Genomes and Genes
Summary: A parasexual process in BACTERIA; ALGAE; FUNGI; and ciliate EUKARYOTA for achieving exchange of chromosome material during fusion of two cells. In bacteria, this is a uni-directional transfer of genetic material; in protozoa it is a bi-directional exchange. In algae and fungi, it is a form of sexual reproduction, with the union of male and female gametes.
- Garcillán Barcia M, Francia M, de la Cruz F. The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol Rev. 2009;33:657-87 pubmed..We hope our effort will provide researchers with a useful tool for further mining and analysing the plasmid universe both experimentally and in silico. ..
- Garcillán Barcia M, de la Cruz F. Why is entry exclusion an essential feature of conjugative plasmids?. Plasmid. 2008;60:1-18 pubmed publisher..Additionally, it avoids competition in a host among identical plasmid backbones. Conversely, the lack of entry exclusion in conjugative transposons can be understood as a means of generating rapid evolutionary change. ..
- Gonzalez Perez B, Lucas M, Cooke L, Vyle J, de la Cruz F, Moncalian G. Analysis of DNA processing reactions in bacterial conjugation by using suicide oligonucleotides. EMBO J. 2007;26:3847-57 pubmed..Thus, only Y18 was used for initiation. Y26 was specifically used in the second transesterification that leads to strand transfer, thus catalyzing the termination reaction that occurs in the recipient cell. ..
- Pan J, Ye R, Wang H, Xiang H, Zhang W, Yu X, et al. Vibrio cholerae O139 multiple-drug resistance mediated by Yersinia pestis pIP1202-like conjugative plasmids. Antimicrob Agents Chemother. 2008;52:3829-36 pubmed publisher..Careful tracking of these plasmids in the microbial ecosystem is warranted...
- Aronica L, Bednenko J, Noto T, DeSouza L, Siu K, Loidl J, et al. Study of an RNA helicase implicates small RNA-noncoding RNA interactions in programmed DNA elimination in Tetrahymena. Genes Dev. 2008;22:2228-41 pubmed publisher..We propose that Ema1p functions in DNA elimination by stimulating base-pairing interactions between scnRNAs and noncoding transcripts in both parental and developing new macronuclei. ..
- Lin T, Lee C, Hsieh P, Tsai S, Wang J. Characterization of integrative and conjugative element ICEKp1-associated genomic heterogeneity in a Klebsiella pneumoniae strain isolated from a primary liver abscess. J Bacteriol. 2008;190:515-26 pubmed..Therefore, ICEKp1 may contribute to the transmission of the HPI and result in K. pneumoniae PLA infection-associated genomic heterogeneity. ..
- Lili L, Britton N, Feil E. The persistence of parasitic plasmids. Genetics. 2007;177:399-405 pubmed
- Hekman K, Guja K, Larkin C, Schildbach J. An intrastrand three-DNA-base interaction is a key specificity determinant of F transfer initiation and of F TraI relaxase DNA recognition and cleavage. Nucleic Acids Res. 2008;36:4565-72 pubmed publisher..Oligonucleotide cleavage assay results suggest the essential function of the three-base interaction may be to position the scissile phosphate for cleavage, rather than to directly contribute to binding affinity. ..
- Scrascia M, Pugliese N, Maimone F, Mohamud K, Grimont P, Materu S, et al. Clonal relationship among Vibrio cholerae O1 El Tor strains isolated in Somalia. Int J Med Microbiol. 2009;299:203-7 pubmed publisher..These findings indicated that the group of strains active in Somalia in the late 1990s had a clonal origin...
- Heap J, Pennington O, Cartman S, Carter G, Minton N. The ClosTron: a universal gene knock-out system for the genus Clostridium. J Microbiol Methods. 2007;70:452-64 pubmed..The procedure is highly efficient and reproducible, and should revolutionize functional genomic studies in clostridia. ..
- Song B, Shoemaker N, Gardner J, Salyers A. Integration site selection by the Bacteroides conjugative transposon CTnBST. J Bacteriol. 2007;189:6594-601 pubmed..Thus, in contrast to well-studied site-specific recombinases which require homology throughout the crossover region, integration of CTnBST requires homology at one end of the crossover region but not at the other end. ..
- Meyer R. The r1162 mob proteins can promote conjugative transfer from cryptic origins in the bacterial chromosome. J Bacteriol. 2009;191:1574-80 pubmed publisher..Transfer of chromosomal DNA due to the presence of a plasmid in the cytoplasm describes a previously unrecognized potential for the exchange of bacterial DNA...
