Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence
Abstract 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 ev...
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2024-11-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-024-05777-z |
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| author | Kuan-Ting Hsin Yu-Hsuan Lee Kai-Chun Lin Wei Chen Yi-Sheng Cheng |
| author_facet | Kuan-Ting Hsin Yu-Hsuan Lee Kai-Chun Lin Wei Chen Yi-Sheng Cheng |
| author_sort | Kuan-Ting Hsin |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-db3dcfc86f7b439faa565cbed17e22b8 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-db3dcfc86f7b439faa565cbed17e22b82024-11-17T12:18:00ZengBMCBMC Plant Biology1471-22292024-11-0124111710.1186/s12870-024-05777-zSpecific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergenceKuan-Ting Hsin0Yu-Hsuan Lee1Kai-Chun Lin2Wei Chen3Yi-Sheng Cheng4Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and TechnologyDepartment of Life Science, College of Life Science, National Taiwan UniversityInstitute of Plant Biology, College of Life Science, National Taiwan UniversityInstitute of Plant Biology, College of Life Science, National Taiwan UniversityDepartment of Life Science, College of Life Science, National Taiwan UniversityAbstract 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.https://doi.org/10.1186/s12870-024-05777-zCircadian clockDNA binding preferenceConservationProtein-DNA interaction |
| spellingShingle | Kuan-Ting Hsin Yu-Hsuan Lee Kai-Chun Lin Wei Chen Yi-Sheng Cheng Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence BMC Plant Biology Circadian clock DNA binding preference Conservation Protein-DNA interaction |
| title | Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence |
| title_full | Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence |
| title_fullStr | Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence |
| title_full_unstemmed | Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence |
| title_short | Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence |
| title_sort | specific binding between arabidopsis thaliana phytochrome interacting factor 3 atpif3 bhlh and g box originated prior to embryophyte emergence |
| topic | Circadian clock DNA binding preference Conservation Protein-DNA interaction |
| url | https://doi.org/10.1186/s12870-024-05777-z |
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