New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp MP131-18

Paulus C, Rebets Y, Tokovenko B, Nadmid S, Terekhova LP, Myronovskyi M, Zotchev SB, Rückert C, Braig S, Zahler S, Kalinowski J, et al. (2017)
SCIENTIFIC REPORTS 7(1): 42382.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Paulus, Constanze; Rebets, Yuriy; Tokovenko, Bogdan; Nadmid, Suvd; Terekhova, Larisa P.; Myronovskyi, Maksym; Zotchev, Sergey B.; Rückert, ChristianUniBi ; Braig, Simone; Zahler, Stefan; Kalinowski, JörnUniBi; Luzhetskyy, Andriy
Alle
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski
Abstract / Bemerkung
Marine actinobacteria are drawing more and more attention as a promising source of new natural products. Here we report isolation, genome sequencing and metabolic profiling of new strain Streptomyces sp. MP131-18 isolated from marine sediment sample collected in the Trondheim Fjord, Norway. The 16S rRNA and multilocus phylogenetic analysis showed that MP131-18 belongs to the genus Streptomyces. The genome of MP131-18 isolate was sequenced, and 36 gene clusters involved in the biosynthesis of 18 different types of secondary metabolites were predicted using antiSMASH analysis. The combined genomics-metabolics profiling of the strain led to the identification of several new biologically active compounds. As a result, the family of bisindole pyrroles spiroindimicins was extended with two new members, spiroindimicins E and F. Furthermore, prediction of the biosynthetic pathway for unusual alpha-pyrone lagunapyrone isolated from MP131-18 resulted in foresight and identification of two new compounds of this family - lagunapyrones D and E. The diversity of identified and predicted compounds from Streptomyces sp. MP131-18 demonstrates that marine-derived actinomycetes are not only a promising source of new natural products, but also represent a valuable pool of genes for combinatorial biosynthesis of secondary metabolites.
Erscheinungsjahr
2017
Zeitschriftentitel
SCIENTIFIC REPORTS
Band
7
Ausgabe
1
Art.-Nr.
42382
Urheberrecht / Lizenzen
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0)
ISSN
2045-2322
Page URI
https://pub.uni-bielefeld.de/record/2909070

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Paulus C, Rebets Y, Tokovenko B, et al. New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp MP131-18. SCIENTIFIC REPORTS. 2017;7(1): 42382.
Paulus, C., Rebets, Y., Tokovenko, B., Nadmid, S., Terekhova, L. P., Myronovskyi, M., Zotchev, S. B., et al. (2017). New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp MP131-18. SCIENTIFIC REPORTS, 7(1), 42382. doi:10.1038/srep42382
Paulus, Constanze, Rebets, Yuriy, Tokovenko, Bogdan, Nadmid, Suvd, Terekhova, Larisa P., Myronovskyi, Maksym, Zotchev, Sergey B., et al. 2017. “New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp MP131-18”. SCIENTIFIC REPORTS 7 (1): 42382.
Paulus, C., Rebets, Y., Tokovenko, B., Nadmid, S., Terekhova, L. P., Myronovskyi, M., Zotchev, S. B., Rückert, C., Braig, S., Zahler, S., et al. (2017). New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp MP131-18. SCIENTIFIC REPORTS 7:42382.
Paulus, C., et al., 2017. New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp MP131-18. SCIENTIFIC REPORTS, 7(1): 42382.
C. Paulus, et al., “New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp MP131-18”, SCIENTIFIC REPORTS, vol. 7, 2017, : 42382.
Paulus, C., Rebets, Y., Tokovenko, B., Nadmid, S., Terekhova, L.P., Myronovskyi, M., Zotchev, S.B., Rückert, C., Braig, S., Zahler, S., Kalinowski, J., Luzhetskyy, A.: New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp MP131-18. SCIENTIFIC REPORTS. 7, : 42382 (2017).
Paulus, Constanze, Rebets, Yuriy, Tokovenko, Bogdan, Nadmid, Suvd, Terekhova, Larisa P., Myronovskyi, Maksym, Zotchev, Sergey B., Rückert, Christian, Braig, Simone, Zahler, Stefan, Kalinowski, Jörn, and Luzhetskyy, Andriy. “New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp MP131-18”. SCIENTIFIC REPORTS 7.1 (2017): 42382.

