Architecture of Burkholderia cepacia complex σ70 gene family: Evidence of alternative primary and clade-specific factors, and genomic instability

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Menard, Aymeric ^a,b   de los Santos, Paulina ^a,b   Graindorge, Arnault ^a,b   Cournoyer, Benoit ^a,b  

^a UNIVERSITÉ DE LYON   (France)

^b University of Lyon   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; BACTERIAL RNA; FLAGELLIN; HEAT SHOCK PROTEIN; SIGMA FACTOR; SIGMA FACTOR RPOS; DNA DIRECTED RNA POLYMERASE; RNA POLYMERASE SIGMA 70; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; BURKHOLDERIA CEPACIA COMPLEX; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; CHROMOSOME INVERSION; GENE EXPRESSION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; MESSENGER RNA SYNTHESIS; MOLECULAR CLONING; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PROMOTER REGION; PSEUDOMONAS AERUGINOSA; SEQUENCE ANALYSIS; STRAIN DIFFERENCE; BACTERIAL GENE; BURKHOLDERIA CEPACIA; CLASSIFICATION; GENETICS; GENOMIC INSTABILITY; PHYLOGENY; SPECIES DIFFERENCE;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BURKHOLDERIA; BURKHOLDERIA CENOCEPACIA; BURKHOLDERIA CEPACIA COMPLEX; PROTEOBACTERIA; PSEUDOMONAS AERUGINOSA;

BURKHOLDERIA CEPACIA; DNA-DIRECTED RNA POLYMERASES; EVOLUTION, MOLECULAR; GENES, BACTERIAL; GENOMIC INSTABILITY; PHYLOGENY; SIGMA FACTOR; SPECIES SPECIFICITY;

EID: 38049181090     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-308     Document Type: Article

References (66)

