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Abstract
The ancestral strain of Bacillus subtilis NCIB3610 (3610) bears a large, low-copy-number plasmid, called pBS32, that was lost during the domestication of laboratory strain derivatives. Selection against pBS32 may have been because it encodes a potent inhibitor of natural genetic competence (ComI), as laboratory strains were selected for high-frequency transformation. Previous studies have shown that pBS32 and its sibling, pLS32 in Bacillus subtilis subsp. natto, encode a replication initiation protein (RepN), a plasmid partitioning system (AlfAB), a biofilm inhibitor (RapP), and an alternative sigma factor (SigN) that can induce plasmid-mediated cell death in response to DNA damage. Here, we review the literature on pBS32/pLS32, the genes found on it, and their associated phenotypes.
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Kopac S, Wang Z, Wiedenbeck J, Sherry J, Wu M, Cohan FM. Genomic heterogeneity and ecological speciation within one subspecies of Bacillus subtilis. Appl Environ Microbiol 2014; 80:4842-53. [PMID: 24907327 PMCID: PMC4135754 DOI: 10.1128/aem.00576-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/23/2014] [Indexed: 02/06/2023] Open
Abstract
Closely related bacterial genomes usually differ in gene content, suggesting that nearly every strain in nature may be ecologically unique. We have tested this hypothesis by sequencing the genomes of extremely close relatives within a recognized taxon and analyzing the genomes for evidence of ecological distinctness. We compared the genomes of four Death Valley isolates plus the laboratory strain W23, all previously classified as Bacillus subtilis subsp. spizizenii and hypothesized through multilocus analysis to be members of the same ecotype (an ecologically homogeneous population), named putative ecotype 15 (PE15). These strains showed a history of positive selection on amino acid sequences in 38 genes. Each of the strains was under a different regimen of positive selection, suggesting that each strain is ecologically unique and represents a distinct ecological speciation event. The rate of speciation appears to be much faster than can be resolved with multilocus sequencing. Each PE15 strain contained unique genes known to confer a function for bacteria. Remarkably, no unique gene conferred a metabolic system or subsystem function that was not already present in all the PE15 strains sampled. Thus, the origin of ecotypes within this clade shows no evidence of qualitative divergence in the set of resources utilized. Ecotype formation within this clade is consistent with the nanoniche model of bacterial speciation, in which ecotypes use the same set of resources but in different proportions, and genetic cohesion extends beyond a single ecotype to the set of ecotypes utilizing the same resources.
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Affiliation(s)
- Sarah Kopac
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
| | - Zhang Wang
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Jane Wiedenbeck
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
| | - Jessica Sherry
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
| | - Martin Wu
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
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Srivastava P, Singh P, Narayanan N, Deb J. Physiological and biochemical consequences of host–plasmid interaction – A case study with Corynebacterium renale, a multiple cryptic plasmid containing strain. Plasmid 2011; 65:110-7. [DOI: 10.1016/j.plasmid.2010.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/29/2010] [Accepted: 11/08/2010] [Indexed: 11/17/2022]
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4
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Presence of pRI1: A Small Cryptic Mobilizable Plasmid Isolated from Enterococcus faecium of Human and Animal Origin. Curr Microbiol 2008; 58:95-100. [DOI: 10.1007/s00284-008-9266-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 08/13/2008] [Accepted: 08/25/2008] [Indexed: 02/03/2023]
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5
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Olubajo B, Bacon CW. Electrotransformation of Bacillus mojavensis with fluorescent protein markers. J Microbiol Methods 2008; 74:102-5. [DOI: 10.1016/j.mimet.2008.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Revised: 03/20/2008] [Accepted: 03/26/2008] [Indexed: 10/22/2022]
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6
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Earl AM, Losick R, Kolter R. Ecology and genomics of Bacillus subtilis. Trends Microbiol 2008; 16:269-75. [PMID: 18467096 DOI: 10.1016/j.tim.2008.03.004] [Citation(s) in RCA: 252] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2007] [Revised: 03/27/2008] [Accepted: 03/28/2008] [Indexed: 01/26/2023]
Abstract
Bacillus subtilis is a remarkably diverse bacterial species that is capable of growth within many environments. Recent microarray-based comparative genomic analyses have revealed that members of this species also exhibit considerable genomic diversity. The identification of strain-specific genes might explain how B. subtilis has become so broadly adapted. The goal of identifying ecologically adaptive genes could soon be realized with the imminent release of several new B. subtilis genome sequences. As we embark upon this exciting new era of B. subtilis comparative genomics we review what is currently known about the ecology and evolution of this species.
