StreptomeDB 2.0 - An extended resource of natural products produced by streptomycetes

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D509-D514

  Klementz, Dennis ^a   Döring, Kersten ^a   Lucas, Xavier ^a,b   Telukunta, Kiran K ^a   Erxleben, Anika ^a   Deubel, Denise ^a   Erber, Astrid ^a   Santillana, Irene ^a   Thomas, Oliver S ^a   Bechthold, Andreas ^a   Günther, Stefan ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL COMPOUND; MOLECULAR SCAFFOLD; NATURAL PRODUCT; RNA 16S; BIOLOGICAL PRODUCT;

ARTICLE; DATA BASE; HOST; MASS SPECTROMETRY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHYLOGENETIC TREE; PRIORITY JOURNAL; RNA SEQUENCE; STREPTOMEDB 2.0; STREPTOMYCETACEAE; CHEMICAL DATABASE; CHEMISTRY; CLASSIFICATION; GENETICS; METABOLISM; PHYLOGENY; STREPTOMYCES;

BIOLOGICAL PRODUCTS; DATABASES, CHEMICAL; PHYLOGENY; STREPTOMYCES;

EID: 84976875272     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1319     Document Type: Article

References (42)

1. Banerjee, P., Erehman, J., Gohlke, B.O., Wilhelm, T., Preissner, R. and Dunkel, M. (2015) Super Natural II - a database of natural products. Nucleic Acids Res., 43, D935-D939.
2. Nakamura, Y., Afendi, F.M., Parvin, A.K., Ono, N., Tanaka, K., Morita, A., Sato, T., Sugiura, T., Altaf-Ul-Amin, M. and Kanaya, S. (2013) KNApSAcK metabolite activity database for retrieving the relationships between metabolites and biological activities. Plant Cell Physiol., 55, e7.
3. Gu, J., Gui, Y., Chen, L., Yuan, G., Lu, H.Z. and Xu, X. (2013) Use of natural products as chemical library for drug discovery and network pharmacology. PLoS One, 8, e62839.
4. Caboche, S., Pupin, M., Leclère, V., Fontaine, A., Jacques, P. and Kucherov, G. (2008) NORINE: a database of nonribosomal peptides. Nucleic Acids Res., 36, D326-D331.
5. Hopwood, D.A. (2006) Soil to genomics: the Streptomyces chromosome. Annu. Rev. Genet., 40, 1-23.
6. Zetterström, R. (2007) Selman A. Waksman (1888-1973) Nobel Prize in 1952 for the discovery of streptomycin, the first antibiotic effective against tuberculosis. Acta Paediatr., 96, 317-319.
7. Procópio, R.E., Silva, I.R., Martins, M.K., Azevedo, J.L. and Araújo, J.M. (2012) Antibiotics produced by Streptomyces. Braz. J. Infect. Dis., 16, 466-471.
8. Kose, L.P., Gülçin, İ., Özdemir, H., Atasever, A., Alwasel, S.H. and Supuran, C.T. (2015) The effects of some avermectins on bovine carbonic anhydrase enzyme. J. Enzyme Inhib. Med. Chem., doi:10.3109/14756366.2015.1064406.
9. Krenzien, F., ElKhal, A., Quante, M., Rodriguez Cetina Biefer, H., Hirofumi, U., Gabardi, S. and Tullius, S.G. (2015) A rationale for age-adapted immunosuppression in organ transplantation. Transplantation, 99, 2258-2268.
10. Bai, T., Zhang, D., Lin, S., Long, Q., Wang, Y., Ou, H., Kang, Q., Deng, Z., Liu, W. and Tao, M. (2014) Operon for biosynthesis of lipstatin, the beta-lactone inhibitor of human pancreatic lipase. Appl. Environ. Microbiol., 80, 7473-7483.
11. Lucas, X., Senger, C., Erxleben, A., Grüning, B.A., Döring, K., Mosch, J., Flemming, S. and Günther, S. (2013) StreptomeDB: a resource for natural compounds isolated from Streptomyces species. Nucleic Acids Res., 41, D1130-D1136.
12. Kling, A., Lukat, P., Almeida, D.V., Bauer, A., Fontaine, E., Sordello, S., Zaburannyi, N., Herrmann, J., Wenzel, S.C., König, C. et al. (2015) Targeting DnaN for tuberculosis therapy using novel griselimycins. Science, 348, 1106-1112.
13. Butler, M.S. and Buss, A.D. (2006) Natural products-the future scaffolds for novel antibiotics? Biochem. Pharmacol., 71, 919-929.
14. Karthikeyan, M. and Vyas, R. (2015) Role of open source tools and resources in virtual screening for drug discovery. Comb. Chem. High Throughput Screen., 18, 528-543.
15. Lucas, X., Grüning, B.A., Bleher, S. and Günther, S. (2015) The purchasable chemical space: a detailed picture. J. Chem. Inf. Model., 55, 915-924.
16. Lucas, X. and Günther, S. (2014) Using chiral molecules as an approach to address low-druggability recognition sites. J. Comput. Chem., 35, 2114-2121.
17. Ribeiro, A.R., Maia, A.S., Cass, Q.B. and Tiritan, M.E. (2014) Enantioseparation of chiral pharmaceuticals in biomedical and environmental analyses by liquid chromatography: an overview. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci., 968, 8-21.
18. Yamada, Y., Arima, S., Nagamitsu, T., Johmoto, K., Uekusa, H., Eguchi, T., Shin-ya, K., Cane, D.E. and Ikeda, H. (2015) Novel terpenes generated by heterologous expression of bacterial terpene synthase genes in an engineered Streptomyces host. J. Antibiot. (Tokyo)., 68, 385-394.
