Beyond DNA binding: single C2H2 zinc fingers with adjacent β-strands mediate dimerization in Drosophila transcription factors.
| Title: | Beyond DNA binding: single C2H2 zinc fingers with adjacent β-strands mediate dimerization in Drosophila transcription factors. |
|---|---|
| Authors: | Balagurov KI; Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia.; Mariasina SS; Center for Magnetic Tomography and Spectroscopy, Chemistry Department, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.; Research and Educational Resource Center 'Pharmacy', RUDN University, Moscow 117198, Russia.; Dukhalin SD; Center for Magnetic Tomography and Spectroscopy, Chemistry Department, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.; Sluchanko NN; A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.; Golovnina AA; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia.; Khrustaleva AM; Group of the Bioinformatics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.; Maksimenko OG; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia.; Arkova OV; Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia.; Stepanenko AA; Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia.; Bocharov EV; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia.; Moscow Center for Advanced Studies, 20 Kulakova St., Moscow 123592, Russia.; Polshakov VI; Center for Magnetic Tomography and Spectroscopy, Chemistry Department, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.; Georgiev PG; Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia.; Bonchuk AN; Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia. |
| Source: | Nucleic acids research [Nucleic Acids Res] 2026 Jan 05; Vol. 54 (1). |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE |
| Imprint Name(s): | Publication: 1992- : Oxford : Oxford University Press; Original Publication: London, Information Retrieval ltd. |
| MeSH Terms: | Drosophila Proteins*/chemistry ; Drosophila Proteins*/genetics ; Drosophila Proteins*/metabolism ; Transcription Factors*/chemistry ; Transcription Factors*/metabolism ; Transcription Factors*/genetics ; DNA-Binding Proteins*/chemistry ; DNA-Binding Proteins*/genetics ; DNA-Binding Proteins*/metabolism ; Protein Multimerization* ; CYS2-HIS2 Zinc Fingers*; DNA/metabolism ; Drosophila melanogaster/genetics ; Animals ; Protein Binding ; Models, Molecular ; Protein Conformation, beta-Strand ; Amino Acid Sequence |
| Abstract: | C2H2 proteins, characterized by DNA-binding C2H2-type zinc finger domains, constitute the largest group of transcription factors. In addition to binding DNA, C2H2 domains can mediate protein-protein interactions, facilitating the oligomerization of C2H2 proteins. In this study, we identified eight C2H2 proteins in the Drosophila genome that feature a unique single C2H2 domain containing a conserved "CGxΦ" motif. Yeast two-hybrid assays, size-exclusion chromatography coupled with multi-angle light scattering, and chemical cross-linking experiments revealed a strong propensity of these domains to form dimers. Using NMR spectroscopy, we determined the solution structure of the dimeric C2H2 domain from the IMZF (Immune-mediated Zinc Finger) protein, providing structural evidence for the dimerization of C2H2 domains. Dimerization is mediated by the interface between the core C2H2 fold and