Transcriptional profile of Bacillus subtilis sigF-mutant during vegetative growth

PLoS ONE

Volumn 10, Issue 10, 2015, Pages

  Overkamp, Wout ^a,b   Kuipers, Oscar P ^a,b  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b KLUYVER CENTRE FOR GENOMICS OF INDUSTRIAL FERMENTATION   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

FATTY ACID; TRANSCRIPTOME; BACTERIAL PROTEIN; FLIA PROTEIN, BACTERIA; SIGMA FACTOR;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM MUTANT; DOWN REGULATION; FATTY ACID METABOLISM; GENE DISRUPTION; GENE MUTATION; MICROARRAY ANALYSIS; NONHUMAN; SIGF GENE; SPORANGIUM; SPOROGENESIS; TRANSCRIPTION REGULATION; UPREGULATION; VEGETATIVE GROWTH; BACTERIAL SPORE; BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MUTATION; PROMOTER REGION;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; MUTATION; PROMOTER REGIONS, GENETIC; SIGMA FACTOR; SPORES, BACTERIAL; TRANSCRIPTION, GENETIC;

EID: 84949599525     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0141553     Document Type: Article

References (48)

1. Nicholson WL, Munakata N, Horneck G, Melosh HJ, Setlow P. Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiol Mol Biol Rev MMBR. 2000; 64: 548-572. PMID: 10974126
2. Errington J. Regulation of endospore formation in Bacillus subtilis. Nat Rev Microbiol. 2003; 1: 117-126. doi: 10.1038/nrmicro750 PMID: 15035041
3. Higgins D, Dworkin J. Recent progress in Bacillus subtilis sporulation. FEMS Microbiol Rev. 2012; 36: 131-148. doi: 10.1111/j.1574-6976.2011.00310.x PMID: 22091839
4. Piggot PJ, Losick R. Sporulation genes and intercompartmental regulation. In: Sonenshein AL, Hoch JA, Losick R, editors. Bacillus subtilis and Its Closest Relative: From Genes to Cells. Washington, DC: ASM Press; 2002. pp. 483-518.
5. Molle V, Fujita M, Jensen ST, Eichenberger P, Gonzalez-Pastor JE, Liu JS, et al. The Spo0A regulon of Bacillus subtilis. Mol Microbiol. 2003; 50: 1683-1701. PMID: 14651647
6. Fawcett P, Eichenberger P, Losick R, Youngman P. The transcriptional profile of early to middle sporulation in Bacillus subtilis. Proc Natl Acad Sci U S A. 2000; 97: 8063-8068. PMID: 10869437
7. Burbulys D, Trach KA, Hoch JA. Initiation of sporulation in B. subtilis is controlled by a multicomponent phosphorelay. Cell. 1991; 64: 545-552. PMID: 1846779
8. Ireton K, Rudner DZ, Siranosian KJ, Grossman AD. Integration of multiple developmental signals in Bacillus subtilis through the Spo0A transcription factor. Genes Dev. 1993; 7: 283-294. PMID: 8436298
9. Hilbert DW, Piggot PJ. Compartmentalization of Gene Expression during Bacillus subtilis Spore Formation. Microbiol Mol Biol Rev. 2004; 68: 234-262. doi: 10.1128/MMBR.68.2.234-262.2004 PMID: 15187183
10. Stragier P, Losick R. Molecular genetics of sporulation in Bacillus subtilis. Annu Rev Genet. 1996; 30: 297-241. doi: 10.1146/annurev.genet.30.1.297 PMID: 8982457
11. Margolis P, Driks A, Losick R. Establishment of cell type by compartmentalized activation of a transcription factor. Science. 1991; 254: 562-565. PMID: 1948031
12. Fort P, Piggot PJ. Nucleotide sequence of sporulation locus spoIIA in Bacillus subtilis. J Gen Microbiol. 1984; 130: 2147-2153. PMID: 6088674
13. Duncan L, Losick R. SpoIIAB is an anti-sigma factor that binds to and inhibits transcription by regulatory protein sigma F from Bacillus subtilis. Proc Natl Acad Sci U S A. 1993; 90: 2325-2329. PMID: 8460142
14. Duncan L, Alper S, Losick R. SpoIIAA governs the release of the cell-type specific transcription factor sigma F from its anti-sigma factor SpoIIAB. J Mol Biol. 1996; 260: 147-164. doi: 10.1006/jmbi.1996. 0389 PMID: 8764397
15. Schmidt R, Margolis P, Duncan L, Coppolecchia R, Moran CP Jr, Losick R. Control of developmental transcription factor sigma F by sporulation regulatory proteins SpoIIAA and SpoIIAB in Bacillus subtilis. Proc Natl Acad Sci U S A. 1990; 87: 9221-9225. PMID: 2123551
16. Illing N, Errington J. Genetic regulation of morphogenesis in Bacillus subtilis: roles of sigma E and sigma F in prespore engulfment. J Bacteriol. 1991; 173: 3159-3169. PMID: 1902463
17. Setlow B, Magill N, Febbroriello P, Nakhimovsky L, Koppel DE, Setlow P. Condensation of the forespore nucleoid early in sporulation of Bacillus species. J Bacteriol. 1991; 173: 6270-6278. PMID: 1917859
18. Dworkin J, Losick R. Developmental Commitment in a Bacterium. Cell. 2005; 121: 401-409. doi: 10. 1016/j.cell.2005.02.032 PMID: 15882622
19. Steil L, Serrano M, Henriques AO, Völker U. Genome-wide analysis of temporally regulated and compartment- specific gene expression in sporulating cells of Bacillus subtilis. Microbiol Read Engl. 2005; 151: 399-420. doi: 10.1099/mic.0.27493-0
