Journal of Microbiology and Biotechnology

  • 제29권7호
  • /
  • Pages.1144-1154
  • /
  • 2019
  • /
  • 1017-7825(pISSN)
  • /
  • 1738-8872(eISSN)
한국미생물·생명공학회 (The Korean Society for Microbiology and Biotechnology)
권호 표지
DOI QR코드

DOI QR Code

Draft Genome Analysis of Antimicrobial Streptomyces Isolated from Himalayan Lichen

  • Kim, Byeollee (Department of Life Science and Biochemical Engineering, SunMoon University) ;
  • Han, So-Ra (Department of Life Science and Biochemical Engineering, SunMoon University) ;
  • Lamichhane, Janardan (Department of Biotechnology, Kathmandu University) ;
  • Park, Hyun (Unit of Polar Genomics, Korea Polar Research Institute) ;
  • Oh, Tae-Jin (Department of Life Science and Biochemical Engineering, SunMoon University)
  • 투고 : 2019.06.17
  • 심사 : 2019.07.09
  • 발행 : 2019.07.28
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

There have been several studies regarding lichen-associated bacteria obtained from diverse environments. Our screening process identified 49 bacterial species in two lichens from the Himalayas: 17 species of Actinobacteria, 19 species of Firmicutes, and 13 species of Proteobacteria. We discovered five types of strong antimicrobial agent-producing bacteria. Although some strains exhibited weak antimicrobial activity, NP088, NP131, NP132, NP134, and NP160 exhibited strong antimicrobial activity against all multidrug-resistant strains. Polyketide synthase (PKS) fingerprinting revealed results for 69 of 148 strains; these had similar genes, such as fatty acid-related PKS, adenylation domain genes, PfaA, and PksD. Although the association between antimicrobial activity and the PKS fingerprinting results is poorly resolved, NP160 had six types of PKS fingerprinting genes, as well as strong antimicrobial activity. Therefore, we sequenced the draft genome of strain NP160, and predicted its secondary metabolism using antiSMASH version 4.2. NP160 had 46 clusters and was predicted to produce similar secondary metabolites with similarities of 5-100%. Although NP160 had 100% similarity with the alkylresorcinol biosynthetic gene cluster, our results showed low similarity with existing members of this biosynthetic gene cluster, and most have not yet been revealed. In conclusion, we expect that lichen-associated bacteria from the Himalayas can produce new secondary metabolites, and we found several secondary metabolite-related biosynthetic gene clusters to support this hypothesis.

키워드

참고문헌

  1. White PA, Oliveira RC, Oliveira AP, Serafini MR, Araujo AA, Gelain DP, et al. 2014. Antioxidant activity and mechanisms of action of natural compounds, isolated from lichens: a systematic review. Molecules 19: 14496-14527. https://doi.org/10.3390/molecules190914496
  2. He H, Bigelis R, Yang HY, Chang LP, Singh MP. 2005. Lichenicolins A and B, new bisnaphthopyrones from an unidentified lichenicolous fungus, strain LL-RB0668. J. Antibiot. Tokyo 58: 731-736. https://doi.org/10.1038/ja.2005.99
  3. Oksanen I, Jokela J, Fewer DP, Wahlsten M, Rikkinen J, Sivonen K. 2004. Discovery of rare and highly toxic microcystins from lichen-associated cyanobacterium Nostoc sp. strain IO-102-I. Appl. Environ. Microbiol. 70: 5756-5763. https://doi.org/10.1128/AEM.70.10.5756-5763.2004
  4. Mushegian AA, Peterson CN, Baker CC, Pringle A. 2011. Bacterial diversity across individual lichens. Appl. Environ. Microbiol. 77: 4249-4252. https://doi.org/10.1128/AEM.02850-10
  5. Parrot D, Legrave N, Delmail D, Grube M, Suzuki M, Tomasi S. 2016. Review - lichen-associated bacteria as a hot spot of chemodiversity: focus on uncialamycin, a promising compound for future medicinal applications. Planta Med. 82: 1143-1152. https://doi.org/10.1055/s-0042-105571
  6. Parrot D, Intertaglia L, Jehan P, Grube M, Suzuki MT, Tomasi S. 2018. Chemical analysis of the alphaproteobacterium strain MOLA1416 associated with the marine lichen Lichina pygmaea. Phytochemistry 145: 57-67. https://doi.org/10.1016/j.phytochem.2017.10.005
  7. Bertrand RL, Sorensen JL. 2018. A comprehensive catalogue of polyketide synthase gene clusters in lichenizing fungi. J. Ind. Microbiol. Biotechnol. 45: 1067-1081. https://doi.org/10.1007/s10295-018-2080-y
  8. Miyanaga A, Kudo F, Eguchi T. 2018. Protein-protein interactions in polyketide synthase-nonribosomal peptide synthetase hybrid assembly lines. Nat. Prod. Rep. 35: 1185-1209. https://doi.org/10.1039/C8NP00022K
  9. Zhang W, Zhang F, Li Z, Miao X, Meng Q, Zhang X. 2009. Investigation of bacteria with polyketide synthase genes and antimicrobial activity isolated from South China Sea sponges. J. Appl. Microbiol. 107: 567-575. https://doi.org/10.1111/j.1365-2672.2009.04241.x
  10. Ayuso-Sacido A, Genilloud O. 2005. New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb. Ecol. 49: 10-24. https://doi.org/10.1007/s00248-004-0249-6
  11. Sigurbjornsdottir MA, Vilhelmsson O. 2016. Selective isolation of potentially phosphate-mobilizing, biosurfactant-producing and biodegradative bacteria associated with a sub-Artic, terricolous lichen, Peltigera membranacea. FEMS Microbiol. Ecol. 92(6): fiw090. https://doi.org/10.1093/femsec/fiw090
  12. Sigurbjornsdottir MA, Heiomarsson S, Jonsdottir AR, Vilhelmsson O. 2014. Novel bacteria associated with Arctic seashore lichens have potential roles in nutrient scavenging. Can. J. Microbiol. 60: 307-317. https://doi.org/10.1139/cjm-2013-0888
  13. Baniya CB, Solhoy T, Gauslaa Y, Palmer MW. 2010. The elevation gradient of lichen species richness in Nepal. Lichenologist 42: 83-96. https://doi.org/10.1017/S0024282909008627
  14. Devkota S, Chaudhary RP, Werth S, Scheidegger C. 2017. Indigenous knowledge and use of lichens by the lichenophilic communities of the Nepal Himalaya. J. Ethnobiol. Ethnomed. 13: 1-10. https://doi.org/10.1186/s13002-016-0106-y
  15. Jha BN, Shrestha M, Pandey DP, Bhattarai T, Bhattarai HD, Paudel B. 2017. Investigation of antioxidant, antimicrobial and toxicity activities of lichens from high altitude regions of Nepal. BMC Complement Altern. Med. 17(1): 282 doi: 10.1186/s12906-017-1797-x.
  16. Bates ST, Cropsey GW, Caporaso JG, Knight R, Fierer N. 2011. Bacterial communities associated with the lichen symbiosis. Appl. Environ. Microbiol. 77: 1309-1314. https://doi.org/10.1128/AEM.02257-10
  17. Han SR, Yu SC, Ahn DH, Park H, Oh TJ. 2016. Complete genome sequence of Burkholderia sp. strain PAMC28687, a potential octopine-utilizing bacterium isolated from Antarctica lichen. J. Biotechnol. 226: 16-17. https://doi.org/10.1016/j.jbiotec.2016.03.043
