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Callens M, Rose CJ, Finnegan M, Gatchitch F, Simon L, Hamet J, Pradier L, Dubois MP, Bedhomme S. Hypermutator emergence in experimental Escherichia coli populations is stress-type dependent. Evol Lett 2023; 7:252-261. [PMID: 37475751 PMCID: PMC10355175 DOI: 10.1093/evlett/qrad019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/04/2023] [Accepted: 04/21/2023] [Indexed: 07/22/2023] Open
Abstract
Genotypes exhibiting an increased mutation rate, called hypermutators, can propagate in microbial populations because they can have an advantage due to the higher supply of beneficial mutations needed for adaptation. Although this is a frequently observed phenomenon in natural and laboratory populations, little is known about the influence of parameters such as the degree of maladaptation, stress intensity, and the genetic architecture for adaptation on the emergence of hypermutators. To address this knowledge gap, we measured the emergence of hypermutators over ~1,000 generations in experimental Escherichia coli populations exposed to different levels of osmotic or antibiotic stress. Our stress types were chosen based on the assumption that the genetic architecture for adaptation differs between them. Indeed, we show that the size of the genetic basis for adaptation is larger for osmotic stress compared to antibiotic stress. During our experiment, we observed an increased emergence of hypermutators in populations exposed to osmotic stress but not in those exposed to antibiotic stress, indicating that hypermutator emergence rates are stress type dependent. These results support our hypothesis that hypermutator emergence is linked to the size of the genetic basis for adaptation. In addition, we identified other parameters that covaried with stress type (stress level and IS transposition rates) that might have contributed to an increased hypermutator provision and selection. Our results provide a first comparison of hypermutator emergence rates under varying stress conditions and point towards complex interactions of multiple stress-related factors on the evolution of mutation rates.
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Affiliation(s)
- Martijn Callens
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
- Animal Sciences Unit—Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food, Oostende, Belgium
| | - Caroline J Rose
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
| | - Michael Finnegan
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
| | | | - Léna Simon
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
- Université Clermont Auvergne, VetAgro Sup, Lempdes, France
| | - Jeanne Hamet
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
| | - Léa Pradier
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
| | | | - Stéphanie Bedhomme
- Corresponding author: CEFE, 1919 route de Mende, 34293 Montpellier, France.
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Wedel E, Bernabe-Balas C, Ares-Arroyo M, Montero N, Santos-Lopez A, Mazel D, Gonzalez-Zorn B. Insertion Sequences Determine Plasmid Adaptation to New Bacterial Hosts. mBio 2023:e0315822. [PMID: 37097157 DOI: 10.1128/mbio.03158-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Plasmids facilitate the vertical and horizontal spread of antimicrobial resistance genes between bacteria. The host range and adaptation of plasmids to new hosts determine their impact on the spread of resistance. In this work, we explore the mechanisms driving plasmid adaptation to novel hosts in experimental evolution. Using the small multicopy plasmid pB1000, usually found in Pasteurellaceae, we studied its adaptation to a host from a different bacterial family, Escherichia coli. We observed two different mechanisms of adaptation. One mechanism is single nucleotide polymorphisms (SNPs) in the origin of replication (oriV) of the plasmid, which increase the copy number in E. coli cells, elevating the stability, and resistance profile. The second mechanism consists of two insertion sequences (ISs), IS1 and IS10, which decrease the fitness cost of the plasmid by disrupting an uncharacterized gene on pB1000 that is harmful to E. coli. Both mechanisms increase the stability of pB1000 independently, but only their combination allows long-term maintenance. Crucially, we show that the mechanisms have a different impact on the host range of the plasmid. SNPs in oriV prevent the replication in the original host, resulting in a shift of the host range. In contrast, the introduction of ISs either shifts or expands the host range, depending on the IS. While IS1 leads to expansion, IS10 cannot be reintroduced into the original host. This study gives new insights into the relevance of ISs in plasmid-host adaptation to understand the success in spreading resistance. IMPORTANCE ColE1-like plasmids are small, mobilizable plasmids that can be found across at least four orders of Gammaproteobacteria and are strongly associated with antimicrobial resistance genes. Plasmid pB1000 carries the gene blaROB-1, conferring high-level resistance to penicillins and cefaclor. pB1000 has been described in various species of the family Pasteurellaceae, for example, in Haemophilus influenzae, which can cause diseases such as otitis media, meningitis, and pneumonia. To understand the resistance spread through horizontal transfer, it is essential to study the mechanisms of plasmid adaptation to novel hosts. In this work we identify that a gene from pB1000, which encodes a peptide that is toxic for E. coli, and the low plasmid copy number (PCN) of pB1000 in E. coli cells are essential targets in the described plasmid-host adaptation and therefore limit the spread of pB1000-encoded blaROB-1. Furthermore, we show how the interplay of two adaptation mechanisms leads to successful plasmid maintenance in a different bacterial family.
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Affiliation(s)
- Emilia Wedel
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Cristina Bernabe-Balas
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Manuel Ares-Arroyo
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Natalia Montero
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Alfonso Santos-Lopez
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Didier Mazel
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
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3
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Nukagawa Y, Wakinaka T, Mogi Y, Watanabe J. Targeted Screening for Spontaneous Insertion Mutations in a Lactic Acid Bacterium, Tetragenococcus halophilus. Appl Environ Microbiol 2023; 89:e0200522. [PMID: 36809065 PMCID: PMC10056959 DOI: 10.1128/aem.02005-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/19/2023] [Indexed: 02/23/2023] Open
Abstract
Studies on the microorganisms used in food production are of interest because microbial genotypes are reflected in food qualities such as taste, flavor, and yield. However, several microbes are nonmodel organisms, and their analysis is often limited by the lack of genetic tools. Tetragenococcus halophilus, a halophilic lactic acid bacterium used in soy sauce fermentation starter culture, is one such microorganism. The lack of DNA transformation techniques for T. halophilus makes gene complementation and disruption assays difficult. Here, we report that the endogenous insertion sequence ISTeha4, belonging to the IS4 family, is translocated at an extremely high frequency in T. halophilus and causes insertional mutations at various loci. We developed a method named targeting spontaneous insertional mutations in genomes (TIMING), which combines high-frequency insertional mutations and efficient PCR screening, enabling the isolation of gene mutants of interest from a library. The method provides a reverse genetics and strain improvement tool, does not require the introduction of exogenous DNA constructs, and enables the analysis of nonmodel microorganisms lacking DNA transformation techniques. Our results highlight the important role of insertion sequences as a source of spontaneous mutagenesis and genetic diversity in bacteria. IMPORTANCE Genetic and strain improvement tools to manipulate a gene of interest are required for the nontransformable lactic acid bacterium Tetragenococcus halophilus. Here, we demonstrate that an endogenous transposable element, ISTeha4, is transposed into the host genome at an extremely high frequency. A genotype-based and non-genetically engineered screening system was constructed to isolate knockout mutants using this transposable element. The method described enables a better understanding of the genotype-phenotype relationship and serves as a tool to develop food-grade-appropriate mutants of T. halophilus.