the adjacent β-strand containing the CGxΦ motif, which was further validated by structure-guided mutagenesis. A bioinformatic survey showed that "CGxΦ"-type C2H2 domains are specific to Diptera. Finally, our predictions demonstrate that dimerizing C2H2 domains containing additional structural elements could be widespread among eukaryotic taxa, with the highest prevalence in insects. These findings establish that single C2H2 domains can mediate self-association and identify the CGxΦ-type C2H2 domains as a distinct structural subclass specific to dipteran insects.; (© The Author(s) 2026. Published by Oxford University Press.) |
| References: | J Comput Biol. 2000;7(6):761-76. (PMID: 11382360); Bioinformatics. 2007 Nov 1;23(21):2947-8. (PMID: 17846036); Oncogene. 1998 Nov 12;17(19):2473-84. (PMID: 9824158); Protein Sci. 2018 Jan;27(1):129-134. (PMID: 28875543); Nucleic Acids Res. 2023 Jan 6;51(D1):D445-D451. (PMID: 36350662); Nucleic Acids Res. 2007 Jan;35(Database issue):D5-12. (PMID: 17170002); J Mol Biol. 2006 Apr 7;357(4):1167-83. (PMID: 16483601); Subcell Biochem. 2011;52:261-77. (PMID: 21557087); FEBS J. 2016 Jun;283(11):2004-17. (PMID: 27062441); Front Genet. 2022 Dec 01;13:1081088. (PMID: 36531247); Bioessays. 2022 Apr;44(4):e2100191. (PMID: 35195290); Nucleic Acids Res. 2025 Jan 6;53(D1):D609-D617. (PMID: 39552041); J Biomol NMR. 2000 Jan;16(1):23-8. (PMID: 10718609); Science. 2018 Oct 12;362(6411):. (PMID: 30190310); J Vis Exp. 2022 Dec 23;(190):. (PMID: 36622017); J Magn Reson. 1997 Mar;125(1):171-7. (PMID: 9245376); Biochemistry. 2020 May 26;59(20):1909-1926. (PMID: 32352758); Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21. (PMID: 9757107); Methods Mol Biol. 2012;831:453-83. (PMID: 22167687); Mol Cell. 2003 Feb;11(2):459-70. (PMID: 12620233); Science. 2010 Dec 24;330(6012):1787-97. (PMID: 21177974); Genetics. 2024 May 7;227(1):. (PMID: 38301657); FEBS J. 2007 Aug;274(16):4223-37. (PMID: 17651434); Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15229-34. (PMID: 22949637); Mol Cell Biol. 2001 Jun;21(11):3609-15. (PMID: 11340155); Nucleic Acids Res. 2003 Jan 15;31(2):532-50. (PMID: 12527760); Imeta. 2024 Apr 05;3(3):e191. (PMID: 38898985); EMBO J. 1996 Oct 1;15(19):5358-69. (PMID: 8895580); Curr Biol. 1998 Apr 23;8(9):508-15. (PMID: 9560339); Nat Commun. 2023 Jul 25;14(1):4470. (PMID: 37491363); Nature. 2018 Oct;562(7728):538-544. (PMID: 30323286); J Biomol NMR. 1994 Sep;4(5):727-34. (PMID: 7919956); Trends Biochem Sci. 2007 Feb;32(2):63-70. (PMID: 17210253); Annu Rev Biophys Biomol Struct. 2000;29:183-212. (PMID: 10940247); Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):583-8. (PMID: 15644435); Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844); Mol Cell. 2024 Jul 11;84(13):2490-2510.e9. (PMID: 38996459); J Biomol NMR. 1995 Nov;6(3):277-93. (PMID: 8520220); Mol Cell Biol. 1996 Jun;16(6):2802-13. (PMID: 8649389); Trends Biochem Sci. 2000 Sep;25(9):421-3. (PMID: 10973053); J Mol Evol. 1994 Sep;39(3):306-14. (PMID: 7932792); Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5690-5. (PMID: 21402926); EMBO J. 1997 Apr 15;16(8):2004-13. (PMID: 9155026); Nucleic Acids Res. 2018 Jul 2;46(W1):W200-W204. (PMID: 29905871); Nucleic Acids Res. 2024 Jul 8;52(12):6886-6905. (PMID: 38769058); J Biol Chem. 2003 Oct 24;278(43):42419-26. (PMID: 12917396); Cell Mol Life Sci. 2001 Apr;58(4):625-35. (PMID: 11361095); J Biol Chem. 2021 Aug;297(2):100947. (PMID: 34270961); Adv Exp Med Biol. 2012;747:105-21. (PMID: 22949114); IUBMB Life. 2002 Dec;54(6):351-5. (PMID: 12665246); Acta Naturae. 