SporeWeb: An interactive journey through the complete sporulation cycle of Bacillus subtilis

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Eijlander, Robyn T ^a,b   De Jong, Anne ^a,b   Krawczyk, Antonina O ^a,b   Holsappel, Siger ^b   Kuipers, Oscar P ^b  

^a TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BACILLUS SUBTILIS; BACTERIAL SPORE; DATA BASE; GENE CONTROL; GENE EXPRESSION; GENE REGULATORY NETWORK; GENE SEQUENCE; GERMINATION; GRAM POSITIVE BACTERIUM; NONHUMAN; PRIORITY JOURNAL; REVIEW; SPOREWEB DATA BASE; SPOROGENESIS; TRANSCRIPTION REGULATION; APPLICATION SERVICE PROVIDER; ARTICLE; COMPUTER INTERFACE; INFORMATION PROCESSING; REGULON; SPOREWEB; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; GROWTH, DEVELOPMENT AND AGING; INTERNET; PHYSIOLOGY;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); POSIBACTERIA;

BACILLUS SUBTILIS; DATABASES, GENETIC; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; INTERNET; REGULON; SPORES, BACTERIAL;

EID: 84891767234     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1007     Document Type: Review

References (45)

1. Eijlander, R.T., Abee, T. and Kuipers, O.P. (2011) Bacterial spores in food: how phenotypic variability complicates prediction of spore properties and bacterial behavior. Curr. Opin. Biotechnol., 22, 180-186.
2. Augustin, J.C. (2011) Challenges in risk assessment and predictive microbiology of foodborne spore-forming bacteria. Food Microbiol., 28, 209-213.
3. Mock, M. and Fouet, A. (2001) Anthrax. Annu. Rev. Microbiol., 55, 647-671.
4. Schnepf, E., Crickmore, N., Van Rie, J., Lereclus, D., Baum, J., Feitelson, J., Zeigler, D.R. and Dean, D.H. (1998) Bacillus thuringiensis and its pesticidal crystal proteins. Microbiol. Mol. Biol. Rev., 62, 775-806.
5. Amuguni, H. and Tzipori, S. (2012) Bacillus subtilis: a temperature resistant and needle free delivery system of immunogens. Hum. Vaccin. Immunother., 8, 979-986.
6. Bader, J., Albin, A. and Stahl, U. (2012) Spore-forming bacteria and their utilisation as probiotics. Benef. Microbes., 3, 67-75.
7. Permpoonpattana, P., Hong, H.A., Khaneja, R. and Cutting, S.M. (2012) Evaluation of Bacillus subtilis strains as probiotics and their potential as a food ingredient. Benef. Microbes., 3, 127-135.
8. Gould, G.W. (2006) History of science-spores. J. Appl. Microbiol., 101, 507-513.
9. Higgins, D. and Dworkin, J. (2012) Recent progress in Bacillus subtilis sporulation. FEMS Microbiol. Rev., 36, 131-148.
10. Errington, J. (2010) From spores to antibiotics via the cell cycle. Microbiology, 156, 1-13.
11. Hilbert, D.W. and Piggot, P.J. (2004) Compartmentalization of gene expression during Bacillus subtilis spore formation. Microbiol. Mol. Biol. Rev., 68, 234-262.
12. Moir, A. (2006) How do spores germinate? J. Appl. Microbiol., 101, 526-530.
13. Liu, H., Bergman, N.H., Thomason, B., Shallom, S., Hazen, A., Crossno, J., Rasko, D.A., Ravel, J., Read, T.D., Peterson, S.N. et al. (2004) Formation and composition of the Bacillus anthracis endospore. J. Bacteriol., 186, 164-178.
14. Fisher, N. and Hanna, P. (2005) Characterization of Bacillus anthracis germinant receptors in vitro. J. Bacteriol., 187, 8055-8062.
15. van der Voort, M., Garcia, D., Moezelaar, R. and Abee, T. (2010) Germinant receptor diversity and germination responses of four strains of the Bacillus cereus group. Int. J. Food Microbiol., 139, 108-115.
16. Vries de, Y.P., Hornstra, L.M., de Vos, W.M. and Abee, T. (2004) Growth and sporulation of Bacillus cereus ATCC 14579 under defined conditions: temporal expression of genes for key sigma factors. Appl. Environ. Microbiol., 70, 2514-2519.
17. Xiao, Y., Francke, C, Abee, T. and Wells-Bennik, M.H. (2011) Clostridial spore germination versus bacilli: genome mining and current insights. Food Microbiol., 28, 266-274.
18. Paredes-Sabja, D., Setlow, P. and Sarker, M.R. (2011) Germination of spores of Bacillales and Clostridials species: mechanisms and proteins involved. Trends Microbiol, 19, 85-94.
19. Steiner, E., Dago, A.E., Young, D.I., Heap, J.T., Minton, N.P., Hoch, JA. and Young, M. (2011) Multiple orphan histidine kinases interact directly with Spo0A to control the initiation of endospore formation in Clostridium acetobutylicum. Mol. Microbiol., 80, 641-654.
20. Burns, DA. and Minton, N.P. (2011) Sporulation studies in Clostridium difficile. J. Microbiol. Methods, 87, 133-138.
21. Rosenbusch, K.E., Bakker, D., Kuijper, E.J. and Smits, W.K. (2012) C. difficile 630Aerm Spo0A regulates sporulation, but does not contribute to toxin production, by direct high-affinity binding to target DNA. PLoS One, 7, e48608.
