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Bonchuk A, Boyko K, Fedotova A, Nikolaeva A, Lushchekina S, Khrustaleva A, Popov V, Georgiev P. Structural basis of diversity and homodimerization specificity of zinc-finger-associated domains in Drosophila. Nucleic Acids Res 2021; 49:2375-2389. [PMID: 33638995 PMCID: PMC7913770 DOI: 10.1093/nar/gkab061] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
In arthropods, zinc finger-associated domains (ZADs) are found at the N-termini of many DNA-binding proteins with tandem arrays of Cys2-His2 zinc fingers (ZAD-C2H2 proteins). ZAD-C2H2 proteins undergo fast evolutionary lineage-specific expansion and functional diversification. Here, we show that all ZADs from Drosophila melanogaster form homodimers, but only certain ZADs with high homology can also heterodimerize. CG2712, for example, is unable to heterodimerize with its paralog, the previously characterized insulator protein Zw5, with which it shares 46% homology. We obtained a crystal structure of CG2712 protein's ZAD domain that, in spite of a low sequence homology, has similar spatial organization with the only known ZAD structure (from Grauzone protein). Steric clashes prevented the formation of heterodimers between Grauzone and CG2712 ZADs. Using detailed structural analysis, site-directed mutagenesis, and molecular dynamics simulations, we demonstrated that rapid evolutionary acquisition of interaction specificity was mediated by the more energy-favorable formation of homodimers in comparison to heterodimers, and that this specificity was achieved by multiple amino acid substitutions resulting in the formation or breaking of stabilizing interactions. We speculate that specific homodimerization of ZAD-C2H2 proteins is important for their architectural role in genome organization.
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Affiliation(s)
- Artem Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Konstantin Boyko
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anna Fedotova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Alena Nikolaeva
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- National Research Center «Kurchatov Institute», Moscow 123182, Russia
| | - Sofya Lushchekina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anastasia Khrustaleva
- Department of the Bioinformatics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Vladimir Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
- National Research Center «Kurchatov Institute», Moscow 123182, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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Fedotova AA, Bonchuk AN, Mogila VA, Georgiev PG. C2H2 Zinc Finger Proteins: The Largest but Poorly Explored Family of Higher Eukaryotic Transcription Factors. Acta Naturae 2017; 9:47-58. [PMID: 28740726 PMCID: PMC5509000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 12/03/2022] Open
Abstract
The emergence of whole-genome assays has initiated numerous genome-wide studies of transcription factor localizations at genomic regulatory elements (enhancers, promoters, silencers, and insulators), as well as facilitated the uncovering of some of the key principles of chromosomal organization. However, the proteins involved in the formation and maintenance of the chromosomal architecture and the organization of regulatory domains remain insufficiently studied. This review attempts to collate the available data on the abundant but still poorly understood family of proteins with clusters of the C2H2 zinc finger domains. One of the best known proteins of this family is a well conserved protein known as CTCF, which plays a key role in the establishment of the chromosomal architecture in vertebrates. The distinctive features of C2H2 zinc finger proteins include strong and specific binding to a long and unique DNA recognition target sequence and rapid expansion within various animal taxa during evolution. The reviewed data support a proposed model according to which many of the C2H2 proteins have functions that are similar to those of the CTCF in the organization of the chromatin architecture.
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Affiliation(s)
- A. A. Fedotova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Str., 34/5, Moscow, 119334, Russia
| | - A. N. Bonchuk
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Str., 34/5, Moscow, 119334, Russia
| | - V. A. Mogila
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Str., 34/5, Moscow, 119334, Russia
| | - P. G. Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Str., 34/5, Moscow, 119334, Russia
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Yamane M, Fujii S, Ohtsuka S, Niwa H. Zscan10 is dispensable for maintenance of pluripotency in mouse embryonic stem cells. Biochem Biophys Res Commun 2015; 468:826-31. [DOI: 10.1016/j.bbrc.2015.11.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/07/2015] [Indexed: 01/22/2023]
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Liang Y, Huimei Hong F, Ganesan P, Jiang S, Jauch R, Stanton LW, Kolatkar PR. Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206. Nucleic Acids Res 2012; 40:8721-32. [PMID: 22735705 PMCID: PMC3458555 DOI: 10.1093/nar/gks611] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Zfp206 (also named as Zscan10) belongs to the subfamily of C2H2 zinc finger transcription factors, which is characterized by the N-terminal SCAN domain. The SCAN domain mediates self-association and association between the members of SCAN family transcription factors, but the structural basis and selectivity determinants for complex formation is unknown. Zfp206 is important for maintaining the pluripotency of embryonic stem cells presumably by combinatorial assembly of itself or other SCAN family members on enhancer regions. To gain insights into the folding topology and selectivity determinants for SCAN dimerization, we solved the 1.85 Å crystal structure of the SCAN domain of Zfp206. In vitro binding studies using a panel of 20 SCAN proteins indicate that the SCAN domain Zfp206 can selectively associate with other members of SCAN family transcription factors. Deletion mutations showed that the N-terminal helix 1 is critical for heterodimerization. Double mutations and multiple mutations based on the Zfp206SCAN–Zfp110SCAN model suggested that domain swapped topology is a possible preference for Zfp206SCAN–Zfp110SCAN heterodimer. Together, we demonstrate that the Zfp206SCAN constitutes a protein module that enables C2H2 transcription factor dimerization in a highly selective manner using a domain-swapped interface architecture and identify novel partners for Zfp206 during embryonal development.
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Affiliation(s)
- Yu Liang
- Laboratory for Structural Biochemistry, Stem Cell and Developmental Biology, Genome Institute of Singapore, Genome, 60 Biopolis Street, Singapore
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