A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

BMC Evolutionary Biology

Volumn 6, Issue , 2006, Pages

  Wilson, James W ^a   Nickerson, Cheryl A ^a  

^a TULANE UNIVERSITY HEALTH SCIENCES CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; DATA ANALYSIS; EVOLUTION; GENE EXPRESSION; GENE TRANSFER; GENOMIC ISLAND; GRAM NEGATIVE BACTERIUM; HORIZONTAL GENE TRANSFER; HOST; HOST RANGE; MOLECULAR CLONING; NONHUMAN; SALMONELLA TYPHIMURIUM; BACTERIUM; CLASSIFICATION; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; SALMONELLA TYPHIMURIUM;

BACTERIAL DNA; BACTERIAL RNA; TRANSFER RNA;

BACTERIA; CLONING, MOLECULAR; CONSERVED SEQUENCE; DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; PHYLOGENY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, TRANSFER; SALMONELLA TYPHIMURIUM;

EID: 32044467135     PISSN: 14712148     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-6-2     Document Type: Article

References (43)

1. Burrus V, Waldor MK: Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 2004, 155(5):376-386.
2. Dobrindt U, Hochhut B, Hentschel U, Hacker J: Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2004, 2(5):414-424.
3. Hacker J, Kaper JB: Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 2000, 54:641-679.
4. Ochman H, Lawrence JG, Groisman EA: Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405(6784):299-304.
5. van der Meer JR, Sentchilo V: Genomic islands and the evolution of catabolic pathways in bacteria. Curr Opin Biotechnol 2003, 14(3):248-254.
6. Galan JE: Salmonella interactions with host cells: type III secretion at work. Annu Rev Cell Dev Biol 2001, 17:53-86.
7. Porwollik S, Wong RM, McClelland M: Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis. Proc Natl Acad Sci U S A 2002, 99(13):8956-8961.
8. Chan K, Baker S, Kim CC, Detweiler CS, Dougan G, Falkow S: Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray. J Bacteriol 2003, 185(2):553-563.
9. Whittam TS, Bumbaugh AC: Inferences from whole-genome sequences of bacterial pathogens. Curr Opin Genet Dev 2002, 12(6):719-725.
10. Koonin EV, Makarova KS, Aravind L: Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 2001, 55:709-742.
11. Mantri Y, Williams KP: Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res 2004, 32(Database issue):D55-8.
12. McDaniel TK, Kaper JB: A cloned pathogenicity island from enteropathogenic Escherichia coli confers the attaching and effacing phenotype on E. coli K-12. Mol Microbiol 1997, 23(2):399-407.
13. Hansen-Wester I, Chakravortty D, Hensel M: Functional transfer of Salmonella pathogenicity island 2 to Salmonella bongori and Escherichia coli. Infect Immun 2004, 72(5):2879-2888.
14. Hansen-Wester I, Hensel M: Genome-based identification of chromosomal regions specific for Salmonella spp. Infect Immun 2002, 70(5):2351-2360.
15. McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK: Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 2001, 413(6858):852-856.
16. Wilson JW, Figurski DH, Nickerson CA: VEX-capture: a new technique that allows in vivo excision, cloning, and broadhost-range transfer of large bacterial genomic DNA segments. J Microbiol Methods 2004, 57(3):297-308.
17. Gulig PA, Curtiss R: Plasmid-associated virulence of Salmonella typhimurium. Infect Immun 1987, 55(12):2891-2901.
18. Beuzon CR, Casadesus J: Conserved structure of IS200 elements in Salmonella. Nucleic Acids Res 1997, 25(7):1355-1361.
19. Beuzon CR, Chessa D, Casadesus J: IS200: an old and still bacterial transposon. Int Microbiol 2004, 7(1):3-12.