1. Mahenthiralingam E Urban TA Goldberg JB The multifarious, multireplicon Burkholderia cepacia complex Nat Rev Microbiol 2005, 3(2):144-156. 10.1038/nrmicro1085 15643431
2. Isles A Maclusky I Corey M Gold R Prober C Fleming P Levison H Pseudomonas cepacia infection in cystic fibrosis: An emerging problem J Pediatr 1984, 104(2):206-210. 10.1016/S0022-3476(84)80993-2 6420530
3. LiPuma JJ Mortensen JE Dasen SE Edlind TD Schidlow DV Burns JL Stull TL Ribotype analysis of Pseudomonas cepacia from cystic fibrosis treatment centers J Pediatr 1988, 113(5):859-862. 10.1016/S0022-3476(88)80018-0 2903229
4. Coenye T Spilker T Van Schoor A LiPuma JJ Vandamme P Recovery of Burkholderia cenocepacia strain PHDC from cystic fibrosis patients in Europe Thorax 2004, 59(11):952-954. 10.1136/thx.2003.019810 15516470
5. GOLD: Genomes OnLine database V.2 http://www.genomesonline.org
6. Martinez-Bueno MA Tobes R Rey M Ramos JL Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01 Environ Microbiol 2002, 4(12):842-855. 10.1046/ j.1462-2920.2002.00371.x 12534467
7. Rojo F Mechanisms of transcriptional repression Curr Opin Microbiol 2001, 4(2):145-151. 10.1016/S1369-5274(00)00180-6 11282469
8. Lonetto MA Rhodius V Lamberg K Kiley P Busby S Gross C Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase sigma70 subunit J Mol Biol 1998, 284(5):1353-1365. 10.1006/jmbi.1998.2268 9878355
9. Bentley SD Chater KF Cerdeno-Tarraga AM Challis GL Thomson NR James KD Harris DE Quail MA Kieser H Harper D Bateman A Brown S Chandra G Chen CW Collins M Cronin A Fraser A Goble A Hidalgo J Hornsby T Howarth S Huang CH Kieser T Larke L Murphy L Oliver K O'Neil S Rabbinowitsch E Rajandream MA Rutherford K Rutter S Seeger K Saunders D Sharp S Squares R Squares S Taylor K Warren T Wietzorrek A Woodward J Barrell BG Parkhill J Hopwood DA Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) Nature 2002, 417(6885):141-147. 10.1038/ 417141a 12000953
10. Himmelreich R Hilbert H Plagens H Pirkl E Li BC Herrmann R Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae Nucleic Acids Res 1996, 24(22):4420-4449. 146264 8948633 10.1093/nar/ 24.22.4420
11. Dandekar T Huynen M Regula JT Ueberle B Zimmermann CU Andrade MA Doerks T Sanchez-Pulido L Snel B Suyama M Yuan YP Herrmann R Bork P Re-annotating the Mycoplasma pneumoniae genome sequence: Adding value, function and reading frames Nucleic Acids Res 2000, 28(17):3278-3288. 110705 10954595 10.1093/nar/28.17.3278
12. Lonetto M Gribskov M Gross CA The sigma 70 family: Sequence conservation and evolutionary relationships J Bacteriol 1992, 174(12):3843-3849. 206090 1597408
13. Lavire C Blaha D Cournoyer B Selection of unusual actinomycetal primary sigma 70 factors by plant-colonizing Frankia strains Appl Environ Microbiol 2004, 70(2):991-998. 348808 14766581 10.1128/ AEM.70.2.991-998.2004
14. Maeda H Fujita N Ishihama A Competition among seven Escherichia coli sigma subunits: Relative binding affinities to the core RNA polymerase Nucleic Acids Res 2000, 28(18):3497-3503. 110723 10982868 10.1093/nar/ 28.18.3497
15. Lavenir R Jocktane D Laurent F Nazaret S Cournoyer B Improved reliability of Pseudomonas aeruginosa PCR detection by the use of the species-specific ecfX gene target J Microbiol Methods 2007, 70(1):20-29. 10.1016/j.mimet.2007.03.008 17490767
16. Aguilar C Bertani I Venturi V Quorum-sensing system and stationary-phase sigma factor (rpoS) of the onion pathogen Burkholderia cepacia genomovar I type strain, ATCC 25416 Appl Environ Microbiol 2003, 69(3):1739-1747. 150111 12620866 10.1128/AEM.69.3.1739-1747.2003
17. Subsin B Thomas MS Katzenmeier G Shaw JG Tungpradabkul S Kunakorn M Role of the stationary growth phase sigma factor RpoS of Burkholderia pseudomallei in response to physiological stress conditions J Bacteriol 2003, 185(23):7008-7014. 262693 14617667 10.1128/JB.185.23.7008-7014.2003
18. DeMaio J Zhang Y Ko C Young DB Bishai WR A stationary-phase stress-response sigma factor from Mycobacterium tuberculosis Proc Natl Acad Sci U S A 1996, 93(7):2790-2794. 39711 8610119 10.1073/ pnas.93.7.2790
19. Potuckova L Kelemen GH Findlay KC Lonetto MA Buttner MJ Kormanec J A new RNA polymerase sigma factor, sigma F, is required for the late stages of morphological differentiation in Streptomyces spp Mol Microbiol 1995, 17(1):37-48. 10.1111/j.1365-2958.1995.mmi_17010037.x 7476207
