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Cornet F, Blanchais C, Dusfour-Castan R, Meunier A, Quebre V, Sekkouri Alaoui H, Boudsoq F, Campos M, Crozat E, Guynet C, Pasta F, Rousseau P, Ton Hoang B, Bouet JY. DNA Segregation in Enterobacteria. EcoSal Plus 2023; 11:eesp00382020. [PMID: 37220081 PMCID: PMC10729935 DOI: 10.1128/ecosalplus.esp-0038-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/13/2023] [Indexed: 01/28/2024]
Abstract
DNA segregation ensures that cell offspring receive at least one copy of each DNA molecule, or replicon, after their replication. This important cellular process includes different phases leading to the physical separation of the replicons and their movement toward the future daughter cells. Here, we review these phases and processes in enterobacteria with emphasis on the molecular mechanisms at play and their controls.
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Affiliation(s)
- François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Corentin Blanchais
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Romane Dusfour-Castan
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Alix Meunier
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Valentin Quebre
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Hicham Sekkouri Alaoui
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - François Boudsoq
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Manuel Campos
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Estelle Crozat
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Franck Pasta
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Bao Ton Hoang
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
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2
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Xu X, Usher B, Gutierrez C, Barriot R, Arrowsmith TJ, Han X, Redder P, Neyrolles O, Blower TR, Genevaux P. MenT nucleotidyltransferase toxins extend tRNA acceptor stems and can be inhibited by asymmetrical antitoxin binding. Nat Commun 2023; 14:4644. [PMID: 37591829 PMCID: PMC10435456 DOI: 10.1038/s41467-023-40264-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Mycobacterium tuberculosis, the bacterium responsible for human tuberculosis, has a genome encoding a remarkably high number of toxin-antitoxin systems of largely unknown function. We have recently shown that the M. tuberculosis genome encodes four of a widespread, MenAT family of nucleotidyltransferase toxin-antitoxin systems. In this study we characterize MenAT1, using tRNA sequencing to demonstrate MenT1 tRNA modification activity. MenT1 activity is blocked by MenA1, a short protein antitoxin unrelated to the MenA3 kinase. X-ray crystallographic analysis shows blockage of the conserved MenT fold by asymmetric binding of MenA1 across two MenT1 protomers, forming a heterotrimeric toxin-antitoxin complex. Finally, we also demonstrate tRNA modification by toxin MenT4, indicating conserved activity across the MenT family. Our study highlights variation in tRNA target preferences by MenT toxins, selective use of nucleotide substrates, and diverse modes of MenA antitoxin activity.
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Affiliation(s)
- Xibing Xu
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Ben Usher
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Roland Barriot
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Tom J Arrowsmith
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Xue Han
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Peter Redder
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Tim R Blower
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK.
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
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3
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Hu L, Rech J, Bouet JY, Liu J. Spatial control over near-critical-point operation ensures fidelity of ParABS-mediated DNA partition. Biophys J 2021; 120:3911-3924. [PMID: 34418367 PMCID: PMC8511131 DOI: 10.1016/j.bpj.2021.08.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/26/2021] [Accepted: 08/13/2021] [Indexed: 01/20/2023] Open
Abstract
In bacteria, most low-copy-number plasmid and chromosomally encoded partition systems belong to the tripartite ParABS partition machinery. Despite the importance in genetic inheritance, the mechanisms of ParABS-mediated genome partition are not well understood. Combining theory and experiment, we provided evidence that the ParABS system-DNA partitioning in vivo via the ParA-gradient-based Brownian ratcheting-operates near a transition point in parameter space (i.e., a critical point), across which the system displays qualitatively different motile behaviors. This near-critical-point operation adapts the segregation distance of replicated plasmids to the half length of the elongating nucleoid, ensuring both cell halves to inherit one copy of the plasmids. Further, we demonstrated that the plasmid localizes the cytoplasmic ParA to buffer the partition fidelity against the large cell-to-cell fluctuations in ParA level. The spatial control over the near-critical-point operation not only ensures both sensitive adaptation and robust execution of partitioning but also sheds light on the fundamental question in cell biology: how do cells faithfully measure cellular-scale distance by only using molecular-scale interactions?
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Affiliation(s)
- Longhua Hu
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jérôme Rech
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse, France.
