The Bacillus subtilis genome sequence: The molecular blueprint of a soil bacterium

FEMS Microbiology Ecology

Volumn 28, Issue 1, 1999, Pages 1-9

  Wipat, Anil ^a   Harwood, Colin R ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Bacillus species; Genome organization; Microbial ecology; Plant growth promoting rhizobacterium; Reporter gene; Root colonization; Soil bacterium

Indexed keywords

BACILLUS SUBTILIS; DNA SEQUENCE; ECOLOGY; ENVIRONMENT; GENOME; NONHUMAN; PLANT GROWTH; PRIORITY JOURNAL; REVIEW; RHIZOBIUM; SOIL MICROFLORA;

EID: 0032919153     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(98)00080-4     Document Type: Review

References (50)

1. Kunst, F. et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390, 249-256.
2. Priest, F. (1993) Systematics and ecology of Bacillus. In: Bacillus subtilis and Other Gram-positive Bacteria (Sonenshein, A.L., Hoch, J.A. and Losick, R., Eds.), pp. 3-16. American Society for Microbiology, Washington, DC.
3. Jordan, D., McNicol, P. and Marshall, M. (1978) Biological nitrogen fixation in the terrestrial environment of a high Arctic ecosystem (Truelove Lowland, Devon Island, N.W.T.). Can. J. Microbiol. 24, 643-649.
4. Broadbent, P., Baker, K.F. and Waterworth, Y. (1977) Effect of Bacillus spp. on increased growth of seedlings in steamed and non-treated soil. Phytopathology 67, 1027-1034.
5. Harwood, C.R. (1992) Bacillus subtilis and its relatives - Molecular biological and industrial workhorses. Trends Biotechnol. 10, 247-256.
6. Vullo, D.L., Coto, C.E. and Sineriz, F. (1991) Characteristics of an inulinase produced by Bacillus subtilis-430a, a strain isolated from the rhizosphere of Vernonia herbacea (Vell-Rusby). Appl. Environ. Microbiol. 57, 2392-2394.
7. Lilley, A.K., Fry, J.C., Bailey, M.J. and Day, M.J. (1996) Comparison of aerobic heterotrophic taxa isolated from four root domains of mature sugar beet (Beta vulgaris). FEMS Microbiol. Ecol. 21, 231-242.
8. Pandey, A. and Palni, L.M.S. (1997) Bacillus species: The dominant bacteria of the rhizosphere of established tea bushes. Microbiol. Res. 152, 359-365.
9. Mahaffee, W.F. and Backman, P.A. (1993) Effect of seed factors on spermosphere and rhizosphere colonization of cotton by Bacillus subtilis GB03. Ecol. Epidemiol. 83, 1120-1125.
10. Ridge, E.H. and Rovira, A.D. (1968) in: Transactions of the 9th International Congress of Soil Science (International Society of Soil Science, Ed.), Vol. 3, pp. 473-481. Elsevier, Amsterdam.
11. Kloepper, J.W., Lifshitz, R. and Zablotowicz, M. (1989) Free-living bacterial inocula for enhancing crop productivity. Trends Biotechnol. 7, 39-44.
12. Kajimura, Y., Sugiyama, M. and Kaneda, M. (1995) Bacillopeptins, new cyclic lipopeptide antibiotics from Bacillus subtilis Fr-2. J. Antibiot. 48, 1095-1103.
13. Turner, J.T. and Backman, P.A. (1991) Factors relating to peanut yield increases after seed treatment with Bacillus subtilis. Plant Dis. 75, 347-353.
14. Wasinger, V.C., Cordwell, S.J., Cerpa-Poljak, A., Yan, J.X., Gooley, A.A., Wilkins, M.R., Duncan, M.W., Harris, R., Williams, K.L. and Humphery-Smith, I. (1995) Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16, 1090-1094.
15. Burkholder, P.R. and Giles, N. H. (1947) Induced biochemical mutants in Bacillus subtilis. Am. J. Bot. 34, 345-348.
16. Hemphil, H.E. and Whitely, H.R. (1975) Bacteriophage of Bacillus subtilis. Bacteriol. Rev. 39, 257-315.
