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Breidenstein A, Lamy A, Bader CP, Sun WS, Wanrooij PH, Berntsson RPA. PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs. Life Sci Alliance 2024; 7:e202402693. [PMID: 38811160 PMCID: PMC11137577 DOI: 10.26508/lsa.202402693] [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: 03/05/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded type IV secretion systems (T4SSs). Many conjugative plasmids encode for a single-stranded DNA-binding protein (SSB) together with their T4SS. Some of these SSBs have been suggested to aid in establishing the plasmid in the recipient cell, but for many, their function remains unclear. Here, we characterize PrgE, a proposed SSB from the Enterococcus faecalis plasmid pCF10. We show that PrgE is not essential for conjugation. Structurally, it has the characteristic OB-fold of SSBs, but it has very unusual DNA-binding properties. Our DNA-bound structure shows that PrgE binds ssDNA like beads on a string supported by its N-terminal tail. In vitro studies highlight the plasticity of PrgE oligomerization and confirm the importance of the N-terminus. Unlike other SSBs, PrgE binds both double- and single-stranded DNA equally well. This shows that PrgE has a quaternary assembly and DNA-binding properties that are very different from the prototypical bacterial SSB, but also different from eukaryotic SSBs.
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Affiliation(s)
- Annika Breidenstein
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- https://ror.org/05kb8h459 Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Anaïs Lamy
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- https://ror.org/05kb8h459 Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Cyrielle Pj Bader
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Wei-Sheng Sun
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- https://ror.org/05kb8h459 Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Paulina H Wanrooij
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Ronnie P-A Berntsson
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- https://ror.org/05kb8h459 Wallenberg Centre for Molecular Medicine and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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2
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Cooke MB, Herman C. Conjugation's Toolkit: the Roles of Nonstructural Proteins in Bacterial Sex. J Bacteriol 2023; 205:e0043822. [PMID: 36847532 PMCID: PMC10029717 DOI: 10.1128/jb.00438-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Bacterial conjugation, a form of horizontal gene transfer, relies on a type 4 secretion system (T4SS) and a set of nonstructural genes that are closely linked. These nonstructural genes aid in the mobile lifestyle of conjugative elements but are not part of the T4SS apparatus for conjugative transfer, such as the membrane pore and relaxosome, or the plasmid maintenance and replication machineries. While these nonstructural genes are not essential for conjugation, they assist in core conjugative functions and mitigate the cellular burden on the host. This review compiles and categorizes known functions of nonstructural genes by the stage of conjugation they modulate: dormancy, transfer, and new host establishment. Themes include establishing a commensalistic relationship with the host, manipulating the host for efficient T4SS assembly and function and assisting in conjugative evasion of recipient cell immune functions. These genes, taken in a broad ecological context, play important roles in ensuring proper propagation of the conjugation system in a natural environment.
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Affiliation(s)
- Matthew B. Cooke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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3
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Couturier A, Virolle C, Goldlust K, Berne-Dedieu A, Reuter A, Nolivos S, Yamaichi Y, Bigot S, Lesterlin C. Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer. Nat Commun 2023; 14:294. [PMID: 36653393 PMCID: PMC9849209 DOI: 10.1038/s41467-023-35978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells, which contributes to the dissemination of antibiotic resistance. Here, we use live-cell microscopy to visualise the intracellular dynamics of conjugative transfer of F-plasmid in E. coli, in real time. We show that the transfer of plasmid in single-stranded form (ssDNA) and its subsequent conversion into double-stranded DNA (dsDNA) are fast and efficient processes that occur with specific timing and subcellular localisation. Notably, the ssDNA-to-dsDNA conversion determines the timing of plasmid-encoded protein production. The leading region that first enters the recipient cell carries single-stranded promoters that allow the early and transient synthesis of leading proteins immediately upon entry of the ssDNA plasmid. The subsequent conversion into dsDNA turns off leading gene expression, and activates the expression of other plasmid genes under the control of conventional double-stranded promoters. This molecular strategy allows for the timely production of factors sequentially involved in establishing, maintaining and disseminating the plasmid.
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Affiliation(s)
- Agathe Couturier
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Chloé Virolle
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Kelly Goldlust
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Annick Berne-Dedieu
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Audrey Reuter
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Sophie Nolivos
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Yoshiharu Yamaichi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France.
| | - Christian Lesterlin
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France.
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4
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Virolle C, Goldlust K, Djermoun S, Bigot S, Lesterlin C. Plasmid Transfer by Conjugation in Gram-Negative Bacteria: From the Cellular to the Community Level. Genes (Basel) 2020; 11:genes11111239. [PMID: 33105635 PMCID: PMC7690428 DOI: 10.3390/genes11111239] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms, and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic lifestyle, virulence, biofilm formation, resistance to heavy metals, and, most importantly, resistance to antibiotics. These properties make conjugation a fundamentally important process, and it is thus the focus of extensive study. Here, we review the key steps of plasmid transfer by conjugation in Gram-negative bacteria, by following the life cycle of the F factor during its transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.
