Address of Corresponding Author

J Mol Microbiol Biotechnol 2004;7:204-211 (DOI: 10.1159/000079829)

  Key Words

• Bacillus licheniformis DSM13
• Genome sequence
• Bacillus subtilis
• Industrial enzymes
• Industrial fermentation

  Abstract

The genome of Bacillus licheniformis DSM13 consists of a single chromosome that has a size of 4,222,748 base pairs. The average G+C ratio is 46.2%. 4,286 open reading frames, 72 tRNA genes, 7 rRNA operons and 20 transposase genes were identified. The genome shows a marked co-linearity with Bacillus subtilis but contains defined inserted regions that can be identified at the sequence as well as at the functional level. B. licheniformis DSM13 has a well-conserved secretory system, no polyketide biosynthesis, but is able to form the lipopeptide lichenysin. From the further analysis of the genome sequence, we identified conserved regulatory DNA motives, the occurrence of the glyoxylate bypass and the presence of anaerobic ribonucleotide reductase explaining that B. licheniformis is able to grow on acetate and 2,3-butanediol as well as anaerobically on glucose. Many new genes of potential interest for biotechnological applications were found in B. licheniformis; candidates include proteases, pectate lyases, lipases and various polysaccharide degrading enzymes.

Copyright © 2004 S. Karger AG, Basel

  References

1.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. 1990. Basic local alignment search tool. J Mol Biol 215:403-410.

2.

Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., et al. 2004. The Pfam protein families database. Nucl Acids Res 32 Database issue, D138-D141.

3.

Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Wheeler, D.L. 2004. GenBank: update. Nucl Acids Res 32 Database issue, D23-D26.

4.

Brüggemann, H., Bäumer, S., Fricke, W.F., Wiezer, A., Liesegang, H., Decker, I., Herzberg, C., Martinez-Arias, R., Merkl, R., Henne, A., Gottschalk, G. 2003. The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc Natl Acad Sci USA 100:1316-1321.

5.

Declerck, N., Machius, M., Wiegand, G., Huber, R., Gaillardin, C. 2000. Probing structural determinants specifying high thermostability in Bacillus licheniformis -amylase. J Mol Biol 301:1041-1057.

6.

Delcher, A.L., Phillippy, A., Carlton, J., Salzberg, S.L. 2002. Fast algorithms for large-scale genome alignment and comparison. Nucl Acids Res 30:2478-2483.

7.

Ehrenreich, A., Widdel, F. 1994. Anaerobic oxidation of ferrous iron by purple bacteria, a new type of phototrophic metabolism. Appl Environ Microbiol 60:4517-4526.

8.

Ewing, B., Hillier, L., Wendl, M.C., Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175-185.

9.

Froyshov, O., Laland, S.G. 1974. On the biosynthesis of bacitracin by a soluble enzyme complex from Bacillus licheniformis. Eur J Biochem 46:235-242.

10.

Fründ, C., Priefert, H., Steinbüchel, A., Schlegel, H.G. 1989. Biochemical and genetic analyses of acetoin catabolism in Alcaligenes eutrophus. J Bacteriol 171:6539-6548.

11.

Gottschalk, G. 1986. Bacterial Metabolism, ed 2. New York, Springer.

12.

Gray, G.L., Mainzer, S.E., Rey, M.W., Lamsa, M.H., Kindle, K.L., Carmona, C., Requadt, C. 1986. Structural genes encoding the thermophilic -amylases of Bacillus stearothermophilus and Bacillus licheniformis. J Bacteriol 166:635-643.

13.

Helmann, J.D., Moran, C.P., Jr. 2002. RNA polymerase and sigma factors; in Sonenhein A.L. (ed): Bacillus subtilis and Its Closest Relatives. Washington, ASM Press.

14.

Hofmann, K., Stoffel, W. 1993. TMbase - A database of membrane spanning protein segments. Biol Chem Hoppe-Seyler 374:166.

15.

Hulo, N., Sigrist, C.J., Le Saux, V., Langendijk-Genevaux, P.S., Bordoli, L., Gattiker, A., De Castro, E., Bucher, P., Bairoch, A. 2004. Recent improvements to the PROSITE database. Nucl Acids Res 32 Database issue, D134-D137.

16.

Huynen, M.A., Bork, P. 1998. Measuring genome evolution. Proc Natl Acad Sci USA 95:5849-5856.

17.

Ivanova, N., Sorokin, A., Anderson, I., Galleron, N., Candelon, B., Kapatral, V., Bhattacharyya, A., Reznik, G., Mikhailova, N., Lapidus, A., et al. 2003. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423:87-91.

18.

