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Niault T, Czarnecki J, Lambérioux M, Mazel D, Val ME. Cell cycle-coordinated maintenance of the Vibrio bipartite genome. EcoSal Plus 2023; 11:eesp00082022. [PMID: 38277776 PMCID: PMC10729929 DOI: 10.1128/ecosalplus.esp-0008-2022] [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] [Indexed: 01/28/2024]
Abstract
To preserve the integrity of their genome, bacteria rely on several genome maintenance mechanisms that are co-ordinated with the cell cycle. All members of the Vibrio family have a bipartite genome consisting of a primary chromosome (Chr1) homologous to the single chromosome of other bacteria such as Escherichia coli and a secondary chromosome (Chr2) acquired by a common ancestor as a plasmid. In this review, we present our current understanding of genome maintenance in Vibrio cholerae, which is the best-studied model for bacteria with multi-partite genomes. After a brief overview on the diversity of Vibrio genomic architecture, we describe the specific, common, and co-ordinated mechanisms that control the replication and segregation of the two chromosomes of V. cholerae. Particular attention is given to the unique checkpoint mechanism that synchronizes Chr1 and Chr2 replication.
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Affiliation(s)
- Théophile Niault
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Jakub Czarnecki
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| | - Morgan Lambérioux
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Didier Mazel
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| | - Marie-Eve Val
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
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2
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Goudin A, Ferat JL, Possoz C, Barre FX, Galli E. Recovery of Vibrio cholerae polarized cellular organization after exit from a non-proliferating spheroplast state. PLoS One 2023; 18:e0293276. [PMID: 37883451 PMCID: PMC10602287 DOI: 10.1371/journal.pone.0293276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Vibrio cholerae, the causative agent of cholera epidemics, is a rod-shaped bacterium with a highly polarized cellular organization. It can survive harmful growth conditions by entering a non-proliferating spheroplast state, which involves loss of the cell envelope and polarity. How polarized rod organization cells are formed when the spheroplasts exit the non-proliferating state remains largely uncharacterized. To address this question, we investigated how L-arabinose-induced V. cholerae spheroplasts return to growth. We found that de novo morphogenesis started with the elimination of an excess of periplasm, which was immediately followed by cell elongation and the formation of cell branches with a diameter similar to that of normal V. cholerae cells. Periplasm elimination was driven by bifunctional peptidoglycan synthases involved in cell-wall maintenance, the aPBPs. Elongation and branching relied on the MreB-associated monofunctional peptidoglycan synthase PBP2. The cell division monofunctional peptidoglycan synthase FtsI was not involved in any of these processes. However, the FtsK cell division protein specifically targeted the sites of vesicle extrusion. Genetic material was amplified by synchronous waves of DNA replication as periplasmic elimination began. The HubP polarity factor targeted the tip of the branches as they began to form. However, HubP-mediated polarization was not involved in the efficiency of the recovery process. Finally, our results suggest that the positioning of HubP and the activities of the replication terminus organizer of the two V. cholerae chromosomes, MatP, are independent of cell division. Taken together, these results confirm the interest of L-arabinose-induced V. cholerae spheroplasts to study how cell shape is generated and shed light on the de novo establishment of the intracellular organization and cell polarization in V. cholerae.
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Affiliation(s)
- Anthony Goudin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Jean-Luc Ferat
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Christophe Possoz
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - François-Xavier Barre
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Elisa Galli
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
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3
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Kaljević J, Tesseur C, Le TBK, Laloux G. Cell cycle-dependent organization of a bacterial centromere through multi-layered regulation of the ParABS system. PLoS Genet 2023; 19:e1010951. [PMID: 37733798 PMCID: PMC10547168 DOI: 10.1371/journal.pgen.1010951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/03/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023] Open
Abstract
The accurate distribution of genetic material is crucial for all organisms. In most bacteria, chromosome segregation is achieved by the ParABS system, in which the ParB-bound parS sequence is actively partitioned by ParA. While this system is highly conserved, its adaptation in organisms with unique lifestyles and its regulation between developmental stages remain largely unexplored. Bdellovibrio bacteriovorus is a predatory bacterium proliferating through polyploid replication and non-binary division inside other bacteria. Our study reveals the subcellular dynamics and multi-layered regulation of the ParABS system, coupled to the cell cycle of B. bacteriovorus. We found that ParA:ParB ratios fluctuate between predation stages, their balance being critical for cell cycle progression. Moreover, the parS chromosomal context in non-replicative cells, combined with ParB depletion at cell division, critically contribute to the unique cell cycle-dependent organization of the centromere in this bacterium, highlighting new levels of complexity in chromosome segregation and cell cycle control.
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Affiliation(s)
| | | | - Tung B. K. Le
- John Innes Centre, Department of Molecular Microbiology, Norwich, United Kingdom
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4
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Brück P, Wasser D, Soppa J. Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes. Genes (Basel) 2023; 14:1437. [PMID: 37510340 PMCID: PMC10379091 DOI: 10.3390/genes14071437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Vibrio natriegens is the fastest-growing bacterium, with a doubling time of approximately 12-14 min. It has a high potential for basic research and biotechnological applications, e.g., it can be used for the cell-free production of (labeled) heterologous proteins, for synthetic biological applications, and for the production of various compounds. However, the ploidy level in V. natriegens remains unknown. At nine time points throughout the growth curve, we analyzed the numbers of origins and termini of both chromosomes with qPCR and the relative abundances of all genomic sites with marker frequency analyses. During the lag phase until early exponential growth, the origin copy number and origin/terminus ratio of chromosome 1 increased severalfold, but the increase was lower for chromosome 2. This increase was paralleled by an increase in cell volume. During the exponential phase, the origin/terminus ratio and cell volume decreased again. This highly dynamic and fast regulation has not yet been described for any other species. In this study, the gene dosage increase in origin-adjacent genes during the lag phase is discussed together with the nonrandom distribution of genes on the chromosomes of V. natriegens. Taken together, the results of this study provide the first comprehensive overview of the chromosome dynamics in V. natriegens and will guide the optimization of molecular biological characterization and biotechnological applications.
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Affiliation(s)
- Patrik Brück
- Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Daniel Wasser
- Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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5
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Chodha SS, Brooks AC, Davis PJ, Ramachandran R, Chattoraj D, Hwang L. Kinetic principles of ParA2-ATP cycling guide dynamic subcellular localizations in Vibrio cholerae. Nucleic Acids Res 2023; 51:5603-5620. [PMID: 37140034 PMCID: PMC10287910 DOI: 10.1093/nar/gkad321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
Dynamic protein gradients are exploited for the spatial organization and segregation of replicated chromosomes. However, mechanisms of protein gradient formation and how that spatially organizes chromosomes remain poorly understood. Here, we have determined the kinetic principles of subcellular localizations of ParA2 ATPase, an essential spatial regulator of chromosome 2 segregation in the multichromosome bacterium, Vibrio cholerae. We found that ParA2 gradients self-organize in V. cholerae cells into dynamic pole-to-pole oscillations. We examined the ParA2 ATPase cycle and ParA2 interactions with ParB2 and DNA. In vitro, ParA2-ATP dimers undergo a rate-limiting conformational switch, catalysed by DNA to achieve DNA-binding competence. This active ParA2 state loads onto DNA cooperatively as higher order oligomers. Our results indicate that the midcell localization of ParB2-parS2 complexes stimulate ATP hydrolysis and ParA2 release from the nucleoid, generating an asymmetric ParA2 gradient with maximal concentration toward the poles. This rapid dissociation coupled with slow nucleotide exchange and conformational switch provides for a temporal lag that allows the redistribution of ParA2 to the opposite pole for nucleoid reattachment. Based on our data, we propose a 'Tug-of-war' model that uses dynamic oscillations of ParA2 to spatially regulate symmetric segregation and positioning of bacterial chromosomes.
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Affiliation(s)
- Satpal S Chodha
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Adam C Brooks
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Peter J Davis
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Revathy Ramachandran
- Basic Research Laboratory, Centre for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4260, USA
| | - Dhruba K Chattoraj
- Basic Research Laboratory, Centre for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4260, USA
| | - Ling Chin Hwang
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Medical Technology Research Centre, School of Medicine, Faculty of Health, Education, Medicine & Social Care, Anglia Ruskin University, Chelmsford, UK
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6
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Mishra D, Srinivasan R. Catching a Walker in the Act-DNA Partitioning by ParA Family of Proteins. Front Microbiol 2022; 13:856547. [PMID: 35694299 PMCID: PMC9178275 DOI: 10.3389/fmicb.2022.856547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/28/2022] [Indexed: 12/01/2022] Open
Abstract
Partitioning the replicated genetic material is a crucial process in the cell cycle program of any life form. In bacteria, many plasmids utilize cytoskeletal proteins that include ParM and TubZ, the ancestors of the eukaryotic actin and tubulin, respectively, to segregate the plasmids into the daughter cells. Another distinct class of cytoskeletal proteins, known as the Walker A type Cytoskeletal ATPases (WACA), is unique to Bacteria and Archaea. ParA, a WACA family protein, is involved in DNA partitioning and is more widespread. A centromere-like sequence parS, in the DNA is bound by ParB, an adaptor protein with CTPase activity to form the segregation complex. The ParA ATPase, interacts with the segregation complex and partitions the DNA into the daughter cells. Furthermore, the Walker A motif-containing ParA superfamily of proteins is associated with a diverse set of functions ranging from DNA segregation to cell division, cell polarity, chemotaxis cluster assembly, cellulose biosynthesis and carboxysome maintenance. Unifying principles underlying the varied range of cellular roles in which the ParA superfamily of proteins function are outlined. Here, we provide an overview of the recent findings on the structure and function of the ParB adaptor protein and review the current models and mechanisms by which the ParA family of proteins function in the partitioning of the replicated DNA into the newly born daughter cells.
