Genome-wide analysis of chlamydiae for promoters that phylogenetically footprint

Research in Microbiology

Volumn 158, Issue 8-9, 2007, Pages 685-693

  Grech, Brian ^a   Maetschke, Stefan ^a   Mathews, Sarah ^a   Timms, Peter ^a  

^a QUEENSLAND UNIVERSITY OF TECHNOLOGY   (Australia)

Author keywords

Bioinformatics; Chlamydia; Phylogenetic footprinting; Promoter

Indexed keywords

ARTICLE; BACTERIAL GENOME; BIOINFORMATICS; CHLAMYDIA TRACHOMATIS; CHLAMYDIACEAE; DNA FOOTPRINTING; GENE MAPPING; GENETIC CODE; GENOME ANALYSIS; METHODOLOGY; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION;

BASE SEQUENCE; CHLAMYDIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROMOTER REGIONS (GENETICS); TRANSCRIPTION INITIATION SITE;

BACTERIA (MICROORGANISMS); CHLAMYDIA; CHLAMYDIA TRACHOMATIS; CHLAMYDIAE;

EID: 36749044857     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2007.08.005     Document Type: Article

References (35)

1. Azuma Y., Hirakawa H., Yamashita A., Cai Y., Rahman M.A., Suzuki H., Mitaku S., Toh H., Goto S., Murakami T., Sugi K., Hayashi H., Fukushi H., Hattori M., Kuhara S., and Shirai M. Genome sequence of the cat pathogen, Chlamydophila felis. DNA Res. 13 (2006) 15-23
2. Belland R.J., Zhong G., Crane D.D., Hogan D., Sturdevant D., Sharma J., Beatty W.L., and Caldwell H.D. Genomic transcriptional profiling of the developmental cycle of Chlamydia trachomatis. Proc. Natl. Acad. Sci. USA 100 (2003) 8478-8483
3. Berg O.G., and von Hippel P.H. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193 (1987) 723-750
4. Carlson J.H., Porcella S.F., McClarty G., and Caldwell H.D. Comparative genomic analysis of Chlamydia trachomatis oculotropic and genitotropic strains. Infect. Immun. 73 (2005) 6407-6418
5. Eskin E., Keich U., Gelfand M.S., and Pevzner P.A. Genome-wide analysis of bacterial promoter regions. Pac. Symp. Biocomput. (2003) 29-40
6. Gelfand M.S. Recognition of regulatory sites by genomic comparison. Res. Microbiol. 150 (1999) 755-771
7. Gelfand M.S., Koonin E.V., and Mironov A.A. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res. 28 (2000) 695-705
8. Gelfand M.S., Novichkov P.S., Novichkova E.S., and Mironov A.A. Comparative analysis of regulatory patterns in bacterial genomes. Brief Bioinform. 1 (2000) 357-371
9. Geng M.M., Schuhmacher A., Muehldorfer I., Bensch K.W., Schaefer K.P., Schneider S., Pohl T., Essig A., Marre R., and Melchers K. The Genome Sequence of Chlamydia pneumoniae TW183 and Comparison with Other Chlamydia Strains Based on Whole Genome Sequence Analysis (2003), Byk Gulden Pharmaceuticals
10. Gershenzon N.I., Stormo G.D., and Ioshikhes I.P. Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Res. 33 (2005) 2290-2301
11. Gordon J.J., Towsey M.W., Hogan J.M., Mathews S.A., and Timms P. Improved prediction of bacterial transcription start sites. Bioinformatics 22 (2006) 142-148
12. Harley C.B., and Reynolds R.P. Analysis of E. coli promoter sequences. Nucleic Acids Res. 15 (1987) 2343-2361
13. Kalman S., Mitchell W., Marathe R., Lammel C., Fan J., Hyman R.W., Olinger L., Grimwood J., Davis R.W., and Stephens R.S. Comparative genomes of Chlamydia pneumoniae and Chlamydia trachomatis. Nat. Genet. 21 (1999) 385-389
14. Koehler J.E., Burgess R.R., Thompson N.E., and Stephens R.S. Chlamydia trachomatis RNA polymerase major sigma subunit. Sequence and structural comparison of conserved and unique regions with Escherichia coli sigma-70 and Bacillus subtilis sigma-43. J. Biol. Chem. 265 (1990) 13206-13214
15. Lambden P.R., Everson J.S., Ward M.E., and Clarke I.N. Sulfur-rich proteins of Chlamydia trachomatis: developmentally regulated transcription of polycistronic mRNA from tandem promoters. Gene 87 (1990) 105-112
