Prevalence, nucleotide sequence and expression studies of two proteins of a 5.6kb, Class III, Bacteroides plasmid frequently found in clinical isolates from European countries

Plasmid

Volumn 63, Issue 2, 2010, Pages 86-97

  Sóki, József ^a   Wareham, David W ^b   Rátkai, Csilla ^a   Aduse Opoku, Joseph ^b   Urbán, Edit ^a   Nagy, Elisabeth ^a  

^a UNIVERSITY OF SZEGED   (Hungary)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Bacteroides; Cryptic plasmid(s); Lipoprotein; Plasmid functions

Indexed keywords

BACTERIAL PROTEIN; OPEN READING FRAME 1 PROTEIN; OPEN READING FRAME 2 PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIUM ISOLATION; BACTEROIDES; CONTROLLED STUDY; EUROPE; GENE EXPRESSION; GEOGRAPHIC DISTRIBUTION; HUNGARY; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID; PROTEIN EXPRESSION; PROTEIN STABILITY; SCREENING; TAXONOMY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BACTEROIDES; BASE SEQUENCE; DNA REPLICATION; EUROPE; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PLASMIDS;

BACTEROIDES; ESCHERICHIA COLI;

EID: 75549089203     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2009.12.002     Document Type: Article

References (47)

1. Beul H.A., von Eichel-Streiber C., Schreiner M., Schwindling F.P., Weinblum D., Zöllner E.J., Dierich M. Characterization of cryptic plasmids in clinical isolates of Bacteroides fragilis. J. Med. Microbiol. 1985, 20:39-48.
2. Callihan D.R., Young F.R., Clark V.L. Identification of three homology classes of small, cryptic plasmids in intestinal Bacteroides species. Plasmid 1983, 9:17-30.
3. Cerdeño-Tarraga A.M., Patrick S., Crossman L.C., Blakely G., Abratt V., Lennard N., Poxton I., Duerden B., Harris B., Quail M.A., Barron A., Clark L., Corton C., Doggett J., Holden M.T.G., Larke N., Line A., Lord A., Norbertczak H., Ormond D., Price C., Rabbinowitsch E., Woodward J., Barrell B., Parkhill J. Extensive DNA inversions in the Bacteroides fragilis genome control variable gene expression. Science 2005, 307:1463-1465.
4. del Solar G., Girlando R., Ruiz-Echevaría M.J., Espinosa M., Díaz-Orejas R. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 1998, 62:434-464.
5. Dupont C., Thompson K., Heuer C., Gicquel B., Murray A. Identification and characterization of an immunogenic 22 kDa exported protein of Mycobacterium avium subspecies paratuberculosis. J. Med. Microbiol. 2006, 54:1083-1092.
6. Francia M.V., Varsaki A., Garcillaán-Barcia M.P., Latorre A., Drainas C., de la Cruz F. A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol. Rev. 2004, 28:79-100.
7. Garcillán-Barcia M.P., de la Cruz F. Why is entry exclusion an essential feature of conjugative plasmids?. Plasmid 2008, 60:1-18.
8. Hatt C., Ward M.E., Clarke I.N. Analysis of the entire nucleotide sequence of the cryptic plasmid of Chlamydia trachomatis serovar L1. Evidence for involvement in DNA replication. Nucleic Acids Res. 1998, 16:4053-4067.
9. Hooper L.V. Bacterial contributions to mammalian gut development. Trends Microbiol. 2004, 12:129-134.
10. Ihalin R., Karched M., Enslätt K., Asikainen S. Characterization of immunoaffinity purified peptidoglycan-associated lipoprotein of Actinobacillus actinomycetemcomitans. J. Chromotogr. B 2006, 831:116-125.
11. Ito K., Inaba K. The disulphide bond formation (Dsb) system. Curr. Opin. Struct. Biol. 2008, 18:450-458.