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Affiliation(s)
- Yuya Nukagawa
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
| | | | - Yoshinobu Mogi
- Manufacturing Division, Yamasa Corporation, Choshi, Japan
| | - Jun Watanabe
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
- Manufacturing Division, Yamasa Corporation, Choshi, Japan
- Institute of Fermentation Sciences, Fukushima University, Fukushima, Japan
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Fan C, Wu YH, Decker CM, Rohani R, Gesell Salazar M, Ye H, Cui Z, Schmidt F, Huang WE. Defensive Function of Transposable Elements in Bacteria. ACS Synth Biol 2019; 8:2141-2151. [PMID: 31375026 DOI: 10.1021/acssynbio.9b00218] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It has been widely debated whether transposable elements have a positive or a negative effect on their host cells. This study demonstrated that transposable elements, specifically insertion sequences (ISs), can adopt a defensive role in Escherichia coli. In three different E. coli strains (S17, DH5α, and Nissle 1917), IS1 and IS10 rapidly disrupted the I-CeuI gene (encoding I-CeuI endonuclease) on the plasmid pLO11-ICeuI as early as the first generation, despite the gene-circuit being under control of an arabinose promoter. Proteomics analysis showed that the protein abundance profile of E. coli DH5α with pLO11-ICeuI in the fifth generation was nearly opposite to that of control strain (E. coli with pLO11, no I-CeuI). The DNA damage caused by the leaky expression of I-CeuI was enough to trigger a SOS response and alter lipid synthesis, ribosomal activity, RNA/DNA metabolism, central dogma and cell cycle processes in E. coli DH5α. After the ISs disrupted the expression of I-CeuI, cells fully recovered by the 31st generation had a protein abundance profile similar to that of the control strain. This study showed that ISs readily mutated a harmful gene which subsequently restored host fitness. These observations have implications for the stability of designed gene circuits in synthetic biology.
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Affiliation(s)
- Catherine Fan
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Yin-Hu Wu
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Christoph M. Decker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Reza Rohani
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Hua Ye
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Zhanfeng Cui
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
- Proteomics Core, Weill Cornel Medicine-Qatar, Education City, PO 24144 Doha, Qatar
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, United Kingdom
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5
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Bedhomme S, Amorós-Moya D, Valero LM, Bonifaci N, Pujana MÀ, Bravo IG. Evolutionary Changes after Translational Challenges Imposed by Horizontal Gene Transfer. Genome Biol Evol 2019; 11:814-831. [PMID: 30753446 PMCID: PMC6427688 DOI: 10.1093/gbe/evz031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 01/24/2023] Open
Abstract
Genes acquired by horizontal gene transfer (HGT) may provide the recipient organism with potentially new functions, but proper expression level and integration of the transferred genes in the novel environment are not granted. Notably, transferred genes can differ from the receiving genome in codon usage preferences, leading to impaired translation and reduced functionality. Here, we characterize the genomic and proteomic changes undergone during experimental evolution of Escherichia coli after HGT of three synonymous versions, presenting very different codon usage preference, of an antibiotic resistance gene. The experimental evolution was conducted with and without the corresponding antibiotic and the mutational patterns and proteomic profiles after 1,000 generations largely depend on the experimental growth conditions (e.g., mutations in antibiotic off-target genes), and on the synonymous gene version transferred (e.g., mutations in genes responsive to translational stress). The transfer of an exogenous gene extensively modifies the whole proteome, and these proteomic changes are different for the different version of the transferred gene. Additionally, we identified conspicuous changes in global regulators and in intermediate metabolism, confirmed the evolutionary ratchet generated by mutations in DNA repair genes and highlighted the plasticity of bacterial genomes accumulating large and occasionally transient duplications. Our results support a central role of HGT in fuelling evolution as a powerful mechanism promoting rapid, often dramatic genotypic and phenotypic changes. The profound reshaping of the pre-existing geno/phenotype allows the recipient bacteria to explore new ways of functioning, far beyond the mere acquisition of a novel function.
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Affiliation(s)
- Stéphanie Bedhomme
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD, France
| | - Dolors Amorós-Moya
- Experimental Molecular Evolution, Institute for Evolution and Biodiversity, Westfälische-Wilhelms Universität Münster, Germany
| | - Luz M Valero
- Secció de Proteomica, SCSIE Universitat de Valencia, Spain
| | - Nùria Bonifaci
- ProCURE, Catalan Institute of Oncology (ICO), Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Miquel-Àngel Pujana
- ProCURE, Catalan Institute of Oncology (ICO), Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Ignacio G Bravo
- Centre National de la Recherche Scientifique (CNRS), Laboratory MIVEGEC (UMR CNRS, IRD, UM), Montpellier, France
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6
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Vandecraen J, Chandler M, Aertsen A, Van Houdt R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol 2017; 43:709-730. [PMID: 28407717 DOI: 10.1080/1040841x.2017.1303661] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new niches. This review focuses on the impact of insertion sequences (IS), arguably the smallest TE, on bacterial genome plasticity and concomitant adaptability of phenotypic traits, including resistance to antibacterial agents, virulence, pathogenicity and catabolism. The direct consequence of IS transposition is the insertion of one DNA sequence into another. This event can result in gene inactivation as well as in modulation of neighbouring gene expression. The latter is usually mediated by de-repression or by the introduction of a complete or partial promoter located within the element. Furthermore, transcription and transposition of IS are affected by host factors and in some cases by environmental signals offering the host an adaptive strategy and promoting genetic variability to withstand the environmental challenges.
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Affiliation(s)
- Joachim Vandecraen
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium.,b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Michael Chandler
- c Laboratoire de Microbiologie et Génétique Moléculaires, Centre national de la recherche scientifique , Toulouse , France
| | - Abram Aertsen
- b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Rob Van Houdt
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium
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7
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González-Prieto C, Agúndez L, Llosa M. Chloramphenicol Selection of IS10 Transposition in the cat Promoter Region of Widely Used Cloning Vectors. PLoS One 2015; 10:e0138615. [PMID: 26375469 PMCID: PMC4574204 DOI: 10.1371/journal.pone.0138615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/01/2015] [Indexed: 11/19/2022] Open
Abstract
The widely used pSU8 family of cloning vectors is based on a p15A replicon and a chloramphenicol acetyltransferase (cat) gene conferring chloramphenicol resistance. We frequently observed an increase in the size of plasmids derived from these vectors. Analysis of the bigger molecular species shows that they have an IS10 copy inserted at a specific site between the promoter and the cat open reading frame. Promoter activity from both ends of IS10 has been reported, suggesting that the insertion events could lead to higher CAT production. Insertions were observed in certain constructions containing inserts that could lead to plasmid instability. To test the possibility that IS10 insertions were selected as a response to chloramphenicol selection, we have grown these constructs in the presence of different amounts of antibiotic and we observed that insertions arise promptly under higher chloramphenicol selective pressure. IS10 is present in many E. coli laboratory strains, so the possibility of insertion in constructions involving cat-containing vectors should be taken into account. Using lower chloramphenicol concentrations could solve this problem.