Jacobs, M., Eliasson, M., Uhlen, M., Flock, J.I. 1985. Cloning, sequencing and expression of subtilisin Carlsberg from Bacillus licheniformis. Nucl Acids Res 13:8913-8926.

19.

Kakudo, S., Kikuchi, N., Kitadokoro, K., Fujiwara, T., Nakamura, E., Okamoto, H., Shin, M., Tamaki, M., Teraoka, H., Tsuzuki, H., et al. 1992. Purification, characterization, cloning, and expression of a glutamic acid-specific protease from Bacillus licheniformis ATCC 14580. J Biol Chem 267:23782-23788.

20.

Kandra, L., Gyemant, G., Remenyik, J., Hovanszki, G., Liptak, A. 2002. Action pattern and subsite mapping of Bacillus licheniformis -amylase (BLA) with modified maltooligosaccharide substrates. FEBS Lett 518:79-82.

21.

Kim, I.C., Cha, J.H., Kim, J.R., Jang, S.Y., Seo, B.C., Cheong, T.K., Lee, D.S., Choi, Y.D., Park, K.H. 1992. Catalytic properties of the cloned amylase from Bacillus licheniformis. J Biol Chem 267:22108-22114.

22.

Konz, D., Doekel, S., Marahiel, M.A. 1999. Molecular and biochemical characterization of the protein template controlling biosynthesis of the lipopeptide lichenysin. J Bacteriol 181:133-140.

23.

Kulikova, T., Aldebert, P., Althorpe, N., Baker, W., Bates, K., Browne, P., van den Broek, A., Cochrane, G., Duggan, K., Eberhardt, R., et al. 2004. The EMBL Nucleotide Sequence Database. Nucl Acids Res 32 Database issue, D27-D30.

24.

Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V., Bertero, M.G., Bessieres, P., Bolotin, A., Borchert, S., et al. 1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249-256.

25.

Kurtz, S., Phillippy, A., Delcher, A.L., Smoot, M., Shumway, M., Antonescu, C., Salzberg, S.L. 2004. Versatile and open software for comparing large genomes. Genome Biol 5:R12.

26.

Lathe, W.C. 3rd, Snel, B., Bork, P. 2000. Gene context conservation of a higher order than operons. Trends Biochem Sci 25:474-479.

27.

Lobry, J.R. 1996. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13:660-665.

28.

Martinez, J.L., Herrero, M., de Lorenzo, V. 1994. The organization of intercistronic regions of the aerobactin operon of pColV-K30 may account for the differential expression of the iucABCD iutA genes. J Mol Biol 238:288-293.

29.

Merkl, R. 2004. Score-based identification of genomic islands. BMC Bioinformatics 5:22.

30.

Moss, J.E., Cardozo, T.J., Zychlinsky, A., Groisman, E.A. 1999. The selC-associated SHI-2 pathogenicity island of Shigella flexneri. Mol Microbiol 33:74-83.

31.

Oppermann, F.B., Steinbüchel, A., Schlegel, H.G. 1989. Evidence for oxidative thiolytic cleavage of acetoin in Pelobacter carbinolicus analogous to aerobic oxidative decarboxylation of pyruvate. FEMS Microbiol Lett 51:113-118.

32.

O'Sullivan, D., Twomey, D.P., Coffey, A., Hill, C., Fitzgerald, G.F., Ross, R.P. 2000. Novel type I restriction specificities through domain shuffling of HsdS subunits in Lactococcus lactis. Mol Microbiol 36:866-875.

33.

Overbeek, R., Larsen, N., Walunas, T., D'Souza, M., Pusch, G., Selkov, E. Jr., Liolios, K., Joukov, V., Kaznadzey, D., Anderson, I., et al. 2003. The ERGO genome analysis and discovery system. Nucl Acids Res 31:164-171.

34.

Pearson, W.R. 1994. Using the FASTA program to search protein and DNA sequence databases. Methods Mol Biol 25:365-389.

35.

Rasko, D.A., Ravel, J., Okstad, O.A., Helgason, E., Cer, R.Z., Jiang, L., Shores, K.A., Fouts, D.E., Tourasse, N.J., Angiuoli, S.V., et al. 2004. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucl Acids Res 32:977-988.

36.

Read, T.D., Peterson, S.N., Tourasse, N., Baillie, L.W., Paulsen, I.T., Nelson, K.E., Tettelin, H., Fouts, D.E., Eisen, J.A., Gill, S.R., et al. 2003. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81-86.

37.

Sandeman, R.A., Hynes, M.J., Fincham, J.R., Connerton, I.F. 1991. Molecular organisation of the malate synthase genes of Aspergillus nidulans and Neurospora crassa. Mol Gen Genet 228:445-452.

38.

