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Liljegren MM, Gama JA, Johnsen PJ, Harms K. The recombination initiation functions DprA and RecFOR suppress microindel mutations in Acinetobacter baylyi ADP1. Mol Microbiol 2024; 122:1-10. [PMID: 38760330 DOI: 10.1111/mmi.15277] [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] [Received: 11/22/2023] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024]
Abstract
Short-Patch Double Illegitimate Recombination (SPDIR) has been recently identified as a rare mutation mechanism. During SPDIR, ectopic DNA single-strands anneal with genomic DNA at microhomologies and get integrated during DNA replication, presumably acting as primers for Okazaki fragments. The resulting microindel mutations are highly variable in size and sequence. In the soil bacterium Acinetobacter baylyi, SPDIR is tightly controlled by genome maintenance functions including RecA. It is thought that RecA scavenges DNA single-strands and renders them unable to anneal. To further elucidate the role of RecA in this process, we investigate the roles of the upstream functions DprA, RecFOR, and RecBCD, all of which load DNA single-strands with RecA. Here we show that all three functions suppress SPDIR mutations in the wildtype to levels below the detection limit. While SPDIR mutations are slightly elevated in the absence of DprA, they are strongly increased in the absence of both DprA and RecA. This SPDIR-avoiding function of DprA is not related to its role in natural transformation. These results suggest a function for DprA in combination with RecA to avoid potentially harmful microindel mutations, and offer an explanation for the ubiquity of dprA in the genomes of naturally non-transformable bacteria.
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Affiliation(s)
- Mikkel M Liljegren
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - João A Gama
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Pål J Johnsen
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - Klaus Harms
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
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2
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Garoña A, Santer M, Hülter NF, Uecker H, Dagan T. Segregational drift hinders the evolution of antibiotic resistance on polyploid replicons. PLoS Genet 2023; 19:e1010829. [PMID: 37535631 PMCID: PMC10399855 DOI: 10.1371/journal.pgen.1010829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/14/2023] [Indexed: 08/05/2023] Open
Abstract
The emergence of antibiotic resistance under treatment depends on the availability of resistance alleles and their establishment in the population. Novel resistance alleles are encoded either in chromosomal or extrachromosomal genetic elements; both types may be present in multiple copies within the cell. However, the effect of polyploidy on the emergence of antibiotic resistance remains understudied. Here we show that the establishment of resistance alleles in microbial populations depends on the ploidy level. Evolving bacterial populations under selection for antibiotic resistance, we demonstrate that resistance alleles in polyploid elements are lost frequently in comparison to alleles in monoploid elements due to segregational drift. Integrating the experiments with a mathematical model, we find a remarkable agreement between the theoretical and empirical results, confirming our understanding of the allele segregation process. Using the mathematical model, we further show that the effect of polyploidy on the establishment probability of beneficial alleles is strongest for low replicon copy numbers and plateaus for high replicon copy numbers. Our results suggest that the distribution of fitness effects for mutations that are eventually fixed in a population depends on the replicon ploidy level. Our study indicates that the emergence of antibiotic resistance in bacterial pathogens depends on the pathogen ploidy level.
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Affiliation(s)
- Ana Garoña
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Mario Santer
- Institute of General Microbiology, Kiel University, Kiel, Germany
- Research group Stochastic Evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Nils F. Hülter
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Hildegard Uecker
- Research group Stochastic Evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
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3
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Garoña A, Hülter NF, Romero Picazo D, Dagan T. Segregational drift constrains the evolutionary rate of prokaryotic plasmids. Mol Biol Evol 2021; 38:5610-5624. [PMID: 34550379 PMCID: PMC8662611 DOI: 10.1093/molbev/msab283] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plasmids are extrachromosomal genetic elements in prokaryotes that have been recognized as important drivers of microbial ecology and evolution. Plasmids are found in multiple copies inside their host cell where independent emergence of mutations may lead to intracellular genetic heterogeneity. The intracellular plasmid diversity is thus subject to changes upon cell division. However, the effect of plasmid segregation on plasmid evolution remains understudied. Here, we show that genetic drift during cell division—segregational drift—leads to the rapid extinction of novel plasmid alleles. We established a novel experimental approach to control plasmid allele frequency at the levels of a single cell and the whole population. Following the dynamics of plasmid alleles in an evolution experiment, we find that the mode of plasmid inheritance—random or clustered—is an important determinant of plasmid allele dynamics. Phylogenetic reconstruction of our model plasmid in clinical isolates furthermore reveals a slow evolutionary rate of plasmid-encoded genes in comparison to chromosomal genes. Our study provides empirical evidence that genetic drift in plasmid evolution occurs at multiple levels: the host cell and the population of hosts. Segregational drift has implications for the evolutionary rate heterogeneity of extrachromosomal genetic elements.
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Affiliation(s)
- Ana Garoña
- Institute of General Microbiology, Kiel University, Kiel, 24118, Germany
| | - Nils F Hülter
- Institute of General Microbiology, Kiel University, Kiel, 24118, Germany
| | | | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, 24118, Germany
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4
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Racharaks R, Arnold W, Peccia J. Development of CRISPR-Cas9 knock-in tools for free fatty acid production using the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973. J Microbiol Methods 2021; 189:106315. [PMID: 34454980 DOI: 10.1016/j.mimet.2021.106315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022]
Abstract
Synechococcus elongatus UTEX 2973 has one of the fastest measured doubling time of cyanobacteria making it an important candidate for metabolic engineering. Traditional genetic engineering methods, which rely on homologous recombination, however, are inefficient, labor-intensive, and time-consuming due to the oligoploidy or polyploidy nature of cyanobacteria and the reliance on unique antibiotic resistance markers. CRISPR-Cas9 has emerged as an effective and versatile editing platform in a wide variety of organisms, but its application for cyanobacterial engineering is limited by the inherent toxicity of Cas9 resulting in poor transformation efficiencies. Here, we demonstrated that a single-plasmid CRISPR-Cas9 system, pCRISPOmyces-2, can effectively knock-in a truncated thioesterase gene from Escherichia coli to generate free fatty acid (FFA) producing mutants of Syn2973. To do so, three parameters were evaluated on the effect of generating recipient colonies after conjugation with pCRISPOmyces-2-based plasmids: 1) a modified conjugation protocol termed streaked conjugation, 2) the deletion of the gene encoding RecJ exonuclease, and 3) single guide RNA (sgRNA) sequence. With the use of the streaked conjugation protocol and a ΔrecJ mutant strain of Syn2973, the conjugation efficiency for the pCRISPomyces-2 plasmid could be improved by 750-fold over the wildtype (WT) for a conjugation efficiency of 2.0 × 10-6 transconjugants/recipient cell. While deletion of the RecJ exonuclease alone increased the conjugation efficiency by 150-fold over the WT, FFA generation was impaired in FFA-producing mutants with the ΔrecJ background, and the large number of poor FFA-producing isolates indicated the potential increase in spontaneous mutation rates. The sgRNA sequence was found to be critical in achieving the desired CRISPR-Cas9-mediated knock-in mutation as the sgRNA impacts conjugation efficiency, likelihood of homogenous recombinants, and free fatty acid production in engineered strains.