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Affiliation(s)
- Coral González-Prieto
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC-SODERCAN), Santander, Spain
| | - Leticia Agúndez
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC-SODERCAN), Santander, Spain
- Department of Genetics, University College London, Institute of Ophthalmology, London, United Kingdom
| | - Matxalen Llosa
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC-SODERCAN), Santander, Spain
- * E-mail:
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8
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Xiang X, Huang X, Wang H, Huang L. pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements. Life (Basel) 2015; 5:506-20. [PMID: 25686154 PMCID: PMC4390865 DOI: 10.3390/life5010506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/04/2015] [Indexed: 11/30/2022] Open
Abstract
Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading.
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Affiliation(s)
- Xiaoyu Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
| | - Xiaoxing Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
| | - Haina Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
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9
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Complete genome sequence of Salmonella enterica serovar Typhimurium VNP20009, a strain engineered for tumor targeting. J Biotechnol 2014; 192 Pt A:177-8. [DOI: 10.1016/j.jbiotec.2014.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/03/2014] [Indexed: 11/18/2022]
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10
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Sousa A, Bourgard C, Wahl LM, Gordo I. Rates of transposition in Escherichia coli. Biol Lett 2013; 9:20130838. [PMID: 24307531 PMCID: PMC3871371 DOI: 10.1098/rsbl.2013.0838] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 11/08/2013] [Indexed: 11/12/2022] Open
Abstract
The evolutionary role of transposable elements (TEs) is still highly controversial. Two key parameters, the transposition rate (u and w, for replicative and non-replicative transposition) and the excision rate (e) are fundamental to understanding their evolution and maintenance in populations. We have estimated u, w and e for six families of TEs (including eight members: IS1, IS2, IS3, IS4, IS5, IS30, IS150 and IS186) in Escherichia coli, using a mutation accumulation (MA) experiment. In this experiment, mutations accumulate essentially at the rate at which they appear, during a period of 80 500 (1610 generations × 50 lines) generations, and spontaneous transposition events can be detected. This differs from other experiments in which insertions accumulated under strong selective pressure or over a limited genomic target. We therefore provide new estimates for the spontaneous rates of transposition and excision in E. coli. We observed 25 transposition and three excision events in 50 MA lines, leading to overall rate estimates of u ∼ 1.15 × 10(-5), w ∼ 4 × 10(-8) and e ∼ 1.08 × 10(-6) (per element, per generation). Furthermore, extensive variation between elements was found, consistent with previous knowledge of the mechanisms and regulation of transposition for the different elements.
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Affiliation(s)
- Ana Sousa
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Lindi M. Wahl
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Department of Applied Mathematics, Western University, London, Ontario, Canada
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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11
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Ross JA, Wardle SJ, Haniford DB. Tn10/IS10 transposition is downregulated at the level of transposase expression by the RNA-binding protein Hfq. Mol Microbiol 2010; 78:607-21. [PMID: 20815820 DOI: 10.1111/j.1365-2958.2010.07359.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We show in this work that disruption of the hfq gene in Escherichia coli causes a large increase in IS10 transposition when IS10 is present on a multi-copy plasmid. Hfq is an RNA-binding protein that regulates the expression of a large number of genes at the post-transcriptional level by promoting the pairing of mRNAs with partially complementary short RNAs. As the translation of IS10 transposase mRNA (RNA-IN) is inhibited by an IS10-encoded anti-sense RNA (RNA-OUT), it seemed likely that Hfq would negatively regulate Tn10/IS10 transposition by promoting anti-sense inhibition of RNA-IN translation. Consistent with this, we show that Hfq promotes pairing of RNA-IN and RNA-OUT in vitro and downregulates RNA-IN expression in vivo. However, we also show that Hfq negatively regulates Tn10 transposition when no functional anti-sense RNA is produced. Taken together, the results suggest that Hfq acts at two distinct steps to inhibit Tn10/IS10 transposition. This is the first example of Hfq regulating a bacterial transposition reaction.
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Affiliation(s)
- Joseph A Ross
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
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13
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Wagner A. Cooperation is fleeting in the world of transposable elements. PLoS Comput Biol 2007; 2:e162. [PMID: 17140282 PMCID: PMC1676026 DOI: 10.1371/journal.pcbi.0020162] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Accepted: 10/13/2006] [Indexed: 11/29/2022] Open
Abstract
Composite transposons are key vehicles for the worldwide spreading of genes that allow bacteria to survive toxic compounds. Composite transposons consist of two smaller transposable elements called insertion sequences (ISs), which flank the genes that permit such survival. Each IS in a composite transposon can either transpose alone, selfishly, or it can transpose cooperatively, jointly with the other IS. Cooperative transposition can enhance an IS's chance of survival, but it also carries the risk of transposon destruction. I use game theory to show that the conditions under which cooperative transposition is an evolutionarily stable strategy (ESS) are not biologically realistic. I then analyze the distribution of thousands of ISs in more than 200 bacterial genomes to test the following prediction of the game-theoretical model: if cooperative transposition was an ESS, then the closely spaced ISs that characterize composite transposons should be more abundant in genomes than expected by chance. The data show that this is not the case. Cooperativity can only be maintained in a transitional, far-from-equilibrium state shortly after a selection pressure first arises. This is the case in the spreading of antibiotic resistance, where we are witnessing a fleeting moment in evolution, a moment in which cooperation among selfish DNA molecules has provided a means of survival. Because such cooperation does not pay in the long run, the vehicles of such survival will eventually disappear again. My analysis demonstrates that game theory can help explain behavioral strategies even for mobile DNA. Molecules can display cooperation and selfish behavior. Wagner investigates cooperative behavior in mobile DNA molecules called transposable elements, which can “hop” among cells, which aids the worldwide spreading of antibiotic resistance genes. A composite transposon consists of two smaller mobile DNA molecules, M, that flank another gene, G, M-G-M. The molecules M are able to change location alone and selfishly. They are also able to change location jointly and cooperatively, thus taking the gene G with them. Cooperation facilitates the spreading of the gene G and of M itself. Cooperativity is advantageous to M. However, Wagner's paper shows that cooperativity is short-lived and not stable on evolutionary time scales. Cooperativity can only be maintained in a transitional, far-from-equilibrium state shortly after a selection pressure first arises. This is the case in the spreading of antibiotic resistance, where we are witnessing a fleeting moment in evolution, a moment in which cooperation among selfish DNA molecules has provided a means of survival. Because such cooperation does not pay in the long run, the vehicles of such survival will eventually disappear again.
