1
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Ramming L, Stukenberg D, Sánchez Olmos MDC, Glatter T, Becker A, Schindler D. Rationally designed chromosome fusion does not prevent rapid growth of Vibrio natriegens. Commun Biol 2024; 7:519. [PMID: 38698198 PMCID: PMC11066055 DOI: 10.1038/s42003-024-06234-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
DNA replication is essential for the proliferation of all cells. Bacterial chromosomes are replicated bidirectionally from a single origin of replication, with replication proceeding at about 1000 bp per second. For the model organism, Escherichia coli, this translates into a replication time of about 40 min for its 4.6 Mb chromosome. Nevertheless, E. coli can propagate by overlapping replication cycles with a maximum short doubling time of 20 min. The fastest growing bacterium known, Vibrio natriegens, is able to replicate with a generation time of less than 10 min. It has a bipartite genome with chromosome sizes of 3.2 and 1.9 Mb. Is simultaneous replication from two origins a prerequisite for its rapid growth? We fused the two chromosomes of V. natriegens to create a strain carrying one chromosome with a single origin of replication. Compared to the parental, this strain showed no significant deviation in growth rate. This suggests that the split genome is not a prerequisite for rapid growth.
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Affiliation(s)
- Lea Ramming
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniel Stukenberg
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | | | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Anke Becker
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
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2
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Doan A, Chatterjee S, Kothapalli R, Khan Z, Sen S, Kedei N, Jha JK, Chattoraj DK, Ramachandran R. The replication enhancer crtS depends on transcription factor Lrp for modulating binding of initiator RctB to ori2 of Vibrio cholerae. Nucleic Acids Res 2024; 52:708-723. [PMID: 38000366 PMCID: PMC10810183 DOI: 10.1093/nar/gkad1111] [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: 04/08/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Replication of Vibrio cholerae chromosome 2 (Chr2) initiates when the Chr1 locus, crtS (Chr2 replication triggering site) duplicates. The site binds the Chr2 initiator, RctB, and the binding increases when crtS is complexed with the transcription factor, Lrp. How Lrp increases the RctB binding and how RctB is subsequently activated for initiation by the crtS-Lrp complex remain unclear. Here we show that Lrp bends crtS DNA and possibly contacts RctB, acts that commonly promote DNA-protein interactions. To understand how the crtS-Lrp complex enhances replication, we isolated Tn-insertion and point mutants of RctB, selecting for retention of initiator activity without crtS. Nearly all mutants (42/44) still responded to crtS for enhancing replication, exclusively in an Lrp-dependent manner. The results suggest that the Lrp-crtS controls either an essential function or more than one function of RctB. Indeed, crtS modulates two kinds of RctB binding to the origin of Chr2, ori2, both of which we find to be Lrp-dependent. Some point mutants of RctB that are optimally modulated for ori2 binding without crtS still remained responsive to crtS and Lrp for replication enhancement. We infer that crtS-Lrp functions as a unit, which has an overarching role, beyond controlling initiator binding to ori2.
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Affiliation(s)
- Alexander Doan
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Soniya Chatterjee
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Roopa Kothapalli
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zaki Khan
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shaanit Sen
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noemi Kedei
- Collaborative Protein Technology Resource, OSTP, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jyoti K Jha
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dhruba K Chattoraj
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Revathy Ramachandran
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- College of Medicine, Mohammed Bin Rashid University, Dubai, UAE
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3
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Zumkeller C, Schindler D, Felder J, Waldminghaus T. Modular Assembly of Synthetic Secondary Chromosomes. Methods Mol Biol 2024; 2819:157-187. [PMID: 39028507 DOI: 10.1007/978-1-0716-3930-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The development of novel DNA assembly methods in recent years has paved the way for the construction of synthetic replicons to be used for basic research and biotechnological applications. A learning-by-building approach can now answer questions about how chromosomes must be constructed to maintain genetic information. Here we describe an efficient pipeline for the design and assembly of synthetic, secondary chromosomes in Escherichia coli based on the popular modular cloning (MoClo) system.
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Affiliation(s)
- Celine Zumkeller
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Jennifer Felder
- Technische Universität Darmstadt, Faculty of Biology, Darmstadt, Germany
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4
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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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5
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Abstract
Maintaining proper chromosome inheritance after the completion of each cell cycle is paramount for bacterial survival. Mechanistic details remain incomplete for how bacteria manage to retain complete chromosomes after each cell cycle. In this study, we examined the potential roles of the partitioning protein ParA on chromosomal maintenance that go beyond triggering the onset of chromosome segregation in Caulobacter crescentus. Our data revealed that increasing the levels of ParA result in cells with multiple origins of replication in a DnaA-ATP-dependent manner. This ori supernumerary is retained even when expressing variants of ParA that are deficient in promoting chromosome segregation. Our data suggest that in Caulobacter ParA's impact on replication initiation is likely indirect, possibly through the effect of other cell cycle events. Overall, our data provide new insights into the highly interconnected network that drives the forward progression of the bacterial cell cycle. IMPORTANCE The successful generation of a daughter cell containing a complete copy of the chromosome requires the exquisite coordination of major cell cycle events. Any mistake in this coordination can be lethal, making these processes ideal targets for novel antibiotics. In this study, we focused on the coordination between the onset of chromosome replication, and the partitioning protein ParA. We demonstrate that altering the cellular levels of ParA causes cells to accumulate multiple origins of replication in Caulobacter crescentus. Our work provides important insights into the complex regulation involved in the coordination of the bacterial cell cycle.
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6
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Murase K, Arakawa E, Izumiya H, Iguchi A, Takemura T, Kikuchi T, Nakagawa I, Thomson NR, Ohnishi M, Morita M. Genomic dissection of the Vibrio cholerae O-serogroup global reference strains: reassessing our view of diversity and plasticity between two chromosomes. Microb Genom 2022; 8. [PMID: 35930328 PMCID: PMC9484750 DOI: 10.1099/mgen.0.000860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Approximately 200 O-serogroups of Vibrio cholerae have already been identified; however, only 2 serogroups, O1 and O139, are strongly related to pandemic cholera. The study of non-O1 and non-O139 strains has hitherto been limited. Nevertheless, there are other clinically and epidemiologically important serogroups causing outbreaks with cholera-like disease. Here, we report a comprehensive genome analysis of the whole set of V. cholerae O-serogroup reference strains to provide an overview of this important bacterial pathogen. It revealed structural diversity of the O-antigen biosynthesis gene clusters located at specific loci on chromosome 1 and 16 pairs of strains with almost identical O-antigen biosynthetic gene clusters but differing in serological patterns. This might be due to the presence of O-antigen biosynthesis-related genes at secondary loci on chromosome 2.
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Affiliation(s)
- Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Eiji Arakawa
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hidemasa Izumiya
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Japan
| | - Taichiro Takemura
- Vietnam Research Station, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Taisei Kikuchi
- Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Hinxton, UK.,London School of Hygiene and Tropical Medicine, London, UK
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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7
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Kothapalli R, Ghirlando R, Khan ZA, Chatterjee S, Kedei N, Chattoraj D. The dimerization interface of initiator RctB governs chaperone and enhancer dependence of Vibrio cholerae chromosome 2 replication. Nucleic Acids Res 2022; 50:4529-4544. [PMID: 35390166 PMCID: PMC9071482 DOI: 10.1093/nar/gkac210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/01/2022] [Accepted: 03/20/2022] [Indexed: 11/13/2022] Open
Abstract
Protein function often requires remodeling of protein structure. In the well-studied iteron-containing plasmids, the initiator of replication has a dimerization interface that undergoes chaperone-mediated remodeling. This remodeling reduces dimerization and promotes DNA replication, since only monomers bind origin DNA. A structurally homologs interface exists in RctB, the replication initiator of Vibrio cholerae chromosome 2 (Chr2). Chaperones also promote Chr2 replication, although both monomers and dimers of RctB bind to origin, and chaperones increase the binding of both. Here we report how five changes in the dimerization interface of RctB affect the protein. The mutants are variously defective in dimerization, more active as initiator, and except in one case, unresponsive to chaperone (DnaJ). The results indicate that chaperones also reduce RctB dimerization and support the proposal that the paradoxical chaperone-promoted dimer binding likely represents sequential binding of monomers on DNA. RctB is also activated for replication initiation upon binding to a DNA site, crtS, and three of the mutants are also unresponsive to crtS. This suggests that crtS, like chaperones, reduces dimerization, but additional evidence suggests that the remodelling activities function independently. Involvement of two remodelers in reducing dimerization signifies the importance of dimerization in limiting Chr2 replication.