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Affiliation(s)
- Ratanachat Racharaks
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Wyatt Arnold
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA.
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5
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Kloos J, Johnsen PJ, Harms K. Tn 1 transposition in the course of natural transformation enables horizontal antibiotic resistance spread in Acinetobacter baylyi. MICROBIOLOGY-SGM 2020; 167. [PMID: 33270000 PMCID: PMC8116780 DOI: 10.1099/mic.0.001003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Transposons are genetic elements that change their intracellular genomic position by transposition and are spread horizontally between bacteria when located on plasmids. It was recently discovered that transposition from fully heterologous DNA also occurs in the course of natural transformation. Here, we characterize the molecular details and constraints of this process using the replicative transposon Tn1 and the naturally competent bacterium Acinetobacter baylyi. We find that chromosomal insertion of Tn1 by transposition occurs at low but detectable frequencies and preferably around the A. baylyi terminus of replication. We show that Tn1 transposition is facilitated by transient expression of the transposase and resolvase encoded by the donor DNA. RecA protein is essential for the formation of a circular, double-stranded cytoplasmic intermediate from incoming donor DNA, and RecO is beneficial but not essential in this process. Absence of the recipient RecBCD nuclease stabilizes the double-stranded intermediate. Based on these results, we suggest a mechanistic model for transposition during natural transformation.
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Affiliation(s)
- Julia Kloos
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Pål J Johnsen
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Klaus Harms
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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6
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Zhou H, Zhang L, Xu Q, Zhang L, Yu Y, Hua X. The mismatch repair system (mutS and mutL) in Acinetobacter baylyi ADP1. BMC Microbiol 2020; 20:40. [PMID: 32111158 PMCID: PMC7048072 DOI: 10.1186/s12866-020-01729-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 02/14/2020] [Indexed: 02/06/2023] Open
Abstract
Background Acinetobacter baylyi ADP1 is an ideal bacterial strain for high-throughput genetic analysis as the bacterium is naturally transformable. Thus, ADP1 can be used to investigate DNA mismatch repair, a mechanism for repairing mismatched bases. We used the mutS deletion mutant (XH439) and mutL deletion mutant (XH440), and constructed a mutS mutL double deletion mutant (XH441) to investigate the role of the mismatch repair system in A. baylyi. Results We determined the survival rates after UV irradiation and measured the mutation frequencies, rates and spectra of wild-type ADP1 and mutSL mutant via rifampin resistance assay (RifR assay) and experimental evolution. In addition, transformation efficiencies of genomic DNA in ADP1 and its three mutants were determined. Lastly, the relative growth rates of the wild type strain, three constructed deletion mutants, as well as the rifampin resistant mutants obtained from RifR assays, were measured. All three mutants had higher survival rates after UV irradiation than wild type, especially the double deletion mutant. Three mutants showed higher mutation frequencies than ADP1 and favored transition mutations in RifR assay. All three mutants showed increased mutation rates in the experimental evolution. However, only XH439 and XH441 had higher mutation rates than the wild type strain in RifR assay. XH441 showed higher transformation efficiency than XH438 when donor DNA harbored transition mutations. All three mutants showed higher growth rates than wild-type, and these four strains displayed higher growth rates than almost all their rpoB mutants. The growth rate results showed different amino acid mutations in rpoB resulted in different extents of reduction in the fitness of rifampin resistant mutants. However, the fitness cost brought by the same mutation did not vary with strain background. Conclusions We demonstrated that inactivation of both mutS and mutL increased the mutation rates and frequencies in A. baylyi, which would contribute to the evolution and acquirement of rifampicin resistance. The mutS deletion is also implicated in increased mutation rates and frequencies, suggesting that MutL may be activated even in the absence of mutS. The correlation between fitness cost and rifampin resistance mutations in A. baylyi is firstly established.
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Affiliation(s)
- Hua Zhou
- Department of Respiratory Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Linyue Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Qingye Xu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Linghong Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.
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7
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Resistance to UV Irradiation Caused by Inactivation of nurA and herA Genes in Thermus thermophilus. J Bacteriol 2018; 200:JB.00201-18. [PMID: 29844033 DOI: 10.1128/jb.00201-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/23/2018] [Indexed: 11/20/2022] Open
Abstract
NurA and HerA are thought to be essential proteins for DNA end resection in archaeal homologous recombination systems. Thermus thermophilus, an extremely thermophilic eubacterium, has proteins that exhibit significant sequence similarity to archaeal NurA and HerA. To unveil the cellular function of NurA and HerA in T. thermophilus, we performed phenotypic analysis of disruptant mutants of nurA and herA with or without DNA-damaging agents. The nurA and herA genes were not essential for survival, and their deletion had no effect on cell growth and genome integrity. Unexpectedly, these disruptants of T. thermophilus showed increased resistance to UV irradiation and mitomycin C treatment. Further, these disruptants and the wild type displayed no difference in sensitivity to oxidative stress and a DNA replication inhibitor. T. thermophilus NurA had nuclease activity, and HerA had ATPase. The overexpression of loss-of-function mutants of nurA and herA in the respective disruptants showed no complementation, suggesting their enzymatic activities were involved in the UV sensitivity. In addition, T. thermophilus NurA and HerA interacted with each other in vitro and in vivo, forming a complex with 2:6 stoichiometry. These results suggest that the NurA-HerA complex has an architecture similar to that of archaeal counterparts but that it impairs, rather than promotes, the repair of photoproducts and DNA cross-links in T. thermophilus cells. This cellular function is distinctly different from that of archaeal NurA and HerA.IMPORTANCE Many nucleases and helicases are engaged in homologous recombination-mediated DNA repair. Previous in vitro analyses in archaea indicated that NurA and HerA are the recombination-related nuclease and helicase. However, their cellular function had not been fully understood, especially in bacterial cells. In this study, we performed in vivo analyses to address the cellular function of nurA and herA in an extremely thermophilic bacterium, Thermus thermophilus As a result, T. thermophilus NurA and HerA exhibited an interfering effect on the repair of several instances of DNA damage in the cell, which is in contrast to the results in archaea. This finding will facilitate our understanding of the diverse cellular functions of the recombination-related nucleases and helicases.