12. Janssens S., Beyaert R. Role of Toll-like receptors in pathogen recognition. Clin. Microbiol. Rev. 2003, 16:637-646.
13. Jin R., Fernandez-Beros M.-E., Novick R.P. Why is the initiation nick site of an AT-rich rolling circle plasmid at a tip of a GC-rich cruciform?. EMBO J. 1997, 16:4456-4466.
14. Johnson J.L. Taxonomy of Bacteroides I. Deoxyribonucleic acid homologies among Bacteroides fragilis and other saccharolytitic Bacteroides species. Int. J. Syst. Bacteriol. 1978, 28:245-256.
15. Khan S.A. Rolling-circle replication. Plasmid Biology 2004, 63-78. ASM Press, Washington, DC. B.E. Funnell, G.J. Phillips (Eds.).
16. Kobayashi I. Genetic addiction: a principle of gene symbiosis in a genome. Plasmid Biology 2004, 105-144. ASM Press, Washington, DC. B.E. Funnell, G.J. Phillips (Eds.).
17. Korch C., Hagblom P., öman H., Göransson M., Normark S. Cryptic plasmids of Neisseria gonorrhoeae: complete nucleotide sequence and genetic organization. J. Bacteriol. 1985, 163:430-438.
18. Krinos C.M., Coyne M.J., Weinacht K.G., Tzianabos A.O., Kasper D.L., Comstock L.E. Extensive surface diversity of a commensal microorganism by multiple DNA inversions. Nature 2001, 414:555-558.
19. Kuwahara T., Yamashita A., Hirakawa H., Nakayama H., Toh H., Okada N., Kuhara S., Hattori M., Hayashi T., Ohnishi Y. Genomic analysis of Bacteroides fragilis reveals DNA inversions regulating cell surface adaptation. Proc. Natl. Acad. Sci. USA 2004, 101:14919-14924.
20. Leung K.-P., Lewis A.S., Concannon S.P., Yoshimoto H., Fukushima H. Prevotella intermedia native plasmid can be mobilized by an Escherichia coli conjugal IncP plasmid. Plasmid 2002, 48:64-72.
21. Lewenza S., Mhlanga M.M., Pugsley A.P. Novel inner membrane retention signals in Pseudomonas aeruginosa lipoproteins. J. Bacteriol. 2008, 190:6119-6125.
22. Ley R.E., Lozupone C.A., Hamady M., Knight R.D., Gordon J.I. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat. Rev. Microbiol. 2008, 6:776-788.
23. Löfmark S., Fang H., Hedberg M., Edlund C. Inducible metronidazole resistance and nim genes in clinical Bacteroides fragilis group isolates. Agents Chemother. 2005, 49:1253-1256.
24. Marchler-Bauer A., Anderson J.B., Derbyshire M.K., DeWeeze-Scott C., Gonzales N.R., Gwadz M., Hao L., He S., Hurwitz D.I., Jackson J.D., Ke Z., Krylov D., Lanczycki D.I., Liebert C.A., Liu C., Lu F., Lu S., Marchler G.H., Mullokandov M., Song J.S., Thanki N., Yamashita R.A., Yin J.J., Zhang D., Bryant S. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 2007, 35:D237-D240.
25. Mueller S., Saunier K., Hanisch C., Norin E., Alm L., Midtvedt T., Cresci A., Silvi S., Orpianesi C., Verdenelli M.C., Clavel T., Koebnick C., Zunft H.-J.F., Doré J., Blaut M. Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl. Environ. Microbiol. 2006, 72:1027-1033.
26. Nagy E., Dányi é;., Földes J. Plasmid analysis of clinical isolates of Bacteroides fragilis group strains. Acta Microbiol. Hung. 1990, 37:367-373.
27. Narita S.-I., Matsuyama S., Tokuda H. Lipoprotein trafficking in Escherichia coli. Arch. Microbiol. 2004, 182:1-6.
28. Novicki T.J., Hecht D.W. Characterization and DNA sequence of the mobilization region of pLV22a from Bacteroides fragilis. J. Bacteriol. 1995, 177:4466-4473.
