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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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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3
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Budimir I, Giampieri E, Saccenti E, Suarez-Diez M, Tarozzi M, Dall'Olio D, Merlotti A, Curti N, Remondini D, Castellani G, Sala C. Intraspecies characterization of bacteria via evolutionary modeling of protein domains. Sci Rep 2022; 12:16595. [PMID: 36198716 PMCID: PMC9534902 DOI: 10.1038/s41598-022-21036-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/22/2022] [Indexed: 12/04/2022] Open
Abstract
The ability to detect and characterize bacteria within a biological sample is crucial for the monitoring of infections and epidemics, as well as for the study of human health and its relationship with commensal microorganisms. To this aim, a commonly used technique is the 16S rRNA gene targeted sequencing. PCR-amplified 16S sequences derived from the sample of interest are usually clustered into the so-called Operational Taxonomic Units (OTUs) based on pairwise similarities. Then, representative OTU sequences are compared with reference (human-made) databases to derive their phylogeny and taxonomic classification. Here, we propose a new reference-free approach to define the phylogenetic distance between bacteria based on protein domains, which are the evolving units of proteins. We extract the protein domain profiles of 3368 bacterial genomes and we use an ecological approach to model their Relative Species Abundance distribution. Based on the model parameters, we then derive a new measurement of phylogenetic distance. Finally, we show that such model-based distance is capable of detecting differences between bacteria in cases in which the 16S rRNA-based method fails, providing a possibly complementary approach , which is particularly promising for the analysis of bacterial populations measured by shotgun sequencing.
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Affiliation(s)
- Iva Budimir
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Enrico Giampieri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Martina Tarozzi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Daniele Dall'Olio
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Alessandra Merlotti
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Nico Curti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy.
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
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4
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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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5
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Kang M, Lim JY, Kim J, Hwang I, Goo E. Influence of genomic structural variations and nutritional conditions on the emergence of quorum sensing-dependent gene regulation defects in Burkholderia glumae. Front Microbiol 2022; 13:950600. [PMID: 35910611 PMCID: PMC9335073 DOI: 10.3389/fmicb.2022.950600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
Bacteria often change their genetic and physiological traits to survive in harsh environments. To determine whether, in various strains of Burkholderia glumae, genomic diversity is associated with the ability to adapt to ever-changing environments, whole genomes of 44 isolates from different hosts and regions were analyzed. Whole-genome phylogenetic analysis of the 44 isolates revealed six clusters and two divisions. While all isolates possessed chromosomes 1 and 2, strains BGR80S and BGR81S had one chromosome resulting from the merging of the two chromosomes. Upon comparison of genomic structures to the prototype BGR1, inversions, deletions, and rearrangements were found within or between chromosomes 1 and/or 2 in the other isolates. When three isolates—BGR80S, BGR15S, and BGR21S, representing clusters III, IV, and VI, respectively—were grown in Luria-Bertani medium, spontaneous null mutations were identified in qsmR encoding a quorum-sensing master regulator. Six days after subculture, qsmR mutants were found at detectable frequencies in BGR15S and BGR21S, and reached approximately 40% at 8 days after subculture. However, the qsmR mutants appeared 2 days after subculture in BGR80S and dominated the population, reaching almost 80%. No qsmR mutant was detected at detectable frequency in BGR1 or BGR13S. The spontaneous qsmR mutants outcompeted their parental strains in the co-culture. Daily addition of glucose or casamino acids to the batch cultures of BGR80S delayed emergence of qsmR mutants and significantly reduced their incidence. These results indicate that spontaneous qsmR mutations are correlated with genomic structures and nutritional conditions.
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Affiliation(s)
- Minhee Kang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Jae Yun Lim
- School of Systems Biomedical Science, Soongsil University, Seoul, South Korea
| | - Jinwoo Kim
- Department of Plant Medicine and Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Eunhye Goo
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Eunhye Goo,
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6
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Possoz C, Yamaichi Y, Galli E, Ferat JL, Barre FX. Vibrio cholerae Chromosome Partitioning without Polar Anchoring by HubP. Genes (Basel) 2022; 13:genes13050877. [PMID: 35627261 PMCID: PMC9140986 DOI: 10.3390/genes13050877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
Partition systems are widespread among bacterial chromosomes. They are composed of two effectors, ParA and ParB, and cis acting sites, parS, located close to the replication origin of the chromosome (oriC). ParABS participate in chromosome segregation, at least in part because they serve to properly position sister copies of oriC. A fourth element, located at cell poles, is also involved in some cases, such as HubP for the ParABS1 system of Vibrio cholerae chromosome 1 (ch1). The polar anchoring of oriC of ch1 (oriC1) is lost when HubP or ParABS1 are inactivated. Here, we report that in the absence of HubP, ParABS1 actively maintains oriC1 at mid-cell, leading to the subcellular separation of the two ch1 replication arms. We further show that parS1 sites ectopically inserted in chromosome 2 (ch2) stabilize the inheritance of this replicon in the absence of its endogenous partition system, even without HubP. We also observe the positioning interference between oriC1 and oriC of ch2 regions when their positionings are both driven by ParABS1. Altogether, these data indicate that ParABS1 remains functional in the absence of HubP, which raises questions about the role of the polar anchoring of oriC1 in the cell cycle.
