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PreprintCited by 90Plant Molecular Biology ResearchProtein Structure and DynamicsGenomics and Chromatin Dynamics

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Plant-TFClass: a structural classification for plant transcription factors

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Blanc-Mathieu, Romain, Dumas, Renaud, Turchi, Laura, Lucas, Jérémy, Parcy, François·2022·Trends in Plant Science
DOI 10.1101/2022.11.22.517060

Preprint — published as 10.1016/j.tplants.2023.06.023

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Abstract

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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Metadata

Authors
Blanc-Mathieu, R., Dumas, R., Turchi, L., Lucas, J., & Parcy, F.
Affiliations
Centre National de la Recherche Scientifique (FR)
Corresponding author
Parcy, François
ORCID
Venue
Trends in Plant Science
Publisher
openRxiv
Published
2022-11-24
Volume
29
Issue
1
Pages
40-51
ISSN
1360-1385 (ISSN-L)
DOI
10.1101/2022.11.22.517060
OpenAlex
W4385146208
Cited by
90
References
1
Citations by year
2026: 32 · 2025: 32 · 2024: 21 · 2023: 5
FWCI
1.33
Type
journal article
Language
en
Open access
Locations
  • Trends in Plant Science (acceptedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, other-oa)
  • HAL (submittedVersion, cc-by-nc)
Funders
  • Agence Nationale de la Recherche (ANR-17-EURE-0003, IDEX-02, ANR‐15‐IDEX‐02, ANR-18-CE12-0014, ANR-21-CE20-0024, ANR18, ANR-17-CE20-0014, ANR-15-IDEX-0002, 0014-01, ANR-17, 15-IDEX-02)
  • Centre National de la Recherche Scientifique (Prime80, ANR-15-IDEX-02)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
plant transcription factors, DNA-binding domain, structural classification, protein structure, gene expression regulation
MeSH terms
Animals, Binding Sites, DNA, DNA-Binding Proteins, Humans, Mammals, Transcription Factors

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