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Affiliation(s)
- Andreas Wagner
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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14
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Abstract
Bacterial insertion sequences (ISs) are the simplest kinds of bacterial mobile DNA. Evolutionary studies need consistent IS annotation across many different genomes. We have developed an open-source software package, IScan, to identify bacterial ISs and their sequence elements—inverted and target direct repeats—in multiple genomes using multiple flexible search parameters. We applied IScan to 438 completely sequenced bacterial genomes and 20 IS families. The resulting data show that ISs within a genome are extremely similar, with a mean synonymous divergence of Ks = 0.033. Our analysis substantially extends previously available information, and suggests that most ISs have entered bacterial genomes recently. By implication, their population persistence may depend on horizontal transfer. We also used IScan's ability to analyze the statistical significance of sequence similarity among many IS inverted repeats. Although the inverted repeats of insertion sequences are evolutionarily highly flexible parts of ISs, we show that this ability can be used to enrich a dataset for ISs that are likely to be functional. Applied to the thousands of genomes that will soon be available, IScan could be used for many purposes, such as mapping the evolutionary history and horizontal transfer patterns of different ISs.
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Affiliation(s)
- Andreas Wagner
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 27-J-54, CH-8057 Zurich, Switzerland.
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15
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Watanabe S, Ito T, Morimoto Y, Takeuchi F, Hiramatsu K. Precise excision and self-integration of a composite transposon as a model for spontaneous large-scale chromosome inversion/deletion of the Staphylococcus haemolyticus clinical strain JCSC1435. J Bacteriol 2007; 189:2921-5. [PMID: 17237177 PMCID: PMC1855803 DOI: 10.1128/jb.01485-06] [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] [Indexed: 11/20/2022] Open
Abstract
Large-scale chromosomal inversions (455 to 535 kbp) or deletions (266 to 320 kbp) were found to accompany spontaneous loss of beta-lactam resistance during drug-free passage of the multiresistant Staphylococcus haemolyticus clinical strain JCSC1435. Identification and sequencing of the rearranged chromosomal loci revealed that ISSha1 of S. haemolyticus is responsible for the chromosome rearrangements.
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Affiliation(s)
- Shinya Watanabe
- Department of Infection Control Science, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan
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16
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Abstract
Tn10 is a bacterial transposon that transposes through a non-replicative mechanism. This mode of DNA transposition is widely used in bacteria and is also used by "DNA-based" transposons in eukaryotes. Tn10 has served as a paradigm for this mode of transposition and continues to provide novel insights into how steps in transposition reactions occur and how these steps are regulated. A common feature of transposition reactions is that they require the formation of a higher order protein-DNA complex called a transpososome. A major objective in the last few years has been to better understand the dynamics of transpososome assembly and progression through the course of transposition reactions. This problem is particularly interesting in the Tn10 system because two important host proteins, IHF and H-NS, have been implicated in regulating transpososome assembly and/or function. Interestingly, H-NS is an integral part of stress response pathways in bacteria, and its function is known to be sensitive to changes in environmental conditions. Consequently, H-NS may provide a means of allowing Tn10 to responed to changing environmental conditions. The current review focuses on the roles of both IHF and H-NS on Tn10 transposition.
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Affiliation(s)
- David B Haniford
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada.
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17
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Wagner A. Periodic Extinctions of Transposable Elements in Bacterial Lineages: Evidence from Intragenomic Variation in Multiple Genomes. Mol Biol Evol 2005; 23:723-33. [PMID: 16373392 DOI: 10.1093/molbev/msj085] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most previous work on the evolution of mobile DNA was limited by incomplete sequence information. Whole genome sequences allow us to overcome this limitation. I study the nucleotide diversity of prominent members of five insertion sequence families whose transposition activity is encoded by a single transposase gene. Eighteen among 376 completely sequenced bacterial genomes and plasmids carry between 3 and 20 copies of a given insertion sequence. I show that these copies generally show very low DNA divergence. Specifically, more than 68% of the transposase genes are identical within a genome. The average number of amino acid replacement substitutions at amino acid replacement sites is Ka = 0.013, that at silent sites is Ks = 0.1. This low intragenomic diversity stands in stark contrast to a much higher divergence of the same insertion sequences among distantly related genomes. Gene conversion among protein-coding genes is unlikely to account for this lack of diversity. The relation between transposition frequencies and silent substitution rates suggests that most insertion sequences in a typical genome are evolutionarily young and have been recently acquired. They may undergo periodic extinction in bacterial lineages. By implication, they are detrimental to their host in the long run. This is also suggested by the highly skewed and patchy distribution of insertion sequences among genomes. In sum, one can think of insertion sequences as slow-acting infectious diseases of cell lineages.
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Affiliation(s)
- Andreas Wagner
- Department of Biology, The University of New Mexico, USA.
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18
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Blount ZD, Grogan DW. New insertion sequences of Sulfolobus: functional properties and implications for genome evolution in hyperthermophilic archaea. Mol Microbiol 2005; 55:312-25. [PMID: 15612937 DOI: 10.1111/j.1365-2958.2004.04391.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analyses of complete genomes indicate that insertion sequences (ISs) are abundant and widespread in hyperthermophilic archaea, but few experimental studies have measured their activities in these hosts. As a way to investigate the impact of ISs on Sulfolobus genomes, we identified seven transpositionally active ISs in a widely distributed Sulfolobus species, and measured their functional properties. Six of the seven were found to be distinct from previously described ISs of Sulfolobus, and one of the six could not be assigned to any known IS family. A type II 'Miniature Inverted-repeat Transposable Element' (MITE) related to one of the ISs was also recovered. Rates of transposition of the different ISs into the pyrEF region of their host strains varied over a 250-fold range. The Sulfolobus ISs also differed with respect to target-site selectivity, although several shared an apparent preference for the pyrEF promoter region. Despite the number of distinct ISs assayed and their molecular diversity, only one demonstrated precise excision from the chromosomal target region. The fact that this IS is the only one lacking inverted repeats and target-site duplication suggests that the observed precise excision may be promoted by the IS itself. Sequence searches revealed previously unidentified partial copies of the newly identified ISs in the Sulfolobus tokodaii and Sulfolobus solfataricus genomes. The structures of these fragmentary copies suggest several distinct molecular mechanisms which, in the absence of precise excision, inactivate ISs and gradually eliminate the defective copies from Sulfolobus genomes.
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Affiliation(s)
- Zachary D Blount
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
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19
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Tanaka MM. Evidence for positive selection on Mycobacterium tuberculosis within patients. BMC Evol Biol 2004; 4:31. [PMID: 15355550 PMCID: PMC518962 DOI: 10.1186/1471-2148-4-31] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Accepted: 09/09/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While the pathogenesis and epidemiology of tuberculosis are well studied, relatively little is known about the evolution of the infectious agent Mycobacterium tuberculosis, especially at the within-host level. The insertion sequence IS6110 is a genetic marker that is widely used to track the transmission of tuberculosis between individuals. This and other markers may also facilitate our understanding of the disease within patients. RESULTS This article presents three lines of evidence supporting the action of positive selection on M. tuberculosis within patients. The arguments are based on a comparison between empirical findings from molecular epidemiology, and population genetic models of evolution. Under the hypothesis of neutrality of genotypes, 1) the mutation rate of the marker IS6110 is unusually high, 2) the time it takes for substitutions to occur within patients is too short, and 3) the amount of polymorphism within patients is too low. CONCLUSIONS Empirical observations are explained by the action of positive selection during infection, or alternatively by very low effective population sizes. I discuss the possible roles of antibiotic treatment, the host immune system and extrapulmonary dissemination in creating opportunities for positive selection.
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Affiliation(s)
- Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia.
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20
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Pomerantsev AP, Kalnin KV, Osorio M, Leppla SH. Phosphatidylcholine-specific phospholipase C and sphingomyelinase activities in bacteria of the Bacillus cereus group. Infect Immun 2003; 71:6591-606. [PMID: 14573681 PMCID: PMC219565 DOI: 10.1128/iai.71.11.6591-6606.2003] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2003] [Revised: 06/13/2003] [Accepted: 08/10/2003] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis is nonhemolytic, even though it is closely related to the highly hemolytic Bacillus cereus. Hemolysis by B. cereus results largely from the action of phosphatidylcholine-specific phospholipase C (PC-PLC) and sphingomyelinase (SPH), encoded by the plc and sph genes, respectively. In B. cereus, these genes are organized in an operon regulated by the global regulator PlcR. B. anthracis contains a highly similar cereolysin operon, but it is transcriptionally silent because the B. anthracis PlcR is truncated at the C terminus. Here we report the cloning, expression, purification, and enzymatic characterization of PC-PLC and SPH from B. cereus and B. anthracis. We also investigated the effects of expressing PlcR on the expression of plc and sph. In B. cereus, PlcR was found to be a positive regulator of plc but a negative regulator of sph. Replacement of the B. cereus plcR gene by its truncated orthologue from B. anthracis eliminated the activities of both PC-PLC and SPH, whereas introduction into B. anthracis of the B. cereus plcR gene with its own promoter did not activate cereolysin expression. Hemolytic activity was detected in B. anthracis strains containing the B. cereus plcR gene on a multicopy plasmid under control of the strong B. anthracis protective antigen gene promoter or in a strain carrying a multicopy plasmid containing the entire B. cereus plc-sph operon. Slight hemolysis and PC-PLC activation were found when PlcR-producing B. anthracis strains were grown under anaerobic-plus-CO(2) or especially under aerobic-plus-CO(2) conditions. Unmodified parental B. anthracis strains did not demonstrate obvious hemolysis under the same conditions.
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Affiliation(s)
- A P Pomerantsev
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-4350, USA
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21
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Hill F, Gemünd C, Benes V, Ansorge W, Gibson TJ. An estimate of large-scale sequencing accuracy. EMBO Rep 2000; 1:29-31. [PMID: 11256620 PMCID: PMC1083690 DOI: 10.1093/embo-reports/kvd015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2000] [Revised: 05/23/2000] [Accepted: 05/25/2000] [Indexed: 11/14/2022] Open
Abstract
The accuracy of large-scale DNA sequencing is difficult to estimate without redundant effort. We have found that the mobile genetic element IS10, a component of the transposon Tn10, has contaminated a significant number of clones in the public databases, as a result of the use of the transposon in bacterial cloning strain construction. These contaminations need to be annotated as such. More positively, by defining the range of sequence variation in IS10, we have been able to determine that the rate of sequencing errors is very low, most likely surpassing the stated aim of one error or less in ten thousand bases.
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Affiliation(s)
- F Hill
- European Molecular Biology Laboratory, Heidelberg, Germany.
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22
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Kleckner N, Chalmers RM, Kwon D, Sakai J, Bolland S. Tn10 and IS10 transposition and chromosome rearrangements: mechanism and regulation in vivo and in vitro. Curr Top Microbiol Immunol 1996; 204:49-82. [PMID: 8556869 DOI: 10.1007/978-3-642-79795-8_3] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- N Kleckner
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138, USA
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23
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Eichenbaum Z, Livneh Z. Intermolecular transposition of IS10 causes coupled homologous recombination at the transposition site. Genetics 1995; 140:861-74. [PMID: 7672587 PMCID: PMC1206671 DOI: 10.1093/genetics/140.3.861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Interplasmid and chromosome to plasmid transposition of IS10 were studied by assaying inactivation of the phage 434 cI gene, carried on a low copy number plasmid. This was detected by the activity of the tet gene expressed from the phage 434 PR promoter. Each interplasmid transposition resulted in the fusion of the donor and acceptor plasmids into cointegrate structure, with a 9-bp duplication of the target DNA at the insertion site. Cointegrate formation was abolished in delta recA strains, although simple insertions of IS10 were observed. This suggests a two-stage mechanism involving IS10 conservative transposition, followed by homologous recombination between the donor and the acceptor. Two plasmids carrying inactive IS10 sequences were fused to cointegrates at a 100-fold lower frequency, suggesting that homologous recombination is coupled to and stimulated by the transposition event. Each IS10 transposition from the chromosome to the acceptor plasmid involved replicon fusion, providing a mechanism for IS10-mediated integration of extrachromosomal elements into the chromosome. This was accompanied by the formation of an additional copy of IS10 in the chromosome. Thus, like replicative transposition, conservative transposition of IS10 is accompanied by cointegrate formation and results in duplication of the IS10.
