Skip to main content
Log in

Implication of PKS type I gene and chromatographic strategy for the biodiscovery of antimicrobial polyketide metabolites from endosymbiotic Nocardiopsis prasina CLA68

  • Original Paper
  • Published:
The Science of Nature Aims and scope Submit manuscript

Abstract

Advanced approach in probing for polyketide antimicrobials requires novel genomics and chromatographic strategies. An endophytic strain CLA68 was isolated from the root of Combretum latifolium Blume (Combretaceae) collected from the Western Ghats of Southern India. Strain CLA68 was then identified as Nocardiopsis prasina by its characteristic culture morphology and analysis of 16S rRNA gene sequence. Biosynthetic polyketide synthase genes were investigated using two pairs of degenerate primers. Ethyl acetate extract of CLA68 exhibited broad spectrum activity against a panel of test human pathogens. PKS type-I gene detection and chromatographic strategy yielded a robust polyketide antimicrobial compound which identified as nocapyrone E. Minimum inhibitory concentration of the purified compound against MRSA and other human pathogens ranged between 25 and 100 μg/ml. The present work highlights the utility of N. prasina CLA68 as potential source for antimicrobial polyketide nocapyrone E which could help to combat multidrug-resistant pathogens. This study demonstrates feasibility of PKS type-I gene-based molecular approach and chemical investigation by chromatographic approach is the best method for prediction and rapid discovery of novel polyketides from endosymbiotic actinomycetes. The sequence data of this endosymbiotic actinomycete is deposited in GenBank under the accession no. KP269077.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Anibou M, Zyadi A, Chait A, Benharref A, Ouhdouch Y (2008) Actinomycetes from Moroccan habitats: isolation and screening for cytotoxic activities. World J Microbiol Biotechnol 24:2019–2025

    Article  Google Scholar 

  • Atlas RM (2010) Handbook of microbiological media, 4th edn. CRC Press, London

    Book  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Bennur N, Kumar AR, Zinjarde S, Javdekar V (2015) Nocardiopsis species: incidence, ecological roles and adaptations. Microbiol Res 174:33–47

    Article  PubMed  Google Scholar 

  • Chairat M, Bremner JB, Samosorn S, Sajomsang W, Chongkraijak W, Saisara A (2015) Effects of additives on the dyeing of cotton yarn with the aqueous extract of Combretum latifolium Blume stems. Color Technol 131:310–315

    Article  CAS  Google Scholar 

  • Chen YG, Zhang YQ, Tang SK, Liu ZX, Xu LH, Zhang LX, Li WJ (2010) Nocardiopsis terrae sp. nov., a halophilic actinomycete isolated from saline soil. Antonie Van Leeuwenhoek 98:31–38

    Article  PubMed  Google Scholar 

  • Chooi Y, Tang Y (2012) Navigating the fungal polyketide chemical space: from genes to molecules. J Org Chem 77:9933–9953

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Christina A, Christapher V, Bhore SJ (2013) Endophytic bacteria as a source of novel antibiotics: an overview. Pharmacogn Rev 7:11–16

    Article  PubMed  PubMed Central  Google Scholar 

  • Chun J, Bae KS, Moon EY, Jung SO, Lee HK, Kim SJ (2000) Nocardiopsis kunsanensis sp. nov., a moderately halophilic actinomycete isolated from a saltern. Int J Syst Evol Microbiol 50:1909–1913

    Article  CAS  PubMed  Google Scholar 

  • Cragg GM, Newman DJ (2013) Natural products: a continuing source of novel drug leads. Biochim Biophys Acta 1830:3670–3695

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74:417–433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Debnath B, Debnath A, Shilsharma A, Paul C (2014) Ethnomedicinal knowledge of Mog and Reang communities of south district of Tripura, India. Indian J Adv Plant Res 1:49–54

    Google Scholar 

  • Deepika VB, Murali TS, Satyamoorthy K (2016) Modulation of genetic clusters for synthesis of bioactive molecules in fungal endophytes: a review. Microbiol Res 182:125–140

    Article  CAS  PubMed  Google Scholar 

  • Ding ZG, Zhao JY, Li MG, Huang R, Li QM, Cui XL, Zhu HJ, Wen ML (2012) Griseusins F and G, spiro-naphthoquinones from a tin mine tailings-derived alkalophilic Nocardiopsis species. J Nat Prod 75:1994–1998

    Article  CAS  PubMed  Google Scholar 

  • Engelhardt K, Degnes KF, Kemmler M, Bredholt H, Fjaervik E, Klinkenberg G, Sletta H, Ellingsen TE, Zotchev SB (2010) Production of a new thiopeptide antibiotic TP-1161, by a marine Nocardiopsis species. Appl Environ Microbiol 76:4969–4976