16. Lee P.S., and Lee K.H. Genomic analysis. Curr. Opin. Biotechnol. 11 (2000) 171-175
17. Lisser S., and Margalit H. Compilation of E. coli mRNA promoter sequences. Nucleic Acids Res. 21 (1993) 1507-1516
18. Lonetto M., Gribskov M., and Gross C.A. The sigma-70 family: sequence conservation and evolutionary relationships. J. Bacteriol. 174 (1992) 3843-3849
19. Mathews S.A., and Timms P. Identification and mapping of sigma-54 promoters in Chlamydia trachomatis. J. Bacteriol. 182 (2000) 6239-6242
20. Mathews S.A., and Timms P. In silico identification of chlamydial promoters and their role in regulation and development. In: Bavoil P.M., and Wyrick P.B. (Eds). Chlamydia: Genomics and Pathogenesis, Horizon Bioscience (2006) 133-156
21. Read T.D., Brunham R.C., Shen C., Gill S.R., Heidelberg J.F., White O., Hickey E.K., 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 S.L., Eisen J., and Fraser C.M. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 28 (2000) 1397-1406
22. Read T.D., Myers G.S., Brunham R.C., Nelson W.C., Paulsen I.T., Heidelberg J., Holtzapple E., Khouri H., Federova N.B., Carty H.A., Umayam L.A., Haft D.H., Peterson J., Beanan M.J., White O., Salzberg S.L., Hsia R.C., McClarty G., Rank R.G., Bavoil P.M., and Fraser C.M. Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic Acids Res. 31 (2003) 2134-2147
23. Sardinia L.M., Engel J.N., and Ganem D. Chlamydial gene encoding a 70-kilodalton antigen in Escherichia coli: analysis of expression signals and identification of the gene product. J. Bacteriol. 171 (1989) 335-341
24. Schneider T.D., Stormo G.D., Gold L., and Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188 (1986) 415-431
25. Shen L., Shi Y., Douglas A.L., Hatch T.P., O'Connell C.M., Chen J.M., and Zhang Y.X. Identification and characterization of promoters regulating tuf expression in Chlamydia trachomatis serovar F. Arch. Biochem. Biophys. 379 (2000) 46-56
26. Shirai M., Hirakawa H., Kimoto M., Tabuchi M., Kishi F., Ouchi K., Shiba T., Ishii K., Hattori M., Kuhara S., and Nakazawa T. Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA. Nucleic Acids Res. 28 (2000) 2311-2314
27. Stephens R.S., Kalman S., Lammel C., Fan J., Marathe R., Aravind L., Mitchell W., Olinger L., Tatusov R.L., Zhao Q., Koonin E.V., and Davis R.W. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282 (1998) 754-759
28. Stormo G.D. DNA binding sites: representation and discovery. Bioinformatics 16 (2000) 16-23
29. Stormo G.D., and Hartzell G.W. Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. USA 86 (1989) 1183-1187
30. Tan M., Gaal T., Gourse R.L., and Engel J.N. Mutational analysis of the Chlamydia trachomatis rRNA P1 promoter defines four regions important for transcription in vitro. J. Bacteriol. 180 (1998) 2359-2366
31. Tan M., Wong B., and Engel J.N. Transcriptional organization and regulation of the dnaK and groE operons of Chlamydia trachomatis. J. Bacteriol. 178 (1996) 6983-6990
32. Thomson N.R., Yeats C., Bell K., Holden M.T., Bentley S.D., Livingstone M., Cerdeno-Tarraga A.M., Harris B., Doggett J., Ormond D., Mungall K., Clarke K., Feltwell T., Hance Z., Sanders M., Quail M.A., Price C., Barrell B.G., Parkhill J., and Longbottom D. The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation. Genome Res. 15 (2005) 629-640
33. van Helden J. Regulatory sequence analysis tools. Nucleic Acids Res. 31 (2003) 3593-3596
34. Wels M., Francke C., Kerkhoven R., Kleerebezem M., and Siezen R.J. Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res. 34 (2006) 1947-1958
35. Wichlan D.G., and Hatch T.P. Identification of an early-stage gene of Chlamydia psittaci 6BC. J. Bacteriol. 175 (1993) 2936-2942