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Elucidating Recombination Mediator Function Using Biophysical Tools. BIOLOGY 2021; 10:biology10040288. [PMID: 33916151 PMCID: PMC8066028 DOI: 10.3390/biology10040288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary This review recapitulates the initial knowledge acquired with genetics and biochemical experiments on Recombination mediator proteins in different domains of life. We further address how recent in vivo and in vitro biophysical tools were critical to deepen the understanding of RMPs molecular mechanisms in DNA and replication repair, and unveiled unexpected features. For instance, in bacteria, genetic and biochemical studies suggest a close proximity and coordination of action of the RecF, RecR and RecO proteins in order to ensure their RMP function, which is to overcome the single-strand binding protein (SSB) and facilitate the loading of the recombinase RecA onto ssDNA. In contrary to this expectation, using single-molecule fluorescent imaging in living cells, we showed recently that RecO and RecF do not colocalize and moreover harbor different spatiotemporal behavior relative to the replication machinery, suggesting distinct functions. Finally, we address how new biophysics tools could be used to answer outstanding questions about RMP function. Abstract The recombination mediator proteins (RMPs) are ubiquitous and play a crucial role in genome stability. RMPs facilitate the loading of recombinases like RecA onto single-stranded (ss) DNA coated by single-strand binding proteins like SSB. Despite sharing a common function, RMPs are the products of a convergent evolution and differ in (1) structure, (2) interaction partners and (3) molecular mechanisms. The RMP function is usually realized by a single protein in bacteriophages and eukaryotes, respectively UvsY or Orf, and RAD52 or BRCA2, while in bacteria three proteins RecF, RecO and RecR act cooperatively to displace SSB and load RecA onto a ssDNA region. Proteins working alongside to the RMPs in homologous recombination and DNA repair notably belongs to the RAD52 epistasis group in eukaryote and the RecF epistasis group in bacteria. Although RMPs have been studied for several decades, molecular mechanisms at the single-cell level are still not fully understood. Here, we summarize the current knowledge acquired on RMPs and review the crucial role of biophysical tools to investigate molecular mechanisms at the single-cell level in the physiological context.
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Abstract
The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how organisms exchange DNA segments that share extended regions of homology. The λ Red system proved useful as a system to study because recombinants could be easily generated by co-infection of genetically marked phages. What emerged from these studies was the recognition that replication of phage DNA was required for substantial Red-promoted recombination in vivo, and the critical role that double-stranded DNA ends play in allowing the Red proteins access to the phage DNA chromosomes. In the past 16 years, however, the λ Red recombination system has gained a new notoriety. When expressed independently of other λ functions, the Red system is able to promote recombination of linear DNA containing limited regions of homology (∼50 bp) with the Escherichia coli chromosome, a process known as recombineering. This review explains how the Red system works during a phage infection, and how it is utilized to make chromosomal modifications of E. coli with such efficiency that it changed the nature and number of genetic manipulations possible, leading to advances in bacterial genomics, metabolic engineering, and eukaryotic genetics.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
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Curtis FA, Malay AD, Trotter AJ, Wilson LA, Barradell-Black MMH, Bowers LY, Reed P, Hillyar CRT, Yeo RP, Sanderson JM, Heddle JG, Sharples GJ. Phage ORF family recombinases: conservation of activities and involvement of the central channel in DNA binding. PLoS One 2014; 9:e102454. [PMID: 25083707 PMCID: PMC4118853 DOI: 10.1371/journal.pone.0102454] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 06/17/2014] [Indexed: 01/05/2023] Open
Abstract
Genetic and biochemical evidence suggests that λ Orf is a recombination mediator, promoting nucleation of either bacterial RecA or phage Redβ recombinases onto single-stranded DNA (ssDNA) bound by SSB protein. We have identified a diverse family of Orf proteins that includes representatives implicated in DNA base flipping and those fused to an HNH endonuclease domain. To confirm a functional relationship with the Orf family, a distantly-related homolog, YbcN, from Escherichia coli cryptic prophage DLP12 was purified and characterized. As with its λ relative, YbcN showed a preference for binding ssDNA over duplex. Neither Orf nor YbcN displayed a significant preference for duplex DNA containing mismatches or 1-3 nucleotide bulges. YbcN also bound E. coli SSB, although unlike Orf, it failed to associate with an SSB mutant lacking the flexible C-terminal tail involved in coordinating heterologous protein-protein interactions. Residues conserved in the Orf family that flank the central cavity in the λ Orf crystal structure were targeted for mutagenesis to help determine the mode of DNA binding. Several of these mutant proteins showed significant defects in DNA binding consistent with the central aperture being important for substrate recognition. The widespread conservation of Orf-like proteins highlights the importance of targeting SSB coated ssDNA during lambdoid phage recombination.
