The distinctive signatures of promoter regions and operon junctions across prokaryotes

Nucleic Acids Research

Volumn 34, Issue 14, 2006, Pages 3980-3987

  Janga, Sarath Chandra ^b   Lamboy, Warren F ^c   Huerta, Araceli M ^d   Moreno Hagelsieb, Gabriel ^a  

^a WILFRID LAURIER UNIVERSITY   (Canada)

^b INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

^d DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; DNA DIRECTED RNA POLYMERASE; RNA POLYMERASE SIGMA 70; SIGMA FACTOR;

ACCURACY; ANIMAL CELL; ARTICLE; BACILLUS SUBTILIS; CHLAMYDIA TRACHOMATIS; CONTROLLED STUDY; CORRELATION ANALYSIS; ESCHERICHIA COLI; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC TRANSCRIPTION; HALOBACTERIUM; HELICOBACTER PYLORI; MATHEMATICAL COMPUTING; MICROARRAY ANALYSIS; NONHUMAN; OPERON; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROKARYOTE; PROMOTER REGION; QUALITY CONTROL; SYNECHOCYSTIS; BACTERIAL GENE; BACTERIAL GENOME; BACTERIUM; BIOLOGY; EVALUATION; GENETICS; GENOME; GENOMICS; METABOLISM; METHODOLOGY;

PROKARYOTA;

BACILLUS SUBTILIS; BACTERIA; COMPUTATIONAL BIOLOGY; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; GENE EXPRESSION; GENES, BACTERIAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOMICS; OPERON; PHYLOGENY; PROMOTER REGIONS (GENETICS); SIGMA FACTOR;

EID: 33748569118     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl563     Document Type: Article

References (48)

