Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence.

Publisher: BioMed Central Country of Publication: England NLM ID: 100967807 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2229 (Electronic) Linking ISSN: 14712229 NLM ISO Abbreviation: BMC Plant Biol Subsets: MEDLINE

Original Publication: London : BioMed Central, [2001-

Arabidopsis Proteins*/metabolism ; Arabidopsis Proteins*/genetics ; Arabidopsis*/metabolism ; Arabidopsis*/genetics ; Basic Helix-Loop-Helix Transcription Factors*/metabolism ; Basic Helix-Loop-Helix Transcription Factors*/genetics; Protein Binding ; Amino Acid Sequence ; Evolution, Molecular

Competing Interests: DeclarationsEthics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare no competing interests.
The basic helix-loop-helix (bHLH) domain via critical amino acid residues on basic region binding to E-box (5'-CANNTG-3') is known in embryophyte. However, the dictated E-box types selection by bHLH dimers and the significant impact of these critical amino acid residues along embryophyte evolution remain unclear. The Arabidopsis thaliana PIF3-bHLH (AtPIF3-bHLH) recombinant protein and a series of AtPIF3-bHLH mutants were synthesized and analyzed. The reduced DNA binding ability and affinity of AtPIF3-bHLH point-mutation proteins, observed via fluorescence-based electrophoretic mobility shift assay (fEMSA) and isothermal titration calorimetry (ITC), suggest the critical role of these DNA-recognition sites in maintaining the AtPIF3-bHLH-DNA interaction. The purifying selection signals and the DNA-recognition-site conservation at the species level suggest the invariant roles of these sites throughout embryophyte evolution. The G-box outcompeted other types of E-box for binding in our competitive fEMSAs. The dynamic hydrogen bond formed between AtPIF3-bHLH and the G-box core indicates flexible identification of the core region. These features highlight a fast fixation of the bHLH-G-box recognition mechanism through embryophyte evolution and serve as a blueprint for studying DNA recognition determinants of other TF families.
(© 2024. The Author(s).)

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NSTC 112-2311-B-002-005 National Science and Technology Council

Keywords: Circadian clock; Conservation; DNA binding preference; Protein-DNA interaction

0 (Arabidopsis Proteins)
0 (Basic Helix-Loop-Helix Transcription Factors)
0 (PIF3 protein, Arabidopsis)

Date Created: 20241110 Date Completed: 20241110 Latest Revision: 20241116

20250114

PMC11552376

10.1186/s12870-024-05777-z

39523297