Complete genome sequence of Rhodococcus sp. strain WMMA185, a marine sponge-associated bacterium

Genome Announcements

Volumn 4, Issue 6, 2016, Pages

  Adnani, Navid ^a   Braun, Doug R ^a   McDonald, Bradon R ^a   Chevrette, Marc G ^a   Currie, Cameron R ^a   Bugni, Tim S ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85010723228     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.01406-16     Document Type: Article

References (25)

1. Centers for Disease Control and Prevention. 2013. Antibiotic resistance threats in the United States, 2013. U.S. Department of Health and Human Services, CDC.
2. Adnani N, Vazquez-Rivera E, Adibhatla SN, Ellis GA, Braun DR, Bugni TS. 2015. Investigation of interspecies interactions within marine Micromonosporaceae using an improved co-culture approach. Mar Drugs 13:6082-6098. http://dx.doi.org/10.3390/md13106082.
3. Bertrand S, Bohni N, Schnee S, Schumpp O, Gindro K, Wolfender JL. 2014 Metabolite induction via microorganism co-culture: A potential way to enhance chemical diversity for drug discovery. Biotechnol Adv 32:1180-1204. http://dx.doi.org/10.1016/j.biotechadv.2014.03.001.
4. Netzker T, Fischer J, Weber J, Mattern DJ, König CC, Valiante V, Schroeckh V, Brakhage AA. 2015. Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters. Front Microbiol 6:299. http://dx.doi.org/10.3389/fmicb.2015.00299.
5. Demain AL. 2014. Importance of microbial natural products and the need to revitalize their discovery. J Ind Microbiol Biotechnol 41:185-201. http://dx.doi.org/10.1007/s10295-013-1325-z.
6. Pettit RK. 2009. Mixed fermentation for natural product drug discovery. Appl Microbiol Biotechnol 83:19-25. http://dx.doi.org/10.1007/s00253-009-1916-9.
7. Larkin MJ, Kulakov LA, Allen CCR. 2005. Biodegradation and Rhodococcus-masters of catabolic versatility. Curr Opin Biotechnol 16: 282-290. http://dx.doi.org/10.1016/j.copbio.2005.04.007.
8. Larkin MJ, Kulakov LA, Allen CCR. 2006. Biodegradation by members of the genus Rhodococcus: biochemistry, physiology, and genetic adaptation. Adv Appl Microbiol 59:1-29. http://dx.doi.org/10.1016/S0065-2164(06)59001-X.
9. De Carvalho CCCR, Costa SS, Fernandes P, Couto I, Viveiros M. 2014. Membrane transport systems and the biodegradation potential and pathogenicity of genus Rhodococcus. Front Physiol 5:133. http://dx.doi.org/10.3389/fphys.2014.00133.
10. Yam KC, Okamoto S, Roberts JN, Eltis LD. 2011. Adventures in Rhodococcus-from steroids to explosives. Can J Microbiol 57:155-168. http://dx.doi.org/10.1139/W10-115.
11. Wang X, Coulson GB, Miranda-CasoLuengo AA, Miranda-CasoLuengo R, Hondalus MK, Meijer WG. 2014. IcgA is a virulence factor of Rhodococcus equi That modulates intracellular growth. Infect Immun 82: 1793-1800. http://dx.doi.org/10.1128/IAI.01670-13.
12. Letek M, González P, MacArthur I, Rodríguez H, Freeman TC, Valero-Rello A, Blanco M, Buckley T, Cherevach I, Fahey R, Hapeshi A, Holdstock J, Leadon D, Navas J, Ocampo A, Quail MA, Sanders M, Scortti MM, Prescott JF, Fogarty U, Meijer WG, Parkhill J, Bentley SD, Vázquez-Boland JA. 2010. The genome of a pathogenic Rhodococcus: cooptive virulence underpinned by key gene acquisitions. PLoS Genet 6:e1001145. http://dx.doi.org/10.1371/journal.pgen.1001145.
13. Kulakov LA, Larkin MJ. 2002. Genomic organization of rhodococcus in genomics of GC-rich Gram-positive bacteria, pp 15-46. A. Danchin (ed), Academic Press, Norfolk, United Kingdom.
14. Kurosawa K, Ghiviriga I, Sambandan TG, Lessard PA, Barbara JE, Rha C, Sinskey AJ. 2008. Rhodostreptomycins, antibiotics biosynthesized following horizontal gene transfer from Streptomyces padanus to Rhodococcus fascians. J Am Chem Soc 130:1126-1127. http://dx.doi.org/10.1021/ja077821p.
15. Onaka H, Mori Y, Igarashi Y, Furumai T. 2011. Mycolic acid-containing bacteria induce natural-product biosynthesis in streptomyces species. Appl Environ Microbiol 77:400-406. http://dx.doi.org/10.1128/AEM.01337-10.
16. Ge F, Wang LS, Kim J. 2005. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol 3:e316. http://dx.doi.org/10.1371/journal.pbio.0030316.
17. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. 2010 Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. http://dx.doi.org/10.1186/1471-2105-11-119.
18. Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E. 2013. TIGRFAMs and genome properties in 2013. Nucleic Acids Res 41: D387-D395. http://dx.doi.org/10.1093/nar/gks1234.
19. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2014 Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42:D199-D205. http://dx.doi.org/10.1093/nar/gkt1076.
20. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2016. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:D457-D462. http://dx.doi.org/10.1093/nar/gkv1070.
21. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer ELL, Tate J, Punta M. 2014. Pfam: the protein families database. Nucleic Acids Res 42:D222-D230. http://dx.doi.org/10.1093/nar/gkt1223.
22. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44:D279-D285. http://dx.doi.org/10.1093/nar/gkv1344.
23. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R. 2011. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339-W346. http://dx.doi.org/10.1093/nar/gkr466.
24. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH. 2015. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43: W237-W243. http://dx.doi.org/10.1093/nar/gkv437.
25. Skinnider MA, Dejong CA, Rees PN, Johnston CW, Li H, Webster ALH, Wyatt MA, Magarvey NA. 2015. Genomes to natural products PRediction informatics for secondary metabolomes (PRISM). Nucleic Acids Res 43:9645-9662. http://dx.doi.org/10.1093/nar/gkv1012.