- Pugliese N, Maimone F, Scrascia M, Materu S, Pazzani C. SXT-related integrating conjugative element and IncC plasmids in Vibrio cholerae O1 strains in Eastern Africa. J Antimicrob Chemother. 2009;63:438-42 pubmed publisher..The objective of this study was to investigate the extent of resistance patterns and associated mobile genetic elements in epidemic V. cholerae O1 El Tor strains isolated from Eastern Africa in the late 1990s...
- de la Cruz F, Frost L, Meyer R, Zechner E. Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev. 2010;34:18-40 pubmed publisher..Here, we review the biochemistry of relaxosomes and ponder some of the remaining questions about the nature of the signal that begins the process. ..
- Marrero J, Waldor M. Determinants of entry exclusion within Eex and TraG are cytoplasmic. J Bacteriol. 2007;189:6469-73 pubmed..These observations suggest that complex topological rearrangements of conjugative proteins must occur during mating to enable these domains to interact. ..
- Kim S, Hu J, Gautom R, Kim J, Lee B, Boyle D. CTX-M extended-spectrum beta-lactamases, Washington State. Emerg Infect Dis. 2007;13:513-4 pubmed
- Cattoir V, Weill F, Poirel L, Fabre L, Soussy C, Nordmann P. Prevalence of qnr genes in Salmonella in France. J Antimicrob Chemother. 2007;59:751-4 pubmed..This strain was probably from East Africa. No qnrB or qnrS genes were identified. Whereas plasmid-mediated quinolone resistance of the Qnr type is emerging in Enterobacteriaceae worldwide, it remains rare in Salmonella in France. ..
- Vo A, van Duijkeren E, Fluit A, Gaastra W. A novel Salmonella genomic island 1 and rare integron types in Salmonella Typhimurium isolates from horses in The Netherlands. J Antimicrob Chemother. 2007;59:594-9 pubmed..The data demonstrate the capability of Salmonella Typhimurium to acquire additional antibiotic resistance determinants and underline the need for the prudent use of antimicrobials. ..
- Golding G, Olson A, Doublet B, Cloeckaert A, Christianson S, Graham M, et al. The effect of the Salmonella genomic island 1 on in vitro global gene expression in Salmonella enterica serovar Typhimurium LT2. Microbes Infect. 2007;9:21-7 pubmed..This is the first report examining gene expression within the SGI1, as well as its potential effect on global gene expression, and sets the foundation for future studies involving the effect of SGI1 in other Salmonella spp. ..
- Dionisio F, Conceição I, Marques A, Fernandes L, Gordo I. The evolution of a conjugative plasmid and its ability to increase bacterial fitness. Biol Lett. 2005;1:250-2 pubmed..Our results suggest that even if general usage of antibiotics is halted, conjugative plasmids that have been selected with antibiotics in previous years can still persist among bacterial populations or even invade new strains. ..
- Ahmed A, Hussein A, Shimamoto T. Proteus mirabilis clinical isolate harbouring a new variant of Salmonella genomic island 1 containing the multiple antibiotic resistance region. J Antimicrob Chemother. 2007;59:184-90 pubmed..In this study, we identified a new variant SGI1 containing the multiple resistance genomic region in a multidrug-resistant strain of P. mirabilis. This is the first report for SGI1 in a genus other than Salmonella. ..
- Fernandez Lopez R, Garcillán Barcia M, Revilla C, Lazaro M, Vielva L, de la Cruz F. Dynamics of the IncW genetic backbone imply general trends in conjugative plasmid evolution. FEMS Microbiol Rev. 2006;30:942-66 pubmed..Starting from the phage paradigm, our analysis articulates novel concepts that apply to plasmid evolution. ..
- Tolonen A, Liszt G, Hess W. Genetic manipulation of Prochlorococcus strain MIT9313: green fluorescent protein expression from an RSF1010 plasmid and Tn5 transposition. Appl Environ Microbiol. 2006;72:7607-13 pubmed..These genetic advances provide a basis for future genetic studies with Prochlorococcus, a microbe of ecological importance in the world's oceans. ..
- Gomis Ruth F, Coll M. Cut and move: protein machinery for DNA processing in bacterial conjugation. Curr Opin Struct Biol. 2006;16:744-52 pubmed..In particular, structural biology is revealing the detailed molecular architecture of several of the pieces involved. ..
- Garcillán Barcia M, Jurado P, Gonzalez Perez B, Moncalian G, Fernandez L, de la Cruz F. Conjugative transfer can be inhibited by blocking relaxase activity within recipient cells with intrabodies. Mol Microbiol. 2007;63:404-16 pubmed..These findings demonstrate that the transferred relaxase plays an important role in the recipient cell and open a new approach to identify specific inhibitors of bacterial conjugation. ..