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Cox KEL, Schildbach JF. Sequence of the R1 plasmid and comparison to F and R100. Plasmid 2017; 91:53-60. [PMID: 28359666 DOI: 10.1016/j.plasmid.2017.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/13/2017] [Accepted: 03/26/2017] [Indexed: 12/29/2022]
Abstract
The R1 antibiotic resistance plasmid, originally discovered in a clinical Salmonella isolate in London, 1963, has served for decades as a key model for understanding conjugative plasmids. Despite its scientific importance, a complete sequence of this plasmid has never been reported. We present the complete genome sequence of R1 along with a brief review of the current knowledge concerning its various genetic systems and a comparison to the F and R100 plasmids. R1 is 97,566 nucleotides long and contains 120 genes. The plasmid consists of a backbone largely similar to that of F and R100, a Tn21-like transposon that is nearly identical to that of R100, and a unique 9-kb sequence that bears some resemblance to sequences found in certain Klebsiella oxytoca strains. These three regions of R1 are separated by copies of the insertion sequence IS1. Overall, the structure of R1 and comparison to F and R100 suggest a fairly stable shared conjugative plasmid backbone into which a variety of mobile elements have inserted to form an "accessory" genome, containing multiple antibiotic resistance genes, transposons, remnants of phage genes, and genes whose functions remain unknown.
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Affiliation(s)
- Katherine E L Cox
- Department of Biology, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218, USA.
| | - Joel F Schildbach
- Department of Biology, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218, USA.
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6
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Zong Z, Ginn AN, Dobiasova H, Iredell JR, Partridge SR. Different IncI1 plasmids from Escherichia coli carry ISEcp1-blaCTX-M-15 associated with different Tn2-derived elements. Plasmid 2015; 80:118-26. [PMID: 25929173 DOI: 10.1016/j.plasmid.2015.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 02/05/2023]
Abstract
The bla(CTX-M-15) gene, encoding the globally dominant CTX-M-15 extended-spectrum β-lactamase, has generally been found in a 2.971-kb ISEcp1-bla(CTX-M-15)-orf477Δ transposition unit, with ISEcp1 providing a promoter. In available IncF plasmid sequences from Escherichia coli, this transposition unit interrupts a truncated copy of transposon Tn2 that lies within larger multiresistance regions. In E. coli, bla(CTX-M-15) is also commonly associated with IncI1 plasmids and here three such plasmids from E. coli clinical isolates from western Sydney 2006-2007 have been sequenced. The plasmid backbones are organised similarly to those of other IncI1 plasmids, but have insertions and/or deletions and sequence differences. Each plasmid also has a different insertion carrying bla(CTX-M-15). pJIE113 (IncI1 sequence type ST31) is almost identical to plasmids isolated from the 2011 E. coli O104:H4 outbreak in Europe, where the typical bla(CTX-M-15) transposition unit interrupts a complete Tn2 inserted directly in the plasmid backbone. In the novel plasmid pJIE139 (ST88), ISEcp1-blaC(TX-M-15)-orf477Δ lies within a Tn2/3 hybrid transposon. Homologous recombination could explain movement of ISEcp1-bla(CTX-M-15)-orf477Δ between copies of Tn2 on IncF and IncI1 plasmids and generation of the Tn2/3 hybrid. pJIE174 (ST37) is almost identical to pESBL-12 from the Netherlands and in these plasmids bla(CTX-M-15) is flanked by two copies of IS26 that truncate the transposition unit within a larger region bounded by the ends of Tn2. bla(CTX-M-15) and the associated ISEcp1-derived promoter may be able to move from this structure by the actions of IS26, independently of both ISEcp1 and Tn2.
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Affiliation(s)
- Zhiyong Zong
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, The University of Sydney and Westmead Hospital, Westmead, NSW 2145, Australia; Department of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Andrew N Ginn
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, The University of Sydney and Westmead Hospital, Westmead, NSW 2145, Australia
| | - Hana Dobiasova
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, The University of Sydney and Westmead Hospital, Westmead, NSW 2145, Australia; Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic; CEITEC VFU, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, The University of Sydney and Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, The University of Sydney and Westmead Hospital, Westmead, NSW 2145, Australia.
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Seventeen Sxy-dependent cyclic AMP receptor protein site-regulated genes are needed for natural transformation in Haemophilus influenzae. J Bacteriol 2012; 194:5245-54. [PMID: 22821979 DOI: 10.1128/jb.00671-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Natural competence is the ability of bacteria to actively take up extracellular DNA. This DNA can recombine with the host chromosome, transforming the host cell and altering its genotype. In Haemophilus influenzae, natural competence is induced by energy starvation and the depletion of nucleotide pools. This induces a 26-gene competence regulon (Sxy-dependent cyclic AMP receptor protein [CRP-S] regulon) whose expression is controlled by two regulators, CRP and Sxy. The role of most of the CRP-S genes in DNA uptake and transformation is not known. We have therefore created in-frame deletions of each CRP-S gene and studied their competence phenotypes. All but one gene (ssb) could be deleted. Although none of the remaining CRP-S genes were required for growth in rich medium or survival under starvation conditions, DNA uptake and transformation were abolished or reduced in most of the mutants. Seventeen genes were absolutely required for transformation, with 14 of these genes being specifically required for the assembly and function of the type IV pilus DNA uptake machinery. Only five genes were dispensable for both competence and transformation. This is the first competence regulon for which all genes have been mutationally characterized.