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Affiliation(s)
- Ashlee M Earl
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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7
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Jones BV, Marchesi JR. Accessing the mobile metagenome of the human gut microbiota. MOLECULAR BIOSYSTEMS 2007; 3:749-58. [PMID: 17940657 DOI: 10.1039/b705657e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This article outlines current and possible future strategies to access the mobile metagenome of bacterial ecosystems. Evidence for the role of this genetic resource in development and maintenance of core community functions of the human gut microbiota is reviewed.
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Affiliation(s)
- Brian V Jones
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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Guglielmetti S, Mora D, Parini C. Small rolling circle plasmids in Bacillus subtilis and related species: Organization, distribution, and their possible role in host physiology. Plasmid 2007; 57:245-64. [PMID: 17064773 DOI: 10.1016/j.plasmid.2006.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 07/28/2006] [Accepted: 09/05/2006] [Indexed: 11/25/2022]
Abstract
Bacillus subtilis and related species (Bacillus licheniformis, Bacillus pumilus, Bacillus amyloliquefaciens, and Bacillus mojavensis) represent a group of bacteria largely studied and widely employed by industry. Small rolling circle replicating plasmids of this group of bacteria have been intensively studied as they represent a convenient model for genetic research and for the construction of molecular tools for the genetic modification of their hosts. Through the computational analysis of the available plasmid sequences to date, the first part of this review focuses on the main stages that the present model for rolling circle replication involves, citing the research data which helped to elucidate the mechanism by which these molecules replicate. Analysis of the distribution and phylogeny of the small RC plasmids inside the Bacillus genus is then considered, emphasizing the low level of diversity observed among these plasmids through the in silico analysis of their organization and the sequence divergence of their replication module. Finally, the parasitic vs. mutualistic nature of small rolling circle plasmids is briefly discussed.
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Affiliation(s)
- S Guglielmetti
- Department of Food Science and Microbiology, Industrial Microbiology Section, University of Milan, Via Celoria 2, Milan, Italy.
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Jones BV, Marchesi JR. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods 2006; 4:55-61. [PMID: 17128268 DOI: 10.1038/nmeth964] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2006] [Accepted: 09/15/2006] [Indexed: 12/13/2022]
Abstract
The bacterial community of the human gut is a complex ecosystem composed of >1,000 species, the majority of which are Gram positive and uncultured. To study plasmids resident within this community, we developed a culture-independent transposon aided capture method (TRACA), which does not rely on any plasmid-encoded traits. TRACA facilitated acquisition of plasmids from metagenomic DNA extracts, and subsequent maintenance and selection in an Escherichia coli host. We confirmed the presence of the transposon in captured plasmids and demonstrate that these plasmids are mainly of a Gram-positive origin. Sequencing of plasmids designated pTRACA10 (7 kb) and pTRACA17 (2.7 kb) revealed genes involved in plasmid mobilization and replication. From the homologies of these genes we conclude that pTRACA17 originates from a Gram-positive host belonging to the Firmicute division. pTRACA10 had two additional open reading frames with similarity to a conserved hypothetical protein and phosphoesterase or phosphohydrolase enzymes (Clusters of Orthologous Groups number 4186). Both plasmids lacked any conventional selectable markers.
