Frequency and diversity of small cryptic plasmids in the genus Rahnella

BMC Microbiology

Volumn 10, Issue , 2010, Pages

  Rozhon, Wilfried ^a   Petutschnig, Elena ^b   Khan, Mamoona ^a   Summers, David K ^c   Poppenberger, Brigitte ^a  

^a UNIVERSITY OF VIENNA   (Austria)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENT; RNA; BACTERIAL PROTEIN; ROM PROTEIN, BACTERIA;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL STRAIN; CELL DIVISION; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA ISOLATION; DNA REPLICATION ORIGIN; ERWINIA; EVOLUTIONARY HOMOLOGY; GENETIC CODE; GENUS; HORIZONTAL GENE TRANSFER; HOST; MICROBIAL COMMUNITY; MOBILIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORIENTATION; PHOTORHABDUS LUMINESCENS; PLASMID; RAHNELLA; REGULATORY RNA SEQUENCE; SEQUENCE HOMOLOGY; SYNTHESIS; BIOLOGICAL MODEL; CHEMISTRY; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; MULTIGENE FAMILY; PHYLOGENY; SEQUENCE ALIGNMENT; VEGETABLE;

BACTERIA (MICROORGANISMS); ENTEROBACTERIACEAE; ERWINIA; PHOTORHABDUS LUMINESCENS; RAHNELLA;

BACTERIAL PROTEINS; BASE SEQUENCE; CLONING, MOLECULAR; GENE TRANSFER, HORIZONTAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; PLASMIDS; RAHNELLA; SEQUENCE ALIGNMENT; VEGETABLES;

EID: 77649302989     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-10-56     Document Type: Article

References (60)

