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Qu Y, Lim CJ, Whang YR, Liu J, Yan J. Mechanism of DNA organization by Mycobacterium tuberculosis protein Lsr2. Nucleic Acids Res 2013; 41:5263-72. [PMID: 23580555 PMCID: PMC3664827 DOI: 10.1093/nar/gkt249] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bacterial nucleoid-associated proteins, such as H-NS-like proteins in Enterobacteriaceae, are abundant DNA-binding proteins that function in chromosomal DNA organization and gene transcription regulation. The Mycobacterium tuberculosis Lsr2 protein has been proposed to be the first identified H-NS analogue in Gram-positive bacteria based on its capability to complement numerous in vivo functions of H-NS. Here, we report that Lsr2 cooperatively binds to DNA forming a rigid Lsr2 nucleoprotein complex that restricts DNA accessibility, similar to H-NS. On large DNA, the rigid Lsr2 nucleoprotein complexes can mediate DNA condensation into highly compact DNA conformations. In addition, the responses of Lsr2 nucleoprotein complex to environmental factors (salt concentration, temperature and pH) were studied over physiological ranges. These results provide mechanistic insights into how Lsr2 may mediate its gene silencing, genomic DNA protection and organization functions in vivo. Finally, our results strongly support that Lsr2 is an H-NS-like protein in Gram-positive bacteria from a structural perspective.
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Affiliation(s)
- Yuanyuan Qu
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
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52
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Lyonnais S, Gorelick RJ, Heniche-Boukhalfa F, Bouaziz S, Parissi V, Mouscadet JF, Restle T, Gatell JM, Le Cam E, Mirambeau G. A protein ballet around the viral genome orchestrated by HIV-1 reverse transcriptase leads to an architectural switch: from nucleocapsid-condensed RNA to Vpr-bridged DNA. Virus Res 2013; 171:287-303. [PMID: 23017337 PMCID: PMC3552025 DOI: 10.1016/j.virusres.2012.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 12/15/2022]
Abstract
HIV-1 reverse transcription is achieved in the newly infected cell before viral DNA (vDNA) nuclear import. Reverse transcriptase (RT) has previously been shown to function as a molecular motor, dismantling the nucleocapsid complex that binds the viral genome as soon as plus-strand DNA synthesis initiates. We first propose a detailed model of this dismantling in close relationship with the sequential conversion from RNA to double-stranded (ds) DNA, focusing on the nucleocapsid protein (NCp7). The HIV-1 DNA-containing pre-integration complex (PIC) resulting from completion of reverse transcription is translocated through the nuclear pore. The PIC nucleoprotein architecture is poorly understood but contains at least two HIV-1 proteins initially from the virion core, namely integrase (IN) and the viral protein r (Vpr). We next present a set of electron micrographs supporting that Vpr behaves as a DNA architectural protein, initiating multiple DNA bridges over more than 500 base pairs (bp). These complexes are shown to interact with NCp7 bound to single-stranded nucleic acid regions that are thought to maintain IN binding during dsDNA synthesis, concurrently with nucleocapsid complex dismantling. This unexpected binding of Vpr conveniently leads to a compacted but filamentous folding of the vDNA that should favor its nuclear import. Finally, nucleocapsid-like aggregates engaged in dsDNA synthesis appear to efficiently bind to F-actin filaments, a property that may be involved in targeting complexes to the nuclear envelope. More generally, this article highlights unique possibilities offered by in vitro reconstitution approaches combined with macromolecular imaging to gain insights into the mechanisms that alter the nucleoprotein architecture of the HIV-1 genome, ultimately enabling its insertion into the nuclear chromatin.
