DOI QR코드

DOI QR Code

Genetic Transformation of Geobacillus kaustophilus HTA426 by Conjugative Transfer of Host-Mimicking Plasmids

  • Suzuki, Hirokazu (Organization of Advanced Science and Technology, Kobe University) ;
  • Yoshida, Ken-Ichi (Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University)
  • Received : 2012.03.12
  • Accepted : 2012.05.10
  • Published : 2012.09.28

Abstract

We established an efficient transformation method for thermophile Geobacillus kaustophilus HTA426 using conjugative transfer from Escherichia coli of host-mimicking plasmids that imitate DNA methylation of strain HTA426 to circumvent its DNA restriction barriers. Two conjugative plasmids, pSTE33T and pUCG18T, capable of shuttling between E. coli and Geobacillus spp., were constructed. The plasmids were first introduced into E. coli BR408, which expressed one inherent DNA methylase gene (dam) and two heterologous methylase genes from strain HTA426 (GK1380-GK1381 and GK0343-GK0344). The plasmids were then directly transferred from E. coli cells to strain HTA426 by conjugative transfer using pUB307 or pRK2013 as a helper plasmid. pUCG18T was introduced very efficiently (transfer efficiency, $10^{-5}-10^{-3}\;recipient^{-1}$). pSTE33T showed lower efficiency ($10^{-7}-10^{-6}\;recipient^{-1}$) but had a high copy number and high segregational stability. Methylase genes in the donor substantially affected the transfer efficiency, demonstrating that the host-mimicking strategy contributes to efficient transformation. The transformation method, along with the two distinguishing plasmids, increases the potential of G. kaustophilus HTA426 as a thermophilic host to be used in various applications and as a model for biological studies of this genus. Our results also demonstrate that conjugative transfer is a promising approach for introducing exogenous DNA into thermophiles.