20. Ellermeier CD, Slauch JM: RtsA and RtsB coordinately regulate expression of the invasion and flagellar genes in Salmonella enterica serovar Typhimurium. J Bacteriol 2003, 185(17):5096-5108.
21. Groisman EA: The pleiotropic two-component regulatory system PhoP-PhoQ. J Bacteriol 2001, 183(6):1835-1842.
22. Ehrbar K, Hardt WD: Bacteriophage-encoded type III effectors in Salmonella enterica subspecies 1 serovar Typhimurium. Infect Genet Evol 2005, 5(1):1-9.
23. Worley MJ, Ching KH, Heffron F: Salmonella SsrB activates a global regulon of horizontally acquired genes. Mol Microbiol 2000, 36(3):749-761.
24. Mahan MJ, Slauch JM, Mekalanos JJ: Environmental regulation of virulence gene expression in Escherichia coli, Salmonella, and Shigella spp. In Escherichia coli and Salmonella: cellular and molecular biology Volume 2. 2nd edition. Edited by: Neidhardt FC, Curtiss R, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE. Washington, DC , ASM Press; 1996.
25. Hoch JA, Silhavey TJ: Two-Component Signal Transduction. Washington D.C. , ASM Press; 1995.
26. Montgomery DM, Dean AC, Wiffen P, Macaskie LE: Phosphatase production and activity in Citrobacter freundii and a naturally occurring, heavy-metal-accumulating Citrobacter sp. Microbiology 1995, 141 ( Pt 10):2433-2441.
27. Uchiya KI, Tohsuji M, Nikai T, Sugihara H, Sasakawa C: Identification and characterization of phoN-Sf, a gene on the large plasmid of Shigella flexneri 2a encoding a nonspecific phosphatase. J Bacteriol 1996, 178(15):4548-4554.
28. Ausubel FM, al: Current Protocols in Molecular Biology. John Wiley and Sons, Inc.; 1996.
29. Chen LM, Kaniga K, Galan JE: Salmonella spp. are cytotoxic for cultured macrophages. Mol Microbiol 1996, 21(5):1101-1115.
30. Schmidhauser TJ, Helinski DR: Regions of broad-host-range plasmid RK2 involved in replication and stable maintenance in nine species of gram-negative bacteria. J Bacteriol 1985, 164(1):446-455.
31. Sambrook J, Fritsch EF, Maniatis T: Molecular cloning: a laboratory manual. 2nd edition. Plainview, NY , Cold Spring Harbor Press; 1989.
32. Nickerson CA, Curtiss R: Role of sigma factor RpoS in initial stages of Salmonella typhimurium infection. Infect Immun 1997, 65(5):1814-1823.
33. Halford WP, Falco VC, Gebhardt BM, Carr DJ: The inherent quantitative capacity of the reverse transcription-polymerase chain reaction. Anal Biochem 1999, 266(2):181191.
34. Wilson JW, Ramamurthy R, Porwollik S, McClelland M, Hammond T, Allen P, Ott CM, Pierson DL, Nickerson CA: Microarray analysis identifies Salmonella genes belonging to the low-shear modeled microgravity regulon. Proc Natl Acad Sci U S A 2002, 99(21):13807-13812.
35. Wilson JW, Sia EA, Figurski DH: The kilE locus of promiscuous IncP alpha plasmid RK2 is required for stable maintenance in Pseudomonas aeruginosa. J Bacteriol 1997, 179(7):2339-2347.
36. Simons RW, Houman F, Kleckner N: Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 1987, 53(1):85-96.
37. Miller JH: A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria. Cold Spring Harbor Laboratory Press; 1992.
38. Brodskii LI, Ivanov VV, Kalaidzidis Ia L, Leontovich AM, Nikolaev VK, Feranchuk SI, Drachev VA: [GeneBee-NET: An Internet based server for biopolymer structure analysis]. Biokhimiia 1995, 60(8):1221-1230.
39. Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000, 17(4):540-552.
40. Felsenstein J: Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981, 17(6):368-376.
41. Olsen GJ, Matsuda H, Hagstrom R, Overbeek R: fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 1994, 10(1):41-48.
42. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
43. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673-4680.