A Maize Gene Regulatory Network for Phenolic Metabolism

Abstract

The translation of the genotype into phenotype, represented for example by the expression of genes encoding enzymes required for the biosynthesis of phytochemicals that are important for interaction of plants with the environment, is largely carried out by transcription factors (TFs) that recognize specific cis-regulatory elements in the genes that they control. TFs and their target genes are organized in gene regulatory networks (GRNs), and thus uncovering GRN architecture presents an important biological challenge necessary to explain gene regulation. Linking TFs to the genes they control, central to understanding GRNs, can be carried out using gene- or TF-centered approaches. In this study, we employed a gene-centered approach utilizing the yeast one-hybrid assay to generate a network of protein-DNA interactions that participate in the transcriptional control of genes involved in the biosynthesis of maize phenolic compounds including general phenylpropanoids, lignins, and flavonoids. We identified 1100 protein-DNA interactions involving 54 phenolic gene promoters and 568 TFs. A set of 11 TFs recognized 10 or more promoters, suggesting a role in coordinating pathway gene expression. The integration of the gene-centered network with information derived from TF-centered approaches provides a foundation for a phenolics GRN characterized by interlaced feed-forward loops that link developmental regulators with biosynthetic genes.

Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Populus trichocarpa

“…In a TF TRN, high-level TFs act as master switches or key receptors to activate the network and initiate a coordinated process and control mid-level TFs that, in turn, regulate effector genes (e.g., cell wall component genes) at the bottom of the network that are directly responsible for implementing specific processes (e.g., wood formation; Yu and Gerstein, 2006;Bhardwaj et al, 2010;Yan et al, 2010;Lin et al, 2013;Song et al, 2016;Yang et al, 2017). Typically, three to five hierarchical layers may be involved in TRNs for growth and development in animals (Gerstein et al, 2010;Roy and The modEncode Consortium et al, 2010;Cheng et al, 2011;Niu et al, 2011) or in plants (Lin et al, 2013;Lu et al, 2013;Taylor-Teeples et al, 2015;Song et al, 2016;Yang et al, 2017).…”

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

“…The B73 reference genome (AGPv4) is a chromosome-level high-quality assembly with wellcurated gene ontology (GO)-based functional annotations (Jiao et al, 2017;Wimalanathan et al, 2018). The maize TFome project provides an invaluable resource of over 2,000 maize TF clones to facilitate high-throughput studies, including a recent Y1H (yeast one-hybrid) screen that identified over a thousand TF-target interactions in the maize phenolic metabolic pathway (Burdo et al, 2014;Yang et al, 2017). Previous efforts in characterizing GRNs in maize have provided insights into regulatory networks (Li et al, 2010;Zhan et al, 2015;Walley et al, 2016;Huang et al, 2018).…”

Genetic elucidation of complex biochemical traits mediating maize innate immunity

“…Flavonoids are predominant protective biochemicals in nearly all plants, are fungal-regulated in maize and commonly co-occur with terpenoids 49–51 . The up-regulated production of simple flavonoids, such as narigenin and apigenin, are associated with increased protein levels of phenylalanine ammonia lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI) and flavone synthase (FNS) family members 52 many of which parallel Zx pathway activation (Fig. 5d).…”