Skip to main content
Applied and Environmental Microbiology logoLink to Applied and Environmental Microbiology
. 1997 Apr;63(4):1406–1420. doi: 10.1128/aem.63.4.1406-1420.1997

Genetic manipulation of Bacillus methanolicus, a gram-positive, thermotolerant methylotroph.

D Cue 1, H Lam 1, R L Dillingham 1, R S Hanson 1, M C Flickinger 1
PMCID: PMC168436  PMID: 9097439

Abstract

We report the fist genetic transformation system, shuttle vectors, and integrative vectors for the thermotolerant, methylotrophic bacterium Bacillus methanolicus. By using a polyethylene glycol-mediated transformation procedure, we have successfully transformed B. methanolicus with both integrative and multicopy plasmids. For plasmids with a single BmeTI recognition site, dam methylation of plasmid DNA (in vivo or in vitro) was found to enhance transformation efficiency from 7- to 11-fold. Two low-copy-number Escherichia coli-B, methanolicus shuttle plasmids, pDQ507 and pDQ508, are described. pDQ508 caries the replication origin cloned from a 17-kb endogenous B. methanolicus plasmid, pBM1. pDQ507 carries a cloned B. methanolicus DNA fragment, pmr-1, possibly of chromosomal origin, that supports maintenance of pDQ507 as a circular, extrachromosomal DNA molecule. Deletion analysis of pDQ507 indicated two regions required for replication, i.e., a 90-bp AT-rich segment containing a 46-bp imperfect, inverted repeat sequence and a second region 65% homologous to the B. subtilis dpp operon. We also evaluated two E. coli-B. subtilis vectors, pEN1 and pHP13, for use as E. coli-B. methanolicus shuttle vectors. The plasmids pHP13, pDQ507, and pDQ508 were segregationally and structurally stable in B. methanolicus for greater than 60 generations of growth under nonselective conditions; pEN1 was segregationally unstable. Single-stranded plasmid DNA was detected in B. methanolicus transformants carrying either pEN1, pHP13, or pDQ508, suggesting that pDQ508, like the B. subtilis plasmids, is replicated by a rolling-circle mechanism. These studies provide the basic tools for the genetic manipulation of B. methanolicus.