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Affiliation(s)
- Dipika Mishra
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
- Homi Bhabha National Institutes, Mumbai, India
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
- Homi Bhabha National Institutes, Mumbai, India
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7
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Possoz C, Yamaichi Y, Galli E, Ferat JL, Barre FX. Vibrio cholerae Chromosome Partitioning without Polar Anchoring by HubP. Genes (Basel) 2022; 13:genes13050877. [PMID: 35627261 PMCID: PMC9140986 DOI: 10.3390/genes13050877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
Partition systems are widespread among bacterial chromosomes. They are composed of two effectors, ParA and ParB, and cis acting sites, parS, located close to the replication origin of the chromosome (oriC). ParABS participate in chromosome segregation, at least in part because they serve to properly position sister copies of oriC. A fourth element, located at cell poles, is also involved in some cases, such as HubP for the ParABS1 system of Vibrio cholerae chromosome 1 (ch1). The polar anchoring of oriC of ch1 (oriC1) is lost when HubP or ParABS1 are inactivated. Here, we report that in the absence of HubP, ParABS1 actively maintains oriC1 at mid-cell, leading to the subcellular separation of the two ch1 replication arms. We further show that parS1 sites ectopically inserted in chromosome 2 (ch2) stabilize the inheritance of this replicon in the absence of its endogenous partition system, even without HubP. We also observe the positioning interference between oriC1 and oriC of ch2 regions when their positionings are both driven by ParABS1. Altogether, these data indicate that ParABS1 remains functional in the absence of HubP, which raises questions about the role of the polar anchoring of oriC1 in the cell cycle.
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8
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Benler S, Koonin EV. Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes. Front Mol Biosci 2022; 9:821197. [PMID: 35402511 PMCID: PMC8987985 DOI: 10.3389/fmolb.2022.821197] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
Prokaryotic genomes are replete with mobile genetic elements (MGE) that span a continuum of replication autonomy. On numerous occasions during microbial evolution, diverse MGE lose their autonomy altogether but, rather than being quickly purged from the host genome, assume a new function that benefits the host, rendering the immobilized MGE subject to purifying selection, and resulting in its vertical inheritance. This mini-review highlights the diversity of the repurposed (exapted) MGE as well as the plethora of cellular functions that they perform. The principal contribution of the exaptation of MGE and their components is to the prokaryotic functional systems involved in biological conflicts, and in particular, defense against viruses and other MGE. This evolutionary entanglement between MGE and defense systems appears to stem both from mechanistic similarities and from similar evolutionary predicaments whereby both MGEs and defense systems tend to incur fitness costs to the hosts and thereby evolve mechanisms for survival including horizontal mobility, causing host addiction, and exaptation for functions beneficial to the host. The examples discussed demonstrate that the identity of an MGE, overall mobility and relationship with the host cell (mutualistic, symbiotic, commensal, or parasitic) are all factors that affect exaptation.
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Affiliation(s)
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
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9
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Kaljević J, Saaki TNV, Govers SK, Remy O, van Raaphorst R, Lamot T, Laloux G. Chromosome choreography during the non-binary cell cycle of a predatory bacterium. Curr Biol 2021; 31:3707-3720.e5. [PMID: 34256020 PMCID: PMC8445325 DOI: 10.1016/j.cub.2021.06.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/13/2021] [Accepted: 06/09/2021] [Indexed: 12/03/2022]
Abstract
In bacteria, the dynamics of chromosome replication and segregation are tightly coordinated with cell-cycle progression and largely rely on specific spatiotemporal arrangement of the chromosome. Whereas these key processes are mostly investigated in species that divide by binary fission, they remain mysterious in bacteria producing larger number of descendants. Here, we establish the predatory bacterium Bdellovibrio bacteriovorus as a model to investigate the non-binary processing of a circular chromosome. We found that its single chromosome is highly compacted in a polarized nucleoid that excludes freely diffusing proteins during the non-proliferative stage of the cell cycle. A binary-like cycle of DNA replication and asymmetric segregation is followed by multiple asynchronous rounds of replication and progressive ParABS-dependent partitioning, uncoupled from cell division. Finally, we provide the first evidence for an on-off behavior of the ParB protein, which localizes at the centromere in a cell-cycle-regulated manner. Altogether, our findings support a model of complex chromosome choreography leading to the generation of variable, odd, or even numbers of offspring and highlight the adaptation of conserved mechanisms to achieve non-binary reproduction. The Bdellovibrio chromosome is polarized, with ori located near the invasive pole The highly compacted nucleoid excludes cytosolic proteins in non-replicative cells Replication and segregation of chromosomes are uncoupled from cell division The centromeric protein ParB localizes at parS in a cell-cycle-dependent manner
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Affiliation(s)
- Jovana Kaljević
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Terrens N V Saaki
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Sander K Govers
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ophélie Remy
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | | | - Thomas Lamot
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Géraldine Laloux
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium.
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Daniel S, Goldlust K, Quebre V, Shen M, Lesterlin C, Bouet JY, Yamaichi Y. Vertical and Horizontal Transmission of ESBL Plasmid from Escherichia coli O104:H4. Genes (Basel) 2020; 11:genes11101207. [PMID: 33081159 PMCID: PMC7602700 DOI: 10.3390/genes11101207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/05/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
Multidrug resistance (MDR) often results from the acquisition of mobile genetic elements (MGEs) that encode MDR gene(s), such as conjugative plasmids. The spread of MDR plasmids is founded on their ability of horizontal transference, as well as their faithful inheritance in progeny cells. Here, we investigated the genetic factors involved in the prevalence of the IncI conjugative plasmid pESBL, which was isolated from the Escherichia coli O104:H4 outbreak strain in Germany in 2011. Using transposon-insertion sequencing, we identified the pESBL partitioning locus (par). Genetic, biochemical and microscopic approaches allowed pESBL to be characterized as a new member of the Type Ib partitioning system. Inactivation of par caused mis-segregation of pESBL followed by post-segregational killing (PSK), resulting in a great fitness disadvantage but apparent plasmid stability in the population of viable cells. We constructed a variety of pESBL derivatives with different combinations of mutations in par, conjugational transfer (oriT) and pnd toxin-antitoxin (TA) genes. Only the triple mutant exhibited plasmid-free cells in viable cell populations. Time-lapse tracking of plasmid dynamics in microfluidics indicated that inactivation of pnd improved the survival of plasmid-free cells and allowed oriT-dependent re-acquisition of the plasmid. Altogether, the three factors—active partitioning, toxin-antitoxin and conjugational transfer—are all involved in the prevalence of pESBL in the E. coli population.
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Affiliation(s)
- Sandra Daniel
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (S.D.); (M.S.)
| | - Kelly Goldlust
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France; (K.G.); (C.L.)
| | - Valentin Quebre
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université de Toulouse, UPS, 31062 Toulouse, France; (V.Q.); (J.-Y.B.)
| | - Minjia Shen
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (S.D.); (M.S.)
- Graduate School of Structure and Dynamics of Living Systems, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Christian Lesterlin
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007 Lyon, France; (K.G.); (C.L.)
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, Université de Toulouse, UPS, 31062 Toulouse, France; (V.Q.); (J.-Y.B.)
| | - Yoshiharu Yamaichi
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (S.D.); (M.S.)
- Correspondence:
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11
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Anand D, Schumacher D, Søgaard-Andersen L. SMC and the bactofilin/PadC scaffold have distinct yet redundant functions in chromosome segregation and organization in Myxococcus xanthus. Mol Microbiol 2020; 114:839-856. [PMID: 32738827 DOI: 10.1111/mmi.14583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/22/2020] [Indexed: 12/20/2022]
Abstract
In bacteria, ParABS systems and structural maintenance of chromosome (SMC) condensin-like complexes are important for chromosome segregation and organization. The rod-shaped Myxococcus xanthus cells have a unique chromosome arrangement in which a scaffold composed of the BacNOP bactofilins and PadC positions the essential ParB∙parS segregation complexes and the DNA segregation ATPase ParA in the subpolar regions. We identify the Smc and ScpAB subunits of the SMC complex in M. xanthus and demonstrate that SMC is conditionally essential, with Δsmc or ΔscpAB mutants being temperature sensitive. Inactivation of SMC caused defects in chromosome segregation and organization. Lack of the BacNOP/PadC scaffold also caused chromosome segregation defects but this scaffold is not essential for viability. Inactivation of SMC was synthetic lethal with lack of the BacNOP/PadC scaffold. Lack of SMC interfered with formation of the BacNOP/PadC scaffold while lack of this scaffold did not interfere with chromosome association by SMC. Altogether, our data support that three systems function together to enable chromosome segregation in M. xanthus. ParABS constitutes the basic and essential machinery. SMC and the BacNOP/PadC scaffold have different yet redundant roles in chromosome segregation with SMC supporting individualization of daughter chromosomes and BacNOP/PadC making the ParABS system operate more robustly.