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8
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An Increase of Abundance and Transcriptional Activity for Acinetobacter junii Post Wastewater Treatment. WATER 2018. [DOI: 10.3390/w10040436] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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9
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Wein T, Dagan T, Fraune S, Bosch TCG, Reusch TBH, Hülter NF. Carrying Capacity and Colonization Dynamics of Curvibacter in the Hydra Host Habitat. Front Microbiol 2018; 9:443. [PMID: 29593687 PMCID: PMC5861309 DOI: 10.3389/fmicb.2018.00443] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/26/2018] [Indexed: 01/29/2023] Open
Abstract
Most eukaryotic species are colonized by a microbial community – the microbiota – that is acquired during early life stages and is critical to host development and health. Much research has focused on the microbiota biodiversity during the host life, however, empirical data on the basic ecological principles that govern microbiota assembly is lacking. Here we quantify the contribution of colonizer order, arrival time and colonization history to microbiota assembly on a host. We established the freshwater polyp Hydra vulgaris and its dominant colonizer Curvibacter as a model system that enables the visualization and quantification of colonizer population size at the single cell resolution, in vivo, in real time. We estimate the carrying capacity of a single Hydra polyp as 2 × 105Curvibacter cells, which is robust among individuals and time. Colonization experiments reveal a clear priority effect of first colonizers that depends on arrival time and colonization history. First arriving colonizers achieve a numerical advantage over secondary colonizers within a short time lag of 24 h. Furthermore, colonizers primed for the Hydra habitat achieve a numerical advantage in the absence of a time lag. These results follow the theoretical expectations for any bacterial habitat with a finite carrying capacity. Thus, Hydra colonization and succession processes are largely determined by the habitat occupancy over time and Curvibacter colonization history. Our experiments provide empirical data on the basic steps of host-associated microbiota establishment – the colonization stage. The presented approach supplies a framework for studying habitat characteristics and colonization dynamics within the host–microbe setting.
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Affiliation(s)
- Tanita Wein
- Institute of Microbiology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Tal Dagan
- Institute of Microbiology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Sebastian Fraune
- Institute of Zoology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Thomas C G Bosch
- Institute of Zoology, Christian-Albrechts University of Kiel, Kiel, Germany
| | | | - Nils F Hülter
- Institute of Microbiology, Christian-Albrechts University of Kiel, Kiel, Germany
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10
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Ambur OH, Engelstädter J, Johnsen PJ, Miller EL, Rozen DE. Steady at the wheel: conservative sex and the benefits of bacterial transformation. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0528. [PMID: 27619692 PMCID: PMC5031613 DOI: 10.1098/rstb.2015.0528] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2016] [Indexed: 12/25/2022] Open
Abstract
Many bacteria are highly sexual, but the reasons for their promiscuity remain obscure. Did bacterial sex evolve to maximize diversity and facilitate adaptation in a changing world, or does it instead help to retain the bacterial functions that work right now? In other words, is bacterial sex innovative or conservative? Our aim in this review is to integrate experimental, bioinformatic and theoretical studies to critically evaluate these alternatives, with a main focus on natural genetic transformation, the bacterial equivalent of eukaryotic sexual reproduction. First, we provide a general overview of several hypotheses that have been put forward to explain the evolution of transformation. Next, we synthesize a large body of evidence highlighting the numerous passive and active barriers to transformation that have evolved to protect bacteria from foreign DNA, thereby increasing the likelihood that transformation takes place among clonemates. Our critical review of the existing literature provides support for the view that bacterial transformation is maintained as a means of genomic conservation that provides direct benefits to both individual bacterial cells and to transformable bacterial populations. We examine the generality of this view across bacteria and contrast this explanation with the different evolutionary roles proposed to maintain sex in eukaryotes. This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Ole Herman Ambur
- Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, 1478 Oslo, Norway
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Pål J Johnsen
- Faculty of Health Sciences, Department of Pharmacy, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Eric L Miller
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Daniel E Rozen
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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11
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Reduced Mutation Rate and Increased Transformability of Transposon-Free Acinetobacter baylyi ADP1-ISx. Appl Environ Microbiol 2017; 83:AEM.01025-17. [PMID: 28667117 DOI: 10.1128/aem.01025-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/21/2017] [Indexed: 01/02/2023] Open
Abstract
The genomes of most bacteria contain mobile DNA elements that can contribute to undesirable genetic instability in engineered cells. In particular, transposable insertion sequence (IS) elements can rapidly inactivate genes that are important for a designed function. We deleted all six copies of IS1236 from the genome of the naturally transformable bacterium Acinetobacter baylyi ADP1. The natural competence of ADP1 made it possible to rapidly repair deleterious point mutations that arose during strain construction. In the resulting ADP1-ISx strain, the rates of mutations inactivating a reporter gene were reduced by 7- to 21-fold. This reduction was higher than expected from the incidence of new IS1236 insertions found during a 300-day mutation accumulation experiment with wild-type ADP1 that was used to estimate spontaneous mutation rates in the strain. The extra improvement appears to be due in part to eliminating large deletions caused by IS1236 activity, as the point mutation rate was unchanged in ADP1-ISx. Deletion of an error-prone polymerase (dinP) and a DNA damage response regulator (umuDAb [the umuD gene of A. baylyi]) from the ADP1-ISx genome did not further reduce mutation rates. Surprisingly, ADP1-ISx exhibited increased transformability. This improvement may be due to less autolysis and aggregation of the engineered cells than of the wild type. Thus, deleting IS elements from the ADP1 genome led to a greater than expected increase in evolutionary reliability and unexpectedly enhanced other key strain properties, as has been observed for other clean-genome bacterial strains. ADP1-ISx is an improved chassis for metabolic engineering and other applications.IMPORTANCEAcinetobacter baylyi ADP1 has been proposed as a next-generation bacterial host for synthetic biology and genome engineering due to its ability to efficiently take up DNA from its environment during normal growth. We deleted transposable elements that are capable of copying themselves, inserting into other genes, and thereby inactivating them from the ADP1 genome. The resulting "clean-genome" ADP1-ISx strain exhibited larger reductions in the rates of inactivating mutations than expected from spontaneous mutation rates measured via whole-genome sequencing of lineages evolved under relaxed selection. Surprisingly, we also found that IS element activity reduces transformability and is a major cause of cell aggregation and death in wild-type ADP1 grown under normal laboratory conditions. More generally, our results demonstrate that domesticating a bacterial genome by removing mobile DNA elements that have accumulated during evolution in the wild can have unanticipated benefits.