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Affiliation(s)
- Fiona A. Curtis
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Ali D. Malay
- Heddle Initiative Research Unit, RIKEN, Wako, Saitama, Japan
| | - Alexander J. Trotter
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Lindsay A. Wilson
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Michael M. H. Barradell-Black
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Laura Y. Bowers
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Patricia Reed
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Christopher R. T. Hillyar
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - Robert P. Yeo
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | - John M. Sanderson
- Department of Chemistry, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
| | | | - Gary J. Sharples
- School of Biological and Biomedical Sciences, Biophysical Sciences Institute, Durham University, Durham, United Kingdom
- * E-mail:
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De Paepe M, Hutinet G, Son O, Amarir-Bouhram J, Schbath S, Petit MA. Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases. PLoS Genet 2014; 10:e1004181. [PMID: 24603854 PMCID: PMC3945230 DOI: 10.1371/journal.pgen.1004181] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 01/04/2014] [Indexed: 01/13/2023] Open
Abstract
Bacteriophages (or phages) dominate the biosphere both numerically and in terms of genetic diversity. In particular, genomic comparisons suggest a remarkable level of horizontal gene transfer among temperate phages, favoring a high evolution rate. Molecular mechanisms of this pervasive mosaicism are mostly unknown. One hypothesis is that phage encoded recombinases are key players in these horizontal transfers, thanks to their high efficiency and low fidelity. Here, we associate two complementary in vivo assays and a bioinformatics analysis to address the role of phage encoded recombinases in genomic mosaicism. The first assay allowed determining the genetic determinants of mosaic formation between lambdoid phages and Escherichia coli prophage remnants. In the second assay, recombination was monitored between sequences on phage λ, and allowed to compare the performance of three different Rad52-like recombinases on the same substrate. We also addressed the importance of homologous recombination in phage evolution by a genomic comparison of 84 E. coli virulent and temperate phages or prophages. We demonstrate that mosaics are mainly generated by homology-driven mechanisms that tolerate high substrate divergence. We show that phage encoded Rad52-like recombinases act independently of RecA, and that they are relatively more efficient when the exchanged fragments are divergent. We also show that accessory phage genes orf and rap contribute to mosaicism. A bioinformatics analysis strengthens our experimental results by showing that homologous recombination left traces in temperate phage genomes at the borders of recently exchanged fragments. We found no evidence of exchanges between virulent and temperate phages of E. coli. Altogether, our results demonstrate that Rad52-like recombinases promote gene shuffling among temperate phages, accelerating their evolution. This mechanism may prove to be more general, as other mobile genetic elements such as ICE encode Rad52-like functions, and play an important role in bacterial evolution itself.
