High-resolution mapping of plasmid transcriptomes in different host bacteria

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Miyakoshi, Masatoshi ^a,c   Nishida, Hiromi ^b   Shintani, Masaki ^a   Yamane, Hisakazu ^a   Nojiri, Hideaki ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c TOHOKU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CARBAZOLE CATABOLIC PLASMID PCAR1; SINGLE STRANDED DNA; SUCCINIC ACID; TRANSCRIPTOME; UNCLASSIFIED DRUG; BACTERIAL RNA; CARBAZOLE; CARBAZOLE DERIVATIVE;

ARTICLE; BACTERIAL GENETICS; BACTERIAL GROWTH; CARBON SOURCE; CONTROLLED STUDY; GENE CLUSTER; GENE MAPPING; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PHENOTYPE; PLASMID; PSEUDOMONAS; PSEUDOMONAS PUTIDA; PSEUDOMONAS RESINOVORANS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION; UPREGULATION; BACTERIAL GENE; CHROMOSOME MAP; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MULTIGENE FAMILY;

BACTERIA (MICROORGANISMS); PROKARYOTA; PSEUDOMONAS RESINOVORANS;

CARBAZOLES; CHROMOSOME MAPPING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPERON; PLASMIDS; PSEUDOMONAS; RNA, BACTERIAL; TRANSCRIPTION, GENETIC;

EID: 60549092956     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-12     Document Type: Article

References (31)