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8
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Jain S, Zweig M, Peeters E, Siewering K, Hackett KT, Dillard JP, van der Does C. Characterization of the single stranded DNA binding protein SsbB encoded in the Gonoccocal Genetic Island. PLoS One 2012; 7:e35285. [PMID: 22536367 PMCID: PMC3334931 DOI: 10.1371/journal.pone.0035285] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 03/14/2012] [Indexed: 11/18/2022] Open
Abstract
Background Most strains of Neisseria gonorrhoeae carry a Gonococcal Genetic Island which encodes a type IV secretion system involved in the secretion of ssDNA. We characterize the GGI-encoded ssDNA binding protein, SsbB. Close homologs of SsbB are located within a conserved genetic cluster found in genetic islands of different proteobacteria. This cluster encodes DNA-processing enzymes such as the ParA and ParB partitioning proteins, the TopB topoisomerase, and four conserved hypothetical proteins. The SsbB homologs found in these clusters form a family separated from other ssDNA binding proteins. Methodology/Principal Findings In contrast to most other SSBs, SsbB did not complement the Escherichia coli ssb deletion mutant. Purified SsbB forms a stable tetramer. Electrophoretic mobility shift assays and fluorescence titration assays, as well as atomic force microscopy demonstrate that SsbB binds ssDNA specifically with high affinity. SsbB binds single-stranded DNA with minimal binding frames for one or two SsbB tetramers of 15 and 70 nucleotides. The binding mode was independent of increasing Mg2+ or NaCl concentrations. No role of SsbB in ssDNA secretion or DNA uptake could be identified, but SsbB strongly stimulated Topoisomerase I activity. Conclusions/Significance We propose that these novel SsbBs play an unknown role in the maintenance of genetic islands.
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Affiliation(s)
- Samta Jain
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Maria Zweig
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Katja Siewering
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kathleen T. Hackett
- Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Joseph P. Dillard
- Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Chris van der Does
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
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Garcillán-Barcia MP, Alvarado A, de la Cruz F. Identification of bacterial plasmids based on mobility and plasmid population biology. FEMS Microbiol Rev 2011; 35:936-56. [PMID: 21711366 DOI: 10.1111/j.1574-6976.2011.00291.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Plasmids contain a backbone of core genes that remains relatively stable for long evolutionary periods, making sense to speak about plasmid species. The identification and characterization of the core genes of a plasmid species has a special relevance in the study of its epidemiology and modes of transmission. Besides, this knowledge will help to unveil the main routes that genes, for example antibiotic resistance (AbR) genes, use to travel from environmental reservoirs to human pathogens. Global dissemination of multiple antibiotic resistances and virulence traits by plasmids is an increasing threat for the treatment of many bacterial infectious diseases. To follow the dissemination of virulence and AbR genes, we need to identify the causative plasmids and follow their path from reservoirs to pathogens. In this review, we discuss how the existing diversity in plasmid genetic structures gives rise to a large diversity in propagation strategies. We would like to propose that, using an identification methodology based on plasmid mobility types, we can follow the propagation routes of most plasmids in Gammaproteobacteria, as well as their cargo genes, in complex ecosystems. Once the dissemination routes are known, designing antidissemination drugs and testing their efficacy will become feasible. We discuss in this review how the existing diversity in plasmid genetic structures gives rise to a large diversity in propagation strategies. We would like to propose that, by using an identification methodology based on plasmid mobility types, we can follow the propagation routes of most plasmids in ?-proteobacteria, as well as their cargo genes, in complex ecosystems.
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Affiliation(s)
- Maria Pilar Garcillán-Barcia
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC-IDICAN, C. Herrera Oria s/n, Santander, Spain
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10
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te Poele EM, Samborskyy M, Oliynyk M, Leadlay PF, Bolhuis H, Dijkhuizen L. Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded. Plasmid 2008; 59:202-16. [PMID: 18295883 DOI: 10.1016/j.plasmid.2008.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Revised: 12/21/2007] [Accepted: 01/06/2008] [Indexed: 10/22/2022]
Abstract
Actinomycete integrative and conjugative elements (AICEs) are present in diverse genera of the actinomycetes, the most important bacterial producers of bioactive secondary metabolites. Comparison of pMEA100 of Amycolatopsis mediterranei, pMEA300 of Amycolatopsis methanolica and pSE211 of Saccharopolyspora erythraea, and other AICEs, revealed a highly conserved structural organisation, consisting of four functional modules (replication, excision/integration, regulation, and conjugative transfer). Features conserved in all elements, or specific for a single element, are discussed and analysed. This study also revealed two novel putative AICEs (named pSE222 and pSE102) in the Sac. erythraea genome, related to the previously described pSE211 and pSE101 elements. Interestingly, pSE102 encodes a putative aminoglycoside phosphotransferase which may confer antibiotic resistance to the host. Furthermore, two of the six pSAM2-like insertions in the Streptomyces coelicolor genome described by Bentley et al. [Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., et al., 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141-147] could be functional AICEs. Homologues of various AICE proteins were found in other actinomycetes, in Frankia species and in the obligate marine genus Salinispora and may be part of novel AICEs as well. The data presented provide a better understanding of the origin and evolution of these elements, and their functional properties. Several AICEs are able to mobilise chromosomal markers, suggesting that they play an important role in horizontal gene transfer and spread of antibiotic resistance, but also in evolution of genome plasticity.
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Affiliation(s)
- Evelien M te Poele
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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11
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Bendtsen JD, Nilsson AS, Lehnherr H. Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein. J Virol 2002; 76:9695-701. [PMID: 12208948 PMCID: PMC136491 DOI: 10.1128/jvi.76.19.9695-9701.2002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit and does not represent a recent acquisition of the phage. The P1 and E. coli SSB proteins are fully functionally interchangeable. SSB-P1 is nonessential for phage growth in an exponentially growing E. coli host, and it is sufficient to promote bacterial growth in the absence of the E. coli SSB protein. Expression studies showed that the P1 ssb gene is transcribed only, in an rpoS-independent fashion, during stationary-phase growth in E. coli. Mixed infection experiments demonstrated that a wild-type phage has a selective advantage over an ssb-null mutant when exposed to a bacterial host in the stationary phase. These results reconciled the observed evolutionary conservation with the seemingly redundant presence of ssb genes in many bacteriophages and conjugative plasmids.
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Affiliation(s)
- Jannick Dyrløv Bendtsen
- Department of Genetics and Biochemistry, Institute of Microbiology, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany
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12
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Beaber JW, Hochhut B, Waldor MK. Genomic and functional analyses of SXT, an integrating antibiotic resistance gene transfer element derived from Vibrio cholerae. J Bacteriol 2002; 184:4259-69. [PMID: 12107144 PMCID: PMC135215 DOI: 10.1128/jb.184.15.4259-4269.2002] [Citation(s) in RCA: 190] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SXT is representative of a family of conjugative-transposon-like mobile genetic elements that encode multiple antibiotic resistance genes. In recent years, SXT-related conjugative, self-transmissible integrating elements have become widespread in Asian Vibrio cholerae. We have determined the 100-kb DNA sequence of SXT. This element appears to be a chimera composed of transposon-associated antibiotic resistance genes linked to a variety of plasmid- and phage-related genes, as well as to many genes from unknown sources. We constructed a nearly comprehensive set of deletions through the use of the one-step chromosomal gene inactivation technique to identify SXT genes involved in conjugative transfer and chromosomal excision. SXT, unlike other conjugative transposons, utilizes a conjugation system related to that encoded by the F plasmid. More than half of the SXT genome, including the composite transposon-like structure that contains its antibiotic resistance genes, was not required for its mobility. Two SXT loci, designated setC and setD, whose predicted amino acid sequences were similar to those of the flagellar regulators FlhC and FlhD, were found to encode regulators that activate the transcription of genes required for SXT excision and transfer. Another locus, designated setR, whose gene product bears similarity to lambdoid phage CI repressors, also appears to regulate SXT gene expression.
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Affiliation(s)
- John W Beaber
- Division of Geographic Medicine/Infectious Diseases, New England Medical Center and Tufts University, and Howard Hughes Medical Institute, Boston, Massachusetts 02111, USA
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13
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Murata T, Ohnishi M, Ara T, Kaneko J, Han CG, Li YF, Takashima K, Nojima H, Nakayama K, Kaji A, Kamio Y, Miki T, Mori H, Ohtsubo E, Terawaki Y, Hayashi T. Complete nucleotide sequence of plasmid Rts1: implications for evolution of large plasmid genomes. J Bacteriol 2002; 184:3194-202. [PMID: 12029035 PMCID: PMC135101 DOI: 10.1128/jb.184.12.3194-3202.2002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rts1, a large conjugative plasmid originally isolated from Proteus vulgaris, is a prototype for the IncT plasmids and exhibits pleiotropic thermosensitive phenotypes. Here we report the complete nucleotide sequence of Rts1. The genome is 217,182 bp in length and contains 300 potential open reading frames (ORFs). Among these, the products of 141 ORFs, including 9 previously identified genes, displayed significant sequence similarity to known proteins. The set of genes responsible for the conjugation function of Rts1 has been identified. A broad array of genes related to diverse processes of DNA metabolism were also identified. Of particular interest was the presence of tus-like genes that could be involved in replication termination. Inspection of the overall genome organization revealed that the Rts1 genome is composed of four large modules, providing an example of modular evolution of plasmid genomes.
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Affiliation(s)
- Takahiro Murata
- Department of Bacteriology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
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Lehnherr H, Bendtsen JD, Preuss F, Ilyina TV. Identification and characterization of the single-stranded DNA-binding protein of bacteriophage P1. J Bacteriol 1999; 181:6463-8. [PMID: 10515938 PMCID: PMC103783 DOI: 10.1128/jb.181.20.6463-6468.1999] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of bacteriophage P1 harbors a gene coding for a 162-amino-acid protein which shows 66% amino acid sequence identity to the Escherichia coli single-stranded DNA-binding protein (SSB). The expression of the P1 gene is tightly regulated by P1 immunity proteins. It is completely repressed during lysogenic growth and only weakly expressed during lytic growth, as assayed by an ssb-P1/lacZ fusion construct. When cloned on an intermediate-copy-number plasmid, the P1 gene is able to suppress the temperature-sensitive defect of an E. coli ssb mutant, indicating that the two proteins are functionally interchangeable. Many bacteriophages and conjugative plasmids do not rely on the SSB protein provided by their host organism but code for their own SSB proteins. However, the close relationship between SSB-P1 and the SSB protein of the P1 host, E. coli, raises questions about the functional significance of the phage protein.
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Affiliation(s)
- H Lehnherr
- Institute of Molecular Biology, University of Southern Denmark, Main Campus Odense University, DK-5230 Odense M, Denmark.
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15
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De Vries J, Genschel J, Urbanke C, Thole H, Wackernagel W. The single-stranded-DNA-binding proteins (SSB) of Proteus mirabilis and Serratia marcescens. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 224:613-22. [PMID: 7925378 DOI: 10.1111/j.1432-1033.1994.00613.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The single-stranded-DNA-binding (SSB) proteins from Proteus mirabilis and Serratia marcescens were purified from overproducing Escherichia coli strains, which were devoid of their own ssb gene. The strains harboured an endA insertion mutation and a xonA mutation resulting in the absence of endonuclease I and exonuclease I activities from the preparations. The amino acid sequences of the SSB of all three species are nearly identical in the N-terminal parts of the proteins that contain the DNA-binding domain, but differ in the C-terminal parts. Both proteins have an apparent binding-site size of 65 and 35 nucleotides at high and low salt concentrations, respectively. The association-rate constant for binding to poly(dT) is 3.2 x 10(8) M-1 s-1 for P. mirabilis SSB (PmiSSB) and 3.4 x 10(8) M-1 s-1 for S. marcescens SSB (SmaSSB). These binding parameters are very similar to those of E. coli SSB (EcoSSB). The structural similarity of the proteins is also documented by the finding that they can exchange subunits among each other to form mixed tetramers. The transcriptional regulation of the ssb and uvrA genes from P. mirabilis and S. marcescens in SOS-induced E. coli cells was studied using lacZ fusions. While the uvrA genes were inducible, there was no induction of the ssb genes transcribed divergently from the uvrA genes. Apparently, regions with nucleotide sequence similarity to the E. coli SOS-box preceding the ssb genes of P. mirabilis and S. marcescens had no gross effect on the transcription. Studies on growth of the cells and recovery from ultraviolet damage indicate that the heterologous SSB proteins support DNA replication and recombinational DNA repair of E. coli with the same efficiency as the E. coli SSB protein. Interactions with other E. coli proteins involved in these processes either do not occur, or are not impeded.
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Affiliation(s)
- J De Vries
- Genetik, Fachbereich Biologie, Universität Oldenburg, Germany
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16
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de Vries J, Wackernagel W. Cloning and sequencing of the Serratia marcescens gene encoding a single-stranded DNA-binding protein (SSB) and its promoter region. Gene X 1993; 127:39-45. [PMID: 8486286 DOI: 10.1016/0378-1119(93)90614-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The gene (ssb) coding for a single-stranded DNA-binding protein (SSB) was identified on a 1.2-kb EcoRI-SalI fragment cloned from chromosomal DNA of Serratia marcescens. The cloned fragment conferred increased resistance against UV and mitomycin C (MC) to ssb- mutants of Escherichia coli. The nucleotide (nt) sequence revealed that SSB consists of 175 amino acids (aa) and has an M(r) of 18,677. It shows 89% aa sequence homology with the SSB of E. coli. The nt sequence preceding the gene contains three promoters. Two of them overlap with a presumptive SOS box, and the distal one overlaps with a second SOS box that coincides with the promoter of the adjacent uvrA (gene encoding the UvrA protein). The uvrA is transcribed in a direction opposite to that of ssb. The sequence coding for the N terminus of the UvrA of S. marcescens indicates that the first 74 aa are identical to those of the E. coli protein. The results suggest that the two bacterial SSBs are members of a group which differs from the known SSBs of prokaryotic transmissible plasmids, because their aa sequence homology with these proteins is only about 60%.
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Affiliation(s)
- J de Vries
- Fachbereich Biologie, Universität Oldenburg, Germany
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17
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Jovanovic OS, Ayres EK, Figurski DH. The replication initiator operon of promiscuous plasmid RK2 encodes a gene that complements an Escherichia coli mutant defective in single-stranded DNA-binding protein. J Bacteriol 1992; 174:4842-6. [PMID: 1624472 PMCID: PMC206285 DOI: 10.1128/jb.174.14.4842-4846.1992] [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: 12/27/2022] Open
Abstract
The amino acid sequence of the 13-kDa polypeptide (P116) encoded by the first gene of the trfA operon of IncP plasmid RK2 shows significant similarity to several known single-stranded DNA-binding proteins. We found that unregulated expression of this gene from its natural promoter (trfAp) or induced expression from a strong heterologous promoter (trcp) was sufficient to complement the temperature-sensitive growth phenotype of an Escherichia coli ssb-1 mutant. The RK2 ssb gene is the first example of a plasmid single-stranded DNA-binding protein-encoding gene that is coregulated with replication functions, indicating a possible role in plasmid replication.
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Affiliation(s)
- O S Jovanovic
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, New York 10032
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18
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Chernin LS, Terentyev MA, Ovadis MI. RecP, a new minor pathway of general recombination in Escherichia coli encoded by plasmid R1drd-19. Plasmid 1992; 27:93-104. [PMID: 1319595 DOI: 10.1016/0147-619x(92)90010-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Plasmid R1drd-19 markedly improves the recombination deficiency of recB and recBrecC mutants of Escherichia coli K12 as measured by Hfr crosses and increases their resistance to uv inactivation. The effect correlates with the production of an ATP-dependent ds DNA exonuclease in recB/R1drd-19 cells. This paper further investigates the suppressive effect of plasmid R1drd-19 on the recB mutation of E. coli. The gene(s) responsible for the effect was localized to the 13.1-kb EcoRI-C fragment of the resistance transfer factor (RTF) portion of R1drd-19. The plasmid-encoded activity does not merely replace the RecBCD enzyme failure but differs in several significant ways. It promotes a hyper-recombinogenic phenotype, as judged by the phenomenon of super oligomerization of the tester pACYC184 plasmid in recB/R1drd-19 cells and two inter- and intramolecular plasmid recombination test systems. It is probably not inhibited by lambda Gam protein and does not restrict plating of T4gp2 mutant. No significant homology between the E. coli chromosomal fragment carrying recBrecCrecD genes and the EcoRI-C fragment of R1drd-19 was observed. It is suggested that the plasmid-encoded recombination activity is involved in a new minor recombination pathway (designated RecP, for Plasmid). RecP resembles in some traits the RecBCD-independent pathways RecE and RecF but differs in activity and perhaps substrate specificity from the main RecBCD pathway.
