Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic

Schneider O, Simic N, Aachmann FL, Rückert C, Kristiansen KA, Kalinowski J, Jiang Y, Wang L, Jiang C-L, Lale R, Zotchev SB (2018)
FRONTIERS IN MICROBIOLOGY 9: 3139.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ; ; ; ; ; ; ; ; ;
Abstract / Bemerkung
Streptomyces bacteria are recognized as an important source for antibiotics with broad applications in human medicine and animal health. Here, we report the isolation of a new lichen-associating Streptomyces sp. YIM 130001 from the tropical rainforest in Xishuangbanna (Yunnan, China), which displayed antibacterial activity against Bacillus subtilis. The draft genome sequence of this isolate strain revealed 18 putative biosynthetic gene clusters (BGCs) for secondary metabolites, which is an unusually low number compared to a typical streptomycete. Inactivation of a (antibiotic dehydrogenase-encoding gene from the BGC presumed to govern biosynthesis of a thiopeptide resulted in the loss of bioactivity. Using comparative HPLC analysis, two peaks in the chromatogram were identified in the extract from the wild-type strain, which were missing in the extract from the mutant. The compounds corresponding to the identified peaks were purified, and structure of one compound was elucidated using NMR. The compound, designated geninthiocin B, showed high similarity to several 35-membered macrocyclic thiopeptides geninthiocin, Val-geninthiocin and berninamycin A. Bioinformatics analysis of the geninthiocin B BGC revealed its close homology to that of berninamycins.
Erscheinungsjahr
Zeitschriftentitel
FRONTIERS IN MICROBIOLOGY
Band
9
Art.-Nr.
3139
ISSN
PUB-ID

Zitieren

Schneider O, Simic N, Aachmann FL, et al. Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic. FRONTIERS IN MICROBIOLOGY. 2018;9: 3139.
Schneider, O., Simic, N., Aachmann, F. L., Rückert, C., Kristiansen, K. A., Kalinowski, J., Jiang, Y., et al. (2018). Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic. FRONTIERS IN MICROBIOLOGY, 9, 3139. doi:10.3389/fmicb.2018.03139
Schneider, O., Simic, N., Aachmann, F. L., Rückert, C., Kristiansen, K. A., Kalinowski, J., Jiang, Y., Wang, L., Jiang, C. - L., Lale, R., et al. (2018). Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic. FRONTIERS IN MICROBIOLOGY 9:3139.
Schneider, O., et al., 2018. Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic. FRONTIERS IN MICROBIOLOGY, 9: 3139.
O. Schneider, et al., “Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic”, FRONTIERS IN MICROBIOLOGY, vol. 9, 2018, : 3139.
Schneider, O., Simic, N., Aachmann, F.L., Rückert, C., Kristiansen, K.A., Kalinowski, J., Jiang, Y., Wang, L., Jiang, C.-L., Lale, R., Zotchev, S.B.: Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic. FRONTIERS IN MICROBIOLOGY. 9, : 3139 (2018).
Schneider, Olha, Simic, Nebojsa, Aachmann, Finn Lillelund, Rückert, Christian, Kristiansen, Kare Andre, Kalinowski, Jörn, Jiang, Yi, Wang, Lisong, Jiang, Cheng-Lin, Lale, Rahmi, and Zotchev, Sergey B. “Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic”. FRONTIERS IN MICROBIOLOGY 9 (2018): 3139.

1 Zitation in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Streptomyces monashensis sp. nov., a novel mangrove soil actinobacterium from East Malaysia with antioxidative potential.
Law JW, Ser HL, Ab Mutalib NS, Saokaew S, Duangjai A, Khan TM, Chan KG, Goh BH, Lee LH., Sci Rep 9(1), 2019
PMID: 30816228

53 References

Daten bereitgestellt von Europe PubMed Central.

