BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Griffiths, Emma ^a   Ventresca, Michael S ^a   Gupta, Radhey S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; BIOLOGICAL MARKER;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL INFECTION; BACTERIAL STRAIN; CHLAMYDIA; CHLAMYDIACEAE; CHLAMYDOPHILA; CONTROLLED STUDY; GENE LOCUS; GENE LOSS; GENE TRANSFER; GENETIC CONSERVATION; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PATHOGENICITY; PREVALENCE; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTOCHLAMYDIA AMOEBOPHILA; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; UNINDEXED SEQUENCE; ALGORITHM; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETICS; GENOME; METHODOLOGY;

BACTERIA (MICROORGANISMS); CHLAMYDIA; CHLAMYDIACEAE; CHLAMYDIAE; CHLAMYDIALES; CHLAMYDOPHILA;

ALGORITHMS; CHLAMYDIA; CHLAMYDIACEAE; CHLAMYDIALES; CHLAMYDOPHILA; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENOME; SEQUENCE ANALYSIS, DNA; SOFTWARE; SPECIES SPECIFICITY;

EID: 33645017409     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-14     Document Type: Article

References (79)

1. Kalayoglu MV, Byrne GI: Chlamydia. In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, 3rd edition, release 3.7, http://link.springer-ny.com/link/service/books/10125/. 3rd edition. Edited by: Dworkin M. New York, Springer-Verlag; 2001.
2. Everett KD, Bush RM, Andersen AA: Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms. Int J Syst Bacteriol 1999, 49 Pt 2:415-440.
3. Rurangirwa FR, Dilbeck PM, Crawford TB, McGuire TC, McElwain TF: Analysis of the 16S rRNA gene of micro-organism WSU 86-1044 from an aborted bovine foetus reveals that it is a member of the order Chlamydiales: proposal of Waddliaceae fam. nov., Waddlia chondrophila gen. nov., sp. nov. Int J Syst Bacteriol 1999, 49 Pt 2:577-581.
4. Everett KD: Chlamydia and Chlamydiales: more than meets the eye. Vet Microbiol 2000, 75:109-126.
5. Kahane S, Greenberg D, Friedman MG, Haikin H, Dagan R: High prevalence of "Simkania Z," a novel Chlamydia-like bacterium, in infants with acute bronchiolitis. J Infect Dis 1998, 177:1425-1429.
6. Horn M, Wagner M, Muller KD, Schmid EN, Fritsche TR, Schleifer KH, Michel R: Neochlamydia hartmannellae gen. nov., sp. nov. (Parachlamydiaceae), an endoparasite of the amoeba Hartmannella vermiformis. Microbiology 2000, 146 (Pt 5):1231-1239.
7. Corsaro D, Venditti D: Emerging chlamydial infections. Crit Rev Microbiol 2004, 30:75-106.
8. Corsaro D, Valassina M, Venditti D: Increasing diversity within Chlamydiae. Crit Rev Microbiol 2003, 29:37-78.
9. Horn M, Wagner M: Evidence for additional genus-level diversity of Chlamydiales in the environment. FEMS Microbiol Lett 2001, 204:71-74.
10. Fritsche TR, Horn M, Wagner M, Herwig RP, Schleifer KH, Gautom RK: Phylogenetic diversity among geographically dispersed Chlamydiales endosymbionts recovered from clinical and environmental isolates of Acanthamoeba spp. Appl Environ Microbiol 2000, 66:2613-2619.
11. Horn M, Collingro A, Schmitz-Esser S, Beier CL, Purkhold U, Fartmann B, Brandt P, Nyakatura GJ, Droege M, Frishman D, Rattei T, Mewes HW, Wagner M: Illuminating the evolutionary history of chlamydiae. Science 2004, 304:728-730.
12. Greub G, Raoult D: Parachlamydiaceae: potential emerging pathogens. Emerg Infect Dis 2002, 8:625-630.
13. Stephens RS, Kalman S, Lammel C, Fan J, Marathe R, Aravind L, Mitchell W, Olinger L, Tatusov RL, Zhao Q, Koonin EV, Davis RW: Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 1998, 282:754-759.
14. Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, DeBoy R, Kolonay J, McClarty G, Salzberg SL, Eisen J, Fraser CM: Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res 2000, 28:1397-1406.
15. Read TD, Myers GS, Brunham RC, Nelson WC, Paulsen IT, Heidelberg J, Holtzapple E, Khouri H, Federova NB, Carty HA, Umayam LA, Haft DH, Peterson J, Beanan MJ, White O, Salzberg SL, Hsia RC, McClarty G, Rank RG, Bavoil PM, Fraser CM: Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic Acids Res 2003, 31:2134-2147.
16. Thomson NR, Yeats C, Bell K, Holden MT, Bentley SD, Livingstone M, Cerdeno-Tarraga AM, Harris B, Doggett J, Ormond D, Mungall K, Clarke K, Feltwell T, Hance Z, Sanders M, Quail MA, Price C, Barrell BG, Parkhill J, Longbottom D: The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation. Genome Res 2005, 15:629-640.
17. Collingro A, Toenshoff ER, Taylor MW, Fritsche TR, Wagner M, Horn M: 'Candidatus Protochlamydia amoebophila', an endosmbiont of Acanthamoeba spp. Int J Syst Evol Microbiol 2005, 55:1863-1866.
18. Kalman S, Mitchell W, Marathe R, Lammel C, Fan J, Hyman RW, Olinger L, Grimwood J, Davis RW, Stephens RS: Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat Genet 1999, 21:385-389.
19. Griffiths E, Gupta RS: Protein signatures distinctive of chlamydial species: horizontal transfers of cell wall biosynthesis genes glmU from archaea to chlamydiae and murA between chlamydiae and Streptomyces. Microbiology 2002, 148:2541-2549.
20. Gupta RS: Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 1998, 62:1435-1491.
21. Gupta RS: Protein signatures distinctive of Alpha proteobacteria and its subgroups and a model for Alpha proteobacterial evolution. Crit Rev Microbiol 2005, 31:135.
22. Gupta RS, Griffiths E: Critical issues in bacterial phylogeny. Theor Popul Biol 2002, 61:423-434.
23. Griffiths E, Gupta RS: The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga-Flavobacterium-Bacteroides division. Microbiology 2001, 147:2611-2622.
24. Gupta Lab's Bacterial Phylogeny Website: http://www.bacterialphylogeny.com. http://www bacterialphylogeny com 2005.
25. Griffiths E, Petrich A, Gupta RS: Conserved Indels in Essential Proteins that are Distinctive Characteristics of Chlamydiales and provide novel means for their identification. Microbiology 2005, 151:2647-2657.
26. Doerks T, von Mering C, Bork P: Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucleic Acids Res 2004, 32:6321-6326.
27. Koehler JE, Birkelund S, Stephens RS: Overexpression and surface localization of the Chlamydia trachomatis major outer membrane protein in Escherichia coli. Mol Microbiol 1992, 6:1087-1094.
28. Everett KD, Hatch TP: Architecture of the cell envelope of Chlamydia psittaci 6BC. J Bacteriol 1995, 177:877-882.
29. Hatch TP: Disulfide cross-linked envelope proteins: the functional equivalent of peptidoglycan in chlamydiae? J Bacteriol 1996, 178:1-5.
30. Weisburg WG, Hatch TP, Woese CR: Eubacterial origin of chlamydiae. J Bacteriol 1986, 167:570-574.
31. Staley JT, Fuerst JA, Giovannoni S, Schlesner H: The order Planctomycetales and the genera Planctomyces, Pirellula, Gemmata and Isosphaera. In The Prokaryotes Volume I. 2nd edition. Edited by: Balows A, Truper HG, Dworkin M, Harder W and Schleifer KH. New York, Springer-Verlag; 1992:3710-3731.
32. Ward NL, Rainey FA, Hedlund BP, Staley JT, Ludwig W, Stackebrandt E: Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny. International Journal of Systematic Bacteriology 2000, 50:1965-1972.