| | - Jian Liu
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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4
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Xu Y, Zhang J, Wang M, Liu M, Liu G, Qu H, Liu J, Deng Z, Sun J, Ou HY, Qu J. Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae. Genome Med 2021; 13:119. [PMID: 34294113 PMCID: PMC8299605 DOI: 10.1186/s13073-021-00936-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/09/2021] [Indexed: 11/28/2022] Open
Abstract
Background Klebsiella pneumoniae, as a global priority pathogen, is well known for its capability of acquiring mobile genetic elements that carry resistance and/or virulence genes. Its virulence plasmid, previously deemed nonconjugative and restricted within hypervirulent K. pneumoniae (hvKP), has disseminated into classic K. pneumoniae (cKP), particularly carbapenem-resistant K. pneumoniae (CRKP), which poses alarming challenges to public health. However, the mechanism underlying its transfer from hvKP to CRKP is unclear. Methods A total of 28 sequence type (ST) 11 bloodstream infection-causing CRKP strains were collected from Ruijin Hospital in Shanghai, China, and used as recipients in conjugation assays. Transconjugants obtained from conjugation assays were confirmed by XbaI and S1 nuclease pulsed-field gel electrophoresis, PCR detection and/or whole-genome sequencing. The plasmid stability of the transconjugants was evaluated by serial culture. Genetically modified strains and constructed mimic virulence plasmids were employed to investigate the mechanisms underlying mobilization. The level of extracellular polysaccharides was measured by mucoviscosity assays and uronic acid quantification. An in silico analysis of 2608 plasmids derived from 814 completely sequenced K. pneumoniae strains available in GenBank was performed to investigate the distribution of putative helper plasmids and mobilizable virulence plasmids. Results A nonconjugative virulence plasmid was mobilized by the conjugative plasmid belonging to incompatibility group F (IncF) from the hvKP strain into ST11 CRKP strains under low extracellular polysaccharide-producing conditions or by employing intermediate E. coli strains. The virulence plasmid was mobilized via four modes: transfer alone, cotransfer with the conjugative IncF plasmid, hybrid plasmid formation due to two rounds of single-strand exchanges at specific 28-bp fusion sites or homologous recombination. According to the in silico analysis, 31.8% (242) of the putative helper plasmids and 98.8% (84/85) of the virulence plasmids carry the 28-bp fusion site. All virulence plasmids carry the origin of the transfer site. Conclusions The nonconjugative virulence plasmid in ST11 CRKP strains is putatively mobilized from hvKP or E. coli intermediates with the help of conjugative IncF plasmids. Our findings emphasize the importance of raising public awareness of the rapid dissemination of virulence plasmids and the consistent emergence of hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) strains. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00936-5.
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Affiliation(s)
- Yanping Xu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Jianfeng Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Meng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Meng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Guitian Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Hongping Qu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jialin Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jingyong Sun
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China.
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5
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Walter JC, Lepage T, Dorignac J, Geniet F, Parmeggiani A, Palmeri J, Bouet JY, Junier I. Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex. PLoS Comput Biol 2021; 17:e1008869. [PMID: 33861734 PMCID: PMC8092679 DOI: 10.1371/journal.pcbi.1008869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/03/2021] [Accepted: 03/11/2021] [Indexed: 11/18/2022] Open
Abstract
ParABS, the most widespread bacterial DNA segregation system, is composed of a centromeric sequence, parS, and two proteins, the ParA ATPase and the ParB DNA binding proteins. Hundreds of ParB proteins assemble dynamically to form nucleoprotein parS-anchored complexes that serve as substrates for ParA molecules to catalyze positioning and segregation events. The exact nature of this ParBS complex has remained elusive, what we address here by revisiting the Stochastic Binding model (SBM) introduced to explain the non-specific binding profile of ParB in the vicinity of parS. In the SBM, DNA loops stochastically bring loci inside a sharp cluster of ParB. However, previous SBM versions did not include the negative supercoiling of bacterial DNA, leading to use unphysically small DNA persistences to explain the ParB binding profiles. In addition, recent super-resolution microscopy experiments have revealed a ParB cluster that is significantly smaller than previous estimations and suggest that it results from a liquid-liquid like phase separation. Here, by simulating the folding of long (≥ 30 kb) supercoiled DNA molecules calibrated with realistic DNA parameters and by considering different possibilities for the physics of the ParB cluster assembly, we show that the SBM can quantitatively explain the ChIP-seq ParB binding profiles without any fitting parameter, aside from the supercoiling density of DNA, which, remarkably, is in accord with independent measurements. We also predict that ParB assembly results from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., ParB clusters behave like liquid-like protein condensates with unconventional “leaky” boundaries. In bacteria, faithful genome inheritance requires the two replicated DNA molecules to be segregated at the opposite halves of the cell. ParABS, the most widespread bacterial DNA segregation system, is composed of a centromere sequence, parS, and two proteins, the ParA ATPase and the ParB DNA binding protein. Hundreds of ParB assemble dynamically to form clusters around parS, which then serve as substrates for ParA molecules to catalyze the positioning and segregation events. The nature of these clusters and their interaction with DNA have remained elusive. Here, we propose a realistic minimal model that captures quantitatively the peculiar DNA binding profile of ParB in the vicinity of parS in Escherichia coli. From the viewpoint of DNA, the only fitting parameter is the in vivo supercoiling density resulting from the removal of DNA helices by toposiomerases, which is in accord with previous independent estimations. From the viewpoint of ParB clusters, we predict that they behave like liquid-like protein condensates with unconventional boundaries. Namely, we predict boundaries to be leaky (i.e. not sharp) as a result of the non-equilibrium protein production, diffusion and dilution. Altogether, our work provides novel insights into bacterial DNA organization and intracellular liquid-liquid phase separation.
