Factors influencing the identification of transcription factor binding sites by cross-species comparison

Genome Research

Volumn 12, Issue 10, 2002, Pages 1523-1532

  McCue, Lee Ann ^a   Thompson, William ^a   Steven Carmack, C ^a   Lawrence, Charles E ^a,b  

^a WADSWORTH CENTER   (United States)

^b RENSSELAER POLYTECHNIC INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ACIDITHIOBACILLUS FERROXIDANS; ARTICLE; BINDING SITE; BUCHNERA; CONTROLLED STUDY; ESCHERICHIA COLI; GENETIC DISTANCE; GRAM NEGATIVE BACTERIUM; HAEMOPHILUS INFLUENZAE; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN FOOTPRINTING; PROTEIN MOTIF; PSEUDOMONAS AERUGINOSA; RANDOMIZATION; SALMONELLA ENTERICA; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SHEWANELLA; SIMULATION; SPECIES DIFFERENCE; SPECIES HABITAT; STATISTICAL ANALYSIS; VIBRIO CHOLERAE; XYLELLA FASTIDIOSA; YERSINIA PESTIS;

BINDING SITES; COMPUTATIONAL BIOLOGY; DNA FOOTPRINTING; GAMMAPROTEOBACTERIA; GENES, BACTERIAL; GENOME, BACTERIAL; GRAM-NEGATIVE BACTERIA; LIKELIHOOD FUNCTIONS; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; TRANSCRIPTION FACTORS;

ACIDITHIOBACILLUS; ACIDITHIOBACILLUS FERROOXIDANS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; GAMMAPROTEOBACTERIA; HAEMOPHILUS; HAEMOPHILUS INFLUENZAE; NEGIBACTERIA; PROTEOBACTERIA; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA; SALMONELLA; SALMONELLA ENTERICA; SHEWANELLA; VIBRIO; VIBRIO CHOLERAE; XYLELLA FASTIDIOSA; YERSINIA; YERSINIA PESTIS;

EID: 0036798220     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.323602     Document Type: Article

References (41)

