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Nishiyama A, Shimizu M, Narita T, Kodera N, Ozeki Y, Yokoyama A, Mayanagi K, Yamaguchi T, Hakamata M, Shaban A, Tateishi Y, Ito K, Matsumoto S. Dynamic action of an intrinsically disordered protein in DNA compaction that induces mycobacterial dormancy. Nucleic Acids Res 2024; 52:816-830. [PMID: 38048321 PMCID: PMC10810275 DOI: 10.1093/nar/gkad1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023] Open
Abstract
Mycobacteria are the major human pathogens with the capacity to become dormant persisters. Mycobacterial DNA-binding protein 1 (MDP1), an abundant histone-like protein in dormant mycobacteria, induces dormancy phenotypes, e.g. chromosome compaction and growth suppression. For these functions, the polycationic intrinsically disordered region (IDR) is essential. However, the disordered property of IDR stands in the way of clarifying the molecular mechanism. Here we clarified the molecular and structural mechanism of DNA compaction by MDP1. Using high-speed atomic force microscopy, we observed that monomeric MDP1 bundles two adjacent DNA duplexes side-by-side via IDR. Combined with coarse-grained molecular dynamics simulation, we revealed the novel dynamic DNA cross-linking model of MDP1 in which a stretched IDR cross-links two DNA duplexes like double-sided tape. IDR is able to hijack HU function, resulting in the induction of strong mycobacterial growth arrest. This IDR-mediated reversible DNA cross-linking is a reasonable model for MDP1 suppression of the genomic function in the resuscitable non-replicating dormant mycobacteria.
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Affiliation(s)
- Akihito Nishiyama
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Masahiro Shimizu
- Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1192, Japan
- Division of Quantum Beam Material Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Tomoyuki Narita
- Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Akira Yokoyama
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Kouta Mayanagi
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takehiro Yamaguchi
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Department of Pharmacology, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan
| | - Mariko Hakamata
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Department of Respiratory Medicine and Infectious Disease, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Amina Kaboso Shaban
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Yoshitaka Tateishi
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Kosuke Ito
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
- Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl. Mulyorejo, Surabaya, East Java 60115, Indonesia
- Division of Research Aids, Hokkaido University Institute for Vaccine Research & Development, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
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