1. Huerta,A.M. and Collado-Vides,J. (2003) Sigma70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals. J. Mol. Biol., 333, 261-278.
2. Jacob,F., Perrin,D., Sanchez,C. and Monod,J. (1960) [Operon: A group of genes with the expression coordinated by an operator.]. C R Hebd. Seances Acad. Sci., 250, 1727-1729.
3. Jacob,F., Perrin,D., Sanchez,C., Monod,J. and Edelstein,S. (2005) [The operon: A group of genes with expression coordinated by an operator. C.R.Acad. Sci. Paris 250 (1960) 1727-1729]. C. R. Biol., 328, 514-520.
4. Plaskon,R.R. and Wartell,R.M. (1987) Sequence distributions associated with DNA curvature are found upstream of strong E. coli promoters. Nucleic Acids Res., 15, 785-796.
5. Espinosa-Urgel,M. and Tormo,A. (1993) Sigma s-dependent promoters in Escherichia coli are located in DNA regions with intrinsic curvature. Nucleic Acids Res., 21, 3667-3670.
6. Carmona,M. and Magasanik,B. (1996) Activation of transcription at sigma 54-dependent promoters on linear templates requires intrinsic or induced bending of the DNA. J. Mol. Biol., 261, 348-356.
7. Gabrielian,A.E., Landsman,D. and Bolshoy,A. (1999) Curved DNA in promoter sequences. In Silico Biol., 1, 183-196.
8. Bolshoy,A. and Nevo,E. (2000) Ecologic genomics of DNA: Upstream bending in prokaryotic promoters. Genome Res., 10, 1185-1193.
9. Ussery,D., Larsen,T.S., Wilkes,K.T., Friis,C., Worning,P., Krogh,A. and Brunak,S. (2001) Genome organisation and chromatin structure in Escherichia coli. Biochimie, 83, 201-212.
10. Jauregui,R., Abreu-Goodger,C., Moreno-Hagelsieb,G., Collado-Vides,J. and Merino,E. (2003) Conservation of DNA curvature signals in regulatory regions of prokaryotic genes. Nucleic Acids Res., 31,6770-6777.
11. Ussery,D.W., Tindbaek,N. and Hallin,P.F. (2004) Genome update: Promoter profiles. Microbiology, 150, 2791-2793.
12. Olivares-Zavaleta,N., Jauregui,R. and Merino,E. (2006) Genome analysis of Escherichia coli promoter sequences evidences that DNA static curvature plays a more important role in gene transcription than has previously been anticipated. Genomics, 87, 329-337.
13. Pedersen,A.G., Jensen,L.J., Brunak,S., Staerfeldt,H.H. and Ussery,D.W. (2000) A DNA structural atlas for Escherichia coli. J. Mol. Biol., 299, 907-930.
14. Mitchison,G. (2005) The regional rule for bacterial base composition. Trends Genet., 21, 440-443.
15. Moreno-Hagelsieb,G., Trevino,V., Perez-Rueda,E., Smith,T.F. and Collado-Vides,J. (2001) Transcription unit conservation in the three domains of life: A perspective from Escherichia coli. Trends Genet., 17, 175-177.
16. Ermolaeva,M.D., White,O. and Salzberg,S.L. (2001) Prediction of operons in microbial genomes. Nucleic Acids Res., 29, 1216-1221.
17. Janga,S.C. and Moreno-Hagelsieb,G. (2004) Conservation of adjacency as evidence of paralogous operons. Nucleic Acids Res., 32, 5392-5397.
18. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
19. Huerta,A.M., Salgado,H., Thieffry,D. and Collado-Vides,J. (1998) RegulonDB: A database on transcriptional regulation in Escherichia coli. Nucleic Acids Res., 26, 55-59.
20. Salgado,H., Gama-Castro,S., Peralta-Gil,M., Diaz-Peredo,E., Sanchez-Solano,F., Santos-Zavaleta,A., Martinez-Flores,I., Jimenez-Jacinto,V., Bonavides-Martinez,C., Segura-Salazar J. et al. (2006) RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res., 34, D394-D397.
21. Blattner,F.R., Plunkett,G.,3rd, Bloch,C.A., Perna,N.T., Burland,V., Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1474.
22. Moreno-Hagelsieb,G. and Collado-Vides,J. (2002) A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics, 18, S329-S336.
23. Salgado,H., Moreno-Hagelsieb,G., Smith,T.F. and Collado-Vides,J. (2000) Operons in Escherichia coli: Genomic analyses and predictions. Proc. Natl Acad. Sci. USA, 97, 6652-6657.
24. Maglott,D.R., Katz,K.S., Sicotte,H. and Pruitt,K.D. (2000) NCBI's LocusLink and RefSeq. Nucleic Acids Res., 28, 126-128.
25. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2005) NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-D504.
26. Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
27. Huynen,M., Snel,B., Lathe,W.,3rd and Bork,P. (2000) Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res., 10, 1204-1210.
28. Karlin,S., Campbell,A.M. and Mrazek,J. (1998) Comparative DNA analysis across diverse genomes. Annu. Rev. Genet., 32, 185-225.
29. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
30. Gattiker,A., Michoud,K., Rivoire,C., Auchincloss,A.H., Coudert,E., Lima,T., Kersey,P., Pagni,M., Sigrist,C.J., Lachaize,C. et al. (2003) Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem., 27, 49-58.
31. Perez-Rueda,E., Collado-Vides,J. and Segovia,L. (2004) Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput. Biol. Chem., 28, 341-350.
32. Cherry,J.L. (2003) Genome size and operon content. J. Theor. Biol., 221, 401-410.
33. van Nimwegen,E. (2003) Scaling laws in the functional content of genomes. Trends Genet., 19, 479-484.
34. Babu,M.M., Luscombe,N.M., Aravind,L., Gerstein,M. and Teichmann,S.A. (2004) Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol, 14, 283-291.
35. Ranea,J.A., Buchan,D.W., Thornton,J.M. and Orengo,C.A. (2004) Evolution of protein superfamilies and bacterial genome size. J. Mol. Biol., 336, 871-887.
36. Skovgaard,M., Jensen,L.J., Brunak,S., Ussery,D. and Krogh,A. (2001) On the total number of genes and their length distribution in complete microbial genomes. Trends Genet., 17, 425-428.
37. R_Development_Core_Team (2006) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria. ISBN 3-900051-07-0.
38. Ogata,H., Goto,S., Fujibuchi,W. and Kanehisa,M. (1998) Computation with the KEGG pathway database. Biosystems, 47, 119-128.
39. Kanehisa,M., Goto,S., Kawashima,S., Okuno,Y. and Hattori,M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32, D277-D280.
40. Snel,B., Lehmann,G., Bork,P, and Huynen,M.A. (2000) STRING: A web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res., 28, 3442-3444.
41. Prico,M.N., Huang,K.H., Alm,E.J. and Arkin,A.P. (2005) A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res., 33, 880-892.
42. Craven,M., Page,D., Shavlik,J., Bockhorst,J. and Glasner,J. (2000) A probabilistic learning approach to whole-genome operon prediction. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8, 116-127.
43. Bockhorst,J., Qiu,Y., Glasner,J., Liu,M., Blattner,F. and Craven,M. (2003) Predicting bacterial transcription units using sequence and expression data. Bioinformatics, 19, I34-I43.
44. Chen,X., Su,Z., Xu,Y. and Jiang,T. (2004) Computational prediction of operons in Synechococcus sp. WH8102. Genome Inform Ser. Workshop Genome Inform., 15, 211-222.
45. De Hoon,M.J., Imoto,S., Kobayashi,K., Ogasawara,N. and Miyano,S. (2004) Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information. Pac. Symp. Biocomp., 9, 276-287.
46. Romero,P.R. and Karp,P.D. (2004) Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinformatics, 20, 709-717.
47. Jacob,E., Sasikumar,R. and Nair,K.N. (2005) A fuzzy guided genetic algorithm for operon prediction. Bioinformatics, 21, 1403-1407.
48. Westover,B.P., Buhler,J.D., Sonnenburg,J.L. and Gordon,J.I. (2005) Operon prediction without a training set. Bioinformatics, 21, 880-888.