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Jäckel C, Hertwig S, Scholz HC, Nöckler K, Reetz J, Hammerl JA. Prevalence, Host Range, and Comparative Genomic Analysis of Temperate Ochrobactrum Phages. Front Microbiol 2017; 8:1207. [PMID: 28713341 PMCID: PMC5492332 DOI: 10.3389/fmicb.2017.01207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/14/2017] [Indexed: 11/13/2022] Open
Abstract
Ochrobactrum and Brucella are closely related bacteria that populate different habitats and differ in their pathogenic properties. Only little is known about mobile genetic elements in these genera which might be important for survival and virulence. Previous studies on Brucella lysogeny indicated that active phages are rare in this genus. To gain insight into the presence and nature of prophages in Ochrobactrum, temperate phages were isolated from various species and characterized in detail. In silico analyses disclosed numerous prophages in published Ochrobactrum genomes. Induction experiments showed that Ochrobactrum prophages can be induced by various stress factors and that some strains released phage particles even under non-induced conditions. Sixty percent of lysates prepared from 125 strains revealed lytic activity. The host range and DNA similarities of 19 phages belonging to the families Myoviridae, Siphoviridae, or Podoviridae were determined suggesting that they are highly diverse. Some phages showed relationship to the temperate Brucella inopinata phage BiPB01. The genomic sequences of the myovirus POA1180 (41,655 bp) and podovirus POI1126 (60,065 bp) were analyzed. Phage POA1180 is very similar to a prophage recently identified in a Brucella strain isolated from an exotic frog. The POA1180 genome contains genes which may confer resistance to chromate and the ability to take up sulfate. Phage POI1126 is related to podoviruses of Sinorhizobium meliloti (PCB5), Erwinia pyrifoliae (Pep14), and Burkholderia cenocepacia (BcepIL02) and almost identical to an unnamed plasmid of the Ochrobactrum intermedium strain LMG 3301. Further experiments revealed that the POI1126 prophage indeed replicates as an extrachromosomal element. The data demonstrate for the first time that active prophages are common in Ochrobactrum and suggest that atypical brucellae also may be a reservoir for temperate phages.
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Affiliation(s)
- Claudia Jäckel
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Stefan Hertwig
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Holger C Scholz
- German Center for Infection Research, Bundeswehr Institute of MicrobiologyMunich, Germany
| | - Karsten Nöckler
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Jochen Reetz
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Jens A Hammerl
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
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Hammerl JA, Göllner C, Al Dahouk S, Nöckler K, Reetz J, Hertwig S. Analysis of the First Temperate Broad Host Range Brucellaphage (BiPBO1) Isolated from B. inopinata. Front Microbiol 2016; 7:24. [PMID: 26858702 PMCID: PMC4729917 DOI: 10.3389/fmicb.2016.00024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022] Open
Abstract
Brucella species are important human and animal pathogens. Though, only little is known about mobile genetic elements of these highly pathogenic bacteria. To date, neither plasmids nor temperate phages have been described in brucellae. We analyzed genomic sequences of various reference and type strains and identified a number of putative prophages residing within the Brucella chromosomes. By induction, phage BiPBO1 was isolated from Brucella inopinata. BiPBO1 is a siphovirus that infects several Brucella species including Brucella abortus and Brucella melitensis. Integration of the phage genome occurs adjacent to a tRNA gene in chromosome 1 (chr 1). The bacterial (attB) and phage (attP) attachment sites comprise an identical sequence of 46 bp. This sequence exists in many Brucella and Ochrobactrum species. The BiPBO1 genome is composed of a 46,877 bp double-stranded DNA. Eighty-seven putative gene products were determined, of which 32 could be functionally assigned. Strongest similarities were found to a temperate phage residing in the chromosome of Ochrobactrum anthropi ATCC 49188 and to prophages identified in several families belonging to the order rhizobiales. The data suggest that horizontal gene transfer may occur between Brucella and Ochrobactrum and underpin the close relationship of these environmental and pathogenic bacteria.
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Affiliation(s)
- Jens A. Hammerl
- Department of Biological Safety, Federal Institute for Risk AssessmentBerlin, Germany
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Van der Henst C, de Barsy M, Zorreguieta A, Letesson JJ, De Bolle X. The Brucella pathogens are polarized bacteria. Microbes Infect 2013; 15:998-1004. [PMID: 24141086 DOI: 10.1016/j.micinf.2013.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 10/01/2013] [Accepted: 10/03/2013] [Indexed: 11/30/2022]
Abstract
Brucella pathogens are responsible for brucellosis, a worldwide zoonosis. They are facultative intracellular pathogens characterized by their asymmetric division and their unipolar growth. This growth modality generates poles with specialized functions (through polar recruitment of polar adhesins or of cell cycle regulators) and progeny cells with potentially different fates.