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Affiliation(s)
- Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
- * E-mail: (J-CW); (IJ)
| | | | - Jérôme Dorignac
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Frédéric Geniet
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Andrea Parmeggiani
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
- LPHI, Univ. Montpellier, CNRS, Montpellier, France
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | | | - Ivan Junier
- CNRS, Univ. Grenoble Alpes, TIMC, Grenoble, France
- * E-mail: (J-CW); (IJ)
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6
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Guilhas B, Walter JC, Rech J, David G, Walliser NO, Palmeri J, Mathieu-Demaziere C, Parmeggiani A, Bouet JY, Le Gall A, Nollmann M. ATP-Driven Separation of Liquid Phase Condensates in Bacteria. Mol Cell 2020; 79:293-303.e4. [PMID: 32679076 DOI: 10.1016/j.molcel.2020.06.034] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/08/2020] [Accepted: 06/22/2020] [Indexed: 12/18/2022]
Abstract
Liquid-liquid phase-separated (LLPS) states are key to compartmentalizing components in the absence of membranes; however, it is unclear whether LLPS condensates are actively and specifically organized in the subcellular space and by which mechanisms. Here, we address this question by focusing on the ParABS DNA segregation system, composed of a centromeric-like sequence (parS), a DNA-binding protein (ParB), and a motor (ParA). We show that parS and ParB associate to form nanometer-sized, round condensates. ParB molecules diffuse rapidly within the nucleoid volume but display confined motions when trapped inside ParB condensates. Single ParB molecules are able to rapidly diffuse between different condensates, and nucleation is strongly favored by parS. Notably, the ParA motor is required to prevent the fusion of ParB condensates. These results describe a novel active mechanism that splits, segregates, and localizes non-canonical LLPS condensates in the subcellular space.
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Affiliation(s)
- Baptiste Guilhas
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France
| | - Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | - Jerome Rech
- LMGM, CBI, CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Gabriel David
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | - Nils Ole Walliser
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | | | - Andrea Parmeggiani
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France; LPHI, CNRS, Université de Montpellier, Montpellier, France
| | - Jean-Yves Bouet
- LMGM, CBI, CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Antoine Le Gall
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France.
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France.
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7
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Cai Y, Usher B, Gutierrez C, Tolcan A, Mansour M, Fineran PC, Condon C, Neyrolles O, Genevaux P, Blower TR. A nucleotidyltransferase toxin inhibits growth of Mycobacterium tuberculosis through inactivation of tRNA acceptor stems. SCIENCE ADVANCES 2020; 6:eabb6651. [PMID: 32923609 PMCID: PMC7450476 DOI: 10.1126/sciadv.abb6651] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/12/2020] [Indexed: 05/12/2023]
Abstract
Toxin-antitoxin systems are widespread stress-responsive elements, many of whose functions remain largely unknown. Here, we characterize the four DUF1814-family nucleotidyltransferase-like toxins (MenT1-4) encoded by the human pathogen Mycobacterium tuberculosis. Toxin MenT3 inhibited growth of M. tuberculosis when not antagonized by its cognate antitoxin, MenA3. We solved the structures of toxins MenT3 and MenT4 to 1.6 and 1.2 Å resolution, respectively, and identified the biochemical activity and target of MenT3. MenT3 blocked in vitro protein expression and prevented tRNA charging in vivo. MenT3 added pyrimidines (C or U) to the 3'-CCA acceptor stems of uncharged tRNAs and exhibited strong substrate specificity in vitro, preferentially targeting tRNASer from among the 45 M. tuberculosis tRNAs. Our study identifies a previously unknown mechanism that expands the range of enzymatic activities used by bacterial toxins, uncovering a new way to block protein synthesis and potentially treat tuberculosis and other infections.
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Affiliation(s)
- Yiming Cai
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31400 Toulouse, France
| | - Ben Usher
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Anastasia Tolcan
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Moise Mansour
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31400 Toulouse, France
| | - Peter C. Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Bio-protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Ciarán Condon
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31400 Toulouse, France
| | - Tim R. Blower
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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8
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Abstract
Plasmids are ubiquitous in the microbial world and have been identified in almost all species of bacteria that have been examined. Their localization inside the bacterial cell has been examined for about two decades; typically, they are not randomly distributed, and their positioning depends on copy number and their mode of segregation. Low-copy-number plasmids promote their own stable inheritance in their bacterial hosts by encoding active partition systems, which ensure that copies are positioned in both halves of a dividing cell. High-copy plasmids rely on passive diffusion of some copies, but many remain clustered together in the nucleoid-free regions of the cell. Here we review plasmid localization and partition (Par) systems, with particular emphasis on plasmids from Enterobacteriaceae and on recent results describing the in vivo localization properties and molecular mechanisms of each system. Partition systems also cause plasmid incompatibility such that distinct plasmids (with different replicons) with the same Par system cannot be stably maintained in the same cells. We discuss how partition-mediated incompatibility is a consequence of the partition mechanism.