1. Frost LS Leplae R Summers AO Toussaint A Mobile genetic elements: The agents of open source evolution Nat Rev Microbiol 2005, 3:722-732. 10.1038/nrmicro1235 16138100
2. Harr B Schlötterer C Gene expression analysis indicates extensive genotype-specific crosstalk between the conjugative F-plasmid and the E. coli chromosome BMC Microbiol 2006, 6:80. 1590023 16981998 10.1186/ 1471-2180-6-80
3. Doyle M Fookes M Ivens A Mangen MW Wain J Dorman CJ An H-NS-like stealth protein aids horizontal DNA transmission in bacteria Science 2007, 315:251-252. 10.1126/science.1137550 17218529
4. Miyakoshi M Shintani M Terabayashi T Kai S Yamane H Nojiri H Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1 J Bacteriol 2007, 189:6849-6860. 2045235 17675379 10.1128/JB.00684-07
5. Thomas CM Transcription regulatory circuits in bacterial plasmids Biochem Soc Trans 2006, 34:1072-1074. 10.1042/BST0341072 17073753
6. Williams PA Jones RM Zylstra G Genomics of catabolic plasmid Pseudomonas Kluwer Academic/Plenum Publishers Ramos JL 2004, 1:165-195.
7. Ramos JL Marqués S Timmis KN Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators Annu Rev Microbiol 1997, 51:341-372. 10.1146/annurev.micro.51.1.341 9343354
8. Ouchiyama N Zhang Y Omori T Kodama T Biodegradation of carbazole by Pseudomonas spp. CA06 and CA10 Biosci Biotechnol Biochem 1993, 57:455-460.
9. Nojiri H Sekiguchi H Maeda K Urata M Nakai S Yoshida T Habe H Omori T Genetic characterization and evolutionary implications of a car gene cluster in the carbazole degrader Pseudomonas sp. strain CA10 J Bacteriol 2001, 183:3663-3679. 95244 11371531 10.1128/ JB.183.12.3663-3679.2001
10. Maeda K Nojiri H Shintani M Yoshida T Habe H Omori T Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676 J Mol Biol 2003, 326:21-33. 10.1016/ S0022-2836(02)01400-6 12547188
11. Urata M Miyakoshi M Kai S Maeda K Habe H Omori T Yamane H Nojiri H Transcriptional regulation of the ant operon, encoding two-component anthranilate 1,2-dioxygenase, on the carbazole-degradative plasmid pCAR1 of Pseudomonas resinovorans strain CA10 J Bacteriol 2004, 186:6815-6823. 522213 15466034 10.1128/JB.186.20.6815-6823.2004
12. Miyakoshi M Urata M Habe H Omori T Yamane H Nojiri H Differentiation of carbazole catabolic operons by replacement of the regulated promoter via transposition of an insertion sequence J Biol Chem 2006, 281:8450-8457. 10.1074/jbc.M600234200 16455652
13. Nelson KE Weinel C Paulsen IT Dodson RJ Hilbert H Martins dos Santos VAP Fouts DE Gill SR Pop M Holmes M Brinkac L Beanan M DeBoy RT Daugherty S Kolonay J Madupu R Nelson W White O Peterson J Khouri H Hance I Chris Lee P Holtzapple E Scanlan D Tran K Moazzez A Utterback T Rizzo M Lee K Kosack D Moestl D Wedler H Lauber J Stjepandic D Hoheisel J Straetz M Heim S Kiewitz C Eisen J Timmis KN Düsterhöft A Tümmler B Fraser CM Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 Environ Microbiol 2002, 4:799-808. 10.1046/j.1462-2920.2002.00366.x 12534463
14. Shintani M Yano H Habe H Omori T Yamane H Tsuda M Nojiri H Characterization of the replication, maintenance, and transfer features of the IncP-7 plasmid pCAR1, which carries genes involved in carbazole and dioxin degradation Appl Environ Microbiol 2006, 72:3206-3216. 1472330 16672459 10.1128/AEM.72.5.3206-3216.2006
15. Kapranov P Willingham AT Gingeras TR Genome-wide transcription and the implications for genomic organization Nat Rev Genet 2007, 8:413-423. 10.1038/nrg2083 17486121
16. Selinger DW Cheung KJ Mei R Johansson EM Richmond CS Blattner FR Lockhart DJ Church GM RNA expression analysis using a 30 base pair resolution Escherichia coli genome array Nat Biotechnol 2000, 18:1262-1268. 10.1038/82367 11101804
17. McGrath PT Lee H Zhang L Iniesta AA Hottes AK Tan MH Hillson NJ Hu P Shapiro L McAdams HH High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons Nat Biotechnol 2007, 25:584-592. 10.1038/nbt1294 17401361
18. Kampa D Cheng J Kapranov P Yamanaka M Brubaker S Cawley S Drenkow J Piccolboni A Bekiranov S Helt G Tammana H Gingeras TR Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosome 21 and 22 Genome Res 2004. 14:331-342. 353210 14993201 10.1101/gr.2094104
19. Johnson JM Edwards S Shoemaker D Schadt EE Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments Trends Genet 2005, 21:93-102. 10.1016/j.tig.2004.12.009 15661355
20. Shintani M Yoshida T Habe H Omori T Nojiri H Large plasmid pCAR2 and class II transposon Tn4676 are functional mobile genetic elements to distribute the carbazole/dioxin-degradative car gene cluster in different bacteria Appl Microbiol Biotechnol 2005, 67:370-382. 10.1007/ s00253-004-1778-0 15856217
21. Li W Shi J Wang X Han Y Tong W Ma L Liu B Cai B Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6 Gene 2004, 336:231-240. 10.1016/ j.gene.2004.03.027 15246534
22. Yano H Garruto CE Sota M Ohtsubo Y Nagata Y Zylstra GJ Williams PA Tsuda M Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic organization of IncP-7 TOL plasmid pWW53 and related mobile genetic elements J Mol Biol 2007, 369:11-26. 10.1016/j.jmb.2007.02.098 17408691
23. Shintani M Habe H Tsuda M Omori T Yamane T Nojiri H Recipient range of IncP-7 conjugative plasmid pCAR2 from Pseudomonas putida HS01 is broader than from other Pseudomonas strains Biotechnol Lett 2005, 27:1847-1853. 10.1007/s10529-005-3892-1 16328978
24. Leplae R Hebrant A Wodak SJ Toussaint A ACLAME: A classification of mobile genetic elements Nucleic Acid Res 2004, 32:D45-49. 308818 14681355 10.1093/nar/gkh084
25. Gilmour MW Thompson NR Sanders M Parkhill J Taylor DE The complete nucleotide sequence of the resistance plasmid R478: Defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics Plasmid 2004, 52:182-202. 10.1016/ j.plasmid.2004.06.006 15518875
26. Murata T Ohnishi M Ara T Kaneko J Han C-G 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, 184:3194-3202. 135101 12029035 10.1128/JB.184.12.3194-3202.2002
27. 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, 184:4259-4269. 135215 12107144 10.1128/ JB.184.15.4259-4269.2002
28. Böltner D MacMahon C Pembroke T Strike P Osborn AM R391: A conjugative integrating mosaic comprised of phage, plasmid, and transposon elements J Bacteriol 2002, 184:5158-5169. 135318 12193633 10.1128/JB.184.18.5158-5169.2002
29. Snider J Houry WA MoxR AAA+ ATPases: A novel family of molecular chaperones? J Struct Biol 2006, 156:200-209. 16677824
30. Whittaker CA Hynes RO Distribution and evolution of von Willebrand/ integrin A domains: Widely dispersed domains with roles in cell adhesion and elsewhere Mol Biol Cell 2002, 13:3369-3387. 129952 12388743 10.1091/ mbc.E02-05-0259
31. Rozen S Skaletsky HJ Primer3 on the WWW for general users and for biologist programmers Bioinformatics Methods and Protocols: Methods in Molecular Biology Totowa: Humana Press Krawetz S, Misener S 2000, 365-386.