1
|
Rua AJ, Whitehead RD, Alexandrescu AT. NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol X 2023; 8:100093. [PMID: 37655311 PMCID: PMC10465944 DOI: 10.1016/j.yjsbx.2023.100093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
ZNF750 is a nuclear transcription factor that activates skin differentiation and has tumor suppressor roles in several cancers. Unusually, ZNF750 has only a single zinc-finger (ZNF) domain, Z*, with an amino acid sequence that differs markedly from the CCHH family consensus. Because of its sequence differences Z* is classified as degenerate, presumed to have lost the ability to bind the zinc ion required for folding. AlphaFold predicts an irregular structure for Z* with low confidence. Low confidence predictions are often inferred to be intrinsically disordered regions of proteins, which would be the case if Z* did not bind Zn2+. We use NMR and CD spectroscopy to show that a 25-51 segment of ZNF750 corresponding to the Z* domain folds into a well-defined antiparallel ββα tertiary structure with a pM dissociation constant for Zn2+ and a thermal stability >80 °C. Of three alternative Zn2+ ligand sets, Z* uses a CCHC rather than the expected CCHH ligating motif. The switch in the last ligand maintains the folding topology and hydrophobic core of the classical ZNF motif. CCHC ZNFs are typically associated with protein-protein interactions, raising the possibility that ZNF750 interacts with DNA through other proteins rather than directly. The structure of Z* provides context for understanding the function of the domain and its cancer-associated mutations. We expect other ZNFs currently classified as degenerate could be CCHC-type structures like Z*.
Collapse
Affiliation(s)
- Antonio J. Rua
- Department of Molecular and Cellular Biology, University of Connecticut, United States
| | - Richard D. Whitehead
- Department of Molecular and Cellular Biology, University of Connecticut, United States
| | | |
Collapse
|
2
|
Negi S, Imanishi M, Hamori M, Kawahara-Nakagawa Y, Nomura W, Kishi K, Shibata N, Sugiura Y. The past, present, and future of artificial zinc finger proteins: design strategies and chemical and biological applications. J Biol Inorg Chem 2023; 28:249-261. [PMID: 36749405 PMCID: PMC9903285 DOI: 10.1007/s00775-023-01991-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/25/2023] [Indexed: 02/08/2023]
Abstract
Zinc finger proteins are abundant in the human proteome and are responsible for a variety of functions. The domains that constitute zinc finger proteins are compact spherical structures, each comprising approximately 30 amino acid residues, but they also have precise molecular factor functions: zinc binding and DNA recognition. Due to the biological importance of zinc finger proteins and their unique structural and functional properties, many artificial zinc finger proteins have been created and are expected to improve their functions and biological applications. In this study, we review previous studies on the redesign and application of artificial zinc finger proteins, focusing on the experimental results obtained by our research group. In addition, we systematically review various design strategies used to construct artificial zinc finger proteins and discuss in detail their potential biological applications, including gene editing. This review will provide relevant information to researchers involved or interested in the field of artificial zinc finger proteins as a potential new treatment for various diseases.
Collapse
Affiliation(s)
- Shigeru Negi
- Faculty of Pharmaceutical Science, Doshisha Women's University Kyotanabe, Kyoto, 610-0395, Japan.