19. Komatsu, M., Komatsu, K., Koiwai, H., Yamada, Y., Kozone, I., Izumikawa, M., Hashimoto, J., Takagi, M., Omura, S., Shin-ya, K. et al. (2013) Engineered Streptomyces avermitilis host for heterologous expression of biosynthetic gene cluster for secondary metabolites. ACS Synth. Biol., 2, 384-396.
20. Liu, W., Zhang, Q., Guo, J., Chen, Z., Li, J. and Wen, Y. (2015) Increasing avermectin production in Streptomyces avermitilis by manipulating the expression of a novel TetR-family regulator and its target gene product. Appl. Environ. Microbiol., 81, 5157-5173.
21. Phelan, R.M., Sekurova, O.N., Keasling, J.D. and Zotchev, S.B. (2015) Engineering terpene biosynthesis in Streptomyces for production of the advanced biofuel precursor bisabolene. ACS Synth. Biol., 4, 393-399.
22. Beller, H.R., Lee, T.S. and Katz, L. (2015) Natural products as biofuels and bio-based chemicals: fatty acids and isoprenoids. Nat. Prod. Rep., 32, 1508-1526.
23. Peralta-Yahya, P.P., Ouellet, M., Chan, R., Mukhopadhyay, A., Keasling, J.D. and Lee, T.S. (2011) Identification and microbial production of a terpene-based advanced biofuel. Nat. Commun., 2, doi:10.1038/ncomms1494.
24. Dhakal, D. and Sohng, J.K. (2015) Commentary: Toward a new focus in antibiotic and drug discovery from the Streptomyces arsenal. Front. Microbiol., 6, doi:10.3389/fmicb.2015.00727.
25. Kiske, C., Erxleben, A., Lucas, X., Willmann, L., Klementz, D., Günther, S., Römer, W. and Kammerer, B. (2014) Metabolic pathway monitoring of phenalinolactone biosynthesis from Streptomyces sp. Tü6071 by liquid chromatography/mass spectrometry coupling. Rapid Commun. Mass Spectrom., 28, 1459-1467.
26. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. and Glöckner, F.O. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res., 41, D590-D596.
27. Cochrane, G., Alako, B., Amid, C., Bower, L., Cerdeño-Tárraga, A., Cleland, I., Gibson, R., Goodgame, N., Jang, M., Kay, S. et al. (2013) Facing growth in the European Nucleotide Archive. Nucleic Acids Res., 41, D30-D35.
28. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T.L. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, doi:10.1186/1471-2105-10-421.
29. Cock, P.J., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B. et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423.
30. McWilliam, H., Li, W., Uludag, M., Squizzato, S., Park, Y.M., Buso, N., Cowley, A.P. and Lopez, R. (2013) Analysis Tool Web Services from the EMBL-EBI. Nucleic Acids Res., 41, W597-W600.
31. Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol., 30, 2725-2729.
32. Sukumaran, J. and Holder, M.T. (2010) DendroPy: a Python library for phylogenetic computing. Bioinformatics, 26, 1569-1571.
33. Huerta-Cepas, J., Dopazo, J. and Gabaldón, T. (2010) ETE: a python Environment for Tree Exploration. BMC Bioinformatics, 11, doi:10.1186/1471-2105-11-24.
34. Ichikawa, N., Sasagawa, M., Yamamoto, M., Komaki, H., Yoshida, Y., Yamazaki, S. and Fujita, N. (2013) DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters. Nucleic Acids Res., 41, D408-D414.
35. Medema, M.H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J.B., Blin, K., de Bruijn, I., Chooi, Y.H., Claesen, J., Coates, R.C. et al. (2015) Minimum information about a biosynthetic gene cluster. Nat. Chem. Biol., 11, 625-631.
36. Benson, D.A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Sayers, E.W. (2013) GenBank. Nucleic Acids Res., 41, D36-D42.
37. Sayers, E.W., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S. et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37, D5-D15.
38. Langdon, S.R., Brown, N. and Blagg, J. (2011) Scaffold diversity of exemplified medicinal chemistry space. J. Chem. Inf. Model., 51, 2174-2185.
39. Allen, F., Greiner, R. and Wishart, D. (2014) Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification. Metabolomics, 11, 98-110.
40. Coenye, T. and Vandamme, P. (2003) Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol. Lett., 228, 45-49.
41. Lucas, X., Grüning, B.A. and Günther, S. (2014) ChemicalToolBoX and its application on the study of the drug like and purchasable space. J. Cheminform., 6, P51.
42. Land, M., Hauser, L., Jun, S.R., Nookaew, I., Leuze, M.R., Ahn, T.H., Karpinets, T., Lund, O., Kora, G., Wassenaar, T. et al. (2015) Insights from 20 years of bacterial genome sequencing. Funct. Integr. Genomics, 15, 141-161.