Evolution of competence and DNA uptake specificity in the Pasteurellaceae

BMC Evolutionary Biology

Volumn 6, Issue , 2006, Pages

  Redfield, Rosemary J ^a   Findlay, Wendy A ^b   Bossé, Janine ^c   Kroll, J Simon ^c   Cameron, Andrew D S ^a   Nash, John H E ^b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA FRAGMENT; BACTERIAL PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BULKED SEGREGANT ANALYSIS; CONTROLLED STUDY; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; HAEMOPHILUS INFLUENZAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PASTEURELLACEAE; PHYLOGENY; BACTERIUM TRANSFORMATION; CHEMISTRY; CLASSIFICATION; EVOLUTION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; PHYSIOLOGY;

ACTINOBACILLUS ACTINOMYCETEMCOMITANS; HAEMOPHILUS INFLUENZAE; MANNHEIMIA SUCCINICIPRODUCENS; PASTEURELLA MULTOCIDA; PASTEURELLACEAE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BIOLOGICAL EVOLUTION; DNA; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; MUTATION; PASTEURELLACEAE; TRANSFORMATION, BACTERIAL;

EID: 33750531455     PISSN: 14712148     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-6-82     Document Type: Article

References (57)

1. Chen I, Dubnau D: DNA uptake during bacterial transformation. Nat Rev Microbiol 2004, 2(3):241-249.
2. Solomon JM, Grossman AD: Who's competent and when: regulation of natural genetic competence in bacteria. Trends Genet 1996, 12(4):150-155.
3. Sikorski J, Teschner N, Wackernagel W: Highly different levels of natural transformation are associated with genomic subgroups within a local population of Pseudomonas stutzeri from soil. Appl Environ Microbiol 2002, 68(2):865-873.
4. Gromkova RC, Mottalini TC, Dove MG: Genetic transformation in Haemophilus parainfluenzae clinical isolates. Curr Microbiol 1998, 37(2):123-126.
5. Sexton JA, Vogel JP: Regulation of hypercompetence in Legionella pneumophila. J Bacteriol 2004, 186(12):3814-3825.
6. Fujise O, Lakio L, Wang Y, Asikainen S, Chen C: Clonal distribution of natural competence in Actinobacillus actinomycetemcomitans. Oral Microbiol Immunol 2004, 19(5):340-342.
7. Smith HO, Gwinn ML, Salzberg SL: DNA uptake signal sequences in naturally transformable bacteria. Res Microbiol 1999, 150(9-10):603-616.
8. Davidsen T, Rodland EA, Lagesen K, Seeberg E, Rognes T, Tonjum T: Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Res 2004, 32(3):1050-1058.
9. Smith HO, Tomb JF, Dougherty BA, Fleischmann RD, Venter JC: Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome. Science 1995, 269(5223):538-540.
10. Elkins C, Thomas CE, Seifert HS, Sparling PF: Species-specific uptake of DNA by gonococci is mediated by a 10-base-pair sequence. J Bacteriol 1991, 173(12):3911-3913.
11. Karlin S, Mrazek J, Campbell AM: Frequent oligonucleotides and peptides of the Haemophilus influenzae genome. Nucleic Acids Res 1996, 24(21):4263-4272.
12. Wang Y, Goodman SD, Redfield RJ, Chen C: Natural transformation and DNA uptake signal sequences in Actinobacillus actinomycetemcomitans. J Bacteriol 2002, 184(13):3442-3449.
13. Bakkali M, Chen TY, Lee HC, Redfield RJ: Evolutionary stability of DNA uptake signal sequences in the Pasteurellaceae. Proc Natl Acad Sci U S A 2004, 101(13):4513-4518.
14. Barouki R, Smith HO: Initial steps in Haemophilus influenzae transformation. Donor DNA binding in the com10 mutant. J Biol Chem 1986, 261(19):8617-8623.