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Mami Hamori
- Faculty of Pharmaceutical Science, Doshisha Women's University Kyotanabe, Kyoto, 610-0395, Japan
| | - Yuka Kawahara-Nakagawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-Cho, Ako-Gun, Hyogo, 678-1297, Japan
| | - Wataru Nomura
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-Ku, Hiroshima, 734-8553, Japan
| | - Kanae Kishi
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-Ku, Hiroshima, 734-8553, Japan
| | - Nobuhito Shibata
- Faculty of Pharmaceutical Science, Doshisha Women's University Kyotanabe, Kyoto, 610-0395, Japan
| | - Yukio Sugiura
- Faculty of Pharmaceutical Science, Doshisha Women's University Kyotanabe, Kyoto, 610-0395, Japan
| |
Collapse
|
3
|
Refactoring transcription factors for metabolic engineering. Biotechnol Adv 2022; 57:107935. [PMID: 35271945 DOI: 10.1016/j.biotechadv.2022.107935] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/04/2022] [Accepted: 03/03/2022] [Indexed: 12/19/2022]
Abstract
Due to the ability to regulate target metabolic pathways globally and dynamically, metabolic regulation systems composed of transcription factors have been widely used in metabolic engineering and synthetic biology. This review introduced the categories, action principles, prediction strategies, and related databases of transcription factors. Then, the application of global transcription machinery engineering technology and the transcription factor-based biosensors and quorum sensing systems are overviewed. In addition, strategies for optimizing the transcriptional regulatory tools' performance by refactoring transcription factors are summarized. Finally, the current limitations and prospects of constructing various regulatory tools based on transcription factors are discussed. This review will provide theoretical guidance for the rational design and construction of transcription factor-based metabolic regulation systems.
Collapse
|
4
|
Kluska K, Adamczyk J, Krężel A. Metal binding properties, stability and reactivity of zinc fingers. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
5
|
Belczyk-Ciesielska A, Csipak B, Hajdu B, Sparavier A, Asaka MN, Nagata K, Gyurcsik B, Bal W. Nickel(ii)-promoted specific hydrolysis of zinc finger proteins. Metallomics 2018; 10:1089-1098. [DOI: 10.1039/c8mt00098k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The (S/T)XH sequence in Cys2His2zinc fingers can be hydrolytically cleaved by Ni(ii) ions. This reaction can be applied for purification, inhibition or activation of designed zinc finger fusion proteins.
Collapse
Affiliation(s)
| | - Brigitta Csipak
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | - Bálint Hajdu
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | | | - Masamitsu N. Asaka
- Nagata Special Laboratory
- Faculty of Medicine
- University of Tsukuba
- Tsukuba 305-8575
- Japan
| | - Kyosuke Nagata
- Nagata Special Laboratory
- Faculty of Medicine
- University of Tsukuba
- Tsukuba 305-8575
- Japan
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics
- Polish Academy of Sciences
- Warsaw
- Poland
| |
Collapse
|
6
|
Imanishi M. [Design of artificial DNA binding proteins toward control and elucidation of cellular functions]. YAKUGAKU ZASSHI 2014. [PMID: 23208050 DOI: 10.1248/yakushi.12-00228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An artificial transcription factor that can regulate the expression of specific genes at a desired time is very useful for research in chemical biology, cell biology, and future gene therapy. A C2H2 zinc finger motif, one of zinc-containing proteins, is known as the most ubiquitous DNA binding motif. The motif is attractive for designing artificial transcription factors with desired DNA binding specificities because of its characteristic DNA binding properties: (1) recognition of 3 bp per motif, (2) tandemly connected modular structure, and (3) binding to non-palindrome sequences as a monomer. Taking advantage of these properties, artificial DNA binding proteins with new DNA binding characteristics have been designed. By changing the linker region between two 3-zinc finger domains, artificial 6-zinc finger proteins were developed and shown to skip DNA sequences. Zinc-responsive transcription factors were created by altering one of the zinc ligands. An artificial zinc finger transcription factor targeting a core clock gene induced phase shifts of the cellular "circadian rhythm". Herein, I will summarize creation and function of the above-mentioned artificial zinc finger-type DNA binding proteins and transcription factors.