1. Rahnella aquatilis, a nitrogen-fixing enteric bacterium associated with the rhizosphere of wheat and maize. O Berge T Heulin W Achouak C Richard R Bally J Balandreau, Can J Microbiol 1991 37 195 203
2. 2-fixing bacteria associated with wheat rhizosphere in French soils. T Heulin O Berge P Mavingui L Gouzou KP Hebbar J Balandreau, Eur J Soil Biol 1994 30 35 42
3. Characterization of five phyllosphere bacteria isolated from Rosa rugosa leaves, and their phenotypic and metabolic properties. Y Hashidoko E Itoh K Yokota T Yoshida S Tahara, Biosci Biotechnol Biochem 2002 66 2474 2478 10.1271/bbb.66.2474 12506991
4. Bacterial endophytes from seeds of Norway spruce (Picea abies L. Karst). K Cankar H Kraigher M Ravnikar M Rupnik, FEMS Microbiol Lett 2005 244 341 345 10.1016/j.femsle.2005.02.008 15766788
5. Occurrence of indole-3-acetic acid producing bacteria on pear trees and their association with fruit russet. SE Lindow C Desurmont R Elkins G McGourty E Clark MT Brandl, Phytopathology 1998 88 1149 1157 10.1094/PHYTO.1998.88.11.1149 18944847
6. Isolation and characterization of pHW15, a small cryptic plasmid from Rahnella genomospecies 2. WM Rozhon EK Petutschnig C Jonak, Plasmid 2006 56 202 215 16844220
7. Comparison of methods for determining the numbers and species distribution of coliform bacteria in well water samples. RM Niemi MP Heikkilä K Lahti S Kalso SI Niemelä J Appl Microbiol 2001 90 850 858 10.1046/j.1365-2672.2001.01314.x 11412314
8. Two new Rahnella genomospecies that cannot be phenotypically differentiated from Rahnella aquatilis. DJ Brenner HE Müller AG Steigerwalt AM Whitney CM O'Hara P Kämpfer, Int J Syst Bacteriol 1998 48 141 149 9542084
9. Identification of bacterial isolates from intestinal contents associated with 12,000-year-old mastodon remains. AN Rhodes JW Urbance H Youga H Corlew-Newman CA Reddy MJ Klug JM Tiedje DC Fisher, Appl Environ Microbiol 1998 64 651 658 9464403
10. Uranium biomineralization as a result of bacterial phosphatase activity: Insights from bacterial isolates from a contaminated subsurface. MJ Beazley RJ Martinez PA Sobecky SM Webb M Teillefert, Environ Sci Technol 2007 41 5701 5707 10.1021/es070567g 17874776
11. Biological control of bacterial spot of tomato caused by Xanthomonas campestris pv. vesicatoria by Rahnella aquatilis. HH El-Hendawy ME Osman NM Sorour, Microbial Res 2005 160 343 352 10.1016/j.micres.2005.02.008 (Pubitemid 41266929)
12. Biological control of fire blight by using Rahnella aquatilis Ra39 and Pseudomonas spec. R1. P Laux Baysal W Zeller, Acta Hort 2002 590 225 229
13. Rahnella aquatilis, a bacterium isolated from soybean rhizosphere, can solubilize hydroxyapatite. KY Kim D Jordan HB Krishnan, FEMS Microbiol Lett 1997 153 273 277
14. Enzymatic characterization of a recombinant levansucrase from Rahnella aquatilis ATCC 15552. H Kim H-E Park M-J Kim HG Lee J-Y Yang J Cha, J Microbiol Biotechnol 2003 13 230 235
15. Production of polysaccharide by Rahnella aquatilis with whey feedstock. ME Pintado AIE Pintado FX Malcata, J Food Sci 1999 64 348 352 10.1111/j.1365-2621.1999.tb15898.x
16. Molecular characterization of the growth phase-dependent expression of the lsrA gene, encoding levansucrase of Rahnella aquatilis. J-W Seo K-H Jang SA Kang K-B Song EK Jang B-S Park CH Kim S-K Rhee, J Bacteriol 2002 184 5862 5870 10.1128/JB.184.21.5862-5870.2002 12374819
17. Rahnella aquatilis baceteremia in a patient with relapsed acute lymphoblastic leukemia. JE Carinder JD Chua RB Corales AJ Taege GW Procop, Scand J Infect Dis 2001 33 471 473 10.1080/00365540152029972 11450870
18. Rahnella aquatilis sepsis in an immunocompetent adult. CL Chang J Jeong JH Shin EY Lee HC Son, J Clin Microbiol 1999 37 4161 4162 10565953
19. Rahnella aquatilis bacetremia from a suspected urinary source. K Tash, J Clin Microbiol 2005 43 2526 2528 10.1128/JCM.43.5.2526-2528.2005 15872303