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Affiliation(s)
- Deepak Anand
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Dominik Schumacher
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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12
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Espinosa E, Paly E, Barre FX. High-Resolution Whole-Genome Analysis of Sister-Chromatid Contacts. Mol Cell 2020; 79:857-869.e3. [PMID: 32681820 DOI: 10.1016/j.molcel.2020.06.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
Sister-chromatid cohesion describes the orderly association of newly replicated DNA molecules behind replication forks. It plays an essential role in the maintenance and faithful transmission of genetic information. Cohesion is created by DNA topological links and proteinaceous bridges, whose formation and deposition could be potentially affected by many processes. Current knowledge on cohesion has been mainly gained by fluorescence microscopy observation. However, the resolution limit of microscopy and the restricted number of genomic positions that can be simultaneously visualized considerably hampered progress. Here, we present a high-throughput methodology to monitor sister-chromatid contacts (Hi-SC2). Using the multi-chromosomal Vibrio cholerae bacterium as a model, we show that Hi-SC2 permits to monitor local variations in sister-chromatid cohesion at a high resolution over a whole genome.
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Affiliation(s)
- Elena Espinosa
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Evelyne Paly
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - François-Xavier Barre
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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13
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Sozhamannan S, Waldminghaus T. Exception to the exception rule: synthetic and naturally occurring single chromosome Vibrio cholerae. Environ Microbiol 2020; 22:4123-4132. [PMID: 32237026 DOI: 10.1111/1462-2920.15002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/25/2020] [Indexed: 12/26/2022]
Abstract
The genome of Vibrio cholerae, the etiological agent of cholera, is an exception to the single chromosome rule found in the vast majority of bacteria and has its genome partitioned between two unequally sized chromosomes. This unusual two-chromosome arrangement in V. cholerae has sparked considerable research interest since its discovery. It was demonstrated that the two chromosomes could be fused by deliberate genome engineering or forced to fuse spontaneously by blocking the replication of Chr2, the secondary chromosome. Recently, natural isolates of V. cholerae with chromosomal fusion have been found. Here, we summarize the pertinent findings on this exception to the exception rule and discuss the potential utility of single-chromosome V. cholerae to address fundamental questions on chromosome biology in general and DNA replication in particular.
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Affiliation(s)
- Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, CBRND-Enabling Biotechnologies, 110 Thomas Johnson Drive, Frederick, MD, 21702, USA.,Logistics Management Institute, Tysons, VA, 22102, USA
| | - Torsten Waldminghaus
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
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14
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Physical Views on ParABS-Mediated DNA Segregation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1267:45-58. [PMID: 32894476 DOI: 10.1007/978-3-030-46886-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this chapter, we will focus on ParABS: an apparently simple, three-component system, required for the segregation of bacterial chromosomes and plasmids. We will specifically describe how biophysical measurements combined with physical modeling advanced our understanding of the mechanism of ParABS-mediated complex assembly, segregation and positioning.
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15
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Two-step chromosome segregation in the stalked budding bacterium Hyphomonas neptunium. Nat Commun 2019; 10:3290. [PMID: 31337764 PMCID: PMC6650430 DOI: 10.1038/s41467-019-11242-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/28/2019] [Indexed: 12/11/2022] Open
Abstract
Chromosome segregation typically occurs after replication has finished in eukaryotes but during replication in bacteria. Here, we show that the alphaproteobacterium Hyphomonas neptunium, which proliferates by bud formation at the tip of a stalk-like cellular extension, segregates its chromosomes in a unique two-step process. First, the two sister origin regions are targeted to opposite poles of the mother cell, driven by the ParABS partitioning system. Subsequently, once the bulk of chromosomal DNA has been replicated and the bud exceeds a certain threshold size, the cell initiates a second segregation step during which it transfers the stalk-proximal origin region through the stalk into the nascent bud compartment. Thus, while chromosome replication and segregation usually proceed concurrently in bacteria, the two processes are largely uncoupled in H. neptunium, reminiscent of eukaryotic mitosis. These results indicate that stalked budding bacteria have evolved specific mechanisms to adjust chromosome segregation to their unusual life cycle.
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16
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Random Chromosome Partitioning in the Polyploid Bacterium Thermus thermophilus HB27. G3-GENES GENOMES GENETICS 2019; 9:1249-1261. [PMID: 30792193 PMCID: PMC6469415 DOI: 10.1534/g3.119.400086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Little is known about chromosome segregation in polyploid prokaryotes. In this study, whether stringent or variable chromosome segregation occurs in polyploid thermophilic bacterium Thermus thermophilus was analyzed. A stable heterozygous strain (HL01) containing two antibiotic resistance markers at one gene locus was generated. The inheritance of the two alleles in the progeny of the heterozygous strain was then followed. During incubation without selection pressure, the fraction of heterozygous cells decreased and that of homozygous cells increased, while the relative abundance of each allele in the whole population remained constant, suggesting chromosome segregation had experienced random event. Consistently, in comparison with Bacillus subtilis in which the sister chromosomes were segregated equally, the ratios of DNA content in two daughter cells of T. thermophilus had a broader distribution and a larger standard deviation, indicating that the DNA content in the two daughter cells was not always identical. Further, the protein homologs (i.e., ParA and MreB) which have been suggested to be involved in bacterial chromosome partitioning did not actively participate in the chromosome segregation in T. thermophilus. Therefore, it seems that protein-based chromosome segregation machineries are less critical for the polyploid T. thermophilus, and chromosome segregation in this bacterium are not stringently controlled but tend to be variable, and random segregation can occur.
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17
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In Vivo Imaging of the Segregation of the 2 Chromosomes and the Cell Division Proteins of Rhodobacter sphaeroides Reveals an Unexpected Role for MipZ. mBio 2019; 10:mBio.02515-18. [PMID: 30602584 PMCID: PMC6315104 DOI: 10.1128/mbio.02515-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Cell division has to be coordinated with chromosome segregation to ensure the stable inheritance of genetic information. We investigated this coordination in the multichromosome bacterium Rhodobacter sphaeroides. By examining the origin and terminus regions of the two chromosomes, the ParA-like ATPase MipZ and FtsZ, we showed that chromosome 1 appears to be the “master” chromosome connecting DNA segregation and cell division, with MipZ being critical for coordination. MipZ shows an unexpected localization pattern, with MipZ monomers interacting with ParB of the chromosome 1 at the cell poles whereas MipZ dimers colocalize with FtsZ at midcell during constriction, both forming dynamic rings. These data suggest that MipZ has roles in R. sphaeroides in both controlling septation and coordinating chromosome segregation with cell division. Coordinating chromosome duplication and segregation with cell division is clearly critical for bacterial species with one chromosome. The precise choreography required is even more complex in species with more than one chromosome. The alpha subgroup of bacteria contains not only one of the best-studied bacterial species, Caulobacter crescentus, but also several species with more than one chromosome. Rhodobacter sphaeroides is an alphaproteobacterium with two chromosomes, but, unlike C. crescentus, it divides symmetrically rather than buds and lacks the complex CtrA-dependent control mechanism. By examining the Ori and Ter regions of both chromosomes and associated ParA and ParB proteins relative to cell division proteins FtsZ and MipZ, we have identified a different pattern of chromosome segregation and cell division. The pattern of chromosome duplication and segregation resembles that of Vibrio cholerae, not that of Agrobacterium tumefaciens, with duplication of the origin and terminus regions of chromosome 2 controlled by chromosome 1. Key proteins are localized to different sites compared to C. crescentus. OriC1 and ParB1 are localized to the old pole, while MipZ and FtsZ localize to the new pole. Movement of ParB1 to the new pole following chromosome duplication releases FtsZ, which forms a ring at midcell, but, unlike reports for other species, MipZ monomers do not form a gradient but oscillate between poles, with the nucleotide-bound monomer and the dimer localizing to midcell. MipZ dimers form a single ring (with a smaller diameter) close to the FtsZ ring at midcell and constrict with the FtsZ ring. Overproduction of the dimer form results in filamentation, suggesting that MipZ dimers are regulating FtsZ activity and thus septation. This is an unexpected role for MipZ and provides a new model for the integration of chromosome segregation and cell division.
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18
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de Lemos Martins F, Fournes F, Mazzuoli MV, Mazel D, Val ME. Vibrio cholerae chromosome 2 copy number is controlled by the methylation-independent binding of its monomeric initiator to the chromosome 1 crtS site. Nucleic Acids Res 2018; 46:10145-10156. [PMID: 30184118 PMCID: PMC6212839 DOI: 10.1093/nar/gky790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/20/2018] [Accepted: 08/22/2018] [Indexed: 12/13/2022] Open
Abstract
Bacteria contain a primary chromosome and, frequently, either essential secondary chromosomes or dispensable megaplasmids of plasmid origin. Incoming plasmids are often poorly adapted to their hosts and their stabilization requires integration with the host's cellular mechanisms in a process termed domestication. All Vibrio, including pathogenic species, carry a domesticated secondary chromosome (Chr2) where replication is coordinated with that of the primary chromosome (Chr1). Chr2 replication is triggered by the replication of an intergenic sequence (crtS) located on Chr1. Yet, the molecular mechanisms by which crtS replication controls the initiation of Chr2 replication are still largely unknown. In this study, we show that crtS not only regulates the timing of Chr2 initiation but also controls Chr2 copy number. We observed and characterized the direct binding of the Chr2 initiator (RctB) on crtS. RctB binding to crtS is independent of its methylation state. RctB molecules, which naturally form dimers, preferentially bind to crtS as monomers, with DnaK/J protein chaperones shown to stimulate binding of additional RctB monomers on crtS. In this study, we addressed various hypothesis of how replication of crtS could trigger Chr2 replication and provide new insights into its mode of action.
