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Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology

The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown th...

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Autores principales: Zhou, Haiying, Hwarari, Delight, Ma, Hongyu, Xu, Haibin, Yang, Liming, Luo, Yuming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9682074/
https://www.ncbi.nlm.nih.gov/pubmed/36437962
http://dx.doi.org/10.3389/fgene.2022.1060546
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author Zhou, Haiying
Hwarari, Delight
Ma, Hongyu
Xu, Haibin
Yang, Liming
Luo, Yuming
author_facet Zhou, Haiying
Hwarari, Delight
Ma, Hongyu
Xu, Haibin
Yang, Liming
Luo, Yuming
author_sort Zhou, Haiying
collection PubMed
description The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown their presence in early land plants. In this paper, we performed a comparative discussion on the current knowledge of the TCP Transcription Factors in lower and higher plants: their evolutionary history based on the phylogenetics of 849 TCP proteins from 37 plant species, duplication events, and biochemical roles in some of the plants species. Phylogenetics investigations confirmed the classification of TCP TFs into Class I (the PCF1/2), and Class II (the C- clade) factors; the Class II factors were further divided into the CIN- and CYC/TB1- subclade. A trace in the evolution of the TCP Factors revealed an absence of the CYC/TB1subclade in lower plants, and an independent evolution of the CYC/TB1subclade in both eudicot and monocot species. 54% of the total duplication events analyzed were biased towards the dispersed duplication, and we concluded that dispersed duplication events contributed to the expansion of the TCP gene family. Analysis in the TCP factors functional roles confirmed their involvement in various biochemical processes which mainly included promoting cell proliferation in leaves in Class I TCPs, and cell division during plant development in Class II TCP Factors. Apart from growth and development, the TCP Factors were also shown to regulate hormonal and stress response pathways. Although this paper does not exhaust the present knowledge of the TCP Transcription Factors, it provides a base for further exploration of the gene family.
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spelling pubmed-96820742022-11-24 Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology Zhou, Haiying Hwarari, Delight Ma, Hongyu Xu, Haibin Yang, Liming Luo, Yuming Front Genet Genetics The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown their presence in early land plants. In this paper, we performed a comparative discussion on the current knowledge of the TCP Transcription Factors in lower and higher plants: their evolutionary history based on the phylogenetics of 849 TCP proteins from 37 plant species, duplication events, and biochemical roles in some of the plants species. Phylogenetics investigations confirmed the classification of TCP TFs into Class I (the PCF1/2), and Class II (the C- clade) factors; the Class II factors were further divided into the CIN- and CYC/TB1- subclade. A trace in the evolution of the TCP Factors revealed an absence of the CYC/TB1subclade in lower plants, and an independent evolution of the CYC/TB1subclade in both eudicot and monocot species. 54% of the total duplication events analyzed were biased towards the dispersed duplication, and we concluded that dispersed duplication events contributed to the expansion of the TCP gene family. Analysis in the TCP factors functional roles confirmed their involvement in various biochemical processes which mainly included promoting cell proliferation in leaves in Class I TCPs, and cell division during plant development in Class II TCP Factors. Apart from growth and development, the TCP Factors were also shown to regulate hormonal and stress response pathways. Although this paper does not exhaust the present knowledge of the TCP Transcription Factors, it provides a base for further exploration of the gene family. Frontiers Media S.A. 2022-11-09 /pmc/articles/PMC9682074/ /pubmed/36437962 http://dx.doi.org/10.3389/fgene.2022.1060546 Text en Copyright © 2022 Zhou, Hwarari, Ma, Xu, Yang and Luo. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Zhou, Haiying
Hwarari, Delight
Ma, Hongyu
Xu, Haibin
Yang, Liming
Luo, Yuming
Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology
title Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology
title_full Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology
title_fullStr Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology
title_full_unstemmed Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology
title_short Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology
title_sort genomic survey of tcp transcription factors in plants: phylogenomics, evolution and their biology
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9682074/
https://www.ncbi.nlm.nih.gov/pubmed/36437962
http://dx.doi.org/10.3389/fgene.2022.1060546
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