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Affiliation(s)
- Roopa Kothapalli
- Basic Research Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA
| | - Zaki Ali Khan
- Basic Research Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Soniya Chatterjee
- Basic Research Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Noemi Kedei
- Collaborative Protein Technology Resource, OSTP, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Dhruba K Chattoraj
- Basic Research Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
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8
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Convergent evolution in two bacterial replicative helicase loaders. Trends Biochem Sci 2022; 47:620-630. [DOI: 10.1016/j.tibs.2022.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
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9
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Homma M, Nishikino T, Kojima S. Achievements in bacterial flagellar research with focus on Vibrio species. Microbiol Immunol 2021; 66:75-95. [PMID: 34842307 DOI: 10.1111/1348-0421.12954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/01/2022]
Abstract
In 1980's, the most genes involved in the bacterial flagellar function and formation had been isolated though many of their functions or roles were not clarified. Bacterial flagella are the primary locomotive organ and are not necessary for growing in vitro but are probably essential for living in natural condition and are involved in the pathogenicity. In vitro, the flagella-deficient strains can grow at rates similar to wild-type strains. More than 50 genes are responsible for flagellar function, and the flagellum is constructed by more than 20 structural proteins. The maintenance cost of flagellum is high as several genes are required for its development. The fact that it evolved as a motor organ even with such the high cost shows that the motility is indispensable to survive under the harsh environment of Earth. In this review, we focus on flagella-related research conducted by the authors for about 40 years and flagellar research focused on Vibrio spp. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University
| | | | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University
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10
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Fournes F, Niault T, Czarnecki J, Tissier-Visconti A, Mazel D, Val ME. The coordinated replication of Vibrio cholerae's two chromosomes required the acquisition of a unique domain by the RctB initiator. Nucleic Acids Res 2021; 49:11119-11133. [PMID: 34643717 PMCID: PMC8565311 DOI: 10.1093/nar/gkab903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/30/2021] [Accepted: 09/22/2021] [Indexed: 12/21/2022] Open
Abstract
Vibrio cholerae, the pathogenic bacterium that causes cholera, has two chromosomes (Chr1, Chr2) that replicate in a well-orchestrated sequence. Chr2 initiation is triggered only after the replication of the crtS site on Chr1. The initiator of Chr2 replication, RctB, displays activities corresponding with its different binding sites: initiator at the iteron sites, repressor at the 39m sites, and trigger at the crtS site. The mechanism by which RctB relays the signal to initiate Chr2 replication from crtS is not well-understood. In this study, we provide new insights into how Chr2 replication initiation is regulated by crtS via RctB. We show that crtS (on Chr1) acts as an anti-inhibitory site by preventing 39m sites (on Chr2) from repressing initiation. The competition between these two sites for RctB binding is explained by the fact that RctB interacts with crtS and 39m via the same DNA-binding surface. We further show that the extreme C-terminal tail of RctB, essential for RctB self-interaction, is crucial for the control exerted by crtS. This subregion of RctB is conserved in all Vibrio, but absent in other Rep-like initiators. Hence, the coordinated replication of both chromosomes likely results from the acquisition of this unique domain by RctB.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites
- Binding, Competitive
- Chromosomes, Bacterial/chemistry
- Chromosomes, Bacterial/metabolism
- Cloning, Molecular
- DNA Replication
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Models, Molecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Replication Origin
- Sequence Alignment
- Sequence Homology, Amino Acid
- Signal Transduction
- Vibrio cholerae/genetics
- Vibrio cholerae/metabolism
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Affiliation(s)
- Florian Fournes
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
| | - Theophile Niault
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris 75005, France
| | - Jakub Czarnecki
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
- University of Warsaw, Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, Warsaw 02-096, Poland
| | - Alvise Tissier-Visconti
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
| | - Didier Mazel
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
| | - Marie-Eve Val
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
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11
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Nishikino T, Kojima S, Homma M. [Flagellar related genes and functions in Vibrio]. Nihon Saikingaku Zasshi 2021; 75:195-214. [PMID: 33390367 DOI: 10.3412/jsb.75.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteria can move or swim by flagella. On the other hand, the motile ability is not necessary to live at all. In laboratory, the flagella-deficient strains can grow just like the wild-type strains. The flagellum is assembled from more than 20 structural proteins and there are more than 50 genes including the structural genes to regulate or support the flagellar formation. The cost to construct the flagellum is so expensive. The fact that it evolved as a motor organ means even at such the large cost shows that the flagellum is essential for survival in natural condition. In this review, we would like to focus on the flagella-related researches conducted by the authors and the flagellar research on Vibrio spp.
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Affiliation(s)
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University
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12
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Maurya GK, Chaudhary R, Pandey N, Misra HS. Molecular insights into replication initiation in a multipartite genome harboring bacterium Deinococcus radiodurans. J Biol Chem 2021; 296:100451. [PMID: 33626388 PMCID: PMC7988490 DOI: 10.1016/j.jbc.2021.100451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 11/23/2022] Open
Abstract
Deinococcus radiodurans harbors a multipartite ploid genome system consisting of two chromosomes and two plasmids present in multiple copies. How these discrete genome elements are maintained and inherited is not well understood. PprA, a pleiotropic protein involved in radioresistance, has been characterized for its roles in DNA repair, genome segregation, and cell division in this bacterium. Here, we show that PprA regulates ploidy of chromosome I and II and inhibits the activity of drDnaA, the initiator protein in D. radiodurans. We found that pprA deletion resulted in an increased genomic content and ploidy of both the chromosomal elements. Expression of PprA in trans rescued the phenotypes of the pprA mutant. To understand the molecular mechanism underlying these phenotypes, we characterized drDnaA and drDnaB. As expected for an initiator protein, recombinant drDnaA showed sequence-specific interactions with the putative oriC sequence in chromosome I (oriCI). Both drDnaA and drDnaB showed ATPase activity, also typical of initiator proteins, but only drDnaB exhibited 5'→3' dsDNA helicase activity in vitro. drDnaA and drDnaB showed homotypic and heterotypic interactions with each other, which were perturbed by PprA. Interestingly, PprA has inhibited the ATPase activity of drDnaA but showed no effect on the activity of drDnaB. Regulation of chromosome copy number and inhibition of the initiator protein functions by PprA strongly suggest that it plays a role as a checkpoint regulator of the DNA replication initiation in D. radiodurans perhaps through its interaction with the replication initiation machinery.
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Affiliation(s)
- Ganesh K Maurya
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India; Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India; Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Neha Pandey
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India; Life Sciences, University of Mumbai, Mumbai, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India; Life Sciences, Homi Bhabha National Institute, Mumbai, India.
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13
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Chatterjee S, Jha JK, Ciaccia P, Venkova T, Chattoraj DK. Interactions of replication initiator RctB with single- and double-stranded DNA in origin opening of Vibrio cholerae chromosome 2. Nucleic Acids Res 2020; 48:11016-11029. [PMID: 33035310 DOI: 10.1093/nar/gkaa826] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022] Open
Abstract
Studies of bacterial chromosomes and plasmids indicate that their replication initiator proteins bind to origins of replication at many double-stranded sites and also at AT-rich regions where single-stranded DNA is exposed during origin opening. Single-strand binding apparently promotes origin opening by stabilizing an open structure, but how the initiator participates in this process and the contributions of the several binding sites remain unclear. Here, we show that the initiator protein of Vibrio cholerae specific to chromosome 2 (Chr2) also has single-strand binding activity in the AT-rich region of its origin. Binding is strand specific, depends on repeats of the sequence 5'ATCA and is greatly stabilized in vitro by specific double-stranded sites of the origin. The stability derives from the formation of ternary complexes of the initiator with the single- and double-stranded sites. An IHF site lies between these two kinds of sites in the Chr2 origin and an IHF-induced looping out of the intervening DNA mediates their interaction. Simultaneous binding to two kinds of sites in the origin appears to be a common mechanism by which bacterial replication initiators stabilize an open origin.
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Affiliation(s)
- Soniya Chatterjee
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4260, USA
| | - Jyoti K Jha
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4260, USA
| | - Peter Ciaccia
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4260, USA
| | - Tatiana Venkova
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4260, USA
| | - Dhruba K Chattoraj
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-4260, USA
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14
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Maurya GK, Misra HS. Characterization of ori and parS-like functions in secondary genome replicons in Deinococcus radiodurans. Life Sci Alliance 2020; 4:4/1/e202000856. [PMID: 33199509 PMCID: PMC7671480 DOI: 10.26508/lsa.202000856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/27/2022] Open
Abstract
The mechanisms underlying multipartite genome maintenance and its functional significance in extraordinary radioresistance of Deinococcus radiodurans are not well understood. The sequences upstream to parAB operons in chrII (cisII) and MP (cisMP) could stabilize an otherwise, non-replicative colE1 plasmid, in D. radiodurans DnaA and cognate ParB proteins bound specifically with cisII and cisMP elements. The ΔcisII and ΔcisMP cells showed the reduced copy number of cognate replicons and radioresistance as compared with wild type. Fluorescent reporter-operator system inserted in chrI, chrII, and MP in wild type and cisII mutants showed the presence of all three replicons in wild-type cells. Although chrI was present in all the ΔcisII and ΔcisMP cells, nearly half of these cells had chrII and MP, respectively, and the other half had the reduced number of foci representing these replications. These results suggested that cisII and cisMP elements contain both origin of replication and parS-like functions and the secondary genome replicons (chrII and MP) are maintained independent of chrI and have roles in radioresistance of D. radiodurans.
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Affiliation(s)
- Ganesh K Maurya
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India .,Homi Bhabha National Institute, Mumbai, India
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15
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Sperlea T, Muth L, Martin R, Weigel C, Waldminghaus T, Heider D. gammaBOriS: Identification and Taxonomic Classification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning. Sci Rep 2020; 10:6727. [PMID: 32317695 PMCID: PMC7174414 DOI: 10.1038/s41598-020-63424-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/31/2020] [Indexed: 01/23/2023] Open
Abstract
The biology of bacterial cells is, in general, based on information encoded on circular chromosomes. Regulation of chromosome replication is an essential process that mostly takes place at the origin of replication (oriC), a locus unique per chromosome. Identification of high numbers of oriC is a prerequisite for systematic studies that could lead to insights into oriC functioning as well as the identification of novel drug targets for antibiotic development. Current methods for identifying oriC sequences rely on chromosome-wide nucleotide disparities and are therefore limited to fully sequenced genomes, leaving a large number of genomic fragments unstudied. Here, we present gammaBOriS (Gammaproteobacterial oriC Searcher), which identifies oriC sequences on gammaproteobacterial chromosomal fragments. It does so by employing motif-based machine learning methods. Using gammaBOriS, we created BOriS DB, which currently contains 25,827 gammaproteobacterial oriC sequences from 1,217 species, thus making it the largest available database for oriC sequences to date. Furthermore, we present gammaBOriTax, a machine-learning based approach for taxonomic classification of oriC sequences, which was trained on the sequences in BOriS DB. Finally, we extracted the motifs relevant for identification and classification decisions of the models. Our results suggest that machine learning sequence classification approaches can offer great support in functional motif identification.
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Affiliation(s)
- Theodor Sperlea
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032, Marburg, Lahn, Germany
| | - Lea Muth
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032, Marburg, Lahn, Germany
| | - Roman Martin
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032, Marburg, Lahn, Germany
| | - Christoph Weigel
- Institute of Biotechnology, Faculty III, Technische Universität Berlin (TUB), Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Torsten Waldminghaus
- Chromosome Biology Group, LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35043, Marburg, Lahn, Germany
| | - Dominik Heider
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032, Marburg, Lahn, Germany.
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16
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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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17
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Abstract
While the model bacteria Escherichia coli and Bacillus subtilis harbor single chromosomes, which is known as monoploidy, some freshwater cyanobacteria contain multiple chromosome copies per cell throughout their cell cycle, which is known as polyploidy. In the model cyanobacteria Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803, chromosome copy number (ploidy) is regulated in response to growth phase and environmental factors. In S. elongatus 7942, chromosome replication is asynchronous both among cells and chromosomes. Comparative analysis of S. elongatus 7942 and S. sp. 6803 revealed a variety of DNA replication mechanisms. In this review, the current knowledge of ploidy and DNA replication mechanisms in cyanobacteria is summarized together with information on the features common with plant chloroplasts. It is worth noting that the occurrence of polyploidy and its regulation are correlated with certain cyanobacterial lifestyles and are shared between some cyanobacteria and chloroplasts. ABBREVIATIONS NGS: next-generation sequencing; Repli-seq: replication sequencing; BrdU: 5-bromo-2'-deoxyuridine; TK: thymidine kinase; GCSI: GC skew index; PET: photosynthetic electron transport; RET: respiration electron transport; Cyt b6f complex: cytochrome b6f complex; PQ: plastoquinone; PC: plastocyanin.
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Affiliation(s)
- Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture , Tokyo, Japan
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18
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Wang R, Lou J, Li J. A mobile restriction modification system consisting of methylases on the IncA/C plasmid. Mob DNA 2019; 10:26. [PMID: 31182978 PMCID: PMC6555945 DOI: 10.1186/s13100-019-0168-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/31/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND IncA/C plasmids play important roles in the development and dissemination of multidrug resistance in bacteria. These plasmids carry three methylase genes, two of which show cytosine specificity. The effects of such a plasmid on the host methylome were observed by single-molecule, real-time (SMRT) and bisulfite sequencing in this work. RESULTS The results showed that the numbers of methylation sites on the host chromosomes were changed, as were the sequences recognized by MTase. The host chromosomes were completely remodified by the plasmid with a methylation pattern different from that of the host itself. When the three dcm genes were deleted, the transferability of the plasmid into other Vibrio cholerae and Escherichia coli strains was lost. During deletion of the dcm genes, except for the wild-type strains and the targeted deletion strains, 18.7%~ 38.5% of the clones lost the IncA/C plasmid and changed from erythromycin-, azithromycin- and tetracycline-resistant strains to strains that were sensitive to these antibiotics. CONCLUSIONS Methylation of the IncA/C plasmid was a new mobile restriction modification (RM) barrier against foreign DNA. By actively changing the host's methylation pattern, the plasmid crossed the barrier of the host's RM system, and this might be the simplest and most universal method by which plasmids acquire a broad host range. Elimination of plasmids by destruction of plasmid stability could be a new effective strategy to address bacterial multidrug resistance.
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Affiliation(s)
- Ruibai Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206 People’s Republic of China
| | - Jing Lou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206 People’s Republic of China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206 People’s Republic of China
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19
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Characterisation of ParB encoded on multipartite genome in Deinococcus radiodurans and their roles in radioresistance. Microbiol Res 2019; 223-225:22-32. [DOI: 10.1016/j.micres.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/27/2019] [Accepted: 03/16/2019] [Indexed: 01/05/2023]
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20
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Kemter FS, Schallopp N, Sperlea T, Serrania J, Sobetzko P, Fritz G, Waldminghaus T. Stringent response leads to continued cell division and a temporal restart of DNA replication after initial shutdown in Vibrio cholerae. Mol Microbiol 2019; 111:1617-1637. [PMID: 30873684 DOI: 10.1111/mmi.14241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2019] [Indexed: 11/29/2022]
Abstract
Vibrio cholerae is an aquatic bacterium with the potential to infect humans and cause the cholera disease. While most bacteria have single chromosomes, the V. cholerae genome is encoded on two replicons of different size. This study focuses on the DNA replication and cell division of this bi-chromosomal bacterium during the stringent response induced by starvation stress. V. cholerae cells were found to initially shut DNA replication initiation down upon stringent response induction by the serine analog serine hydroxamate. Surprisingly, cells temporarily restart their DNA replication before finally reaching a state with fully replicated single chromosome sets. This division-replication pattern is very different to that of the related single chromosome model bacterium Escherichia coli. Within the replication restart phase, both chromosomes of V. cholerae maintained their known order of replication timing to achieve termination synchrony. Using flow cytometry combined with mathematical modeling, we established that a phase of cellular regrowth be the reason for the observed restart of DNA replication after the initial shutdown. Our study shows that although the stringent response induction itself is widely conserved, bacteria developed different ways of how to react to the sensed nutrient limitation, potentially reflecting their individual lifestyle requirements.
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Affiliation(s)
- 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
| | - Theodor Sperlea
- LOEWE Center for Synthetic Microbiology - SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Javier Serrania
- LOEWE Center for Synthetic Microbiology - SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology - SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Georg Fritz
- 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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21
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Marczynski GT, Petit K, Patel P. Crosstalk Regulation Between Bacterial Chromosome Replication and Chromosome Partitioning. Front Microbiol 2019; 10:279. [PMID: 30863373 PMCID: PMC6399470 DOI: 10.3389/fmicb.2019.00279] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 02/04/2019] [Indexed: 12/14/2022] Open
Abstract
Despite much effort, the bacterial cell cycle has proved difficult to study and understand. Bacteria do not conform to the standard eukaryotic model of sequential cell-cycle phases. Instead, for example, bacteria overlap their phases of chromosome replication and chromosome partitioning. In “eukaryotic terms,” bacteria simultaneously perform “S-phase” and “mitosis” whose coordination is absolutely required for rapid growth and survival. In this review, we focus on the signaling “crosstalk,” meaning the signaling mechanisms that advantageously commit bacteria to start both chromosome replication and chromosome partitioning. After briefly reviewing the molecular mechanisms of replication and partitioning, we highlight the crosstalk research from Bacillus subtilis, Vibrio cholerae, and Caulobacter crescentus. As the initiator of chromosome replication, DnaA also mediates crosstalk in each of these model bacteria but not always in the same way. We next focus on the C. crescentus cell cycle and describe how it is revealing novel crosstalk mechanisms. Recent experiments show that the novel nucleoid associated protein GapR has a special role(s) in starting and separating the replicating chromosomes, so that upon asymmetric cell division, the new chromosomes acquire different fates in C. crescentus’s distinct replicating and non-replicating cell types. The C. crescentus PopZ protein forms a special cell-pole organizing matrix that anchors the chromosomes through their centromere-like DNA sequences near the origin of replication. We also describe how PopZ anchors and interacts with several key cell-cycle regulators, thereby providing an organized subcellular environment for more novel crosstalk mechanisms.
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Affiliation(s)
- Gregory T Marczynski
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Kenny Petit
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Priya Patel
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
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22
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Chase J, Catalano A, Noble AJ, Eng ET, Olinares PD, Molloy K, Pakotiprapha D, Samuels M, Chait B, des Georges A, Jeruzalmi D. Mechanisms of opening and closing of the bacterial replicative helicase. eLife 2018; 7:41140. [PMID: 30582519 PMCID: PMC6391071 DOI: 10.7554/elife.41140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and closing of the helicase, which enable and restrict access to an internal chamber, are not known. Here, we investigate these mechanisms in the Escherichia coli DnaB helicase•bacteriophage λ helicase loader (λP) complex. We show that five copies of λP bind at DnaB subunit interfaces and reconfigure the helicase into an open spiral conformation that is intermediate to previously observed closed ring and closed spiral forms; reconfiguration also produces openings large enough to admit ssDNA into the inner chamber. The helicase is also observed in a restrained inactive configuration that poises it to close on activating signal, and transition to the translocation state. Our findings provide insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.
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Affiliation(s)
- Jillian Chase
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States
| | - Andrew Catalano
- Department of Chemistry and Biochemistry, City College of New York, New York, United States
| | - Alex J Noble
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Edward T Eng
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Paul Db Olinares
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Kelly Molloy
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Danaya Pakotiprapha
- Department of Biochemistry, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Martin Samuels
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Brian Chait
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Amedee des Georges
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Biology, The Graduate Center of the City University of New York, New York, United States
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23
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Bruhn M, Schindler D, Kemter FS, Wiley MR, Chase K, Koroleva GI, Palacios G, Sozhamannan S, Waldminghaus T. Functionality of Two Origins of Replication in Vibrio cholerae Strains With a Single Chromosome. Front Microbiol 2018; 9:2932. [PMID: 30559732 PMCID: PMC6284228 DOI: 10.3389/fmicb.2018.02932] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/14/2018] [Indexed: 12/16/2022] Open
Abstract
Chromosomal inheritance in bacteria usually entails bidirectional replication of a single chromosome from a single origin into two copies and subsequent partitioning of one copy each into daughter cells upon cell division. However, the human pathogen Vibrio cholerae and other Vibrionaceae harbor two chromosomes, a large Chr1 and a small Chr2. Chr1 and Chr2 have different origins, an oriC-type origin and a P1 plasmid-type origin, respectively, driving the replication of respective chromosomes. Recently, we described naturally occurring exceptions to the two-chromosome rule of Vibrionaceae: i.e., Chr1 and Chr2 fused single chromosome V. cholerae strains, NSCV1 and NSCV2, in which both origins of replication are present. Using NSCV1 and NSCV2, here we tested whether two types of origins of replication can function simultaneously on the same chromosome or one or the other origin is silenced. We found that in NSCV1, both origins are active whereas in NSCV2 ori2 is silenced despite the fact that it is functional in an isolated context. The ori2 activity appears to be primarily determined by the copy number of the triggering site, crtS, which in turn is determined by its location with respect to ori1 and ori2 on the fused chromosome.
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Affiliation(s)
- Matthias Bruhn
- LOEWE Centre for Synthetic Microbiology-SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Daniel Schindler
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Franziska S Kemter
- LOEWE Centre for Synthetic Microbiology-SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Michael R Wiley
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Kitty Chase
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Galina I Koroleva
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Frederick, MD, United States.,The Tauri Group, LLC, Alexandria, VA, United States
| | - Torsten Waldminghaus
- LOEWE Centre for Synthetic Microbiology-SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
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24
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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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25
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Abstract
The causes and consequences of spatiotemporal variation in mutation rates remain to be explored in nearly all organisms. Here we examine relationships between local mutation rates and replication timing in three bacterial species whose genomes have multiple chromosomes: Vibrio fischeri, Vibrio cholerae, and Burkholderia cenocepacia. Following five mutation accumulation experiments with these bacteria conducted in the near absence of natural selection, the genomes of clones from each lineage were sequenced and analyzed to identify variation in mutation rates and spectra. In lineages lacking mismatch repair, base substitution mutation rates vary in a mirrored wave-like pattern on opposing replichores of the large chromosomes of V. fischeri and V. cholerae, where concurrently replicated regions experience similar base substitution mutation rates. The base substitution mutation rates on the small chromosome are less variable in both species but occur at similar rates to those in the concurrently replicated regions of the large chromosome. Neither nucleotide composition nor frequency of nucleotide motifs differed among regions experiencing high and low base substitution rates, which along with the inferred ~800-kb wave period suggests that the source of the periodicity is not sequence specific but rather a systematic process related to the cell cycle. These results support the notion that base substitution mutation rates are likely to vary systematically across many bacterial genomes, which exposes certain genes to elevated deleterious mutational load. That mutation rates vary within bacterial genomes is well known, but the detailed study of these biases has been made possible only recently with contemporary sequencing methods. We applied these methods to understand how bacterial genomes with multiple chromosomes, like those of Vibrio and Burkholderia, might experience heterogeneous mutation rates because of their unusual replication and the greater genetic diversity found on smaller chromosomes. This study captured thousands of mutations and revealed wave-like rate variation that is synchronized with replication timing and not explained by sequence context. The scale of this rate variation over hundreds of kilobases of DNA strongly suggests that a temporally regulated cellular process may generate wave-like variation in mutation risk. These findings add to our understanding of how mutation risk is distributed across bacterial and likely also eukaryotic genomes, owing to their highly conserved replication and repair machinery.
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26
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Fournes F, Val ME, Skovgaard O, Mazel D. Replicate Once Per Cell Cycle: Replication Control of Secondary Chromosomes. Front Microbiol 2018; 9:1833. [PMID: 30131796 PMCID: PMC6090056 DOI: 10.3389/fmicb.2018.01833] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/23/2018] [Indexed: 12/13/2022] Open
Abstract
Faithful vertical transmission of genetic information, especially of essential core genes, is a prerequisite for bacterial survival. Hence, replication of all the replicons is tightly controlled to ensure that all daughter cells get the same genome copy as their mother cell. Essential core genes are very often carried by the main chromosome. However they can occasionally be found on secondary chromosomes, recently renamed chromids. Chromids have evolved from non-essential megaplasmids, and further acquired essential core genes and a genomic signature closed to that of the main chromosome. All chromids carry a plasmidic replication origin, belonging so far to either the iterons or repABC type. Based on these differences, two categories of chromids have been distinguished. In this review, we focus on the replication initiation controls of these two types of chromids. We show that the sophisticated mechanisms controlling their replication evolved from their plasmid counterparts to allow a timely controlled replication, occurring once per cell cycle.
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Affiliation(s)
- Florian Fournes
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, Paris, France
| | - Marie-Eve Val
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, Paris, France
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Didier Mazel
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, Paris, France
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27
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Hagemann M, Gärtner K, Scharnagl M, Bolay P, Lott SC, Fuss J, Huettel B, Reinhardt R, Klähn S, Hess WR. Identification of the DNA methyltransferases establishing the methylome of the cyanobacterium Synechocystis sp. PCC 6803. DNA Res 2018; 25:343-352. [PMID: 29444255 PMCID: PMC6105098 DOI: 10.1093/dnares/dsy006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/24/2018] [Indexed: 11/12/2022] Open
Abstract
DNA methylation in bacteria is important for defense against foreign DNA, but is also involved in DNA repair, replication, chromosome partitioning, and regulatory processes. Thus, characterization of the underlying DNA methyltransferases in genetically tractable bacteria is of paramount importance. Here, we characterized the methylome and orphan methyltransferases in the model cyanobacterium Synechocystis sp. PCC 6803. Single molecule real-time (SMRT) sequencing revealed four DNA methylation recognition sequences in addition to the previously known motif m5CGATCG, which is recognized by M.Ssp6803I. For three of the new recognition sequences, we identified the responsible methyltransferases. M.Ssp6803II, encoded by the sll0729 gene, modifies GGm4CC, M.Ssp6803III, encoded by slr1803, represents the cyanobacterial dam-like methyltransferase modifying Gm6ATC, and M.Ssp6803V, encoded by slr6095 on plasmid pSYSX, transfers methyl groups to the bipartite motif GGm6AN7TTGG/CCAm6AN7TCC. The remaining methylation recognition sequence GAm6AGGC is probably recognized by methyltransferase M.Ssp6803IV encoded by slr6050. M.Ssp6803III and M.Ssp6803IV were essential for the viability of Synechocystis, while the strains lacking M.Ssp6803I and M.Ssp6803V showed growth similar to the wild type. In contrast, growth was strongly diminished of the Δsll0729 mutant lacking M.Ssp6803II. These data provide the basis for systematic studies on the molecular mechanisms impacted by these methyltransferases.
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Affiliation(s)
- Martin Hagemann
- Institute of Biosciences, Plant Physiology, University of Rostock, Rostock, Germany
| | - Katrin Gärtner
- Institute of Biosciences, Plant Physiology, University of Rostock, Rostock, Germany
| | - Matthias Scharnagl
- Institute of Biosciences, Plant Physiology, University of Rostock, Rostock, Germany
| | - Paul Bolay
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Steffen C Lott
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Janina Fuss
- Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Bruno Huettel
- Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Richard Reinhardt
- Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Stephan Klähn
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Wolfgang R Hess
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Freiburg Institute for Advanced Studies, University of Freiburg, Germany
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28
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Ramachandran R, Ciaccia PN, Filsuf TA, Jha JK, Chattoraj DK. Chromosome 1 licenses chromosome 2 replication in Vibrio cholerae by doubling the crtS gene dosage. PLoS Genet 2018; 14:e1007426. [PMID: 29795553 PMCID: PMC5991422 DOI: 10.1371/journal.pgen.1007426] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/06/2018] [Accepted: 05/17/2018] [Indexed: 12/20/2022] Open
Abstract
Initiation of chromosome replication in bacteria is precisely timed in the cell cycle. Bacteria that harbor multiple chromosomes face the additional challenge of orchestrating replication initiation of different chromosomes. In Vibrio cholerae, the smaller of its two chromosomes, Chr2, initiates replication after Chr1 such that both chromosomes terminate replication synchronously. The delay is due to the dependence of Chr2 initiation on the replication of a site, crtS, on Chr1. The mechanism by which replication of crtS allows Chr2 replication remains unclear. Here, we show that blocking Chr1 replication indeed blocks Chr2 replication, but providing an extra crtS copy in replication-blocked Chr1 permitted Chr2 replication. This demonstrates that unreplicated crtS copies have significant activity, and suggests that a role of replication is to double the copy number of the site that sufficiently increases its activity for licensing Chr2 replication. We further show that crtS activity promotes the Chr2-specific initiator function and that this activity is required in every cell cycle, as would be expected of a cell-cycle regulator. This study reveals how increase of gene dosage through replication can be utilized in a critical regulatory switch.
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Affiliation(s)
- Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter N. Ciaccia
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tara A. Filsuf
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jyoti K. Jha
- 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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29
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Myka KK, McGlynn P, Ferguson GP. Insights into the initiation of chromosome II replication of the pressure-loving deep-sea bacterium Photobacterium profundum SS9. MICROBIOLOGY-SGM 2018; 164:920-933. [PMID: 29757128 DOI: 10.1099/mic.0.000663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
How DNA metabolism is adapted to survival of organisms such as the bacterium Photobacterium profundum SS9 at high pressure is unknown. Previously, a high pressure-sensitive P. profundum SS9 transposon mutant (FL31) was identified, with an insertion in a putative rctB gene. The Vibrio cholerae RctB protein is essential for replication initiation at the origin of chromosome II, oriCII. Using a plasmid-based system in E. coli we have identified the replication origin of chromosome II from P. profundum SS9 and have shown that the putative rctB gene, disrupted in FL31, is essential for oriCII function. Moreover, we found that a region corresponding to the V. cholerae oriCII incompatibility region (incII) exerts an inhibitory effect on P. profundum oriCII. The truncated rctB gene in FL31 confers insensitivity to incII inhibition, indicating that the C-terminus of RctB is important for the negative regulation of replication. The RctB proteins of V. cholerae and P. profundum are partially interchangeable, but full functionality is achieved only with the cognate origin. Our findings provide the first characterization of the replication origin of chromosome II in a deep-sea bacterium.
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Affiliation(s)
- Kamila K Myka
- Present address: Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Peter McGlynn
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.,Present address: Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Gail P Ferguson
- School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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30
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Kemter FS, Messerschmidt SJ, Schallopp N, Sobetzko P, Lang E, Bunk B, Spröer C, Teschler JK, Yildiz FH, Overmann J, Waldminghaus T. Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae. PLoS Genet 2018; 14:e1007251. [PMID: 29505558 PMCID: PMC5854411 DOI: 10.1371/journal.pgen.1007251] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/15/2018] [Accepted: 02/13/2018] [Indexed: 11/18/2022] Open
Abstract
Vibrio cholerae, the causative agent of the cholera disease, is commonly used as a model organism for the study of bacteria with multipartite genomes. Its two chromosomes of different sizes initiate their DNA replication at distinct time points in the cell cycle and terminate in synchrony. In this study, the time-delayed start of Chr2 was verified in a synchronized cell population. This replication pattern suggests two possible regulation mechanisms for other Vibrio species with different sized secondary chromosomes: Either all Chr2 start DNA replication with a fixed delay after Chr1 initiation, or the timepoint at which Chr2 initiates varies such that termination of chromosomal replication occurs in synchrony. We investigated these two models and revealed that the two chromosomes of various Vibrionaceae species terminate in synchrony while Chr2-initiation timing relative to Chr1 is variable. Moreover, the sequence and function of the Chr2-triggering crtS site recently discovered in V. cholerae were found to be conserved, explaining the observed timing mechanism. Our results suggest that it is beneficial for bacterial cells with multiple chromosomes to synchronize their replication termination, potentially to optimize chromosome related processes as dimer resolution or segregation.