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Affiliation(s)
- Marianne De Paepe
- INRA, UMR1319, Micalis, domaine de Vilvert, Jouy en Josas, France
- AgroParisTech, UMR1319, Micalis, domaine de Vilvert, Jouy en Josas, France
| | - Geoffrey Hutinet
- INRA, UMR1319, Micalis, domaine de Vilvert, Jouy en Josas, France
- AgroParisTech, UMR1319, Micalis, domaine de Vilvert, Jouy en Josas, France
| | - Olivier Son
- INRA, UMR1319, Micalis, domaine de Vilvert, Jouy en Josas, France
- AgroParisTech, UMR1319, Micalis, domaine de Vilvert, Jouy en Josas, France
| | - Jihane Amarir-Bouhram
- INRA, UMR1319, Micalis, domaine de Vilvert, Jouy en Josas, France
- AgroParisTech, UMR1319, Micalis, domaine de Vilvert, Jouy en Josas, France
| | - Sophie Schbath
- INRA, UR1077, MIG, domaine de Vilvert, Jouy en Josas, France
| | - Marie-Agnès Petit
- INRA, UMR1319, Micalis, domaine de Vilvert, Jouy en Josas, France
- AgroParisTech, UMR1319, Micalis, domaine de Vilvert, Jouy en Josas, France
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Abstract
The homologous recombination systems of linear double-stranded (ds)DNA bacteriophages are required for the generation of genetic diversity, the repair of dsDNA breaks, and the formation of concatemeric chromosomes, the immediate precursor to packaging. These systems have been studied for decades as a means to understand the basic principles of homologous recombination. From the beginning, it was recognized that these recombinases are linked intimately to the mechanisms of phage DNA replication. In the last decade, however, investigators have exploited these recombination systems as tools for genetic engineering of bacterial chromosomes, bacterial artificial chromosomes, and plasmids. This recombinational engineering technology has been termed "recombineering" and offers a new paradigm for the genetic manipulation of bacterial chromosomes, which is far more efficient than the classical use of nonreplicating integration vectors for gene replacement. The phage λ Red recombination system, in particular, has been used to construct gene replacements, deletions, insertions, inversions, duplications, and single base pair changes in the Escherichia coli chromosome. This chapter discusses the components of the recombination systems of λ, rac prophage, and phage P22 and properties of single-stranded DNA annealing proteins from these and other phage that have been instrumental for the development of this technology. The types of genetic manipulations that can be made are described, along with proposed mechanisms for both double-stranded DNA- and oligonucleotide-mediated recombineering events. Finally, the impact of this technology to such diverse fields as bacterial pathogenesis, metabolic engineering, and mouse genomics is discussed.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
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Curtis FA, Reed P, Wilson LA, Bowers LY, Yeo RP, Sanderson JM, Walmsley AR, Sharples GJ. The C-terminus of the phage λ Orf recombinase is involved in DNA binding. J Mol Recognit 2010; 24:333-40. [PMID: 21360615 DOI: 10.1002/jmr.1079] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 07/27/2010] [Accepted: 07/28/2010] [Indexed: 11/11/2022]
Abstract
Phage λ Orf substitutes for the activities of the Escherichia coli RecFOR proteins in vivo and is therefore implicated as a recombination mediator, encouraging the assembly of bacterial RecA onto single-stranded DNA (ssDNA) coated with SSB. Orf exists as a dimer in solution, associates with E. coli SSB and binds preferentially to ssDNA. To help identify interacting domains we analysed Orf and SSB proteins carrying mutations or truncations in the C-terminal region. A cluster of acidic residues at the carboxy-terminus of SSB is known to attract multiple protein partners to assist in DNA replication and repair. In this case an alternative domain must be utilized since Orf association with SSB was unaffected by an SSB113 point mutant (P176S) or removal of the last ten residues (ΔC10). Structurally the Orf C-terminus consists of a helix with a flexible tail that protrudes from each side of the dimer and could serve as a binding site for either SSB or DNA. Eliminating the six residue flexible tail (ΔC6) or the entire helix (ΔC19) had no significant impact on the Orf-SSB interaction. However, the OrfΔC6 protein exhibited reduced DNA binding, a feature shared by single amino acid substitutions within (W141F) or adjacent (R140A) to this region. The OrfΔC19 mutant bound poorly to DNA and secondary structure analysis in solution revealed that this truncation induces protein misfolding and aggregation. The results show that the carboxy-terminus of Orf is involved in nucleic acid recognition and also plays an unexpected role in maintaining structural integrity.