The structures of sulfomycin I and berninamycin A.
Abe H., Kushida K., Shiobara Y., Kodama M.., 1988
Thiopeptide antibiotics.
Bagley MC, Dale JW, Merritt EA, Xiong X., Chem. Rev. 105(2), 2005
PMID: 15700961
Taxonomy, Physiology, and Natural Products of Actinobacteria.
Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk HP, Clement C, Ouhdouch Y, van Wezel GP., Microbiol. Mol. Biol. Rev. 80(1), 2015
PMID: 26609051
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
antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de Los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH., Nucleic Acids Res. 45(W1), 2017
PMID: 28460038
Rare actinomycete bacteria from the shallow water sediments of the Trondheim fjord, Norway: isolation, diversity and biological activity.
Bredholdt H, Galatenko OA, Engelhardt K, Fjaervik E, Terekhova LP, Zotchev SB., Environ. Microbiol. 9(11), 2007
PMID: 17922759
A prevalent peptide-binding domain guides ribosomal natural product biosynthesis.
Burkhart BJ, Hudson GA, Dunbar KL, Mitchell DA., Nat. Chem. Biol. 11(8), 2015
PMID: 26167873
YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function.
Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA., Chem. Rev. 117(8), 2017
PMID: 28256131
Genome Mining and Activation of a Silent PKS/NRPS Gene Cluster Direct the Production of Totopotensamides.
Chen R, Zhang Q, Tan B, Zheng L, Li H, Zhu Y, Zhang C., Org. Lett. 19(20), 2017
PMID: 29019409
Origins and evolution of antibiotic resistance.
Davies J, Davies D., Microbiol. Mol. Biol. Rev. 74(3), 2010
PMID: 20805405
Will 10 Million People Die a Year due to Antimicrobial Resistance by 2050?
de Kraker ME, Stewardson AJ, Harbarth S., PLoS Med. 13(11), 2016
PMID: 27898664
The molecular basis of the inhibitory activities of type A and type B synergimycins and related antibiotics on ribosomes.
Di Giambattista M, Chinali G, Cocito C., J. Antimicrob. Chemother. 24(4), 1989
PMID: 2515187
Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis.
Dunbar KL, Chekan JR, Cox CL, Burkhart BJ, Nair SK, Mitchell DA., Nat. Chem. Biol. 10(10), 2014
PMID: 25129028
YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations.
Dunbar KL, Melby JO, Mitchell DA., Nat. Chem. Biol. 8(6), 2012
PMID: 22522320
Production of a new thiopeptide antibiotic, TP-1161, by a marine Nocardiopsis species.
Engelhardt K, Degnes KF, Kemmler M, Bredholt H, Fjaervik E, Klinkenberg G, Sletta H, Ellingsen TE, Zotchev SB., Appl. Environ. Microbiol. 76(15), 2010
PMID: 20562278
Isolation and characterization of the gene cluster for biosynthesis of the thiopeptide antibiotic TP-1161.
Engelhardt K, Degnes KF, Zotchev SB., Appl. Environ. Microbiol. 76(21), 2010
PMID: 20851988
Enediyne compounds - new promises in anticancer therapy.
Gredicak M, Jeric I., Acta Pharm 57(2), 2007
PMID: 17507311
Characterization of Streptomyces spp. isolated from the sea surface microlayer in the Trondheim Fjord, Norway.
Hakvag S, Fjaervik E, Josefsen KD, Ian E, Ellingsen TE, Zotchev SB., Mar Drugs 6(4), 2008
PMID: 19172199
Secondary metabolites overproduction through transcriptional gene cluster refactoring.
Horbal L, Marques F, Nadmid S, Mendes MV, Luzhetskyy A., Metab. Eng. 49(), 2018
PMID: 30240601
Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis.
Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S., Nat. Biotechnol. 21(5), 2003
PMID: 12692562
Thiopeptide engineering: a multidisciplinary effort towards future drugs.
Just-Baringo X, Albericio F, Alvarez M., Angew. Chem. Int. Ed. Engl. 53(26), 2014
PMID: 24861213
Natural product discovery: past, present, and future.
Katz L, Baltz RH., J. Ind. Microbiol. Biotechnol. 43(2-3), 2016
PMID: 26739136
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Kumar S, Stecher G, Tamura K., Mol. Biol. Evol. 33(7), 2016
PMID: 27004904
Phylogenetic study of the species within the family Streptomycetaceae.
Labeda DP, Goodfellow M, Brown R, Ward AC, Lanoot B, Vanncanneyt M, Swings J, Kim SB, Liu Z, Chun J, Tamura T, Oguchi A, Kikuchi T, Kikuchi H, Nishii T, Tsuji K, Yamaguchi Y, Tase A, Takahashi M, Sakane T, Suzuki KI, Hatano K., Antonie Van Leeuwenhoek 101(1), 2011
PMID: 22045019
Berninamycins B, C, and D, minor metabolites from Streptomyces bernensis.
Lau RC, Rinehart KL., J. Antibiot. 47(12), 1994
PMID: 7844041
Multiple oxidative routes towards the maturation of nosiheptide.
Liu W, Xue Y, Ma M, Wang S, Liu N, Chen Y., Chembiochem 14(13), 2013
PMID: 23939763
The posttranslational modification cascade to the thiopeptide berninamycin generates linear forms and altered macrocyclic scaffolds.
Malcolmson SJ, Young TS, Ruby JG, Skewes-Cox P, Walsh CT., Proc. Natl. Acad. Sci. U.S.A. 110(21), 2013
PMID: 23650400
Ribosomally synthesized thiopeptide antibiotics targeting elongation factor Tu.
Morris RP, Leeds JA, Naegeli HU, Oberer L, Memmert K, Weber E, LaMarche MJ, Parker CN, Burrer N, Esterow S, Hein AE, Schmitt EK, Krastel P., J. Am. Chem. Soc. 131(16), 2009
PMID: 19338336
Generation of a cluster-free Streptomyces albus chassis strains for improved heterologous expression of secondary metabolite clusters.
Myronovskyi M, Rosenkranzer B, Nadmid S, Pujic P, Normand P, Luzhetskyy A., Metab. Eng. 49(), 2018
PMID: 30196100
Antibiotic A10255 (thioplabin) enhances fibrin binding and activation of plasminogen.
Ohyama S, Wada Y, Hasumi K., J. Antibiot. 55(1), 2002
PMID: 11918071
Hopanoids are formed during transition from substrate to aerial hyphae in Streptomyces coelicolor A3(2).
Poralla K, Muth G, Hartner T., FEMS Microbiol. Lett. 189(1), 2000
PMID: 10913872
Diversity of the ectoines biosynthesis genes in the salt tolerant Streptomyces and evidence for inductive effect of ectoines on their accumulation.
Sadeghi A, Soltani BM, Nekouei MK, Jouzani GS, Mirzaei HH, Sadeghizadeh M., Microbiol. Res. 169(9-10), 2014
PMID: 24629523
Val-Geninthiocin: structure elucidation and msn fragmentation of thiopeptide antibiotics produced by Streptomyces sp. RSF18.
Sajid I., Shaaban K., Frauendorf H., Hasnain S., Laatscha H.., 2008

