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Barakat S, Ezen E, Devecioğlu İ, Gezen M, Piepoli S, Erman B. Dimerization choice and alternative functions of ZBTB transcription factors. FEBS J 2024; 291:237-255. [PMID: 37450366 DOI: 10.1111/febs.16905] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 06/09/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Zinc Finger DNA-binding domain-containing proteins are the most populous family among eukaryotic transcription factors. Among these, members of the BTB domain-containing ZBTB sub-family are mostly known for their transcriptional repressive functions. In this Viewpoint article, we explore molecular mechanisms that potentially diversify the function of ZBTB proteins based on their homo and heterodimerization, alternative splicing and post-translational modifications. We describe how the BTB domain is as much a scaffold for the assembly of co-repressors, as a domain that regulates protein stability. We highlight another mechanism that regulates ZBTB protein stability: phosphorylation in the zinc finger domain. We explore the non-transcriptional, structural roles of ZBTB proteins and highlight novel findings that describe the ability of ZBTB proteins to associate with poly adenosine ribose in the nucleus during the DNA damage response. Herein, we discuss the contribution of BTB domain scaffolds to the formation of transcriptional repressive complexes, to chromosome compartmentalization and their non-transcriptional, purely structural functions in the nucleus.
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Affiliation(s)
- Sarah Barakat
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Ege Ezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - İzem Devecioğlu
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Melike Gezen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Sofia Piepoli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
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Structural insights into the recognition of telomeric variant repeat TTGGGG by broad-complex, tramtrack and bric-à-brac - zinc finger protein ZBTB10. J Biol Chem 2023; 299:102918. [PMID: 36657642 PMCID: PMC9958480 DOI: 10.1016/j.jbc.2023.102918] [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: 10/30/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/17/2023] Open
Abstract
Multiple proteins bind to telomeric DNA and are important for the role of telomeres in genome stability. A recent study established a broad-complex, tramtrack and bric-à-brac - zinc finger (BTB-ZF) protein, ZBTB10 (zinc finger and BTB domain-containing protein 10), as a telomeric variant repeat-binding protein at telomeres that use an alternative method for lengthening telomeres). ZBTB10 specifically interacts with the double-stranded telomeric variant repeat sequence TTGGGG by employing its tandem C2H2 zinc fingers (ZF1-2). Here, we solved the crystal structure of human ZBTB10 ZF1-2 in complex with a double-stranded DNA duplex containing the sequence TTGGGG to assess the molecular details of this interaction. Combined with calorimetric analysis, we identified the vital residues in TTGGGG recognition and determined the specific recognition mechanisms that are different from those of TZAP (telomere zinc finger-associated protein), a recently defined telomeric DNA-binding protein. Following these studies, we further identified a single amino-acid mutant (Arg767Gln) of ZBTB10 ZF1-2 that shows a preference for the telomeric DNA repeat TTAGGG sequence. We solved the cocrystal structure, providing a structural basis for telomeric DNA recognition by C2H2 ZF proteins.
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Piepoli S, Barakat S, Nogay L, Şimşek B, Akkose U, Taskiran H, Tolay N, Gezen M, Yeşilada CY, Tuncay M, Adebali O, Atilgan C, Erman B. Sibling rivalry among the ZBTB transcription factor family: homodimers versus heterodimers. Life Sci Alliance 2022; 5:5/11/e202201474. [PMID: 36096675 PMCID: PMC9468604 DOI: 10.26508/lsa.202201474] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
BTB domains potentially can form homo- or heterodimers. The study examines the dimerization choice of several BTB domains and finds only one heterodimer, while all tested pairs can homodimerize. The BTB domain is an oligomerization domain found in over 300 proteins encoded in the human genome. In the family of BTB domain and zinc finger–containing (ZBTB) transcription factors, 49 members share the same protein architecture. The N-terminal BTB domain is structurally conserved among the family members and serves as the dimerization site, whereas the C-terminal zinc finger motifs mediate DNA binding. The available BTB domain structures from this family reveal a natural inclination for homodimerization. In this study, we investigated the potential for heterodimer formation in the cellular environment. We selected five BTB homodimers and four heterodimer structures. We performed cell-based binding assays with fluorescent protein–BTB domain fusions to assess dimer formation. We tested the binding of several BTB pairs, and we were able to confirm the heterodimeric physical interaction between the BTB domains of PATZ1 and PATZ2, previously reported only in an interactome mapping experiment. We also found this pair to be co-expressed in several immune system cell types. Finally, we used the available structures of BTB domain dimers and newly constructed models in extended molecular dynamics simulations (500 ns) to understand the energetic determinants of homo- and heterodimer formation. We conclude that heterodimer formation, although frequently described as less preferred than homodimers, is a possible mechanism to increase the combinatorial specificity of this transcription factor family.
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Affiliation(s)
- Sofia Piepoli
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Sarah Barakat
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Liyne Nogay
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Büşra Şimşek
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Umit Akkose
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Hakan Taskiran
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Nazife Tolay
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Melike Gezen
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Canberk Yarkın Yeşilada
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Mustafa Tuncay
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
| | - Ogün Adebali
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul, Turkey
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Orth B, Sander B, Möglich A, Diederichs K, Eilers M, Lorenz S. Identification of an atypical interaction site in the BTB domain of the MYC-interacting zinc-finger protein 1. Structure 2021; 29:1230-1240.e5. [PMID: 34186024 DOI: 10.1016/j.str.2021.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/26/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
The repurposing of structurally conserved protein domains in different functional contexts is thought to be a driving force in the evolution of complex protein interaction networks. The BTB/POZ domain is such a versatile binding module that occurs over 200 times in the human proteome with diverse protein-specific adaptations. In BTB-zinc-finger transcription factors, the BTB domain drives homo- and heterodimerization as well as interactions with non-BTB-domain-containing proteins. Which mechanisms encode specificity in these interactions at a structural level is incompletely understood. Here, we uncover an atypical peptide-binding site in the BTB domain of the MYC-interacting zinc-finger protein 1 (MIZ1) that arises from local flexibility of the core BTB fold and may provide a target site for MIZ1-directed therapeutic approaches. Intriguingly, the identified binding mode requires the BTB domain to be in a homodimeric state, thus holding opportunities for functional discrimination between homo- and heterodimers of MIZ1 in the cell.
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Affiliation(s)
- Barbara Orth
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany; Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Bodo Sander
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Andreas Möglich
- Lehrstuhl für Biochemie, University of Bayreuth, 95447 Bayreuth, Germany
| | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Martin Eilers
- Lehrstuhl für Biochemie, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sonja Lorenz
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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