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MESH Headings
- DNA Packaging
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Genome, Viral
- HIV Integrase/genetics
- HIV Integrase/metabolism
- HIV Reverse Transcriptase/genetics
- HIV Reverse Transcriptase/metabolism
- HIV-1/chemistry
- HIV-1/enzymology
- HIV-1/genetics
- HIV-1/metabolism
- Humans
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Reverse Transcription
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
- vpr Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program; SAIC-Frederick, Inc.; Frederick National Laboratory for Cancer Research; Frederick, MD USA
| | - Fatima Heniche-Boukhalfa
- Maintenance des génomes, Microscopies Moléculaire et Bionanosciences; UMR 8126 CNRS-Université Paris Sud, Villejuif, F-94805, France
| | - Serge Bouaziz
- Laboratoire de Cristallographie et RMN biologiques; UMR 8015 CNRS-Université Paris Descartes; Paris, F-75006, France
| | - Vincent Parissi
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, UMR5234 CNRS-Université Bordeaux Segalen, France
| | | | - Tobias Restle
- Institute of Molecular Medicine, University of Lübeck, Center for Structural and Cell Biology in Medicine (CSCM), D-23538 Lübeck, Germany
| | | | - Eric Le Cam
- Maintenance des génomes, Microscopies Moléculaire et Bionanosciences; UMR 8126 CNRS-Université Paris Sud, Villejuif, F-94805, France
| | - Gilles Mirambeau
- AIDS Research Group; IDIBAPS; E-08036 Barcelona, Spain
- Faculté de Biologie; UPMC Sorbonne Universités; Paris, F-75005, France
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53
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Lim CJ, Lee SY, Teramoto J, Ishihama A, Yan J. The nucleoid-associated protein Dan organizes chromosomal DNA through rigid nucleoprotein filament formation in E. coli during anoxia. Nucleic Acids Res 2012. [PMID: 23180762 PMCID: PMC3553945 DOI: 10.1093/nar/gks1126] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Dan is a transcription factor that regulates the ttd operon encoding tartrate dehydratase. During anaerobic conditions, its copy number increases by 100-fold, making Dan an abundant nucleoid-associated protein. However, little is known about the mode of Dan–DNA interaction. To understand its cellular functions, we used single-molecule manipulation and imaging techniques to show that Dan binds cooperatively along DNA, resulting in formation of a rigid periodic nucleoprotein filament that strongly restricts accessibility to DNA. Furthermore, in the presence of physiologic levels of magnesium, these filaments interact with each other to cause global DNA condensation. Overall, these results shed light on the architectural role of Dan in the compaction of Escherichia coli chromosomal DNA under anaerobic conditions. Formation of the nucleoprotein filament provides a basis in understanding how Dan may play roles in both chromosomal DNA protection and gene regulation.
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Affiliation(s)
- Ci Ji Lim
- National University of Singapore, Graduate School for Integrative Sciences and Engineering, Singapore
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54
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Driessen RPC, Meng H, Suresh G, Shahapure R, Lanzani G, Priyakumar UD, White MF, Schiessel H, van Noort J, Dame RT. Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends. Nucleic Acids Res 2012; 41:196-205. [PMID: 23155062 PMCID: PMC3592393 DOI: 10.1093/nar/gks1053] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Archaeal chromatin proteins share molecular and functional similarities with both bacterial and eukaryotic chromatin proteins. These proteins play an important role in functionally organizing the genomic DNA into a compact nucleoid. Cren7 and Sul7 are two crenarchaeal nucleoid-associated proteins, which are structurally homologous, but not conserved at the sequence level. Co-crystal structures have shown that these two proteins induce a sharp bend on binding to DNA. In this study, we have investigated the architectural properties of these proteins using atomic force microscopy, molecular dynamics simulations and magnetic tweezers. We demonstrate that Cren7 and Sul7 both compact DNA molecules to a similar extent. Using a theoretical model, we quantify the number of individual proteins bound to the DNA as a function of protein concentration and show that forces up to 3.5 pN do not affect this binding. Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein–DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins.