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Affiliation(s)
- Brian V Jones
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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Ricci G, Borgo F, Fortina MG. Plasmids from Lactobacillus helveticus: distribution and diversity among natural isolates. Lett Appl Microbiol 2006; 42:254-8. [PMID: 16478513 DOI: 10.1111/j.1472-765x.2005.01847.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To investigate the distribution and the level of diversity of extrachromosomal molecules in Lactobacillus helveticus strains in relation to their different ecological niches. METHODS AND RESULTS The plasmid profile of 22 Lact. helveticus strains, isolated from five different Italian cheeses, was determined. Among the tested strains, there was a variable presence of plasmids: eight plasmid-free strains and the remaining with several plasmids that could be differentiated on the basis of number and molecular weight. The profiles showed between one and five plasmid bands, which size ranged between 2.3 and 31 kb. Four of these plasmids were further analyzed by restriction digestion and compared with the plasmids from Lact. helveticus ATCC 15009(T). Analyses and comparison of their primary structures and hybridization experiments revealed the presence of different DNA homology groups. CONCLUSIONS This study indicates that within Lact. helveticus species, there is a high degree of variability in relation to the presence of plasmid molecules. Moreover, the structural diversity found among some of these plasmids allows to hypothesize the presence of different evolutionary lineages. SIGNIFICANCE AND IMPACT OF THE STUDY Studies on plasmid distribution and diversity should be considered as an essential component in a continuing effort to explore microbial diversity as well as to understand the real role of plasmids in the flow of genetic information in natural bacterial communities.
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Affiliation(s)
- G Ricci
- Industrial Microbiology Section, Department of Food Science and Microbiology, University of Milan, Milan, Italy
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Guglielmetti S, Mora D, Manachini PL, Parini C. Genetic relationship among Bacillus licheniformis rolling-circle-replicating plasmids and complete nucleotide sequence of pBL63.1, an atypical replicon. Plasmid 2005; 54:93-103. [PMID: 16122558 DOI: 10.1016/j.plasmid.2005.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 01/13/2005] [Accepted: 01/13/2005] [Indexed: 10/25/2022]
Abstract
The degree of biodiversity among Bacillus licheniformis plasmids and their relation to other Bacillus subtilis group plasmids has been evaluated. To attain this goal we surveyed the diversity and linkage of replication modules in a collection of 21 naturally occurring plasmids of B. licheniformis strains, isolated from different geographical areas. On the basis of rep gene sequence analysis it was possible to group the B. licheniformis plasmids rep genes in two main cluster. Comparison with known rep genes from Bacillus rolling-circle-replicating (RCR) plasmids revealed the presence in B. licheniformis plasmids of replication genes with a DNA sequence peculiar to B. licheniformis species together with rep genes with a very high sequence similarity to B. subtilis plasmids. Furthermore, the molecular organization of an atypical replicon, pBL63.1, was shown. This plasmid did not display any significant similarity with known Bacillus RCR plasmids. The complete nucleotide sequence evidenced a replication module with an unexpected similarity with Rep proteins from RCR plasmids of bacterial species phylogenetically distantly related to Bacillus. pBL63.1 represents an exception to the low-level diversity hypothesis among Bacillus RC replicons.