Collapse
Affiliation(s)
- Miki Imanishi
- Institute for Chemical Research, Kyoto University, Kyoto, Japan.
| |
Collapse
|
7
|
Imanishi M, Matsumura K, Tsuji S, Nakaya T, Negi S, Futaki S, Sugiura Y. Zn(II) binding and DNA binding properties of ligand-substituted CXHH-type zinc finger proteins. Biochemistry 2012; 51:3342-8. [PMID: 22482427 DOI: 10.1021/bi300236m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CCHH-type zinc fingers are among the most common DNA binding motifs found in eukaryotes. In a previous report, we substituted the second ligand cysteine residue with aspartic acid, producing a Zn(II)-responsive transcription factor; this indicates that a ligand substitution is a possible design target of an engineered zinc finger peptide. Despite the importance of Zn(II) binding with respect to the folding and DNA binding properties of a zinc finger peptide, no study about the effects of ligand substitution on both Zn(II) binding and DNA binding properties has been reported. Here, we substituted a conserved cysteine (C) with other zinc-coordinated amino acid residues, histidine (H), aspartic acid (D), and glutamic acid (E), to create CXHH-type zinc finger peptides (X = C, H, D, and E). The Zn(II)-dependent conformational change was observed in all peptides; however, the Zn(II) binding affinity and metal coordination geometry of the peptides were different. Gel mobility shift assays showed that the Zn(II)-bound forms of the ligand-substituted derivatives retain DNA binding ability, while the DNA binding affinity decreased in the following manner: CCHH > CDHH > CEHH ≫ CHHH. The DNA binding sequence preferences of the ligand-substituted derivatives were similar to that of the wild type in the context of the full three-finger DNA-binding domain of transcription factor Zif268. These results indicate that artificial zinc finger proteins with various DNA binding affinities that respond to a diverse range of Zn(II) concentrations can be designed by substituting the Zn(II) ligand.
Collapse
Affiliation(s)
- Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | | | | | | | | | | | | |
Collapse
|
8
|
Murase S, Ishino S, Ishino Y, Tanaka T. Control of enzyme reaction by a designed metal-ion-dependent α-helical coiled-coil protein. J Biol Inorg Chem 2012; 17:791-9. [PMID: 22466407 DOI: 10.1007/s00775-012-0896-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 03/20/2012] [Indexed: 01/01/2023]
Abstract
Regulation of protein function by external stimuli is a fascinating target for de novo design. We have constructed a peptide that assembles into a homotrimer in the presence of metal ions, such as Ni(2+), Cu(2+), and Zn(2+). We fused the peptide construct to the DNA-binding domain (DBD) of the heat shock factor from Saccharomyces cerevisiae, which binds tandem repeats of the heat shock element (HSE). However, the fusion protein bound to the natural three tandem HSEs even in the absence of metal ions, although mainly as the dimerized protein. Using "skipped" HSEs containing six additional nucleotides inserted between two adjacent HSEs, to prevent interactions between the DBDs, we found the fusion protein bound to the new DNA target in a metal-ion-dependent manner, as monitored by a HindIII protection assay. The fusion protein containing two metal binding sites in the metal-ion-controlled domain inhibited RNA transcription by T7 RNA polymerase in the presence of metal ions, in a template containing skipped HSEs downstream of the T7 promoter. The designed protein therefore regulates the functions of the enzyme in a metal-ion-dependent manner.
Collapse
Affiliation(s)
- Shigeo Murase
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya, 466-8555, Japan
| | | | | | | |
Collapse
|
9
|
Towards artificial metallonucleases for gene therapy: recent advances and new perspectives. Future Med Chem 2011; 3:1935-66. [DOI: 10.4155/fmc.11.139] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.
Collapse
|
10
|
Negi S, Imanishi M, Sasaki M, Tatsutani K, Futaki S, Sugiura Y. An Arginine Residue Instead of a Conserved Leucine Residue in the Recognition Helix of the Finger 3 of Zif268 Stabilizes the Domain Structure and Mediates DNA Binding. Biochemistry 2011; 50:6266-72. [DOI: 10.1021/bi200697p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shigeru Negi
- Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Koudo, Kyotanabe-Shi 610-0395, Japan
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Maeko Sasaki
- Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Koudo, Kyotanabe-Shi 610-0395, Japan
| | - Kazuya Tatsutani
- Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Yukio Sugiura
- Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Koudo, Kyotanabe-Shi 610-0395, Japan
| |
Collapse
|