A Phylogenetic Study of the ANT Family Points to a preANT Gene as the Ancestor of Basal and euANT Transcription Factors in Land Plants

Abstract

Comparative genomics has revealed that members of early divergent lineages of land plants share a set of highly conserved transcription factors (TFs) with flowering plants. While gene copy numbers have expanded through time, it has been predicted that diversification, co-option, and reassembly of gene regulatory networks implicated in development are directly related to morphological innovations that led to more complex land plant bodies. Examples of key networks have been deeply studied in Arabidopsis thaliana, such as those involving the AINTEGUMENTA (ANT) gene family that encodes AP2-type TFs. These TFs play significant roles in plant development such as the maintenance of stem cell niches, the correct development of the embryo and the formation of lateral organs, as well as fatty acid metabolism. Previously, it has been hypothesized that the common ancestor of mosses and vascular plants encoded two ANT genes that later diversified in seed plants. However, algae and bryophyte sequences have been underrepresented from such phylogenetic analyses. To understand the evolution of ANT in a complete manner, we performed phylogenetic analyses of ANT protein sequences of representative species from across the Streptophyta clade, including algae, liverworts, and hornworts, previously unrepresented. Moreover, protein domain architecture, selection analyses, and regulatory cis elements prediction, allowed us to propose a scenario of how the evolution of ANT genes occurred. In this study we show that a duplication of a preANT-like gene in the ancestor of embryophytes may have given rise to the land plant-exclusive basalANT and euANT lineages. We hypothesize that the absence of euANT-type and basalANT-type sequences in algae, and its presence in extant land plant species, suggests that the divergence of pre-ANT into basal and eu-ANT clades in embryophytes may have influenced the conquest of land by plants, as ANT TFs play important roles in tolerance to desiccation and the establishment, maintenance, and development of complex multicellular structures which either became more complex or appeared in land plants.

Expansion and Molecular Characterization of AP2/ERF Gene Family in Wheat (Triticum aestivum L.)

“…TaAP2/ERF gene family is supposed to have a critical role in signal transduction and transcriptional adjustment because most of the genes of this family are predicted to be present in the nucleus as compared with T. durum which is a close relative to T. aestivum Figure 5B ( Faraji et al, 2020 ). As it is clear from the previous results that AP2/ERF gene family plays a critical role in plant growth and development ( Scheres and Krizek, 2018 ; Dipp-álvarez and Cruz-Ramírez, 2019 ; Jiang et al, 2019 ; Wang et al, 2019 ). So, our study about AP2/ERF genes in wheat will be useful for improving the wheat crop from different biotic and abiotic stresses in the future.…”

TaAP2-15, An AP2/ERF Transcription Factor, Is Positively Involved in Wheat Resistance to Puccinia striiformis f. sp. tritici

“…The conserved AP2 DNA binding domains of amino acids 57-66 characterize the AP2/ERF superfamily [ 41 ]. In accordance with the double AP2 domain amino acid sequence and the nuclear location sequence, the AP2 family was subdivided into euAP2, eu-AINTEGUMENTA (euANT) and basalANT groups, respectively [ 42 , 43 , 44 ]. AP2 TFs play a number of roles in plant developmental processes and stress responses, such as vegetative and reproductive growth, cell proliferation, abiotic and biotic stress responses, and plant hormone responses [ 14 , 15 , 16 ].…”

Genome-Wide Identification and Analysis of the AP2 Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

“…Accumulating evidence showed that AP2 family genes play pivotal roles in regulating plant growth and development (Scheres and Krizek, 2018; Dipp-Alvarez and Cruz-Ramirez, 2019; Jiang et al, 2019; Wang et al, 2019a). Arabidopsis AtANT was one of the first genes in the family that were functionally characterized; it regulates organ size, floral meristem patterning, and plant defense pathways (Elliott et al, 1996; Krizek et al, 2016).…”

“…The AP2 family proteins contain two repeated AP2 domains; the ERF family proteins contain a single AP2 domain; the RAV (related to ABI3/VP1) family proteins contain two different DNA binding domains, AP2 and B3 (Sakuma et al, 2002; Nakano et al, 2006). The AP2 family was subdivided into the euAP2, eu-AINTEGUMENTA (euANT) and basalANT groups according to the amino acid sequence of the double AP2 domain and the nuclear localization sequence (Shigyo et al, 2006; Wang et al, 2016a; Dipp-Alvarez and Cruz-Ramirez, 2019).…”