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Affiliation(s)
- S Guglielmetti
- Department of Food Science and Microbiology, Industrial Microbiology Section, University of Milan, Via Celoria 2, 20133 Milan, Italy
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Wichmann G, Ritchie D, Kousik CS, Bergelson J. Reduced genetic variation occurs among genes of the highly clonal plant pathogen Xanthomonas axonopodis pv. vesicatoria, including the effector gene avrBs2. Appl Environ Microbiol 2005; 71:2418-32. [PMID: 15870329 PMCID: PMC1087534 DOI: 10.1128/aem.71.5.2418-2432.2005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Accepted: 11/18/2004] [Indexed: 11/20/2022] Open
Abstract
The bacterial plant pathogen Xanthomonas axonopodis pv. vesicatoria, also known as Xanthomonas campestris pv. vesicatoria group A, is the causal agent of bacterial spot in pepper and tomato. In order to test different models that may explain the coevolution of avrBs2 with its host plants, we sequenced avrBs2 and six chromosomal loci (total of 5.5 kb per strain) from a global sample of 55 X. axonopodis pv. vesicatoria strains collected from diseased peppers. We found an extreme lack of genetic variation among all X. axonopodis pv. vesicatoria genomic loci (average nucleotide diversity, pi = 9.1 x 10(-5)), including avrBs2. This lack of diversity is consistent with X. axonopodis pv. vesicatoria having undergone a recent population bottleneck and/or selective sweep followed by population expansion. Coalescent analysis determined that approximately 1.4 x 10(4) to 7.16 x 10(4) bacterial generations have passed since the most recent common ancestor (MRCA) of the current X. axonopodis pv. vesicatoria population. Assuming a range of 50 to 500 bacterial generations per year, only 28 to 1,432 years have passed since the MRCA. This time frame coincides with human intervention with the pathogen's host plants, from domestication to modern agricultural practices. Examination of 19 mutated (loss-of-function) avrBs2 alleles detected nine classes of mutations. All mutations affected protein coding, while no synonymous changes were found. The nature of at least one of the avrBs2 mutations suggests that it may be possible to observe one stage of an evolutionary arms race as X. axonopodis pv. vesicatoria responds to selection pressure to alter avrBs2 to escape host plant resistance.
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Affiliation(s)
- Gale Wichmann
- Committee on Genetics, University of Chicago, Illinois, USA.
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13
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McSpadden Gardener BB. Ecology of Bacillus and Paenibacillus spp. in Agricultural Systems. PHYTOPATHOLOGY 2004; 94:1252-8. [PMID: 18944463 DOI: 10.1094/phyto.2004.94.11.1252] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
ABSTRACT Diverse populations of aerobic endospore-forming bacteria occur in agricultural fields and may directly and indirectly contribute to crop productivity. This paper describes recent advances in our understanding of the ecology of Bacillus and Paenibacillus spp. and how different subpopulations of these two genera can promote crop health. The abundance, diversity, and distribution of native populations and inoculant strains in agricultural fields have been characterized using a variety of methods. While native populations of these two genera occur abundantly in most agricultural soils, plant tissues are differentially colonized by distinct subpopulations. Multiple Bacillus and Paenibacillus spp. can promote crop health in a variety of ways. Some populations suppress plant pathogens and pests by producing antibiotic metabolites, while others may directly stimulate plant host defenses prior to infection. Some strains can also stimulate nutrient uptake by plants, either by promoting rhizobial and mycorrhizal symbioses or by fixing atmospheric nitrogen directly. Despite a wealth of new information on the genetics and physiology of Bacillus and related species, a better understanding of the microbial ecology of these two genera must be developed. To this end, several important, but unanswered, questions related to the ecological significance and potential for managing the beneficial activities of these bacteria are discussed.
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Parini C, Guglielmetti S, Mora D, Ricci G. Homologies among three Bacillus licheniformis plasmids and molecular characterization of their replication module. Microbiol Res 2004; 159:211-7. [PMID: 15462521 DOI: 10.1016/j.micres.2004.04.003] [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: 11/20/2022]
Abstract
To assess to what extent three Bacillus licheniformis plasmids had the same molecular organization a physical map of the 9.34, 8.40 and 7.90 kb plasmids was achieved by using seventeen restriction enzymes. Southern hybridization was performed on plasmids using restriction fragments of the smallest plasmid as probes. Data from different hybridization patterns show a close homology among the three plasmids hypothesizing a similar molecular organization. The lack of plasmid diversity observed, seem to support the hypothesis of a similar phylogeny among these plasmids. This investigation provides more information concerning phylogeny, interrelationships and level of diversity among Bacillus plasmids and a molecular characterization of three plasmids useful for the construction of cloning vectors.
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Affiliation(s)
- Carlo Parini
- Department of Food Science and Microbiology, Industrial Microbiology Section, University of Milan, Via Celoria 2, Milan 20133, Italy.
