A universal operon predictor for prokaryotic genomes

Journal of Bioinformatics and Computational Biology

Volumn 7, Issue 1, 2009, Pages 19-38

  Li, Guojun ^a,b   Che, Dongsheng ^a   Xu, Ying ^a  

^a University of Georgia ^*  (United States)

^b SHANDONG UNIVERSITY   (China)

Author keywords

Bipartite graph matching; Operon; Prokaryotes

Indexed keywords

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENOME; COMPUTER PROGRAM; ESCHERICHIA COLI K 12; GENE CLUSTER; GENE EXPRESSION PROFILING; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC DISTANCE; NONHUMAN; OPERON; PREDICTION; PROKARYOTE; PSEUDOMONAS AERUGINOSA; RHIZOBIUM RADIOBACTER; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; GENOME, ARCHAEAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; OPERON; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

BACILLUS SUBTILIS; ESCHERICHIA COLI; PROKARYOTA;

EID: 65449136663     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720009003984     Document Type: Article

References (55)

1. Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL, Duke K, Kiraly M et al., A global analysis of Caenorhabditis elegans operons, Nature 417 851-854, 2002.
2. Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J, Operons in Escherichia coli: Genomic analyses and predictions, Proc Natl Acad Sci USA 97:6652-6657, 2000.
3. Ermolaeva MD, White O, Salzberg SL, Prediction of operons in microbial genomes, Nucleic Acids Res 29:1216-1221, 2001.
4. Janga SC, Lamboy WF, Huerta AM, Moreno-Hagelsieb G, The distinctive signatures of promoter regions and operon junctions across prokaryotes, Nucleic Acids Res 34:3980-3987, 2006.
5. Chen X, Su Z, Dam P, Palenik B, Xu Y, Jiang T, Operon prediction by comparative genomics: An application to the Synechococcus sp. WH8102 genome, Nucleic Acids Res 32:2147-2157, 2004.
6. Craven M, Page D, Shavlik J, Bockhorst J, Glasner J, A probabilistic learning approach to whole-genome operon prediction, Proc Int Conf Intell Syst Mol Biol 8:116-127, 2000.
7. Price MN, Huang KH, Alm EJ, Arkin AP, A novel method for accurate operon predictions in all sequenced prokaryotes, Nucleic Acids Res 33 880-892, 2005.
8. Chen X, Su Z, Xu Y, Jiang T, Computational prediction of operons in Synechococcus sp. WH8102, Genome Inform Ser Workshop Genome Inform 15:211-222, 2004.
9. Bockhorst J, Craven M, Page D, Shavlik J, Glasner J, A Bayesian network approach to operon prediction, Bioinformatics 19:1227-1235, 2003.
10. Sabatti C, Rohlin L, Oh MK, Liao JC, Co-expression pattern from DNA microarray experiments as a tool for operon prediction, Nucleic Acids Res 30:2886-2893, 2002.
11. Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S, Computational identification of operons in microbial genomes, Genome Res 12 1221-1230, 2002.
12. Jacob E, Sasikumar R, Nair KN, A fuzzy guided genetic algorithm for operon prediction, Bioinformatics 21:1403-1407, 2005.
13. Westover BP, Buhler JD, Sonnenburg JL, Gordon JI, Operon prediction without a training set, Bioinformatics 21:880-888, 2005.
14. Tran TT, Dam P, Su Z, Poole FL, Adams MW, Zhou GT, Xu Y, Operon prediction in Pyrococcus furiosus, Nucleic Acids Res 35 11-20, 2007.
15. Yada T, Nakao M, Totoki Y, Nakai K, Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models, Bioinformatics 15:987-993, 1999.
16. Dam P, Olman V, Harris K, Su Z, Xu Y, Operon prediction using both genome-specific and general genomic information, Nucleic Acids Res 35:288-298, 2007.
17. Edwards MT, Rison SC, Stoker NG, Wernisch L, A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context, Nucleic Acids Res 33:3253-3262, 2005.