17. Kappes, R., Kempf, B. and Bremer, E. (1996) Three transport systems for the osmoprotectant glycine betaine operate in Bacillus subtilis: characterisation of OpuD. J. Bacteriol. 178, 5071-5079.
18. Boch, J., Kempf, B., Schmid, R. and Bremer, E. (1996) Synthesis of the osmoprotectant glycine betaine in Bacillus subtilis - Characterization of the gbsAB genes. J. Bacteriol. 178, 5121-5129.
19. Hecker, M., Schumann, W. and Volker, U. (1996) Heat-shock and general stress response in Bacillus subtilis. Mol. Microbiol. 19, 417-428.
20. Graumann, P., Wendrich, T.M., Weber, M.H.W., Schroder, K. and Marahiel, M.A. (1997) A family of cold shock proteins in Bacillus subtilis is essential for cellular growth and for efficient protein synthesis at optimal and low temperatures. Mol. Microbiol. 25, 741-756.
21. Gothel, S.F., Schmid, R., Wipat, A., Carter, N.M., Emmerson, P.T., Harwood, C.R. and Marahiel, M.A. (1997) An internal FK506-binding domain is the catalytic core of the prolyl isomerase activity associated with the Bacillus subtilis trigger factor. Eur. J. Biochem. 244, 59-65.
22. Rainey, P., Heithoff, D. and Mahan, M. (1997) Single-step conjugative cloning of bacterial gene fusions involved in microbe-host interactions. Mol. Gen. Genet. 256, 84-87.
23. Shenker, O., Gat, O., Sonenshein, A.L. and Shoham, Y. (1997) in: Abstracts of the 9th International Conference on Bacilli, Institut de Génétique et de Biologie Microbiennes, University de Lausanne, Lausanne.
24. Wray, L.V., Ferson, A.E. and Fisher, S.H. (1997) Expression of the Bacillus subtilis ureABC operon is controlled by multiple regulatory factors including CodY, GlnR, TnrA and Spo0H. J. Bacteriol. 179, 5494-5501.
25. Fisher, S.H. (1993) Utilisation of amino acids and other nitrogen-containing compounds. In: Bacillus subtilis and Other Gram-positive Bacteria (Sonenshein, A.L., Hoch, J.A. and Losick, R., Eds.), pp. 221-228. American Society for Microbiology, Washington, DC.
26. Kim, K.S. and Farrand, S.K. (1996) Ti plasmid-encoded genes responsible for catabolism of the crown gall opine mannopine by Agrobacterium tumefaciens: Are homologs of the T-region genes responsible for synthesis of this opine by the plant tumor? J. Bacteriol. 178, 3275-3284.
27. Hulett, F. (1993) in: Bacillus subtilis and Other Gram-positive Bacteria (Sonenshein, A.L., Hoch, J.A. and Losick, R., Eds.), pp. 229-236. American Society for Microbiology, Washington, DC.
28. Eymann, C., Mach, H., Harwood, C.R. and Hecker, M. (1996) Phosphate-starvation-inducible proteins in Bacillus subtilis - a 2-dimensional gel-electrophoresis study. Microbiology (UK) 142, 3163-3170.
29. Kirby, J.R., Kristich, C.J., Feinberg, S.L. and Ordal, G.W. (1997) Methanol production during chemotaxis to amino acids in Bacillus subtilis. Mol. Microbiol. 24, 869-878.
30. Chumakov, M.I. (1996) Involvement of superficial polysaccharides and proteins of Rhizobiaceae in attachment to plant surfaces. Microbiology 65, 631-643.
31. Swart, S., Lugtenberg, B.J.J., Smit, G. and Kijne, J.W. (1994) Rhicadhesin-mediated attachment and virulence of an Agrobacterium tumefaciens chvB mutant can be restored by growth in a highly osmotic medium. J. Bacteriol. 176, 3816-3819.
32. DeFlaun, M.F., Tanzer, A.S., McAteer, A.L., Marshall, B. and Levy, S.B. (1990) Development of an adhesion assay and characterization of an adhesion deficient mutant of Pseudomonas fluorescens. Appl. Environ. Microbiol. 56, 112-119.