Full Text

The Full Text of this article is available as a PDF (2.3 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson L. M., Ruley H. E., Bott K. F. Isolation of an autonomously replicating DNA fragment from the region of defective bacteriophage PBSX of Bacillus subtilis. J Bacteriol. 1982 Jun;150(3):1280–1286. doi: 10.1128/jb.150.3.1280-1286.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arfman N., Dijkhuizen L., Kirchhof G., Ludwig W., Schleifer K. H., Bulygina E. S., Chumakov K. M., Govorukhina N. I., Trotsenko Y. A., White D. Bacillus methanolicus sp. nov., a new species of thermotolerant, methanol-utilizing, endospore-forming bacteria. Int J Syst Bacteriol. 1992 Jul;42(3):439–445. doi: 10.1099/00207713-42-3-439. [DOI] [PubMed] [Google Scholar]
  3. Chang S., Cohen S. N. High frequency transformation of Bacillus subtilis protoplasts by plasmid DNA. Mol Gen Genet. 1979 Jan 5;168(1):111–115. doi: 10.1007/BF00267940. [DOI] [PubMed] [Google Scholar]
  4. Cue D., Lam H., Hanson R. S., Flickinger M. C. Characterization of a restriction-modification system of the thermotolerant methylotroph Bacillus methanolicus. Appl Environ Microbiol. 1996 Mar;62(3):1107–1111. doi: 10.1128/aem.62.3.1107-1111.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. De Rossi E., Brigidi P., Rossi M., Matteuzzi D., Riccardi G. Characterization of gram-positive broad host-range plasmids carrying a thermophilic replicon. Res Microbiol. 1991 May;142(4):389–396. doi: 10.1016/0923-2508(91)90108-m. [DOI] [PubMed] [Google Scholar]
  6. Diaz R., Barnsley P., Pritchard R. H. Location and characterisation of a new replication origin in the E. coli K12 chromosome. Mol Gen Genet. 1979 Sep;175(2):151–157. doi: 10.1007/BF00425531. [DOI] [PubMed] [Google Scholar]
  7. Grandjean V., Nguyen J., Hauck Y., Hirschbein L. Establishment of a new replicon generated from an integrational plasmid and a cryptic pUB110 origin-like region in Bacillus subtilis. Plasmid. 1993 Jul;30(1):1–13. doi: 10.1006/plas.1993.1029. [DOI] [PubMed] [Google Scholar]
  8. Haima P., Bron S., Venema G. The effect of restriction on shotgun cloning and plasmid stability in Bacillus subtilis Marburg. Mol Gen Genet. 1987 Sep;209(2):335–342. doi: 10.1007/BF00329663. [DOI] [PubMed] [Google Scholar]
  9. Hanahan D., Jessee J., Bloom F. R. Plasmid transformation of Escherichia coli and other bacteria. Methods Enzymol. 1991;204:63–113. doi: 10.1016/0076-6879(91)04006-a. [DOI] [PubMed] [Google Scholar]
  10. Itaya M., Kondo K., Tanaka T. A neomycin resistance gene cassette selectable in a single copy state in the Bacillus subtilis chromosome. Nucleic Acids Res. 1989 Jun 12;17(11):4410–4410. doi: 10.1093/nar/17.11.4410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lidstrom M. E., Stirling D. I. Methylotrophs: genetics and commercial applications. Annu Rev Microbiol. 1990;44:27–58. doi: 10.1146/annurev.mi.44.100190.000331. [DOI] [PubMed] [Google Scholar]
  12. Macaluso A., Mettus A. M. Efficient transformation of Bacillus thuringiensis requires nonmethylated plasmid DNA. J Bacteriol. 1991 Feb;173(3):1353–1356. doi: 10.1128/jb.173.3.1353-1356.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Mathiopoulos C., Mueller J. P., Slack F. J., Murphy C. G., Patankar S., Bukusoglu G., Sonenshein A. L. A Bacillus subtilis dipeptide transport system expressed early during sporulation. Mol Microbiol. 1991 Aug;5(8):1903–1913. doi: 10.1111/j.1365-2958.1991.tb00814.x. [DOI] [PubMed] [Google Scholar]
  14. Matsubara K., Kaiser A. D. Lambda dv: an autonomously replicating DNA fragment. Cold Spring Harb Symp Quant Biol. 1968;33:769–775. doi: 10.1101/sqb.1968.033.01.088. [DOI] [PubMed] [Google Scholar]
  15. Mills D. A., Flickinger M. C. Cloning and sequence analysis of the meso-diaminopimelate decarboxylase gene from Bacillus methanolicus MGA3 and comparison to other decarboxylase genes. Appl Environ Microbiol. 1993 Sep;59(9):2927–2937. doi: 10.1128/aem.59.9.2927-2937.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Moriya S., Atlung T., Hansen F. G., Yoshikawa H., Ogasawara N. Cloning of an autonomously replicating sequence (ars) from the Bacillus subtilis chromosome. Mol Microbiol. 1992 Feb;6(3):309–315. doi: 10.1111/j.1365-2958.1992.tb01473.x. [DOI] [PubMed] [Google Scholar]
  17. Nelson M., Raschke E., McClelland M. Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res. 1993 Jul 1;21(13):3139–3154. doi: 10.1093/nar/21.13.3139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Perkins J. B., Dean D. H. Transfection of Bacillus subtilis protoplasts by bacteriophage phi do7 DNA. J Bacteriol. 1983 Nov;156(2):931–933. doi: 10.1128/jb.156.2.931-933.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sanford J. C., Smith F. D., Russell J. A. Optimizing the biolistic process for different biological applications. Methods Enzymol. 1993;217:483–509. doi: 10.1016/0076-6879(93)17086-k. [DOI] [PubMed] [Google Scholar]
  20. Schendel F. J., Bremmon C. E., Flickinger M. C., Guettler M., Hanson R. S. L-lysine production at 50 degrees C by mutants of a newly isolated and characterized methylotrophic Bacillus sp. Appl Environ Microbiol. 1990 Apr;56(4):963–970. doi: 10.1128/aem.56.4.963-970.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Schendel F. J., Flickinger M. C. Cloning and nucleotide sequence of the gene coding for aspartokinase II from a thermophilic methylotrophic Bacillus sp. Appl Environ Microbiol. 1992 Sep;58(9):2806–2814. doi: 10.1128/aem.58.9.2806-2814.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Slack F. J., Serror P., Joyce E., Sonenshein A. L. A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon. Mol Microbiol. 1995 Feb;15(4):689–702. doi: 10.1111/j.1365-2958.1995.tb02378.x. [DOI] [PubMed] [Google Scholar]
  23. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  24. Sternberg N., Austin S. Isolation and characterization of P1 minireplicons, lambda-P1:5R and lambda-P1:5L. J Bacteriol. 1983 Feb;153(2):800–812. doi: 10.1128/jb.153.2.800-812.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Streips U. N., Welker N. E. Infection of Bacillus stearothermophilus with bacteriophage deoxyribonucleic acid. J Bacteriol. 1969 Jul;99(1):344–346. doi: 10.1128/jb.99.1.344-346.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tani Y. Production of useful chemicals by methylotrophs. Biotechnology. 1991;18:253–270. doi: 10.1016/b978-0-7506-9188-8.50018-8. [DOI] [PubMed] [Google Scholar]
  27. Tsutsui H., Fujiyama A., Murotsu T., Matsubara K. Role of nine repeating sequences of the mini-F genome for expression of F-specific incompatibility phenotype and copy number control. J Bacteriol. 1983 Jul;155(1):337–344. doi: 10.1128/jb.155.1.337-344.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Vogelstein B., Gillespie D. Preparative and analytical purification of DNA from agarose. Proc Natl Acad Sci U S A. 1979 Feb;76(2):615–619. doi: 10.1073/pnas.76.2.615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Vrijbloed J. W., Jelínková M., Hessels G. I., Dijkhuizen L. Identification of the minimal replicon of plasmid pMEA300 of the methylotrophic actinomycete Amycolatopsis methanolica. Mol Microbiol. 1995 Oct;18(1):21–31. doi: 10.1111/j.1365-2958.1995.mmi_18010021.x. [DOI] [PubMed] [Google Scholar]
  30. 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(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  31. Yee T. W., Smith D. W. Pseudomonas chromosomal replication origins: a bacterial class distinct from Escherichia coli-type origins. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1278–1282. doi: 10.1073/pnas.87.4.1278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Zhang M., Nakai H., Imanaka T. Useful Host-Vector Systems in Bacillus stearothermophilus. Appl Environ Microbiol. 1988 Dec;54(12):3162–3164. doi: 10.1128/aem.54.12.3162-3164.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Applied and Environmental Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES