1
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Wagner M, Döhlemann J, Geisel D, Sobetzko P, Serrania J, Lenz P, Becker A. Engineering a Sinorhizobium meliloti Chassis with Monopartite, Single Replicon Genome Configuration. ACS Synth Biol 2024; 13:2515-2532. [PMID: 39109796 DOI: 10.1021/acssynbio.4c00281] [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: 08/17/2024]
Abstract
Multipartite bacterial genomes pose challenges for genome engineering and the establishment of additional replicons. We simplified the tripartite genome structure (3.65 Mbp chromosome, 1.35 Mbp megaplasmid pSymA, 1.68 Mbp chromid pSymB) of the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Strains with bi- and monopartite genome configurations were generated by targeted replicon fusions. Our design preserved key genomic features such as replichore ratios, GC skew, KOPS, and coding sequence distribution. Under standard culture conditions, the growth rates of these strains and the wild type were nearly comparable, and the ability for symbiotic nitrogen fixation was maintained. Spatiotemporal replicon organization and segregation were maintained in the triple replicon fusion strain. Deletion of the replication initiator-encoding genes, including the oriVs of pSymA and pSymB from this strain, resulted in a monopartite genome with oriC as the sole origin of replication, a strongly unbalanced replichore ratio, slow growth, aberrant cellular localization of oriC, and deficiency in symbiosis. Suppressor mutation R436H in the cell cycle histidine kinase CckA and a 3.2 Mbp inversion, both individually, largely restored growth, but only the genomic rearrangement recovered the symbiotic capacity. These strains will facilitate the integration of secondary replicons in S. meliloti and thus be useful for genome engineering applications, such as generating hybrid genomes.
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Affiliation(s)
- Marcel Wagner
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Johannes Döhlemann
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - David Geisel
- Department of Physics, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Patrick Sobetzko
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Peter Lenz
- Department of Physics, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany
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2
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Won C, Yim SS. Emerging methylation-based approaches in microbiome engineering. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:96. [PMID: 38987811 PMCID: PMC11238421 DOI: 10.1186/s13068-024-02529-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
Bacterial epigenetics, particularly through DNA methylation, exerts significant influence over various biological processes such as DNA replication, uptake, and gene regulation in bacteria. In this review, we explore recent advances in characterizing bacterial epigenomes, accompanied by emerging strategies that harness bacterial epigenetics to elucidate and engineer diverse bacterial species with precision and effectiveness. Furthermore, we delve into the potential of epigenetic modifications to steer microbial functions and influence community dynamics, offering promising opportunities for understanding and modulating microbiomes. Additionally, we investigate the extensive diversity of DNA methyltransferases and emphasize their potential utility in the context of the human microbiome. In summary, this review highlights the potential of DNA methylation as a powerful toolkit for engineering microbiomes.
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Affiliation(s)
- Changhee Won
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sung Sun Yim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, Republic of Korea.
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea.
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
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3
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Richard E, Darracq B, Littner E, Millot GA, Conte V, Cokelaer T, Engelstädter J, Rocha EPC, Mazel D, Loot C. Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons. PLoS Genet 2024; 20:e1011231. [PMID: 38578806 PMCID: PMC11023631 DOI: 10.1371/journal.pgen.1011231] [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: 10/20/2023] [Revised: 04/17/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
Integrons are adaptive devices that capture, stockpile, shuffle and express gene cassettes thereby sampling combinatorial phenotypic diversity. Some integrons called sedentary chromosomal integrons (SCIs) can be massive structures containing hundreds of cassettes. Since most of these cassettes are non-expressed, it is not clear how they remain stable over long evolutionary timescales. Recently, it was found that the experimental inversion of the SCI of Vibrio cholerae led to a dramatic increase of the cassette excision rate associated with a fitness defect. Here, we question the evolutionary sustainability of this apparently counter selected genetic context. Through experimental evolution, we find that the integrase is rapidly inactivated and that the inverted SCI can recover its original orientation by homologous recombination between two insertion sequences (ISs) present in the array. These two outcomes of SCI inversion restore the normal growth and prevent the loss of cassettes, enabling SCIs to retain their roles as reservoirs of functions. These results illustrate a nice interplay between gene orientation, genome rearrangement, bacterial fitness and demonstrate how integrons can benefit from their embedded ISs.
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Affiliation(s)
- Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Eloi Littner
- Sorbonne Université, ED515, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
| | - Gael A. Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Valentin Conte
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, Plateforme Technologique Biomics, Paris, France
| | - Jan Engelstädter
- School of the Environment, The University of Queensland, Brisbane, Australia
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
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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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Gao Q, Lu S, Wang Y, He L, Wang M, Jia R, Chen S, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Sun D, Tian B, Cheng A. Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria. Front Microbiol 2023; 14:1129437. [PMID: 37032876 PMCID: PMC10073500 DOI: 10.3389/fmicb.2023.1129437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
Epigenetics modulates expression levels of various important genes in both prokaryotes and eukaryotes. These epigenetic traits are heritable without any change in genetic DNA sequences. DNA methylation is a universal mechanism of epigenetic regulation in all kingdoms of life. In bacteria, DNA methylation is the main form of epigenetic regulation and plays important roles in affecting clinically relevant phenotypes, such as virulence, host colonization, sporulation, biofilm formation et al. In this review, we survey bacterial epigenomic studies and focus on the recent developments in the structure, function, and mechanism of several highly conserved bacterial DNA methylases. These methyltransferases are relatively common in bacteria and participate in the regulation of gene expression and chromosomal DNA replication and repair control. Recent advances in sequencing techniques capable of detecting methylation signals have enabled the characterization of genome-wide epigenetic regulation. With their involvement in critical cellular processes, these highly conserved DNA methyltransferases may emerge as promising targets for developing novel epigenetic inhibitors for biomedical applications.
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Affiliation(s)
- Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Shuwei Lu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuwei Wang
- Key Laboratory of Livestock and Poultry Provenance Disease Research in Mianyang, Sichuan, China
| | - Longgui He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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6
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Funnell BE. Chromosome dynamics: Rearranging the choreography of a multipartite bacterial genome. Curr Biol 2022; 32:R889-R891. [PMID: 35998600 DOI: 10.1016/j.cub.2022.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A new study identifies a novel fusion between a linear and a circular bacterial chromosome, with unusual requirements for DNA recombination and replication. Understanding how cells accommodate this chromosome promises to inform analyses and elucidate mechanisms of chromosome dynamics in bacteria.
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Affiliation(s)
- Barbara E Funnell
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.
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7
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Liao Q, Ren Z, Wiesler EE, Fuqua C, Wang X. A dicentric bacterial chromosome requires XerC/D site-specific recombinases for resolution. Curr Biol 2022; 32:3609-3618.e7. [PMID: 35797999 PMCID: PMC9398967 DOI: 10.1016/j.cub.2022.06.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/24/2022] [Accepted: 06/15/2022] [Indexed: 12/18/2022]
Abstract
Unlike eukaryotes and archaea, which have multiple replication origins on their chromosomes, bacterial chromosomes usually contain a single replication origin.1 Here, we discovered a dicentric bacterial chromosome with two replication origins, which has resulted from the fusion of the circular and linear chromosomes in Agrobacterium tumefaciens. The fused chromosome is well tolerated, stably maintained, and retains similar subcellular organization and genome-wide DNA interactions found for the bipartite chromosomes. Strikingly, the two replication origins and their partitioning systems are both functional and necessary for cell survival. Finally, we discovered that the site-specific recombinases XerC and XerD2 are essential in cells harboring the fused chromosome but not in cells with bipartite chromosomes. Analysis of actively dividing cells suggests a model in which XerC/D are required to recombine the sister fusion chromosomes when the two centromeres on the same chromosome are segregated to opposite cell poles. Thus, faithful segregation of dicentric chromosomes in bacteria can occur because of site-specific recombination between the sister chromatids during chromosome partitioning. Our study provides a natural comparative platform to examine a bacterial chromosome with multiple origins and a possible explanation for the fundamental difference in bacterial genome architecture relative to eukaryotes and archaea.1.
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Affiliation(s)
- Qin Liao
- Department of Biology, Indiana University, 1001 E 3(rd) Street, Bloomington, IN 47405, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, 1001 E 3(rd) Street, Bloomington, IN 47405, USA
| | - Emma E Wiesler
- Department of Biology, Indiana University, 1001 E 3(rd) Street, Bloomington, IN 47405, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, 1001 E 3(rd) Street, Bloomington, IN 47405, USA
| | - Xindan Wang
- Department of Biology, Indiana University, 1001 E 3(rd) Street, Bloomington, IN 47405, USA.
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8
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Mori JF, Kanaly RA. Natural Chromosome-Chromid Fusion across rRNA Operons in a Burkholderiaceae Bacterium. Microbiol Spectr 2022; 10:e0222521. [PMID: 34985328 PMCID: PMC8729776 DOI: 10.1128/spectrum.02225-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/07/2021] [Indexed: 12/31/2022] Open
Abstract
Chromids (secondary chromosomes) in bacterial genomes that are present in addition to the main chromosome appear to be evolutionarily conserved in some specific bacterial groups. In rare cases among these groups, a small number of strains from Rhizobiales and Vibrionales were shown to possess a naturally fused single chromosome that was reported to have been generated through intragenomic homologous recombination between repeated sequences on the chromosome and chromid. Similar examples have never been reported in the family Burkholderiaceae, a well-documented group that conserves chromids. Here, an in-depth genomic characterization was performed on a Burkholderiaceae bacterium that was isolated from a soil bacterial consortium maintained on diesel fuel and mutagenic benzo[a]pyrene. This organism, Cupriavidus necator strain KK10, was revealed to carry a single chromosome with unexpectedly large size (>6.6 Mb), and results of comparative genomics with the genome of C. necator N-1T indicated that the single chromosome of KK10 was generated through fusion of the prototypical chromosome and chromid at the rRNA operons. This fusion hypothetically occurred through homologous recombination with a crossover between repeated rRNA operons on the chromosome and chromid. Some metabolic functions that were likely expressed from genes on the prototypical chromid region were indicated to be retained. If this phenomenon-the bacterial chromosome-chromid fusion across the rRNA operons through homologous recombination-occurs universally in prokaryotes, the multiple rRNA operons in bacterial genomes may not only contribute to the robustness of ribosome function, but also provide more opportunities for genomic rearrangements through frequent recombination. IMPORTANCE A bacterial chromosome that was naturally fused with the secondary chromosome, or "chromid," and presented as an unexpectedly large single replicon was discovered in the genome of Cupriavidus necator strain KK10, a biotechnologically useful member of the family Burkholderiaceae. Although Burkholderiaceae is a well-documented group that conserves chromids in their genomes, this chromosomal fusion event has not been previously reported for this family. This fusion has hypothetically occurred through intragenomic homologous recombination between repeated rRNA operons and, if so, provides novel insight into the potential of multiple rRNA operons in bacterial genomes to lead to chromosome-chromid fusion. The harsh conditions under which strain KK10 was maintained-a genotoxic hydrocarbon-enriched milieu-may have provided this genotype with a niche in which to survive.
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Affiliation(s)
- Jiro F. Mori
- Graduate School of Nanobiosicences, Yokohama City University, Yokohama, Japan
| | - Robert A. Kanaly
- Graduate School of Nanobiosicences, Yokohama City University, Yokohama, Japan
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9
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Soler-Bistué A, Aguilar-Pierlé S, Garcia-Garcerá M, Val ME, Sismeiro O, Varet H, Sieira R, Krin E, Skovgaard O, Comerci DJ, Rocha EPC, Mazel D. Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae. BMC Biol 2020; 18:43. [PMID: 32349767 PMCID: PMC7191768 DOI: 10.1186/s12915-020-00777-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/31/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In fast-growing bacteria, the genomic location of ribosomal protein (RP) genes is biased towards the replication origin (oriC). This trait allows optimizing their expression during exponential phase since oriC neighboring regions are in higher dose due to multifork replication. Relocation of s10-spc-α locus (S10), which codes for most of the RP, to ectopic genomic positions shows that its relative distance to the oriC correlates to a reduction on its dosage, its expression, and bacterial growth rate. However, a mechanism linking S10 dosage to cell physiology has still not been determined. RESULTS We hypothesized that S10 dosage perturbations impact protein synthesis capacity. Strikingly, we observed that in Vibrio cholerae, protein production capacity was independent of S10 position. Deep sequencing revealed that S10 relocation altered chromosomal replication dynamics and genome-wide transcription. Such changes increased as a function of oriC-S10 distance. Since RP constitutes a large proportion of cell mass, lower S10 dosage could lead to changes in macromolecular crowding, impacting cell physiology. Accordingly, cytoplasm fluidity was higher in mutants where S10 is most distant from oriC. In hyperosmotic conditions, when crowding differences are minimized, the growth rate and replication dynamics were highly alleviated in these strains. CONCLUSIONS The genomic location of RP genes ensures its optimal dosage. However, besides of its essential function in translation, their genomic position sustains an optimal macromolecular crowding essential for maximizing growth. Hence, this could be another mechanism coordinating DNA replication to bacterial growth.
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Affiliation(s)
- Alfonso Soler-Bistué
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde," CONICET - Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | | | - Marc Garcia-Garcerá
- Microbial Evolutionary Genomics, Département Génomes et Génétique, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique UMR3525, Paris, France
- Department of Fundamental Microbiology, University of Lausanne, Quartier SORGE, 1003, Lausanne, Switzerland
| | - Marie-Eve Val
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Plate-forme Transcriptome et Épigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France
| | - Hugo Varet
- Institut Pasteur, Plate-forme Transcriptome et Épigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France
| | - Rodrigo Sieira
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Evelyne Krin
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Diego J Comerci
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde," CONICET - Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Département Génomes et Génétique, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique UMR3525, Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France.
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10
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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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11
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Das B, Chattoraj DK. Commentary: Functionality of Two Origins of Replication in Vibrio cholerae Strains With a Single Chromosome. Front Microbiol 2019; 10:1314. [PMID: 31275259 PMCID: PMC6594386 DOI: 10.3389/fmicb.2019.01314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/27/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
- Bhabatosh Das
- Translational Health Science and Technology Institute, Faridabad, India
| | - Dhruba K Chattoraj
- Center of Cancer Research (CCR), National Cancer Institute (NCI) and National Institute Health (NIH), Bethesda, MD, United States
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12
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Abstract
Bacterial chromosomes harbour a unique origin of bidirectional replication, oriC. They are almost always circular, with replication terminating in a region diametrically opposite to oriC, the terminus. The oriC-terminus organisation is reflected by the orientation of the genes and by the disposition of DNA-binding protein motifs implicated in the coordination of chromosome replication and segregation with cell division. Correspondingly, the E. coli and B. subtilis model bacteria possess a replication fork trap system, Tus/ter and RTP/ter, respectively, which enforces replication termination in the terminus region. Here, we show that tus and rtp are restricted to four clades of bacteria, suggesting that tus was recently domesticated from a plasmid gene. We further demonstrate that there is no replication fork system in Vibrio cholerae, a bacterium closely related to E. coli. Marker frequency analysis showed that replication forks originating from ectopic origins were not blocked in the terminus region of either of the two V. cholerae chromosomes, but progressed normally until they encountered an opposite fork. As expected, termination synchrony of the two chromosomes is disrupted by these ectopic origins. Finally, we show that premature completion of the primary chromosome replication did not modify the choreography of segregation of its terminus region.