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9
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The Tcp plasmids of Clostridium perfringens require the resP gene to ensure stable inheritance. Plasmid 2020; 107:102461. [DOI: 10.1016/j.plasmid.2019.102461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 11/23/2022]
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10
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Abstract
Bacterial toxin–antitoxin (TA) systems, in which a labile antitoxin binds and inhibits the toxin, can promote adaptation and persistence by modulating bacterial growth in response to stress. Some atypical TA systems, known as tripartite toxin–antitoxin–chaperone (TAC) modules, include a molecular chaperone that facilitates folding and protects the antitoxin from degradation. Here we use a TAC module from Mycobacterium tuberculosis as a model to investigate the molecular mechanisms by which classical TAs can become ‘chaperone-addicted'. The chaperone specifically binds the antitoxin at a short carboxy-terminal sequence (chaperone addiction sequence, ChAD) that is not present in chaperone-independent antitoxins. In the absence of chaperone, the ChAD sequence destabilizes the antitoxin, thus preventing toxin inhibition. Chaperone–ChAD pairs can be transferred to classical TA systems or to unrelated proteins and render them chaperone-dependent. This mechanism might be used to optimize the expression and folding of heterologous proteins in bacterial hosts for biotechnological or medical purposes. Some bacterial toxin-antitoxin systems consist of a labile antitoxin that inhibits a toxin, and a chaperone that stabilizes the antitoxin. Here, Bordes et al. identify a sequence within the antitoxin to which the chaperone binds and which can be transferred to other proteins to make them chaperone-dependent.
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11
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The IntXO-PSL Recombination System Is a Key Component of the Second Maintenance System for Bacillus anthracis Plasmid pXO1. J Bacteriol 2016; 198:1939-1951. [PMID: 27137503 DOI: 10.1128/jb.01004-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/25/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED We previously identified three noncontiguous regions on Bacillus anthracis plasmid pXO1 that comprise a system for accurate plasmid partitioning and maintenance. However, deletion of these regions did not decrease retention of certain shortened pXO1 plasmids during vegetative growth. Using two genetic tools developed for DNA manipulation in B. anthracis (the Cre-loxP and Flp-FRT systems), we found two other noncontiguous pXO1 regions that together are sufficient for plasmid stability. This second pXO1 maintenance system includes the tubZ and tubR genes, characteristic of a type III partitioning system, and the IntXO recombinase gene (GBAA_RS29165), encoding a tyrosine recombinase, along with its adjacent 37-bp perfect stem-loop (PSL) target. Insertion of either the tubZ and tubR genes or the IntXO-PSL system into an unstable mini-pXO1 plasmid did not restore plasmid stability. The need for the two components of the second pXO1 maintenance system follows from the sequential roles of IntXO-PSL in generating monomeric circular daughter pXO1 molecules (thereby presumably preventing dimer catastrophe) and of TubZ/TubR in partitioning the monomers during cell division. We show that the IntXO recombinase deletes DNA regions located between two PSL sites in a manner similar to the actions of the Cre-loxP and Flp-FRT systems. IMPORTANCE Tyrosine recombinases catalyze cutting and joining reactions between short specific DNA sequences. Three types of reactions occur: integration and excision of DNA segments, inversion of DNA segments, and separation of monomeric forms from replicating circular DNA molecules. Here we show that the newly discovered site-specific IntXO-PSL recombinase system that contributes to the maintenance of the B. anthracis plasmid pXO1 can be used for genome engineering in a manner similar to that of the Cre-loxP or Flp-FRT system.
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Abstract
One of the disadvantages of circular plasmids and chromosomes is their high sensitivity to rearrangements caused by homologous recombination. Odd numbers of crossing-over occurring during or after replication of a circular replicon result in the formation of a dimeric molecule in which the two copies of the replicon are fused. If they are not converted back to monomers, the dimers of replicons may fail to correctly segregate at the time of cell division. Resolution of multimeric forms of circular plasmids and chromosomes is mediated by site-specific recombination, and the enzymes that catalyze this type of reaction fall into two families of proteins: the serine and tyrosine recombinase families. Here we give an overview of the variety of site-specific resolution systems found on circular plasmids and chromosomes.