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12
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Hülter N, Sørum V, Borch-Pedersen K, Liljegren MM, Utnes ALG, Primicerio R, Harms K, Johnsen PJ. Costs and benefits of natural transformation in Acinetobacter baylyi. BMC Microbiol 2017; 17:34. [PMID: 28202049 PMCID: PMC5312590 DOI: 10.1186/s12866-017-0953-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 02/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background Natural transformation enables acquisition of adaptive traits and drives genome evolution in prokaryotes. Yet, the selective forces responsible for the evolution and maintenance of natural transformation remain elusive since taken-up DNA has also been hypothesized to provide benefits such as nutrients or templates for DNA repair to individual cells. Results We investigated the immediate effects of DNA uptake and recombination on the naturally competent bacterium Acinetobacter baylyi in both benign and genotoxic conditions. In head-to-head competition experiments between DNA uptake-proficient and -deficient strains, we observed a fitness benefit of DNA uptake independent of UV stress. This benefit was found with both homologous and heterologous DNA and was independent of recombination. Recombination with taken-up DNA reduced survival of transformed cells with increasing levels of UV-stress through interference with nucleotide excision repair, suggesting that DNA strand breaks occur during recombination attempts with taken-up DNA. Consistent with this, we show that absence of RecBCD and RecFOR recombinational DNA repair pathways strongly decrease natural transformation. Conclusions Our data show a physiological benefit of DNA uptake unrelated to recombination. In contrast, recombination during transformation is a strand break inducing process that represents a previously unrecognized cost of natural transformation. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0953-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nils Hülter
- Genomic Microbiology, Institute of Microbiology, Christian-Albrechts-University Kiel, Am Botanischen Garten 11, 24118, Kiel, Germany.,Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Vidar Sørum
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Kristina Borch-Pedersen
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 8146 Dep, 0033, Oslo, Norway
| | - Mikkel M Liljegren
- Centre for Ecolgical and Evolutionary Synthesis, Faculty of Mathematics and Natural Sciences, University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway
| | - Ane L G Utnes
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Raul Primicerio
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway
| | - Klaus Harms
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway. .,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, Tromsø, Norway.
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13
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Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms. Proc Natl Acad Sci U S A 2016; 113:15066-15071. [PMID: 27956618 DOI: 10.1073/pnas.1615819114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.
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Cheng K, Zhao Y, Chen X, Li T, Wang L, Xu H, Tian B, Hua Y. A Novel C-Terminal Domain of RecJ is Critical for Interaction with HerA in Deinococcus radiodurans. Front Microbiol 2015; 6:1302. [PMID: 26648913 PMCID: PMC4663267 DOI: 10.3389/fmicb.2015.01302] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/06/2015] [Indexed: 01/09/2023] Open
Abstract
Homologous recombination (HR) generates error-free repair products, which plays an important role in double strand break repair and replication fork rescue processes. DNA end resection, the critical step in HR, is usually performed by a series of nuclease/helicase. RecJ was identified as a 5'-3' exonuclease involved in bacterial DNA end resection. Typical RecJ possesses a conserved DHH domain, a DHHA1 domain, and an oligonucleotide/oligosaccharide-binding (OB) fold. However, RecJs from Deinococcus-Thermus phylum, such as Deinococcus radiodurans RecJ (DrRecJ), possess an extra C-terminal domain (CTD), of which the function has not been characterized. Here, we showed that a CTD-deletion of DrRecJ (DrRecJΔC) could not restore drrecJ mutant growth and mitomycin C (MMC)-sensitive phenotypes, indicating that this domain is essential for DrRecJ in vivo. DrRecJΔC displayed reduced DNA nuclease activity and DNA binding ability. Direct interaction was identified between DrRecJ-CTD and DrHerA, which stimulates DrRecJ nuclease activity by enhancing its DNA binding affinity. Moreover, DrNurA nuclease, another partner of DrHerA, inhibited the stimulation of DrHerA on DrRecJ nuclease activity by interaction with DrHerA. Opposing growth and MMC-resistance phenotypes between the recJ and nurA mutants were observed. A novel modulation mechanism among DrRecJ, DrHerA, and DrNurA was also suggested.
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Affiliation(s)
- Kaiying Cheng
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Ye Zhao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Xuanyi Chen
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Tao Li
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Liangyan Wang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Hong Xu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Bing Tian
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University Hangzhou, China
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15
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Biswas I. Genetic tools for manipulating Acinetobacter baumannii genome: an overview. J Med Microbiol 2015; 64:657-669. [PMID: 25948809 DOI: 10.1099/jmm.0.000081] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Acinetobacter baumannii is an emerging nosocomial pathogen involved in a variety of infections ranging from minor soft-tissue infections to more severe infections such as ventilator-associated pneumonia and bacteraemia. A. baumannii has become resistant to most of the commonly used antibiotics and multidrug-resistant isolates are becoming a severe problem in the healthcare setting. In the past few years, whole-genome sequences of >200 A. baumannii isolates have been generated. Several methods and molecular tools have been used for genetic manipulation of various Acinetobacter spp. Here, we review recent developments of various genetic tools used for modification of the A. baumannii genome, including various ways to inactivate gene function, chromosomal integration and transposon mutagenesis.
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Affiliation(s)
- Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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16
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Kurth D, Belfiore C, Gorriti MF, Cortez N, Farias ME, Albarracín VH. Genomic and proteomic evidences unravel the UV-resistome of the poly-extremophile Acinetobacter sp. Ver3. Front Microbiol 2015; 6:328. [PMID: 25954258 PMCID: PMC4406064 DOI: 10.3389/fmicb.2015.00328] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/01/2015] [Indexed: 12/20/2022] Open
Abstract
Ultraviolet radiation can damage biomolecules, with detrimental or even lethal effects for life. Even though lower wavelengths are filtered by the ozone layer, a significant amount of harmful UV-B and UV-A radiation reach Earth's surface, particularly in high altitude environments. high-altitude Andean lakes (HAALs) are a group of disperse shallow lakes and salterns, located at the Dry Central Andes region in South America at altitudes above 3,000 m. As it is considered one of the highest UV-exposed environments, HAAL microbes constitute model systems to study UV-resistance mechanisms in environmental bacteria at various complexity levels. Herein, we present the genome sequence of Acinetobacter sp. Ver3, a gammaproteobacterium isolated from Lake Verde (4,400 m), together with further experimental evidence supporting the phenomenological observations regarding this bacterium ability to cope with increased UV-induced DNA damage. Comparison with the genomes of other Acinetobacter strains highlighted a number of unique genes, such as a novel cryptochrome. Proteomic profiling of UV-exposed cells identified up-regulated proteins such as a specific cytoplasmic catalase, a putative regulator, and proteins associated to amino acid and protein synthesis. Down-regulated proteins were related to several energy-generating pathways such as glycolysis, beta-oxidation of fatty acids, and electronic respiratory chain. To the best of our knowledge, this is the first report on a genome from a polyextremophilic Acinetobacter strain. From the genomic and proteomic data, an "UV-resistome" was defined, encompassing the genes that would support the outstanding UV-resistance of this strain.