33. Bateman A, Bycroft M: The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MItD). J Mol Biol 2000, 299:1113-1119.
34. Ghuysen JM, Goffin C: Lack of cell wall peptidoglycan versus penicillin sensitivity: new insights into the chlamydial anomaly. Antimicrob Agents Chemother 1999, 43:2339-2344.
35. Fox A, Rogers JC, Gilbart J, Morgan S, Davis CH, Knight S, Wyrick PB: Muramic acid is not detectable in Chlamydia psittaci or Chlamydia trachomatis by gas chromatography-mass spectrometry. Infect Immun 1990, 58:835-837.
36. Vandahl BB, Birkelund S, Christiansen G: Genome and proteome analysis of Chlamydia. Proteomics 2004, 4:2831-2842.
37. Fields KA, Mead DJ, Dooley CA, Hackstadt T: Chlamydia trachomatis type III secretion: evidence for a functional apparatus during early-cycle development. Mol Microbiol 2003, 48:671-683.
38. Rockey DD, Lenart J, Stephens RS: Genome sequencing and our understanding of chlamydiae. Infect Immun 2000, 68:5473-5479.
39. Hatch T: Chlamydia: old ideas crushed, new mysteries bared. Science 1998, 282:638-639.
40. NCBI Conserved Domain (YjgP_YjgQ) Website: http:// www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid= pfam03739&version=v2.03. 2006.
41. Ceccarelli EA, Arakaki AK, Cortez N, Carrillo N: Functional plasticity and catalytic efficiency in plant and bacterial ferredoxin-NADP(H) reductases. Biochim Biophys Acta 2004, 1698:155-165.
42. Kaul R, Hoang A, Yau P, Bradbury EM, Wenman WM: The chlamydial EUO gene encodes a histone HI-specific protease. J Bacteriol 1997, 179:5928-5934.
43. Zhang L, Douglas AL, Hatch TP: Characterization of a Chlamydia psittaci DNA binding protein (EUO) synthesized during the early and middle phases of the developmental cycle. Infect Immun 1998, 66:1167-1173.
44. Barry CEIII, Brickman TJ, Hackstadt T: Hcl-mediated effects on DNA structure: a potential regulator of chlamydial development. Mol Microbiol 1993, 9:273-283.
45. Thomas NS, Lusher M, Storey CC, Clarke IN: Plasmid diversity in Chlamydia. Microbiology 1997, 143 (Pt 6):1847-1854.
46. Comanducci M, Ricci S, Cevenini R, Ratti G: Diversity of the Chlamydia trachomatis common plasmid in biovars with different pathogenicity. Plasmid 1990, 23:149-154.
47. Fahr MJ, Douglas AL, Xia W, Hatch TP: Characterization of late gene promoters of Chlamydia trachomatis. J Bacteriol 1995, 177:4252-4260.
48. Tanzer RJ, Hatch TP: Characterization of outer membrane proteins in Chlamydia trachomatis LGV serovar L2. J Bacteriol 2001, 183:2686-2690.
49. Kaltenboeck B, Kousoulas KG, Storz J: Structures of and allelic diversity and relationships among the major outer membrane protein (ompA) genes of the four chlamydial species. J Bacteriol 1993, 175:487-502.
50. Starnbach MN, Loomis WP, Ovendale P, Regan D, Hess B, Alderson MR, Fling SP: An inclusion membrane protein from Chlamydia trachomatis enters the MHC class I pathway and stimulates a CD8+ T cell response. J Immunol 2003, 171:4742-4749.
51. Kawa DE, Schachter J, Stephens RS: Immune response to the Chlamydia trachomatis outer membrane protein PorB. Vaccine 2004, 22:4282-4286.
52. Rockey DD, Scidmore MA, Bannantine JP, Brown WJ: Proteins in the chlamydial inclusion membrane. Microbes Infect 2002, 4:333-340.
53. Hackstadt T, Fischer ER, Scidmore MA, Rockey DD, Heinzen RA: Origins and functions of the chlamydial inclusion. Trends Microbiol 1997, 5:288-293.
54. Bannantine JP, Rockey DD, Hackstadt T: Tandem genes of Chlamydia psittaci that encode proteins localized to the inclusion membrane. Mol Microbiol 1998, 28:1017-1026.