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Diaz R, Rech J, Bouet JY. Imaging centromere-based incompatibilities: Insights into the mechanism of incompatibility mediated by low-copy number plasmids. Plasmid 2015; 80:54-62. [DOI: 10.1016/j.plasmid.2015.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/24/2015] [Accepted: 03/30/2015] [Indexed: 11/15/2022]
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Ah-Seng Y, Rech J, Lane D, Bouet JY. Defining the role of ATP hydrolysis in mitotic segregation of bacterial plasmids. PLoS Genet 2013; 9:e1003956. [PMID: 24367270 PMCID: PMC3868542 DOI: 10.1371/journal.pgen.1003956] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 09/30/2013] [Indexed: 11/21/2022] Open
Abstract
Hydrolysis of ATP by partition ATPases, although considered a key step in the segregation mechanism that assures stable inheritance of plasmids, is intrinsically very weak. The cognate centromere-binding protein (CBP), together with DNA, stimulates the ATPase to hydrolyse ATP and to undertake the relocation that incites plasmid movement, apparently confirming the need for hydrolysis in partition. However, ATP-binding alone changes ATPase conformation and properties, making it difficult to rigorously distinguish the substrate and cofactor roles of ATP in vivo. We had shown that mutation of arginines R36 and R42 in the F plasmid CBP, SopB, reduces stimulation of SopA-catalyzed ATP hydrolysis without changing SopA-SopB affinity, suggesting the role of hydrolysis could be analyzed using SopA with normal conformational responses to ATP. Here, we report that strongly reducing SopB-mediated stimulation of ATP hydrolysis results in only slight destabilization of mini-F, although the instability, as well as an increase in mini-F clustering, is proportional to the ATPase deficit. Unexpectedly, the reduced stimulation also increased the frequency of SopA relocation over the nucleoid. The increase was due to drastic shortening of the period spent by SopA at nucleoid ends; average speed of migration per se was unchanged. Reduced ATP hydrolysis was also associated with pronounced deviations in positioning of mini-F, though time-averaged positions changed only modestly. Thus, by specifically targeting SopB-stimulated ATP hydrolysis our study reveals that even at levels of ATPase which reduce the efficiency of splitting clusters and the constancy of plasmid positioning, SopB still activates SopA mobility and plasmid positioning, and sustains near wild type levels of plasmid stability. Genes enabling bacteria to survive and thrive in challenging environments are very often found on small, non-essential DNA molecules called plasmids. Many plasmids are naturally present in the cell in very few copies and so risk being lost from one of the daughter cells upon division. These plasmids elaborate a partition system, functionally similar to mitosis, which assures their faithful inheritance. Chromosomes also generally possess such systems. We know that partition systems involve two proteins, that one (B) stimulates the other (A) to hydrolyse ATP, and that upon binding to A protein ATP confers properties needed for partition. ATP's double action, as hydrolysis substrate and cofactor, complicates definition of its role in the mechanism. The novelty of our approach lies in use of B protein mutants that do not stimulate hydrolysis. Our results reveal that the major function of ATP hydrolysis is not to displace plasmid molecules to their positions in each cell half, as generally thought, but to split initial sibling plasmid pairs and prevent their reforming. This study is the first to dissect ATPase activity in vivo using normal A-protein ATPase, and so opens a new avenue to exploration of the mechanisms that ensure plasmid and chromosome inheritance.
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Affiliation(s)
- Yoan Ah-Seng
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de Recherche Scientifique et l'Université Paul Sabatier, Toulouse, France
| | - Jérôme Rech
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de Recherche Scientifique et l'Université Paul Sabatier, Toulouse, France
| | - David Lane
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de Recherche Scientifique et l'Université Paul Sabatier, Toulouse, France
- * E-mail:
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de Recherche Scientifique et l'Université Paul Sabatier, Toulouse, France
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15
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Sanchez A, Rech J, Gasc C, Bouet JY. Insight into centromere-binding properties of ParB proteins: a secondary binding motif is essential for bacterial genome maintenance. Nucleic Acids Res 2013; 41:3094-103. [PMID: 23345617 PMCID: PMC3597684 DOI: 10.1093/nar/gkt018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
ParB proteins are one of the three essential components of partition systems that actively segregate bacterial chromosomes and plasmids. In binding to centromere sequences, ParB assembles as nucleoprotein structures called partition complexes. These assemblies are the substrates for the partitioning process that ensures DNA molecules are segregated to both sides of the cell. We recently identified the sopC centromere nucleotides required for binding to the ParB homologue of plasmid F, SopB. This analysis also suggested a role in sopC binding for an arginine residue, R219, located outside the helix-turn-helix (HTH) DNA-binding motif previously shown to be the only determinant for sopC-specific binding. Here, we demonstrated that the R219 residue is critical for SopB binding to sopC during partition. Mutating R219 to alanine or lysine abolished partition by preventing partition complex assembly. Thus, specificity of SopB binding relies on two distinct motifs, an HTH and an arginine residue, which define a split DNA-binding domain larger than previously thought. Bioinformatic analysis over a broad range of chromosomal ParBs generalized our findings with the identification of a non-HTH positively charged residue essential for partition and centromere binding, present in a newly identified highly conserved motif. We propose that ParB proteins possess two DNA-binding motifs that form an extended centromere-binding domain, providing high specificity.