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15
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Parini C, Guglielmetti S, Mora D, Ricci G. Complete sequence and structural organization of pFL5 and pFL7, two cryptic plasmids from Bacillus licheniformis. Plasmid 2004; 51:192-202. [PMID: 15109826 DOI: 10.1016/j.plasmid.2004.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 02/09/2004] [Indexed: 10/26/2022]
Abstract
The complete nucleotide sequences of two plasmids, pFL5 and pFL7, isolated from soil bacteria, Bacillus licheniformis FL5 and FL7, have been determined. The plasmids pFL5 and pFL7 were analyzed and found to be 9150 and 7853 bp in size with a G+C content of 41.0 and 43.6 mol%, respectively. Computer assisted analysis of sequence data revealed 11 possible ORFs in pFL5, four of which could be assigned no function from homology searches. Instead, eight putative ORFs were identified in pFL7, two of which appeared to have no biological function. All the ORFs were preceded by a ribosome binding site. The ORFs 9.5 and 6.7, each of 340 amino acids, were postulated to encode a replication protein similar to known replication proteins of rolling circle replicons, particularly those of the pC194 family. The structural organization of the two pFL plasmids is similar to the pTA plasmids family, with only a few putative coding regions that cannot be attributed to these plasmid backbone genes. In contrast to pTA plasmids, the majority of the genes have an orientation of transcription opposite to the direction of replication. The identified probable sso sequences seem to belong to a different group of those found in Bacillus plasmids; in fact, a significant level of homology was found with ssoA group sequences. These plasmids seem to be related to plasmids identified within the Bacillus subtilis group, confirming the low-level diversity among these replicons.
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Affiliation(s)
- C Parini
- Department of Food Science and Microbiology, University of Milan, Via Celoria 2, 20133, Italy.
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Strömsten NJ, Benson SD, Burnett RM, Bamford DH, Bamford JKH. The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state. J Bacteriol 2004; 185:6985-9. [PMID: 14617663 PMCID: PMC262720 DOI: 10.1128/jb.185.23.6985-6989.2003] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Bam35, a 15-kbp double-stranded DNA phage, infects Bacillus thuringiensis. Recently, sequencing of the related Bacillus cereus revealed a 15.1-kbp linear plasmid, pBClin15. We show that pBClin15 closely resembles Bam35 and demonstrate conversion of Bam35 to a prophage. This state is common, as several B. thuringiensis strains release Bam35-related viruses.
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Affiliation(s)
- Nelli J Strömsten
- Department of Biosciences and Institute of Biotechnology, Biocenter 2, FIN-00014, University of Helsinki, Finland
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Dionisio F, Matic I, Radman M, Rodrigues OR, Taddei F. Plasmids spread very fast in heterogeneous bacterial communities. Genetics 2002; 162:1525-32. [PMID: 12524329 PMCID: PMC1462386 DOI: 10.1093/genetics/162.4.1525] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Conjugative plasmids can mediate gene transfer between bacterial taxa in diverse environments. The ability to donate the F-type conjugative plasmid R1 greatly varies among enteric bacteria due to the interaction of the system that represses sex-pili formations (products of finOP) of plasmids already harbored by a bacterial strain with those of the R1 plasmid. The presence of efficient donors in heterogeneous bacterial populations can accelerate plasmid transfer and can spread by several orders of magnitude. Such donors allow millions of other bacteria to acquire the plasmid in a matter of days whereas, in the absence of such strains, plasmid dissemination would take years. This "amplification effect" could have an impact on the evolution of bacterial pathogens that exist in heterogeneous bacterial communities because conjugative plasmids can carry virulence or antibiotic-resistance genes.
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Affiliation(s)
- Francisco Dionisio
- Faculté de Médicine Necker-Enfants Malade, INSERM U571, Université Paris V, 75730 Paris Cedex 15, France.