  18. Kim MK, Park H, Oh TJ. 2014. Antibacterial and antioxidant capacity of polar microorganisms isolated from Arctic lichen Ochrolechia sp. Pol. J. Microbiol. 63: 317-322. https://doi.org/10.33073/pjm-2014-042
  19. Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120. https://doi.org/10.1007/BF01731581
  20. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35: 1547-1549. https://doi.org/10.1093/molbev/msy096
  21. Bauer AW, Kirby MM, Sherris JC, Truck M. 1966. Antibiotic susceptibility testing by a standardized single disk method. Am. J. Clinic. Pathol. 45: 493-496. https://doi.org/10.1093/ajcp/45.4_ts.493
  22. Zhao K, Penttinen P, Guan T, Xiao J, Chen Q, Xu J, et al. 2011. The diversity and anti-microbial activity of endophytic actinomycetes isolated from medicinal plants in Panxi plateau, China. Curr. Microbiol. 62: 182-190. https://doi.org/10.1007/s00284-010-9685-3
  23. Gaber AA, Badr OM, Emara SA, Ibrahim AM. 2015. Antitumor activity of two Streptomyces extracts (Ag18 & Ag20) on Ehrlich ascites tumor in mice: in vitro and in vivo studies. J. Biosci. Appl. Res. 1: 20-29. https://doi.org/10.21608/jbaar.2015.105946
  24. Wawrik B, Kerkhof L, Zylstra GJ, Kukor JJ. 2005. Identification of unique type II polyketide synthase genes in soil. Appl. Environ. Microbiol. 71: 2232-2238. https://doi.org/10.1128/AEM.71.5.2232-2238.2005
  25. Han SR, Lee JH, Kang S, Park H, Oh TJ. 2016. Complete genome sequence of opine-utilizing Variovorax sp. strain PAMC28711 isolated from an Antarctic lichen. J. Biotechnol. 225: 46-47. https://doi.org/10.1016/j.jbiotec.2016.03.042
  26. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75. https://doi.org/10.1186/1471-2164-9-75
  27. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, et al. 2017. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 45: W36-W41. https://doi.org/10.1093/nar/gkx319
  28. Ayuso A, Clark D, Gonzalez I, Salazar O, Anderson A, Genilloud O. 2005. A novel actinomycete strain de-replication approach based on the diversity of polyketide synthase and nonribosomal peptide synthetase biosynthetic pathways. Appl. Microbiol. Biotechnol. 67: 795-806. https://doi.org/10.1007/s00253-004-1828-7
  29. Zheng KX, Jiang Y, Jiang JX, Huang R, He J, Wu SH. 2019. A new phthalazinone derivative and a new isoflavonid glycoside from lichen-associated Amycolatopsis sp. Fitoterapia 135: 85-89. https://doi.org/10.1016/j.fitote.2019.04.011
  30. Sigurbjornsdottir MA, Andresson OS, Vilhelmsson O. 2016. Nutrient scavenging activity and antagonistic factors of non-photobiont lichen-associated bacteria: a review. World J. Microbiol. Biotechnol. 32: 68. https://doi.org/10.1007/s11274-016-2019-2
  31. Butcher RA, Schroeder FC, Fischbach MA, Straight PD, Kolter R, Walsh CT, Clardy J. 2007. The identification of bacillaene, the product of the PksX megacomplex in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 104: 1506-1509. https://doi.org/10.1073/pnas.0610503104
  32. Schneider O, Simic N, Aachmann FL, Ruckert C, Kristiansen KA, Kalinowski J, et al. 2018. Genome mining of Streptomyces sp. YIM 130001 isolated from lichen affords new thiopeptide antibiotic. Front Microbiol. 9: 3139. https://doi.org/10.3389/fmicb.2018.03139
  33. Jeon BJ, Kim JD, Han JW, Kim BS. 2016. Antifungal activity of rimocidin and a new rimocidin derivative BU16 produced by Streptomyces mauvecolor BU16 and their effects on pepper anthracnose. J. Appl. Microbiol. 120: 1219-1228. https://doi.org/10.1111/jam.13071
  34. Calcott MJ, Ackerley DF, Knight A, Keyzers RA, Owen JG. 2018. Secondary metabolism in the lichen symbiosis. Chem. Soc. Rev. 47: 1730-1760. https://doi.org/10.1039/C7CS00431A

피인용 문헌

  1. Properties of Modestobacter deserti sp. nov., a Kind of Novel Phosphate-Solubilizing Actinobacteria Inhabited in the Desert Biological Soil Crusts vol.12, 2021, https://doi.org/10.3389/fmicb.2021.742798