33. Dintilhac, A., Alloing, G., Granadel, C. and Claverys, J.P. (1997) Competence and virulence of Streptococcus pneumoniae: adc and psaA mutants exhibit a requirement for Zn and Mn resulting from inactivation of putative ABC metal permeases. Mol. Microbiol. 25, 727-739.
34. Heilmann, C., Schweitzer, O., Gerke, C., Vanittanakom, N., Mack, D. and Gotz, F. (1996) Molecular-basis of intercellular-adhesion in the biofilm-forming Staphylococcus epidermidis. Mol. Microbiol. 20, 1083-1091.
35. Tosato, V., Albertini, A.M., Zotti, M., Sonda, S. and Bruschi, C.V. (1997) Sequence completion, identification and definition of the fengycin operon in Bacillus subtilis 168. Microbiology (UK) 143, 3443-3450.
36. Nagai, T. and Itoh, H. (1997) Characterization of a generalized transducing phage of poly-glutamic acid-producing Bacillus subtilis and its application for analysis of Tn917-LTV1 insertional mutants defective in polyglutamic acid production. Appl. Environ. Microbiol. 63, 4087-4089.
37. Srinivasan, M., Petersen, D.J. and Holl, F.B. (1997) Nodulation of Phaseolus vulgaris by Rhizobium etli is enhanced by the presence of Bacillus. Can. J. Microbiol. 43, 1-8.
38. Relic, B., Perret, X., Estradagarcia, M.T., Kopcinska, J., Golinowski, W., Krishnan, H.B., Pueppke, S.G. and Broughton, W.J. (1994) Nod factors of Rhizobium are a key to the legume door. Mol. Microbiol. 13, 171-178.
39. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
40. Doolittle, R. (1998) Microbial genomes opened up. Nature 392, 339-342.
41. Harwood, C.R. and Wipat, A. (1996) Sequencing and functional analysis of the genome of Bacillus subtilis strain 168. FEBS Lett. 389, 84-87.
42. Zhu, Y.M., Pierson, L.S. and Hawes, M.C. (1997) Induction of microbial genes for pathogenesis and symbiosis by chemicals from root border cells. Plant Physiol. 115, 1691-1698.
43. Kragelund, L., Hosbond, C. and Nybroe, O. (1997) Distribution of metabolic activity and phosphate starvation response of lux-tagged Pseudomonas fluorescens reporter bacteria in the barley rhizosphere. Appl. Environ. Microbiol. 63, 4920-4928.
44. Egener, T., Hurek, T. and Reinhold, B. (1998) Use of green fluorescent protein to detect expression of nif genes of Azoarcus sp. BH72, a grass-associated diazotroph, on rice roots. Mol. Plant-Microbiol. Interact. 11, 71-75.
45. Slauch, J.M., Mahan, M.J. and Mekalanos, J.J. (1994) In vivo expression technology for selection of bacterial genes specifically induced in host tissues. Methods Enzymol. 235, 481-492.
46. Mahan, M.J., Tobias, J.W., Slauch, J.M., Hanna, P.C., Collier, R.J. and Mekalanos, J.J. (1995) Antibiotic-based selection for bacterial genes that are specifically induced during infection of a host. Proc. Natl. Acad. Sci. USA 92, 669-673.
47. Mahan, M.J., Slauch, J.M. and Mekalanos, J.J. (1993) Selection of bacterial virulence genes that are specifically induced in host tissues. Science 259, 666-668.
48. Shoemaker, D.D., Lashkari, D.A., Morris, D., Mittmann, M. and Davis, R.W. (1996) Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nature Genet. 14, 450-456.
49. Horton, H. and Brown, E.L. (1996) Expression monitoring by hybridisation to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1645-1680.
50. Hancock, J. (1996) Simple sequences in a minimal genome. Nature Genet. 14, 14-15.