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Mason VP, Syrett N, Hassanali T, Osborn A. Diversity and linkage of replication and mobilisation genes in Bacillus rolling circle-replicating plasmids from diverse geographical origins. FEMS Microbiol Ecol 2002; 42:235-41. [DOI: 10.1111/j.1574-6941.2002.tb01013.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Beeson KE, Erdner DL, Bagwell CE, Lovell CR, Sobecky PA. Differentiation of plasmids in marine diazotroph assemblages determined by randomly amplified polymorphic DNA analysis. MICROBIOLOGY (READING, ENGLAND) 2002; 148:179-189. [PMID: 11782510 DOI: 10.1099/00221287-148-1-179] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nitrogen fixation by diazotrophic bacteria is a significant source of new nitrogen in salt marsh ecosystems. Recent studies have characterized the physiological and phylogenetic diversity of oxygen-utilizing diazotrophs isolated from the rhizoplanes of spatially separated intertidal macrophyte habitats. However, there is a paucity of information regarding the traits encoded by and the diversity of plasmids occurring in this key ecological functional group. Five-hundred and twenty-one isolates cultivated from the rhizoplanes of Juncus roemarianus, Spartina patens and different growth forms (short-form and tall-form) of Spartina alterniflora were screened for the presence of plasmids. One-hundred and thirty-four diazotrophs carrying plasmids that ranged in size from 2 to >100 kbp were identified. The majority of the marine bacteria contained one plasmid. Diazotrophs from the short-form S. alterniflora rhizoplane contained significantly fewer plasmids relative to isolates from tall-form S. alterniflora, J. roemarianus and S. patens. Although some plasmids exhibited homology to a nifH gene probe, the majority of the plasmids were classified as cryptic. Two oligonucleotide primers were developed to facilitate genotypic typing of the endogenously isolated marine plasmids by the randomly amplified polymorphic DNA (RAPD)-PCR technique. These primers proved to be more effective than 21 commercially available primers tested to generate RAPD-PCR patterns. Analysis of the RAPD-PCR patterns indicated as many as 71 different plasmid genotypes occurring in diazotroph bacterial assemblages within and between the four different salt marsh grass rhizoplane habitats investigated in this study.
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Affiliation(s)
- Keri E Beeson
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA1
| | - Deana L Erdner
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA1
| | - Christopher E Bagwell
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA2
| | - Charles R Lovell
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA2
| | - Patricia A Sobecky
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA1
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Luo Y, Leisinger T, Wasserfallen A. Comparative sequence analysis of plasmids pME2001 and pME2200 of methanothermobacter marburgensis strains Marburg and ZH3. Plasmid 2001; 45:18-30. [PMID: 11319928 DOI: 10.1006/plas.2000.1493] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Comparison of the updated complete nucleotide sequences of the two related plasmids pME2001 and pME2200 from the thermophilic archaeon Methanothermobacter marburgensis (formerly Methanobacterium thermoautotrophicum) strains Marburg and ZH3, respectively, revealed an almost identical common backbone structure and five plasmid-specific inserted fragments (IFs), four of which are flanked by perfect or nearly perfect direct repeats 25-52 bp in length. A 4354-bp minimal replicon was derived from the alignment of the two plasmids, which encodes one putative antisense RNA related to replication control and five open reading frames (ORFs) organized in two operons. The first operon consists of four ORFs, the third of which, i.e. ORF3, contains a helix-turn-helix motif and a purine NTP-binding motif often found in proteins involved in DNA metabolic processes. The database search results suggest that ORF3 might function as a replication initiator protein. The large putative Rep protein encoded by pME2001 was overexpressed in Escherichia coli as an N-terminal His-tagged version using pET28a and a compatible helper plasmid that coexpresses minor tRNAs, argU and ileX to compensate for codon usage difference. ORFs 1, 2, and 3 are organized in a sequence reminiscent of that described in E. coli plasmids of the R1 family, cop-tap-rep. ORF6 encoded by IF1, one of the pME2200-specific elements, showed significant similarity to ORF6 encoded by archaeal phage psiM2 of M. marburgensis strain Marburg and may confer the apparent immunity of its host strain ZH3 to infection by phage psiM2. Our data indicate that M. marburgensis plasmids may evolve by a series of gene duplication and excision events.
