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RNA-seq Analysis of Antibiotic-Producing Bacillus subtilis SC-8 in Response to Signal Peptide PapR of Bacillus cereus

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Abstract

Bacillus subtilis SC-8 produces an antibiotic that has narrow antagonistic activity against bacteria in the Bacillus cereus group. In B. cereus group bacteria, peptide-activating PlcR (PapR) plays a significant role in regulating the transcription of virulence factors. When B. subtilis SC-8 and B. cereus are co-cultured, PapR is assumed to stimulate antibiotic production by B. subtilis SC-8. To better understand the effect of PapR on this interspecies interaction, the global transcriptome profile of B. subtilis SC-8 was analyzed in the presence of PapR. Significant changes were detected in 12.8 % of the total transcripts. Genes related to amino acid transport and metabolism (16.5 %) and transcription (15 %) were mainly upregulated, whereas genes involved in carbohydrate transport and metabolism (12.7 %) were markedly downregulated. The expression of genes related to transcription, including several transcriptional regulators and proteins involved in tRNA biosynthesis, was increased. The expression levels of genes associated with several transport systems, such as antibiotic, cobalt, and iron complex transporters, was also significantly altered. Among the downregulated genes were transcripts associated with spore formation, the subtilosin A gene cluster, and nitrogen metabolism.

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References

  1. Lee, N. K., Park, J. W., Cho, I. J., Kim, B. Y., Kwon, K. O., & Hahm, Y. T. (2008). Korean Journal Food Science and Technology, 40, 669–673.

    Google Scholar 

  2. Lee, N. K., Yeo, I. C., Park, J. W., Kang, B. S., & Hahm, Y. T. (2010). Journal of Bioscience and Bioengineering, 110, 298–303.

    Article  CAS  Google Scholar 

  3. Yeo, I. C., Lee, N. K., Cha, C. J., & Hahm, Y. T. (2012). Applied Biochemistry and Biotechnology, 166, 700–710.

    Article  CAS  Google Scholar 

  4. Waters, C. M., & Bassler, B. L. (2005). Annual Review of Cell Developmental Biology, 21, 319–346.

    Article  CAS  Google Scholar 

  5. Kleerebezem, M., Quadri, L. E., Kuipers, O. P., & de Vos, W. M. (1997). Molecular Microbiology, 24, 895–904.

    Article  CAS  Google Scholar 

  6. Lereclus, D., Agaisse, H., Gominet, M., Salamitou, S., & Sanchis, V. (1996). Journal of Bacteriology, 178, 2749–2756.

    CAS  Google Scholar 

  7. Økstad, O. A., Gominet, M., Purnelle, B., Rose, M., Lereclus, D., & Kolstø, A. B. (1999). Microbiology, 145, 3129–3138.

    Article  Google Scholar 

  8. Slamti, L., & Lereclus, D. (2002). EMBO Jorunal, 21, 4550–4559.

    Article  CAS  Google Scholar 

  9. Declerck, N., Bouillant, L., Chaix, D., Rugani, N., Slamti, L., Hoh, F., et al. (2007). Proceedings of the National Academy of Science of the United States of America, 104, 18490–18495.

    Article  CAS  Google Scholar 

  10. Bouillaut, L., Perchat, S., Arold, S., Zorrilla, S., Slamti, L., Henry, C., et al. (2008). Nucleic Acids Research, 36, 3791–3801.

    Article  CAS  Google Scholar 

  11. Gohar, M., Faegri, K., Perchat, S., Ravnum, S., Økstad, O. A., Gominet, M., et al. (2008). PLoS One, 3, e2793.

    Article  Google Scholar 

  12. Yeo, I. C., Lee, N. K., & Hahm, Y. T. (2012). Journal of Bacteriology, 194, 536–537.

    Article  CAS  Google Scholar 

  13. Schroeder, A., Mueller, O., Stocker, S., Salowsky, R., Leiber, M., Gassmann, M., et al. (2006). BMC Molecular Biology, 7, 1–14.

    Article  Google Scholar 

  14. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008). Nature Methods, 5, 621–628.

    Article  CAS  Google Scholar 

  15. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., et al. (2000). Nature Genetics, 25, 25–29.

    Article  CAS  Google Scholar 

  16. Livak, K. J., & Schmittgen, T. D. (2001). Methods, 25, 402–408.

    Article  CAS  Google Scholar 

  17. González–Pastor, J. E., Hobbs, E. C., & Losick, R. (2003). Science, 301, 510–513.

    Article  Google Scholar 

  18. Fawcett, P., Eichenberger, P., Losick, R., & Youngman, P. (2000). Proceeding of the National Academy of Science of the USA, 97, 8063–8068.