Keywords

References

  1. Arsene, F., T. Tomoyasu, and B. Bukau. 2000. The heat shock response of Escherichia coli. Int. J. Food Microbiol. 55: 3-9. https://doi.org/10.1016/S0168-1605(00)00206-3
  2. Bart, A., M. W. J. van Passel, K. van Amsterdam, and A. van der Ende. 2005. Direct detection of methylation in genomic DNA. Nucleic Acids Res. 33: e124. https://doi.org/10.1093/nar/gni121
  3. Bennett, P. M., J. Grinsted, and M. H. Richmond. 1977. Transposition of TnA does not generate deletions. Mol. Gen. Genet. 154: 205-211. https://doi.org/10.1007/BF00330839
  4. Cava, F., A. Hidalgo, and J. Berenguer. 2009. Thermus thermophilus as biological model. Extremophiles 13: 213-231. https://doi.org/10.1007/s00792-009-0226-6
  5. Cripps, R. E., K. Eley, D. J. Leak, B. Rudd, M. Taylor, M. Todd, S. Boakes, S. Martin, and T. Atkinson. 2009. Metabolic engineering of Geobacillus thermoglucosidasius for high yield ethanol production. Metab. Eng. 11: 398-408. https://doi.org/10.1016/j.ymben.2009.08.005
  6. Cuebas, M., D. Sannino, and E. Bini. 2011. Isolation and characterization of an arsenic resistant Geobacillus kaustophilus strain from geothermal soils. J. Basic Microbiol. 51: 364-371. https://doi.org/10.1002/jobm.201000314
  7. De Rossi, E., P. Brigidi, N. E. Welker, G. Riccardi, and D. Matteuzzi. 1994. New shuttle vector for cloning in Bacillus stearothermophilus. Res. Microbiol. 145: 579-583. https://doi.org/10.1016/0923-2508(94)90074-4
  8. Ehrlich, M., G. G. Wilson, K. C. Kuo, and C. W. Gehrke. 1987. $N^4$-Methylcytosine as a minor base in bacterial DNA. J. Bacteriol. 169: 939-943. https://doi.org/10.1128/jb.169.3.939-943.1987
  9. Feng, L., W. Wang, J. Cheng, Y. Ren, G. Zhao, C. Gao, et al. 2007. Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deepsubsurface oil reservoir. Proc. Natl. Acad. Sci. USA 104: 5602-5607. https://doi.org/10.1073/pnas.0609650104
  10. Figurski, D. H. and D. R. Helinski. 1979. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc. Natl. Acad. Sci. USA 76: 1648-1652. https://doi.org/10.1073/pnas.76.4.1648
  11. Flusberg, B. A., D. R. Webster, J. H. Lee, K. J. Travers, E. C. Olivares, T. A. Clark, et al. 2010. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7: 461-467. https://doi.org/10.1038/nmeth.1459
  12. Higuchi, R., B. Krummel, and R. K. Saiki. 1988. A general method of in vitro preparation and specific mutagenesis of DNA fragments: Study of protein and DNA interactions. Nucleic Acids Res. 16: 7351-7367. https://doi.org/10.1093/nar/16.15.7351
  13. Kato, T., A. Miyanaga, S. Kanaya, and M. Morikawa. 2010. Gene cloning and characterization of an aldehyde dehydrogenase from long-chain alkane-degrading Geobacillus thermoleovorans B23. Extremophiles 14: 33-39. https://doi.org/10.1007/s00792-009-0285-8
  14. McMullan, G., J. M. Christie, T. J. Rahman, I. M. Banat, N. G. Ternan, and R. Marchant. 2004. Habitat, applications and genomics of the aerobic, thermophilic genus Geobacillus. Biochem. Soc. Trans. 32: 214-217. https://doi.org/10.1042/BST0320214
  15. Miller, J. F., E. Lanka, and M. H. Malamy. 1985. F factor inhibition of conjugal transfer of broad-host-range plasmid RP4: Requirement for the protein product of pif operon regulatory gene pifC. J. Bacteriol. 163: 1067-1073.
  16. Nagaraja, V., M. Stieger, C. Nager, S. M. Hadi, and T. A. Bickle. 1985. The nucleoside sequence recognized by the Escherichia coli D type I restriction and modification enzyme. Nucleic Acids Res. 13: 389-399. https://doi.org/10.1093/nar/13.2.389
  17. Nakayama, N., I. Narumi, S. Nakamoto, and H. Kihara. 1992. A new shuttle vector for Bacillus stearothermophilus and Escherichia coli. Biotechnol. Lett. 14: 649-652. https://doi.org/10.1007/BF01021636
  18. Narumi, I., N. Nakayama, S. Nakamoto, T. Kimura, T. Yanagisawa, and H. Kihara. 1993. Construction of a new shuttle vector pSTE33 and its stabilities in Bacillus stearothermophilus, Bacillus subtilis, and Escherichia coli. Biotechnol. Lett. 15: 815-820.
  19. Narumi, I., K. Sawakami, S. Nakamoto, N. Nakayama, T. Yanagisawa, N. Takahashi, and H. Kihara. 1992. A newly isolated Bacillus stearothermophilus K1041 and its transformation by electroporation. Biotechnol. Tech. 6: 83-86. https://doi.org/10.1007/BF02438695
  20. Nazina, T. N., T. P. Tourova, A. B. Poltaraus, E. V. Novikova, A. A. Grigoryan, A. E. Ivanova, et al. 2001. Taxonomic study of aerobic thermophilic bacilli: Descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans. Int. J. Syst. Evol. Microbiol. 51: 433-446. https://doi.org/10.1099/00207713-51-2-433
  21. Roberts, R. J., M. Belfort, T. Bestor, A. S. Bhagwat, T. A. Bickle, J. Bitinaite, et al. 2003. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 31: 1805-1812. https://doi.org/10.1093/nar/gkg274
  22. Roberts, R. J., T. Vincze, J. Posfai, and D. Macelis. 2010. REBASE - a database for DNA restriction and modification: Enzymes, genes and genomes. Nucleic Acids Res. 38: D234-D236. https://doi.org/10.1093/nar/gkp874
  23. Ryu, J. and E. Rowsell. 2008. Quick identification of Type I restriction enzyme isoschizomers using newly developed pTypeI and reference plasmids. Nucleic Acids Res. 36: e81. https://doi.org/10.1093/nar/gkn056
  24. Sato, T., T. Fukui, H. Atomi, and T. Imanaka. 2005. Improved and versatile transformation system allowing multiple genetic manipulations of the hyperthermophilic archaeon Thermococcus kodakaraensis. Appl. Environ. Microbiol. 71: 3889-3899. https://doi.org/10.1128/AEM.71.7.3889-3899.2005
  25. Suzuki, H., S. Takahashi, H. Osada, and K. Yoshida. 2011. Improvement of transformation efficiency by strategic circumvention of restriction barriers in Streptomyces griseus. J. Microbiol. Biotechnol. 21: 675-678. https://doi.org/10.4014/jmb.1102.02038
  26. Takami, H., A. Inoue, F. Fuji, and K. Horikoshi. 1997. Microbial flora in the deepest sea mud of the Mariana Trench. FEMS Microbiol. Lett. 152: 279-285. https://doi.org/10.1111/j.1574-6968.1997.tb10440.x
  27. Takami, H., S. Nishi, J. Lu, S. Shinamura, and Y. Takaki. 2004. Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench. Extremophiles 8: 351-356. https://doi.org/10.1007/s00792-004-0394-3
  28. Takami, H., Y. Takaki, G. J. Chee, S. Nishi, S. Shimamura, H. Suzuki, et al. 2004. Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucleic Acids Res. 32: 6292-6303. https://doi.org/10.1093/nar/gkh970
  29. Taylor, M. P., C. D. Esteban, and D. J. Leak. 2008. Development of a versatile shuttle vector for gene expression in Geobacillus spp. Plasmid 60: 45-52. https://doi.org/10.1016/j.plasmid.2008.04.001
  30. Wiegel, J. and L. G. Ljungdahl. 1986. The importance of thermophilic bacteria in biotechnology. Crit. Rev. Biotechnol. 3: 39-108.
  31. Wu, L. J. and N. E. Welker. 1989. Protoplast transformation of Bacillus stearothermophilus NUB36 by plasmid DNA. J. Gen. Microbiol. 135: 1315-1324.