20. Brochier C Bapteste E Moreira D Philippe H Eubacterial phylogeny based on translational apparatus proteins Trends Genet 2002, 18(1):1-5. 10.1016/S0168-9525(01)02522-7 11750686
21. Kim J Kang Y Choi O Jeong Y Jeong JE Lim JY Kim M Moon JS Suga H Hwang I Regulation of polar flagellum genes is mediated by quorum sensing and FlhDC in Burkholderia glumae Mol Microbiol 2007, 64(1):165-179. 10.1111/ j.1365-2958.2007.05646.x 17376080
22. Martin DW Holloway BW Deretic V Characterization of a locus determining the mucoid status of Pseudomonas aeruginosa: AlgU shows sequence similarities with a Bacillus sigma factor J Bacteriol 1993, 175(4):1153-1164. 193032 8432708
23. Devescovi G Venturi V The Burkholderia cepacia rpoE gene is not involved in exopolysaccharide production and onion pathogenicity Can J Microbiol 2006, 52(3):260-265. 10.1139/w05-119 16604122
24. Mahenthiralingam E Simpson DA Speert DP Identification and characterization of a novel DNA marker associated with epidemic Burkholderia cepacia strains recovered from patients with cystic fibrosis J Clin Microbiol 1997, 35(4):808-816. 229681 9157133
25. Kurtz S Phillippy A Delcher AL Smoot M Shumway M Antonescu C Salzberg SL Versatile and open software for comparing large genomes Genome Biol 2004, 5(2):R12. 395750 14759262 10.1186/gb-2004-5-2-r12
26. IS Finder http://www-is.biotoul.fr/
27. Echeita MA Usera MA Chromosomal rearrangements in Salmonella enterica serotype typhi affecting molecular typing in outbreak investigations J Clin Microbiol 1998, 36(7):2123-2126. 104999 9650981
28. Stibitz S Yang MS Genomic plasticity in natural populations of Bordetella pertussis J Bacteriol 1999, 181(17):5512-5515. 94064 10464229
29. Romling U Schmidt KD Tummler B Large genome rearrangements discovered by the detailed analysis of 21 Pseudomonas aeruginosa clone C isolates found in environment and disease habitats J Mol Biol 1997 271 3 386 404 10.1006/jmbi.1997.1186 9268667
30. Hughes D Evaluating genome dynamics: The constraints on rearrangements within bacterial genomes Genome Biol 2000, 1:6. REVIEWS0006 138892 11380986 10.1186/gb-2000-1-6-reviews0006
31. Burger M Woods RG McCarthy C Beacham IR Temperature regulation of protease in Pseudomonas fluorescens LS107d2 by an ECF sigma factor and a transmembrane activator Microbiology 2000, 146(Pt 12):3149-3155. 11101673
32. Agnoli K Lowe CA Farmer KL Husnain SI Thomas MS The ornibactin biosynthesis and transport genes of Burkholderia cenocepacia are regulated by an extracytoplasmic function sigma factor which is a part of the Fur regulon J Bacteriol 2006, 188(10):3631-3644. 1482860 16672617 10.1128/JB.188.10.3631-3644.2006
33. Enz S Mahren S Stroeher UH Braun V Surface signaling in ferric citrate transport gene induction: Interaction of the FecA, FecR, and FecI regulatory proteins J Bacteriol 2000, 182(3):637-646. 94325 10633096 10.1128/JB.182.3.637-646.2000
34. Mahren S Schnell H Braun V Occurrence and regulation of the ferric citrate transport system in Escherichia coli B, Klebsiella pneumoniae, Enterobacter aerogenes, and Photorhabdus luminescens Arch Microbiol 2005, 184(3):175-186. 10.1007/s00203-005-0035-y 16193283
35. Whitby PW Vanwagoner TM Springer JM Morton DJ Seale TW Stull TL Burkholderia cenocepacia utilizes ferritin as an iron source J Med Microbiol 2006, 55(Pt 6):661-668. 10.1099/jmm.0.46199-0 16687582
36. Carver TJ RKM Berriman M, Rajandream MA, Barrell BG, Parkhill J ACT: The Artemis Comparison Tool Bioinformatics 2005, 21:3422-3423. 10.1093/ bioinformatics/bti553 15976072
37. Meyer JM Van VT Stintzi A Berge O Winkelmann G Ornibactin production and transport properties in strains of Burkholderia vietnamiensis and Burkholderia cepacia (formerly Pseudomonas cepacia) Biometals 1995, 8(4):309-317. 10.1007/BF00141604 7580051
38. FramePlot 2.3.2 http://www.nih.go.jp/~jun/cgi-bin/frameplot.pl
39. ORF Finder http://www.ncbi.nlm.nih.gov/gorf/gorf.html
40. Fickett JW Recognition of protein coding regions in DNA sequences Nucleic Acids Res 1982, 10(17):5303-5318. 320873 7145702 10.1093/nar/ 10.17.5303
41. Basic Local Alignment Search Tool http://www.ncbi.nlm.nih.gov/BLAST
42. Marchler-Bauer A Anderson JB Cherukuri PF DeWeese-Scott C Geer LY Gwadz M He S Hurwitz DI Jackson JD Ke Z Lanczycki CJ Liebert CA Liu C Lu F Marchler GH Mullokandov M Shoemaker BA Simonyan V Song JS Thiessen PA Yamashita RA Yin JJ Zhang D Bryant SH CDD: A Conserved Domain Database for protein classification Nucleic Acids Res 2005, 33: Database issue D192-6. 540023 15608175 10.1093/nar/gki069