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Affiliation(s)
- Francisco de Lemos Martins
- Bacterial Genome Plasticity, Genomes & Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Florian Fournes
- Bacterial Genome Plasticity, Genomes & Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Maria-Vittoria Mazzuoli
- Bacterial Genome Plasticity, Genomes & Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Didier Mazel
- Bacterial Genome Plasticity, Genomes & Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Marie-Eve Val
- Bacterial Genome Plasticity, Genomes & Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
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19
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Muraleedharan S, Freitas C, Mann P, Glatter T, Ringgaard S. A cell length-dependent transition in MinD-dynamics promotes a switch in division-site placement and preservation of proliferating elongated Vibrio parahaemolyticus
swarmer cells. Mol Microbiol 2018; 109:365-384. [DOI: 10.1111/mmi.13996] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Samada Muraleedharan
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
| | - Carolina Freitas
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
| | - Petra Mann
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
| | - Timo Glatter
- Core facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
| | - Simon Ringgaard
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
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20
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Misra HS, Maurya GK, Kota S, Charaka VK. Maintenance of multipartite genome system and its functional significance in bacteria. J Genet 2018; 97:1013-1038. [PMID: 30262715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacteria are unicellular organisms that do not show compartmentalization of the genetic material and other cellular organelles as seen in higher organisms. Earlier, bacterial genomes were defined as single circular chromosome and extrachromosomal plasmids. Recently, many bacteria were found harbouringmultipartite genome system and the numbers of copies of genome elements including chromosomes vary from one to several per cell. Interestingly, it is noticed that majority of multipartite genome-harbouring bacteria are either stress tolerant or pathogens. Further, it is observed that the secondary genomes in these bacteria encode proteins that are involved in bacterial genome maintenance and also contribute to higher stress tolerance, and pathogenicity in pathogenic bacteria. Surprisingly, in some bacteria the genes encoding the proteins of classical homologous recombination pathways are present only on the secondary chromosomes, and some do not have either of the classical homologous recombination pathways. This review highlights the presence of ploidy and multipartite genomes in bacterial system, the underlying mechanisms of genome maintenance and the possibilities of these features contributing to higher abiotic and biotic stress tolerance in these bacteria.
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Affiliation(s)
- Hari Sharan Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
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21
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Misra HS, Maurya GK, Kota S, Charaka VK. Maintenance of multipartite genome system and its functional significance in bacteria. J Genet 2018. [DOI: 10.1007/s12041-018-0969-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Alvarado A, Kjær A, Yang W, Mann P, Briegel A, Waldor MK, Ringgaard S. Coupling chemosensory array formation and localization. eLife 2017; 6:31058. [PMID: 29058677 PMCID: PMC5706961 DOI: 10.7554/elife.31058] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 10/22/2017] [Indexed: 11/13/2022] Open
Abstract
Chemotaxis proteins organize into large, highly ordered, chemotactic signaling arrays, which in Vibrio species are found at the cell pole. Proper localization of signaling arrays is mediated by ParP, which tethers arrays to a cell pole anchor, ParC. Here we show that ParP’s C-terminus integrates into the core-unit of signaling arrays through interactions with MCP-proteins and CheA. Its intercalation within core-units stimulates array formation, whereas its N-terminal interaction domain enables polar recruitment of arrays and facilitates its own polar localization. Linkage of these domains within ParP couples array formation and localization and results in controlled array positioning at the cell pole. Notably, ParP’s integration into arrays modifies its own and ParC’s subcellular localization dynamics, promoting their polar retention. ParP serves as a critical nexus that regulates the localization dynamics of its network constituents and drives the localized assembly and stability of the chemotactic machinery, resulting in proper cell pole development. Many bacteria live in a liquid environment and explore their surroundings by swimming. When in search of food, bacteria are able to swim toward the highest concentration of food molecules in the environment by a process called chemotaxis. Proteins important for chemotaxis group together in large networks called chemotaxis arrays. In the bacterium Vibrio cholerae chemotaxis arrays are placed at opposite ends (at the “cell poles”) of the bacterium by a protein called ParP. This makes sure that when the bacterium divides, each new cell receives a chemotaxis array and can immediately search for food. In cells that lack ParP, the chemotaxis arrays are no longer placed correctly at the cell poles and the bacteria search for food much less effectively. To understand how ParP is able to direct chemotaxis arrays to the cell poles in V. cholerae Alvarado et al. searched for partner proteins that could help ParP position the arrays. The search revealed that ParP interacts with other proteins in the chemotaxis arrays. This enables ParP to integrate into the arrays and stimulate new arrays to form. Alvarado et al. also discovered that ParP consists of two separate parts that have different roles. One part directs ParP to the cell pole while the other part integrates ParP into the arrays. By performing both of these roles, ParP links the positioning of the arrays at the cell pole to their formation at this site. The findings presented by Alvarado et al. open many further questions. For instance, it is not understood how ParP affects how other chemotaxis proteins within the arrays interact with each other. As well as enabling many species of bacteria to spread through their environment, chemotaxis is also important for the disease-causing properties of many human pathogens – like V. cholerae. As a result, learning how chemotaxis is regulated could potentially identify new ways to stop the spread of infectious bacteria and prevent human infections.
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Affiliation(s)
- Alejandra Alvarado
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Andreas Kjær
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Wen Yang
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Petra Mann
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ariane Briegel
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Simon Ringgaard
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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23
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Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome. Int J Genomics 2017; 2017:8724304. [PMID: 28951866 PMCID: PMC5603330 DOI: 10.1155/2017/8724304] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/15/2017] [Accepted: 06/22/2017] [Indexed: 11/18/2022] Open
Abstract
The genetic make-up of most bacteria is encoded in a single chromosome while about 10% have more than one chromosome. Among these, Vibrio cholerae, with two chromosomes, has served as a model system to study various aspects of chromosome maintenance, mainly replication, and faithful partitioning of multipartite genomes. Here, we describe the genomic characterization of strains that are an exception to the two chromosome rules: naturally occurring single-chromosome V. cholerae. Whole genome sequence analyses of NSCV1 and NSCV2 (natural single-chromosome vibrio) revealed that the Chr1 and Chr2 fusion junctions contain prophages, IS elements, and direct repeats, in addition to large-scale chromosomal rearrangements such as inversions, insertions, and long tandem repeats elsewhere in the chromosome compared to prototypical two chromosome V. cholerae genomes. Many of the known cholera virulence factors are absent. The two origins of replication and associated genes are generally intact with synonymous mutations in some genes, as are recA and mismatch repair (MMR) genes dam, mutH, and mutL; MutS function is probably impaired in NSCV2. These strains are ideal tools for studying mechanistic aspects of maintenance of chromosomes with multiple origins and other rearrangements and the biological, functional, and evolutionary significance of multipartite genome architecture in general.
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24
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Díaz-Orejas R, Espinosa M, Yeo CC. The Importance of the Expendable: Toxin-Antitoxin Genes in Plasmids and Chromosomes. Front Microbiol 2017; 8:1479. [PMID: 28824602 PMCID: PMC5543033 DOI: 10.3389/fmicb.2017.01479] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/24/2017] [Indexed: 02/01/2023] Open
Abstract
Toxin–antitoxin (TA) genes were first reported in plasmids and were considered expendable genetic cassettes involved in the stable maintenance of the plasmid replicon by interfering with growth and/or viability of bacteria in which the plasmid was lost. TAs were later found in bacterial chromosomes and also in integrated mobile genetic elements; they were proposed to be involved in the bacterial response to stressful situations. At present, 100s of TAs have been identified and classified in up to six families (I to VI), with those belonging to the type II (constituted by two protein components) being the most studied. Based on well-characterized examples of several type II TAs, we discuss in this review that irrespective of their locations in plasmids or chromosomes, TAs functionally overlap as indicated by: (i) in both locations they can mediate the maintenance of genetic elements to which they are physical linked, and (ii) they can induce persistence or virulence in response to stress situations. Examples of functional confluences in homologous TA systems with different locations are also given. We also consider whether the physiological role of TAs is due to their genetic organization as operons or to their inherent properties, like the short lifespan of the antitoxin component.