20. Biochemical-genetic characterization of the chromosomally encoded extended-spectrum class A -lactamase from Rahnella aquatilis. S Bellais L Poirel N Fortineau JW Decousser P Nordmann, Antimicrob Agents Chemother 2001 45 2965 2968 10.1128/AAC.45.10.2965-2968.2001 11557504 (Pubitemid 32906706)
21. Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes. A-M Lindberg Ljungh S Ahrné S Löfdahl G Molin, Int J Food Microbiol 1998 39 11 17 10.1016/S0168-1605(97)00104-9 9562874
22. Natural antibiotic susceptibility of Rahnella aquatilis and R. aquatilis-related strains. I Stock T Grüger B Wiedemann, J Chemother 2000 12 30 39 10768513
23. Species differences in plasmid carriage in the Enterobacteriaceae. M Sherley DM Gordon PJ Collignon, Plasmid 2003 49 79 85 10.1016/S0147-619X(02) 00107-5 12584004
24. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. PC Fineran TR Blower IJ Foulds DP Humphreys KS Lilley GP Salmond, Proc Natl Acad Sci USA 2009 106 894 899 10.1073/pnas.0808832106 19124776
25. Multicopy plasmid instability: the dimer catastrophe hypothesis. DK Summers CW Beton HL Withers, Mol Microbiol 1993 8 1031 1038 10.1111/j.1365-2958. 1993.tb01648.x 8361350
26. Multimerization of high copy number plasmids causes instability: ColE1 encodes a determinant essential for plasmid monomerization and stability. DK Summers DJ Sherratt, Cell 1984 36 1097 1103 10.1016/0092-8674(84)90060-6 6323019
27. -2 related recombinases are required for site-specific recombination at dif and cer in Escherichia coli K12. G Blakely G May R McCulloch LK Arciszewska M Burke ST Lovett DJ Sherratt, Cell 1993 75 351 361 10.1016/0092-8674(93)80076-Q 8402918
28. Recombination at ColE1 cer requires the Escherichia coli xerC gene product, a member of the lambda integrase family. SD Colloms P Sykora G Szatmari DJ Sherratt, J Bacteriol 1990 172 6973 6980 2254268
29. xerB, an Escherichia coli gene required for plasmid ColE1 site-specific recombination is identical to pepA, encoding aminopeptidase A, a protein with substantial similarity to bovine lens leucine aminopeptidase. CJ Stirling SD Colloms JF Collins G Szatmari DJ Sherratt, EMBO Journal 1989 8 1623 1627 2670557
30. The arginine repressor is essential for plasmid stabilizing site-specific recombination at the ColE1 cer locus. CJ Stirling G Szatmari G Stewart MCM Smith DJ Sherratt, EMBO Journal 1988 7 4389 4395 3149585
31. Nucleoprotein architecture and ColE1 dimer resolution: a hypothesis. TC Hodgman H Griffiths DK Summers, Mol Microbiol 1998 29 545 558 10.1046/j.1365-2958.1998.00948.x 9720871
32. Resolution of ColE1 dimers requires a DNA sequence implicated in the three-dimensional organization of the cer site. DK Summers DJ Sherratt, EMBO Journal 1988 7 851 858 3294000
33. ColE1 multimer formation triggers inhibition of E. coli cell division. ME Patient DK Summers, Mol Microbiol 1993 8 1089 1095 10.1111/j.1365-2958.1993. tb01238.x
34. Indole signalling contributes to the stable maintenance of Escherichia coli multicopy plasmids. EL Chant DK Summers, Mol Microbiol 2007 63 35 43 10.1111/j.1365-2958.2006.05481.x 17163976
35. The role of FIS in the Rcd checkpoint and stable maintenance of plasmid ColE1. IK Blaby DK Summers, Microbiology 2009 155 2676 2682 10.1099/mic.0. 029777-0 19443546
36. Replication forks blocked by protein-DNA complexes have limited stability in vitro. P McGlynn CP Guy, J Mol Biol 2008 381 249 255 10.1016/j.jmb.2008.05. 053 18602646
37. Mechanisms of transcription-replication collisions in bacteria. EV Mirkin SM Mirkin, Mol Cell Biol 2005 25 888 895 10.1128/MCB.25.3.888-895.2005 15657418
38. Nucleotide sequence and gene organization of ColE1 DNA. PT Chan H Ohmori J Tomizawa J Lebowitz, J Biol Chem 1985 260 8925 8935 2991225
39. A ColE1-encoded gene directs entry exclusion of the plasmid. Y Yamada M Yamada A Nakazawa, J Bacteriol 1995 177 6064 6068 7592368