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Affiliation(s)
- Z Eichenbaum
- Department of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
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24
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Signon L, Kleckner N. Negative and positive regulation of Tn10/IS10-promoted recombination by IHF: two distinguishable processes inhibit transposition off of multicopy plasmid replicons and activate chromosomal events that favor evolution of new transposons. Genes Dev 1995; 9:1123-36. [PMID: 7744253 DOI: 10.1101/gad.9.9.1123] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Tn10 is a composite transposon; inverted repeats of insertion sequence IS10 flank a tetracycline-resistance determinant. Previous work has identified several regulatory processes that modulate the interaction between Tn10 and its host. Among these, host-specified DNA adenine methylation, an IS10-encoded antisense RNA and preferential cis action of transposase are particularly important. We now find that the accessory host protein IHF and the sequences that encode the IHF-binding site in IS10 are also important regulators of the Tn10 transposition reaction in vivo and that these determinants are involved in two distinguishable regulatory processes. First, IHF and the IHF-binding site of IS10, together with other host components (e.g., HU), negatively regulate the normal intermolecular transposition process. Such negative regulation is prominent only for elements present on multicopy plasmid replicons. This multicopy plasmid-specific regulation involves effects both on the transposition reaction per se and on transposase gene expression. Second, specific interaction of IHF with its binding site stimulates transposon-promoted chromosome rearrangements but not transposition of a short Tn10-length chromosomal element. However, additional considerations predict that IHF action should favor chromosomal transposition for very long composite elements. On the basis of these and other observations we propose that, for chromosomal events, the major role of IHF is to promote the evolution of new IS10-based composite transposons.
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Affiliation(s)
- L Signon
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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25
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KARCHER SUSANJ. TRANSPOSON MUTAGENESIS OF Escherichia coli. Mol Biol 1995. [DOI: 10.1016/b978-012397720-5.50035-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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26
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Fonstein M, Nikolskaya T, Zaporojets D, Nikolsky Y, Kulakauskas S, Mironov A. Tn10-mediated inversions fuse uridine phosphorylase (udp) and rRNA genes of Escherichia coli. J Bacteriol 1994; 176:2265-71. [PMID: 7512551 PMCID: PMC205348 DOI: 10.1128/jb.176.8.2265-2271.1994] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Two strains carrying metE::Tn10 insertions (upstream of the udp gene) were used to isolate mutants of Escherichia coli overexpressing udp. These strains differ in their gene order; one contains an inversion between the rrnD and rrnE rRNA operons. Selection was based on the ability of overexpressed Udp to complement thymine auxotrophy. Chromosomal rearrangements that connect the udp gene and promoters of different rrn operons were obtained by this selection. Seven of 14 independent mutants selected in one of the initial strains contained similar inversions of the metE-rrnD segment of the chromosome (about 12% of its length). Another mutant contained traces of a more complicated event, inversion between rrnB and rrnG operons, which was followed by reinversion of the segment between metE and the hybrid rrnG/B operon. Similar inversions (udp-rrn) in a strain already carrying an rrnE-rrnD inversion flip the chromosomal segment between metE and rrnD/E in the opposite direction. In this case, inversions are also accompanied by duplications of the chromosomal region between the rrnA and hybrid udp-rrnD/E operons. PCR amplification with a set of oligonucleotides from the rrn, Tn5, and met genes was used for more detailed mapping. Amplified fragments of the rearranged chromosomes connecting rrnD sequences and insertion elements were sequenced, and inversion endpoints were established.
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27
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Benada O, Navrátil O. Electron microscopic analysis of two nonconjugative derivatives of plasmid R1drd-19Km- from Escherichia coli. Folia Microbiol (Praha) 1992; 37:347-52. [PMID: 1337331 DOI: 10.1007/bf02815660] [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: 12/26/2022]
Abstract
The plasmids pON5300 and pON5304, nonconjugative variants of the plasmid R1drd-19Km, were analyzed by electron microscopy. It was found by heteroduplex mapping that a 1.4 kb DNA segment was inserted into EcoRI E fragment of both plasmids, where some tra-genes and oriT are localized. Although this DNA segment was mapped to the same region its orientation was different in each of the two plasmids. The inserted DNA segment was identified as an IS10R sequence on the basis of analysis of self-annealed molecules of pON5304 and their cleavage with EcoRV restriction enzyme. These methods enable us not only to map IS10R sequences on 87 kb pON5300 and 65 kb pON5304 molecules, respectively, but also to define their orientation.
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Affiliation(s)
- O Benada
- Institute of Microbiology, Czechoslovak Academy of Sciences, Prague
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28
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Hinton JC, Santos DS, Seirafi A, Hulton CS, Pavitt GD, Higgins CF. Expression and mutational analysis of the nucleoid-associated protein H-NS of Salmonella typhimurium. Mol Microbiol 1992; 6:2327-37. [PMID: 1406272 DOI: 10.1111/j.1365-2958.1992.tb01408.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The H-NS (H1) protein is a major component of bacterial chromatin. Mutations in the hns (osmZ) gene encoding H-NS are highly pleiotropic, affecting the expression of many unrelated genes in an allele-specific manner. H-NS expression was found not to vary with growth phase or growth medium osmolarity. Additionally, 10 independent hns mutations were isolated and characterized. Five of these mutations were the result of an IS10 insertion, each generating a truncated polypeptide. The other five mutations were the same specific deletion of one amino acid, delta Ala46. The various hns mutations exhibited different phenotypes and influenced DNA topology to variable extents. Implications for the mechanism by which H-NS influences gene expression are discussed.
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Affiliation(s)
- J C Hinton
- Imperial Cancer Research Fund Laboratories, University of Oxford, John Radcliffe Hospital, UK
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29
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Lockman HA, Curtiss R. Isolation and characterization of conditional adherent and non-type 1 fimbriated Salmonella typhimurium mutants. Mol Microbiol 1992; 6:933-45. [PMID: 1351241 DOI: 10.1111/j.1365-2958.1992.tb01543.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mutations in the genes encoding the type 1 fimbriae of Salmonella typhimurium were isolated by selecting for the deletion of Tn10 inserted adjacent to the chromosomal fim+ genes and screening for the loss of mannose-sensitive haemagglutination (HA) activity. S. typhimurium strains with Tn10 insertions in ahp were hypersensitive to peroxides, and tetracycline-sensitive derivatives of ahp::Tn10 mutants displayed two fim mutant phenotypes. The predominant class of fim mutants did not synthesize type 1 fimbriae. A second type of fim mutant synthesized type 1 fimbriae and exhibited a conditional lipoic acid requirement for HA. A fim-lip conditional mutant synthesized type 1 fimbriae when grown in Mueller-Hinton broth but the haemagglutinating activity of the fimbriae was dependent upon the addition of lipoic acid to the growth medium. Independently isolated lip mutations did not demonstrate a similar pleiotropic effect on HA. Western blots of fimbriae extracted from a fim-lip conditional mutant that was grown under permissive and restrictive conditions indicated the presence of 33 and 36.6 kDa proteins in HA+ fimbriae that were absent in HA- fimbriae. The HA+ phenotype of both conditional and non-fimbriated mutants was restored by transformation with cloned genes encoding S. typhimurium type 1 fimbriae.