2021 Jan-Mar;13(1):31-46. (PMID: 33959385); Development. 2017 Aug 1;144(15):2719-2729. (PMID: 28765213); J Biomol NMR. 2013 Jul;56(3):227-41. (PMID: 23728592); Science. 1991 May 10;252(5007):809-17. (PMID: 2028256); Biophys J. 2012 Jan 4;102(1):136-43. (PMID: 22225807); Nucleic Acids Res. 2014 Dec 16;42(22):13997-4005. (PMID: 25414354); J Biol Chem. 2000 Jun 2;275(22):17173-9. (PMID: 10747874); J Biol Chem. 2004 Sep 17;279(38):39789-97. (PMID: 15234987); PLoS Comput Biol. 2009 Mar;5(3):e1000307. (PMID: 19282963); J Biomol NMR. 1996 Dec;8(4):477-86. (PMID: 9008363); Bioessays. 2023 Feb;45(2):e2200179. (PMID: 36449605); Mol Biol Evol. 2020 May 1;37(5):1530-1534. (PMID: 32011700); Bioinformatics. 2009 May 1;25(9):1189-91. (PMID: 19151095); EMBO J. 1985 Jun;4(6):1609-14. (PMID: 4040853); J Mol Biol. 2011 Sep 23;412(3):423-36. (PMID: 21821048); Nucleic Acids Res. 2021 Feb 26;49(4):2375-2389. (PMID: 33638995); Mol Cell Biol. 1998 Apr;18(4):2252-61. (PMID: 9528796); Biopolymers. 1983 Dec;22(12):2577-637. (PMID: 6667333); Elife. 2024 Sep 02;13:. (PMID: 39221775); J Magn Reson B. 1995 Jul;108(1):31-43. (PMID: 7542984); Bioinformatics. 2009 Aug 1;25(15):1972-3. (PMID: 19505945); Biochim Biophys Acta Gene Regul Mech. 2020 Jan;1863(1):194446. (PMID: 31706027); Biochemistry. 2004 Oct 26;43(42):13318-27. (PMID: 15491138); Bioessays. 2024 Aug;46(8):e2400052. (PMID: 38873893); Science. 1993 Sep 24;261(5129):1701-7. (PMID: 8378770); F1000Res. 2013 Sep 18;2:191. (PMID: 24555091); Biochem Biophys Res Commun. 2024 Jan 29;694:149399. (PMID: 38134477); Protein Sci. 1999 Mar;8(3):467-81. (PMID: 10091649); Insect Biochem Mol Biol. 2024 Jul;170:104138. (PMID: 38762126); Cell Biochem Biophys. 2008;50(3):111-31. (PMID: 18253864); J Biol Chem. 2000 Dec 8;275(49):38347-54. (PMID: 10978333); Int J Mol Sci. 2023 Feb 02;24(3):. (PMID: 36769179); PLoS Biol. 2014 Mar 18;12(3):e1001809. (PMID: 24643257); Nucleic Acids Res. 2006;34(22):6505-20. (PMID: 17130173); J Biomol NMR. 2001 May;20(1):71-5. (PMID: 11430757); Nat Struct Biol. 1997 Aug;4(8):605-8. (PMID: 9253405); Bioinformatics. 2021 Sep 29;37(18):3041-3042. (PMID: 33715003); Acta Naturae. 2017 Apr-Jun;9(2):47-58. (PMID: 28740726); Bioinformatics. 2023 Jan 1;39(1):. (PMID: 36413069); Nucleic Acids Res. 2025 Jan 6;53(D1):D444-D456. (PMID: 39565202); Protein Sci. 2018 Jan;27(1):14-25. (PMID: 28710774); Nucleic Acids Res. 2004 Mar 19;32(5):1792-7. (PMID: 15034147); Science. 2021 Jan 1;371(6524):57-64. (PMID: 33384371); Biochemistry. 1992 Apr 28;31(16):3907-17. (PMID: 1567844); Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314. (PMID: 30418610) |
| Grant Information: | 19-74-30026-P Russian Science Foundation; 24-14-00081 Russian Science Foundation |
| Substance Nomenclature: | 0 (Drosophila Proteins); 0 (Transcription Factors); 9007-49-2 (DNA); 0 (DNA-Binding Proteins) |
| Entry Date(s): | Date Created: 20260107 Date Completed: 20260107 Latest Revision: 20260109 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC12774644 |
| DOI: | 10.1093/nar/gkaf1425 |
| PMID: | 41495890 |
| Database: | MEDLINE |
Journal Article