Cited by

  1. A Ternary Conjugation System for the Construction of DNA Libraries forGeobacillus kaustophilusHTA426 vol.77, pp.11, 2013, https://doi.org/10.1271/bbb.130492
  2. Current state of genetic and metabolic engineering of the genus Geobacillus aimed at production of ethanol and organic acids vol.4, pp.3, 2012, https://doi.org/10.1134/s2079059714030046
  3. Bioinformatics analysis of the genome of Geobacillus stearothermophilus 22 Strain isolated from the Garga hot spring, Baikal Region vol.4, pp.4, 2012, https://doi.org/10.1134/s207905971404011x
  4. Transformable facultative thermophile Geobacillus stearothermophilus NUB3621 as a host strain for metabolic engineering vol.98, pp.15, 2012, https://doi.org/10.1007/s00253-014-5746-z
  5. Identification and characterization of a novel Geobacillus thermoglucosidasius bacteriophage, GVE3 vol.160, pp.9, 2012, https://doi.org/10.1007/s00705-015-2497-9
  6. Thermoadaptation-directed evolution of chloramphenicol acetyltransferase in an error-prone thermophile using improved procedures vol.99, pp.13, 2012, https://doi.org/10.1007/s00253-015-6522-4
  7. Unique Plasmids Generated via pUC Replicon Mutagenesis in an Error-Prone Thermophile Derived from Geobacillus kaustophilus HTA426 vol.81, pp.21, 2012, https://doi.org/10.1128/aem.01574-15
  8. Conjugative plasmid transfer from Escherichia coli is a versatile approach for genetic transformation of thermophilic Bacillus and Geobacillus species vol.20, pp.3, 2012, https://doi.org/10.1007/s00792-016-0819-9
  9. Evolutionary engineering of Geobacillus thermoglucosidasius for improved ethanol production vol.113, pp.10, 2016, https://doi.org/10.1002/bit.25983
  10. Microbial and genomic characterization of Geobacillus thermodenitrificans OS27, a marine thermophile that degrades diverse raw seaweeds vol.102, pp.11, 2018, https://doi.org/10.1007/s00253-018-8958-9
  11. A novel method for transforming the thermophilic bacterium Geobacillus kaustophilus vol.17, pp.None, 2012, https://doi.org/10.1186/s12934-018-0969-9
  12. A plasmid vector that directs hyperproduction of recombinant proteins in the thermophiles Geobacillus species vol.24, pp.1, 2012, https://doi.org/10.1007/s00792-019-01142-3
  13. Identification of a repressor for the two iol operons required for inositol catabolism in Geobacillus kaustophilus vol.167, pp.1, 2021, https://doi.org/10.1099/mic.0.001008
  14. Development of a Cas12a-Based Genome Editing Tool for Moderate Thermophiles vol.4, pp.1, 2021, https://doi.org/10.1089/crispr.2020.0086