- Brinkley C, Burland V, Keller R, Rose D, Boutin A, Klink S, et al. Nucleotide sequence analysis of the enteropathogenic Escherichia coli adherence factor plasmid pMAR7. Infect Immun. 2006;74:5408-13 pubmed..This study confirms EPEC's potential for dissemination of virulence attributes by horizontal transfer of the EAF plasmid. ..
- Yamane K, Wachino J, Suzuki S, Kimura K, Shibata N, Kato H, et al. New plasmid-mediated fluoroquinolone efflux pump, QepA, found in an Escherichia coli clinical isolate. Antimicrob Agents Chemother. 2007;51:3354-60 pubmed publisher..coli was first identified. Surveillance of the qepA-harboring clinical isolates should be encouraged to minimize further dissemination of the kind of plasmid-dependent FQ resistance determinants among pathogenic microbes...
- Marrero J, Waldor M. The SXT/R391 family of integrative conjugative elements is composed of two exclusion groups. J Bacteriol. 2007;189:3302-5 pubmed..Unexpectedly, our analyses indicate that there are only two exclusion groups among the diverse members of the SXT/R391 family of integrative conjugative elements. ..
- Bogaerts P, Galimand M, Bauraing C, Deplano A, Vanhoof R, De Mendonca R, et al. Emergence of ArmA and RmtB aminoglycoside resistance 16S rRNA methylases in Belgium. J Antimicrob Chemother. 2007;59:459-64 pubmed..The rapid spread of multidrug-resistant isolates producing both ESBLs and 16S rRNA methylases raises clinical concern and may become a major therapeutic threat in the future. ..
- Kazimierczak K, Scott K. Antibiotics and resistance genes: influencing the microbial ecosystem in the gut. Adv Appl Microbiol. 2007;62:269-92 pubmed
- Cabrera E, Rodriguez R. First report on the occurrence of SHV-12 extended-spectrum beta-lactamase-producing Enterobacteriaceae in the Philippines. J Microbiol Immunol Infect. 2009;42:74-85 pubmed..SHV-12 is the dominating ESBL among the Enterobacteriaceae studied. The gene bla(SHV-12) is carried together with genes for multiple resistance to other classes of antimicrobials in conjugative and nonconjugative plasmids. ..
- Heinaru E, Vedler E, Jutkina J, Aava M, Heinaru A. Conjugal transfer and mobilization capacity of the completely sequenced naphthalene plasmid pNAH20 from multiplasmid strain Pseudomonas fluorescens PC20. FEMS Microbiol Ecol. 2009;70:563-74 pubmed publisher..The characteristics of the strain PC20 and the conjugal transfer/mobilization capacity of pNAH20 (or its backbone) make this strain/plasmid a potentially successful tool for bioremediation applications. ..
- Chuanchuen R, Ajariyakhajorn K, Koowatananukul C, Wannaprasat W, Khemtong S, Samngamnim S. Antimicrobial resistance and virulence genes in Salmonella enterica isolates from dairy cows. Foodborne Pathog Dis. 2010;7:63-9 pubmed publisher..One hundred fifty-nine isolates (98.8%) were positive to the invasion gene invA, whereas the virulence plasmid-associated genes spvC and pefA were found in only two (1.3%) and one (0.6%) Salmonella isolates, respectively. ..
- Steen J, Bannam T, Teng W, Devenish R, Rood J. The putative coupling protein TcpA interacts with other pCW3-encoded proteins to form an essential part of the conjugation complex. J Bacteriol. 2009;191:2926-33 pubmed publisher..Based on these results, we have constructed a model for this unique conjugative transfer apparatus. ..
- Ozgumus O, Sandalli C, Sevim A, Celik Sevim E, Sivri N. Class 1 and class 2 integrons and plasmid-mediated antibiotic resistance in coliforms isolated from ten rivers in northern Turkey. J Microbiol. 2009;47:19-27 pubmed publisher..The actual risk to public health is the transfer of resistance genes from the environmental bacteria to human pathogens. ..
- Timmery S, Modrie P, Minet O, Mahillon J. Plasmid capture by the Bacillus thuringiensis conjugative plasmid pXO16. J Bacteriol. 2009;191:2197-205 pubmed publisher..Taken together, these results emphasize the potential role of plasmid capture played by B. thuringiensis in natural environments. ..
- Argudín M, Fetsch A, Tenhagen B, Hammerl J, Hertwig S, Kowall J, et al. High heterogeneity within methicillin-resistant Staphylococcus aureus ST398 isolates, defined by Cfr9I macrorestriction-pulsed-field gel electrophoresis profiles and spa and SCCmec types. Appl Environ Microbiol. 2010;76:652-8 pubmed publisher..In general, the combination of Cfr9I PFGE with spa and SCCmec typing demonstrated the heterogeneity of the series analyzed and can be further used for outbreak investigations and traceability studies of the MRSA ST398 emerging clone. ..