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. 308517 7984417 10.1093/nar/22.22.4673
44. Kumar S Tamura K Nei M MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment Brief Bioinform 2004, 5(2):150-163. 10.1093/bib/5.2.150 15260895
45. Saitou N Nei M The neighbor-joining method: A new method for reconstructing phylogenetic trees Mol Biol Evol 1987, 4(4):406-425. 3447015
46. HTTP server UMR5557 ECF http://ecomicro.univ-lyon1.fr/poe/ ECF_alignment.fas
47. HTTP server UMR5557 NON ECF http://ecomicro.univ-lyon1.fr/poe/ NON-ECF-alignment.fas
48. Bertani G Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli J Bacteriol 1951, 62(3):293-300. 386127 14888646
49. Pitcher DG Saunders, N.A., Owen, R.J. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate Lett Appl Microbiol 1989, 8:151-156.
50. Sambrook J Fritsch E. F., and Maniatis T. Molecular cloning: A laboratory manual Cold Spring Harbor, N.Y., Cold Spring Harbor Laboratory Press 2nd 1989
51. J. Craig Venter Institute http://www.tigr.org
52. The Joint Genome Institute http://genome.jgi-psf.org/mic_home.html
53. Wellcome Trust Sanger Institute Bacterial Genomes http://www.sanger.ac.uk/Projects/Microbes/
54. Broad Institute http://www.broad.mit.edu
55. Palleroni NJ Holmes B Pseudomonas-cepacia Sp-Nov, Nom-Rev Int J Syst Bacteriol 1981, 31(4):479-481.
56. LiPuma JJ Spilker T Gill LH Campbell PW 3rd Liu L Mahenthiralingam E Disproportionate distribution of Burkholderia cepacia complex species and transmissibility markers in cystic fibrosis Am J Respir Crit Care Med 2001, 164(1):92-96. 11435245
57. Vandamme P Mahenthiralingam E Holmes B Coenye T Hoste B De Vos P Henry D Speert DP Identification and population structure of Burkholderia stabilis sp. nov. (formerly Burkholderia cepacia genomovar IV) J Clin Microbiol 2000, 38(3):1042-1047. 86333 10698993
58. Ramette A LiPuma JJ Tiedje JM Species abundance and diversity of Burkholderia cepacia complex in the environment Appl Environ Microbiol 2005, 71(3):1193-1201. 1065178 15746318 10.1128/AEM.71.3.1193-1201.2005
59. Vandamme P Holmes B Coenye T Goris J Mahenthiralingam E LiPuma JJ Govan JR Burkholderia cenocepacia sp. nov. - a new twist to an old story Res Microbiol 2003, 154(2):91-96. 10.1016/S0923-2508(03)00026-3 12648723
60. Romling U Fiedler B Bosshammer J Grothues D Greipel J von der Hardt H Tummler B Epidemiology of chronic Pseudomonas aeruginosa infections in cystic fibrosis J Infect Dis 1994, 170(6):1616-1621. 7996008
61. Richau JA Leitao JH Correia M Lito L Salgado MJ Barreto C Cescutti P Sa-Correia I Molecular typing and exopolysaccharide biosynthesis of Burkholderia cepacia isolates from a Portuguese cystic fibrosis center J Clin Microbiol 2000, 38(4):1651-1655. 86514 10747161
62. Vandamme P Holmes B Vancanneyt M Coenye T Hoste B Coopman R Revets H Lauwers S Gillis M Kersters K Govan JR Occurrence of multiple genomovars of Burkholderia cepacia in cystic fibrosis patients and proposal of Burkholderia multivorans sp. nov Int J Syst Bacteriol 1997, 47(4):1188-1200. 9336927
63. Gillis M Van Van T Bardin R Goor M Hebbar P Willems A Segers P Kersters K Heulin T Fernandez M Polyphasic taxonomy in the genus Burkholderia leading to an emended description of the genus and proposition of Burkholderia vietnamiensis sp. nov. for N2-fixing isolates from rice in Vietnam Int J Syst Bacteriol 1995, 45:274-289.
64. Menard A Monnez C Estrada de Los Santos P Segonds C Caballero-Mellado J Lipuma JJ Chabanon G Cournoyer B Selection of nitrogen-fixing deficient Burkholderia vietnamiensis strains by cystic fibrosis patients: involvement of nif gene deletions and auxotrophic mutations Environ Microbiol 2007 9 5 1176 1185 10.1111/j.1462-2920.2007.01240.x 17472633
65. Vermis K Coenye T LiPuma JJ Mahenthiralingam E Nelis HJ Vandamme P Proposal to accommodate Burkholderia cepacia genomovar VI as Burkholderia dolosa sp. nov Int J Syst Evol Microbiol 2004, 54(Pt 3):689-691. 10.1099/ijs.0.02888-0 15143009
66. Vandamme P Henry D Coenye T Nzula S Vancanneyt M LiPuma JJ Speert DP Govan JR Mahenthiralingam E Burkholderia anthina sp. nov. and Burkholderia pyrrocinia, two additional Burkholderia cepacia complex bacteria, may confound results of new molecular diagnostic tools FEMS Immunol Med Microbiol 2002, 33(2):143-149. 10.1111/ j.1574-695X.2002.tb00584.x 12052570