7 Zitationen in Europe PMC

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A look into a multifunctional toolbox: endophytic Bacillus species provide broad and underexploited benefits for plants.
Lopes R, Tsui S, Gonçalves PJRO, de Queiroz MV., World J Microbiol Biotechnol 34(7), 2018
PMID: 29900507
Genomics-guided discovery and structure identification of cyclic lipopeptides from the Bacillus siamensis JFL15.
Xu BH, Lu YQ, Ye ZW, Zheng QW, Wei T, Lin JF, Guo LQ., PLoS One 13(8), 2018
PMID: 30169540
Heterologous Expression of the Nybomycin Gene Cluster from the Marine Strain Streptomyces albus subsp. chlorinus NRRL B-24108.
Rodríguez Estévez M, Myronovskyi M, Gummerlich N, Nadmid S, Luzhetskyy A., Mar Drugs 16(11), 2018
PMID: 30400361
Identification and characterization of a biosynthetic gene cluster for tryptophan dimers in deep sea-derived Streptomyces sp. SCSIO 03032.
Ma L, Zhang W, Zhu Y, Zhang G, Zhang H, Zhang Q, Zhang L, Yuan C, Zhang C., Appl Microbiol Biotechnol 101(15), 2017
PMID: 28620687
Current Status and Future Prospects of Marine Natural Products (MNPs) as Antimicrobials.
Choudhary A, Naughton LM, Montánchez I, Dobson ADW, Rai DK., Mar Drugs 15(9), 2017
PMID: 28846659
Antibacterial Activity of Endophytic Actinomycetes Isolated from the Medicinal Plant Vochysia divergens (Pantanal, Brazil).
Gos FMWR, Savi DC, Shaaban KA, Thorson JS, Aluizio R, Possiede YM, Rohr J, Glienke C., Front Microbiol 8(), 2017
PMID: 28932210
Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production.
Remali J, Sarmin N'M, Ng CL, Tiong JJL, Aizat WM, Keong LK, Zin NM., PeerJ 5(), 2017
PMID: 29201559

58 References

Daten bereitgestellt von Europe PubMed Central.

Antimicrobial resistance: impact on clinical and economic outcomes and the need for new antimicrobials.
Thabit AK, Crandon JL, Nicolau DP., Expert Opin Pharmacother 16(2), 2014
PMID: 25496207
Antibiotic resistance threats in the United States: stepping back from the brink.
Solomon SL, Oliver KB., Am Fam Physician 89(12), 2014
PMID: 25162160
Thoughts and facts about antibiotics: where we are now and where we are heading.
Berdy J., J. Antibiot. 65(8), 2012
PMID: 22511224

Solecka, Central European Journal of Biology 7(), 2012
Discovering new bioactive molecules from microbial sources.
Monciardini P, Iorio M, Maffioli S, Sosio M, Donadio S., Microb Biotechnol 7(3), 2014
PMID: 24661414
Statistical research on marine natural products based on data obtained between 1985 and 2008.
Hu GP, Yuan J, Sun L, She ZG, Wu JH, Lan XJ, Zhu X, Lin YC, Chen SP., Mar Drugs 9(4), 2011
PMID: 21731546
Antimicrobial potential of Actinomycetes species isolated from marine environment.
Valli S, Suvathi SS, Aysha OS, Nirmala P, Vinoth KP, Reena A., Asian Pac J Trop Biomed 2(6), 2012
PMID: 23569952
Marine actinobacteria associated with marine organisms and their potentials in producing pharmaceutical natural products.
Valliappan K, Sun W, Li Z., Appl. Microbiol. Biotechnol. 98(17), 2014
PMID: 25064352
Diazepinomicin, a new antimicrobial alkaloid from a marine Micromonospora sp.
Charan RD, Schlingmann G, Janso J, Bernan V, Feng X, Carter GT., J. Nat. Prod. 67(8), 2004
PMID: 15332871
A phase II study of the Ras-MAPK signaling pathway inhibitor TLN-4601 in patients with glioblastoma at first progression.
Mason WP, Belanger K, Nicholas G, Vallieres I, Mathieu D, Kavan P, Desjardins A, Omuro A, Reymond D., J. Neurooncol. 107(2), 2011
PMID: 22048878
Salinosporamide natural products: Potent 20 S proteasome inhibitors as promising cancer chemotherapeutics.
Gulder TA, Moore BS., Angew. Chem. Int. Ed. Engl. 49(49), 2010
PMID: 20927786
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).
Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA., Nature 417(6885), 2002
PMID: 12000953
Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites.
Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M, Takahashi Y, Horikawa H, Nakazawa H, Osonoe T, Kikuchi H, Shiba T, Sakaki Y, Hattori M., Proc. Natl. Acad. Sci. U.S.A. 98(21), 2001
PMID: 11572948
Actinomycetes biosynthetic potential: how to bridge in silico and in vivo?
Rebets Y, Brotz E, Tokovenko B, Luzhetskyy A., J. Ind. Microbiol. Biotechnol. 41(2), 2013
PMID: 24127068
Strategies for the discovery of new natural products by genome mining.
Zerikly M, Challis GL., Chembiochem 10(4), 2009
PMID: 19165837