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Affiliation(s)
- Fiona A Curtis
- School of Biological and Biomedical Sciences, University of Durham, Science Site, Durham DH1 3LE, UK
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Szczepańska AK. Bacteriophage-encoded functions engaged in initiation of homologous recombination events. Crit Rev Microbiol 2010; 35:197-220. [PMID: 19563302 DOI: 10.1080/10408410902983129] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Recombination plays a significant role in bacteriophage biology. Functions promoting recombination are involved in key stages of phage multiplication and drive phage evolution. Their biological role is reflected by the great variety of phages existing in the environment. This work presents the role of recombination in the phage life cycle and highlights the discrete character of phage-encoded recombination functions (anti-RecBCD activities, 5' --> 3' DNA exonucleases, single-stranded DNA binding proteins, single-stranded DNA annealing proteins, and recombinases). The focus of this review is on phage proteins that initiate genetic exchange. Importance of recombination is reviewed based on the accepted coli-phages T4 and lambda models, the recombination system of phage P22, and the recently characterized recombination functions of Bacillus subtilis phage SPP1 and mycobacteriophage Che9c. Key steps of the molecular mechanisms involving phage recombination functions and their application in molecular engineering are discussed.
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Affiliation(s)
- Agnieszka K Szczepańska
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Poteete AR. Expansion of a chromosomal repeat in Escherichia coli: roles of replication, repair, and recombination functions. BMC Mol Biol 2009; 10:14. [PMID: 19236706 PMCID: PMC2656507 DOI: 10.1186/1471-2199-10-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 02/23/2009] [Indexed: 11/21/2022] Open
Abstract
Background Previous studies of gene amplification in Escherichia coli have suggested that it occurs in two steps: duplication and expansion. Expansion is thought to result from homologous recombination between the repeated segments created by duplication. To explore the mechanism of expansion, a 7 kbp duplication in the chromosome containing a leaky mutant version of the lac operon was constructed, and its expansion into an amplified array was studied. Results Under selection for lac function, colonies bearing multiple copies of the mutant lac operon appeared at a constant rate of approximately 4 to 5 per million cells plated per day, on days two through seven after plating. Expansion was not seen in a recA strain; null mutations in recBCD and ruvC reduced the rate 100- and 10-fold, respectively; a ruvC recG double mutant reduced the rate 1000-fold. Expansion occurred at an increased rate in cells lacking dam, polA, rnhA, or uvrD functions. Null mutations of various other cellular recombination, repair, and stress response genes had little effect upon expansion. The red recombination genes of phage lambda could substitute for recBCD in mediating expansion. In the red-substituted cells, expansion was only partially dependent upon recA function. Conclusion These observations are consistent with the idea that the expansion step of gene amplification is closely related, mechanistically, to interchromosomal homologous recombination events. They additionally provide support for recently described models of RecA-independent Red-mediated recombination at replication forks.
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Affiliation(s)
- Anthony R Poteete
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA, USA.
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Poteete AR. Involvement of DNA replication in phage lambda Red-mediated homologous recombination. Mol Microbiol 2008; 68:66-74. [PMID: 18333884 DOI: 10.1111/j.1365-2958.2008.06133.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Crosses between a non-replicating linear bacteriophage lambda chromosome and a replicating plasmid bearing a short cloned segment of lambda DNA were monitored by extracting DNA from infected cells, and analysing it via restriction endonuclease digestion and Southern blots. Recombinant formation resulting from the action of the Red homologous recombination system, observed directly in this way, was found to be fast, efficient, independent of the bacterial recA function and highly dependent upon replication of the target plasmid. These features of the experimental system faithfully model Red-mediated recombination in a lytically infected cell in which phage DNA replication is occurring. Neither of the previously established mechanisms by which the Red system can operate--strand annealing or strand invasion--accounts well for these findings. A third mechanism, replisome invasion, involving replication directly in the recombination mechanism, is invoked as an alternative.
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Affiliation(s)
- Anthony R Poteete
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA, USA.
