Transcription factor family-based reconstruction of singletonregulons and Study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes

Journal of Bacteriology

Volumn 195, Issue 1, 2013, Pages 29-38

  Kazakov, Alexey E ^a,b   Rodionov, Dmitry A ^b,c   Price, Morgan N ^a   Arkin, Adam P ^a   Dubchak, Inna ^a   Novichkov, Pavel S ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^c BURNHAM INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ARSR; TRANSCRIPTION FACTOR CRP; TRANSCRIPTION FACTOR FNR; TRANSCRIPTION FACTOR GNTR; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENOME; BINDING SITE; DESULFOVIBRIONALES; ENZYME BINDING; GENETIC CONSERVATION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN MOTIF; REGULATOR GENE; REGULON; SPECIES DISTRIBUTION; TRANSCRIPTION REGULATION;

AMINO ACID MOTIFS; BACTERIAL PROTEINS; BASE SEQUENCE; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; MULTIGENE FAMILY; PHYLOGENY; PROTEIN BINDING; REGULON; SULFUR-REDUCING BACTERIA; TRANSCRIPTION FACTORS;

DESULFOVIBRIONALES;

EID: 84872011384     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01977-12     Document Type: Article

References (30)

1. Ravcheev DA, Best AA, Tintle N, Dejongh M, Osterman AL, Novichkov PS, Rodionov DA. 2011. Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics- based evidence. J. Bacteriol. 193:3228-3240.
2. Rodionov DA. 2007. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem. Rev. 107:3467-3497.
3. Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin AP, Dubchak I, Osterman AL, Gelfand MS. 2011. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics 12(Suppl. 1):S3. doi:10.1186/1471-2164-12-S1-S3.
4. Mironov AA, Koonin EV, Roytberg MA, Gelfand MS. 1999. Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res. 27:2981-2989.
5. Alkema WB, Lenhard B, Wasserman WW. 2004. Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. Genome Res. 14:1362-1373.
6. Price MN, Dehal PS, Arkin AP. 2008. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol. 9:R4. doi:10.1186/gb-2008-9-1-r4.
7. Treangen TJ, Rocha EP. 2011. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet. 7:e1001284. doi:10.1371/journal.pgen.1001284.
8. Sandelin A, Wasserman WW. 2004. Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol. 338:207-215.
9. Hertz GZ, Hartzell GW III, Stormo GD. 1990. Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci. 6:81-92.
10. Kechris KJ, van Zwet E, Bickel PJ, Eisen MB. 2004. Detecting DNA regulatory motifs by incorporating positional trends in information content. Genome Biol. 5:R50. doi:10.1186/gb-2004-5-7-r50.
11. Liu X, Brutlag DL, Liu JS. 2001. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 2001:127-138.
12. Hershberg R, Yeger-Lotem E, Margalit H. 2005. Chromosomal organization is shaped by the transcription regulatory network. Trends Genet. 21:138-142.
13. Sahota G, Stormo GD. 2010. Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. Bioinformatics 26:2672-2677.
14. Gavrilescu M, Pavel LV, Cretescu I. 2009. Characterization and remediation of soils contaminated with uranium. J. Hazard. Mater. 163:475-510.
15. Hansen TA. 1994. Metabolism of sulfate-reducing prokaryotes. Antonie Van Leeuwenhoek 66:165-185.
16. Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP. 2010. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 38(Suppl 1):D396- D400.
17. Vindal V, Suma K, Ranjan A. 2007. GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization. BMC Genomics 8:289. doi:10.1186/1471-2164-8-289.
18. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
19. Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I. 2010. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 38(Suppl 2):W299- W307.
20. Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. 2004. Reconstruction of regulatory and metabolic pathways in metal-reducing deltaproteobacteria. Genome Biol. 5:R90. doi:10.1186/gb-2004-5-11-r90.
21. Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, Gelfand MS. 2005. Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PLoS Comput. Biol. 1:e55. doi: 10.1371/journal.pcbi.0010055.
22. Pinchuk GE, Rodionov DA, Yang C, Li X, Osterman AL, Dervyn E, Geydebrekht OV, Reed SB, Romine MF, Collart FR, Scott JH, Fredrickson JK, Beliaev AS. 2009. Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. Proc. Natl. Acad. Sci. U. S. A. 106:2874-2879.
23. Lee JW, Helmann JD. 2007. Functional specialization within the Fur family of metalloregulators. Biometals 20:485-499.
24. Nguyen CC, Saier MH, Jr. 1995. Phylogenetic, structural and functional analyses of the LacI-GalR family of bacterial transcription factors. FEBS Lett. 377:98-102.
25. Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Res. 14:1188-1190.
26. Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA. 2010. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 38(Suppl 1):D111-D118.
27. Castillo R, Saier MH, Jr. 2010. Functional promiscuity of homologues of the bacterial ArsA ATPases. Int. J. Microbiol. 2010:187373. doi:10.1155/ 2010/187373.
28. Rigali S, Derouaux A, Giannotta F, Dusart J. 2002. Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J. Biol. Chem. 277:12507-12515.
29. Gebhard S, Cook GM. 2008. Differential regulation of high-affinity phosphate transport systems of Mycobacterium smegmatis: identification of PhnF, a repressor of the phnDCE operon. J. Bacteriol. 190:1335-1343.
30. Dufour YS, Kiley PJ, Donohue TJ. 2010. Reconstruction of the core and extended regulons of global transcription factors. PLoS Genet. 6:e1001027. doi:10.1371/journal.pgen.1001027.