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fu P, Liu P, Qu H, Wang Y, Chen D, Wang H, Li J, Zhu W (2011) α-Pyrones and diketopiperazine derivatives from the marine-derived actinomycete Nocardiopsis dassonvillei HR10-5. J Nat Prod 74:2219–2222

    Article  CAS  PubMed  Google Scholar 

  • Fu P, Liu P, Gong Q, Wang Y, Wanga P, Zhu W (2013) α-Pyrones from the marine-derived actinomycete Nocardiopsis dassonvillei subsp. dassonvillei XG-8-1. RSC Adv. 3:20726–20731

  • Fujii I, Watanabe A, Sankawa U, Ebizuka Y (2001) Identification of a Claisen cyclase domain in fungal polyketide synthase WA, a naphthopyrone synthase of Aspergillus nidulans. Chem Biol 8:189–197

    Article  CAS  PubMed  Google Scholar 

  • Golinska P, Magdalena W, Agarkar G, Rathod D, Dahm H, Rai M (2015) Endophytic actinobacteria of medicinal plants: diversity and bioactivity. Antonie van Leeuwenhoek. 108:267–289

  • Gordon RE, Barnett DA, Handerhan JE, Pang CH (1974) Nocardia coeliaca, Nocardia autotrophica and the Nocardin strain. Int J Syst Bacteriol 24:54–63

    Article  Google Scholar 

  • Grund E, Kroppenstedt RM (1990) Chemotaxonomy and numerical taxonomy of the genus Nocardiopsis Meyer 1976. Int J Syst Bacteriol 40:5–11

    Article  Google Scholar 

  • Jose PA, Jebakumar SR (2012) Phylogenetic diversity of actinomycetes cultured from coastal multipond solar saltern in Tuticorin, India. Aquat Biosyst 8:23–31

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jumpathong J, Seshime Y, Fujii I, Peberdy J, Lumyong S (2011) Genome screening for reducing type I polyketide synthase genes in tropical fungi associated with medicinal plants. World J Microbiol Biotechnol 27:1989–1995

    Article  CAS  Google Scholar 

  • Kapetanovic IM (2008) Computer-aided drug discovery and development (CADDD): In silico-chemico-biological approach. Chem Biol Interact 171:165–176

    Article  CAS  PubMed  Google Scholar 

  • Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA (2000) Practical Streptomyces genetics. John Innes Foundation, Norwich

    Google Scholar 

  • Kim MC, Kwon OW, Park JS, Kim SY, Kwon HC (2013) Nocapyrones H–J, 3,6-disubstituted α-pyrones from the marine actinomycete Nocardiopsis sp. KMF-001. Chem Pharm Bull 61:511–515

    Article  CAS  PubMed  Google Scholar 

  • Kim Y, Ogura H, Akasaka K, Oikawa T, Matsuura N, Imada C, Yasuda H, Igarashi Y (2014) Nocapyrones: α- and γ-Pyrones from a marine-derived Nocardiopsis sp. Mar Drugs 12:4110–4125

    Article  PubMed  PubMed Central  Google Scholar 

  • Kornerup A, Wanscher JH (1978) Methuen handbook of colour. Eyre Methuen, London

    Google Scholar 

  • Kurup PV, Schmitt JA (1973) Numerical taxonomy of Nocardia. Can J Microbiol 19:1035–1048

    Article  CAS  PubMed  Google Scholar 

  • Kusari P, Kusari S, Eckelmann D, Zuhlke S, Kayser O, Spiteller M (2016) Cross-species biosynthesis of maytansine in Maytenus serrata. RSC Adv 6:10011–10016

    Article  CAS  Google Scholar 

  • Li WJ, Kroppenstedt RM, Wang D, Tang SK, Lee JC, Park DJ, Kim CJ, Xu LH, Jiang CL (2006) Five novel species of the genus Nocardiopsis isolated from hyper saline soils and emended description of Nocardiopsis salina. Int J Syst Evol Microbiol 56:1089–1096

    Article  CAS  PubMed  Google Scholar 

  • Li YQ, Li MG, Li W, Zhao JY, Ding ZG, Cui XL, Wen ML (2007) Griseusin D, a new pyranonaphtho-quinone derivative from a alkaphilic Nocardiopsis sp. J Antibiot 60:757–761

    Article  CAS  PubMed  Google Scholar 

  • Li J, Yang J, Zhu WY, He J, Tian XP, Xie Q, Zhang S, Li WJ (2012) Nocardiopsis coralliicola sp. nov., isolated from the gorgonian coral, Menella praelonga. Int J Syst Evol Microbiol 62:1653–1658