    Article  CAS  Google Scholar 

  19. Phillips, Z. E., & Strauch, M. A. (2002). Cellular and Molecular Life Sciences, 59, 392–402.

    Article  CAS  Google Scholar 

  20. Kuwana, R., Kasahara, Y., Fujibayashi, M., Takamatsu, H., Ogasawara, N., & Watabe, K. (2002). Microbiology, 148, 3971–3982.

    CAS  Google Scholar 

  21. Kuwana, R., Yamamura, S., Ikejiri, H., Kobayashi, K., Ogasawara, N., Asai, K., et al. (2003). Microbiology, 149, 3011–3021.

    Article  CAS  Google Scholar 

  22. Cangiano, G., Mazzone, A., Baccigalupi, L., Isticato, R., Eichenberger, P., De Felice, M., et al. (2010). Journal of Bacteriology, 192, 3406–3413.

    Article  CAS  Google Scholar 

  23. Salzberg, L. I., Luo, Y., Hachmann, A. B., Mascher, T., & Helmann, J. D. (2011). Journal of Bacteriology, 193, 5793–5801.

    Article  CAS  Google Scholar 

  24. Cao, M., Wang, T., Ye, R., & Helmann, J. D. (2002). Molecular Microbiology, 45, 1267–1276.

    Article  CAS  Google Scholar 

  25. Mascher, T., Margulis, N. G., Wang, T., Ye, R. W., & Helmann, J. D. (2003). Molecular Microbiology, 50, 1591–1604.

    Article  CAS  Google Scholar 

  26. Lonetto, M. A., Brown, K. L., Rudd, K. E., & Buttner, M. J. (1994). Proceeding of the National Academy of Science of the USA, 91, 7573–7577.

    Article  CAS  Google Scholar 

  27. Hughes, K. T., & Mathee, K. (1998). Annual Reviews Microbiology, 52, 231–286.

    Article  CAS  Google Scholar 

  28. Helmann, J. D. (2002). Advances in Microbial Physiology, 46, 47–110.

    Article  CAS  Google Scholar 

  29. Bashyam, M. D., & Hasnain, S. E. (2004). Infection, Genetics and Evolution, 4, 301–308.

    Article  CAS  Google Scholar 

  30. Liesegang, H., Lemke, K., Siddiqui, R. A., & Schlegel, H. G. (1993). Journal of Bacteriology, 175, 767–778.

    CAS  Google Scholar 

  31. Gorham, H. C., McGowan, S. J., Robson, P. R., & Hodgson, D. A. (1996). Molecular Microbiology, 19, 171–186.

    Article  CAS  Google Scholar 

  32. Paget, M. S., Kang, J. G., Roe, J. H., & Buttner, M. J. (1998). The EMBO Journal, 17, 5776–5782.

    Article  CAS  Google Scholar 

  33. Paget, M. S., Bae, J. B., Hahn, M. Y., Li, W., Kleanthous, C., Roe, J. H., et al. (2001). Molecular Microbiology, 39, 1036–1047.

    Article  CAS  Google Scholar 

  34. Aoki–Kinoshita, K. F., & Kanehisa, M. (2007). Methods in Molecualr Biology, 396, 71–91.

    Article  Google Scholar 

  35. Moussatova, A., Kandt, C., O'Mara, M. L., & Tieleman, D. P. (2008). Biochimica Biophysica Acta, 1778, 1757–1771.

    Article  CAS  Google Scholar 

  36. Méndez, C., & Salas, J. A. (1998). FEMS Microbiology Letters, 158, 1–8.

    Article  Google Scholar 

  37. Méndez, C., & Salas, J. A. (2001). Research in Microbiology, 152, 341–350.

    Article  Google Scholar 

  38. Maqueda, M., Sánchez–Hidalgo, M., Fernández, M., Montalbán–López, M., Valdivia, E., & Martinez–Bueno, M. (2008). FEMS Microbiology Reviews, 32, 2–22.

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2012R1A1B3000933) and by the Chung-Ang University Research Grant in 2013.

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Authors and Affiliations

  1. Department of Systems Biotechnology (BK21 program), Chung-Ang University, An-seong, 456-756, Republic of Korea

    In-Cheol Yeo, Byung Wook Yang & Young Tae Hahm

  2. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA

    In-Cheol Yeo

  3. Research Center for Industrial Development of Biofood Materials, Chonbuk National University, Jeonju, 561-756, Republic of Korea

    Nam Keun Lee

Authors
  1. In-Cheol Yeo
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  2. Nam Keun Lee
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Correspondence to Young Tae Hahm.

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Yeo, IC., Lee, N.K., Yang, B.W. et al. RNA-seq Analysis of Antibiotic-Producing Bacillus subtilis SC-8 in Response to Signal Peptide PapR of Bacillus cereus . Appl Biochem Biotechnol 172, 580–594 (2014). https://doi.org/10.1007/s12010-013-0516-4

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  • DOI: https://doi.org/10.1007/s12010-013-0516-4

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