55. Sappington TW, Raikhel AS: Ligand-binding domains in vitellogenin receptors and other LDL-receptor family members share a common ancestral ordering of cysteine-rich repeats. J Mol Evol 1998, 46:476-487.
56. Scidmore-Carlson MA, Shaw EI, Dooley CA, Fischer ER, Hackstadt T: Identification and characterization of a Chlamydia trachomatis early operon encoding four novel inclusion membrane proteins. Mol Microbiol 1999, 33:753-765.
57. Bush RM, Everett KD: Molecular evolution of the Chlamydiaceae. Int J Syst Evol Microbiol 2001, 51:203-220.
58. Garner SA, Everson JS, Lambden PR, Fane BA, Clarke IN: Isolation, molecular characterisation and genome sequence of a bacteriophage (Chp3) from Chlamydophila pecorum. Virus Genes 2004, 28:207-214.
59. Brinkman FS, Blanchard JL, Cherkasov A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BF, Keeling PJ, Rose AM, Hancock RE, Jones SJ, Greberg H: Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Genome Res 2002, 12:1159-1167.
60. Greub G, Raoult D: History of the ADP/ATP-translocase-encoding gene, a parasitism gene transferred from a Chlamydiales ancestor to plants 1 billion years ago. Appl Environ Microbiol 2003, 69:5530-5535.
61. Zhong J, Douglas AL, Hatch TP: Characterization of integration host factor (IHF) binding upstream of the cysteine-rich protein operon (omcAB) promoter of Chlamydia trachomatis LGV serovar L2. Mol Microbiol 2001, 41:451-462.
62. Newhall WJ: Biosynthesis and disulfide cross-linking of outer membrane components during the growth cycle of Chlamydia trachomatis. Infect Immun 1987, 55:162-168.
63. Nicholson TL, Olinger L, Chong K, Schoolnik G, Stephens RS: Global stage-specific gene regulation during the developmental cycle of Chlamydia trachomatis. J Bacteriol 2003, 185:3179-3189.
64. Daubin V, Ochman H: Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res 2004, 14:1036-1042.
65. Kainth P, Gupta RS: Signature proteins that are distinctive of alpha proteabacteria. BMC Genomics 2005, 6:94.
66. Siew N, Fischer D: Twenty thousand ORFan microbial protein families for the biologist? Structure (Camb) 2003, 11:7-9.
67. Daubin V, Lerat E, Perriere G: The source of laterally transferred genes in bacterial genomes. Genome Biol 2003, 4:R57.
68. Lerat E, Daubin V, Ochman H, Moran NA: Evolutionary Origins of Genomic Repertoires in Bacteria. PLoS Biol 2005, 3:e130.
69. Frost LS, Leplae R, Summers AO, Toussaint A: Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005, 3:722-732.
70. Suyama M, Bork P: Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends Genet 2001, 17:10-13.
71. Everett KD, Hornung LJ, Andersen AA: Rapid detection of the Chlamydiaceae and other families in the order Chlamydiales: three PCR tests. J Clin Microbiol 1999, 37:575-580.
72. Sachse K, Grossmann E, Jager C, Diller R, Hotzel H: Detection of Chlamydia suis from clinical specimens: comparison of PCR, antigen ELISA, and culture. J Microbiol Methods 2003, 54:233-238.
73. Mardh PA: Chlamydia screening-yes, but of whom, when, by whom, and with what? Ann N Y Acad Sci 2000, 900:286-292.
74. Watson EJ, Templeton A, Russell I, Paavonen J, Mardh PA, Stary A, Pederson BS: The accuracy and efficacy of screening tests for Chlamydia trachomatis: a systematic review. J Med Microbiol 2002, 51:1021-1031.
75. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein databases search programs. Nucleic Acids Research 1997, 25:3389-3402.
76. Koski LB, Golding GB: The closest BLAST hit is often not the nearest neighbor. J Mol Evol 2001, 52:540-542.
77. National Center for Biotechnology Information (NCBI) Website [http://www.ncbi.nlm.nih.gov/]. 2005.
78. 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, 22:4673-4680.
79. Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 1992, 89:10915-10919.