15. Danner DB, Deich RA, Sisco KL, Smith HO: An eleven-base-pair sequence determines the specificity of DNA uptake in Haemophilus transformation. Gene 1980, 11(3-4):311-318.
16. Christensen H, Foster G, Christensen JP, Pennycott T, Olsen JE, Bisgaard M: Phylogenetic analysis by 16S rDNA gene sequence comparison of avian taxa of Bisgaard and characterization and description of two new taxa of Pasteurellaceae. J Appl Microbiol 2003, 95(2):354-363.
17. Christensen H, Kuhnert P, Olsen JE, Bisgaard M: Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae. Int J Syst Evol Microbiol 2004, 54(Pt 5):1601-1609.
18. Dewhirst FE, Paster BJ, Olsen I, Fraser GJ: Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences. J Bacteriol 1992, 174(6):2002-2013.
19. Kilian M: Taxonomic Study of Genus Hemophilus, with Proposal of a New Species. Journal of General Microbiology 1976, 93(MAR):9-62.
20. Norskov-Lauritsen N, Bruun B, Kilian M: Multilocus sequence phylogenetic study of the genus Haemophilus with description of Haemophilus pittmaniae sp. nov. Int J Syst Evol Microbiol 2005, 55(Pt 1):449-456.
21. Lee PC, Lee SY, Hong SH, Chang HN: Isolation and characterization of a new succinic acid-producing bacterium, Mannheimia succiniciproducens MBEL55E, from bovine rumen. Appl Microbiol Biotechnol 2002, 58(5):663-8.
22. Hong SH, Kim JS, Lee SY, In YH, Choi SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ: The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat Biotechnol 2004, 22(10):1275-1281.
23. Hong SH, Kim JS, Lee SY, In YH, Choi SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ: Corrigendum: The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat Biotechnol 2004, 22(12):1589.
24. Alexander H, Leidy G: Determination of inherited traits of H. influenzae by desoxyribonucleic acid fractions isolated from type-specific cells. J Exp Med 1951, 93:345-359.
25. Bosse JT, Nash JH, Kroll JS, Langford PR: Harnessing natural transformation in Actinobacillus pleuropneumoniae: a simple method for allelic replacements. FEMS Microbiol Lett 2004, 233(2):277-281.
26. Bigas A, Garrido ME, Rozas AM, Badiola I, Barbe J, Llagostera M: Development of a genetic manipulation system for Haemophilus parasuis. Vet Microbiol 2005, 105(3-4):223-228.
27. Nickel L, Goodgal SH: Effect of Interspecific Transformation on Linkage Relationships of Markers in Haemophilus influenzae and Haemophilus parainfluenzae. J Bacteriol 1964, 88:1538-1544.
28. VanWagoner TM, Whitby PW, Morton DJ, Seale TW, Stull TL: Characterization of three new competence-regulated operons in Haemophilus influenzae. J Bacteriol 2004, 186(19):6409-6421.
29. Redfield RJ, Cameron ADS, Qian Q, Hinds J, Ali TR, Kroll JS, Langford PR: A novel CRP-dependent regulon controls expression of competence genes in Haemophilus influenzae. J Mol Biol 2005, 347(4):735-747.
30. May BJ, Zhang Q, Li LL, Paustian ML, Whittam TS, Kapur V: Complete genomic sequence of Pasteurella multocida, Pm70. Proc Natl Acad Sci U S A 2001, 98(6):3460-3465.
31. Ochman H: Neutral mutations and neutral substitutions in bacterial genomes. Mol Biol Evol 2003, 20(12):2091-2096.
32. Lethem MI, James SL, Marriott C, Burke JF: The origin of DNA associated with mucus glycoproteins in cystic fibrosis sputum. Eur Respir J 1990, 3(1):19-23.
33. Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome Res 2004, 14(6):1188-1190.