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Affiliation(s)
- L S Chernin
- Institute of Chemical Physics, USSR Academy of Sciences, Moscow
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19
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Porter RD, Black S. The single-stranded-DNA-binding protein encoded by the Escherichia coli F factor can complement a deletion of the chromosomal ssb gene. J Bacteriol 1991; 173:2720-3. [PMID: 2013585 PMCID: PMC207845 DOI: 10.1128/jb.173.8.2720-2723.1991] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Genes encoding single-stranded-DNA-binding proteins (SSBs) are carried by a variety of large self-transmissible plasmids, and it previously has been shown that these plasmid-borne genes can complement conditional lethal alleles of the ssb gene on the Escherichia coli chromosome for cellular viability. We have tested one of the plasmid-borne ssb genes, the ssf gene from the E. coli F factor, for its ability to complement total deletion of the chromosomal ssb gene for viability. We have found that ssf can complement the ssb deletion, but only when it is present on a high-copy-number plasmid. Cells that are totally dependent on the F-factor-encoded SSB for viability manifest growth properties indicative of problems in DNA replication.
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Affiliation(s)
- R D Porter
- Department of Molecular and Cell Biology, Pennsylvania State University, University Park 16802
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20
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Ruvolo PP, Keating KM, Williams KR, Chase JW. Single-stranded DNA binding proteins (SSBs) from prokaryotic transmissible plasmids. Proteins 1991; 9:120-34. [PMID: 2008432 DOI: 10.1002/prot.340090206] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The DNA and protein sequences of single-stranded DNA binding proteins (SSBs) encoded by the plP71a, plP231a, and R64 conjugative plasmids have been determined and compared to Escherichia coli SSB and the SSB encoded by F-plasmid. Although the amino acid sequences of all of these proteins are highly conserved within the NH2-terminal two-thirds of the protein, they diverge in the COOH-terminal third region. A number of amino acid residues which have previously been implicated as being either directly or indirectly involved in DNA binding are conserved in all of these SSBs. These residues include Trp-40, Trp-54, Trp-88, His-55, and Phe-60. On the basis of these sequence comparisons and DNA binding studies, a role for Tyr-70 in DNA binding is suggested for the first time. Although the COOH-terminal third of these proteins diverges more than their NH2-terminal regions, the COOH-terminal five amino acid residues of all five of these proteins are identical. In addition, all of these proteins share the characteristic property of having a protease resistant, NH2-terminal core and an acidic COOH-terminal region. Despite the high degree of sequence homology among the plasmid SSB proteins, the F-plasmid SSB appears unique in that it was the only SSB tested that neither bound well to poly(dA) nor was able to stimulate DNA polymerase III holoenzyme elongation rates. Poly [d(A-T)] melting studies suggest that at least three of the plasmid encoded SSBs are better helix-destabilizing proteins than is the E. coli SSB protein.
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Affiliation(s)
- P P Ruvolo
- Department of Molecular Biology and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
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21
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Abstract
The single-stranded DNA-binding protein (SSB) of Escherichia coli is involved in all aspects of DNA metabolism: replication, repair, and recombination. In solution, the protein exists as a homotetramer of 18,843-kilodalton subunits. As it binds tightly and cooperatively to single-stranded DNA, it has become a prototypic model protein for studying protein-nucleic acid interactions. The sequences of the gene and protein are known, and the functional domains of subunit interaction, DNA binding, and protein-protein interactions have been probed by structure-function analyses of various mutations. The ssb gene has three promoters, one of which is inducible because it lies only two nucleotides from the LexA-binding site of the adjacent uvrA gene. Induction of the SOS response, however, does not lead to significant increases in SSB levels. The binding protein has several functions in DNA replication, including enhancement of helix destabilization by DNA helicases, prevention of reannealing of the single strands and protection from nuclease digestion, organization and stabilization of replication origins, primosome assembly, priming specificity, enhancement of replication fidelity, enhancement of polymerase processivity, and promotion of polymerase binding to the template. E. coli SSB is required for methyl-directed mismatch repair, induction of the SOS response, and recombinational repair. During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake.