18. Salgado H, Gama-Castro S, Martinez-Antonio A, Diaz-Peredo E, Sanchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jimenez-Jacinto V, Santos-Zavaleta A, Bonavides-Martinez C, et al., RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12, Nucleic Acids Res 32:D303-D306, 2004.
19. Okuda S, Katayama T, Kawashima S, Goto S, Kanehisa M, ODB: A database of operons accumulating known operons across multiple genomes, Nucleic Acids Res 34:D358-D362, 2006.
20. Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC et al., The Stanford Microarray Database: Data access and quality assessment tools, Nucleic Acids Res 31:94-96, 2003.
21. Cormen TH, Leiserson CE, Rivest RL, Stein C, Introduction to Algorithms, 2nd ed. MIT Press, Cambridge, Mass, 2001.
22. Bagchi G, Chauhan S, Sharma D, Tyagi JS, Transcription and autoregulation of the Rv3134c-devR-devS operon of Mycobacterium tuberculosis, Microbiology 151:4045-4053, 2005.
23. Rosas-Magallanes V, Deschavanne P, Quintana-Murci L, Brosch R, Gicquel B, Neyrolles O, Horizontal transfer of a virulence operon to the ancestor of Mycobacterium tuberculosis, Mol Biol Evol 23 1129-1135, 2006.
24. Braibant M, Lefevre P, de Wit L, Peirs P, Ooms J, Huygen K, Andersen AB, Content J, A Mycobacterium tuberculosis gene cluster encoding proteins of a phosphate transporter homologous to the Escherichia coli Pst system, Gene 176:171-176, 1996.
25. Casali N, White AM, Riley LW, Regulation of the Mycobacterium tuberculosis mce1 operon, J Bacteriol 188:441-449, 2006.
26. Bischoff M, Entenza JM, Giachino P, Influence of a functional sigB operon on the global regulators sar and agr in Staphylococcus aureus, J Bacteriol 183:5171-5179, 2001.
27. Ouyang S, Sau S, Lee CY, Promoter analysis of the cap8 operon, involved in type 8 capsular polysaccharide production in Staphylococcus aureus, J Bacteriol 181:2492-2500, 1999.
28. Gertz S, Engelmann S, Schmid R, Ziebandt AK, Tischer K, Scharf C, Hacker J, Hecker M, Characterization of the sigma(B) regulon in Staphylococcus aureus, J Bacteriol 182:6983-6991, 2000.
29. Kuroda M, Hayashi H, Ohta T, Chromosome-determined zinc-responsible operon czr in Staphylococcus aureus strain 912, Microbiol Immunol 43:115-125, 1999.
30. Nakao A, Imai S, Takano T, Transposon-mediated insertional mutagenesis of the D-alanyl-lipoteichoic acid (dlt) operon raises methicillin resistance in Staphylococcus aureus, Res Microbiol 151 823-829, 2000.
31. Kopp U, Roos M, Wecke J, Labischinski H, Staphylococcal peptidoglycan interpeptide bridge biosynthesis: A novel antistaphylococcal target? Microb Drug Resist 2:29-41, 1996.
32. Cabrera G, Xiong A, Uebel M, Singh VK, Jayaswal RK, Molecular characterization of the iron-hydroxamate uptake system in Staphylococcus aureus, Appl Environ Microbiol 67:1001-1003, 2001.
33. Kuroda M, Kobayashi D, Honda K, Hayashi H, Ohta T, The hsp operons are repressed by the hrc37 of the hsp70 operon in Staphylococcus aureus, Microbiol Immunol 43:19-27, 1999.
34. Breidt F, Jr, Hengstenberg W, Finkeldei U, Stewart GC, Identification of the genes for the lactose-specific components of the phosphotransferase system in the lac operon of Staphylococcus aureus, J Biol Chem 262:16444-16449, 1987.
35. Masalha M, Borovok I, Schreiber R, Aharonowitz Y, Cohen G, Analysis of transcription of the Staphylococcus aureus aerobic class Ib and anaerobic class III ribonucleotide reductase genes in response to oxygen, J Bacteriol 183:7260-7272, 2001.
36. Glanzmann P, Gustafson J, Komatsuzawa H, Ohta K, Berger-Bachi B, glmM operon and methicillin-resistant glmM suppressor mutants in Staphylococcus aureus, Antimicrob Agents Chemother 43:240-245, 1999.