34. Melnikow E, Dornan S, Sargent C, Duszenko M, Evans G, Gunkel N, Selzer PM, Ullrich HJ: Microarray analysis of Haemophilus parasuis gene expression under in vitro growth conditions mimicking the in vivo environment. Vet Microbiol 2005, 110(3-4):255-263.
35. White DC, Leidy G, Jamieson JD, Shope RE: Porcine Contagious Pleuropneumonia. 3. Interrelationship Of Hemophilus pleuropneumoniae To Other Species Of Hemophilus: Nutritional, Metabolic, Transformation, And Electron Microscopy Studies. J Exp Med 1964, 120:1-12.
36. Scocca JJ, Poland RL, Zoon KC: Specificity in deoxyribonucleic acid uptake by transformable Haemophilus influenzae. J Bacteriol 1974, 118(2):369-373.
37. Albritton WL, Setlow JK, Thomas ML, Sottnek FO: Relatedness within the family Pasteurellaceae as determined by genetic transformation. Int J Syst Bact 1986, 36(1):103-106.
38. Kahn ME, Barany F, Smith HO: Transformasomes: specialized membranous structures that protect DNA during Haemophilus transformation. Proc Natl Acad Sci U S A 1983, 80(22):6927-6931.
39. Setlow JK, Boling ME, Allison DP, Beattie KL: Relationship between prophage induction and transformation in Haemophilus influenzae. Journal of Bacteriology 1973, 115(1):153-161.
40. Tanaka MM, Bergstrom CT, Levin BR: The evolution of mutator genes in bacterial populations: the roles of environmental change and timing. Genetics 2003, 164(3):843-854.
41. Harrison A, Dyer DW, Gillaspy A, Ray WC, Mungur R, Carson MB, Zhong H, Gipson J, Gipson M, Johnson LS, Lewis L, Bakaletz LO, Munson RSJ: Genomic sequence of an otitis media isolate of nontypeable Haemophilus influenzae: comparative study with H. influenzae serotype d, strain KW20. J Bacteriol 2005, 187(13):4627-4636.
42. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al.: Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995, 269(5223):496-512.
43. National Center for Biotechnology Information [http://www.ncbi.nlm.nih. gov]
44. Actinobacillus actinomycetemcomitans Strain HK1651 Genome Sequencing [http://www.genome.ou.edu/act.html]
45. DOE Joint Genome Institute [http://www.jgi.doe.gov]
46. Baylor College of Medicine Human Genome Sequencing Center [http://www.hgsc.bcm.tmc.edu]
47. Gioia J, Qin X, Jiang H, Clinkenbeard K, Lo R, Liu Y, Fox GE, Yerrapragada S, McLeod MP, McNeill TZ, Hemphill L, Sodergren E, Wang Q, Muzny DM, Homsi FJ, Weinstock GM, Highlander SK: The Genome Sequence of Mannheimia haemolytica A1: Insights into Virulence, Natural Competence, and Pasteurellaceae Phylogeny. J Bacteriol 2006, 188(20):7257-7266.
48. Glimmer Microbial Gene Finding System [http://cbcb.umd.edu/software/ glimmer]
49. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
50. 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.
51. Felsenstein J: PHYLIP - Phylogeny inference package (version 3.2). Cladistics 1989, 5:164-166.
52. NRC Institute for Biological Sciences: Genomics and Proteomics [http://ibs-isb.nrc-cnrc.gc.ca/glycobiology/group_software_e.html]
53. WebLogo [http://weblogo.berkeley.edu]
54. Poje G, Redfield RJ: Transformation of Haemophilus influenzae. In Haemophilus influenzae Protocols Edited by: Herbert MA, Hood DW, Moxon ER. Totowa NJ , Humana; 2003:57-70.
55. Poje G: DNA uptake specificity of Haemophilus influenzae. In Zoology Vancouver , University of British Columbia; 2000.
56. Sisco KL, Smith HO: Sequence-specific DNA uptake in Haemophilus transformation. Proc Natl Acad Sci U S A 1979, 76(2):972-976.
57. Lerat E, Daubin V, Moran NA: From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biol 2003, 1(1):E19.