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Affiliation(s)
- Daniel Kurth
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Carolina Belfiore
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Marta F Gorriti
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Néstor Cortez
- Centro Científico Tecnológico, IBR - CONICET, Universidad Nacional de Rosario Rosario, Argentina
| | - María E Farias
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Virginia H Albarracín
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina ; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán Argentina
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17
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The adnAB locus, encoding a putative helicase-nuclease activity, is essential in Streptomyces. J Bacteriol 2014; 196:2701-8. [PMID: 24837284 DOI: 10.1128/jb.01513-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Homologous recombination is a crucial mechanism that repairs a wide range of DNA lesions, including the most deleterious ones, double-strand breaks (DSBs). This multistep process is initiated by the resection of the broken DNA ends by a multisubunit helicase-nuclease complex exemplified by Escherichia coli RecBCD, Bacillus subtilis AddAB, and newly discovered Mycobacterium tuberculosis AdnAB. Here we show that in Streptomyces, neither recBCD nor addAB homologues could be detected. The only putative helicase-nuclease-encoding genes identified were homologous to M. tuberculosis adnAB genes. These genes are conserved as a single copy in all sequenced genomes of Streptomyces. The disruption of adnAB in Streptomyces ambofaciens and Streptomyces coelicolor could not be achieved unless an ectopic copy was provided, indicating that adnAB is essential for growth. Both adnA and adnB genes were shown to be inducible in response to DNA damage (mitomycin C) and to be independently transcribed. Introduction of S. ambofaciens adnAB genes in an E. coli recB mutant restored viability and resistance to UV light, suggesting that Streptomyces AdnAB could be a functional homologue of RecBCD and be involved in DNA damage resistance.
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18
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Starikova I, Harms K, Haugen P, Lunde TTM, Primicerio R, Samuelsen Ø, Nielsen KM, Johnsen PJ. A trade-off between the fitness cost of functional integrases and long-term stability of integrons. PLoS Pathog 2012; 8:e1003043. [PMID: 23209414 PMCID: PMC3510236 DOI: 10.1371/journal.ppat.1003043] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 10/05/2012] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer (HGT) plays a major role in bacterial microevolution as evident from the rapid emergence and spread of antimicrobial drug resistance. Few studies have however addressed the population dynamics of newly imported genetic elements after HGT. Here, we show that newly acquired class-1 integrons from Salmonella enterica serovar Typhimurium and Acinetobacter baumannii, free of associated transposable elements, strongly reduce host fitness in Acinetobacter baylyi. Insertional inactivation of the integron intI1 restored fitness, demonstrating that the observed fitness costs were due to the presence of an active integrase. The biological cost of harboring class-1 integrons was rapidly reduced during serial transfers due to intI1 frameshift mutations leading to inactivated integrases. We use a mathematical model to explore the conditions where integrons with functional integrases are maintained and conclude that environmental fluctuations and episodic selection is necessary for the maintenance of functional integrases. Taken together, the presented data suggest a trade-off between the ability to capture gene cassettes and long-term stability of integrons and provide an explanation for the frequent observation of inactive integron-integrases in bacterial populations. Horizontal acquisition of mobile and mobilizable genetic elements plays a major role in the development of antimicrobial drug resistance in bacteria. Despite their causal role in drug treatment failure, there is only limited understanding of how horizontal acquisitions of these elements affect bacterial fitness. A prominent group of such genetic elements are the integrons. These genetic elements harbor an integrase-gene that allows the integron to respond to environmental changes by capture and excision of gene cassettes. Here, we have experimentally determined if horizontal acquisition of an integron affect host fitness. The data demonstrate that the initial costs are substantial. However, inactivation of the integrase gene occurred rapidly by spontaneous mutation alleviating the detrimental effect of the integron on bacterial fitness. The same fitness restoring effects was also shown by targeted inactivation of the integrase gene. The inactivation results in a negative trade-off between host adaptation and loss of the ability to capture new gene cassettes. Importantly, our results explain the frequent observation of inactive integrase genes in integrons found in bacteria of different origins. Finally, we use mathematical modeling to determine the conditions necessary for maintaining functional integrases.
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Affiliation(s)
- Irina Starikova
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Klaus Harms
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Pål Haugen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Tracy T. M. Lunde
- Reference Centre for Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Raul Primicerio
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Ørjan Samuelsen
- Reference Centre for Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Kaare M. Nielsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- GenØk, Center for Biosafety, Research Park, Tromsø, Norway
| | - Pål J. Johnsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- * E-mail:
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Kidane D, Ayora S, Sweasy JB, Graumann PL, Alonso JC. The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery. Crit Rev Biochem Mol Biol 2012; 47:531-55. [PMID: 23046409 DOI: 10.3109/10409238.2012.729562] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as "guardians", protects ssDNA from degradation and limit the RecA recombinase loading. Then, the "mediators" overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by "modulators", catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or "resolver" cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the "rescuers" will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective.
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Affiliation(s)
- Dawit Kidane
- Departments of Therapeutic Radiology and Genetics, Yale University School of Medicine, New Haven, CT, USA
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20
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Domingues S, Harms K, Fricke WF, Johnsen PJ, da Silva GJ, Nielsen KM. Natural transformation facilitates transfer of transposons, integrons and gene cassettes between bacterial species. PLoS Pathog 2012; 8:e1002837. [PMID: 22876180 PMCID: PMC3410848 DOI: 10.1371/journal.ppat.1002837] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 06/19/2012] [Indexed: 12/24/2022] Open
Abstract
We have investigated to what extent natural transformation acting on free DNA substrates can facilitate transfer of mobile elements including transposons, integrons and/or gene cassettes between bacterial species. Naturally transformable cells of Acinetobacter baylyi were exposed to DNA from integron-carrying strains of the genera Acinetobacter, Citrobacter, Enterobacter, Escherichia, Pseudomonas, and Salmonella to determine the nature and frequency of transfer. Exposure to the various DNA sources resulted in acquisition of antibiotic resistance traits as well as entire integrons and transposons, over a 24 h exposure period. DNA incorporation was not solely dependent on integrase functions or the genetic relatedness between species. DNA sequence analyses revealed that several mechanisms facilitated stable integration in the recipient genome depending on the nature of the donor DNA; homologous or heterologous recombination and various types of transposition (Tn21-like and IS26-like). Both donor strains and transformed isolates were extensively characterized by antimicrobial susceptibility testing, integron- and cassette-specific PCRs, DNA sequencing, pulsed field gel electrophoreses (PFGE), Southern blot hybridizations, and by re-transformation assays. Two transformant strains were also genome-sequenced. Our data demonstrate that natural transformation facilitates interspecies transfer of genetic elements, suggesting that the transient presence of DNA in the cytoplasm may be sufficient for genomic integration to occur. Our study provides a plausible explanation for why sequence-conserved transposons, IS elements and integrons can be found disseminated among bacterial species. Moreover, natural transformation of integron harboring populations of competent bacteria revealed that interspecies exchange of gene cassettes can be highly efficient, and independent on genetic relatedness between donor and recipient. In conclusion, natural transformation provides a much broader capacity for horizontal acquisitions of genetic elements and hence, resistance traits from divergent species than previously assumed. Genetic elements, such as transposons and integrons, frequently carry antimicrobial resistance determinants and can be found widely disseminated among pathogenic bacteria. Their distribution pattern suggests dissemination through horizontal gene transfer. The role of natural transformation in horizontal transfer of genetic elements other than those that are self-replicative (plasmids) has remained largely unexplored. We have tested if natural transformation can facilitate transfer of transposons and class 1 integrons between bacterial species. We here provide experimental evidence showing that natural transformation can be a general mechanism for dissemination of genetic elements that by themselves do not encode interspecies transfer functions (e.g. transposons, insertion sequences). We demonstrate that antibiotic resistance determinants present in such genetic elements can spread by natural transformation between species of clinical interest. We show by quantitative data that interspecies exchange of resistance gene cassettes is highly efficient among integron-containing strains and species. Our study also provides a plausible explanation for how sequence-conserved integrons can become distributed among bacterial species.
