The crystal structure of the TCP domain of PCF6 in <i>Oryza sativa</i> L. reveals an RHH‐like fold

Sun, Lifang; Zou, Xiaoming; Jiang, Meiqin; Wu, Xiang-Feng; Chen, Yayu; Wang, Qianchao; Wang, Qin; Chen, Lifei; Wu, Yunkun

doi:10.1002/1873-3468.13727

Cited by 14 publications

(14 citation statements)

References 41 publications

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“…Until recently, these plant-specific TFs were considered similar to bHLH [52]. However, the determination of the crystallographic structure of the DBD of O. sativa PCF6 (5ZKT) revealed they rather belong to Ribbon-Helix-Helix (RHH) TFs [53], a class yet never described in plants that recognize DNA motifs in the major groove thanks to an anti-parallel beta-sheet involved in dimer formation, anchored by alpha-helices [53,54]. We have thus added the RHH class and TCP family to the “beta-Hairpin exposed by an alpha/beta-scaffold” superclass.…”

Section: Introductionmentioning

confidence: 99%

Plant-TFClass: a structural classification for plant transcription factors

Blanc-Mathieu

Dumas

Turchi

et al. 2022

Preprint

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Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved thanks to the DNA-binding domain (DBD) present in each TF. DBDs show a vast diversity of protein folds within and across organisms, ranging from simple long basic alpha helices to complex structural combinations of alpha, beta and loop folds. In mammals, the structural conformation of the DBDs and the way it establishes contact with DNA has been used to organize TFs in a hierarchical classification named TFClass. However, such classification is missing from plants that possess many DBD types absent from mammals. Here, we reviewed the numerous TF DBD 3D-structures and models available for plants to organize all plant TFs types following the TFClass hierarchy (Superclass/Class/Family/Subfamily). We classified most of the 55 recognized plant TF types within the existing TFClass framework. This extended classification led us to add six new classes and 34 new families corresponding to TF DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF and TF binding sites comparison across TF families and across organisms.

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Section: Introductionmentioning

confidence: 99%

Plant-TFClass: a structural classification for plant transcription factors

Blanc-Mathieu

Dumas

Turchi

et al. 2022

Preprint

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“…Nonetheless, the TCP domain structure has remained intact ( Kosugi and Ohashi, 1997 ; Cubas et al, 1999 ). The protein structural analysis of the bHLH TFs has shown that the TCP domain is characterized by a basic residue-rich region forming a typical fold of 3 short β -strands (β1, β2, and β3) and two consecutive α-helices (α-1 and α-2) ( Sun et al, 2020 ). However, the TCP domain is different to the bHLH domain ( Carrara and Dornelas, 2021 ).…”

Section: Tcp Conserved Domainsmentioning

confidence: 99%

“…Interestingly, their analysis in rice OsPCF6 protein, disclosed that the TCP domain dimerize with other two TCP domains, each forming a stable conformation that adopts the ribbon-helix-helix (RHH) fold rather than the bHLH motif previously predicted. Implying that the TCP protein can also be classified into the RHH family ( Liu et al, 2019 ; Sun et al, 2020 ). Although these findings are not conclusive, the homology modelling of TCP protein has also demonstrated their ability to form homodimers and/or heterodimers with other TCP proteins to bind DNA ( Parapunova et al, 2014 ).…”

Section: Tcp Conserved Domainsmentioning

confidence: 99%

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

Zhou

Hwarari

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.

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“…In 2010, a model of the TCP domain bound to a B-form dsDNA with the sequence GTGGTCCC was reported using a DNA-bound MyoD structure as a template ( 9 ); nevertheless, this structural model has been misleading. Recently, the apo structure of the TCP domain from OsPCF6 was solved, and the TCP domain was demonstrated to possess a low-homology bacterial RHH fold by structural comparison ( 26 ). The HLH region of the TCP domain does resemble the bacterial RHH domain, but the basic regions of the two folds are quite distinct.…”

Section: Introductionmentioning

confidence: 99%

DNA–TCP complex structures reveal a unique recognition mechanism for TCP transcription factor families

Zhang

Nie

et al. 2022

Nucleic Acids Research

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Plant-specific TCP transcription factors are key regulators of diverse plant functions. TCP transcription factors have long been annotated as basic helix–loop–helix (bHLH) transcription factors according to remote sequence homology without experimental validation, and their consensus DNA-binding sequences and protein–DNA recognition mechanisms have remained elusive. Here, we report the crystal structures of the class I TCP domain from AtTCP15 and the class II TCP domain from AtTCP10 in complex with different double-stranded DNA (dsDNA). The complex structures reveal that the TCP domain is a distinct DNA-binding motif and the homodimeric TCP domains adopt a unique three-site recognition mode, binding to dsDNA mainly through a central pair of β-strands formed by the dimer interface and two basic flexible loops from each monomer. The consensus DNA-binding sequence for class I TCPs is a perfectly palindromic 11 bp (GTGGGNCCCAC), whereas that for class II TCPs is a near-palindromic 11 bp (GTGGTCCCCAC). The unique DNA binding mode allows the TCP domains to display broad specificity for a range of DNA sequences even shorter than 11 bp, adding further complexity to the regulatory network of plant TCP transcription factors.

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The crystal structure of the TCP domain of PCF6 in Oryza sativa L. reveals an RHH‐like fold

Cited by 14 publications

References 41 publications

Plant-TFClass: a structural classification for plant transcription factors

Plant-TFClass: a structural classification for plant transcription factors

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

DNA–TCP complex structures reveal a unique recognition mechanism for TCP transcription factor families

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