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Affiliation(s)
- R R Meyer
- Department of Biological Sciences, University of Cincinnati, Ohio 45221
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22
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Abstract
Plasmid RP4 is stably maintained in strains of Escherichia coli and other Gram-negative bacteria. Inactivation of the plasmid primase gene (pri) or removal of the PstIC fragment gave RP4 derivatives that are slightly unstably maintained in E. coli. Removal of the Tn 1 multimer resolution system (res and tnpR) did not lead to any detectable plasmid loss. Removal of all three of these regions, however, gave rise to pNJ5000 which is lost at high frequency. We have dissected the mechanisms causing this phenomenon. In contrast to RP4, pNJ5000 accumulates significantly as plasmid multimers in a Rec+ host; in a recA host, multimers are not seen and the plasmid is stably maintained. Multimers therefore appear to form by recA-mediated homologous recombination and cause plasmid instability, perhaps by interfering with partition. We demonstrate a mechanism provided by the PstIC fragment which acts on multimers analogously to the Tn1/3 resolution system on plasmid cointegrates, being effective only when cloned in cis. The loss of pri, on the other hand, can be complemented in trans. Our results are consistent with the view that primase prevents multimers forming (rather than resolving them once formed), perhaps by binding specifically to single-stranded regions of the plasmid and preventing homologous pairing.
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Affiliation(s)
- N J Grinter
- Department of Biochemistry and Soil Science, University College of North Wales, Bangor, Gwynedd, United Kingdom
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23
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Abstract
The IncI1 plasmid ColIb-P9 was found to carry a single-stranded DNA-binding (SSB) protein gene (ssb) that maps about 11 kilobase pairs from the origin of transfer in the region transferred early during bacterial conjugation. The cloned gene was able to suppress the UV and temperature sensitivity of an ssb-1 strain of Escherichia coli K-12. The nucleotide sequence of the ColIb ssb gene was determined, giving a predicted molecular weight of 19,110 for the SSB protein. Sequence data show that ColIb ssb is very similar to the ssb gene on plasmid F, which is also known to map in the leader region. High-level expression of ssb on ColIb required derepression of the transfer (tra) genes and the activity of the positive regulatory system controlling these genes, suggesting that the SSB protein contributes to the conjugative processing of DNA. A mutant of ColIbdrd-1 carrying a Tn903-derived insertion in ssb was constructed, but it was unaffected in the ability to generate plasmid transconjugants and it was maintained apparently stably in donor cells both following mating and during vegetative growth. Hence, no biological role of ColIb SSB protein was detected. However, unlike the parental plasmid, such ColIb ssb mutants conferred a marked Psi+ (plasmid-mediated SOS inhibition) phenotype on recA441 and recA730 strains, implying a functional relationship between SSB and Psi proteins.
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Affiliation(s)
- C J Howland
- Department of Genetics, University of Leicester, England
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24
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Casas-Finet JR, Jhon NI, Khamis MI, Maki AH, Ruvolo PP, Chase JW. An IncY plasmid-encoded single-stranded DNA-binding protein from Escherichia coli shows the identical pattern of stacked tryptophan residues as the chromosomal ssb gene product. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 178:101-7. [PMID: 3060358 DOI: 10.1111/j.1432-1033.1988.tb14434.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In an extension of earlier studies on the Escherichia coli plasmid-encoded single-stranded DNA-binding proteins pIP71a SSB, F SSB and R64 SSB [Khamis, M. I., Casas-Finet, J. R., Maki, A. H., Ruvolo, P. P. & Chase, J. W. (1987) Biochemistry 26, 3347-3354; Casas-Finet, J. R., Khamis, M. I., Maki, A. H., Ruvolo, P. P. & Chase, J. W. (1987) J. Biol. Chem. 262, 8574-8593], we have investigated the binding of pIP231a SSB to natural and heavy-atom-derivatized single-stranded homopolynucleotides. Fluorimetric equilibrium binding isotherms indicate that pIP231a SSB has a greater solubility at low ionic strength than any other plasmid SSB protein investigated. Furthermore, its complex with mercurated poly(uridylic acid) [poly(Hg5U)] shows a greater resistance to disruption by salt than the other plasmid SSB complexes. Essentially complete binding of pIP231a SSB to poly(Hg5U) could be achieved, and time-resolved optically detected triplet-state magnetic resonance (ODMR) techniques could be applied to the complex. These methods allowed complete resolution of the three Trp chromophores of pIP231a SSB. Comparison of wavelength-selected ODMR results with those obtained for the poly(Hg5U) complex of a point-mutated chromosomal ssb gene product (Eco SSB) carrying substitutions of Phe for Trp [Khamis, M. I., Casas-Finet, J. R., Maki, A. H., Murphy, J. B. & Chase, J. W. (1987) J. Biol. Chem. 262, 10938-10945] confirm that Trp40 and Trp54 of pIP231a SSB are stacked in the complex, while Trp88 is not. This is the same distribution of stacked Trp residues found in Eco SSB. These results are confirmed further by specific effects observed on the ODMR signals of pIP231a SSB upon binding to poly(Br5U) and poly(dT), which are known to be caused by the stacking of Trp54 with nucleic acid bases.
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Affiliation(s)
- J R Casas-Finet
- Department of Chemistry, University of California, Davis 95616
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25
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Golub EI, Panzer HA. The F factor of Escherichia coli carries a locus of stable plasmid inheritance stm, similar to the parB locus of plasmid RI. MOLECULAR & GENERAL GENETICS : MGG 1988; 214:353-7. [PMID: 3070354 DOI: 10.1007/bf00337735] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We found that a 1.4 kb fragment of the F factor of Escherichia coli (coordinates 62.8-64.2) considerably increased the stable inheritance of different plasmids which carried it. The fragment has a 589 bp DNA sequence (coordinates 63.3-63.9) with extensive homology to the parB locus of plasmid RI and, probably like the parB region, ensures the presence of plasmids in bacterial populations by killing those cells which have lost the plasmid.