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Affiliation(s)
- Charles Van der Henst
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
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Aujoulat F, Roger F, Bourdier A, Lotthé A, Lamy B, Marchandin H, Jumas-Bilak E. From environment to man: genome evolution and adaptation of human opportunistic bacterial pathogens. Genes (Basel) 2012; 3:191-232. [PMID: 24704914 PMCID: PMC3899952 DOI: 10.3390/genes3020191] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 02/29/2012] [Accepted: 02/29/2012] [Indexed: 02/07/2023] Open
Abstract
Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. The versatility of bacterial life-style involves adaptation to various niches. Adaptation to both open environment and human specific niches is a major challenge that involves intermediate organisms allowing pre-adaptation to humans. The aim of this review is to analyze genomic features of environmental bacteria in order to explain their adaptation to human beings. The genera Pseudomonas, Aeromonas and Ochrobactrum provide valuable examples of opportunistic behavior associated to particular genomic structure and evolution. Particularly, we performed original genomic comparisons among aeromonads and between the strictly intracellular pathogens Brucella spp. and the mild opportunistic pathogens Ochrobactrum spp. We conclude that the adaptation to human could coincide with a speciation in action revealed by modifications in both genomic and population structures. This adaptation-driven speciation could be a major mechanism for the emergence of true pathogens besides the acquisition of specialized virulence factors.
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Affiliation(s)
- Fabien Aujoulat
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Frédéric Roger
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Alice Bourdier
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Anne Lotthé
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Brigitte Lamy
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Hélène Marchandin
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
| | - Estelle Jumas-Bilak
- Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), équipe Pathogènes et Environnements, Montpellier 34093, France.
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Pradella S, Päuker O, Petersen J. Genome organisation of the marine Roseobacter clade member Marinovum algicola. Arch Microbiol 2009; 192:115-26. [PMID: 20039020 DOI: 10.1007/s00203-009-0535-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 11/10/2009] [Accepted: 12/09/2009] [Indexed: 11/30/2022]
Abstract
The Roseobacter clade, belonging to the family Rhodobacteraceae of the class Alphaproteobacteria, is one of the major bacterial groups in marine environments. A remarkable wealth of diverse large plasmids has been detected in members of this lineage. Here, we analysed the genome structure and extrachromosomal DNA content of four strains of the roseobacter species Marinovum algicola by pulsed-field gel electrophoresis. They were originally isolated from toxic dinoflagellates and possess multireplicon genomes with sizes between 5.20 and 5.35 Mb. In addition to the single circular chromosomes (3.60-3.74 Mb), whose organisation seem to be conserved, 9 to 12 extrachromosomal replicons have been detected for each strain. This number is unprecedented for roseobacters and proposes a sophisticated regulation of replication and partitioning to ensure stable maintenance. The plasmid lengths range from 7 to 477 kb and our analyses document a circular conformation for all but one of them, which might represent a linear plasmid-like prophage. In striking contrast to other roseobacters, up to one-third of the genomic information (1.75 Mb) is plasmid borne in Marinovum algicola. The plasmid patterns of some strains are conspicuously different, indicating that recombination and conjugative gene transfer are dominant mechanisms for microevolution within the Roseobacter clade.
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Affiliation(s)
- Silke Pradella
- German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany.
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The MG1363 and IL1403 laboratory strains of Lactococcus lactis and several dairy strains are diploid. J Bacteriol 2009; 192:1058-65. [PMID: 20023021 DOI: 10.1128/jb.00900-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria are normally haploid, maintaining one copy of their genome in one circular chromosome. We have examined the cell cycle of laboratory strains of Lactococcus lactis, and, to our surprise, we found that some of these strains were born with two complete nonreplicating chromosomes. We determined the cellular content of DNA by flow cytometry and by radioactive labeling of the DNA. These strains thus fulfill the criterion of being diploid. Several dairy strains were also found to be diploid while a nondairy strain and several other dairy strains were haploid in slow-growing culture. The diploid and haploid strains differed in their sensitivity toward UV light, in their cell size, and in their D period, the period between termination of DNA replication and cell division.
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MacLean AM, Finan TM, Sadowsky MJ. Genomes of the symbiotic nitrogen-fixing bacteria of legumes. PLANT PHYSIOLOGY 2007; 144:615-22. [PMID: 17556525 PMCID: PMC1914180 DOI: 10.1104/pp.107.101634] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Allyson M MacLean
- Department of Biology, Center for Environmental Genomics, McMaster University, Hamilton, Ontario, Canada L8S 4K1
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Martins-Pinheiro M, Marques RCP, Menck CFM. Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus. BMC Microbiol 2007; 7:17. [PMID: 17352799 PMCID: PMC1839093 DOI: 10.1186/1471-2180-7-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Accepted: 03/12/2007] [Indexed: 11/10/2022] Open
Abstract
Background The integrity of DNA molecules is fundamental for maintaining life. The DNA repair proteins protect organisms against genetic damage, by removal of DNA lesions or helping to tolerate them. DNA repair genes are best known from the gamma-proteobacterium Escherichia coli, which is the most understood bacterial model. However, genome sequencing raises questions regarding uniformity and ubiquity of these DNA repair genes and pathways, reinforcing the need for identifying genes and proteins, which may respond to DNA damage in other bacteria. Results In this study, we employed a bioinformatic approach, to analyse and describe the open reading frames potentially related to DNA repair from the genome of the alpha-proteobacterium Caulobacter crescentus. This was performed by comparison with known DNA repair related genes found in public databases. As expected, although C. crescentus and E. coli bacteria belong to separate phylogenetic groups, many of their DNA repair genes are very similar. However, some important DNA repair genes are absent in the C. crescentus genome and other interesting functionally related gene duplications are present, which do not occur in E. coli. These include DNA ligases, exonuclease III (xthA), endonuclease III (nth), O6-methylguanine-DNA methyltransferase (ada gene), photolyase-like genes, and uracil-DNA-glycosylases. On the other hand, the genes imuA and imuB, which are involved in DNA damage induced mutagenesis, have recently been described in C. crescentus, but are absent in E. coli. Particularly interesting are the potential atypical phylogeny of one of the photolyase genes in alpha-proteobacteria, indicating an origin by horizontal transfer, and the duplication of the Ada orthologs, which have diverse structural configurations, including one that is still unique for C. crescentus. Conclusion The absence and the presence of certain genes are discussed and predictions are made considering the particular aspects of the C. crescentus among other known DNA repair pathways. The observed differences enlarge what is known for DNA repair in the Bacterial world, and provide a useful framework for further experimental studies in this organism.
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Affiliation(s)
- Marinalva Martins-Pinheiro
- Department of Microbiology, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, SP, Brazil
| | - Regina CP Marques
- Department of Microbiology, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, SP, Brazil
| | - Carlos FM Menck
- Department of Microbiology, Institute of Biomedical Sciences, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, SP, Brazil
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Giuntini E, Mengoni A, De Filippo C, Cavalieri D, Aubin-Horth N, Landry CR, Becker A, Bazzicalupo M. Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics 2005; 6:158. [PMID: 16283928 PMCID: PMC1298293 DOI: 10.1186/1471-2164-6-158] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Accepted: 11/10/2005] [Indexed: 12/21/2022] Open
Abstract
Background Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa). This species occupies different ecological niches, being present as a free-living soil bacterium and as a symbiont of plant root nodules. The genome of the type strain Rm 1021 contains one chromosome and two megaplasmids for a total genome size of 6 Mb. We applied comparative genomic hybridisation (CGH) on an oligonucleotide microarrays to estimate genetic variation at the genomic level in four natural strains, two isolated from Italian agricultural soil and two from desert soil in the Aral Sea region. Results From 4.6 to 5.7 percent of the genes showed a pattern of hybridisation concordant with deletion, nucleotide divergence or ORF duplication when compared to the type strain Rm 1021. A large number of these polymorphisms were confirmed by sequencing and Southern blot. A statistically significant fraction of these variable genes was found on the pSymA megaplasmid and grouped in clusters. These variable genes were found to be mainly transposases or genes with unknown function. Conclusion The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in S. meliloti.
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Affiliation(s)
- Elisa Giuntini
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy
| | - Alessio Mengoni
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy
| | - Carlotta De Filippo
- Dipartimento di Farmacologia, Università di Firenze, Viale Pieraccini 6, 50139 Firenze, Italy
| | - Duccio Cavalieri
- Dipartimento di Farmacologia, Università di Firenze, Viale Pieraccini 6, 50139 Firenze, Italy
| | - Nadia Aubin-Horth
- Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - Christian R Landry
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - Anke Becker
- Lehrstuhl fur Genetik, Universitat Bielefeld, 33594 Bielefeld, Germany
| | - Marco Bazzicalupo
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy
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Thanbichler M, Wang SC, Shapiro L. The bacterial nucleoid: A highly organized and dynamic structure. J Cell Biochem 2005; 96:506-21. [PMID: 15988757 DOI: 10.1002/jcb.20519] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent advances in bacterial cell biology have revealed unanticipated structural and functional complexity, reminiscent of eukaryotic cells. Particular progress has been made in understanding the structure, replication, and segregation of the bacterial chromosome. It emerged that multiple mechanisms cooperate to establish a dynamic assembly of supercoiled domains, which are stacked in consecutive order to adopt a defined higher-level organization. The position of genetic loci on the chromosome is thereby linearly correlated with their position in the cell. SMC complexes and histone-like proteins continuously remodel the nucleoid to reconcile chromatin compaction with DNA replication and gene regulation. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress.
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Affiliation(s)
- Martin Thanbichler
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305-5329, USA
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