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Affiliation(s)
- Aurore Sanchez
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, F-31000 Toulouse, France
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Pillet F, Sanchez A, Lane D, Anton Leberre V, Bouet JY. Centromere binding specificity in assembly of the F plasmid partition complex. Nucleic Acids Res 2011; 39:7477-86. [PMID: 21653553 PMCID: PMC3177203 DOI: 10.1093/nar/gkr457] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The segregation of plasmid F of Escherichia coli is highly reliable. The Sop partition locus, responsible for this stable maintenance, is composed of two genes, sopA and sopB and a centromere, sopC, consisting of 12 direct repeats of 43 bp. Each repeat carries a 16-bp inverted repeat motif to which SopB binds to form a nucleoprotein assembly called the partition complex. A database search for sequences closely related to sopC revealed unexpected features that appeared highly conserved. We have investigated the requirements for specific SopB-sopC interactions using a surface plasmon resonance imaging technique. We show that (i) only 10 repeats interact specifically with SopB, (ii) no base outside the 16-bp sopC sites is involved in binding specificity, whereas five bases present in each arm are required for interactions, and (iii) the A-C central bases contribute to binding efficiency by conforming to a need for a purine-pyrimidine dinucleotide. We have refined the SopB-sopC binding pattern by electro-mobility shift assay and found that all 16 bp are necessary for optimal SopB binding. These data and the model we propose, define the basis of the high binding specificity of F partition complex assembly, without which, dispersal of SopB over DNA would result in defective segregation.
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Affiliation(s)
- Flavien Pillet
- Université de Toulouse, INSA, UPS, INP, LISBP, Toulouse, France
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17
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Meile JC, Mercier R, Stouf M, Pages C, Bouet JY, Cornet F. The terminal region of the E. coli chromosome localises at the periphery of the nucleoid. BMC Microbiol 2011; 11:28. [PMID: 21288323 PMCID: PMC3040692 DOI: 10.1186/1471-2180-11-28] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 02/02/2011] [Indexed: 11/23/2022] Open
Abstract
Background Bacterial chromosomes are organised into a compact and dynamic structures termed nucleoids. Cytological studies in model rod-shaped bacteria show that the different regions of the chromosome display distinct and specific sub-cellular positioning and choreographies during the course of the cell cycle. The localisation of chromosome loci along the length of the cell has been described. However, positioning of loci across the width of the cell has not been determined. Results Here, we show that it is possible to assess the mean positioning of chromosomal loci across the width of the cell using two-dimension images from wide-field fluorescence microscopy. Observed apparent distributions of fluorescent-tagged loci of the E. coli chromosome along the cell diameter were compared with simulated distributions calculated using a range of cell width positioning models. Using this method, we detected the migration of chromosome loci towards the cell periphery induced by production of the bacteriophage T4 Ndd protein. In the absence of Ndd production, loci outside the replication terminus were located either randomly along the nucleoid width or towards the cell centre whereas loci inside the replication terminus were located at the periphery of the nucleoid in contrast to other loci. Conclusions Our approach allows to reliably observing the positioning of chromosome loci along the width of E. coli cells. The terminal region of the chromosome is preferentially located at the periphery of the nucleoid consistent with its specific roles in chromosome organisation and dynamics.
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Affiliation(s)
- Jean-Christophe Meile
- Université de Toulouse, Université Paul Sabatier, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
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Gerdes K, Howard M, Szardenings F. Pushing and pulling in prokaryotic DNA segregation. Cell 2010; 141:927-42. [PMID: 20550930 DOI: 10.1016/j.cell.2010.05.033] [Citation(s) in RCA: 225] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 04/11/2010] [Accepted: 05/20/2010] [Indexed: 10/19/2022]
Abstract
In prokaryotes, DNA can be segregated by three different types of cytoskeletal filaments. The best-understood type of partitioning (par) locus encodes an actin homolog called ParM, which forms dynamically unstable filaments that push plasmids apart in a process reminiscent of mitosis. However, the most common type of par locus, which is present on many plasmids and most bacterial chromosomes, encodes a P loop ATPase (ParA) that distributes plasmids equidistant from one another on the bacterial nucleoid. A third type of par locus encodes a tubulin homolog (TubZ) that forms cytoskeletal filaments that move rapidly with treadmill dynamics.
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Affiliation(s)
- Kenn Gerdes
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK.
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19
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Schumacher MA, Piro KM, Xu W. Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes. Nucleic Acids Res 2010; 38:4514-26. [PMID: 20236989 PMCID: PMC2910045 DOI: 10.1093/nar/gkq161] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Accurate DNA segregation is essential for genome transmission. Segregation of the prototypical F plasmid requires the centromere-binding protein SopB, the NTPase SopA and the sopC centromere. SopB displays an intriguing range of DNA-binding properties essential for partition; it binds sopC to form a partition complex, which recruits SopA, and it also coats DNA to prevent non-specific SopA–DNA interactions, which inhibits SopA polymerization. To understand the myriad functions of SopB, we determined a series of SopB–DNA crystal structures. SopB does not distort its DNA site and our data suggest that SopB–sopC forms an extended rather than wrapped partition complex with the SopA-interacting domains aligned on one face. SopB is a multidomain protein, which like P1 ParB contains an all-helical DNA-binding domain that is flexibly attached to a compact (β3–α)2 dimer-domain. Unlike P1 ParB, the SopB dimer-domain does not bind DNA. Moreover, SopB contains a unique secondary dimerization motif that bridges between DNA duplexes. Both specific and non-specific SopB–DNA bridging structures were observed. This DNA-linking function suggests a novel mechanism for in trans DNA spreading by SopB, explaining how it might mask DNA to prevent DNA-mediated inhibition of SopA polymerization.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry and Molecular Biology, University of Texas, M.D. Anderson Cancer Center, Unit 1000, Houston, TX 77030, USA.