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Affiliation(s)
- Y Luo
- Institute of Microbiology, Swiss Federal Institute of Technology Zürich, Schmelzbergstrasse 7, Zürich, CH-8092, Switzerland
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21
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Manachini PL, Fortina MG, Levati L, Parini C. Contribution to phenotypic and genotypic characterization of Bacillus licheniformis and description of new genomovars. Syst Appl Microbiol 1998; 21:520-9. [PMID: 9924820 DOI: 10.1016/s0723-2020(98)80064-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A study of phenotypic and genotypic characteristics was carried out on 182 strains isolated from soil of different geographical areas; the type strains were B. licheniformis, B. subtilis, B. pumilus, B. cereus and B. coagulans. The results showed, primarily on the basis of phenotypic features, that all the isolates belonged to the B. licheniformis species, however DNA relatedness studies revealed only 161 to be genetically related to B. licheniformis, the DNA relatedness levels ranging from 66 to 100%. The other 21 isolates appeared to be genetically distinct not only from B. licheniformis but also from B. subtilis and B. pumilus, where there were low levels of DNA relatedness (from 4 to 37%). Nevertheless the ARDRA results indicate that the 21 atypical isolates were phylogenetically related to B. licheniformis. Our data and the phenotypic homogeneity found suggest the presence of three different genomovars.
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Affiliation(s)
- P L Manachini
- Universià degli Studi di Milano, Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Italy
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Sobecky PA, Mincer TJ, Chang MC, Toukdarian A, Helinski DR. Isolation of broad-host-range replicons from marine sediment bacteria. Appl Environ Microbiol 1998; 64:2822-30. [PMID: 9687436 PMCID: PMC106778 DOI: 10.1128/aem.64.8.2822-2830.1998] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Naturally occurring plasmids isolated from heterotrophic bacterial isolates originating from coastal California marine sediments were characterized by analyzing their incompatibility and replication properties. Previously, we reported on the lack of DNA homology between plasmids from the culturable bacterial population of marine sediments and the replicon probes specific for a number of well-characterized incompatibility and replication groups (P. A. Sobecky, T. J. Mincer, M. C. Chang, and D. R. Helinski, Appl. Environ. Microbiol. 63:888-895, 1997). In the present study we isolated 1.8- to 2.3-kb fragments that contain functional replication origins from one relatively large (30-kb) and three small (<10-kb) naturally occurring plasmids present in different marine isolates. 16S rRNA sequence analyses indicated that the four plasmid-bearing marine isolates belonged to the alpha and gamma subclasses of the class Proteobacteria. Three of the marine sediment isolates are related to the gamma-3 subclass organisms Vibrio splendidus and Vibrio fischeri, while the fourth isolate may be related to Roseobacter litoralis. Sequence analysis of the plasmid replication regions revealed the presence of features common to replication origins of well-characterized plasmids from clinical bacterial isolates, suggesting that there may be similar mechanisms for plasmid replication initiation in the indigenous plasmids of gram-negative marine sediment bacteria. In addition to replication in Escherichia coli DH5alpha and C2110, the host ranges of the plasmid replicons, designated repSD41, repSD121, repSD164, and repSD172, extended to marine species belonging to the genera Achromobacter, Pseudomonas, Serratia, and Vibrio. While sequence analysis of repSD41 and repSD121 revealed considerable stretches of homology between the two fragments, these regions do not display incompatibility properties against each other. The replication origin repSD41 was detected in 5% of the culturable plasmid-bearing marine sediment bacterial isolates, whereas the replication origins repSD164 and repSD172 were not detected in any plasmid-bearing bacteria other than the parental isolates. Microbial community DNA extracted from samples collected in November 1995 and June 1997 and amplified by PCR yielded positive signals when they were hybridized with probes specific for repSD41 and repSD172 replication sequences. In contrast, replication sequences specific for repSD164 were not detected in the DNA extracted from marine sediment microbial communities.
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Affiliation(s)
- P A Sobecky
- Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0634, USA.
