TCP Transcription Factors Predate the Emergence of Land Plants

Abstract

TCP proteins are plant-specific transcription factors identified so far only in angiosperms and shown to be involved in specifying plant morphologies. However, the functions of these proteins remain largely unknown. Our study is the first phylogenetic analysis comparing the TCP genes from higher and lower plants, and it dates the emergence of the TCP family to before the split of the Zygnemophyta. EST database analysis and CODEHOP PCR amplification revealed TCP genes in basal land plant genomes and also in their close freshwater algal relatives. Based on an extensive survey of TCP genes, families of TCP proteins were characterized in the Arabidopsis thaliana, poplar, rice, club-moss, and moss genomes. The phylogenetic trees indicate a continuous expansion of the TCP family during the diversification of the Phragmoplastophyta and a similar degree of expansion in several angiosperm lineages. TCP paralogues were identified in all genomes studied, and Ks values indicate that TCP genes expanded during genome duplication events. MEME and SIMPLE analyses detected conserved motifs and low-complexity regions, respectively, outside of the TCP domain, which reinforced the previous description of a "mosaic" structure of TCP proteins.

TheArabidopsis thalianaTCP transcription factors: A broadening horizon beyond development

“…[4][5][6][7][8] According to the differential features within the plant-specific TCP domain, TCP proteins can be distinguished into 2 divergent types, including the class I (TCP-P) and class II (TCP-C), and the latter is further divided into 2 subgroups, namely ubiquitous CINCINNATA (CIN) and angiosperm-specific CYC/TB1. 2,9 Interestingly, TCP proteins have in common a short a-helical L**LL motif located in the second helix of the DNA-binding domain. 1 In both animals and plants, the hydrophobic face formed by the conserved leucine residues in the L**LL motif has been demonstrated to mediate protein interactions.…”

“…Intriguingly, TCP genes also occur in gymnosperms and non-seed plants, such as pteridophytes, lycophytes, mosses, and algae. 9 Molecular phylogenetic studies reveal that TCP proteins likely emerged first in the Streptophyta lineage prior to the divergence of the Zygnemophyta between 650 and 800 million years ago, as both classes of TCP genes are detectable in Cosmarium sp. (Zygnemophyta), but not in Klebsormidium flaccidum (Klebsormidiophyta), Chlorokybus atmophyticus (Chlorokybophyta) or Mesostigma viride (Mesostygmatophyta).…”

“…(Zygnemophyta), but not in Klebsormidium flaccidum (Klebsormidiophyta), Chlorokybus atmophyticus (Chlorokybophyta) or Mesostigma viride (Mesostygmatophyta). 9 In non-seed plants, TCP genes constitute a small family of 5 to 6 members. 9 During the evolution of land plants, subfunctionalization of duplicated genes, followed by neofunctionalization, expands the TCP gene family to comprise a multitude of members in gymnosperms and angiosperms.…”

“…9 In non-seed plants, TCP genes constitute a small family of 5 to 6 members. 9 During the evolution of land plants, subfunctionalization of duplicated genes, followed by neofunctionalization, expands the TCP gene family to comprise a multitude of members in gymnosperms and angiosperms. 2,9 Duplication and subsequent diversification occurring in the ECE (CYC/TB1) clade of TCP proteins exemplify the evolution of this ancient family.…”

“…9 During the evolution of land plants, subfunctionalization of duplicated genes, followed by neofunctionalization, expands the TCP gene family to comprise a multitude of members in gymnosperms and angiosperms. 2,9 Duplication and subsequent diversification occurring in the ECE (CYC/TB1) clade of TCP proteins exemplify the evolution of this ancient family. 15 Phylogenetic analysis reveals that 3 major copies of CYC have arisen from duplication events predating the core eudicots.…”