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Kawasaki M, Hosoe Y, Kamatari YO, Oda M. Naïve balance between structural stability and DNA-binding ability of c-Myb R2R3 under physiological ionic conditions. Biophys Chem 2020; 258:106319. [DOI: 10.1016/j.bpc.2019.106319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/26/2019] [Accepted: 12/31/2019] [Indexed: 01/22/2023]
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Inaba S, Fukada H, Oda M. Folding thermodynamics of c-Myb DNA-binding domain in correlation with its α-helical contents. Int J Biol Macromol 2016; 82:725-32. [DOI: 10.1016/j.ijbiomac.2015.10.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/12/2015] [Accepted: 10/12/2015] [Indexed: 11/28/2022]
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Uemae Y, Sakamoto J, Hidaka Y, Hiratsuka A, Susa T, Kato Y, Suzuki M. Gene expression, function, and diversity of Nkx2-4 in the rainbow trout, Oncorhynchus mykiss. Gen Comp Endocrinol 2014; 206:193-202. [PMID: 25051213 DOI: 10.1016/j.ygcen.2014.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 06/25/2014] [Accepted: 07/13/2014] [Indexed: 11/27/2022]
Abstract
Nkx2 homeodomain transcription factors are involved in various developmental processes and cell specification: e.g. in mammals, NKX2-1 is essential for thyroid-specific gene expression and thyroid morphogenesis. Among Nkx2 proteins, information is still very limited for Nkx2-4. In the present study, we have identified three distinct cDNAs encoding Nkx2-4 isoforms (Nkx2-4a, -b, and -c) from the rainbow trout thyroid tissue, and characterized their transcriptional properties. The trout Nkx2-4 proteins were all predicted to conserve three characteristic domains: the tinman-like amino terminal decapeptide, the NK2 homeodomain, and the NK2-specific domain, and also share 75-89% amino acid similarity. It was shown by dual luciferase assay that Nkx2-4a and Nkx2-4b, but not Nkx2-4c, significantly activated transcription from a cotransfected rat thyroglobulin (TG) promoter. An electrophoretic mobility shift assay indicated that all the Nkx2-4 isoforms could bind to the TG promoter, implying that the faint transcriptional activity of Nkx2-4c might result from some critical amino acid substitution(s) outside the homeodomain. RT-PCR analysis revealed similar tissue distribution patterns for Nkx2-4a and Nkx2-4b mRNAs. Both mRNAs were expressed abundantly in the thyroid, and weakly in the testis. On the other hand, Nkx2-4c mRNA was detected in the ovary as well as in the thyroid. The expression sites of Nkx2-4c mRNA were localized, by in situ hybridization histochemistry, to the ovarian granulosa cells and to the thyroid follicular cells. The results suggest that in the rainbow trout, Nkx2-4a and Nkx2-4b might play a major role in TG gene transcription whereas Nkx2-4c might have some functions in the ovary as well as the thyroid.
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Affiliation(s)
- Youji Uemae
- Department of Biological Science, Graduate School of Science, Shizuoka University, Ohya 836, Shizuoka City, Shizuoka 422-8529, Japan
| | - Joe Sakamoto
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Ohya 836, Shizuoka City, Shizuoka 422-8529, Japan
| | - Yoshie Hidaka
- Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Ohya 836, Shizuoka City, Shizuoka 422-8529, Japan
| | - Ai Hiratsuka
- Department of Biology, Faculty of Science, Shizuoka University, Ohya 836, Shizuoka City, Shizuoka 422-8529, Japan
| | - Takao Susa
- Department of Life Science, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Kawasaki, Kanagawa 214-8571, Japan
| | - Yukio Kato
- Department of Life Science, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Kawasaki, Kanagawa 214-8571, Japan
| | - Masakazu Suzuki
- Department of Biological Science, Graduate School of Science, Shizuoka University, Ohya 836, Shizuoka City, Shizuoka 422-8529, Japan; Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, Ohya 836, Shizuoka City, Shizuoka 422-8529, Japan; Department of Biology, Faculty of Science, Shizuoka University, Ohya 836, Shizuoka City, Shizuoka 422-8529, Japan.
