Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence

Journal of Bacteriology

Volumn 193, Issue 13, 2011, Pages 3228-3240

  Ravcheev, Dmitry A ^a,b   Best, Aaron A ^c   Tintle, Nathan ^c   DeJongh, Matthew ^c   Osterman, Andrei L ^a   Novichkov, Pavel S ^d   Rodionov, Dmitry A ^a,b  

^a BURNHAM INSTITUTE   (United States)

^b INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^c HOPE COLLEGE   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BACTERIAL GENOME; BACTERIAL VIRULENCE; BINDING SITE; CONTROLLED STUDY; GENE INTERACTION; GENE REGULATORY NETWORK; GENE TARGETING; HOMEOSTASIS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; REGULON; STAPHYLOCOCCUS AUREUS;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, BACTERIAL; GENOMICS; HUMANS; PROTEIN INTERACTION MAPPING; REGULON; STAPHYLOCOCCACEAE; TRANSCRIPTION, GENETIC;

STAPHYLOCOCCACEAE; STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS;

EID: 79959363284     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00350-11     Document Type: Article

References (54)

1. Alkema, W. B., B. Lenhard, and W. W. Wasserman. 2004. Regulog analysis. Detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. Genome Res. 14:1362-1373.
2. Ballal, A., and A. C. Manna. 2009. Expression of the sarA family of genes in different strains of Staphylococcus aureus. Microbiology 155:2342-2352.
3. Barrett, T., et al. 2011. NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res. 39:D1005-D1010.
4. Chang, W., D. A. Small, F. Toghrol, and W. E. Bentley. 2006. Global transcriptome analysis of Staphylococcus aureus response to hydrogen peroxide. J. Bacteriol. 188:1648-1659.
5. Chastanet, A., J. Fert, and T. Msadek. 2003. Comparative genomics reveal novel heat shock regulatory mechanisms in Staphylococcus aureus and other Gram-positive bacteria. Mol. Microbiol. 47:1061-1073.
6. Chen, L., L. Keramati, and J. D. Helmann. 1995. Coordinate regulation of Bacillus subtilis peroxide stress genes by hydrogen peroxide and metal ions. Proc. Natl. Acad. Sci. U. S. A. 92:8190-8194.
7. Cirz, R. T., et al. 2007. Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin. J. Bacteriol. 189:531-539.
8. Dehal, P. S., et al. 2010. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 38:D396-D400.
9. Disz, T., et al. 2010. Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics 11:319.
10. Dunman, P. M., et al. 2004. Uses of Staphylococcus aureus GeneChips in genotyping and genetic composition analysis. J. Clin. Microbiol. 42:4275-4283.
11. Faith, J. J., et al. 2008. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res. 36:D866-D870.
12. Faith, J. J., et al. 2007. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5:e8.
13. Farr, S. B., and T. Kogoma. 1991. Oxidative stress responses in Escherichia coli and Salmonella typhimurium. Microbiol. Rev. 55:561-585.
14. Gelfand, M. S. 2006. Evolution of transcriptional regulatory networks in microbial genomes. Curr. Opin. Struct. Biol. 16:420-429.
15. Giedroc, D. P. 2009. Hydrogen peroxide sensing in Bacillus subtilis: it is all about the (metallo)regulator. Mol. Microbiol. 73:1-4.
16. Grinberg, I., et al. 2009. Functional analysis of the Streptomyces coelicolor NrdR ATP-cone domain: role in nucleotide binding, oligomerization, and DNA interactions. J. Bacteriol. 191:1169-1179.
17. Hecker, M., A. Reder, S. Fuchs, M. Pagels, and S. Engelmann. 2009. Physiological proteomics and stress/starvation responses in Bacillus subtilis and Staphylococcus aureus. Res. Microbiol. 160:245-258.
18. Horsburgh, M. J., M. O. Clements, H. Crossley, E. Ingham, and S. J. Foster. 2001. PerR controls oxidative stress resistance and iron storage proteins and is required for virulence in Staphylococcus aureus. Infect. Immun. 69:3744-3754.
19. Irizarry, R. A., et al. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31:e15.
20. Kazakov, A. E., et al. 2007. RegTransBase-a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 35:D407-D412.
21. Kummerfeld, S. K., and S. A. Teichmann. 2006. DBD: a transcription factor prediction database. Nucleic Acids Res. 34:D74-D81.
22. Layer, G., et al. 2007. SufE transfers sulfur from SufS to SufB for iron-sulfur cluster assembly. J. Biol. Chem. 282:13342-13350.
23. Li, S. J., and J. E. Cronan, Jr. 1993. Growth rate regulation of Escherichia coli acetyl coenzyme A carboxylase, which catalyzes the first committed step of lipid biosynthesis. J. Bacteriol. 175:332-340.