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Affiliation(s)
- Franziska S. Kemter
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Sonja J. Messerschmidt
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Nadine Schallopp
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Elke Lang
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jennifer K. Teschler
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States of America
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States of America
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Centre of Infection Research (DZIF), Partner Site Hannover–Braunschweig, Braunschweig, Germany
| | - Torsten Waldminghaus
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
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31
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Establishing a System for Testing Replication Inhibition of the Vibrio cholerae Secondary Chromosome in Escherichia coli. Antibiotics (Basel) 2017; 7:antibiotics7010003. [PMID: 29295515 PMCID: PMC5872114 DOI: 10.3390/antibiotics7010003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/05/2017] [Accepted: 12/20/2017] [Indexed: 12/29/2022] Open
Abstract
Regulators of DNA replication in bacteria are an attractive target for new antibiotics, as not only is replication essential for cell viability, but its underlying mechanisms also differ from those operating in eukaryotes. The genetic information of most bacteria is encoded on a single chromosome, but about 10% of species carry a split genome spanning multiple chromosomes. The best studied bacterium in this context is the human pathogen Vibrio cholerae, with a primary chromosome (Chr1) of 3 M bps, and a secondary one (Chr2) of about 1 M bps. Replication of Chr2 is under control of a unique mechanism, presenting a potential target in the development of V. cholerae-specific antibiotics. A common challenge in such endeavors is whether the effects of candidate chemicals can be focused on specific mechanisms, such as DNA replication. To test the specificity of antimicrobial substances independent of other features of the V. cholerae cell for the replication mechanism of the V. cholerae secondary chromosome, we establish the replication machinery in the heterologous E. coli system. We characterize an E. coli strain in which chromosomal replication is driven by the replication origin of V. cholerae Chr2. Surprisingly, the E. coli ori2 strain was not inhibited by vibrepin, previously found to inhibit ori2-based replication.
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32
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diCenzo GC, Finan TM. The Divided Bacterial Genome: Structure, Function, and Evolution. Microbiol Mol Biol Rev 2017; 81:e00019-17. [PMID: 28794225 PMCID: PMC5584315 DOI: 10.1128/mmbr.00019-17] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure.
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Affiliation(s)
- George C diCenzo
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Turlough M Finan
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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33
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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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34
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Orlova N, Gerding M, Ivashkiv O, Olinares PDB, Chait BT, Waldor MK, Jeruzalmi D. The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators. Nucleic Acids Res 2017; 45:3724-3737. [PMID: 28031373 PMCID: PMC5397143 DOI: 10.1093/nar/gkw1288] [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: 10/21/2016] [Accepted: 12/18/2016] [Indexed: 01/23/2023] Open
Abstract
The conserved DnaA-oriC system is used to initiate replication of primary chromosomes throughout the bacterial kingdom; however, bacteria with multipartite genomes evolved distinct systems to initiate replication of secondary chromosomes. In the cholera pathogen, Vibrio cholerae, and in related species, secondary chromosome replication requires the RctB initiator protein. Here, we show that RctB consists of four domains. The structure of its central two domains resembles that of several plasmid replication initiators. RctB contains at least three DNA binding winged-helix-turn-helix motifs, and mutations within any of these severely compromise biological activity. In the structure, RctB adopts a head-to-head dimeric configuration that likely reflects the arrangement in solution. Therefore, major structural reorganization likely accompanies complex formation on the head-to-tail array of binding sites in oriCII. Our findings support the hypothesis that the second Vibrionaceae chromosome arose from an ancestral plasmid, and that RctB may have evolved additional regulatory features.
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Affiliation(s)
- Natalia Orlova
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, NY 10016, USA
| | - Matthew Gerding
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Olha Ivashkiv
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA
| | - Paul Dominic B Olinares
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, NY 10021, USA
| | - Brian T Chait
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, NY 10021, USA
| | - Matthew K Waldor
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, NY 10016, USA.,Ph.D. Program in Biology, The Graduate Center of the City University of New York, NY 10016, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, NY 10016, USA
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35
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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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36
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Control of bacterial chromosome replication by non-coding regions outside the origin. Curr Genet 2016; 63:607-611. [PMID: 27942832 DOI: 10.1007/s00294-016-0671-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/01/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
Abstract
Chromosome replication in Eubacteria is initiated by initiator protein(s) binding to specific sites within the replication origin, oriC. Recently, initiator protein binding to chromosomal regions outside the origin has attracted renewed attention; as such binding sites contribute to control the frequency of initiations. These outside-oriC binding sites function in several different ways: by steric hindrances of replication fork assembly, by titration of initiator proteins away from the origin, by performing a chaperone-like activity for inactivation- or activation of initiator proteins or by mediating crosstalk between chromosomes. Here, we discuss initiator binding to outside-oriC sites in a broad range of different taxonomic groups, to highlight the significance of such regions for regulation of bacterial chromosome replication. For Escherichia coli, it was recently shown that the genomic positions of regulatory elements are important for bacterial fitness, which, as we discuss, could be true for several other organisms.
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37
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Random versus Cell Cycle-Regulated Replication Initiation in Bacteria: Insights from Studying Vibrio cholerae Chromosome 2. Microbiol Mol Biol Rev 2016; 81:81/1/e00033-16. [PMID: 27903655 DOI: 10.1128/mmbr.00033-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial chromosomes initiate replication at a fixed time in the cell cycle, whereas there is generally no particular time for plasmid replication initiation or chromosomal replication initiation from integrated plasmids. In bacteria with divided genomes, the replication system of one of the chromosomes typically resembles that of bacteria with undivided genomes, whereas the remaining chromosomes have plasmid-like replication systems. For example, in Vibrio cholerae, a bacterium with two chromosomes (chromosome 1 [Chr1] and Chr2), the Chr1 system resembles that of the Escherichia coli chromosome, and the Chr2 system resembles that of iteron-based plasmids. However, Chr2 still initiates replication at a fixed time in the cell cycle and thus offers an opportunity to understand the molecular basis for the difference between random and cell cycle-regulated modes of replication. Here we review studies of replication control in Chr2 and compare it to those of plasmids and chromosomes. We argue that although the Chr2 control mechanisms in many ways are reminiscent of those of plasmids, they also appear to combine more regulatory features than are found on a typical plasmid, including some that are more typical of chromosomes. One of the regulatory mechanisms is especially novel, the coordinated timing of replication initiation of Chr1 and Chr2, providing the first example of communication between chromosomes for replication initiation.
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38
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Milbredt S, Farmani N, Sobetzko P, Waldminghaus T. DNA Replication in Engineered Escherichia coli Genomes with Extra Replication Origins. ACS Synth Biol 2016; 5:1167-1176. [PMID: 27268399 DOI: 10.1021/acssynbio.6b00064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The standard outline of bacterial genomes is a single circular chromosome with a single replication origin. From the bioengineering perspective, it appears attractive to extend this basic setup. Bacteria with split chromosomes or multiple replication origins have been successfully constructed in the last few years. The characteristics of these engineered strains will largely depend on the respective DNA replication patterns. However, the DNA replication has not been investigated systematically in engineered bacteria with multiple origins or split replicons. Here we fill this gap by studying a set of strains consisting of (i) E. coli strains with an extra copy of the native replication origin (oriC), (ii) E. coli strains with an extra copy of the replication origin from the secondary chromosome of Vibrio cholerae (oriII), and (iii) a strain in which the E. coli chromosome is split into two linear replicons. A combination of flow cytometry, microarray-based comparative genomic hybridization (CGH), and modeling revealed silencing of extra oriC copies and differential timing of ectopic oriII copies compared to the native oriC. The results were used to derive construction rules for future multiorigin and multireplicon projects.