AUTHOR UNKNOWN, 0
Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica.
Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS., Proc. Natl. Acad. Sci. U.S.A. 104(25), 2007
PMID: 17563368

AUTHOR UNKNOWN, 0
Cluster of DnaA boxes involved in regulation of Streptomyces chromosome replication: from in silico to in vivo studies.
Smulczyk-Krawczyszyn A, Jakimowicz D, Ruban-Osmialowska B, Zawilak-Pawlik A, Majka J, Chater K, Zakrzewska-Czerwinska J., J. Bacteriol. 188(17), 2006
PMID: 16923885
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.
Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, Medema MH., Nucleic Acids Res. 43(W1), 2015
PMID: 25948579

AUTHOR UNKNOWN, 0
Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria.
Gao B, Gupta RS., Microbiol. Mol. Biol. Rev. 76(1), 2012
PMID: 22390973

AUTHOR UNKNOWN, 0
Lynamicins A-E, chlorinated bisindole pyrrole antibiotics from a novel marine actinomycete.
McArthur KA, Mitchell SS, Tsueng G, Rheingold A, White DJ, Grodberg J, Lam KS, Potts BC., J. Nat. Prod. 71(10), 2008
PMID: 18842058
Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample.
Pfleiderer A, Lagier JC, Armougom F, Robert C, Vialettes B, Raoult D., Eur. J. Clin. Microbiol. Infect. Dis. 32(11), 2013
PMID: 23728738
Draft genome sequences of three chemically rich actinomycetes isolated from Mediterranean sponges.
Horn H, Cheng C, Edrada-Ebel R, Hentschel U, Abdelmohsen UR., Mar Genomics 24 Pt 3(), 2015
PMID: 26490827
Streptomyces specialis sp. nov.
Kampfer P, Huber B, Buczolits S, Thummes K, Grun-Wollny I, Busse HJ., Int. J. Syst. Evol. Microbiol. 58(Pt 11), 2008
PMID: 18984700
Streptomyces avicenniae sp. nov., a novel actinomycete isolated from the rhizosphere of the mangrove plant Avicennia mariana.
Xiao J, Wang Y, Luo Y, Xie SJ, Ruan JS, Xu J., Int. J. Syst. Evol. Microbiol. 59(Pt 10), 2009
PMID: 19625443
eggNOG v4.0: nested orthology inference across 3686 organisms.
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldon T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24297252
Elucidation of Piericidin A1 biosynthetic locus revealed a thioesterase-dependent mechanism of α-pyridone ring formation.
Liu Q, Yao F, Chooi YH, Kang Q, Xu W, Li Y, Shao Y, Shi Y, Deng Z, Tang Y, You D., Chem. Biol. 19(2), 2012
PMID: 22365607
A bacterial source for mollusk pyrone polyketides.
Lin Z, Torres JP, Ammon MA, Marett L, Teichert RW, Reilly CA, Kwan JC, Hughen RW, Flores M, Tianero MD, Peraud O, Cox JE, Light AR, Villaraza AJ, Haygood MG, Concepcion GP, Olivera BM, Schmidt EW., Chem. Biol. 20(1), 2013
PMID: 23352141
New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products.
Ortega MA, van der Donk WA., Cell Chem Biol 23(1), 2016
PMID: 26933734
Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert.
Elsayed SS, Trusch F, Deng H, Raab A, Prokes I, Busarakam K, Asenjo JA, Andrews BA, van West P, Bull AT, Goodfellow M, Yi Y, Ebel R, Jaspars M, Rateb ME., J. Org. Chem. 80(20), 2015
PMID: 26402731
Evaluation of similarity measures for searching the dictionary of natural products database.
Whittle M, Willett P, Klaffke W, van Noort P., J Chem Inf Comput Sci 43(2), 2003
PMID: 12653508
Indimicins A-E, Bisindole Alkaloids from the Deep-Sea-Derived Streptomyces sp. SCSIO 03032.
Zhang W, Ma L, Li S, Liu Z, Chen Y, Zhang H, Zhang G, Zhang Q, Tian X, Yuan C, Zhang S, Zhang W, Zhang C., J. Nat. Prod. 77(8), 2014
PMID: 25069084
Spiroindimicins A-D: new bisindole alkaloids from a deep-sea-derived actinomycete.
Zhang W, Liu Z, Li S, Yang T, Zhang Q, Ma L, Tian X, Zhang H, Huang C, Zhang S, Ju J, Shen Y, Zhang C., Org. Lett. 14(13), 2012
PMID: 22694269