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Affiliation(s)
- Sara Domingues
- Centre of Pharmaceutical Studies, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Klaus Harms
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - W. Florian Fricke
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Pål J. Johnsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Gabriela J. da Silva
- Centre of Pharmaceutical Studies, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Kaare Magne Nielsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- Genøk-Centre for Biosafety, Tromsø, Norway
- * E-mail:
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21
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Function and biochemical characterization of RecJ in Deinococcus radiodurans. DNA Repair (Amst) 2012; 11:349-56. [DOI: 10.1016/j.dnarep.2011.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Revised: 11/11/2011] [Accepted: 11/12/2011] [Indexed: 12/21/2022]
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22
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Tropodithietic acid production in Phaeobacter gallaeciensis is regulated by N-acyl homoserine lactone-mediated quorum sensing. J Bacteriol 2011; 193:6576-85. [PMID: 21949069 DOI: 10.1128/jb.05818-11] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The production of N-acyl homoserine lactones (AHLs) is widely distributed within the marine Roseobacter clade, and it was proposed that AHL-mediated quorum sensing (QS) is one of the most common cell-to-cell communication mechanisms in roseobacters. The traits regulated by AHL-mediated QS are yet not known for members of the Roseobacter clade, but production of the antibiotic tropodithietic acid (TDA) was supposed to be controlled by AHL-mediated QS in Phaeobacter spp. We describe here for the first time the functional role of luxR and luxI homologous genes of an organism of the Roseobacter clade, i.e., pgaR and pgaI in Phaeobacter gallaeciensis. Our results demonstrate that the AHL synthase gene pgaI is responsible for production of N-3-hydroxydecanoylhomoserine lactone (3OHC(10)-HSL). Insertion mutants of pgaI and pgaR are both deficient in TDA biosynthesis and the formation of a yellow-brown pigment when grown in liquid marine broth medium. This indicates that in P. gallaeciensis the production of both secondary metabolites is controlled by AHL-mediated QS. Quantitative real-time PCR showed that the transcription level of tdaA, which encodes an essential transcriptional regulator for TDA biosynthesis, decreased 28- and 51-fold in pgaI and pgaR genetic backgrounds, respectively. These results suggest that both the response regulator PgaR and the 3OHC(10)-HSL produced by PgaI induce expression of tdaA, which in turn positively regulates expression of the tda genes. Moreover, we confirmed that TDA can also act as autoinducer in P. gallaeciensis, as previously described for Silicibacter sp. strain TM1040, but only in the presence of the response regulator PgaR.
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23
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Singh S, Joshi P, Chopade BA. Pathway Analysis of Acinetobacter baylyi: A Combined Bioinformatic and Genomics Approach. Chem Biol Drug Des 2011; 78:893-905. [DOI: 10.1111/j.1747-0285.2011.01191.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Ayora S, Carrasco B, Cárdenas PP, César CE, Cañas C, Yadav T, Marchisone C, Alonso JC. Double-strand break repair in bacteria: a view from Bacillus subtilis. FEMS Microbiol Rev 2011; 35:1055-81. [PMID: 21517913 DOI: 10.1111/j.1574-6976.2011.00272.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In all living organisms, the response to double-strand breaks (DSBs) is critical for the maintenance of chromosome integrity. Homologous recombination (HR), which utilizes a homologous template to prime DNA synthesis and to restore genetic information lost at the DNA break site, is a complex multistep response. In Bacillus subtilis, this response can be subdivided into five general acts: (1) recognition of the break site(s) and formation of a repair center (RC), which enables cells to commit to HR; (2) end-processing of the broken end(s) by different avenues to generate a 3'-tailed duplex and RecN-mediated DSB 'coordination'; (3) loading of RecA onto single-strand DNA at the RecN-induced RC and concomitant DNA strand exchange; (4) branch migration and resolution, or dissolution, of the recombination intermediates, and replication restart, followed by (5) disassembly of the recombination apparatus formed at the dynamic RC and segregation of sister chromosomes. When HR is impaired or an intact homologous template is not available, error-prone nonhomologous end-joining directly rejoins the two broken ends by ligation. In this review, we examine the functions that are known to contribute to DNA DSB repair in B. subtilis, and compare their properties with those of other bacterial phyla.
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Affiliation(s)
- Silvia Ayora
- Departmento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, Spain
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25
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Bentchikou E, Servant P, Coste G, Sommer S. A major role of the RecFOR pathway in DNA double-strand-break repair through ESDSA in Deinococcus radiodurans. PLoS Genet 2010; 6:e1000774. [PMID: 20090937 PMCID: PMC2806897 DOI: 10.1371/journal.pgen.1000774] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 11/16/2009] [Indexed: 11/19/2022] Open
Abstract
In Deinococcus radiodurans, the extreme resistance to DNA-shattering treatments such as ionizing radiation or desiccation is correlated with its ability to reconstruct a functional genome from hundreds of chromosomal fragments. The rapid reconstitution of an intact genome is thought to occur through an extended synthesis-dependent strand annealing process (ESDSA) followed by DNA recombination. Here, we investigated the role of key components of the RecF pathway in ESDSA in this organism naturally devoid of RecB and RecC proteins. We demonstrate that inactivation of RecJ exonuclease results in cell lethality, indicating that this protein plays a key role in genome maintenance. Cells devoid of RecF, RecO, or RecR proteins also display greatly impaired growth and an important lethal sectoring as bacteria devoid of RecA protein. Other aspects of the phenotype of recFOR knock-out mutants paralleled that of a DeltarecA mutant: DeltarecFOR mutants are extremely radiosensitive and show a slow assembly of radiation-induced chromosomal fragments, not accompanied by DNA synthesis, and reduced DNA degradation. Cells devoid of RecQ, the major helicase implicated in repair through the RecF pathway in E. coli, are resistant to gamma-irradiation and have a wild-type DNA repair capacity as also shown for cells devoid of the RecD helicase; in contrast, DeltauvrD mutants show a markedly decreased radioresistance, an increased latent period in the kinetics of DNA double-strand-break repair, and a slow rate of fragment assembly correlated with a slow rate of DNA synthesis. Combining RecQ or RecD deficiency with UvrD deficiency did not significantly accentuate the phenotype of DeltauvrD mutants. In conclusion, RecFOR proteins are essential for DNA double-strand-break repair through ESDSA whereas RecJ protein is essential for cell viability and UvrD helicase might be involved in the processing of double stranded DNA ends and/or in the DNA synthesis step of ESDSA.