37. Savopoulos JW, Hibbs M, Jones EJ, Mensah L, Richardson C, Fosberry A, Downes R, Fox SG, Brown JR, Jenkins O, Identification, cloning, and expression of a functional phenylalanyl-tRNA synthetase (pheRS) from Staphylococcus aureus, Protein Expr Purif 21:470-484, 2001.
38. Kies S, Otto M, Vuong C, Gotz F, Identification of the sigB operon in Staphylococcus epidermidis: Construction and characterization of a sigB deletion mutant, Infect Immun 69:7933-7936, 2001.
39. Kullik II, Giachino P, The alternative sigma factor sigmaB in Staphylococcus aureus: Regulation of the sigB operon in response to growth phase and heat shock, Arch Microbiol 167:151-159, 1997.
40. Horsburgh MJ, Ingham E, Foster SJ, In Staphylococcus aureus, fur is an interactive regulator with PerR, contributes to virulence, and is necessary for oxidative stress resistance through positive regulation of catalase and iron homeostasis, J Bacteriol 183:468-475, 2001.
41. Morrissey JA, Cockayne A, Hill PJ, Williams P, Molecular cloning and analysis of a putative siderophore ABC transporter from Staphylococcus aureus, Infect Immun 68:6281-6288, 2000.
42. Hiramatsu T, Kodama K, Kuroda T, Mizushima T, Tsuchiya T, A putative multi-subunit Na+/H+ antiporter from Staphylococcus aureus, J Bacteriol 180:6642-6648, 1998.
43. Groicher KH, Firek BA, Fujimoto DF, Bayles KW, The Staphylococcus aureus lrgAB operon modulates murein hydrolase activity and penicillin tolerance, J Bacteriol 182:1794-1801, 2000.
44. Stranden AM, Roos M, Berger-Bachi B, Glutamine synthetase and heteroresistance in methicillin-resistant Staphylococcus aureus, Microb Drug Resist 2:201-207, 1996.
45. Reed SB, Wesson CA, Liou LE, Trumble WR, Schlievert PM, Bohach GA, Bayles KW, Molecular characterization of a novel Staphylococcus aureus serine protease operon, Infect Immun 69:1521-1527, 2001.
46. Brandenberger M, Tschierske M, Giachino P, Wada A, Berger-Bachi B, Inactivation of a novel three-cistronic operon tcaR-tcaA-tcaB increases teicoplanin resistance in Staphylococcus aureus, Biochim Biophys Acta 1523:135-139, 2000.
47. Laing E, Mersinias V, Smith CP, Hubbard SJ, Analysis of gene expression in operons of Streptomyces coelicolor, Genome Biol 7:R46, 2006.
48. de Hoon MJ, Makita Y, Nakai K, Miyano S, Prediction of transcriptional terminators in Bacillus subtilis and related species, PLoS Computational Biology 1:e25, 2005.
49. Karlin S, Brocchieri L, Campbell A, Cyert M, Mrazek J, Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes, Proc Natl Acad Sci USA 102:7309-7314, 2005.
50. Lecompte O, Ripp R, Thierry JC, Moras D, Poch O, Comparative analysis of ribosomal proteins in complete genomes: An example of reductive evolution at the domain scale, Nucleic Acids Res 30 5382-5390, 2002.
51. Aravind L, Walker DR, Koonin EV, Conserved domains in DNA repair proteins and evolution of repair systems, Nucleic Acids Res 27 1223-1242, 1999.
52. White MF, Archaeal DNA repair: Paradigms and puzzles. Biochem Soc Trans 31:690-693, 2003.
53. Constantinesco F, Forterre P, Koonin EV, Aravind L, Elie C, A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea, Nucleic Acids Res 32:1439-1447, 2004.
54. Bardy SL, Ng SY, Jarrell KF, Recent advances in the structure and assembly of the archaeal flagellum, J Mol Microbiol Biotechnol 7:41-51, 2004.
55. Ng SY, Chaban B, Jarrell KF, Archaeal flagella, bacterial flagella and type IV pili: A comparison of genes and posttranslational modifications, J Mol Microbiol Biotechnol 11:167-191, 2006.