20. Wang ST, Setlow B, Conlon EM, Lyon JL, Imamura D, Sato T, et al. The forespore line of gene expression in Bacillus subtilis. J Mol Biol. 2006; 358: 16-37. doi: 10.1016/j.jmb.2006.01.059 PMID: 16497325
21. Piggot PJ, Coote JG. Genetic aspects of bacterial endospore formation. Bacteriol Rev. 1976; 40: 908-962, PMID: 12736
22. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997; 390: 249-256. doi: 10.1038/36786 PMID: 9384377
23. Yanisch-Perron C, Vieira J, Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985; 33: 103-119. PMID: 2985470
24. Guérout-Fleury A-M, Shazand K, Frandsen N, Stragier P. Antibiotic-resistance cassettes for Bacillus subtilis. Gene. 1995; 167: 335-336. doi: 10.1016/0378-1119(95)00652-4 PMID: 8566804
25. Harwood CR, Cutting SM. Molecular Biological Methods for Bacillus. John Wiley & Sons; 1990.
26. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory; 1989.
27. Leskelä S, Kontinen VP, Sarvas M. Molecular analysis of an operon in Bacillus subtilis encoding a novel ABC transporter with a role in exoprotein production, sporulation and competence. Microbiol Read Engl. 1996; 142 (Pt 1): 71-77.
28. Anagnostopoulos C, Spizizen J. Requirements for transformation in Bacillus subtilis. J Bacteriol. 1961; 81: 741-746. PMID: 16561900
29. Lulko AT, Buist G, Kok J, Kuipers OP. Transcriptome Analysis of Temporal Regulation of Carbon Metabolism by CcpA in Bacillus subtilis Reveals Additional Target Genes. J Mol Microbiol Biotechnol. 2007; 12: 82-95. doi: 10.1159/000096463 PMID: 17183215
30. van Hijum SAFT, de Jong A, Baerends RJS, Karsens HA, Kramer NE, Larsen R, et al. A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics. 2005; 6: 77. doi: 10.1186/1471-2164-6-77 PMID: 15907200
31. Long AD, Mangalam HJ, Chan BY, Tolleri L, Hatfield GW, Baldi P. Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem. 2001; 276: 19937-19944. doi: 10.1074/jbc.M010192200 PMID: 11259426
32. van Hijum SAFT, García de la Nava J, Trelles O, Kok J, Kuipers OP. MicroPreP: a cDNA microarray data pre-processing framework. Appl Bioinformatics. 2003; 2: 241-244. PMID: 15130795
33. Blom E-J, Bosman DWJ, van Hijum SAFT, Breitling R, Tijsma L, Silvis R, et al. FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. Bioinforma Oxf Engl. 2007; 23: 1161-1163. doi: 10.1093/bioinformatics/btl658
34. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004; 32: D277-280. doi: 10.1093/nar/gkh063 PMID: 14681412
35. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25: 25-29. doi: 10.1038/75556 PMID: 10802651
36. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997; 278: 631-637. PMID: 9381173
37. Sierro N, Makita Y, de Hoon M, Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 2008; 36: D93-D96. doi: 10.1093/nar/gkm910 PMID: 17962296
38. Fujita M, Losick R. Evidence that entry into sporulation in Bacillus subtilis is governed by a gradual increase in the level and activity of the master regulator Spo0A. Genes Dev. 2005; 19: 2236-2244. doi: 10.1101/gad.1335705 PMID: 16166384
39. Eijlander RT, de Jong A, Krawczyk AO, Holsappel S, Kuipers OP. SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis. Nucleic Acids Res. 2013; doi: 10.1093/nar/gkt1007
40. Flórez LA, Roppel SF, Schmeisky AG, Lammers CR, Stülke J. A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database J Biol Databases Curation. 2009; 2009: bap012. doi: 10.1093/database/bap012
41. Ward JB, Zahler SA. Genetic studies of leucine biosynthesis in Bacillus subtilis. J Bacteriol. 1973; 116: 719-726. PMID: 4200853
42. Ebbole DJ, Zalkin H. Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis. J Biol Chem. 1987; 262: 8274-8287. PMID: 3036807
43. Molle V, Nakaura Y, Shivers RP, Yamaguchi H, Losick R, Fujita Y, et al. Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol. 2003; 185: 1911-1922. PMID: 12618455
44. González-Pastor JE, Hobbs EC, Losick R. Cannibalism by sporulating bacteria. Science. 2003; 301: 510-513. doi: 10.1126/science.1086462 PMID: 12817086
45. Tojo S, Satomura T, Matsuoka H, Hirooka K, Fujita Y. Catabolite repression of the Bacillus subtilis FadR regulon, which is involved in fatty acid catabolism. J Bacteriol. 2011; 193: 2388-2395. doi: 10. 1128/JB.00016-11 PMID: 21398533
46. Matsuoka H, Hirooka K, Fujita Y. Organization and function of the YsiA regulon of Bacillus subtilis involved in fatty acid degradation. J Biol Chem. 2007; 282: 5180-5194. doi: 10.1074/jbc.M606831200 PMID: 17189250
47. Kaneda T. Fatty acids of the genus Bacillus: an example of branched-chain preference. Bacteriol Rev. 1977; 41: 391-418. PMID: 329832
48. Koburger T, Weibezahn J, Bernhardt J, Homuth G, Hecker M. Genome-wide mRNA profiling in glucose starved Bacillus subtilis cells. Mol Genet Genomics. 2005; 274: 1-12. doi: 10.1007/s00438-005-1119-8 PMID: 15809868