22. Labbe, R.G and Durre, P. (2005) Sporulation of clostridia. In: Durre, P. (ed.), Handbook on Clostridia. CRC Press, Taylor & Francis Group, FL, USA, pp. 647-669.
23. de Hoon, M.J.L., Eichenberger, P. and Vitkup, D. (2010) Hierarchical evolution of the bacterial sporulation network. Curr. Biol., 20, R735-R745.
24. Galperin, MY., Mekhedov, S.L., Puigbo, P., Smirnov, S., Wolf, Y.I. and Rigden, D.J. (2012) Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ. Microbiol., 11, 2870-2890.
25. Stragier, P. and Losick, R. (1996) Molecular genetics of sporulation in Bacillus subtilis. Annu. Rev. Genet., 30, 297-241.
26. Piggot, P.J. and Hilbert, D.W. (2004) Sporulation of Bacillus subtilis. Curr. Opin. Microbiol., 7, 579-586.
27. Silvaggi, J.M., Perkins, J.B. and Losick, R. (2006) Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis. J. Bacteriol., 188, 532-541.
28. Schmalisch, M., Maiques, E., Nikolov, L., Camp, A.H, Chevreux, B., Muffler, A., Rodriguez, S., Perkins, J. and Losick, R. (2010) Small genes under sporulation control in the Bacillus subtilis genome. J. Bacteriol., 192, 5402-5412.
29. Liebal, U.W., Millat, T., De Jong, I.G, Kuipers, O.P., Volker, U. and Wolkenhauer, O. (2010) How mathematical modelling elucidates signalling in Bacillus subtilis. Mol. Microbiol., 77, 1083-1095.
30. Jabbari, S., Heap, J.T. and King, J.R. (2011) Mathematical modelling of the sporulation-initiation network in Bacillus subtilis revealing the dual role of the putative quorum-sensing signal molecule PhrA. Bull. Math. Biol., 73, 181-211.
31. Levine, J.H., Fontes, M.E., Dworkin, J. and Elowitz, M.B. (2012) Pulsed feedback defers cellular differentiation. PLoS Biol., 10, e1001252.
32. Rottger, R., Ruckert, U., Taubert, J. and Baumbach, J. (2012) How little do we actually know?-on the size of gene regulatory networks. IEEE/ACM Trans. Comput. Biol. Bioinform., 9, 1293-1300.
33. Mader, U., Schmeisky, A.G., Florez, L.A. and Stulke, J. (2012) SubtiWiki-A comprehensive community resource for the model organism Bacillus subtilis. Nucleic Acids Res., 40, D1278-D1287.
34. Parker, G.F., Daniel, R.A. and Errington, J. (1996) Timing and genetic regulation of commitment to sporulation in Bacillus subtilis. Microbiology, 142(Pt 12), 3445-3452.
35. Steil, L., Serrano, M., Henriques, A.O. and Volker, U. (2005) Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilis. Microbiology, 151, 399-420.
36. Cangiano, G., Mazzone, A., Baccigalupi, L., Isticato, R., Eichenberger, P., De Felice, M. and Ricca, E. (2010) Direct and indirect control of late sporulation genes by GerR of Bacillus subtilis. J. Bacteriol., 192, 3406-3413.
37. Britton, R.A., Eichenberger, P., Gonzalez-Pastor, J.E., Fawcett, P., Monson, R., Losick, R. and Grossman, A.D. (2002) Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis. J. Bacteriol., 184, 4881-4890.
38. Wang, S.T., Setlow, B., Conlon, E.M., Lyon, J.L., Imamura, D., Sato, T., Setlow, P., Losick, R. and Eichenberger, P. (2006) The forespore line of gene expression in Bacillus subtilis. J. Mol. Biol., 358, 16-37.
39. Eichenberger, P., Fujita, M., Jensen, S.T., Conlon, E.M., Rudner, D.Z., Wang, S.T., Ferguson, C., Haga, K., Sato, T., Liu, J.S. et al. (2004) The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol., 2, e328.
40. Eichenberger, P., Jensen, S.T., Conlon, E.M., van Ooij, C., Silvaggi, J., Gonzalez-Pastor, J.E., Fujita, M., Ben-Yehuda, S., Stragier, P., Liu, J.S. et al. (2003) The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis. J. Mol. Biol., 327, 945-972.
41. Molle, V., Fujita, M., Jensen, S.T., Eichenberger, P., Gonzalez-Pastor, J.E., Liu, J.S. and Losick, R. (2003) The Spo0A regulon of Bacillus subtilis. Mol. Microbiol., 50, 1683-1701.
42. Fawcett, P., Eichenberger, P., Losick, R. and Youngman, P. (2000) The transcriptional profile of early to middle sporulation in Bacillus subtilis. Proc. Natl Acad. Sci. USA, 97, 8063-8068.
43. Saito, R., Smoot, M.E., Ono, K., Ruscheinski, J., Wang, P.L., Lotia, S., Pico, A.R., Bader, G.D. and Ideker, T. (2012) A travel guide to Cytoscape plugins. Nat. Methods, 9, 1069-1076.
44. Fujita, M., Gonzalez-Pastor, J.E. and Losick, R. (2005) High-and low-threshold genes of the Spo0A regulon of Bacillus subtilis. J. Bacteriol., 187, 1357-1368.
45. Nicolas, P., Mader, U., Dervyn, E., Rochat, T., Leduc, A., Pigeonneau, N., Bidnenko, E., Marchadier, E., Hoebeke, M., Aymerich, S. et al. (2012) Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science, 335, 1103-1106.