    Article  CAS  PubMed  Google Scholar 

  • Mansson M, Rank C, Frisvad JS, Lasen TO (2011) Dereplication of microbial natural products by LC-DAD-TOFMS. J Nat Prod 74:2338–2348

    Article  PubMed  Google Scholar 

  • Meena B, Rajan LA, Vinithkumar NV, Kirubagaran R (2013) Novel marine actinobacteria from emerald Andaman and Nicobar Islands: a prospective source for industrial and pharmaceutical by products. BMC Microbiol 13:145–161

    Article  PubMed  PubMed Central  Google Scholar 

  • Messaoudi O, Bendahou M, Benamur I, Abdelwouhid D (2015) Identification and preliminary characterization of non-polyene antibiotics secreted by new strain of actinomycete isolated from Sebkha of Kenadsa, Algeria. Asian Pac J Trop Biomed 5:438–445

    Article  Google Scholar 

  • Metsa-Ketela M, Salo V, Halo L, Hautala A, Hakala J, Mantsala P, Ylihonko K (1999) An efficient approach for screening minimal PKS genes from Streptomyces. FEMS Microbiol Lett 180:1–6

    Article  CAS  PubMed  Google Scholar 

  • Meyer J (1976) Nocardiopsis, a new genus of the order Actinomycetales. Int J Syst Bacteriol 26:487–493

    Article  Google Scholar 

  • Myres N, Mittermeier RA, Mittermeier CG, Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858

    Article  Google Scholar 

  • Nopsiri W, Chansakaow S, Putiyanan S, Natakankitkul S, Santiarworn D (2014) Antioxidant and anticancer activities from leaf extracts of four Combretum species from Northern Thailand. CMU J Nat Sci 13:195–205

    Google Scholar 

  • Nopsiri W, Chansakaow S, Putiyanan S, Natakankitkul S, Nantachit K, Khantawa B, Santiarworn D (2015) Chemical constituents and antibacterial activity of volatile oils of Combretum latifolium Bl. and C. quadrangulare Kurz Leaves. CMU J Nat Sci 14:245–256

    Google Scholar 

  • Padhi S, Tayung K (2013) Antimicrobial activity and molecular characterization of an endophytic fungus, Quambalaria sp. isolated from Ipomoea carnea. Ann Microbiol 63:793–800

    Article  CAS  Google Scholar 

  • Passari AK, Mishra VK, Saikia R, Gupta VK, Singh BP (2015) Isolation, abundance and phylogenetic affiliation of endophytic actinomycetes associated with medicinal plants and screening for their in vitro antimicrobial biosynthetic potential. Front Microbiol 6:273. doi:10.3389/fmicb.2015.00273

    Article  PubMed  PubMed Central  Google Scholar 

  • Patra JK, Gouda S, Sahoo SK, Thatoi HN (2012) Chromatography separation, 1H NMR analysis and bioautography screening of methanol extract of Excoecaia agallocha L. from Bhitarkanika, Orissa, India. Asian Pac J Trop Biomed 2(1):S50–S56

  • Pimentel MR, Molina G, Dionisio AP, Marostica Junior MRM, Pastore GM (2011) The use of endophytes to obtain bioactive compounds and their application in biotransformation process. Biotechnol Res Int 2011:576286

    Article  PubMed  Google Scholar 

  • Qin S, Li J, Chen HH, Zhao GZ, Zhu WY, Jiang CL, Xu LH, Li WJ (2009) Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China. Appl Environ Microbiol 75:6176–6186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qin S, Xing K, Jiang J, Xu L, Li W (2011) Biodiversity, bioactive natural products and biotechnological potential of plant-associated endophytic actinobacteria. Appl Microbiol Biotechnol 89:457–473

    Article  CAS  PubMed  Google Scholar 

  • Rakshith D, Santosh P, Tarman K, Gurudatt DM, Satish S (2013) Dereplication strategy for antimicrobial metabolite using thin-layer chromatography–bioautography and LC– PDA–MS analysis. J Planar Chromatogr Mod TLC 26:470–474

    Article  CAS  Google Scholar 

  • Ramesh S, Mathivanan N (2009) Screening of marine actinomycetes isolated from the Bay of Bengal, India for antimicrobial activity and industrial enzymes. World J Microbiol Biotechnol 25:2103–2111

    Article  CAS  Google Scholar 

  • Rao HCY, Satish S (2015) Genomic and chromatographic approach for the discovery of polyketide antimicrobial metabolites from an endophytic Phomopsis liquidambaris CBR-18. Front Life Sci 8:200–207

    Article  CAS  Google Scholar 

  • Rao HCY, Baker S, Rakshith D, Satish S (2015a) Molecular profiling and antimicrobial potential of endophytic Gliomastix polychroma CLB32 inhabiting Combretum latifolium Blume. Mycology 6:176–181