- Bélanger M, Rodrigues P, Progulske Fox A. Genetic manipulation of Porphyromonas gingivalis. Curr Protoc Microbiol. 2007;Chapter 13:Unit13C.2 pubmed publisher..Finally, a description of a noninvasive reporter system allowing the study of gene expression and regulation in P. gingivalis completes this unit. ..
- Moura A, Henriques I, Ribeiro R, Correia A. Prevalence and characterization of integrons from bacteria isolated from a slaughterhouse wastewater treatment plant. J Antimicrob Chemother. 2007;60:1243-50 pubmed publisher..Moreover, water discharges represent a possible risk for dissemination of undesirable genetic traits...
- Pernil R, Picossi S, Mariscal V, Herrero A, Flores E. ABC-type amino acid uptake transporters Bgt and N-II of Anabaena sp. strain PCC 7120 share an ATPase subunit and are expressed in vegetative cells and heterocysts. Mol Microbiol. 2008;67:1067-80 pubmed publisher..Whereas Bgt is dispensable for diazotrophic growth, N-II appears to contribute together with N-I to the diazotrophic physiology of this cyanobacterium. ..
- Adylova A, Chernikova T, Abdukarimov A. [Phenol biodegradation by a Pseudomonas sp. strain tagged with the gfp gene]. Prikl Biokhim Mikrobiol. 2008;44:308-13 pubmed..The change of the population density of the tagged bacteria after their introduction to soil was studied. The potential of the resulting bacterial strain in remediation of phenol-polluted soils is discussed. ..
- Veldman K, Dierikx C, van Essen Zandbergen A, van Pelt W, Mevius D. Characterization of multidrug-resistant, qnrB2-positive and extended-spectrum-beta-lactamase-producing Salmonella Concord and Salmonella Senftenberg isolates. J Antimicrob Chemother. 2010;65:872-5 pubmed publisher..In Salmonella Senftenberg one large plasmid (IncHI2) and in Salmonella Concord two large plasmids (IncHI2 and IncA/C) were responsible for the multidrug resistance. ..
- Goren M, Carmeli Y, Schwaber M, Chmelnitsky I, Schechner V, Navon Venezia S. Transfer of carbapenem-resistant plasmid from Klebsiella pneumoniae ST258 to Escherichia coli in patient. Emerg Infect Dis. 2010;16:1014-7 pubmed publisher..The KPC-3 plasmid was identical in isolates of both species. The patient's gut flora contained a carbapenem-susceptible E. coli strain isogenic with the KPC-3-producing isolate, which suggests horizontal interspecies plasmid transfer. ..
- Guan D, Pettis G. Intergeneric conjugal gene transfer from Escherichia coli to the sweet potato pathogen Streptomyces ipomoeae. Lett Appl Microbiol. 2009;49:67-72 pubmed publisher..ipomoeae. Efficient transfer of genes into S. ipomoeae was achieved here by using an optimized intergeneric mating procedure. The described protocol will facilitate further genetic manipulation of this agriculturally important pathogen. ..
- Barlow M. What antimicrobial resistance has taught us about horizontal gene transfer. Methods Mol Biol. 2009;532:397-411 pubmed publisher..Further studies of HGT and methods for controlling HGT may be necessary to maintain the usefulness of antimicrobials. ..
- Schluter A, Krahn I, Kollin F, Bönemann G, Stiens M, Szczepanowski R, et al. IncP-1-beta plasmid pGNB1 isolated from a bacterial community from a wastewater treatment plant mediates decolorization of triphenylmethane dyes. Appl Environ Microbiol. 2007;73:6345-50 pubmed..The pGNB1-encoded enzyme activity is discussed with respect to bioremediation of sewage polluted with triphenylmethane dyes. ..
- Lorenzo Díaz F, Espinosa M. Lagging-strand DNA replication origins are required for conjugal transfer of the promiscuous plasmid pMV158. J Bacteriol. 2009;191:720-7 pubmed publisher..pneumoniae to Enterococcus faecalis. Thus, it appears that ssoU is a critical factor for pMV158 promiscuity and that the presence of a functional sso plays an essential role in plasmid transfer. ..
- Minarini L, Poirel L, Cattoir V, Darini A, Nordmann P. Plasmid-mediated quinolone resistance determinants among enterobacterial isolates from outpatients in Brazil. J Antimicrob Chemother. 2008;62:474-8 pubmed publisher..This study constitutes the first epidemiological survey of the three known Qnr determinants among Brazilian isolates and shows their low prevalence in that country, with the qnrB2 gene being mostly identified. ..