Yamaguchi et al, 2011) have identified many genes involved in xylem cell differentiation. These include VND family genes and SCW-related genes encoding MYB transcription factors (McCarthy et al, 2010;Ko et al, 2012Ko et al, , 2014Zhong and Ye, 2012;Hussey et al, 2013); based on this information, NAC-MYB-based transcriptional networks have been proposed for xylem vessel cell differentiation . Moreover, proteome data have been reported for xylem tissues of hybrid aspen (Populus spp.…”