1. Azam, T.A. and Ishihama, A. 1999. Twelve species of the nucleoid-associated protein from Escherichia coli: Sequence recognition specificity and DNA binding affinity. J. Biol. Chem. 274: 33105-33113.
2. Behr, M.A., Wilson, M.A., Gill, W.P., Salamon, H., Schoolnik, G.K., Rane, S., and Small, P.M. 1999. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284: 1520-1523.
3. Blanchette, M. and Tompa, M. 2002. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12: 739-748.
4. Blanchette, M., Schwikowski, B., and Tompa, M. 2002. Algorithms for phylogenetic footprinting. J. Comput. Biol. 9: 211-223.
5. Cliften, P.F., Hillier, L.W., Fulton, L., Graves,T., Miner, T., Gish, W.R., Waterston, R.H., and Johnston, M. 2001. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 11: 1175-1186.
6. Doolittle, W.F. 1999. Phylogenetic classification and the universal tree. Science 284: 2124-2129.
7. Eisen, J.A. 2000. Assessing evolutionary relationships among microbes from whole-genome analysis. Curr. Opin. Microbiol. 3: 475-480.
8. Fraser, C. 2000. DOE-funded microbial genome sequencing at the Institute for Genomic Research. Human Genome Program, U.S. Department of Energy, Microbial Genome Program Report. http://www.ornl.gov/hgmis/publicat/microbial/index.html.
9. Galperin, M.Y. and Koonin, E.V. 2000. Who's your neighbor?: New computational approaches for functional genomics. Nat. Biotechnol. 18: 609-613.
10. Gelfand, M.S. 1999. Recognition of regulatory sites by genomic comparison. Res. Microbiol. 150: 755-771.
11. Gelfand, M.S., Koonin, E.V., and Mironov, A.A. 2000. Prediction of transcription regulatory sites in archaea by a comparative genomic approach. Nucleic Acids Res. 28: 695-705.
12. Hardison, R.C., Oeltjen, J., and Miller, W. 1997. Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome. Genome Res. 7: 959-966.
13. Heidelberg, J.F., Eisen, J.A., Nelson, W.C., Clayton, R.A., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hickey, E.K., Peterson, J.D., Umayam, L., et al. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406: 477-483.
14. Holmes, I. and Bruno, W.J. 2001. Evolutionary HMMs: A Bayesian approach to multiple alignment. Bioinformatics 17: 803-820.
15. Huynen, M.A. and Bork, P. 1998. Measuring genome evolution. Proc. Natl. Acad. Sci. 95: 5849-5856.
16. Jeon, Y., Lee, Y.S., Han, J.S., Kim, J.B., and Hwang, D.S. 2001. Multimerization of phosphorylated and non-phosphorylated ArcA is necessary for the response regulator function of the Arc two-component signal transduction system. J. Biol. Chem. 276: 40873-40879.
17. Laikova, O.N., Mironov, A.A., and Gelfand, M.S. 2001. Computational analysis of the transcriptional regulation of pentose utilization systems in the γ subdivision of proteobacteria. FEMS Microbiol. Lett. 205: 315-322.
18. Makarova, K.S., Mironov, A.A., and Gelfand, M.S. 2001. Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol. 2: RESEARCH0013.
19. McCue, L., Thompson, W., Carmack, C., Ryan, M.P., Liu, J.S., Derbyshire, V., and Lawrence, C.E. 2001. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29: 774-782.
20. McGuire, A.M., Hughes, J.D., and Church, G.M. 2000. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 10: 744-757.
21. Miller, W. 2000. So many genomes, so little time. Nat. Biotechnol. 18: 148-149.
22. Mironov, A.A., Koonin, E.V., Roytberg, M.A., and Gelfand, M.S. 1999. Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res. 27: 2981-2989.
23. O'Brien, S.J., Menotti-Raymond, M., Murphy, W.J., Nash, W.G., Wienberg, J., Stanyon, R., Copeland, N.G., Jenkins, N.A., Womack, J.E., and Marshall Graves, J.A. 1999. The promise of comparative genomics in mammals. Science 286: 458-462, 479-481.
24. O'Brien, S.J., Eizirik, E., and Murphy, W.J. 2001. Genomics. On choosing mammalian genomes for sequencing. Science 292: 2264-2266.
25. Panina, E.M., Mironov, A.A., and Gelfand, M.S. 2001a. Comparative analysis of FUR regulons in γ-proteobacteria. Nucleic Acids Res. 29: 5195-5206.
26. Panina, E.M., Vitreschak, A.G., Mironov, A.A., and Gelfand, M.S. 2001b. Regulation of aromatic amino acid biosynthesis in γ-proteobacteria. J. Mol. Microbiol. Biotechnol. 3: 529-543.
27. Park, S.M., Lu, C.D., and Abdelal, A.T. 1997a. Cloning and characterization of argR, a gene that participates in regulation of arginine biosynthesis and catabolism in Pseudomonas aeruginosa PAO1. J. Bacteriol. 179: 5300-5308.
28. Park, S.M., Lu, C.D. and Abdelal, A.T. 1997b. Purification and characterization of an arginine regulatory protein, ArgR, from Pseudomonas aeruginosa and its interactions with the control regions for the car, argF, and aru operons. J. Bacteriol. 179: 5309-5317.
29. Parkhill, J., Dougan, G., James, K.D., Thomson, N.R., Pickard, D., Wain, J., Churcher, C., Mungall, K.L., Bentley, S.D., Holden, M.T., et al. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413: 848-852.
30. Pizza, M., Scarlato, V., Masignani, V., Giuliani, M.M., Arico, B., Comanducci, M., Jennings, G.T., Baldi, L., Bartolini, E., Capecchi, B., et al. 2000. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287: 1816-1820.
31. Porcella, S.F. and Schwan, T.G. 2001. Borrelia burgdorferi and Treponema pallidum: A comparison of functional genomics, environmental adaptations, and pathogenic mechanisms. J. Clin. Invest. 107: 651-656.
32. Rajewsky, N., Socci, N.D., Zapotocky, M., and Siggia, E.D. 2002. The evolution of DNA regulatory regions for proteo-γ bacteria by interspecies comparisons. Genome Res. 12: 298-308.
33. Rodionov, D.A., Mironov, A.A., Rakhmaninova, A.B., and Gelfand, M.S. 2000. Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in γ purple bacteria. Mol. Microbiol. 38: 673-683.
34. Rodionov, D.A., Gelfand, M.S., Mironov, A.A., and Rakhmaninova, A.B. 2001a. Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in γ-proteobacteria. J. Mol. Microbiol. Biotechnol. 3: 319-324.
35. Rodionov, D.A., Mironov, A.A., and Gelfand, M.S. 2001b. Transcriptional regulation of pentose utilisation systems in the Bacillusl/Clostridium group of bacteria. FEMS Microbiol. Lett. 205: 305-314.
36. Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y., and Ishikawa, H. 2000. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407: 81-86.
37. Snel, B., Bork, P., and Huynen, M.A. 1999. Genome phylogeny based on gene content. Nat. Genet. 21: 108-110.
38. Tamames, J. 2001. Evolution of gene order conservation in prokaryotes. Genome Biol. 2: RESEARCH0020.
39. Tan, K., Moreno-Hagelsieb, G., Collado-Vides, J., and Stormo, G.D. 2001. A comparative genomics approach to prediction of new members of regulons. Genome Res. 11: 566-584.
40. Terai, G., Takagi, T., and Nakai, K. 2001. Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species. Genome Biol. 2: RESEARCH0048.1.
41. Zhang, Y.M., Marrakchi, H., and Rock, C.O. 2002. The FabR (YijC) transcription factor regulates unsaturated fatty acid biosynthesis in Escherichia coli. J. Biol. Chem. 277: 15558-15565.