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7
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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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8
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Paredes O, Morales JA, Mendizabal AP, Romo-Vázquez R. Metacode: One code to rule them all. Biosystems 2021; 208:104486. [PMID: 34274462 DOI: 10.1016/j.biosystems.2021.104486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022]
Abstract
The code of codes or metacode is a microcosm where biological layers, as well as their codes, interact together allowing the continuity of information flow in organisms by increasing biological entities' complexity. Through this novel organic code, biological systems scale towards niches with higher informatic freedom building structures that increase the entropy in the universe. Code biology has developed a novel informational framework where biological entities strive themselves through the information flow carried out through organic codes consisting of two molecular or functional landscapes intertwined through arbitrary linkages via an adaptor whose nature is autonomous from molecular determinism. Here we will integrate genomic and epigenomic codes according to the evidence released in ENCODE (phase 3), psychENCODE and GTEx project, outlining the principles of the metacode, to address the continuous nature of biological systems and their inter-layered information flow. This novel complex metacode maps from very constrained sets of elements (i.e., regulation sites modulating gene expression) to new ones with greater freedom of decoding (i.e., a continuous cell phenotypic space). This leads to a new domain in code biology where biological systems are informatic attractors that navigate an energy metaspace through a complexity-noise balance, stalling in emergent niches where organic codes take meaning.
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Affiliation(s)
- Omar Paredes
- Computer Sciences Department, CUCEI, Universidad de Guadalajara, Mexico
| | | | - Adriana P Mendizabal
- Molecular Biology Laboratory, Farmacobiology Department, CUCEI, Universidad de Guadalajara, Mexico
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9
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Hoff J, Daniel B, Stukenberg D, Thuronyi BW, Waldminghaus T, Fritz G. Vibrio natriegens
: an ultrafast‐growing marine bacterium as emerging synthetic biology chassis. Environ Microbiol 2020; 22:4394-4408. [DOI: 10.1111/1462-2920.15128] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Josef Hoff
- School of Molecular Sciences The University of Western Australia Perth Australia
- Center for Synthetic Microbiology Philipps‐Universität Marburg Marburg Germany
| | - Benjamin Daniel
- Center for Synthetic Microbiology Philipps‐Universität Marburg Marburg Germany
- Institute of Microbiology, ETH Zurich Zürich Switzerland
| | - Daniel Stukenberg
- Center for Synthetic Microbiology Philipps‐Universität Marburg Marburg Germany
| | | | - Torsten Waldminghaus
- Centre for Synthetic Biology Technische Universität Darmstadt Darmstadt Germany
- Department of Biology Technische Universität Darmstadt Darmstadt Germany
| | - Georg Fritz
- School of Molecular Sciences The University of Western Australia Perth Australia
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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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Gao F, Leonard AC. Editorial: DNA Replication Origins in Microbial Genomes, Volume 2. Front Microbiol 2019; 10:2416. [PMID: 31708893 PMCID: PMC6819313 DOI: 10.3389/fmicb.2019.02416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/07/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin, China
- Frontier Science Center of Synthetic Biology (MOE), Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Alan C. Leonard
- Laboratory of Microbial Genetics, Department of Biomedical and Chemical Engineering and Science, Florida Institute of Technology, Melbourne, FL, United States
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12
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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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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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Ausiannikava D, Mitchell L, Marriott H, Smith V, Hawkins M, Makarova KS, Koonin EV, Nieduszynski CA, Allers T. Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii. Mol Biol Evol 2018; 35:1855-1868. [PMID: 29668953 PMCID: PMC6063281 DOI: 10.1093/molbev/msy075] [Citation(s) in RCA: 15] [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] [Indexed: 01/22/2023] Open
Abstract
The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins. Three scenarios have been proposed for the evolution of this genome architecture: 1) mutational diversification of a multi-copy chromosome; 2) capture of a new chromosome by horizontal transfer; 3) acquisition of new origins and splitting into two replication-competent chromosomes. We report an example of the third scenario: the multi-origin chromosome of the archaeon Haloferax volcanii has split into two elements via homologous recombination. The newly generated elements are bona fide chromosomes, because each bears "chromosomal" replication origins, rRNA loci, and essential genes. The new chromosomes were stable during routine growth but additional genetic manipulation, which involves selective bottlenecks, provoked further rearrangements. To the best of our knowledge, rearrangement of a naturally evolved prokaryotic genome to generate two new chromosomes has not been described previously.
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Affiliation(s)
- Darya Ausiannikava
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Laura Mitchell
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Hannah Marriott
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Michelle Hawkins
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD
| | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
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15
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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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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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