Dynamic action of an intrinsically disordered protein in DNA compaction that induces mycobacterial dormancy
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 function...
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| Published in | Nucleic acids research Vol. 52; no. 2; pp. 816 - 830 |
|---|---|
| Main Authors | , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
25.01.2024
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0305-1048 1362-4962 1362-4962 |
| DOI | 10.1093/nar/gkad1149 |
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| Abstract | 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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| AbstractList | 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. 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. Graphical Abstract Graphical 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. Graphical 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.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. |
| Author | Shaban, Amina Kaboso Kodera, Noriyuki Shimizu, Masahiro Ito, Kosuke Nishiyama, Akihito Matsumoto, Sohkichi Tateishi, Yoshitaka Yamaguchi, Takehiro Ozeki, Yuriko Yokoyama, Akira Narita, Tomoyuki Mayanagi, Kouta Hakamata, Mariko |
| Author_xml | – sequence: 1 givenname: Akihito orcidid: 0000-0003-4416-7710 surname: Nishiyama fullname: Nishiyama, Akihito email: anishi@med.niigata-u.ac.jp – sequence: 2 givenname: Masahiro orcidid: 0000-0001-6249-1018 surname: Shimizu fullname: Shimizu, Masahiro – sequence: 3 givenname: Tomoyuki surname: Narita fullname: Narita, Tomoyuki – sequence: 4 givenname: Noriyuki orcidid: 0000-0003-4880-8423 surname: Kodera fullname: Kodera, Noriyuki – sequence: 5 givenname: Yuriko orcidid: 0000-0003-0672-1039 surname: Ozeki fullname: Ozeki, Yuriko – sequence: 6 givenname: Akira surname: Yokoyama fullname: Yokoyama, Akira – sequence: 7 givenname: Kouta orcidid: 0000-0001-6157-9093 surname: Mayanagi fullname: Mayanagi, Kouta – sequence: 8 givenname: Takehiro surname: Yamaguchi fullname: Yamaguchi, Takehiro – sequence: 9 givenname: Mariko surname: Hakamata fullname: Hakamata, Mariko – sequence: 10 givenname: Amina Kaboso orcidid: 0000-0001-6306-1298 surname: Shaban fullname: Shaban, Amina Kaboso – sequence: 11 givenname: Yoshitaka surname: Tateishi fullname: Tateishi, Yoshitaka – sequence: 12 givenname: Kosuke orcidid: 0000-0001-5161-1301 surname: Ito fullname: Ito, Kosuke – sequence: 13 givenname: Sohkichi surname: Matsumoto fullname: Matsumoto, Sohkichi email: sohkichi@med.niigata-u.ac.jp |
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Mycobacteria are the major human pathogens with the capacity to become dormant persisters. Mycobacterial DNA-binding protein 1 (MDP1), an abundant... Mycobacteria are the major human pathogens with the capacity to become dormant persisters. Mycobacterial DNA-binding protein 1 (MDP1), an abundant histone-like... |
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| SubjectTerms | DNA Histones Humans Intrinsically Disordered Proteins - genetics Intrinsically Disordered Proteins - metabolism Molecular Biology Mycobacterium - genetics Mycobacterium - metabolism |
| Title | Dynamic action of an intrinsically disordered protein in DNA compaction that induces mycobacterial dormancy |
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