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Ah-Seng Y, Lopez F, Pasta F, Lane D, Bouet JY. Dual role of DNA in regulating ATP hydrolysis by the SopA partition protein. J Biol Chem 2009; 284:30067-75. [PMID: 19740757 DOI: 10.1074/jbc.m109.044800] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In bacteria, mitotic stability of plasmids and many chromosomes depends on replicon-specific systems, which comprise a centromere, a centromere-binding protein and an ATPase. Dynamic self-assembly of the ATPase appears to enable active partition of replicon copies into cell-halves, but for Walker-box partition ATPases the molecular mechanism is unknown. ATPase activity appears to be essential for this process. DNA and centromere-binding proteins are known to stimulate the ATPase activity but molecular details of the stimulation mechanism have not been reported. We have investigated the interactions which stimulate ATP hydrolysis by the SopA partition ATPase of plasmid F. By using SopA and SopB proteins deficient in DNA binding, we have found that the intrinsic ability of SopA to hydrolyze ATP requires direct DNA binding by SopA but not by SopB. Our results show that two independent interactions of SopA act in synergy to stimulate its ATPase. SopA must interact with (i) DNA, through its ATP-dependent nonspecific DNA binding domain and (ii) SopB, which we show here to provide an arginine-finger motif. In addition, the latter interaction stimulates ATPase maximally when SopB is part of the partition complex. Hence, our data demonstrate that DNA acts on SopA in two ways, directly as nonspecific DNA and through SopB as centromeric DNA, to fully activate SopA ATP hydrolysis.
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Affiliation(s)
- Yoan Ah-Seng
- Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, F-31000 Toulouse, France
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21
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Bouet JY, Lane D. Molecular basis of the supercoil deficit induced by the mini-F plasmid partition complex. J Biol Chem 2008; 284:165-173. [PMID: 19001378 DOI: 10.1074/jbc.m802752200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formation of a partition complex on plasmid F by binding of SopB protein to the sopC centromere is the first step in the partition process that ensures stability of F in dividing cells. Establishment of the complex enables nonspecific binding of SopB to neighboring DNA, which extends the partition complex and provokes reduction of negative supercoiling of the plasmid. This reduction is believed to reflect winding of DNA into positive supercoils about SopB to create a nucleoprotein structure of probable importance to partition. We have searched for evidence that SopB alters plasmid topology. Permutation analysis indicated only modest bending of linear DNA fragments, and in vivo DNase I footprinting revealed no enhanced cleavages indicating curvature. In vitro, SopB binding left no topological trace in relaxed-circular DNA treated with topoisomerase I or in nicked circles closed by ligase. In vivo, novobiocin-mediated inhibition of DNA gyrase relaxed a plasmid carrying the partition complex but left no residue of positive supercoils. Hence, SopB does not reduce plasmid supercoiling directly. We did observe that SopB partly prevented removal of negative supercoils from plasmid DNA by topoisomerase I and partly prevented ligation of nicked circles, indicating that it acts as a physical obstacle. The supercoil deficit is thus better explained as SopB recoating of just-replicated DNA, which shelters it from gyrase and from topological changes in SopB-free DNA. This topological simplicity distinguishes the Sop partition complex from other complexes described.
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Affiliation(s)
- Jean-Yves Bouet
- Laboratoire de Microbiologie et Gánátique Moláculaires, CNRS, F-31000 Toulouse, France and LMGM, Universitáde Toulouse, UPS, F-31000 Toulouse, France; Laboratoire de Microbiologie et Gánátique Moláculaires, CNRS, F-31000 Toulouse, France and LMGM, Universitáde Toulouse, UPS, F-31000 Toulouse, France.
| | - David Lane
- Laboratoire de Microbiologie et Gánátique Moláculaires, CNRS, F-31000 Toulouse, France and LMGM, Universitáde Toulouse, UPS, F-31000 Toulouse, France
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22
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Castaing JP, Bouet JY, Lane D. F plasmid partition depends on interaction of SopA with non-specific DNA. Mol Microbiol 2008; 70:1000-11. [PMID: 18826408 DOI: 10.1111/j.1365-2958.2008.06465.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Bacterial ATPases belonging to the ParA family assure partition of their replicons by forming dynamic assemblies which move replicon copies into the new cell-halves. The mechanism underlying partition is not understood for the Walker-box ATPase class, which includes most plasmid and all chromosomal ParAs. The ATPases studied both polymerize and interact with non-specific DNA in an ATP-dependent manner. Previous work showed that in vitro, polymerization of one such ATPase, SopA of plasmid F, is inhibited by DNA, suggesting that interaction of SopA with the host nucleoid could regulate partition. In an attempt to identify amino acids in SopA that are needed for interaction with non-specific DNA, we have found that mutation of codon 340 (lysine to alanine) reduces ATP-dependent DNA binding > 100-fold and correspondingly diminishes SopA activities that depend on it: inhibition of polymer formation and persistence, stimulation of basal-level ATP hydrolysis and localization over the nucleoid. The K340A mutant retained all other SopA properties tested except plasmid stabilization; substitution of the mutant SopA for wild-type nearly abolished mini-F partition. The behaviour of this mutant indicates a causal link between interaction with the cell's non-specific DNA and promotion of the dynamic behaviour that ensures F plasmid partition.
