Comprehensive Bioinformatics and Expression Analysis of TCP Transcription Factors in Liriodendron chinense Reveals Putative Abiotic Stress Regulatory Roles

et al. 2022

Front. Plant Sci.

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The basic leucine zipper (bZIP) is a transcription factor family that plays critical roles in abiotic and biotic stress responses as well as plant development and growth. A comprehensive genome-wide study in Liriodendron chinense was conducted to identify 45 bZIP transcription factors (LchibZIPs), which were divided into 13 subgroups according the phylogenetic analysis. Proteins in the same subgroup shared similar gene structures and conserved domains, and a total of 20 conserved motifs were revealed in LchibZIP proteins. Gene localization analysis revealed that LchibZIP genes were unequally distributed across 16 chromosomes, and that 4 pairs of tandem and 9 segmental gene duplications existed. Concluding that segmental duplication events may be strongly associated with the amplification of the L. chinense bZIP gene family. We also assessed the collinearity of LchibZIPs between the Arabidopsis and Oryza and showed that the LchibZIP is evolutionarily closer to O. sativa as compared to the A. thaliana. The cis-regulatory element analysis showed that LchibZIPs clustered in one subfamily are involved in several functions. In addition, we gathered novel research suggestions for further exploration of the new roles of LchibZIPs from protein-protein interactions and gene ontology annotations of the LchibZIP proteins. Using the RNA-seq data and qRT-PCR we analyzed the gene expression patterns of LchibZIP genes, and showed that LchibZIP genes regulate cold stress, especially LchibZIP4 and LchibZIP7; and LchibZIP2 and LchibZIP28 which were up-regulated and down-regulated by cold stress, respectively. Studies of genetic engineering and gene function in L. chinense can benefit greatly from the thorough investigation and characterization of the L. chinense bZIP gene family.

Section: Methodsmentioning

confidence: 99%

The bZIP transcription factors in Liriodendron chinense: Genome-wide recognition, characteristics and cold stress response

et al. 2022

Front. Plant Sci.

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“…The NCBI-CDD database ( , accessed on 15 September 2022) and SMART website ( , accessed on 15 September 2022) were used to predict the conserved domain of HSPs in L . chinense [ 46 ].…”

Section: Methodsmentioning

confidence: 99%

Genomic Survey of Heat Shock Proteins in Liriodendron chinense Provides Insight into Evolution, Characterization, and Functional Diversities

et al. 2022

IJMS

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Heat shock proteins (HSPs) are conserved molecular chaperones whose main role is to facilitate the regulation of plant growth and stress responses. The HSP gene family has been characterized in most plants and elucidated as generally stress-induced, essential for their cytoprotective roles in cells. However, the HSP gene family has not yet been analyzed in the Liriodendron chinense genome. In current study, 60 HSP genes were identified in the L. chinense genome, including 7 LchiHSP90s, 23 LchiHSP70s, and 30 LchiHSP20s. We investigated the phylogenetic relationships, gene structure and arrangement, gene duplication events, cis-acting elements, 3D-protein structures, protein–protein interaction networks, and temperature stress responses in the identified L. chinense HSP genes. The results of the comparative phylogenetic analysis of HSP families in 32 plant species showed that LchiHSPs are closely related to the Cinnamomum kanehirae HSP gene family. Duplication events analysis showed seven segmental and six tandem duplication events that occurred in the LchiHSP gene family, which we speculated to have played an important role in the LchiHSP gene expansion and evolution. Furthermore, the Ka/Ks analysis indicated that these genes underwent a purifying selection. Analysis in the promoter region evidenced that the promoter region LchiHSPs carry many stress-responsive and hormone-related cis-elements. Investigations in the gene expression patterns of the LchiHSPs using transcriptome data and the qRT-PCR technique indicated that most LchiHSPs were responsive to cold and heat stress. In total, our results provide new insights into understanding the LchiHSP gene family function and their regulatory mechanisms in response to abiotic stresses.

“…Our analysis concurred with previous TCP protein structure investigations (Pilar Cubas et al, 1999). Recently, we have also analysed the TCP protein structure of the L. chinense , and showed that most of the LcTCP proteins carry 2 to 3β-strands, and 2α-helices with alternating hydrophobic regions and are less mobile ( Hwarari et al, 2022 ). Other researches have also exhibited that the TCP protein contain potential sites of phosphorylation and regions linked by a conserved Glycine-Aspartate-Serine residues, highly frequent in loops and Proline ( Cubas et al, 1999 ; Tarczewska and Greb-Markiewicz, 2019 ; Edwards and Gorelick, 2022 ).This result generally confirms that the TCP bHLH domain is rather distinct from the bHLH domain.…”

Section: Tcp Conserved Domainsmentioning

confidence: 99%

“…Although their ancestry remains unknown ( Navaud et al, 2007 ), their biological roles and mode of action are conserved in plant species from the bryophytes to the angiosperms. Up to date, there have been several breakthroughs in the identification and computation of TCP TFs in numerous plant species including: A. thaliana ( Aggarwal et al, 2010 ), G. biloba ( Yu L. et al, 2022 ), P. edulis ( Liu et al, 2018 ), S. lycopersicum ( Parapunova et al, 2014 ), L. chinense ( Hwarari et al, 2022 ), etc. However, in some plant orders, the TCP TFs have not yet been identified ( Manassero et al, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

“…Research on the TCP gene expression have supported the biological functions of TB1, CYC, and PCF genes, tailoring the TCP domain to be involved in DNA binding activities, dimerization, and protein to protein interactions ( Kosugi and Ohashi, 2002 ). Recent reports have shown their involvement in the regulation of biotic and abiotic stresses ( Yu Z. et al, 2022 ; Hwarari et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Zhou

et al. 2022

Front. Genet.

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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.