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Affiliation(s)
- H A Lockman
- Department of Biology, Washington University, St Louis, Missouri 63130-4899
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30
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Abstract
BlnI or AvrII (5'-CCTAGG) sites are very rare in the Salmonella typhimurium LT2 genome. BlnI was used to construct a physical map which was correlated with the genetic map by using three methods. First, Tn10 carries BlnI sites, and the extra restriction sites produced by 34 genetically mapped Tn10 insertions were physically mapped by using pulsed-field gel electrophoresis. Second, six genetically mapped Mud-P22 prophage insertions were used to assign BlnI fragments. Integration of Mud-P22 introduces 30 kb of DNA that can easily be detected by a "shift up" in all but the largest BlnI fragments. Finally, induced Mud-P22 insertions package more than 100 kb of genomic DNA adjacent to one side of the insertion. Some of the smaller BlnI fragments were localized by hybridization to a dot blot array of 52 lysates from induced Mud-P22 insertions. Of the 10 BlnI sites mapped, 6 probably occur in or near the 16S rRNA genes at about 55, 71, 83, 86, 88.5, and 89.5 min. There is one BlnI site in the 90-kb pSLT plasmid. Two additional BlnI fragments of about 7 and 4 kb have not been localized. The size of the genome was estimated as 4.78 Mb (+/- 0.1 Mb) excluding pSLT but including prophages Fels-1 and Fels-2. One BlnI fragment that maps between 55 and 59 min showed a 40-kb reduction in size in a strain cured of the approximately 40-kb Fels-2 prophage.
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Affiliation(s)
- K K Wong
- California Institute of Biological Research, La Jolla 92037
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31
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Gompels UA, Carss AL, Sun N, Arrand JR. Infectivity determinants encoded in a conserved gene block of human herpesvirus-6. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1992; 3:25-39. [PMID: 1333836 DOI: 10.3109/10425179209039693] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The nucleotide sequence was determined for a 9.3 kb BamHI DNA fragment derived from a cosmid clone (Lorist 6) library of the 160 kb human herpesvirus-6 (HHV-6) strain U1102 genome. Analysis of the sequence showed two different sources for the DNA; 8.0 kb was derived from HHV-6, while 1.3 kb was derived from the right repeat of transposon Tn10, the insertion sequence (IS) element IS10R. The IS element sequence is shown to be derived from the host bacteria of the plasmid. The HHV-6 sequence represents a highly conserved part of the genome encoding 15% of the genes conserved among the other human herpesviruses in only 5% of the genome. Six genes were identified, five encoding products with amino acid sequence similarity to homologues in herpes simplex virus (HSV), Varicella Zoster Virus (VZV), human cytomegalovirus (CMV) and Epstein-Barr Virus (EBV). All had closest amino acid similarity to CMV proteins. Three clustered structural genes, included glycoprotein H, a major conserved determinant of infectivity, were jointed to a putative dUTPase homologue in an arrangement distinct to CMV and HHV-6. In the other herpes viruses these genes are separated by over 50 kb. The gene at this point of genetic rearrangement had no sequence similarity to proteins of other herpesviruses. However, there is a protein at this locus in CMV with similar composition and character. Both appear to be highly glycosylated, secreted glycoproteins with repetitive elements similar to those of human mucins. Comparison of sequence available in the HHV-6 GS strain also shows this to be a variable region (5% nucleotide differences) in an overall conserved DNA sequence (0.5%).
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Affiliation(s)
- U A Gompels
- Dept. of Medicine, Addenbrooke's Hospital Level 5, Cambridge, UK
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32
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Abstract
Repetitive sequences were isolated and characterized as double-stranded DNA fragments by treatment with S1 nuclease after denaturation and renaturation of the total DNA of Enterobacter cloacae MD36. One repetitive sequence was identical to the nucleotide sequence of IS10-right (IS10R), which is the active element in the plasmid-associated transposon Tn10. Unexpectedly, 15 copies of IS10R were found in the chromosomal DNA of E. cloacae MD36. One copy of the central region of Tn10 was found in the total DNA of E. cloacae MD36. IS10Rs in restriction fragments isolated from the E. cloacae MD36 total DNA showed 9-bp duplications adjacent to the terminal sequences that are characteristic of Tn10 transposition. This result suggests that many copies of IS10R in E. cloacae MD36 are due to transposition of IS10R alone, not due to transposition of Tn10 or to DNA rearrangement. I also found nine copies of IS10 in Shigella sonnei HH109, two and four copies in two different natural isolates of Escherichia coli, and two copies in E. coli K-12 strain JM109 from the 60 bacterial strains that were examined. All dam sites in the IS10s in E. cloacae MD36 and S. sonnei HH109 were methylated. Tn10 and IS10 transpose by a mechanism in which the element is excised from the donor site and inserted into the new target site without significant replication of the transposing segment; thus, the copy numbers of the elements in the cell are thought to be unchanged in most circumstances. Accumulation of IS10 copies in E. cloacae MD36 has interesting evolutionary implications.
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Affiliation(s)
- S Matsutani
- National Institute of Hygienic Sciences, Tokyo, Japan
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33
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Bender J, Kuo J, Kleckner N. Genetic evidence against intramolecular rejoining of the donor DNA molecule following IS10 transposition. Genetics 1991; 128:687-94. [PMID: 1655563 PMCID: PMC1204543 DOI: 10.1093/genetics/128.4.687] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Tn10 and IS10 transpose by a nonreplicative mechanism in which the transposon is excised from the donor molecule and integrated into a target DNA site, leaving behind a break at the original donor site. The fate of this broken donor DNA molecule is not known. We describe here two experiments that address this issue. One experiment demonstrates that a polar IS10 element gives rise to polarity-relief revertants at less than 1% the frequency of transposition of the same element in the same culture. In a second experiment, transpositions of an IS10 element from one site in the bacterial genome to another are selected and the resulting isolates examined for alterations at the donor site; none of 1088 such isolates exhibited a detectable change at the donor locus. These results are compatible with two possible fates of the transposon donor molecule: degradation ("donor suicide"), or restoration of the original information at the donor site by a recombinational repair mechanism analogous to double-strand break repair. These results argue against the possibility that the donor molecule gap is simply resealed by intramolecular rejoining.
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Affiliation(s)
- J Bender
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
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Abstract
Some transposable elements move by a replicative mechanism involving cointegrate formation. Intramolecular cointegration can generate a product called an "adjacent deletion" in which a contiguous chromosomal segment adjacent to the transposon is deleted while the element responsible remains intact. Insertion sequence IS10 is thought to transpose by a nonreplicative mechanism. In the simplest models, nonreplicative transposition cannot give rise to an adjacent deletion because an intrinsic feature of such transposition is excision of the IS element from the donor location. We report here that IS10 can generate adjacent deletions, but at a frequency which is approximately 1/30th the frequency of transposition for the same element. We suggest that these deletions might arise either by nonreplicative transposition events that involve two IS10 elements located on sister chromosomes or by aberrant nonreplicative events involving cleavage and ligation at only one end of the element.