Sambrook J., Fritsch E., Maniatis T.., 1989
Microbial iron acquisition: marine and terrestrial siderophores.
Sandy M, Butler A., Chem. Rev. 109(10), 2009
PMID: 19772347
Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177T isolated from a marine sponge.
Schaffert L, Albersmeier A, Winkler A, Kalinowski J, Zotchev SB, Ruckert C., Stand Genomic Sci 11(), 2016
PMID: 28031775
Prokka: rapid prokaryotic genome annotation.
Seemann T., Bioinformatics 30(14), 2014
PMID: 24642063
Discovery of pentangular polyphenols hexaricins A-C from marine Streptosporangium sp. CGMCC 4.7309 by genome mining.
Tian J, Chen H, Guo Z, Liu N, Li J, Huang Y, Xiang W, Chen Y., Appl. Microbiol. Biotechnol. 100(9), 2016
PMID: 26754814
Crystallographic analysis of NosA, which catalyzes terminal amide formation in the biosynthesis of nosiheptide.
Wang Y, Liu S, Yao P, Yu Y, Zhang Y, Lan W, Wang C, Ding J, Liu W, Cao C., Acta Crystallogr F Struct Biol Commun 71(Pt 8), 2015
PMID: 26249695
Genomics-inspired discovery of natural products.
Winter JM, Behnken S, Hertweck C., Curr Opin Chem Biol 15(1), 2010
PMID: 21111667
Glycomyces phytohabitans sp. nov., a novel endophytic actinomycete isolated from the coastal halophyte in Jiangsu, East China.
Xing K, Qin S, Zhang WD, Cao CL, Ruan JS, Huang Y, Jiang JH., J. Antibiot. 67(8), 2014
PMID: 24736858
Novel terpenes generated by heterologous expression of bacterial terpene synthase genes in an engineered Streptomyces host.
Yamada Y, Arima S, Nagamitsu T, Johmoto K, Uekusa H, Eguchi T, Shin-ya K, Cane DE, Ikeda H., J. Antibiot. 68(6), 2015
PMID: 25605043
NosA catalyzing carboxyl-terminal amide formation in nosiheptide maturation via an enamine dealkylation on the serine-extended precursor peptide.
Yu Y, Guo H, Zhang Q, Duan L, Ding Y, Liao R, Lei C, Shen B, Liu W., J. Am. Chem. Soc. 132(46), 2010
PMID: 21047073
Biosynthetic Timing and Substrate Specificity for the Thiopeptide Thiomuracin.
Zhang Z, Hudson GA, Mahanta N, Tietz JI, van der Donk WA, Mitchell DA., J. Am. Chem. Soc. 138(48), 2016
PMID: 27700071

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 30619207
PubMed | Europe PMC

Suchen in

Google Scholar