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

doi:10.3389/fgene.2022.1060546

Cited by 15 publications

(13 citation statements)

References 106 publications

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“…In addition, genome-wide analysis allowed the identification of TCP genes in numerous species of commercial interest, as tobacco, banana, Brassica napus , cucumber, watermelon, strawberry, eggplant, Ginkgo biloba , and tea [ 22 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. For the interested reader, an exhaustive analysis of the phylogeny and the evolution of the TCP family in 37 plant species from lower to higher plants was recently reported by Zhou et al [ 39 ].…”

Section: Introductionmentioning

confidence: 99%

Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors

Viola

Alem

Jure

et al. 2023

IJMS

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TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 and 2 (TCP) proteins constitute a plant-specific transcription factors family exerting effects on multiple aspects of plant development, such as germination, embryogenesis, leaf and flower morphogenesis, and pollen development, through the recruitment of other factors and the modulation of different hormonal pathways. They are divided into two main classes, I and II. This review focuses on the function and regulation of class I TCP proteins (TCPs). We describe the role of class I TCPs in cell growth and proliferation and summarize recent progresses in understanding the function of class I TCPs in diverse developmental processes, defense, and abiotic stress responses. In addition, their function in redox signaling and the interplay between class I TCPs and proteins involved in immunity and transcriptional and posttranslational regulation is discussed.

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Section: Introductionmentioning

confidence: 99%

Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors

Viola

Alem

Jure

et al. 2023

IJMS

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“…TCP TFs are a common family with redundant functions in plants ( Zhou et al., 2022 ). With release of the scaffolded genome of C. roseus , it is necessary to annotate the TCP genes at the whole-genome level.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of TCP family genes in Catharanthus roseus

et al. 2023

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IntroductionThe anti-tumor vindoline and catharanthine alkaloids are naturally existed in Catharanthus roseus (C. roseus), an ornamental plant in many tropical countries. Plant-specific TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play important roles in various plant developmental processes. However, the roles of C. roseus TCPs (CrTCPs) in terpenoid indole alkaloid (TIA) biosynthesis are largely unknown.MethodsHere, a total of 15 CrTCP genes were identified in the newly updated C. roseus genome and were grouped into three major classes (P-type, C-type and CYC/TB1).ResultsGene structure and protein motif analyses showed that CrTCPs have diverse intron-exon patterns and protein motif distributions. A number of stress responsive cis-elements were identified in promoter regions of CrTCPs. Expression analysis showed that three CrTCP genes (CrTCP2, CrTCP4, and CrTCP7) were expressed specifically in leaves and four CrTCP genes (CrTCP13, CrTCP8, CrTCP6, and CrTCP10) were expressed specifically in flowers. HPLC analysis showed that the contents of three classic TIAs, vindoline, catharanthine and ajmalicine, were significantly increased by ultraviolet-B (UV-B) and methyl jasmonate (MeJA) in leaves. By analyzing the expression patterns under UV-B radiation and MeJA application with qRT-PCR, a number of CrTCP and TIA biosynthesis-related genes were identified to be responsive to UV-B and MeJA treatments. Interestingly, two TCP binding elements (GGNCCCAC and GTGGNCCC) were identified in several TIA biosynthesis-related genes, suggesting that they were potential target genes of CrTCPs. DiscussionThese results suggest that CrTCPs are involved in the regulation of the biosynthesis of TIAs, and provide a basis for further functional identification of CrTCPs.

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“…The systematic classification of the transcription factor families based on molecular phylogeny facilitates the understanding of functional and genomic studies [40]. To better…”

Section: Phylogenetic Analysis Of Gata Factorsmentioning

confidence: 99%

Systematic Characterization of GATA Transcription Factors in Liriodendron chinense and Functional Validation in Abiotic Stresses

Hwarari

Radani

Guan

et al. 2023

Plants

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The Liriodendron chinense in the Magnoliaceae family is an endangered tree species useful for its socio-economic and ecological benefits. Abiotic stresses (cold, heat, and drought stress), among other factors, affect its growth, development, and distribution. However, GATA transcription factors (TFs) respond to various abiotic stresses and play a significant role in plant acclimatization to abiotic stresses. To determine the function of GATA TFs in L. chinense, we investigated the GATA genes in the genome of L. chinense. In this study, a total of 18 GATA genes were identified, which were randomly distributed on 12 of the total 17 chromosomes. These GATA genes clustered together in four separate groups based on their phylogenetic relationships, gene structures, and domain conservation arrangements. Detailed interspecies phylogenetic analyses of the GATA gene family demonstrated a conservation of the GATAs and a probable diversification that prompted gene diversification in plant species. In addition, the LcGATA gene family was shown to be evolutionarily closer to that of O. sativa, giving an insight into the possible LcGATA gene functions. Investigations of LcGATA gene duplication showed four gene duplicate pairs by the segmental duplication event, and these genes were a result of strong purified selection. Analysis of the cis-regulatory elements demonstrated a significant representation of the abiotic stress elements in the promoter regions of the LcGATA genes. Additional gene expressions through transcriptome and qPCR analyses revealed a significant upregulation of LcGATA17, and LcGATA18 in various stresses, including heat, cold, and drought stress in all time points analyzed. We concluded that the LcGATA genes play a pivotal role in regulating abiotic stress in L. chinense. In summary, our results provide new insights into understanding of the LcGATA gene family and their regulatory functions during abiotic stresses.

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

Cited by 15 publications

References 106 publications

Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors

Physiological Roles and Mechanisms of Action of Class I TCP Transcription Factors

Genome-wide identification and expression analysis of TCP family genes in Catharanthus roseus

Systematic Characterization of GATA Transcription Factors in Liriodendron chinense and Functional Validation in Abiotic Stresses

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