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Babin V, Wang D, Rose RB, Sagui C. Binding polymorphism in the DNA bound state of the Pdx1 homeodomain. PLoS Comput Biol 2013; 9:e1003160. [PMID: 23950697 PMCID: PMC3738460 DOI: 10.1371/journal.pcbi.1003160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/13/2013] [Indexed: 11/18/2022] Open
Abstract
The subtle effects of DNA-protein recognition are illustrated in the homeodomain fold. This is one of several small DNA binding motifs that, in spite of limited DNA binding specificity, adopts crucial, specific roles when incorporated in a transcription factor. The homeodomain is composed of a 3-helix domain and a mobile N-terminal arm. Helix 3 (the recognition helix) interacts with the DNA bases through the major groove, while the N-terminal arm becomes ordered upon binding a specific sequence through the minor groove. Although many structural studies have characterized the DNA binding properties of homeodomains, the factors behind the binding specificity are still difficult to elucidate. A crystal structure of the Pdx1 homeodomain bound to DNA (PDB 2H1K) obtained previously in our lab shows two complexes with differences in the conformation of the N-terminal arm, major groove contacts, and backbone contacts, raising new questions about the DNA recognition process by homeodomains. Here, we carry out fully atomistic Molecular Dynamics simulations both in crystal and aqueous environments in order to elucidate the nature of the difference in binding contacts. The crystal simulations reproduce the X-ray experimental structures well. In the absence of crystal packing constraints, the differences between the two complexes increase during the solution simulations. Thus, the conformational differences are not an artifact of crystal packing. In solution, the homeodomain with a disordered N-terminal arm repositions to a partially specific orientation. Both the crystal and aqueous simulations support the existence of different stable binding conformers identified in the original crystallographic data with different degrees of specificity. We propose that protein-protein and protein-DNA interactions favor a subset of the possible conformations. This flexibility in DNA binding may facilitate multiple functions for the same transcription factor.
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Affiliation(s)
- Volodymyr Babin
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California, United States of America
| | - Dongli Wang
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert B. Rose
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (RBR); (CS)
| | - Celeste Sagui
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (RBR); (CS)
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Zhang LP, Ma BY, Han FX, Wan HL, Wu JP, Yu LH, Wang XR, Zhu JY. Molecular characterization and functional analysis of sheep thyroid transcription factor-1. GENETICS AND MOLECULAR RESEARCH 2012; 11:2585-97. [PMID: 22782632 DOI: 10.4238/2012.june.18.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Thyroid transcription factor-1 (TTF-1), a member of the Nkx2 family of homeodomain-containing proteins, is involved in binding to and in activating the promoters of several important genes in the thyroid, lungs, and brain, and in regulating expression of these tissue-specific genes. We investigated potential roles of sheep (Ovis aries) TTF-1 in regulating cell fate and organ morphogenesis and in controlling puberty and reproductive capability of females. We amplified and cloned the sheep TTF-1 full-length DNA for the first time, analyzed its functional domains and regions, predicted molecular structure of its homeodomain and DNA-binding sites, and examined its expression in pituitary, brain, thyroid gland, ovary, and hypothalamus. We found that sheep TTF-1 has a high degree of homologous identity with that of other mammals, and it has several important domains including domain N, DNA-binding domain, domain C, TN-domain, domain I, and NK2-SD. The DNA-binding domain of sheep TTF-1 has 10 potential DNA-binding sites and is a novel mammalian homeodomain that shows considerable sequence homology with the corresponding rat homeodomain. Several functional regions in sheep TTF-1 share high sequence identity with rat TTF-1, indicating that these regions may have the same activity as in the rat. Expression of TTF-1 in several specific tissues implies that sheep TTF-1 in involved in sheep sexual development and reproductive capability. These results suggest a role of sheep TTF-1 in enhancing sheep reproduction performance and we propose it as a candidate gene for selection.
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Affiliation(s)
- L P Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.
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