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Affiliation(s)
- Sarah Milbredt
- LOEWE Center for Synthetic
Microbiology, SYNMIKRO, Philipps-University, Marburg, Hans-Meerwein-Strasse 6, D-35043 Marburg, Germany
| | - Neda Farmani
- LOEWE Center for Synthetic
Microbiology, SYNMIKRO, Philipps-University, Marburg, Hans-Meerwein-Strasse 6, D-35043 Marburg, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic
Microbiology, SYNMIKRO, Philipps-University, Marburg, Hans-Meerwein-Strasse 6, D-35043 Marburg, Germany
| | - Torsten Waldminghaus
- LOEWE Center for Synthetic
Microbiology, SYNMIKRO, Philipps-University, Marburg, Hans-Meerwein-Strasse 6, D-35043 Marburg, Germany
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39
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Dillon MM, Sung W, Sebra R, Lynch M, Cooper VS. Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri. Mol Biol Evol 2016; 34:93-109. [PMID: 27744412 PMCID: PMC5854121 DOI: 10.1093/molbev/msw224] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera, Vibrio cholerae Here, we present the genome-wide mutation spectra in wild-type and mismatch repair (MMR) defective backgrounds of two Vibrio species, the low-%GC squid symbiont V. fischeri and the pathogen V. cholerae, collected under conditions that greatly minimize the efficiency of natural selection. In apparent contrast to their high diversity in nature, both wild-type V. fischeri and V. cholerae have among the lowest rates for base-substitution mutations (bpsms) and insertion-deletion mutations (indels) that have been measured, below 10-3/genome/generation. Vibrio fischeri and V. cholerae have distinct mutation spectra, but both are AT-biased and produce a surprising number of multi-nucleotide indels. Furthermore, the loss of a functional MMR system caused the mutation spectra of these species to converge, implying that the MMR system itself contributes to species-specific mutation patterns. Bpsm and indel rates varied among genome regions, but do not explain the more rapid evolutionary rates of genes on chromosome 2, which likely result from weaker purifying selection. More generally, the very low mutation rates of Vibrio species correlate inversely with their immense population sizes and suggest that selection may not only have maximized replication fidelity but also optimized other polygenic traits relative to the constraints of genetic drift.
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Affiliation(s)
- Marcus M Dillon
- Microbiology Graduate Program, University of New Hampshire, Durham, NH
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, Charlotte, NC.,Department of Biology, Indiana University, Bloomington, IN
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
| | - Vaughn S Cooper
- Microbiology Graduate Program, University of New Hampshire, Durham, NH .,Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
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Zhou J, Wu R, Xue X, Qin Z. CasHRA (Cas9-facilitated Homologous Recombination Assembly) method of constructing megabase-sized DNA. Nucleic Acids Res 2016; 44:e124. [PMID: 27220470 PMCID: PMC5001600 DOI: 10.1093/nar/gkw475] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/22/2016] [Accepted: 05/11/2016] [Indexed: 01/01/2023] Open
Abstract
Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated 'CasHRA (Cas9-facilitated Homologous Recombination Assembly)' that directly uses large circular DNAs in a one-step in vivo assembly process. The large circular DNAs are co-introduced into Saccharomyces cerevisiae by protoplast fusion, and they are cleaved by RNA-guided Cas9 nuclease to release the linear DNA segments for subsequent assembly by the endogenous homologous recombination system. The CasHRA method allows efficient assembly of multiple large DNA segments in vivo; thus, this approach should be useful in the last stage of genome construction. As a proof of concept, we combined CasHRA with an upstream assembly method (Gibson procedure of genome assembly) and successfully constructed a 1.03 Mb MGE-syn1.0 (Minimal Genome of Escherichia coli) that contained 449 essential genes and 267 important growth genes. We expect that CasHRA will be widely used in megabase-sized genome constructions.
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Affiliation(s)
- Jianting Zhou
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ronghai Wu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoli Xue
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhongjun Qin
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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41
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Adhikari S, Curtis PD. DNA methyltransferases and epigenetic regulation in bacteria. FEMS Microbiol Rev 2016; 40:575-91. [PMID: 27476077 DOI: 10.1093/femsre/fuw023] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 12/21/2022] Open
Abstract
Epigenetics is a change in gene expression that is heritable without a change in DNA sequence itself. This phenomenon is well studied in eukaryotes, particularly in humans for its role in cellular differentiation, X chromosome inactivation and diseases like cancer. However, comparatively little is known about epigenetic regulation in bacteria. Bacterial epigenetics is mainly present in the form of DNA methylation where DNA methyltransferases add methyl groups to nucleotides. This review focuses on two methyltransferases well characterized for their roles in gene regulation: Dam and CcrM. Dam methyltransferase in Escherichia coli is important for expression of certain genes such as the pap operon, as well as other cellular processes like DNA replication initiation and DNA repair. In Caulobacter crescentus and other Alphaproteobacteria, the methyltransferase CcrM is cell cycle regulated and is involved in the cell-cycle-dependent regulation of several genes. The diversity of regulatory targets as well as regulatory mechanisms suggests that gene regulation by methylation could be a widespread and potent method of regulation in bacteria.
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Affiliation(s)
- Satish Adhikari
- Department of Biology, University of Mississippi, University, MS 38677, USA
| | - Patrick D Curtis
- Department of Biology, University of Mississippi, University, MS 38677, USA
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Abstract
The initiation of chromosomal DNA replication starts at a replication origin, which in bacteria is a discrete locus that contains DNA sequence motifs recognized by an initiator protein whose role is to assemble the replication fork machinery at this site. In bacteria with a single chromosome, DnaA is the initiator and is highly conserved in all bacteria. As an adenine nucleotide binding protein, DnaA bound to ATP is active in the assembly of a DnaA oligomer onto these sites. Other proteins modulate DnaA oligomerization via their interaction with the N-terminal region of DnaA. Following the DnaA-dependent unwinding of an AT-rich region within the replication origin, DnaA then mediates the binding of DnaB, the replicative DNA helicase, in a complex with DnaC to form an intermediate named the prepriming complex. In the formation of this intermediate, the helicase is loaded onto the unwound region within the replication origin. As DnaC bound to DnaB inhibits its activity as a DNA helicase, DnaC must dissociate to activate DnaB. Apparently, the interaction of DnaB with primase (DnaG) and primer formation leads to the release of DnaC from DnaB, which is coordinated with or followed by translocation of DnaB to the junction of the replication fork. There, DnaB is able to coordinate its activity as a DNA helicase with the cellular replicase, DNA polymerase III holoenzyme, which uses the primers made by primase for leading strand DNA synthesis.
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Affiliation(s)
- S Chodavarapu
- Michigan State University, East Lansing, MI, United States
| | - J M Kaguni
- Michigan State University, East Lansing, MI, United States.
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Abstract
The DNA of Escherichia coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases, and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during the repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and the regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation, although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential, and, in C. crescentus, it is important for temporal gene expression, which, in turn, is required for coordinating chromosome initiation, replication, and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage, decrease transformation frequency in certain bacteria, and decrease the stability of short direct repeats and are necessary for site-directed mutagenesis and to probe eukaryotic structure and function.
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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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Holm KO, Nilsson K, Hjerde E, Willassen NP, Milton DL. Complete genome sequence of Vibrio anguillarum strain NB10, a virulent isolate from the Gulf of Bothnia. Stand Genomic Sci 2015; 10:60. [PMID: 26380645 PMCID: PMC4572688 DOI: 10.1186/s40793-015-0060-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 08/17/2015] [Indexed: 11/12/2022] Open
Abstract
Vibrio anguillarum causes a fatal hemorrhagic septicemia in marine fish that leads to great economical losses in aquaculture world-wide. Vibrio anguillarum strain NB10 serotype O1 is a Gram-negative, motile, curved rod-shaped bacterium, isolated from a diseased fish on the Swedish coast of the Gulf of Bothnia, and is slightly halophilic. Strain NB10 is a virulent isolate that readily colonizes fish skin and intestinal tissues. Here, the features of this bacterium are described and the annotation and analysis of its complete genome sequence is presented. The genome is 4,373,835 bp in size, consists of two circular chromosomes and one plasmid, and contains 3,783 protein-coding genes and 129 RNA genes.
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Affiliation(s)
- Kåre Olav Holm
- />Department of Chemistry, Faculty of Science and Technology, UiT: The Arctic University of Norway, 9037 Tromsø, NO Norway
| | - Kristina Nilsson
- />Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Department of Molecular Biology, 901 87 Umeå, SE Sweden
| | - Erik Hjerde
- />Department of Chemistry, Faculty of Science and Technology, UiT: The Arctic University of Norway, 9037 Tromsø, NO Norway
| | - Nils-Peder Willassen
- />Department of Chemistry, Faculty of Science and Technology, UiT: The Arctic University of Norway, 9037 Tromsø, NO Norway
| | - Debra L. Milton
- />Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Department of Molecular Biology, 901 87 Umeå, SE Sweden
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Molecular Dissection of the Essential Features of the Origin of Replication of the Second Vibrio cholerae Chromosome. mBio 2015. [PMID: 26220967 PMCID: PMC4551981 DOI: 10.1128/mbio.00973-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Vibrionaceae family members are interesting models for studying DNA replication initiation, as they contain two circular chromosomes. Chromosome II (chrII) replication is governed by two evolutionarily unique yet highly conserved elements, the origin DNA sequence oriCII and the initiator protein RctB. The minimum functional region of oriCII, oriCII-min, contains multiple elements that are bound by RctB in vitro, but little is known about the specific requirements for individual elements during oriCII initiation. We utilized undirected and site-specific mutagenesis to investigate the functionality of mutant forms of oriCII-min and assessed binding to various mutant forms by RctB. Our analyses showed that deletions, point mutations, and changes in RctB target site spacing or methylation all impaired oriCII-min-based replication. RctB displayed a reduced affinity for most of the low-efficacy origins tested, although its characteristic cooperative binding was generally maintained. Mutations that removed or altered the relative positions of origin components other than RctB binding sites (e.g., AT-rich sequence, DnaA target site) also abolished replicative capacity. Comprehensive mutagenesis and deep-sequencing-based screening (OriSeq) allowed the identification of a previously uncharacterized methylated domain in oriCII that is required for origin function. Together, our results reveal the remarkable evolutionary honing of oriCII and provide new insight into the complex interplay between RctB and oriCII. The genome of the enteric pathogen Vibrio cholerae consists of two chromosomes. While the chromosome I replication origin and its cognate replication initiator protein resemble those of Escherichia coli, the factors responsible for chromosome II replication initiation display no similarity to any other known initiation systems. Here, to enhance our understanding of how this DNA sequence, oriCII, and its initiator protein, RctB, function, we used both targeted mutagenesis and a new random-mutagenesis approach (OriSeq) to finely map the oriCII structural features and sequences required for RctB-mediated DNA replication. Collectively, our findings reveal the extraordinary evolutionary honing of the architecture and motifs that constitute oriCII and reveal a new role for methylation in oriCII-based replication. Finally, our findings suggest that the OriSeq approach is likely to be widely applicable for defining critical bases in cis-acting sequences.
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47
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Schindler D, Waldminghaus T. Synthetic chromosomes. FEMS Microbiol Rev 2015; 39:871-91. [DOI: 10.1093/femsre/fuv030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
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Marczynski GT, Rolain T, Taylor JA. Redefining bacterial origins of replication as centralized information processors. Front Microbiol 2015; 6:610. [PMID: 26136739 PMCID: PMC4468827 DOI: 10.3389/fmicb.2015.00610] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/02/2015] [Indexed: 01/06/2023] Open
Abstract
In this review we stress the differences between eukaryotes and bacteria with respect to their different cell cycles, replication mechanisms and genome organizations. One of the most basic and underappreciated differences is that a bacterial chromosome uses only one ori while eukaryotic chromosome uses multiple oris. Consequently, eukaryotic oris work redundantly in a cell cycle divided into separate phases: First inactive replication proteins assemble on eukaryotic oris, and then they await conditions (in the separate “S-phase”) that activate only the ori-bound and pre-assembled replication proteins. S-phase activation (without re-assembly) ensures that a eukaryotic ori “fires” (starts replication) only once and that each chromosome consistently duplicates only once per cell cycle. This precise chromosome duplication does not require precise multiple ori firing in S-phase. A eukaryotic ori can fire early, late or not at all. The single bacterial ori has no such margin for error and a comparable imprecision is lethal. Single ori usage is not more primitive; it is a totally different strategy that distinguishes bacteria. We further argue that strong evolutionary pressures created more sophisticated single ori systems because bacteria experience extreme and rapidly changing conditions. A bacterial ori must rapidly receive and process much information in “real-time” and not just in “cell cycle time.” This redefinition of bacterial oris as centralized information processors makes at least two important predictions: First that bacterial oris use many and yet to be discovered control mechanisms and second that evolutionarily distinct bacteria will use many very distinct control mechanisms. We review recent literature that supports both predictions. We will highlight three key examples and describe how negative-feedback, phospho-relay, and chromosome-partitioning systems act to regulate chromosome replication. We also suggest future studies and discuss using replication proteins as novel antibiotic targets.
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Affiliation(s)
- Gregory T Marczynski
- Department of Microbiology and Immunology, McGill University , Montreal, QC, Canada
| | - Thomas Rolain
- Department of Microbiology and Immunology, McGill University , Montreal, QC, Canada
| | - James A Taylor
- Department of Microbiology and Immunology, McGill University , Montreal, QC, Canada
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Hua ZG, Lin Y, Yuan YZ, Yang DC, Wei W, Guo FB. ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes. Nucleic Acids Res 2015; 43:W85-90. [PMID: 25977299 PMCID: PMC4489317 DOI: 10.1093/nar/gkv491] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/02/2015] [Indexed: 01/09/2023] Open
Abstract
In 2003, we developed an ab initio program, ZCURVE 1.0, to find genes in bacterial and archaeal genomes. In this work, we present the updated version (i.e. ZCURVE 3.0). Using 422 prokaryotic genomes, the average accuracy was 93.7% with the updated version, compared with 88.7% with the original version. Such results also demonstrate that ZCURVE 3.0 is comparable with Glimmer 3.02 and may provide complementary predictions to it. In fact, the joint application of the two programs generated better results by correctly finding more annotated genes while also containing fewer false-positive predictions. As the exclusive function, ZCURVE 3.0 contains one post-processing program that can identify essential genes with high accuracy (generally >90%). We hope ZCURVE 3.0 will receive wide use with the web-based running mode. The updated ZCURVE can be freely accessed from http://cefg.uestc.edu.cn/zcurve/ or http://tubic.tju.edu.cn/zcurveb/ without any restrictions.
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Affiliation(s)
- Zhi-Gang Hua
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yan Lin
- Department of Physics, Tianjin University, Tianjin 300072, China Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin 300072, China Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Ya-Zhou Yuan
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - De-Chang Yang
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wen Wei
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Feng-Biao Guo
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in BioMedicine, University of Electronic Science and Technology of China, Chengdu 610054, China Health Big Data Science Research Center, Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
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The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes. Proc Natl Acad Sci U S A 2015; 112:10185-91. [PMID: 25944937 DOI: 10.1073/pnas.1421397112] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Across eukaryotes, mitochondria exhibit staggering diversity in genomic architecture, including the repeated evolution of multichromosomal structures. Unlike in the nucleus, where mitosis and meiosis ensure faithful transmission of chromosomes, the mechanisms of inheritance in fragmented mitochondrial genomes remain mysterious. Multichromosomal mitochondrial genomes have recently been found in multiple species of flowering plants, including Silene noctiflora, which harbors an unusually large and complex mitochondrial genome with more than 50 circular-mapping chromosomes totaling ∼7 Mb in size. To determine the extent to which such genomes are stably maintained, we analyzed intraspecific variation in the mitochondrial genome of S. noctiflora. Complete genomes from two populations revealed a high degree of similarity in the sequence, structure, and relative abundance of mitochondrial chromosomes. For example, there are no inversions between the genomes, and there are only nine SNPs in 25 kb of protein-coding sequence. Remarkably, however, these genomes differ in the presence or absence of 19 entire chromosomes, all of which lack any identifiable genes or contain only duplicate gene copies. Thus, these mitochondrial genomes retain a full gene complement but carry a highly variable set of chromosomes that are filled with presumably dispensable sequence. In S. noctiflora, conventional mechanisms of mitochondrial sequence divergence are being outstripped by an apparently nonadaptive process of whole-chromosome gain/loss, highlighting the inherent challenge in maintaining a fragmented genome. We discuss the implications of these findings in relation to the question of why mitochondria, more so than plastids and bacterial endosymbionts, are prone to the repeated evolution of multichromosomal genomes.
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