Journal Article

An Arabidopsis gene regulatory network for secondary cell wall synthesis

Tagkopoulos, I., Lamothe, R., Kay, S. A., Wang, C., Ware, D., Xiong, G., Zhang, L., Turco, G., de Lucas, M., Ahnert, S. E., Handakumbura, P. P., Pruneda-Paz, J. L., Tsoukalas, A., Breton, G., Lin, L., Taylor-Teeples, M., Pauly, M., Toal, T. W., Corwin, J., Veling, M. T., Dehesh, K., Hazen, S. P., Young, N. F., Trabucco, G. M., Gaudinier, A., Brady, S. M., Kliebenstein, D. J.

2015

Overview

The 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 thaliana 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. The full complement of transcriptional regulators that affect synthesis of the plant secondary cell wall remains largely undetermined; here, the network of protein–DNA interactions controlling secondary cell wall synthesis of Arabidopsis thaliana is determined, showing that gene expression is regulated by a series of feed-forward loops to ensure that the secondary cell wall is deposited at the right time and in the right place. Secondary cell wall synthesis in Arabidopsis The plant cell wall determines cell shape and mediates communication with the cellular environment. But it is the secondary cell wall — deposited in various cell types including xylem — that is the main source of biomass used for biofuels and in the pulp and paper industry. The full complement of transcriptional regulators that affect biosynthesis of secondary cell wall remains largely undetermined. Siobhan Brady and colleagues describe a gene regulatory network involving hundreds of transcription factors that controls the formation of xylem in the plant Arabidopsis through protein–DNA interactions. Gene expression is regulated by a series of feed-forward loops to ensure that secondary cell wall is deposited at the right time and in the right place. The authors use their gene regulatory network to develop new hypotheses about the effect of abiotic stress, such as salinity and iron deprivation, on secondary cell wall gene regulation, and to validate these hypotheses.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/449/2653 / 631/553/2711 / 64 / 82 / Abiotic stress / Arabidopsis / Arabidopsis - genetics / Arabidopsis - growth & development / Arabidopsis - metabolism / Arabidopsis Proteins - genetics / Arabidopsis Proteins - metabolism / Arabidopsis thaliana / BASIC BIOLOGICAL SCIENCES / Biosynthesis / Cell Wall - metabolism / Cellulose / Deoxyribonucleic acid / DNA / DNA, Plant - genetics / DNA, Plant - metabolism / E2F Transcription Factors - metabolism / Feedback / Flowers & plants / Gene expression / Gene Expression Regulation, Developmental - genetics / Gene Expression Regulation, Plant - genetics / Gene Regulatory Networks - genetics / Genetic aspects / Genetic research / Genetic transcription / Humanities and Social Sciences / Iron - deficiency / Lignin / Methods / multidisciplinary / Organ Specificity / Physiological aspects / Plant biomass / Plant cell walls / plant development / Polymers / Promoter Regions, Genetic - genetics / Proteins / regulatory networks / Reproducibility of Results / Salinity / Science / Structure / Time Factors / Transcription factors / Transcription Factors - metabolism / Xylem - genetics / Xylem - growth & development / Xylem - metabolism