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Martinsohn JT, Radman M, Petit MA. The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism. PLoS Genet 2008; 4:e1000065. [PMID: 18451987 PMCID: PMC2327257 DOI: 10.1371/journal.pgen.1000065] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 04/03/2008] [Indexed: 11/26/2022] Open
Abstract
Genome mosaicism in temperate bacterial viruses (bacteriophages) is so great that it obscures their phylogeny at the genome level. However, the precise molecular processes underlying this mosaicism are unknown. Illegitimate recombination has been proposed, but homeologous recombination could also be at play. To test this, we have measured the efficiency of homeologous recombination between diverged oxa gene pairs inserted into λ. High yields of recombinants between 22% diverged genes have been obtained when the virus Red Gam pathway was active, and 100 fold less when the host Escherichia coli RecABCD pathway was active. The recombination editing proteins, MutS and UvrD, showed only marginal effects on λ recombination. Thus, escape from host editing contributes to the high proficiency of virus recombination. Moreover, our bioinformatics study suggests that homeologous recombination between similar lambdoid viruses has created part of their mosaicism. We therefore propose that the remarkable propensity of the λ-encoded Red and Gam proteins to recombine diverged DNA is effectively contributing to mosaicism, and more generally, that a correlation may exist between virus genome mosaicism and the presence of Red/Gam-like systems. Temperate bacterial viruses alternate between a dormant state, during which viral DNA remains integrated in the host genome, and a lytic state of phage multiplication. Temperate viruses have a characteristic genome organisation known as ‘mosaic’ – they contain ‘foreign’ segments that originate from related viruses. In pairwise alignments between a given virus and its relatives, the overall nucleotide sequence identity is around 50%. In contrast, the mosaic segments are 90% to 100% identical. How mosaics are generated is largely unknown, but it is likely that related viruses meet in the same bacterium and undergo random recombination, with emergence of the most robust recombinatory viruses. The prevalent hypothesis is that mosaics are formed by illegitimate recombination. We propose and demonstrate that an alternative driving mechanism, homologous recombination, is used for mosaic formation between similar but diverged viral sequences. Using the well known Escherichia coli λ virus as a paradigm, we show that such homeologous recombination is remarkably efficient. This finding has important implications in the field of virus genome evolution, as it may explain the high plasticity of viral genomes. It is also applicable to the field of biotechnology, and reveals viruses to be promising vectors for shuffling genes in vivo.
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Affiliation(s)
- Jann T. Martinsohn
- Faculté de Médecine R. Descartes, INSERM U571, Université Paris Descartes, Paris, France
| | - Miroslav Radman
- Faculté de Médecine R. Descartes, INSERM U571, Université Paris Descartes, Paris, France
| | - Marie-Agnès Petit
- Faculté de Médecine R. Descartes, INSERM U571, Université Paris Descartes, Paris, France
- INRA, UR888, Jouy en Josas, France
- * E-mail:
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12
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Seaman PF, Day MJ. Isolation and characterization of a bacteriophage with an unusually large genome from the Great Salt Plains National Wildlife Refuge, Oklahoma, USA. FEMS Microbiol Ecol 2007; 60:1-13. [PMID: 17250749 DOI: 10.1111/j.1574-6941.2006.00277.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In this study we present a bacteriophage isolated from the Great Salt Plains National Wildlife Refuge (GSP) that is shown to have a genome size of 340 kb, unusually large for a bacterial virus. Transmission electron microscopy analysis of the virion showed this to be a Myoviridae, the first reported to infect the genus Halomonas. This temperate phage, PhigspC, exhibits a broad host range, displaying the ability to infect two different Halomonas spp. also isolated from the GSP. The phage infection process demonstrates a high level of tolerance towards temperature, pH and salinity; however, free virions are rapidly inactivated in water unless supplemented with salt. We show that susceptibility to osmotic shock is correlated with the density of the packaged DNA (rho(pack)). Lysogens of Halomonas salina GSP21 were detrimental to host fitness at 10% salinity, but the lysogen was able to grow faster than the wild type at 20% salinity. From these results we propose that the extensive genome of PhigspC may encode environmentally relevant genes (ERGs); genes that are perhaps not essential for the phage life cycle but increase host and phage fitness in some environmental conditions.
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Affiliation(s)
- Paul F Seaman
- Cardiff School of Biosciences, Cardiff University, Park Place, Cardiff, UK
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Poteete AR, Rosadini C, St Pierre C. Gentamicin and other cassettes for chromosomal gene replacement in Escherichia coli. Biotechniques 2006; 41:261-2, 264. [PMID: 16989085 DOI: 10.2144/000112242] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Anthony R Poteete
- University of Massachusetts Medical School, Department of Molecular Genetics & Microbiology, Worcester, MA 01655, USA.
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Maxwell KL, Reed P, Zhang RG, Beasley S, Walmsley AR, Curtis FA, Joachimiak A, Edwards AM, Sharples GJ. Functional similarities between phage lambda Orf and Escherichia coli RecFOR in initiation of genetic exchange. Proc Natl Acad Sci U S A 2005; 102:11260-5. [PMID: 16076958 PMCID: PMC1183564 DOI: 10.1073/pnas.0503399102] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Indexed: 11/18/2022] Open
Abstract
Genetic recombination in bacteriophage lambda relies on DNA end processing by Exo to expose 3'-tailed strands for annealing and exchange by beta protein. Phage lambda encodes an additional recombinase, Orf, which participates in the early stages of recombination by supplying a function equivalent to the Escherichia coli RecFOR complex. These host enzymes assist loading of the RecA strand exchange protein onto ssDNA coated with ssDNA-binding protein. In this study, we purified the Orf protein, analyzed its biochemical properties, and determined its crystal structure at 2.5 angstroms. The homodimeric Orf protein is arranged as a toroid with a shallow U-shaped cleft, lined with basic residues, running perpendicular to the central cavity. Orf binds DNA, favoring single-stranded over duplex and with no obvious preference for gapped, 3'-tailed, or 5'-tailed substrates. An interaction between Orf and ssDNA-binding protein was indicated by far Western analysis. The functional similarities between Orf and RecFOR are discussed in relation to the early steps of recombinational exchange and the interplay between phage and bacterial recombinases.
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Affiliation(s)
- Karen L Maxwell
- Centre for Infectious Diseases, Wolfson Research Institute, University of Durham, Queen's Campus, Stockton-on-Tees TS17 6BH, United Kingdom
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Hayes S, Asai K, Chu AM, Hayes C. NinR- and red-mediated phage-prophage marker rescue recombination in Escherichia coli: recovery of a nonhomologous immlambda DNA segment by infecting lambdaimm434 phages. Genetics 2005; 170:1485-99. [PMID: 15956667 PMCID: PMC1449759 DOI: 10.1534/genetics.105.042341] [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: 12/11/2022] Open
Abstract
We examined the requirement of lambda recombination functions for marker rescue of cryptic prophage genes within the Escherichia coli chromosome. We infected lysogenic host cells with lambdaimm434 phages and selected for recombinant immlambda phages that had exchanged the imm434 region of the infecting phage for the heterologous 2.6-kb immlambda region from the prophage. Phage-encoded activity, provided by either Red or NinR functions, was required for the substitution. Red(-) phages with DeltaNinR, internal NinR deletions of rap-ninH, or orf-ninC were 117-, 12-, and 5-fold reduced for immlambda rescue in a Rec(+) host, suggesting the participation of several NinR activities. RecA was essential for NinR-dependent immlambda rescue, but had slight influence on Red-dependent rescue. The host recombination activities RecBCD, RecJ, and RecQ participated in NinR-dependent recombination while they served to inhibit Red-mediated immlambda rescue. The opposite effects of several host functions toward NinR- and Red-dependent immlambda rescue explains why the independent pathways were not additive in a Rec(+) host and why the NinR-dependent pathway appeared dominant. We measured the influence of the host recombination functions and DnaB on the appearance of orilambda-dependent replication initiation and whether orilambda replication initiation was required for immlambda marker rescue.
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Affiliation(s)
- Sidney Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
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Tan XH, Zhao M, Pan KF, Dong Y, Dong B, Feng GJ, Jia G, Lu YY. Frequent mutation related with overexpression of DNA polymerase beta in primary tumors and precancerous lesions of human stomach. Cancer Lett 2005; 220:101-14. [PMID: 15737693 DOI: 10.1016/j.canlet.2004.07.049] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 07/25/2004] [Accepted: 07/29/2004] [Indexed: 10/26/2022]
Abstract
To explore whether DNA polymerase beta (pol beta) contributes to the malignant transformation of gastric mucosa, we examined pol beta in gastric tumor cell lines, primary tumors and precancerous lesions. Point mutations of pol beta were detected in 6 of 13 cell lines and 23 of 104 tissues including 35.0% (14/40) of gastric cancer (GC), 30.0% (3/10) of dysplasia (Dys), 28.6% (4/14) of intestinal metaplasia (IM) and 10.5% (2/19) of chronic atrophic gastritis (CAG), respectively. A frequent mutation was a T to C transition at nucleotide 889, which was observed in 4 GC cell lines, 7 GC, 2 Dys, and 2 IM. The level of pol beta expression in tumors was higher than that of their matched normal tissues and gradual changes from GC, Dys, CAG to IM. These results indicate that the mutation and overexpression of pol beta may influence the progression during gastric carcinogenesis.
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Affiliation(s)
- Xiao-Hui Tan
- Beijing Molecular Oncology Laboratory, Beijing Institute for Cancer Research, School of Oncology, Peking University, Da-Hong-Luo-Chang Street 1#, Western District, Beijing 100034, People's Republic of China
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Poteete AR, Fenton AC, Nadkarni A. Chromosomal duplications and cointegrates generated by the bacteriophage lamdba Red system in Escherichia coli K-12. BMC Mol Biol 2004; 5:22. [PMID: 15596011 PMCID: PMC545071 DOI: 10.1186/1471-2199-5-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2004] [Accepted: 12/13/2004] [Indexed: 11/30/2022] Open
Abstract
Background An Escherichia coli strain in which RecBCD has been genetically replaced by the bacteriophage λ Red system engages in efficient recombination between its chromosome and linear double-stranded DNA species sharing sequences with the chromosome. Previous studies of this experimental system have focused on a gene replacement-type event, in which a 3.5 kbp dsDNA consisting of the cat gene and flanking lac operon sequences recombines with the E. coli chromosome to generate a chloramphenicol-resistant Lac- recombinant. The dsDNA was delivered into the cell as part of the chromosome of a non-replicating λ vector, from which it was released by the action of a restriction endonuclease in the infected cell. This study characterizes the genetic requirements and outcomes of a variety of additional Red-promoted homologous recombination events producing Lac+ recombinants. Results A number of observations concerning recombination events between the chromosome and linear DNAs were made: (1) Formation of Lac+ and Lac- recombinants depended upon the same recombination functions. (2) High multiplicity and high chromosome copy number favored Lac+ recombinant formation. (3) The Lac+ recombinants were unstable, segregating Lac- progeny. (4) A tetracycline-resistance marker in a site of the phage chromosome distant from cat was not frequently co-inherited with cat. (5) Recombination between phage sequences in the linear DNA and cryptic prophages in the chromosome was responsible for most of the observed Lac+ recombinants. In addition, observations were made concerning recombination events between the chromosome and circular DNAs: (6) Formation of recombinants depended upon both RecA and, to a lesser extent, Red. (7) The linked tetracycline-resistance marker was frequently co-inherited in this case. Conclusions The Lac+ recombinants arise from events in which homologous recombination between the incoming linear DNA and both lac and cryptic prophage sequences in the chromosome generates a partial duplication of the bacterial chromosome. When the incoming DNA species is circular rather than linear, cointegrates are the most frequent type of recombinant.
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Affiliation(s)
- Anthony R Poteete
- Dept. of Molecular Genetics & Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Anita C Fenton
- Dept. of Molecular Genetics & Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Ashwini Nadkarni
- Dept. of Molecular Genetics & Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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