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Affiliation(s)
- Ramón Díaz-Orejas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC)Madrid, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC)Madrid, Spain
| | - Chew Chieng Yeo
- Faculty of Medicine, Biomedical Research Centre, Universiti Sultan Zainal AbidinKuala Terengganu, Malaysia
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25
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An evolutionary perspective on plasmid lifestyle modes. Curr Opin Microbiol 2017; 38:74-80. [DOI: 10.1016/j.mib.2017.05.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 11/19/2022]
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26
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27
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Cass JA, Kuwada NJ, Traxler B, Wiggins PA. Escherichia coli Chromosomal Loci Segregate from Midcell with Universal Dynamics. Biophys J 2017; 110:2597-2609. [PMID: 27332118 DOI: 10.1016/j.bpj.2016.04.046] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/31/2016] [Accepted: 04/28/2016] [Indexed: 12/31/2022] Open
Abstract
The structure of the Escherichia coli chromosome is inherently dynamic over the duration of the cell cycle. Genetic loci undergo both stochastic motion around their initial positions and directed motion to opposite poles of the rod-shaped cell during segregation. We developed a quantitative method to characterize cell-cycle dynamics of the E. coli chromosome to probe the chromosomal steady-state mobility and segregation process. By tracking fluorescently labeled chromosomal loci in thousands of cells throughout the entire cell cycle, our method allows for the statistical analysis of locus position and motion, the step-size distribution for movement during segregation, and the locus drift velocity. The robust statistics of our detailed analysis of the wild-type E. coli nucleoid allow us to observe loci moving toward midcell before segregation occurs, consistent with a replication factory model. Then, as segregation initiates, we perform a detailed characterization of the average segregation velocity of loci. Contrary to origin-centric models of segregation, which predict distinct dynamics for oriC-proximal versus oriC-distal loci, we find that the dynamics of loci were universal and independent of genetic position.
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Affiliation(s)
- Julie A Cass
- Departments of Physics, Bioengineering, and Microbiology, University of Washington, Seattle, Washington
| | - Nathan J Kuwada
- Departments of Physics, Bioengineering, and Microbiology, University of Washington, Seattle, Washington
| | - Beth Traxler
- Departments of Physics, Bioengineering, and Microbiology, University of Washington, Seattle, Washington
| | - Paul A Wiggins
- Departments of Physics, Bioengineering, and Microbiology, University of Washington, Seattle, Washington.
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28
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Late assembly of the Vibrio cholerae cell division machinery postpones septation to the last 10% of the cell cycle. Sci Rep 2017; 7:44505. [PMID: 28300142 PMCID: PMC5353653 DOI: 10.1038/srep44505] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/08/2017] [Indexed: 12/26/2022] Open
Abstract
Bacterial cell division is a highly regulated process, which involves the formation of a complex apparatus, the divisome, by over a dozen proteins. In the few model bacteria in which the division process was detailed, divisome assembly occurs in two distinct steps: a few proteins, including the FtsZ tubulin-like protein, form a membrane associated contractile ring, the Z-ring, at ~30% of the cell cycle. The Z-ring serves as a scaffold for the recruitment of a second series of proteins, including integral membrane and periplasmic cell wall remodelling enzymes, at ~50% of the cell cycle. Actual septation occupies most of the remaining half of the cell cycle. In contrast, we present evidence suggesting that early pre-divisional Z-rings form between 40 and 50% of the cell cycle and mature into fully assembled divisome at about 80% of the cell cycle in Vibrio cholerae. Thus, actual septation is restricted to a very short amount of time. Our results further suggest that late assembly of the divisome probably helps maintain the asymmetric polar organisation of V. cholerae cells by limiting the accumulation of a cell pole marker, HubP, at the nascent cell poles.
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29
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Messerschmidt SJ, Schindler D, Zumkeller CM, Kemter FS, Schallopp N, Waldminghaus T. Optimization and Characterization of the Synthetic Secondary Chromosome synVicII in Escherichia coli. Front Bioeng Biotechnol 2016; 4:96. [PMID: 28066763 PMCID: PMC5179572 DOI: 10.3389/fbioe.2016.00096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/09/2016] [Indexed: 11/15/2022] Open
Abstract
Learning by building is one of the core ideas of synthetic biology research. Consequently, building synthetic chromosomes is the way to fully understand chromosome characteristics. The last years have seen exciting synthetic chromosome studies. We had previously introduced the synthetic secondary chromosome synVicII in Escherichia coli. It is based on the replication mechanism of the secondary chromosome in Vibrio cholerae. Here, we present a detailed analysis of its genetic characteristics and a selection approach to optimize replicon stability. We probe the origin diversity of secondary chromosomes from Vibrionaceae by construction of several new respective replicons. Finally, we present a synVicII version 2.0 with several innovations including its full compatibility with the popular modular cloning (MoClo) assembly system.
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Affiliation(s)
- Sonja J Messerschmidt
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Daniel Schindler
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Celine M Zumkeller
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Franziska S Kemter
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Nadine Schallopp
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Torsten Waldminghaus
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
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30
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Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM. Proc Natl Acad Sci U S A 2016; 113:10412-7. [PMID: 27573843 DOI: 10.1073/pnas.1604693113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nearly all motile bacterial cells use a highly sensitive and adaptable sensory system to detect changes in nutrient concentrations in the environment and guide their movements toward attractants and away from repellents. The best-studied bacterial chemoreceptor arrays are membrane-bound. Many motile bacteria contain one or more additional, sometimes purely cytoplasmic, chemoreceptor systems. Vibrio cholerae contains three chemotaxis clusters (I, II, and III). Here, using electron cryotomography, we explore V. cholerae's cytoplasmic chemoreceptor array and establish that it is formed by proteins from cluster I. We further identify a chemoreceptor with an unusual domain architecture, DosM, which is essential for formation of the cytoplasmic arrays. DosM contains two signaling domains and spans the two-layered cytoplasmic arrays. Finally, we present evidence suggesting that this type of receptor is important for the structural stability of the cytoplasmic array.
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31
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Orderly Replication and Segregation of the Four Replicons of Burkholderia cenocepacia J2315. PLoS Genet 2016; 12:e1006172. [PMID: 27428258 PMCID: PMC4948915 DOI: 10.1371/journal.pgen.1006172] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/15/2016] [Indexed: 11/19/2022] Open
Abstract
Bacterial genomes typically consist of a single chromosome and, optionally, one or more plasmids. But whole-genome sequencing reveals about ten per-cent of them to be multipartite, with additional replicons which by size and indispensability are considered secondary chromosomes. This raises the questions of how their replication and partition is managed without compromising genome stability and of how such genomes arose. Vibrio cholerae, with a 1 Mb replicon in addition to its 3 Mb chromosome, is the only species for which maintenance of a multipartite genome has been investigated. In this study we have explored the more complex genome of Burkholderia cenocepacia (strain J2315). It comprises an extra replicon (c2) of 3.21 Mb, comparable in size to the3.87Mb main chromosome (c1), another extra replicon(c3) of 0.87 Mb and a plasmid of 0.09 Mb. The replication origin of c1 is typically chromosomal and those of c2 and c3 are plasmid-like; all are replicated bidirectionally. Fluorescence microscopy of tagged origins indicates that all initiate replication at mid-cell and segregate towards the cell quarter positions sequentially, c1-c2-p1/c3. c2 segregation is as well-phased with the cell cycle as c1, implying that this plasmid-like origin has become subject to regulation not typical of plasmids; in contrast, c3 segregates more randomly through the cycle. Disruption of individual Par systems by deletion of parAB or by addition of parS sites showed each Par system to govern the positioning of its own replicon only. Inactivation of c1, c2 and c3 Par systems not only reduced growth rate, generated anucleate cells and compromised viability but influenced processes beyond replicon partition, notably regulation of replication, chromosome condensation and cell size determination. In particular, the absence of the c1 ParA protein altered replication of all three chromosomes, suggesting that the partition system of the main chromosome is a major participant in the choreography of the cell cycle. Unlike higher organisms, bacteria typically carry their genetic information on a single chromosome. But in a few bacterial families the genome includes one to three additional chromosome-like DNA molecules. Because these families are rich in pathogenic and environmentally versatile species, it is important to understand how their split genomes evolved and how their maintenance is managed without confusion. We find that mitotic segregation (partition) of all three chromosomes of the cystic fibrosis type strain, Burkholderia cenocepacia J2315, proceeds from mid-cell to cell quarter positions, but that it occurs in a sequential manner, from largest chromosome to smallest. Positioning of each chromosome is specified solely by its own partition proteins. Nevertheless, the partition system of the largest chromosome appears also to play a global role in the cell cycle, by modulating the timing of initiation of replication. In addition, disrupting the partition systems of all three chromosomes induced specific cell abnormalities. Hence, although such bacteria are governed mainly by the largest, housekeeping chromosome, all the Par systems have insinuated themselves into cell cycle regulation to become indispensable for normal growth. Exploration of the underlying mechanisms should allow us to understand their full importance to bacterial life.
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Draft Genome Sequence of an ortho-Nitrophenyl-β-d-Galactoside (ONPG)-Negative Strain of Vibrio cholerae, Isolated from Drakes Bay, California. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00135-16. [PMID: 26988050 PMCID: PMC4796129 DOI: 10.1128/genomea.00135-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We present the draft whole-genome sequence of a Vibrio cholerae strain (Vc25-3) isolated from Drakes Bay, California. This environmental isolate has an atypical morphology and is ortho-nitrophenyl-β-d-galactoside (ONPG)-negative.
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Luo P, He X, Liu Q, Hu C. Developing Universal Genetic Tools for Rapid and Efficient Deletion Mutation in Vibrio Species Based on Suicide T-Vectors Carrying a Novel Counterselectable Marker, vmi480. PLoS One 2015; 10:e0144465. [PMID: 26641275 PMCID: PMC4671572 DOI: 10.1371/journal.pone.0144465] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 11/18/2015] [Indexed: 01/06/2023] Open
Abstract
Despite that Vibrio spp. have a significant impact on the health of humans and aquatic animals, the molecular basis of their pathogenesis is little known, mainly due to the limited genetic tools for the functional research of genes in Vibrio. In some cases, deletion of target DNAs in Vibrio can be achieved through the use of suicide vectors. However, these strategies are time-consuming and lack universality, and the widely used counterselectable gene sacB does not work well in Vibrio cells. In this study, we developed universal genetic tools for rapid and efficient deletion mutations in Vibrio species based on suicide T-Vectors carrying a novel counterselectable marker, vmi480. We explored two uncharacterized genes, vmi480 and vmi470, in a genomic island from Vibrio mimicus VM573 and confirmed that vmi480 and vmi470 constitute a two-component toxin-antitoxin system through deletion and expression of vmi480 and vmi470. The product of vmi480 exhibited strong toxicity to Escherichia coli cells. Based on vmi480 and the PBAD or PTAC promoter system, we constructed two suicide T-vectors, pLP11 and pLP12, and each of these vectors contained a multiple cloning region with two AhdI sites. Both vectors linearized by AhdI digestion could be stored and directly ligated with purified PCR products without a digestion step. By using pLP11 and pLP12 coupled with a highly efficient conjugation system provided by E. coli β2163, six genes from four representative Vibrio species were easily deleted. By using the counterselective marker vmi480, we obtained 3–12 positive colonies (deletion mutants) among no more than 20 colonies randomly selected on counterselection plates. The strategy does not require the digestion of PCR products and suicide vectors every time, and it avoids large-scale screening colonies on counterselective plates. These results demonstrate that we successfully developed universal genetic tools for rapid and efficient gene deletion in Vibrio species.
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Affiliation(s)
- Peng Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Key Laboratory of Applied Marine Biology, Chinese Academy of Sciences, Guangzhou, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
| | - Xiangyan He
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiuting Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chaoqun Hu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Key Laboratory of Applied Marine Biology, Chinese Academy of Sciences, Guangzhou, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
- * E-mail: (CQH)
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Val ME, Soler-Bistué A, Bland MJ, Mazel D. Management of multipartite genomes: the Vibrio cholerae model. Curr Opin Microbiol 2015; 22:120-6. [PMID: 25460805 DOI: 10.1016/j.mib.2014.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 09/29/2014] [Accepted: 10/06/2014] [Indexed: 11/26/2022]
Abstract
A minority of bacterial species has been found to carry a genome divided among several chromosomes. Among these, all Vibrio species harbor a genome split into two chromosomes of uneven size, with distinctive replication origins whose replication firing involves common and specific factors. Most of our current knowledge on replication and segregation in multi-chromosome bacteria has come from the study of Vibrio cholerae, which is now the model organism for this field. It has been firmly established that replication of the two V. cholerae chromosomes is temporally regulated and coupled to the cell cycle, but the mediators of these processes are as yet mostly unknown. The two chromosomes are also organized along different patterns within the cell and occupy different subcellular domains. The selective advantages provided by this partitioning into two replicons are still unclear and are a key motivation for these studies.
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Affiliation(s)
- Marie-Eve Val
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
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Ringgaard S, Hubbard T, Mandlik A, Davis BM, Waldor MK. RpoS and quorum sensing control expression and polar localization of Vibrio cholerae chemotaxis cluster III proteins in vitro and in vivo. Mol Microbiol 2015; 97:660-75. [PMID: 25989366 DOI: 10.1111/mmi.13053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2015] [Indexed: 01/29/2023]
Abstract
The diarrheal pathogen Vibrio cholerae contains three gene clusters that encode chemotaxis-related proteins, but only cluster II appears to be required for chemotaxis. Here, we present the first characterization of V. cholerae's 'cluster III' chemotaxis system. We found that cluster III proteins assemble into foci at bacterial poles, like those formed by cluster II proteins, but the two systems assemble independently and do not colocalize. Cluster III proteins are expressed in vitro during stationary phase and in conjunction with growth arrest linked to carbon starvation. This expression, as well as expression in vivo in suckling rabbits, is dependent upon RpoS. V. cholerae's CAI-1 quorum sensing (QS) system is also required for cluster III expression in stationary phase and modulates its expression in vivo, but is not required for cluster III expression in response to carbon starvation. Surprisingly, even though the CAI-1 and AI-2 QS systems are thought to feed into the same signaling pathway, the AI-2 system inhibited cluster III gene expression, revealing that the outputs of the two QS systems are not always the same. The distinctions between genetic determinants of cluster III expression in vitro and in vivo highlight the distinctive nature of the in vivo environment.
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Affiliation(s)
- Simon Ringgaard
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Troy Hubbard
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anjali Mandlik
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Brigid M Davis
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, 02115, USA
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Characterization of chromosomal and megaplasmid partitioning loci in Thermus thermophilus HB27. BMC Genomics 2015; 16:317. [PMID: 25909452 PMCID: PMC4409726 DOI: 10.1186/s12864-015-1523-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/10/2015] [Indexed: 12/12/2022] Open
Abstract
Background In low-copy-number plasmids, the partitioning loci (par) act to ensure proper plasmid segregation and copy number maintenance in the daughter cells. In many bacterial species, par gene homologues are encoded on the chromosome, but their function is much less understood. In the two-replicon, polyploid genome of the hyperthermophilic bacterium Thermus thermophilus, both the chromosome and the megaplasmid encode par gene homologues (parABc and parABm, respectively). The mode of partitioning of the two replicons and the role of the two Par systems in the replication, segregation and maintenance of the genome copies are completely unknown in this organism. Results We generated a series of chromosomal and megaplasmid par mutants and sGFP reporter strains and analyzed them with respect to DNA segregation defects, genome copy number and replication origin localization. We show that the two ParB proteins specifically bind their cognate centromere-like sequences parS, and that both ParB-parS complexes localize at the cell poles. Deletion of the chromosomal parAB genes did not apparently affect the cell growth, the frequency of cells with aberrant nucleoids, or the chromosome and megaplasmid replication. In contrast, deletion of the megaplasmid parAB operon or of the parB gene was not possible, indicating essentiality of the megaplasmid-encoded Par system. A mutant expressing lower amounts of ParABm showed growth defects, a high frequency of cells with irregular nucleoids and a loss of a large portion of the megaplasmid. The truncated megaplasmid could not be partitioned appropriately, as interlinked megaplasmid molecules (catenenes) could be detected, and the ParBm-parSm complexes in this mutant lost their polar localization. Conclusions We show that in T. thermophilus the chromosomal par locus is not required for either the chromosomal or megaplasmid bulk DNA replication and segregation. In contrast, the megaplasmid Par system of T. thermophilus is needed for the proper replication and segregation of the megaplasmid, and is essential for its maintenance. The two Par sets in T. thermophilus appear to function in a replicon-specific manner. To our knowledge, this is the first analysis of Par systems in a polyploid bacterium. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1523-3) contains supplementary material, which is available to authorized users.
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Ramachandran R, Jha J, Chattoraj DK. Chromosome segregation in Vibrio cholerae. J Mol Microbiol Biotechnol 2015; 24:360-70. [PMID: 25732338 DOI: 10.1159/000368853] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The study of chromosome segregation is currently one of the most exciting research frontiers in cell biology. In this review, we discuss our current knowledge of the chromosome segregation process in Vibrio cholerae, based primarily on findings from fluorescence microscopy experiments. This bacterium is of special interest because of its eukaryotic feature of having a divided genome, a feature shared with 10% of known bacteria. We also discuss how the segregation mechanisms of V. cholerae compare with those in other bacteria, and highlight some of the remaining questions regarding the process of bacterial chromosome segregation.
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Affiliation(s)
- Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Md., USA
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Heinrich K, Leslie DJ, Jonas K. Modulation of bacterial proliferation as a survival strategy. ADVANCES IN APPLIED MICROBIOLOGY 2015; 92:127-71. [PMID: 26003935 DOI: 10.1016/bs.aambs.2015.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The cell cycle is one of the most fundamental processes in biology, underlying the proliferation and growth of all living organisms. In bacteria, the cell cycle has been extensively studied since the 1950s. Most of this research has focused on cell cycle regulation in a few model bacteria, cultured under standard growth conditions. However in nature, bacteria are exposed to drastic environmental changes. Recent work shows that by modulating their own growth and proliferation bacteria can increase their survival under stressful conditions, including antibiotic treatment. Here, we review the mechanisms that allow bacteria to integrate environmental information into their cell cycle. In particular, we focus on mechanisms controlling DNA replication and cell division. We conclude this chapter by highlighting the importance of understanding bacterial cell cycle and growth control for future research as well as other disciplines.
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Bouet JY, Stouf M, Lebailly E, Cornet F. Mechanisms for chromosome segregation. Curr Opin Microbiol 2014; 22:60-5. [DOI: 10.1016/j.mib.2014.09.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/15/2014] [Indexed: 11/25/2022]
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Messerschmidt SJ, Kemter FS, Schindler D, Waldminghaus T. Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae. Biotechnol J 2014; 10:302-14. [PMID: 25359671 DOI: 10.1002/biot.201400031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 10/02/2014] [Accepted: 10/30/2014] [Indexed: 01/25/2023]
Abstract
Recent developments in DNA-assembly methods make the synthesis of synthetic chromosomes a reachable goal. However, the redesign of primary chromosomes bears high risks and still requires enormous resources. An alternative approach is the addition of synthetic chromosomes to the cell. The natural secondary chromosome of Vibrio cholerae could potentially serve as template for a synthetic secondary chromosome in Escherichia coli. To test this assumption we constructed a replicon named synVicII based on the replication module of V. cholerae chromosome II (oriII). A new assay for the assessment of replicon stability was developed based on flow-cytometric analysis of unstable GFP variants. Application of this assay to cells carrying synVicII revealed an improved stability compared to a secondary replicon based on E. coli oriC. Cell cycle analysis and determination of cellular copy numbers of synVicII indicate that replication timing of the synthetic replicon in E. coli is comparable to the natural chromosome II (ChrII) in V. cholerae. The presented synthetic biology work provides the basis to use secondary chromosomes in E. coli to answer basic research questions as well as for several biotechnological applications.
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Affiliation(s)
- Sonja J Messerschmidt
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Germany
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Demarre G, Galli E, Muresan L, Paly E, David A, Possoz C, Barre FX. Differential management of the replication terminus regions of the two Vibrio cholerae chromosomes during cell division. PLoS Genet 2014; 10:e1004557. [PMID: 25255436 PMCID: PMC4177673 DOI: 10.1371/journal.pgen.1004557] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/25/2014] [Indexed: 12/04/2022] Open
Abstract
The replication terminus region (Ter) of the unique chromosome of most bacteria locates at mid-cell at the time of cell division. In several species, this localization participates in the necessary coordination between chromosome segregation and cell division, notably for the selection of the division site, the licensing of the division machinery assembly and the correct alignment of chromosome dimer resolution sites. The genome of Vibrio cholerae, the agent of the deadly human disease cholera, is divided into two chromosomes, chrI and chrII. Previous fluorescent microscopy observations suggested that although the Ter regions of chrI and chrII replicate at the same time, chrII sister termini separated before cell division whereas chrI sister termini were maintained together at mid-cell, which raised questions on the management of the two chromosomes during cell division. Here, we simultaneously visualized the location of the dimer resolution locus of each of the two chromosomes. Our results confirm the late and early separation of chrI and chrII Ter sisters, respectively. They further suggest that the MatP/matS macrodomain organization system specifically delays chrI Ter sister separation. However, TerI loci remain in the vicinity of the cell centre in the absence of MatP and a genetic assay specifically designed to monitor the relative frequency of sister chromatid contacts during constriction suggest that they keep colliding together until the very end of cell division. In contrast, we found that even though it is not able to impede the separation of chrII Ter sisters before septation, the MatP/matS macrodomain organization system restricts their movement within the cell and permits their frequent interaction during septum constriction. The genome of Vibrio cholerae is divided into two circular chromosomes, chrI and chrII. ChrII is derived from a horizontally acquired mega-plasmid, which raised questions on the necessary coordination of the processes that ensure its segregation with the cell division cycle. Here, we show that the MatP/matS macrodomain organization system impedes the separation of sister copies of the terminus region of chrI before the initiation of septum constriction. In its absence, however, chrI sister termini remain sufficiently close to mid-cell to be processed by the FtsK cell division translocase. In contrast, we show that MatP cannot impede the separation of chrII sister termini before constriction. However, it restricts their movements within the cell, which allows for their processing by FtsK at the time of cell division. These results suggest that multiple redundant factors, including MatP in the enterobacteriaceae and the Vibrios, ensure that sister copies of the terminus region of bacterial chromosomes remain sufficiently close to mid-cell to be processed by FtsK.
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Affiliation(s)
- Gaëlle Demarre
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Elisa Galli
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Leila Muresan
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Evelyne Paly
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Ariane David
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Christophe Possoz
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - François-Xavier Barre
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- * E-mail:
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Bacillus subtilis chromosome organization oscillates between two distinct patterns. Proc Natl Acad Sci U S A 2014; 111:12877-82. [PMID: 25071173 DOI: 10.1073/pnas.1407461111] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial chromosomes have been found to possess one of two distinct patterns of spatial organization. In the first, called "ori-ter" and exemplified by Caulobacter crescentus, the chromosome arms lie side-by-side, with the replication origin and terminus at opposite cell poles. In the second, observed in slow-growing Escherichia coli ("left-ori-right"), the two chromosome arms reside in separate cell halves, on either side of a centrally located origin. These two patterns, rotated 90° relative to each other, appear to result from different segregation mechanisms. Here, we show that the Bacillus subtilis chromosome alternates between them. For most of the cell cycle, newly replicated origins are maintained at opposite poles with chromosome arms adjacent to each other, in an ori-ter configuration. Shortly after replication initiation, the duplicated origins move as a unit to midcell and the two unreplicated arms resolve into opposite cell halves, generating a left-ori-right pattern. The origins are then actively segregated toward opposite poles, resetting the cycle. Our data suggest that the condensin complex and the parABS partitioning system are the principal driving forces underlying this oscillatory cycle. We propose that the distinct organization patterns observed for bacterial chromosomes reflect a common organization-segregation mechanism, and that simple modifications to it underlie the unique patterns observed in different species.
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David A, Demarre G, Muresan L, Paly E, Barre FX, Possoz C. The two Cis-acting sites, parS1 and oriC1, contribute to the longitudinal organisation of Vibrio cholerae chromosome I. PLoS Genet 2014; 10:e1004448. [PMID: 25010199 PMCID: PMC4091711 DOI: 10.1371/journal.pgen.1004448] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 05/07/2014] [Indexed: 11/19/2022] Open
Abstract
The segregation of bacterial chromosomes follows a precise choreography of spatial organisation. It is initiated by the bipolar migration of the sister copies of the replication origin (ori). Most bacterial chromosomes contain a partition system (Par) with parS sites in close proximity to ori that contribute to the active mobilisation of the ori region towards the old pole. This is thought to result in a longitudinal chromosomal arrangement within the cell. In this study, we followed the duplication frequency and the cellular position of 19 Vibrio cholerae genome loci as a function of cell length. The genome of V. cholerae is divided between two chromosomes, chromosome I and II, which both contain a Par system. The ori region of chromosome I (oriI) is tethered to the old pole, whereas the ori region of chromosome II is found at midcell. Nevertheless, we found that both chromosomes adopted a longitudinal organisation. Chromosome I extended over the entire cell while chromosome II extended over the younger cell half. We further demonstrate that displacing parS sites away from the oriI region rotates the bulk of chromosome I. The only exception was the region where replication terminates, which still localised to the septum. However, the longitudinal arrangement of chromosome I persisted in Par mutants and, as was reported earlier, the ori region still localised towards the old pole. Finally, we show that the Par-independent longitudinal organisation and oriI polarity were perturbed by the introduction of a second origin. Taken together, these results suggest that the Par system is the major contributor to the longitudinal organisation of chromosome I but that the replication program also influences the arrangement of bacterial chromosomes.
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Affiliation(s)
- Ariane David
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Gaëlle Demarre
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Leila Muresan
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Evelyne Paly
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - François-Xavier Barre
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- * E-mail: (FXB); (CP)
| | - Christophe Possoz
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- * E-mail: (FXB); (CP)
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Abstract
ABSTRACT Bacterial ParA and ParB proteins are best known for their contribution to plasmid and chromosome segregation, but they may also contribute to other cell functions. In segregation, ParA interacts with ParB, which binds to parS centromere-analogous sites. In transcription, plasmid Par proteins can serve as repressors by specifically binding to their own promoters and, additionally, in the case of ParB, by spreading from a parS site to nearby promoters. Here, we have asked whether chromosomal Par proteins can likewise control transcription. Analysis of genome-wide ParB1 binding in Vibrio cholerae revealed preferential binding to the three known parS1 sites and limited spreading of ParB1 beyond the parS1 sites. Comparison of wild-type transcriptomes with those of ΔparA1, ΔparB1, and ΔparAB1 mutants revealed that two out of 20 genes (VC0067 and VC0069) covered by ParB1 spreading are repressed by both ParB1 and ParA1. A third gene (VC0076) at the outskirts of the spreading area and a few genes further away were also repressed, particularly the gene for an outer membrane protein, ompU (VC0633). Since ParA1 or ParB1 binding was not evident near VC0076 and ompU genes, the repression may require participation of additional factors. Indeed, both ParA1 and ParB1 proteins were found to interact with several V. cholerae proteins in bacterial and yeast two-hybrid screens. These studies demonstrate that chromosomal Par proteins can repress genes unlinked to parS and can do so without direct binding to the cognate promoter DNA. IMPORTANCE Directed segregation of chromosomes is essential for their maintenance in dividing cells. Many bacteria have genes (par) that were thought to be dedicated to segregation based on analogy to their roles in plasmid maintenance. It is becoming clear that chromosomal par genes are pleiotropic and that they contribute to diverse processes such as DNA replication, cell division, cell growth, and motility. One way to explain the pleiotropy is to suggest that Par proteins serve as or control other transcription factors. We tested this model by determining how Par proteins affect genome-wide transcription activity. We found that genes implicated in drug resistance, stress response, and pathogenesis were repressed by Par. Unexpectedly, the repression did not involve direct Par binding to cognate promoter DNA, indicating that the repression may involve Par interactions with other regulators. This pleiotropy highlights the degree of integration of chromosomal Par proteins into cellular control circuitries.