    Article  Google Scholar 

  • Rao HCY, Rakshith D, Satish S (2015b) Antimicrobial proprieties of endophytic actinomycetes isolated from Combretum latifolium Blume, a medicinal shrub from Western Ghats of India. Front Biol 10:528–536

    Article  Google Scholar 

  • Rao HCY, Santosh P, Rakshith D, Satish S (2015c) Molecular characterization of an endophytic Phomopsis liquidambaris CBR-15 from Cryptolepis buchanani Roem. and impact of culture media on biosynthesis of antimicrobial metabolites. 3Biotech 5:165–173

    Google Scholar 

  • Schneemann I, Ohlendorf B, Zinecker H, Nagel K, Wiese J, Imhoff JF (2010) Nocapyrones A-D, γ-pyrones from a Nocardiopsis strain isolated from the marine sponge Halichondria panicea. J Nat Prod 73:1444–1447

    Article  CAS  PubMed  Google Scholar 

  • Schumann J, Hertweck C (2006) Advances in cloning, functional analysis and heterologous expression of fungal polyketide synthase genes. J Biotechnol 124:690–703

    Article  PubMed  Google Scholar 

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  • Subramani R, Aalbersberg W (2012) Marine actinomycetes: an ongoing source of novel bioactive metabolites. Microbiol Res 167:571–580

    Article  CAS  PubMed  Google Scholar 

  • Suthari S, Sreeramalu N, Omkar K, Raju VS (2014) The climbing plants of northern Telangana in India and their ethnomedicinal and economic uses. Indian J Plant Sci 3:86–100

    Google Scholar 

  • Tabbene O, Slimene IB, Djebali K, Mangoni ML, Urdaci MC, Limam F (2009) Optimization of medium composition for the production of antimicrobial activity by Bacillus subtilis B38. Biotechnol Prog 25:1267–1274

    Article  CAS  PubMed  Google Scholar 

  • Turner TR, James EK, Poole PS (2013) The plant microbiome. Genome Biol 14:209

    Article  PubMed  PubMed Central  Google Scholar 

  • Valgas C, De Souza SM, Smania EFA, Smania AJ (2007) Screening methods to determine antibacterial activity of natural products. Braz J Microbiol 38:369–380

    Article  Google Scholar 

  • Wang LW, Xu G, Wang JY, Su ZZ, Lin FC, Zhang CL, Kubicek CP (2012) Bioactive metabolites from Phoma species, an endophytic fungus from the Chinese medicinal plant Arisaema erubescens. Appl Microbiol Biotechnol 93:1231–1239

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Wang G, Zhang Y, Zheng B, Zhang C, Wang L (2014) Isolation and identification of an endophytic fungus Pezicula sp. in Forsythia viridissima and its secondary metabolites. World J Microbiol Biotechnol 30:2639–2644

    Article  CAS  PubMed  Google Scholar 

  • Weber T, Welzel K, Pelzer S, Vente A, Wohlleben W (2003) Exploiting the genetic potential of polyketide producing streptomycetes. J Biotechnol 106:221–232

    Article  CAS  PubMed  Google Scholar 

  • Zhao K, Penttinen P, Guan T, Xiao J, Chen Q, Xu J, Lindström K, Zhang L, Zhang X, Strobel GA (2011) The diversity and anti-microbial activity of endophytic actinomycetes isolated from medicinal plants in Panxi plateau, China. Curr Microbiol 62:182–190

    Article  CAS  PubMed  Google Scholar 

  • Zhou J, Tang X, Martin GB (1997) The Pto kinase conferring resistance to tomato bacterial speck disease interacts with proteins that bind a cis-element of pathogenesis-related genes. EMBO J 16:3207–3218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

We are grateful to University Grants Commission (UGC) and University of Mysore, India, for providing financial assistance (order no: DV9/405/Misc/2014-15, dated 24/02/2015) to the first author. We also thank Indian Institute of Science, Bengaluru, India and Institution of Excellence, University of Mysore, India, for providing instrumentation facilities.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sreedharamurthy Satish.

Ethics declarations

Conflict of interest

All authors declares that they have no conflict of interest.

Additional information

Communicated by: Sven Thatje

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOCX 869 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Rao, H.C.Y., Rakshith, D., Gurudatt, D.M. et al. Implication of PKS type I gene and chromatographic strategy for the biodiscovery of antimicrobial polyketide metabolites from endosymbiotic Nocardiopsis prasina CLA68. Sci Nat 103, 45 (2016). https://doi.org/10.1007/s00114-016-1370-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00114-016-1370-3

Keywords

Navigation