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Affiliation(s)
- D E Roberts
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
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Haniford DB, Benjamin HW, Kleckner N. Kinetic and structural analysis of a cleaved donor intermediate and a strand transfer intermediate in Tn10 transposition. Cell 1991; 64:171-9. [PMID: 1846088 DOI: 10.1016/0092-8674(91)90218-n] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Tn10 transposes by a nonreplicative "cut and paste" mechanism. We describe here two protein-DNA complexes that are reaction intermediates in the Tn10 transposition process: a cleaved donor complex whose DNA component consists of transposon sequences cleanly excised from flanking donor DNA, and a strand transfer complex whose DNA component contains transposon termini specifically joined to a target site. The kinetic behavior of the first species suggests that it is an early intermediate in the transposition reaction. These two Tn10 complexes are closely analogous to complexes identified in the pathway for replicative "cointegrate" formation by bacteriophage Mu and thus represent intermediates that may be common to both nonreplicative and replicative transposition. These and other results suggest that the Tn10 and Mu reactions are fundamentally very similar despite their very different biological outcomes. The critical difference between the two reactions is the fate of the DNA strand that is not joined to target DNA.
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Affiliation(s)
- D B Haniford
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
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Abstract
Transposon Tn10 promotes the formation of a circular product containing only transposon sequences. We show that these circles result from an intramolecular transposition reaction in which all of the strand cleavage and ligation events have occurred but newly created transposon/target junctions have not undergone repair. The unligated strand termini at these junctions are those expected according to a simple model in which the target DNA is cleaved by a pair of staggered nicks 9 bp apart, transposon sequences are separated from flanking donor DNA by cleavage at the terminal nucleotides on both strands (at both ends) of the element, and 3' transposon strand ends are ligated to 5' target strand ends. The stability of the unligated junctions suggests that they are protected from cellular processing by transposase and/or host proteins. We propose that the nonreplicative nature of Tn10 transposition is determined by the efficiency with which the nontransferred transposon strand is separated from flanking donor DNA and by the nature of the protein-DNA complexes present at the strand transfer junctions.
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Affiliation(s)
- H W Benjamin
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
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Raleigh EA, Trimarchi R, Revel H. Genetic and physical mapping of the mcrA (rglA) and mcrB (rglB) loci of Escherichia coli K-12. Genetics 1989; 122:279-96. [PMID: 2548920 PMCID: PMC1203701 DOI: 10.1093/genetics/122.2.279] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We have genetically analyzed, cloned and physically mapped the modified cytosine-specific restriction determinants mcrA (rglA) and mcrB (rglB) of Escherichia coli K-12. The independently discovered Rgl and Mcr restriction systems are shown to be identical by three criteria: 1) mutants with the RglA- or RglB- phenotypes display the corresponding McrA- or McrB- phenotypes, and vice versa; 2) the gene(s) for RglA and McrA reside together at one locus, while gene(s) for RglB and McrB are coincident at a different locus; and 3) RglA+ and RglB+ recombinant clones complement for the corresponding Mcr-deficient lesions. The mcrA (rglA) gene(s) is on the excisable element e14, just clockwise of purB at 25 min. The mcrB (rglB) gene(s), at 99 min, is in a cluster of restriction functions that includes hsd and mrr, determinants of host-specific restriction (EcoK) and methyladenine-specific restriction respectively. Gene order is mcrB-hsdS-hsdM-hsdR-mrr-serB. Possible models for the acqusition of these restriction determinants by enteric bacteria are discussed.
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Affiliation(s)
- E A Raleigh
- New England BioLabs, Beverly, Massachusetts 01915-9990
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Case CC, Roels SM, González JE, Simons EL, Simons RW. Analysis of the promoters and transcripts involved in IS10 anti-sense RNA control. Gene 1988; 72:219-36. [PMID: 2468561 DOI: 10.1016/0378-1119(88)90147-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic analysis of eleven mutations affecting the IS10 promoters, pIN and pOUT, involved in anti-sense RNA control of transposase gene expression, and characterization of the transcripts, reveal that: (i) The transposase message (RNA-IN) and the anti-sense RNA (RNA-OUT) have been unambiguously identified in vivo. (ii) Five mutations affect pIN activity, and establish that pIN is the only IS10 promoter transcribing the tnp gene, and the only such IS10 promoter that responds to DNA-adenine methylation. (iii) Six mutations alter pOUT activity, and establish that pOUT is the only IS10 promoter specifying the anti-sense RNA-OUT. (iv) The latter, however, need not be so: heterologous promoters, if properly positioned, can also specify active anti-sense RNAs. (v) These heterologously promoted anti-sense RNAs are processed to species closely resembling native RNA-OUT.
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Affiliation(s)
- C C Case
- Department of Microbiology, University of California, Los Angeles 90024
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Abstract
The presence of transposons Tn10 or Tn5 in the genome increases the frequency with which a silent (promoter-less) gene (hisD) is mutationally activated. The activation frequency is increased 5-25-fold by Tn10 and 30-90-fold by Tn5. Activation of the hisD gene is achieved by transposition of the entire transposon or one of its flanking insertion sequences to a region just upstream of the silent gene, between a Rho-dependent termination site in the adjacent hisG gene and the hisD gene. For both Tn5 and Tn10 the component insertion sequences were found to transpose much more frequently than the entire composite element. Transposons Tn5 and Tn10 have previously been shown to carry promoters which direct transcripts into sequences adjacent to their insertion sites.
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Affiliation(s)
- A Wang
- Department of Biology, University of Utah, Salt Lake City 84112
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Abstract
We describe a cell-free system that promotes Tn10 transposition and transposon circle formation, a related intramolecular event. Tn10 circle formation in vitro has been characterized in detail, and is shown to require a supercoiled substrate and to proceed in the absence of ATP. The reaction requires Tn10 transposase protein, and either of two E. coli proteins, integration host factor (IHF) and HU, which are small DNA binding proteins that change the conformation of DNA. Tn10 is composed of inverted repeats of insertion sequence IS10. Pair-wise combinations of the IS10 "outside" and "inside" ends mediate distinct classes of rearrangements in vivo, and they exhibit different reaction requirements in vitro. In contrast to the Tn10 reaction, which involves two outside ends, circle formation with two inside ends proceeds with a transposase fraction alone, in the absence of added host factors, and is inhibited by methylation of the dam site within each terminus.
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Affiliation(s)
- D Morisato
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
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