40. Comparative analysis of the replicon regions of eleven ColE2-related plasmids. S Hiraga T Sugiyama T Itoh, J Bacteriol 1994 176 7233 7243 7525540
41. pUB6060: a broad-host-range, DNA polymerase-I-independent ColE2-like plasmid. MB Avison TR Walsh PM Bennett, Plasmid 2001 45 88 100 10.1006/plas.2000.1511 11322823
42. A classification scheme for mobilization regions of bacterial plasmids. MV Francia A Varsaki MP Garcilln-Barcia A Latorre C Drainas F de la Cruz, FEMS Microbiol Rev 2004 28 79 100 10.1016/j.femsre.2003.09.001 14975531
43. The genome of Erwinia tasmaniensis strain Et1/99, a non-pathogenic bacterium in the genus Erwinia. M Kube AM Migdoll I Müller H Kuhl A Beck R Reinhardt K Geider, Environ Microbiol 2008 10 2211 2222 10.1111/j.1462-2920. 2008.01639.x 18462403
44. Replication and control of circular bacterial plasmids. G del Solar R Giraldo MJ Ruiz-Echevarría M Espinosa R Díaz-Orejas, Microbiol Mol Biol Rev 1998 62 434 464 9618448
45. Comparative sequence analysis of the icm/dot genes in Legionella. I Morozova X Qu S Shi G Asamani JE Greenberg HA Shuman JJ Russo, Plasmid 2004 51 127 147 10.1016/j.plasmid.2003.12.004 15003709
46. Features of the replicon of plasmid pAM10.6 of Pseudomonas fluorescens. M Peters E Jgi I Suitso T Punnisk A Nurk, Plasmid 2001 46 25 36 10.1006/plas.2001.1524 11535033
47. The family of highly interrelated single-stranded deoxyribonucleic acid plasmids. A Gruss SD Ehrlich, Mirobiol Rev 1989 53 232 241
48. Characterization, sequence and mode of replication of plasmid pNB2 from the thermophilic bacterium Clostridium thermosaccharolyticum. EP Delver NG Belogurova EE Tupikova SD Varfolomeyev AA Belogurov, Mol Gen Genet 1996 253 166 172 10.1007/s004380050309 9003300
49. Complete nucleotide sequence of pT181, a tetracycline-resistance plasmid from Staphylococcus aureus. SA Khan RP Novick, Plasmid 1983 10 251 259 10.1016/0147-619X(83)90039-2 6657777
50. Complete nucleotide sequence and characterization of pUA140, a cryptic plasmid from Streptococcus mutans. X Zou PW Caufield Y Li F Qi, Plasmid 2001 46 77 85 10.1006/plas.2001.1539 11591133
51. Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content. H Heuer C Kopmann CT Binh EM Top K Smalla, Environ Microbiol 2009 11 937 949 10.1111/j.1462-2920.2008.01819.x 19055690
52. The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. E Duchaud C Rusniok L Frangeul C Buchrieser A Givaudan S Taourit S Bocs C Boursaux-Eude M Chandler JF Charles E Dassa R Derose S Derzelle G Freyssinet S Gaudriault C Médigue A Lanois K Powell P Siguier R Vincent V Wingate M Zouine P Glaser N Boemare A Danchin F Kunst, Nat Biotechnol 2003 21 1307 1313 10.1038/nbt886 14528314
53. Analysis of the intestinal microflora in Hepialus gonggaensis larvae using 16S rRNA sequences. H Yu Z Wang L Liu Y Xia Y Cao Y Yin, Curr Microbiol 2008 56 391 396 10.1007/s00284-007-9078-4 18183461
54. Erwinia tasmaniensis sp. nov., a non-phytopathogenic bacterium from apple and pear trees. K Geider G Auling Z Du V Jakovljevic S Jock B Völksch, Int J Syst Bacteriol 2006 56 2937 2943
55. J Sambrook DW Russell, Molecular Cloning: A Laboratory Manual Cold Spring Harbor, Cold Spring Harbor Laboratory Press 2001
56. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738
57. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. T Carver M Berriman A Tivey C Patel U Böhme BG Barrell J Parkhill MA Rajandream, Bioinformatics 2008 24 2672 2676 10.1093/ bioinformatics/btn529 18845581
58. Genomic sequencing. GM Church W Gilbert, Proc Natl Acad Sci USA 1984 81 1991 1995 10.1073/pnas.81.7.1991 6326095
59. Enterobacteriales. DJ Brenner JJ Farmer, Bergey's Manual of Systematic Bacteriology Springer, Brenner D, Krieg NR, Staley JT, Garrity GM, 2005 2 Part B 587 848
60. E' tude taxonomique d'ente'robacte'ries appartenant ou apparente'es au genre Enterobacter. F Gavini C Ferragut B Lefebvre H Leclerc, Ann Microbiol (Paris) 1976 127B 317 335 1020871