Frode, Tetrahedron Letters 35(), 1994
Staurosporine and rebeccamycin aglycones are assembled by the oxidative action of StaP, StaC, and RebC on chromopyrrolic acid.
Howard-Jones AR, Walsh CT., J. Am. Chem. Soc. 128(37), 2006
PMID: 16967980

Lindel, Tetrahedron Letters 37(), 1996
Genomic islands in pathogenic and environmental microorganisms.
Dobrindt U, Hochhut B, Hentschel U, Hacker J., Nat. Rev. Microbiol. 2(5), 2004
PMID: 15100694

AUTHOR UNKNOWN, 0
Aryl Polyenes, a Highly Abundant Class of Bacterial Natural Products, Are Functionally Related to Antioxidative Carotenoids.
Schoner TA, Gassel S, Osawa A, Tobias NJ, Okuno Y, Sakakibara Y, Shindo K, Sandmann G, Bode HB., Chembiochem 17(3), 2016
PMID: 26629877
Enzymatic generation of the chromopyrrolic acid scaffold of rebeccamycin by the tandem action of RebO and RebD.
Howard-Jones AR, Walsh CT., Biochemistry 44(48), 2005
PMID: 16313168
Enzymatic assembly of the bis-indole core of rebeccamycin.
Nishizawa T, Gruschow S, Jayamaha DH, Nishizawa-Harada C, Sherman DH., J. Am. Chem. Soc. 128(3), 2006
PMID: 16417354
The biosynthetic gene cluster for the antitumor rebeccamycin: characterization and generation of indolocarbazole derivatives.
Sanchez C, Butovich IA, Brana AF, Rohr J, Mendez C, Salas JA., Chem. Biol. 9(4), 2002
PMID: 11983340
An iterative type I polyketide synthase PKSN catalyzes synthesis of the decaketide alternapyrone with regio-specific octa-methylation.
Fujii I, Yoshida N, Shimomaki S, Oikawa H, Ebizuka Y., Chem. Biol. 12(12), 2005
PMID: 16356847
Complete reconstitution of a highly reducing iterative polyketide synthase.
Ma SM, Li JW, Choi JW, Zhou H, Lee KK, Moorthie VA, Xie X, Kealey JT, Da Silva NA, Vederas JC, Tang Y., Science 326(5952), 2009
PMID: 19900898
Nafuredin, a novel inhibitor of NADH-fumarate reductase, produced by Aspergillus niger FT-0554.
Ui H, Shiomi K, Yamaguchi Y, Masuma R, Nagamitsu T, Takano D, Sunazuka T, Namikoshi M, Omura S., J. Antibiot. 54(3), 2001
PMID: 11372780
Biosynthesis of α-pyrones.
Schaberle TF., Beilstein J Org Chem 12(), 2016
PMID: 27340449

AUTHOR UNKNOWN, 0
Production of landomycins in Streptomyces globisporus 1912 and S cyanogenus S136 is regulated by genes encoding putative transcriptional activators.
Rebets Y, Ostash B, Luzhetskyy A, Hoffmeister D, Brana A, Mendez C, Salas JA, Bechthold A, Fedorenko V., FEMS Microbiol. Lett. 222(1), 2003
PMID: 12757959
Prokka: rapid prokaryotic genome annotation.
Seemann T., Bioinformatics 30(14), 2014
PMID: 24642063
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23193283
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K, Misawa K, Kuma K, Miyata T., Nucleic Acids Res. 30(14), 2002
PMID: 12136088
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Stamatakis A., Bioinformatics 30(9), 2014
PMID: 24451623
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A., Bioinformatics 28(12), 2012
PMID: 22543367
Determination of minimum inhibitory concentrations.
Andrews JM., J. Antimicrob. Chemother. 48 Suppl 1(), 2001
PMID: 11420333
Circos: an information aesthetic for comparative genomics.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA., Genome Res. 19(9), 2009
PMID: 19541911
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