Browse > Article
http://dx.doi.org/10.4014/jmb.1906.06037

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)
Publication Information
Journal of Microbiology and Biotechnology / v.29, no.7, 2019 , pp. 1144-1154 More about this Journal
Abstract
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.
Keywords
Antimicrobial activity; draft genome sequencing; fingerprinting; Himalayan lichen-associated bacteria; polyketide synthase; secondary metabolites;
Citations & Related Records
연도 인용수 순위
  • Reference
1 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.   DOI
2 Bates ST, Cropsey GW, Caporaso JG, Knight R, Fierer N. 2011. Bacterial communities associated with the lichen symbiosis. Appl. Environ. Microbiol. 77: 1309-1314.   DOI
3 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.   DOI
4 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.   DOI
5 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.   DOI
6 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.   DOI
7 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.   DOI
8 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.   DOI
9 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.   DOI
10 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.   DOI
11 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.   DOI
12 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.   DOI
13 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.   DOI
14 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.   DOI
15 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.   DOI
16 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.   DOI
17 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.   DOI
18 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.   DOI
19 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.   DOI
20 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.   DOI
21 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.   DOI
22 Mushegian AA, Peterson CN, Baker CC, Pringle A. 2011. Bacterial diversity across individual lichens. Appl. Environ. Microbiol. 77: 4249-4252.   DOI
23 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.   DOI
24 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.   DOI
25 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.   DOI
26 Calcott MJ, Ackerley DF, Knight A, Keyzers RA, Owen JG. 2018. Secondary metabolism in the lichen symbiosis. Chem. Soc. Rev. 47: 1730-1760.   DOI
27 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.   DOI
28 Bertrand RL, Sorensen JL. 2018. A comprehensive catalogue of polyketide synthase gene clusters in lichenizing fungi. J. Ind. Microbiol. Biotechnol. 45: 1067-1081.   DOI
29 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.   DOI
30 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.   DOI
31 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.   DOI
32 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.   DOI
33 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.   DOI
34 Baniya CB, Solhoy T, Gauslaa Y, Palmer MW. 2010. The elevation gradient of lichen species richness in Nepal. Lichenologist 42: 83-96.   DOI