29. Pilo P., Martig S., Frey J., Vilei E.M. Antigenic and genetic characterization of lipoprotein IppC from Mycoplasma mycoides subsp. mycoides SC. Vet. Res. 2003, 34:761-775.
30. Pumbwe L., Wareham D.W., Aduse-Opoku J., Brazier J.S., Wexler H.M. Genetic analysis of mechanisms of multidrug resistance in a clinical isolate of Bacteroides fragilis. Clin. Microbiol. Infect. 2006, 13:183-189.
31. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual 1989, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. second ed.
32. Smith J.C., Parker A.C. The transfer origin for Bacteroides mobilizable transposon Tn4555 is related to a plasmid family from Gram-positive bacteria. J. Bacteriol. 1998, 180:435-439.
33. Smith C.J., Rollins L.A., Parker A.C. Nucleotide sequence determination and genetic analysis of the Bacteroides plasmid, pBI143. Plasmid 1995, 34:211-222.
34. Sóki J., Szoke I., Nagy E. Characterisation of a 5.5-kb cryptic plasmid present in different isolates of Bacteroides spp. originating from Hungary. J. Med. Microbiol. 1999, 48:25-31.
35. Sóki J., Kerekes I., Macrczinovits I., Nagy E. Molecular relatedness of the prevalent cryptic plasmids of Bacteroides species isolated in Hungary. Anaerobe 2000, 6:179-185.
36. Sóki J., Gal M., Brazier J.S., Rotimi V.O., Urbán E., Nagy E., Duerden B.I. Molecular investigation of genetic elements contributing to metronidazole resistance in Bacteroides strains. J. Antimicrob. Chemother. 2006, 57:212-220.
37. Sutciffe I.C., Harrington D.J. Lipoproteins of Mycobacterium tuberculosis: an abundant and functionally diverse class of cell envelope components. FEMS Microbiol. Rev. 2004, 28:645-659.
38. Tribble G.D., Parker A.C., Smith J.C. Genetic structure and transcriptional analysis of a mobilizable, antibiotic resistance transposon from Bacteroides. Plasmid 1999, 42:1-12.
39. Trinh S., Reysset G. Identification and DNA sequence of the mobilization region of the 5-nitroimidazole resistance plasmid pIP421 from Bacteroides fragilis. J. Bacteriol. 1997, 179:4071-4074.
40. Trinh S., Haggoud A., Reysset G. Conjugal transfer of the 5-nitroimidazole resistance plasmid pIP417 from Bacteroides vulgatus BV-17: characterization and nucleotide sequence analysis of the mobilization region. J. Bacteriol. 1997, 178:6671-6676.
41. Turnbaugh P.J., Ley R.E., Hamady M., Fraser-Liggett C.M., Knight R.D., Gordon G.I. The human microbiome project. Nature 2007, 449:804-810.
42. Valentine P.J., Shoemaker N.B., Salyers A.A. Mobilization of Bacteroides plasmids by Bacteroides conjugal elements. J. Bacteriol. 1988, 170:1319-1324.
43. Wallace B.L., Bradley J.E., Rogolsky M. Plasmid analysis in clinical isolates of Bacteroides fragilis and other Bacteroides species. J. Clin. Microbiol. 1981, 14:383-388.
44. Wexler H.M. Bacteroides: the good, the bad and the nitty-gritty. Clin. Microbiol. Rev. 2007, 20:593-621.
45. Xu J., Bjursell M.K., Himrod J., Deng S., Carmichael L.K., Chiang H.C., Hooper L.V., Gordon J.I. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 2003, 299:2074-2076.
46. Xu J., Chiang H.C., Bjursell M.K., Gordon J.I. Message from a human gut symbiont: sensitivity is a prerequisite for sharing. Trends Microbiol. 2004, 12:21-28.
47. Xu Q., McShan K., Liang F.T. Essential protective role attributed to surface lipoproteins of Borrelia burgdorferi against innate defences. Mol. Microbiol. 2008, 69:15-29.