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Baek JH, Chattoraj DK. Chromosome I controls chromosome II replication in Vibrio cholerae. PLoS Genet 2014; 10:e1004184. [PMID: 24586205 PMCID: PMC3937223 DOI: 10.1371/journal.pgen.1004184] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 01/02/2014] [Indexed: 11/19/2022] Open
Abstract
Control of chromosome replication involves a common set of regulators in eukaryotes, whereas bacteria with divided genomes use chromosome-specific regulators. How bacterial chromosomes might communicate for replication is not known. In Vibrio cholerae, which has two chromosomes (chrI and chrII), replication initiation is controlled by DnaA in chrI and by RctB in chrII. DnaA has binding sites at the chrI origin of replication as well as outside the origin. RctB likewise binds at the chrII origin and, as shown here, to external sites. The binding to the external sites in chrII inhibits chrII replication. A new kind of site was found in chrI that enhances chrII replication. Consistent with its enhancing activity, the chrI site increased RctB binding to those chrII origin sites that stimulate replication and decreased binding to other sites that inhibit replication. The differential effect on binding suggests that the new site remodels RctB. The chaperone-like activity of the site is supported by the finding that it could relieve the dependence of chrII replication on chaperone proteins DnaJ and DnaK. The presence of a site in chrI that specifically controls chrII replication suggests a mechanism for communication between the two chromosomes for replication. Genome maintenance in dividing cells requires that the chromosomes replicate reliably once per cell cycle, and that this replication be timed to allow for proper segregation of the daughter chromosomes before cell division. In organisms with divided genomes, eukaryotes and a significant class of bacteria, the chromosomes must avoid interference with one another. They exhibit disciplined chromosome choreography, involving several regulators and control circuits that, even in the simplest organisms, are poorly understood. Here we examine the regulatory processes involved in maintaining the two chromosomes of the well-studied and medically important pathogen Vibrio cholerae. We provide evidence that a site in chromosome I can control the frequency and timing of replication of chromosome II. The mechanism involves a DNA-mediated remodeling of the chromosome II-specific initiator of replication by the chromosome I site. The site enhances the activity of the protein by differentially affecting its affinity for inhibitory and stimulatory sites on chromosome II. Our results provide the groundwork for determining whether coordination of replication might be a conserved feature that maintains chromosomes in proliferating cells of higher organisms.
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Affiliation(s)
- Jong Hwan Baek
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dhruba K. Chattoraj
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Youngren B, Nielsen HJ, Jun S, Austin S. The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer. Genes Dev 2014; 28:71-84. [PMID: 24395248 PMCID: PMC3894414 DOI: 10.1101/gad.231050.113] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
At all but the slowest growth rates, Escherichia coli cell cycles overlap, and its nucleoid is segregated to daughter cells as a forked DNA circle with replication ongoing-a state fundamentally different from eukaryotes. We have solved the chromosome organization, structural dynamics, and segregation of this constantly replicating chromosome. It is locally condensed to form a branched donut, compressed so that the least replicated DNA spans the cell center and the newest DNA extends toward the cell poles. Three narrow zones at the cell center and quarters contain both the replication forks and nascent DNA and serve to segregate the duplicated chromosomal information as it flows outward. The overall pattern is smoothly self-replicating, except when the duplicated terminus region is released from the septum and recoils to the center of a sister nucleoid. In circular cross-section of the cell, the left and right arms of the chromosome form separate, parallel structures that lie in each cell half along the radial cell axis. In contrast, replication forks and origin and terminus regions are found mostly at the center of the cross section, balanced by the parallel chromosome arms. The structure is consistent with the model in which the nucleoid is a constrained ring polymer that develops by spontaneous thermodynamics. The ring polymer pattern extrapolates to higher growth rates and also provides a structural basis for the form of the chromosome during very slow growth.
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Affiliation(s)
- Brenda Youngren
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, National Cancer Institute, Frederick, Maryland 21702, USA
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Val ME, Kennedy SP, Soler-Bistué AJ, Barbe V, Bouchier C, Ducos-Galand M, Skovgaard O, Mazel D. Fuse or die: how to survive the loss of Dam inVibrio cholerae. Mol Microbiol 2014; 91:665-78. [DOI: 10.1111/mmi.12483] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Marie-Eve Val
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | | | - Alfonso J. Soler-Bistué
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | | | | | - Magaly Ducos-Galand
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | - Ole Skovgaard
- Department of Science, Systems and Models; Roskilde University; DK-4000 Roskilde Denmark
| | - Didier Mazel
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
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Demidenok OI, Goncharenko AV. Bacterial toxin-antitoxin systems and perspectives for their application in medicine. APPL BIOCHEM MICRO+ 2013. [DOI: 10.1134/s0003683813060070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Harms A, Treuner-Lange A, Schumacher D, Søgaard-Andersen L. Tracking of chromosome and replisome dynamics in Myxococcus xanthus reveals a novel chromosome arrangement. PLoS Genet 2013; 9:e1003802. [PMID: 24068967 PMCID: PMC3778016 DOI: 10.1371/journal.pgen.1003802] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/31/2013] [Indexed: 11/24/2022] Open
Abstract
Cells closely coordinate cell division with chromosome replication and segregation; however, the mechanisms responsible for this coordination still remain largely unknown. Here, we analyzed the spatial arrangement and temporal dynamics of the 9.1 Mb circular chromosome in the rod-shaped cells of Myxococcus xanthus. For chromosome segregation, M. xanthus uses a parABS system, which is essential, and lack of ParB results in chromosome segregation defects as well as cell divisions over nucleoids and the formation of anucleate cells. From the determination of the dynamic subcellular location of six genetic loci, we conclude that in newborn cells ori, as monitored following the ParB/parS complex, and ter regions are localized in the subpolar regions of the old and new cell pole, respectively and each separated from the nearest pole by approximately 1 µm. The bulk of the chromosome is arranged between the two subpolar regions, thus leaving the two large subpolar regions devoid of DNA. Upon replication, one ori region remains in the original subpolar region while the second copy segregates unidirectionally to the opposite subpolar region followed by the rest of the chromosome. In parallel, the ter region of the mother chromosome relocates, most likely passively, to midcell, where it is replicated. Consequently, after completion of replication and segregation, the two chromosomes show an ori-ter-ter-ori arrangement with mirror symmetry about a transverse axis at midcell. Upon completion of segregation of the ParB/parS complex, ParA localizes in large patches in the DNA-free subpolar regions. Using an Ssb-YFP fusion as a proxy for replisome localization, we observed that the two replisomes track independently of each other from a subpolar region towards ter. We conclude that M. xanthus chromosome arrangement and dynamics combine features from previously described systems with new features leading to a novel spatiotemporal arrangement pattern. Work on several model organisms has revealed that bacterial chromosomes are spatially highly arranged throughout the cell cycle in a dynamic yet reproducible manner. These analyses have also demonstrated significant differences between chromosome arrangements and dynamics in different bacterial species. Here, we show that the Myxococcus xanthus genome is arranged about a longitudinal axis with ori in a subpolar region and ter in the opposite subpolar region. Upon replication, one ori remains at the original subpolar region while the second copy in a directed and parABS-dependent manner segregates to the opposite subpolar region followed by the rest of the chromosome. In parallel, ter relocates from a subpolar region to midcell. Replication involves replisomes that track independently of each other from the ori-containing subpolar region towards ter. Moreover, we find that the parABS system is essential in M. xanthus and ParB depletion not only results in chromosome segregation defects but also in cell division defects with cell divisions occurring over nucleoids. In M. xanthus the dynamics of chromosome replication and segregation combine features from previously described systems leading to a novel spatiotemporal arrangement pattern.
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Affiliation(s)
- Andrea Harms
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Anke Treuner-Lange
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Dominik Schumacher
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
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Chao MC, Pritchard JR, Zhang YJ, Rubin EJ, Livny J, Davis BM, Waldor MK. High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data. Nucleic Acids Res 2013; 41:9033-48. [PMID: 23901011 PMCID: PMC3799429 DOI: 10.1093/nar/gkt654] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial growth and survival. We have refined analysis of transposon-insertion sequencing data by normalizing for the effect of DNA replication on sequencing output and using a hidden Markov model (HMM)-based filter to exploit heretofore unappreciated information inherent in all transposon-insertion sequencing data sets. The HMM can smooth variations in read abundance and thereby reduce the effects of read noise, as well as permit fine scale mapping that is independent of genomic annotation and enable classification of loci into several functional categories (e.g. essential, domain essential or ‘sick’). We generated a high-resolution map of genomic loci (encompassing both intra- and intergenic sequences) that are required or beneficial for in vitro growth of the cholera pathogen, Vibrio cholerae. This work uncovered new metabolic and physiologic requirements for V. cholerae survival, and by combining transposon-insertion sequencing and transcriptomic data sets, we also identified several novel noncoding RNA species that contribute to V. cholerae growth. Our findings suggest that HMM-based approaches will enhance extraction of biological meaning from transposon-insertion sequencing genomic data.
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Affiliation(s)
- Michael C Chao
- Division of Infectious Disease, Brigham & Women's Hospital, Boston, MA 02115, USA, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA, Howard Hughes Medical Institute, Boston, MA 02115, USA, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA and Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA 02142, USA
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