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13
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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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14
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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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15
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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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16
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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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17
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Single Circular Chromosome Identified from the Genome Sequence of the Vibrio cholerae O1 bv. El Tor Ogawa Strain V060002. GENOME ANNOUNCEMENTS 2018; 6:6/25/e00564-18. [PMID: 29930068 PMCID: PMC6013637 DOI: 10.1128/genomea.00564-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the complete genome sequence of the Vibrio cholerae O1 bv. El Tor Ogawa strain V060002, isolated in 1997. The data demonstrate that this clinical strain has a single chromosome resulting from recombination of two prototypical chromosomes.
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18
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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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19
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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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20
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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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21
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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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22
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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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23
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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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24
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Val ME, Marbouty M, de Lemos Martins F, Kennedy SP, Kemble H, Bland MJ, Possoz C, Koszul R, Skovgaard O, Mazel D. A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae. SCIENCE ADVANCES 2016; 2:e1501914. [PMID: 27152358 PMCID: PMC4846446 DOI: 10.1126/sciadv.1501914] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/28/2016] [Indexed: 05/04/2023]
Abstract
Bacteria with multiple chromosomes represent up to 10% of all bacterial species. Unlike eukaryotes, these bacteria use chromosome-specific initiators for their replication. In all cases investigated, the machineries for secondary chromosome replication initiation are of plasmid origin. One of the important differences between plasmids and chromosomes is that the latter replicate during a defined period of the cell cycle, ensuring a single round of replication per cell. Vibrio cholerae carries two circular chromosomes, Chr1 and Chr2, which are replicated in a well-orchestrated manner with the cell cycle and coordinated in such a way that replication termination occurs at the same time. However, the mechanism coordinating this synchrony remains speculative. We investigated this mechanism and revealed that initiation of Chr2 replication is triggered by the replication of a 150-bp locus positioned on Chr1, called crtS. This crtS replication-mediated Chr2 replication initiation mechanism explains how the two chromosomes communicate to coordinate their replication. Our study reveals a new checkpoint control mechanism in bacteria, and highlights possible functional interactions mediated by contacts between two chromosomes, an unprecedented observation in bacteria.
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Affiliation(s)
- Marie-Eve Val
- Bacterial Genome Plasticity, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
- CNRS UMR 3525, Paris 75015, France
| | - Martial Marbouty
- CNRS UMR 3525, Paris 75015, France
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
| | - Francisco de Lemos Martins
- Bacterial Genome Plasticity, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
- CNRS UMR 3525, Paris 75015, France
| | | | - Harry Kemble
- Bacterial Genome Plasticity, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
- CNRS UMR 3525, Paris 75015, France
| | - Michael J. Bland
- Bacterial Genome Plasticity, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
- CNRS UMR 3525, Paris 75015, France
| | - Christophe Possoz
- Department of Genome Biology, Institute of Integrative Biology of the Cell (I2BC), Paris-Sud University, CEA, CNRS, Gif-sur-Yvette 91190, France
| | - Romain Koszul
- CNRS UMR 3525, Paris 75015, France
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
| | - Ole Skovgaard
- Department of Science, Systems and Models, Roskilde University, Roskilde DK-4000, Denmark
- Corresponding author. E-mail: (D.M.); (O.S.)
| | - Didier Mazel
- Bacterial Genome Plasticity, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France
- CNRS UMR 3525, Paris 75015, France
- Corresponding author. E-mail: (D.M.); (O.S.)
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Xer Site-Specific Recombination: Promoting Vertical and Horizontal Transmission of Genetic Information. Microbiol Spectr 2016; 2. [PMID: 26104463 DOI: 10.1128/microbiolspec.mdna3-0056-2014] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Two related tyrosine recombinases, XerC and XerD, are encoded in the genome of most bacteria where they serve to resolve dimers of circular chromosomes by the addition of a crossover at a specific site, dif. From a structural and biochemical point of view they belong to the Cre resolvase family of tyrosine recombinases. Correspondingly, they are exploited for the resolution of multimers of numerous plasmids. In addition, they are exploited by mobile DNA elements to integrate into the genome of their host. Exploitation of Xer is likely to be advantageous to mobile elements because the conservation of the Xer recombinases and of the sequence of their chromosomal target should permit a quite easy extension of their host range. However, it requires means to overcome the cellular mechanisms that normally restrict recombination to dif sites harbored by a chromosome dimer and, in the case of integrative mobile elements, to convert dedicated tyrosine resolvases into integrases.
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Abstract
One of the disadvantages of circular plasmids and chromosomes is their high sensitivity to rearrangements caused by homologous recombination. Odd numbers of crossing-over occurring during or after replication of a circular replicon result in the formation of a dimeric molecule in which the two copies of the replicon are fused. If they are not converted back to monomers, the dimers of replicons may fail to correctly segregate at the time of cell division. Resolution of multimeric forms of circular plasmids and chromosomes is mediated by site-specific recombination, and the enzymes that catalyze this type of reaction fall into two families of proteins: the serine and tyrosine recombinase families. Here we give an overview of the variety of site-specific resolution systems found on circular plasmids and chromosomes.
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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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Horton JR, Zhang X, Blumenthal RM, Cheng X. Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression. Nucleic Acids Res 2015; 43:4296-308. [PMID: 25845600 PMCID: PMC4417163 DOI: 10.1093/nar/gkv251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 11/21/2014] [Accepted: 03/11/2015] [Indexed: 12/31/2022] Open
Abstract
DNA adenine methyltransferase (Dam) is widespread and conserved among the γ-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. An unexplained and perplexing observation about Escherichia coli Dam (EcoDam) is that there is no obvious relationship between the genes that are transcriptionally responsive to Dam and the promoter-proximal presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a 5-base pair non-cognate sequence distinct from GATC. The crystal structure of a non-cognate complex allowed us to identify a DNA binding element, GTYTA/TARAC (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some Dam-regulated promoters, including the Pap operon which specifies pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC sequences (i.e. 3/4-site ATC and GAT). Taken together, these results imply that Dam, in addition to being responsible for GATC methylation, could also function as a methylation-independent transcriptional repressor.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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29
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Sánchez-Romero MA, Cota I, Casadesús J. DNA methylation in bacteria: from the methyl group to the methylome. Curr Opin Microbiol 2015; 25:9-16. [PMID: 25818841 DOI: 10.1016/j.mib.2015.03.004] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Formation of C(5)-methyl-cytosine, N(4)-methyl-cytosine, and N(6)-methyl-adenine in bacterial genomes is postreplicative, and occurs at specific targets. Base methylation can modulate the interaction of DNA-binding proteins with their cognate sites, and controls chromosome replication, correction of DNA mismatches, cell cycle-coupled transcription, and formation of epigenetic lineages by phase variation. During four decades, the roles of DNA methylation in bacterial physiology have been investigated by analyzing the contribution of individual methyl groups or small methyl group clusters to the control of DNA-protein interactions. Nowadays, single-molecule real-time sequencing can analyze the DNA methylation of the entire genome (the 'methylome'). Bacterial methylomes provide a wealth of information on the methylation marks present in bacterial genomes, and may open a new era in bacterial epigenomics.
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Affiliation(s)
| | - Ignacio Cota
- Departamento de Genética, Universidad de Sevilla, Apartado 1095, 41080 Seville, Spain
| | - Josep Casadesús
- Departamento de Genética, Universidad de Sevilla, Apartado 1095, 41080 Seville, Spain.