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Affiliation(s)
- Rosalie P C Driessen
- Molecular Genetics, Leiden Institute of Chemistry and Cell Observatory, Physics of Life Processes, Leiden Institute of Physics and Cell Observatory, Leiden University, 2333 CC Leiden, The Netherlands
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55
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Lin J, Chen H, Dröge P, Yan J. Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF). PLoS One 2012; 7:e49885. [PMID: 23166787 PMCID: PMC3498176 DOI: 10.1371/journal.pone.0049885] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 10/15/2012] [Indexed: 11/18/2022] Open
Abstract
The integration host factor (IHF) is an abundant nucleoid-associated protein and an essential co-factor for phage λ site-specific recombination and gene regulation in E. coli. Introduction of a sharp DNA kink at specific cognate sites is critical for these functions. Interestingly, the intracellular concentration of IHF is much higher than the concentration needed for site-specific interactions, suggesting that non-specific binding of IHF to DNA plays a role in the physical organization of bacterial chromatin. However, it is unclear how non-specific DNA association contributes to DNA organization. By using a combination of single DNA manipulation and atomic force microscopy imaging methods, we show here that distinct modes of non-specific DNA binding of IHF result in complex global DNA conformations. Changes in KCl and IHF concentrations, as well as tension applied to DNA, dramatically influence the degree of DNA-bending. In addition, IHF can crosslink DNA into a highly compact DNA meshwork that is observed in the presence of magnesium at low concentration of monovalent ions and high IHF-DNA stoichiometries. Our findings provide important insights into how IHF contributes to bacterial chromatin organization, gene regulation, and biofilm formation.
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Affiliation(s)
- Jie Lin
- Department of Physics, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Hu Chen
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Peter Dröge
- Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (PD); (JY)
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
- * E-mail: (PD); (JY)
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56
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Lim CJ, Lee SY, Kenney LJ, Yan J. Nucleoprotein filament formation is the structural basis for bacterial protein H-NS gene silencing. Sci Rep 2012; 2:509. [PMID: 22798986 PMCID: PMC3396134 DOI: 10.1038/srep00509] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 06/28/2012] [Indexed: 11/23/2022] Open
Abstract
H-NS is an abundant nucleoid-associated protein in bacteria that globally silences genes, including horizontally-acquired genes related to pathogenesis. Although it has been shown that H-NS has multiple modes of DNA-binding, which mode is employed in gene silencing is still unclear. Here, we report that in H-NS mutants that are unable to silence genes, are unable to form a rigid H-NS nucleoprotein filament. These results indicate that the H-NS nucleoprotein filament is crucial for its gene silencing function, and serves as the fundamental structural basis for gene silencing by H-NS and likely other H-NS-like bacterial proteins.
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Affiliation(s)
- Ci Ji Lim
- NUS Graduate school For Integrative Sciences and Engineering, Singapore 119077
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57
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Winardhi RS, Fu W, Castang S, Li Y, Dove SL, Yan J. Higher order oligomerization is required for H-NS family member MvaT to form gene-silencing nucleoprotein filament. Nucleic Acids Res 2012; 40:8942-52. [PMID: 22798496 PMCID: PMC3467065 DOI: 10.1093/nar/gks669] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MvaT from Pseudomonas aeruginosa is a member of the histone-like nucleoid structuring protein (H-NS) family of nucleoid-associated proteins widely spread among Gram-negative bacteria that functions to repress the expression of many genes. Recently, it was reported that H-NS from Escherichia coli can form rigid nucleoproteins filaments on DNA, which are important for their gene-silencing function. This raises a question whether the gene-silencing function of MvaT, which has only ∼18% sequence similarity to H-NS, is also based on the formation of nucleoprotein filaments. Here, using magnetic tweezers and atomic force microscopy imaging, we demonstrate that MvaT binds to DNA through cooperative polymerization to form a nucleoprotein filament that can further organize DNA into hairpins or higher-order compact structures. Furthermore, we studied DNA binding by MvaT mutants that fail to repress gene expression in P. aeruginosa because they are specifically defective for higher-order oligomer formation. We found that, although the mutants can organize DNA into compact structures, they fail to form rigid nucleoprotein filaments. Our findings suggest that higher-order oligomerization of MvaT is required for the formation of rigid nucleoprotein filaments that silence at least some target genes in P. aeruginosa. Further, our findings suggest that formation of nucleoprotein filaments provide a general structural basis for the gene-silencing H-NS family members.
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Affiliation(s)
- Ricksen S Winardhi
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore 117456
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58
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Benza VG, Bassetti B, Dorfman KD, Scolari VF, Bromek K, Cicuta P, Lagomarsino MC. Physical descriptions of the bacterial nucleoid at large scales, and their biological implications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:076602. [PMID: 22790781 DOI: 10.1088/0034-4885/75/7/076602] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation.
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Affiliation(s)
- Vincenzo G Benza
- Dipartimento di Fisica e Matematica, Università dell'Insubria, Como, Italy
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