Schallmey, M., Singh, A., Ward, O.P. 2004. Developments in the use of Bacillus species for industrial production. Can J Microbiol 50:1-17.

39.

Sharma, V., Sharma, S., Hoener zu Bentrup, K., McKinney, J.D., Russell, D.G., Jacobs, W.R. Jr., Sacchettini, J.C. 2000. Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Nat Struct Biol 7:663-668.

40.

Shimizu, T., Ohtani, K., Hirakawa, H., Ohshima, K., Yamashita, A., Shiba, T., Ogasawara, N., Hattori, M., Kuhara, S., Hayashi, H. 2002. Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci USA 99:996-1001.

41.

Smith, E.L., DeLange, R.J., Evans, W.H., Landon, M., Markland, F.S. 1968. Subtilisin Carlsberg. V. The complete sequence: Comparison with subtilisin BPN'; evolutionary relationships. J Biol Chem 243:2184-2191.

42.

Sneath, P.H.A., Mair, N.S., Sharpe, M.E., Holt, J.G. 1986. Bergey's Manual of Sytematic Bacteriology, vol 2. Baltimore, Williams & Wilkins.

43.

Staden, R., Beal, K.F., Bonfield, J.K. 2000. The Staden package, 1998. Methods Mol Biol 132:115-130.

44.

Stephens, M.A., Ortlepp, S.A., Ollington, J.F., McConnell, D.J. 1984. Nucleotide sequence of the 5' region of the Bacillus licheniformis -amylase gene: Comparison with the B. amyloliquefaciens gene. J Bacteriol 158:369-372.

45.

Svendsen, I., Breddam, K. 1992. Isolation and amino acid sequence of a glutamic acid specific endopeptidase from Bacillus licheniformis. Eur J Biochem 204:165-171.

46.

Syed, R., Wu, Z.P., Hogle, J.M., Hilvert, D. 1993. Crystal structure of selenosubtilisin at 2.0-A resolution. Biochemistry 32:6157-6164.

47.

Takami, H., Horikoshi, K. 2000. Analysis of the genome of an alkaliphilic Bacillus strain from an industrial point of view. Extremophiles 4:99-108.

48.

Takami, H., Nakasone, K., Takaki, Y., Maeno, G., Sasaki, R., Masui, N., Fuji, F., Hirama, C., Nakamura, Y., Ogasawara, N., et al. 2000. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucl Acids Res 28:4317-4331.

49.

Tech, M., Merkl, R. 2003. YACOP: Enhanced gene prediction obtained by a combination of existing methods. In Silico Biol 3:441-451.

50.

Tillier, E.R., Collins, R.A. 2000. The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol 50:249-257.

51.

Tjalsma, H., Bolhuis, A., Jongbloed, J.D., Bron, S., van Dijl, J.M. 2000. Signal peptide-dependent protein transport in Bacillus subtilis: A genome-based survey of the secretome. Microbiol Mol Biol Rev 64:515-547.

52.

Torrents, E., Buist, G., Liu, A., Eliasson, R., Kok, J., Gibert, I., Graslund, A., Reichard, P. 2000. The anaerobic (class III) ribonucleotide reductase from Lactococcus lactis. Catalytic properties and allosteric regulation of the pure enzyme system. J Biol Chem 275:2463-2471.

53.

Yuuki, T., Nomura, T., Tezuka, H., Tsuboi, A., Yamagata, H., Tsukagoshi, N., Udaka, S. 1985. Complete nucleotide sequence of a gene coding for heat- and pH-stable -amylase of Bacillus licheniformis: Comparison of the amino acid sequences of three bacterial liquefying -amylases deduced from the DNA sequences. J Biochem (Tokyo) 98:1147-1156.

  Author Contacts

Armin Ehrenreich
Genomics Laboratory and Competence Centre for Genome Research on Bacteria
Institute of Microbiology and Genetics, University of Göttingen
Grisebachstrasse 8, DE-37077 Göttingen (Germany)
Tel. +49 551 393833, Fax +49 551 393793, E-Mail aehrenr@gwdg.de

  Article Information

Number of Print Pages : 8
Number of Figures : 4, Number of Tables : 5, Number of References : 53

  Publication Details

Journal of Molecular Microbiology and Biotechnology

Vol. 7, No. 4, Year 2004 (Cover Date: Released September 2004)

Journal Editor: Saier, M.H., Jr. (La Jolla, Calif.)
ISSN: 1464-1801 (print), 1660-2412 (Online)

For additional information: http://www.karger.com/mmb

  Drug Dosage / Copyright

Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in goverment regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug. Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher or, in the case of photocopying, direct payment of a specified fee to the Copyright Clearance Center.