Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families

Abstract

Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

Identification of plant enhancers and their constituent elements by STARR-seq in tobacco leaves

“…Our approach bypasses the need for a species-specific protoplasting protocol by using transient expression of diverse STARR-seq libraries in tobacco leaves. As transcription factors are highly conserved among plant species 6,7 , the versatile tobacco system can serve as a proxy for many plant species, including crops.…”

“…Our approach bypasses the need for a species-specific protoplasting protocol by using transient expression of diverse STARR-seq libraries in tobacco leaves. As transcription factors are highly conserved among plant species 6,7 , the versatile tobacco system can serve as a proxy for many plant species, including crops.We used a green fluorescent protein (GFP) reporter gene under control of the Cauliflower mosaic virus 35S minimal promoter and the 35S core enhancer 8,9 (subdomains A1 and B1-3) to benchmark the assay.We systematically analyzed the position-and orientation-dependency of the enhancer (Fig. 1a).…”

Principles and characteristics of the Arabidopsis WRKY regulatory network during early MAMP‐triggered immunity

“…A large array of plasma membrane-localized receptors recognize diverse microbe-associated molecular patterns (MAMPs) and thereby trigger appropriate signaling within a deeply interconnected network that ultimately enables proper transcriptional defense outputs (Tsuda and Somssich, 2015;Li et al, 2016a;Yu et al, 2017). Transcription factors (TFs) are among the most largely expanded gene families in plants, and this is also manifested in the increasing number of genes encoding defense-associated TFs including WRKY factors (Lehti-Shiu et al, 2017). The number of WRKY genes increased drastically from only one or two genes in green algae, 19-38 in liverworts and mosses, and expanded up to more than 160 in flowering plants (Mohanta et al, 2016) This expansion is clearly correlated with the multiple levels at which WRKY TFs operate within the complex MAMP-triggered and effector-triggered defense signal transduction cascades (Rushton et al, 2010;Banerjee and Roychoudhury, 2015).…”

Neofunctionalisation of basic helix−loop−helix proteins occurred when embryophytes colonised the land

“…The comparison of land plant (Rensing et al ., ; Banks et al ., ; Bowman et al ., ) and streptophyte algae genomes (Hori et al ., ; Ju et al ., ; Nishiyama et al ., ) has led to the hypothesis that the evolution of the morphological diversity resulted from an increase in the number of regulatory genes within gene families (Floyd & Bowman, ; Lang et al ., ; Pires & Dolan, ,b; Bowman et al ., ; Lehti‐Shiu et al ., ). For example, there are generally more transcription factors in the genomes of the morphologically diverse land plants than in the genomes of the comparatively simple streptophyte algae (Tanabe et al ., ; Navaud et al ., ; Chanderbali et al ., ; Catarino et al ., ; Nishiyama et al ., ).…”