24. Lindsay, J. A., and S. J. Foster. 2001. zur: a Zn(2+)-responsive regulatory element of Staphylococcus aureus. Microbiology 147:1259-1266.
25. Majerczyk, C. D., et al. 2010. Direct targets of CodY in Staphylococcus aureus. J. Bacteriol. 192:2861-2877.
26. Martinez, M. A., et al. 2010. A novel role of malonyl-ACP in lipid homeostasis. Biochemistry 49:3161-3167.
27. Mironov, A. A., N. P. Vinokurova, and M. S. Gel'fand. 2000. Software for analyzing bacterial genomes. Mol. Biol. (Mosk.) 34:253-262.
28. Mostertz, J., C. Scharf, M. Hecker, and G. Homuth. 2004. Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress. Microbiology 150:497-512.
29. Novichkov, P. S., et al. 2010. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 38:D111-D118.
30. Novichkov, P. S., et al. 2010. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 38:W299-W307.
31. Novick, R. P. 2003. Autoinduction and signal transduction in the regulation of staphylococcal virulence. Mol. Microbiol. 48:1429-1449.
32. Novick, R. P., et al. 1995. The agr P2 operon: an autocatalytic sensory transduction system in Staphylococcus aureus. Mol. Gen. Genet. 248:446-458.
33. Osterman, A., and R. Overbeek. 2003. Missing genes in metabolic pathways: a comparative genomics approach. Curr. Opin. Chem. Biol. 7:238-251.
34. Overbeek, R., et al. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33:5691-5702.
35. Pagels, M., et al. 2010. Redox sensing by a Rex-family repressor is involved in the regulation of anaerobic gene expression in Staphylococcus aureus. Mol. Microbiol. 76:1142-1161.
36. Parkinson, H., et al. 2011. ArrayExpress update-an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res. 39:D1002-D1004.
37. Peng, H. L., R. P. Novick, B. Kreiswirth, J. Kornblum, and P. Schlievert. 1988. Cloning, characterization, and sequencing of an accessory gene regulator (agr) in Staphylococcus aureus. J. Bacteriol. 170:4365-4372.
38. Pohl, K., et al. 2009. CodY in Staphylococcus aureus: a regulatory link between metabolism and virulence gene expression. J. Bacteriol. 191:2953-2963.
39. Reiss, D. J., N. S. Baliga, and R. Bonneau. 2006. Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics 7:280.
40. Rodionov, D. A. 2007. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem. Rev. 107:3467-3497.
41. Rodionov, D. A., et al. 2010. Genomic encyclopedia of sugar utilization pathways in the Shewanella genus. BMC Genomics 11:494.
42. Saini, A., D. T. Mapolelo, H. K. Chahal, M. K. Johnson, and F. W. Outten. 2010. SufD and SufC ATPase activity are required for iron acquisition during in vivo Fe-S cluster formation on SufB. Biochemistry 49:9402-9412.
43. Schmid, A. K., M. Pan, K. Sharma, and N. S. Baliga. 2011. Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res. 39:2519-2533.
44. Schujman, G. E., et al. 2006. Structural basis of lipid biosynthesis regulation in Gram-positive bacteria. EMBO J. 25:4074-4083.
45. Schujman, G. E., L. Paoletti, A. D. Grossman, and D. de Mendoza. 2003. FapR, a bacterial transcription factor involved in global regulation of membrane lipid biosynthesis. Dev. Cell 4:663-672.
46. Seidl, K., et al. 2009. Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus. BMC Microbiol. 9:95.
47. Semchyshyn, H., T. Bagnyukova, K. Storey, and V. Lushchak. 2005. Hydrogen peroxide increases the activities of soxRS regulon enzymes and the levels of oxidized proteins and lipids in Escherichia coli. Cell Biol. Int. 29:898-902.
48. Sierro, N., Y. Makita, M. de Hoon, and K. Nakai. 2008. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 36:D93-D96.
49. Somerville, G. A., and R. A. Proctor. 2009. At the crossroads of bacterial metabolism and virulence factor synthesis in staphylococci. Microbiol. Mol. Biol. Rev. 73:233-248.
50. Soutourina, O., et al. 2009. CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulphur source utilization and plays a role in biofilm formation. Mol. Microbiol. 73:194-211.
51. Torrents, E., et al. 2007. NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. J. Bacteriol. 189:5012-5021.
52. Torres, V. J., et al. 2010. Staphylococcus aureus Fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia. Infect. Immun. 78:1618-1628.
53. Wollers, S., et al. 2010. Iron-sulfur (Fe-S) cluster assembly: the SufBCD complex is a new type of Fe-S scaffold with a flavin redox cofactor. J. Biol. Chem. 285:23331-23341.
54. Zhang, Y. M., and C. O. Rock. 2009. Transcriptional regulation in bacterial membrane lipid synthesis. J. Lipid Res. 50(Suppl.):S115-S119.