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Affiliation(s)
- Jean-Philippe Castaing
- Laboratoire de Microbiologie et Génétique Moléculaires, Université Paul Sabatier, F31000 Toulouse, France
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Hoischen C, Bussiek M, Langowski J, Diekmann S. Escherichia coli low-copy-number plasmid R1 centromere parC forms a U-shaped complex with its binding protein ParR. Nucleic Acids Res 2007; 36:607-15. [PMID: 18056157 PMCID: PMC2241845 DOI: 10.1093/nar/gkm672] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Escherichia coli low-copy-number plasmid R1 contains a segregation machinery composed of parC, ParR and parM. The R1 centromere-like site parC contains two separate sets of repeats. By atomic force microscopy (AFM) we show here that ParR molecules bind to each of the 5-fold repeated iterons separately with the intervening sequence unbound by ParR. The two ParR protein complexes on parC do not complex with each other. ParR binds with a stoichiometry of about one ParR dimer per each single iteron. The measured DNA fragment lengths agreed with B-form DNA and each of the two parC 5-fold interon DNA stretches adopts a linear path in its complex with ParR. However, the overall parC/ParR complex with both iteron repeats bound by ParR forms an overall U-shaped structure: the DNA folds back on itself nearly completely, including an angle of ∼150°. Analysing linear DNA fragments, we never observed dimerized ParR complexes on one parC DNA molecule (intramolecular) nor a dimerization between ParR complexes bound to two different parC DNA molecules (intermolecular). This bacterial segrosome is compared to other bacterial segregation complexes. We speculate that partition complexes might have a similar overall structural organization and, at least in part, common functional properties.
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Affiliation(s)
- C Hoischen
- Molecular Biology, FLI, Leibniz-Institute for Age Research, Beutenbergstrasse 11, D-07745 Jena, Germany
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Ringgaard S, Löwe J, Gerdes K. Centromere Pairing by a Plasmid-encoded Type I ParB Protein. J Biol Chem 2007; 282:28216-25. [PMID: 17644524 DOI: 10.1074/jbc.m703733200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The par2 locus of Escherichia coli plasmid pB171 encodes two trans-acting proteins, ParA and ParB, and two cis-acting sites, parC1 and parC2, to which ParB binds cooperatively. ParA is related to MinD and oscillates in helical structures and thereby positions ParB/parC-carrying plasmids regularly over the nucleoid. ParB ribbon-helix-helix dimers bind cooperatively to direct repeats in parC1 and parC2. Using four different assays we obtain solid evidence that ParB can pair parC1- and parC2-encoding DNA fragments in vitro. Convincingly, electron microscopy revealed that ParB mediates binary pairing of parC fragments. In addition to binary complexes, ParB mediated the formation of higher order complexes consisting of several DNA fragments joined by ParB at centromere site parC. N-terminal truncated versions of ParB still possessing specific DNA binding activity were incompetent in pairing, hence identifying the N terminus of ParB as a requirement for ParB-mediated centromere pairing. These observations suggest that centromere pairing is an important intermediate step in plasmid partitioning mediated by the common type I loci.
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Affiliation(s)
- Simon Ringgaard
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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25
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Abstract
The mitotic apparatus that a plasmid uses to ensure its stable inheritance responds to the appearance of an additional copy of the plasmid's centromere by segregating it from the pre-existing copies: if the new copy arises by replication of the plasmid the result is partition, if it arrives on a different plasmid the result is incompatibility. Incompatibility thus serves as a probe of the partition mechanism. Coupling of distinct plasmids via their shared centromeres to form mixed pairs has been the favoured explanation for centromere-based incompatibility, because it supports a long-standing assumption that pairing of plasmid replicas is a prerequisite for their partition into daughter cells. Recent results from molecular genetic and fluorescence microscopy studies challenge this mixed pairing model. Partition incompatibility is seen to result from various processes, including titration, randomized positioning and a form of mixed pairing that is based on co-activation of the same partition event rather than direct contact between partition complexes. The perspectives thus opened onto the partition mechanism confirm the continuing utility of incompatibility as an approach to understanding bacterial mitosis. The results considered are compatible with the view that direct pairing of plasmids is not essential to plasmid partition.
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Affiliation(s)
- Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de Recherche Scientifique, Campus Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France
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