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Affiliation(s)
- E I Golub
- Radiobiology Laboratories, Yale University School of Medicine, New Haven, CT 06510
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26
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Golub E, Bailone A, Devoret R. A gene encoding an SOS inhibitor is present in different conjugative plasmids. J Bacteriol 1988; 170:4392-4. [PMID: 3045095 PMCID: PMC211458 DOI: 10.1128/jb.170.9.4392-4394.1988] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In 9 of 20 conjugative plasmids of different incompatibility groups, including F and R100 (or R6-5), coexist two sequences which are homologous, respectively, to the gene psiB, which encodes an inhibitor of SOS induction, and to the gene ssb, which encodes a single-stranded-DNA-binding protein.
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Affiliation(s)
- E Golub
- Radiobiology Laboratories, Yale University School of Medicine, New Haven, Connecticut 06510
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27
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Christie PJ, Ward JE, Winans SC, Nester EW. The Agrobacterium tumefaciens virE2 gene product is a single-stranded-DNA-binding protein that associates with T-DNA. J Bacteriol 1988; 170:2659-67. [PMID: 2836366 PMCID: PMC211185 DOI: 10.1128/jb.170.6.2659-2667.1988] [Citation(s) in RCA: 156] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Agrobacterium tumefaciens transfers T-DNA into the plant genome by a process mediated by Ti plasmid-encoded vir genes. Cleavage at T-DNA border sequences by the VirD endonuclease generates linear, single-stranded T-DNA molecules. In the work described in this report, we used electrophoretic mobility shift assays to show that the purified virE2 gene product binds to single-stranded DNA. VirE2 protein associates with T-DNA as shown by immunoprecipitation studies with VirE2-specific antiserum. The VirE2 protein was detected primarily in the cytoplasm, but also in the inner and outer membrane and periplasmic fractions. Virulence of a virE2 mutant was restored by mixed infection with strains carrying an intact vir region, but not with virA, virB, virD, virE, or virG mutants or chvA, chvB, or exoC mutants. We propose that the VirE2 protein is involved in the processing of T-DNA and in T-strand protection during transfer to the plant cell.
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Affiliation(s)
- P J Christie
- Department of Microbiology, University of Washington, Seattle 98195
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28
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Egner C, Azhderian E, Tsang SS, Radding CM, Chase JW. Effects of various single-stranded-DNA-binding proteins on reactions promoted by RecA protein. J Bacteriol 1987; 169:3422-8. [PMID: 3301800 PMCID: PMC212412 DOI: 10.1128/jb.169.8.3422-3428.1987] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
To relate the roles of Escherichia coli SSB in recombination in vivo and in vitro, we have studied the mutant proteins SSB-1 and SSB-113, the variant SSBc produced by chymotryptic cleavage, the partially homologous variant F SSB (encoded by the E. coli sex factor), and the protein encoded by gene 32 of bacteriophage T4. All of these, with the exception of SSB-1, augmented both the initial rate of homologous pairing and strand exchange promoted by RecA protein. From these and related observations, we conclude that SSB stimulates the initial formation of joint molecules by nonspecifically promoting the binding of RecA protein to single-stranded DNA; that SSB plays no role in synapsis of the RecA nucleoprotein filament with duplex DNA; that stimulation of strand exchange by SSB is similarly nonspecific; and that all members of the class of proteins represented by SSB, F SSB, and gene 32 protein may play equivalent roles in making single-stranded DNA more accessible to RecA protein.
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29
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Casas-Finet JR, Khamis MI, Maki AH, Ruvolo PP, Chase JW. Optically detected magnetic resonance of tryptophan residues in Escherichia coli ssb gene product and E. coli plasmid-encoded single-stranded DNA-binding proteins and their complexes with poly(deoxythymidylic) acid. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)47452-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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30
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Golub EI, Low KB. Derepression of single-stranded DNA-binding protein genes on plasmids derepressed for conjugation, and complementation of an E. coli ssb- mutation by these genes. MOLECULAR & GENERAL GENETICS : MGG 1986; 204:410-6. [PMID: 2945079 DOI: 10.1007/bf00331017] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Plasmid single-stranded DNA-binding protein genes complement the E. coli ssb-1 mutation, and partially restore capacity for DNA synthesis, DNA repair (direct role as well as role in SOS induction) and general recombination. Plasmid mutants derepressed for fertility derived from R1, R64 and R222 show a higher level of complementation compared to the parental repressed plasmids. Derepressed mutants of R222 synthesize more RNA which hybridizes with the ssb gene of the F factor than does the original R222 plasmid. This indicates that plasmid ssb genes are regulated coordinately with fertility genes.
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31
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Golub EI, Low KB. Unrelated conjugative plasmids have sequences which are homologous to the leading region of the F factor. J Bacteriol 1986; 166:670-2. [PMID: 3009421 PMCID: PMC214657 DOI: 10.1128/jb.166.2.670-672.1986] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Conjugative plasmids from various incompatibility groups which carry DNA homologous to the ssb gene of the F factor were found to have additional homology with the F factor. This region homologous with F was located on both sides of the ssb gene and occupied a considerable part of the leading region, i.e., the 12.9-kilobase portion of F transferred first during conjugation. This region was the only region of the F factor which has a homologous counterpart on many plasmids.
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