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Affiliation(s)
- Esma Bentchikou
- Université Paris-Sud 11, CNRS UMR 8621, LRC CEA 42V, Institut de Génétique et Microbiologie, Orsay, France
| | - Pascale Servant
- Université Paris-Sud 11, CNRS UMR 8621, LRC CEA 42V, Institut de Génétique et Microbiologie, Orsay, France
| | - Geneviève Coste
- Université Paris-Sud 11, CNRS UMR 8621, LRC CEA 42V, Institut de Génétique et Microbiologie, Orsay, France
| | - Suzanne Sommer
- Université Paris-Sud 11, CNRS UMR 8621, LRC CEA 42V, Institut de Génétique et Microbiologie, Orsay, France
- * E-mail:
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26
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Cao Z, Mueller CW, Julin DA. Analysis of the recJ gene and protein from Deinococcus radiodurans. DNA Repair (Amst) 2010; 9:66-75. [DOI: 10.1016/j.dnarep.2009.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 10/26/2009] [Accepted: 10/26/2009] [Indexed: 02/01/2023]
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27
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The evolution of RecD outside of the RecBCD complex. J Mol Evol 2009; 69:360-71. [PMID: 19841849 DOI: 10.1007/s00239-009-9290-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 09/18/2009] [Indexed: 11/26/2022]
Abstract
The common understanding of the function of RecD, as derived predominantly from studies in Escherichia coli, is that RecD is one of three enzymes in the RecBCD double-stranded break repair DNA recombination complex. However, comparative genomics has revealed that many organisms possess a recD gene even though the other members of the complex, recB and recC, are not present. Further, bioinformatic analyses have shown that there is substantial sequence dissimilarity between recD genes associated with recB and recC (recD1), and those that are not associated with recBC (recD2). Deinococcus radiodurans, known for its extraordinary DNA repair capability, is one such organism that does not possess either recB or recC, and yet does possess a recD gene. The recD of D. radiodurans was deleted and this mutant was shown to have a capacity to repair double-stranded DNA breaks equivalent to wild-type. The phylogenetic history of recD was studied using a dataset of 120 recD genes from 91 fully sequenced species. The analysis focused upon the role of gene duplication and functional genomic context in the evolution of recD2, which appears to have undergone numerous independent events resulting in duplicate recD2 genes. The role of RecD as part of the RecBCD complex appears to have a divergence from an earlier ancestral RecD function still preserved in many species including D. radiodurans.
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Sexual isolation in Acinetobacter baylyi is locus-specific and varies 10,000-fold over the genome. Genetics 2009; 182:1165-81. [PMID: 19474200 DOI: 10.1534/genetics.109.103127] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Naturally transformable bacteria acquire chromosomal DNA from related species at lower frequencies than from cognate DNA sources. To determine how genome location affects heterogamic transformation in bacteria, we inserted an nptI marker into random chromosome locations in 19 different strains of the Acinetobacter genus (>24% divergent at the mutS/trpE loci). DNA from a total of 95 nptI-tagged isolates was used to transform the recipient Acinetobacter baylyi strain ADP1. A total of >1300 transformation assays revealed that at least one nptI-tagged isolate for each of the strains/species tested resulted in detectable integration of the nptI marker into the ADP1 genome. Transformation frequencies varied up to approximately 10,000-fold among independent nptI insertions within a strain. The location and local sequence divergence of the nptI flanking regions were determined in the transformants. Heterogamic transformation depended on RecA and was hampered by DNA mismatch repair. Our studies suggest that single-locus-based studies, and inference of transfer frequencies from general estimates of genomic sequence divergence, is insufficient to predict the recombination potential of chromosomal DNA fragments between more divergent genomes. Interspecies differences in overall gene content, and conflicts in local gene organization and synteny are likely important determinants of the genomewide variation in recombination rates between bacterial species.
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Hülter N, Wackernagel W. Frequent integration of short homologous DNA tracks during Acinetobacter baylyi transformation and influence of transcription and RecJ and SbcCD DNases. MICROBIOLOGY-SGM 2009; 154:3676-3685. [PMID: 19047735 DOI: 10.1099/mic.0.2008/021378-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The minimal length of integrated homologous donor DNA tracks in Acinetobacter baylyi transformation and factors influencing the location and length of tracks were determined. Donor DNA contained the nptII gene region (kanamycin resistance, KmR). This region carried nine approximately evenly spaced silent nucleotide sequence tags and was embedded in heterologous DNA. Recipient cells carried the normal nptII gene with a central 10 bp deletion (kanamycin-sensitive). The Km(R) transformants obtained had donor DNA tracks integrated covering on average only 4.6 (2-7) of the nine tags, corresponding to about 60 % of the 959 nt homologous donor DNA segment. The track positions were biased towards the 3' end of nptII. While the replication direction of recipient DNA did not affect track positions, inhibited transcription (by rifampicin) shifted the beginning of tracks towards the nptII promoter. Absence of the RecJ DNase decreased the length of tracks. Absence of SbcCD DNase increased the integration frequency of the 5' part of nptII, which can form hairpin structures of 43-75 nt, suggesting that SbcCD DNase interferes with hairpins in transforming DNA. In homology-facilitated illegitimate recombination events during transformation (in which a homologous DNA segment serves as a recombinational anchor to facilitate illegitimate recombination in neighbouring heterologous DNA), on average only about half of the approximately 800 nt long tagged nptII anchor sequences were integrated. From donor DNA with an approximately 5000 nt long homologous segment having the nptII gene in the middle, most transformants (74 %) had only a part of the donor nptII integrated, showing that short track integration occurs frequently also from large homologous DNA. It is discussed how short track integration steps can also accomplish incorporation of large DNA molecules.
