Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Toxic Pyrene Metabolism in Mycobacterium gilvum PYR-GCK Results in the Expression of Mammalian Cell Entry Genes as Revealed by Transcriptomics Study

  • Badejo, Abimbola Comfort (Department of Molecular and Life Science, Hanyang University) ;
  • Chung, Won Hyong (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Nam Shin (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Se Kye (Department of Molecular and Life Science, Hanyang University) ;
  • Chai, Jin Choul (Department of Molecular and Life Science, Hanyang University) ;
  • Lee, Young Seek (Department of Molecular and Life Science, Hanyang University) ;
  • Jung, Kyoung Hwa (Department of Molecular and Life Science, Hanyang University) ;
  • Kim, Hyo Joon (Department of Molecular and Life Science, Hanyang University) ;
  • Chai, Young Gyu (Department of Molecular and Life Science, Hanyang University)
  • Received : 2013.12.02
  • Accepted : 2014.06.09
  • Published : 2014.09.28
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Abstract

Mycobacterium gilvum PYR-GCK is a bacterial strain under study for its bioremediation use on heavy hydrocarbon pollutants in the environment. During the course of our study, mammalian cell entry (mce) genes, known to facilitate pathogenicity in M. tuberculosis, were highly expressed during a comparative and substrate-related cultural global transcriptomic study. RNA sequencing of the global transcriptome of the test strain in two different substrates, pyrene and glucose, showed high expression of the mce genes based on the differential results. After validating the expression of these genes with quantitative real-time PCR, we arrived at the conclusion that the genes were expressed based on the pyrene substrate (a phytosterol compound), and sterol metabolism is said to activate the expression of the mce genes in some actinomycetes bacteria, M. gilvum PYR-GCK in this case. This study is believed to be important based on the fact that some mycobacterial strains are undergoing a continuous research as a result of their use in practical bioremediation of anthropogenic exposure of toxic organic wastes in the environment.

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References

  1. Arruda S, Bomfim G, Knights R, Huima-Byron T, Riley LW. 1993. Cloning of an M. tuberculosis DNA fragment associated with entry and survival inside cells. Science 261: 1454-1457. https://doi.org/10.1126/science.8367727
  2. Badejo AC, Badejo AO, Shin KH, Chai YG. 2013. A gene expression study of the activities of aromatic ring-cleavage dioxygenases in Mycobacterium gilvum PYR-GCK to changes in salinity and pH during pyrene degradation. Plos One 8: e58066 https://doi.org/10.1371/journal.pone.0058066
  3. Badejo AC, Choi CW, Badejo AO, Shin KH, Hyun JH, Lee YG, et al. 2013. A global proteome study of Mycobacterium gilvum PYR-GCK grown on pyrene and glucose reveals the activation of glyoxylate, shikimate and gluconeogenetic pathways through the central carbon metabolism highway. Biodegradation 24: 741-752. https://doi.org/10.1007/s10532-013-9622-9
  4. Boonchan S, Britz ML, Stanley GA. 2000. Degradation and mineralization of high-molecular-weight polycyclic aromatic hydrocarbons by defined fungal-bacterial cocultures. Appl. Environ. Microbiol. 66: 1007-1019. https://doi.org/10.1128/AEM.66.3.1007-1019.2000
  5. Clark CL, Seipke RF, Prieto P, Willemse J, van Wezel GP, Hutchings MI, Hoskisson PA. 2013. Mammalian cell entry genes in Streptomyces may provide clues to the evolution of bacterial virulence. Sci. Rep. 3: 1109. https://doi.org/10.1038/srep01109
  6. Casali N, Riley LW. 2007. A phylogenomic analysis of the Actinomycetales mce operons. BMC Genom. 8: 60. https://doi.org/10.1186/1471-2164-8-60
  7. Cerniglia CE. 1984. Microbial metabolism of polycyclic aromatic hydrocarbons. Adv. Appl. Microbiol. 30: 31-71. https://doi.org/10.1016/S0065-2164(08)70052-2
  8. Chitale S, Ehrt S, Kawamura I, Fujimura T, Shimono N, Anand N, et al. 2001. Recombinant Mycobacterium tuberculosis protein associated with mammalian cell entry. Cell. Microbiol. 3: 247-254. https://doi.org/10.1046/j.1462-5822.2001.00110.x
  9. Gioffre A, Infante E, Aguilar D, Santangelo MP, Klepp L, Amadio A, et al. 2005. Mutation in mce operons attenuates Mycobacterium tuberculosis virulence. Microb. Infect. 7: 325-334. https://doi.org/10.1016/j.micinf.2004.11.007
  10. Haile Y, Caugant DA, Bjune G, Wiker HG. 2002. Mycobacterium tuberculosis mammalian cell entry operon (mce) homologs in Mycobacterium other than tuberculosis (MOTT). FEMS Immunol. Med. Microbiol. 33: 125-132. https://doi.org/10.1111/j.1574-695X.2002.tb00581.x
  11. Klepp LI, Forrellad MA, Osella AV, Blanco FC, Stella EJ, Bianco MV, et al. 2012. Impact of the deletion of the six mce operons in Mycobacterium smegmatis. Microb. Infect. 14: 590-599. https://doi.org/10.1016/j.micinf.2012.01.007
  12. Krauss M, Wilcke W, Martius C, Bandeira AG, Garcia MV, Amelung W. 2005. Atmospheric versus biological sources of polycyclic aromatic hydrocarbons (PAHs) in a tropical rain forest environment. Environ. Pollut. 135: 143-154. https://doi.org/10.1016/j.envpol.2004.09.012
  13. Kumar A, Bose M, Brahmachari V. 2003. Analysis of expression profile of mammalian cell entry (mce) operons of Mycobacterium tuberculosis. Infect. Immun. 71: 6083-6087. https://doi.org/10.1128/IAI.71.10.6083-6087.2003
  14. Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408. https://doi.org/10.1006/meth.2001.1262
  15. McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, et al. 2006. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc. Natl. Acad. Sci. USA 103: 15582-15587. https://doi.org/10.1073/pnas.0607048103
  16. Mohn WW, van der Geize R, Stewart GR, Okamoto S, Liu J, Dijkhuizen L, Eltis LD. 2008. The actinobacterial mce4 locus encodes a steroid transporter. J. Biol. Chem. 283: 35368-35374. https://doi.org/10.1074/jbc.M805496200
  17. Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5: 621-628. https://doi.org/10.1038/nmeth.1226
  18. Peng RH, Xiong AS, Xue Y, Fu XY, Gao F, Zhao W, et al. 2008. Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol. Rev. 32: 927-955. https://doi.org/10.1111/j.1574-6976.2008.00127.x
  19. Rozen S, Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132: 365-386.
  20. Sassetti CM, Rubin EJ. 2003. Genetic requirements for mycobacterial survival during infection. Proc. Natl. Acad. Sci. USA 100: 12989-12994. https://doi.org/10.1073/pnas.2134250100
  21. Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, et al. 2006. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol. Biol. 7: 3. https://doi.org/10.1186/1471-2199-7-3
  22. Shimono N, Morici L, Casali N, Cantrell S, Sidders B, Ehrt S, Riley LW. 2003. Hypervirulent mutant of Mycobacterium tuberculosis resulting from disruption of the mce1 operon. Proc. Natl. Acad. Sci. USA 100: 15918-15923. https://doi.org/10.1073/pnas.2433882100
  23. Shuttleworth KL, Cerniglia CE. 1995. Environmental aspects of PAH biodegradation. Appl. Biochem. Biotechnol. 54: 291-302. https://doi.org/10.1007/BF02787927
  24. Slaytor M, Bloch K. 1965. Metabolic transformation of cholestenediols. J. Biol. Chem. 240: 4598-4602.
  25. Stingley RL, Brezna B, Khan AA, Cerniglia CE. 2004. Novel organization of genes in a phthalate degradation operon of Mycobacterium vanbaalenii PYR-1. Microbiology 150: 3749-3761. https://doi.org/10.1099/mic.0.27263-0
  26. Tekaia F, Gordon SV, Garnier T, Brosch R, Barrell BG, Cole ST. 1999. Analysis of the proteome of Mycobacterium tuberculosis in silico. Tuber. Lung Dis. 79: 329-342. https://doi.org/10.1054/tuld.1999.0220
  27. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28: 511-515. https://doi.org/10.1038/nbt.1621
  28. Van der Geize R, Yam K, Heuser T, Wilbrink MH, Hara H, Anderton MC, et al. 2007. A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc. Natl. Acad. Sci. USA 104: 1947-1952. https://doi.org/10.1073/pnas.0605728104
  29. Wipperman MF, Yang M, Thomas ST, Sampson NS. 2013. Shrinking the FadE proteome of Mycobacterium tuberculosis: insights into cholesterol metabolism through identification of an alpha2beta2 heterotetrameric acyl coenzyme A dehydrogenase family. J. Bacteriol. 195: 4331-4341. https://doi.org/10.1128/JB.00502-13

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