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30
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Chapman C, Henry M, Bishop-Lilly KA, Awosika J, Briska A, Ptashkin RN, Wagner T, Rajanna C, Tsang H, Johnson SL, Mokashi VP, Chain PSG, Sozhamannan S. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity. PLoS One 2015; 10:e0120311. [PMID: 25794000 PMCID: PMC4368569 DOI: 10.1371/journal.pone.0120311] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/20/2015] [Indexed: 01/08/2023] Open
Abstract
Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.
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Affiliation(s)
- Carol Chapman
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Matthew Henry
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Kimberly A. Bishop-Lilly
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Joy Awosika
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Adam Briska
- OpGen, Inc., Gaithersburg, Maryland, United States of America
| | | | - Trevor Wagner
- OpGen, Inc., Gaithersburg, Maryland, United States of America
| | - Chythanya Rajanna
- University of Florida, Gainesville, Florida, United States of America
| | - Hsinyi Tsang
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Shannon L. Johnson
- Genome Science, Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Vishwesh P. Mokashi
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Patrick S. G. Chain
- Genome Science, Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Shanmuga Sozhamannan
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
- * E-mail:
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31
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Mazel D, Colwell R, Klose K, Oliver J, Crumlish M, McDougald D, Bland MJ, Austin B. VIBRIO 2014 meeting report. Res Microbiol 2014; 165:857-64. [PMID: 25463383 DOI: 10.1016/j.resmic.2014.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 10/15/2014] [Accepted: 10/15/2014] [Indexed: 11/16/2022]
Affiliation(s)
- Didier Mazel
- Unité Plasticité du Génome bactérien and CNRS UMR 3525, Département de Génomes et Génétique, Institut Pasteur, Paris, France.
| | - Rita Colwell
- Maryland Pathogen Research Institute and Center of Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Karl Klose
- Department of Biology, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - James Oliver
- Department of Biology, University North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Mags Crumlish
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | - Diane McDougald
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, The University of New South Wales, Sydney 2052, Australia
| | - Michael J Bland
- Unité Plasticité du Génome bactérien and CNRS UMR 3525, Département de Génomes et Génétique, Institut Pasteur, Paris, France
| | - Brian Austin
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
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32
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DNA methylation in Caulobacter and other Alphaproteobacteria during cell cycle progression. Trends Microbiol 2014; 22:528-35. [DOI: 10.1016/j.tim.2014.05.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 01/20/2023]
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Baharoglu Z, Mazel D. SOS, the formidable strategy of bacteria against aggressions. FEMS Microbiol Rev 2014; 38:1126-45. [PMID: 24923554 DOI: 10.1111/1574-6976.12077] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 05/01/2014] [Accepted: 05/07/2014] [Indexed: 12/22/2022] Open
Abstract
The presence of an abnormal amount of single-stranded DNA in the bacterial cell constitutes a genotoxic alarm signal that induces the SOS response, a broad regulatory network found in most bacterial species to address DNA damage. The aim of this review was to point out that beyond being a repair process, SOS induction leads to a very strong but transient response to genotoxic stress, during which bacteria can rearrange and mutate their genome, induce several phenotypic changes through differential regulation of genes, and sometimes acquire characteristics that potentiate bacterial survival and adaptation to changing environments. We review here the causes and consequences of SOS induction, but also how this response can be modulated under various circumstances and how it is connected to the network of other important stress responses. In the first section, we review articles describing the induction of the SOS response at the molecular level. The second section discusses consequences of this induction in terms of DNA repair, changes in the genome and gene expression, and sharing of genomic information, with their effects on the bacteria's life and evolution. The third section is about the fine tuning of this response to fit with the bacteria's 'needs'. Finally, we discuss recent findings linking the SOS response to other stress responses. Under these perspectives, SOS can be perceived as a powerful bacterial strategy against aggressions.
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Affiliation(s)
- Zeynep Baharoglu
- Institut Pasteur, Département Génomes et Génétique, Unité Plasticité du Génome Bactérien, Paris, France; CNRS, UMR3525, Paris, France
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