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Affiliation(s)
- Nils Hülter
- Genetics, Department of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, D-26111 Oldenburg, Germany
| | - Wilfried Wackernagel
- Genetics, Department of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, D-26111 Oldenburg, Germany
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Harms K, Wackernagel W. The RecBCD and SbcCD DNases suppress homology-facilitated illegitimate recombination during natural transformation of Acinetobacter baylyi. MICROBIOLOGY-SGM 2008; 154:2437-2445. [PMID: 18667576 DOI: 10.1099/mic.0.2008/018382-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
During natural transformation of Acinetobacter baylyi, the genomic integration of foreign (non-homologous) DNA is possible when the DNA contains a single segment homologous to the recipient genome (anchor) through homologous recombination in the anchor facilitating illegitimate recombination in the neighbouring foreign DNA (homology-facilitated illegitimate recombination; HFIR). DNA integration by HFIR occurs about 10 000 times less frequently than fully homologous recombination, but at least 100 000-fold more frequently than integration in the absence of any homology. We investigated the influence of the RecBCD enzyme (DNase/helicase) and SbcCD DNase (DNA-structure-specific single-strand endonuclease and exonuclease) on HFIR. In a recBCD null mutant the acquisition of foreign DNA was elevated 11-fold relative to wild-type cells by a 6.9-fold increased HFIR frequency and by the integration of longer stretches of foreign DNA in each event. In an sbcCD null mutant, the foreign DNA acquisition was 4.5-fold higher than in the wild-type, while homologous transformation with large DNA molecules was unaffected and increased 3.2-fold with small DNA fragments. The sbcCD mutation partially suppressed the high UV sensitivity and low viability of the recBCD mutant and also decreased its foreign DNA acquisition by HFIR to the lower level of the sbcCD mutant. We propose that suppression of HFIR results from the elimination of double-stranded intermediates of the HFIR process during transformation by RecBCD, and by SbcCD interfering with branched molecules. Our results provide evidence that the homologous recombination enzymes RecBCD and SbcCD control the level of foreign DNA acquisition by HFIR.
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Affiliation(s)
- Klaus Harms
- Genetics, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, D-26111 Oldenburg, Germany
| | - Wilfried Wackernagel
- Genetics, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, D-26111 Oldenburg, Germany
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31
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Picardeau M, Bulach DM, Bouchier C, Zuerner RL, Zidane N, Wilson PJ, Creno S, Kuczek ES, Bommezzadri S, Davis JC, McGrath A, Johnson MJ, Boursaux-Eude C, Seemann T, Rouy Z, Coppel RL, Rood JI, Lajus A, Davies JK, Médigue C, Adler B. Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis. PLoS One 2008; 3:e1607. [PMID: 18270594 PMCID: PMC2229662 DOI: 10.1371/journal.pone.0001607] [Citation(s) in RCA: 222] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Accepted: 01/17/2008] [Indexed: 11/19/2022] Open
Abstract
Leptospira biflexa is a free-living saprophytic spirochete present in aquatic environments. We determined the genome sequence of L. biflexa, making it the first saprophytic Leptospira to be sequenced. The L. biflexa genome has 3,590 protein-coding genes distributed across three circular replicons: the major 3,604 chromosome, a smaller 278-kb replicon that also carries essential genes, and a third 74-kb replicon. Comparative sequence analysis provides evidence that L. biflexa is an excellent model for the study of Leptospira evolution; we conclude that 2052 genes (61%) represent a progenitor genome that existed before divergence of pathogenic and saprophytic Leptospira species. Comparisons of the L. biflexa genome with two pathogenic Leptospira species reveal several major findings. Nearly one-third of the L. biflexa genes are absent in pathogenic Leptospira. We suggest that once incorporated into the L. biflexa genome, laterally transferred DNA undergoes minimal rearrangement due to physical restrictions imposed by high gene density and limited presence of transposable elements. In contrast, the genomes of pathogenic Leptospira species undergo frequent rearrangements, often involving recombination between insertion sequences. Identification of genes common to the two pathogenic species, L. borgpetersenii and L. interrogans, but absent in L. biflexa, is consistent with a role for these genes in pathogenesis. Differences in environmental sensing capacities of L. biflexa, L. borgpetersenii, and L. interrogans suggest a model which postulates that loss of signal transduction functions in L. borgpetersenii has impaired its survival outside a mammalian host, whereas L. interrogans has retained environmental sensory functions that facilitate disease transmission through water.
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Affiliation(s)
| | - Dieter M. Bulach
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | | | - Richard L. Zuerner
- Bacterial Diseases of Livestock Research Unit, National Animal Disease Center (NADC), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Ames, Iowa, United States of America
| | - Nora Zidane
- Plate-forme Génomique, Institut Pasteur, Paris, France
| | - Peter J. Wilson
- Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, St. Lucia, Queensland, Australia
| | - Sophie Creno
- Plate-forme Génomique, Institut Pasteur, Paris, France
| | - Elizabeth S. Kuczek
- Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, St. Lucia, Queensland, Australia
| | | | - John C. Davis
- Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, St. Lucia, Queensland, Australia
| | - Annette McGrath
- Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, St. Lucia, Queensland, Australia
| | - Matthew J. Johnson
- Australian Genome Research Facility, Gehrmann Laboratories, University of Queensland, St. Lucia, Queensland, Australia
| | | | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
| | - Zoé Rouy
- Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant, Laboratoire de Génomique Comparative, Institut de Génomique, Genoscope, Evry, France
| | - Ross L. Coppel
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Julian I. Rood
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Aurélie Lajus
- Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant, Laboratoire de Génomique Comparative, Institut de Génomique, Genoscope, Evry, France
| | - John K. Davies
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Claudine Médigue
- Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant, Laboratoire de Génomique Comparative, Institut de Génomique, Genoscope, Evry, France
- Centre National de la Recherche Scientifique (CNRS) UMR8030, Génomique Métabolique, Evry, France
| | - Ben Adler
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton, Victoria, Australia
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Hülter N, Wackernagel W. Double illegitimate recombination events integrate DNA segments through two different mechanisms during natural transformation of Acinetobacter baylyi. Mol Microbiol 2008; 67:984-95. [PMID: 18194157 DOI: 10.1111/j.1365-2958.2007.06096.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acquisition of foreign DNA by horizontal gene transfer is seen as a major source of genetic diversity in prokaryotes. However, strongly divergent DNA is not genomically integrated by homologous recombination and would depend on illegitimate recombination (IR) events which are rare. We show that, by two mechanisms, during natural transformation of Acinetobacter baylyi two IR events can integrate DNA segments. One mechanism is double illegitimate recombination (DIR) acting in the absence of any homology (frequency: 7 x 10(-13) per cell). It occurs about 10(10)-fold less frequent than homologous transformation. The other mechanism is homology-facilitated double illegitimate recombination (HFDIR) being about 440-fold more frequent (3 x 10(-10) per cell) than DIR. HFDIR depends on a homologous sequence located between the IR sites and on recA(+). In HFDIR two IR events act on the same donor DNA molecule as shown by the joint inheritance of molecular DNA tags. While the IR events in HFDIR occurred at microhomologies, in DIR microhomologies were not used. The HFDIR phenomenon indicates that a temporal recA-dependent association of donor DNA at a homology in recipient DNA may facilitate two IR events on the 5' and 3' heterologous parts of the transforming DNA molecule.
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Affiliation(s)
- Nils Hülter
- Genetics, Department of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, D-26111 Oldenburg, Germany
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33
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Abstract
A mutant derived from Acinetobacter baylyi ADP1 was isolated from a screen for genes involved in the response to DNA damage. This derivative has an insertion in the mpl gene which encodes a peptidoglycan-recycling protein. We demonstrate that the insertion renders cells sensitive to mitomycin C and to UV.
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