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Meijer WJ, Wisman GB, Terpstra P, Thorsted PB, Thomas CM, Holsappel S, Venema G, Bron S. Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from gram-positive bacteria. FEMS Microbiol Rev 1998; 21:337-68. [PMID: 9532747 DOI: 10.1111/j.1574-6976.1998.tb00357.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Most small plasmids of Gram-positive bacteria use the rolling-circle mechanism of replication and several of these have been studied in considerable detail at the DNA level and for the function of their genes. Although most of the common laboratory Bacillus subtilis 168 strains do not contain plasmids, several industrial strains and natural soil isolates do contain rolling-circle replicating (RCR) plasmids. So far, knowledge about these plasmids was mainly limited to: (i) a classification into seven groups, based on size and restriction patterns; and (ii) DNA sequences of the replication region of a limited number of them. To increase the knowledge, also with respect to other functions specified by these plasmids, we have determined the complete DNA sequence of four plasmids, representing different groups, and performed computer-assisted and experimental analyses on the possible function of their genes. The plasmids analyzed are pTA1015 (5.8 kbp), pTA1040 (7.8 kbp), pTA1050 (8.4 kbp), and pTA1060 (8.7 kbp). These plasmids have a structural organization similar to most other known RCR plasmids. They contain highly related replication functions, both for leading and lagging strand synthesis. pTA1015 and pTA1060 contain a mobilization gene enabling their conjugative transfer. Strikingly, in addition to the conserved replication modules, these plasmids contain unique module(s) with genes which are not present on known RCR plasmids of other Gram-positive bacteria. Examples are genes encoding a type I signal peptidase and genes encoding proteins belonging to the family of response regulator aspartate phosphatases. The latter are likely to be involved in the regulation of post-exponential phase processes. The presence of these modules on plasmids may reflect an adaptation to the special conditions to which the host cells were exposed.
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Affiliation(s)
- W J Meijer
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Haren, The Netherlands
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Souza V, Eguiarte LE. Bacteria gone native vs. bacteria gone awry?: plasmidic transfer and bacterial evolution. Proc Natl Acad Sci U S A 1997; 94:5501-3. [PMID: 9159098 PMCID: PMC33669 DOI: 10.1073/pnas.94.11.5501] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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Wernegreen JJ, Harding EE, Riley MA. Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum. Proc Natl Acad Sci U S A 1997; 94:5483-8. [PMID: 9144264 PMCID: PMC24705 DOI: 10.1073/pnas.94.10.5483] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Lateral transfer of bacterial plasmids is thought to play an important role in microbial evolution and population dynamics. However, this assumption is based primarily on investigations of medically or agriculturally important bacterial species. To explore the role of lateral transfer in the evolution of bacterial systems not under intensive, human-mediated selection, we examined the association of genotypes at plasmid-encoded and chromosomal loci of native Rhizobium, the nitrogen-fixing symbiont of legumes. To this end, Rhizobium leguminosarum strains nodulating sympatric species of native Trifolium were characterized genetically at plasmid-encoded symbiotic (sym) regions (nodulation AB and nodulation CIJT loci) and a repeated chromosomal locus not involved in the symbiosis with legumes. Restriction fragment length polymorphism analysis was used to distinguish genetic groups at plasmid and chromosomal loci. The correlation between major sym and chromosomal genotypes and the distribution of genotypes across host plant species and sampling location were determined using chi2 analysis. In contrast to findings of previous studies, a strict association existed between major sym plasmid and chromosomal genetic groups, suggesting a lack of successful sym plasmid transfer between major Rhizobium chromosomal types. These data indicate that previous observations of sym plasmid transfer in agricultural settings may seriously overestimate the rates of successful conjugation in systems not impacted by human activities. In addition, a nonrandom distribution of Rhizobium genotypes across host plant species and sampling site demonstrates the importance of both factors in shaping Rhizobium population dynamics.
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Affiliation(s)
- J J Wernegreen
- Department of Biology, Yale University, New Haven, CT 06511, USA.
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