Abstract
Here we report the draft genome sequence of Nocardiopsis sp. strain TP-A0876, isolated from marine sediment, which produces polyketide-derived pyrones called nocapyrones. The genome contains three polyketide synthase (PKS) gene clusters, one of which was proposed to be responsible for nocapyrone biosynthesis. This genome sequence will facilitate the study of the potential for secondary metabolism in Nocardiopsis strains.
GENOME ANNOUNCEMENT
Marine actinomycetes are promising sources of bioactive compounds (1–3). In our screening for discovering new adiponectin inducers, Nocardiopsis sp. strain TP-A0876 was isolated from marine sediment and found to produce four pyrone compounds of polyketide origin: nocapyrones B, H, L, and R (14). To identify their biosynthetic gene cluster, we performed whole-genome shotgun sequencing of the strain. Herein we present its draft genome sequence.
Nocardiopsis sp. TP-A0876 was deposited to the NBRC culture collection and registered as NBRC 110039. The whole genome of Nocardiopsis sp. TP-A0876 was read by using a combined strategy of shotgun sequencing with GS FLX+ (Roche; 20 Mb sequences, 3.5-fold coverage) and pair-end sequencing with MiSeq (Illumina; 772 Mb, 128-fold coverage). These reads were assembled using Newbler v2.6 software and subsequently finished using GenoFinisher software (4), which led to a final assembly of 25 scaffold sequences of >500 bp each. The total size of the assembly was 5,861,114 bp, with a G+C content of 68.8%. Coding sequences were predicted by Prodigal (5), and domains related to polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) were searched for using the SMART and PFAM domain databases. PKS and NRPS gene clusters and their domain organizations were determined manually. The genome was found to contain two type-I PKS gene clusters, one type-II PKS gene cluster, one NRPS gene cluster, and one hybrid PKS/NRPS gene cluster.
The 16S rRNA gene sequence (GenBank accession no. AB488799) of Nocardiopsis sp. TP-A0876 showed 100% identity to that of Nocardiopsis alba DSM 43377T. To examine the taxonomical identity of our strain with this species, the average nucleotide identity (ANI) was analyzed by JSpecies (version 1.2.1) (6), using currently available genome sequences of two N. alba strains, drainage-derived DSM 43377T (7) and honeybee gut-derived ATCC BAA-2165 (8). The ANI values between strain TP-A0876 and the two N. alba strains were 98.35% to 99.04%. Based on these similarities, TP-A0876 was identified as N. alba (9). The two N. alba strains also possess gene clusters homologous to the five PKS and NRPS gene clusters found in the TP-A0876 genome.
During our genome analysis of Nocardiopisis sp. TP-A0876, Lin et al. reported a putative nocapyrone biosynthetic gene cluster, ncpA-D, in N. alba CR167, isolated from the venom duct of a cone snail (10). One (orf181 to orf178 in scaffold009) of the two type-I PKS gene clusters in Nocardiopisis sp. TP-A0876 is homologous to ncpA-D. We assume that this cluster is responsible for nocapyrone biosynthesis in strain TP-A0876. Interestingly, a variety of pyrone derivatives were isolated from marine-derived Nocardiopsis strains (11–14). The actual products of the remaining four PKS and NRPS gene clusters have not been isolated or characterized from our strain. The genome sequence of Nocardiopisis sp. TP-A0876 will serve as a valuable reference to elucidate the potential of marine-derived Nocardiopisis strains as promising sources for bioactive secondary metabolites.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. BAZE00000000. The version described in this paper is the first version, BAZE01000000.
ACKNOWLEDGMENTS
This research was supported by a Grant-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, and Technology of Japan to Y.I.
We are grateful to Machi Sasagawa for finding nocapyrone-synthetic gene clusters and for her helpful comments. We also thank Yuko Kitahashi for finishing genome sequences and annotating PKS and NRPS genes.
Footnotes
Citation Komaki H, Ichikawa N, Hosoyama A, Fujita N, Igarashi Y. 2014. Draft genome sequence of marine-derived actinomycete Nocardiopsis sp. strain TP-A0876, a producer of polyketide pyrones. Genome Announc. 2(4):e00665-14. doi:10.1128/genomeA.00665-14.
REFERENCES
- 1. Fenical W, Jensen PR. 2006. Developing a new resource for drug discovery: marine actinomycete bacteria. Nat. Chem. Biol. 2:666–673. 10.1038/nchembio841 [DOI] [PubMed] [Google Scholar]
- 2. Jensen PR, Mincer TJ, Williams PG, Fenical W. 2005. Marine actinomycete diversity and natural product discovery. Antonie Van Leeuwenhoek 87:43–48. 10.1007/s10482-004-6540-1 [DOI] [PubMed] [Google Scholar]
- 3. Lam KS. 2006. Discovery of novel metabolites from marine actinomycetes. Curr. Opin. Microbiol. 9:245–251. 10.1016/j.mib.2006.03.004 [DOI] [PubMed] [Google Scholar]
- 4. Ohtsubo Y, Maruyama F, Mitsui H, Nagata Y, Tsuda M. 2012. Complete genome sequence of Acidovorax sp. strain KKS102, a polychlorinated-biphenyl degrader. J. Bacteriol. 194:6970–6971. 10.1128/JB.01848-12 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. 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. 10.1186/1471-2105-11-119 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U. S. A. 106:19126–19131. 10.1073/pnas.0906412106 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Li HW, Zhi XY, Yao JC, Zhou Y, Tang SK, Klenk HP, Zhao J, Li WJ. 2013. Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability. PLoS One 8:e61528. 10.1371/journal.pone.0061528 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Qiao J, Chen L, Li Y, Wang J, Zhang W, Chen S. 2012. Whole-genome sequence of Nocardiopsis alba strain ATCC BAA-2165, associated with honeybees. J. Bacteriol. 194:6358–6359. 10.1128/JB.01522-12 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57:81–91. 10.1099/ijs.0.64483-0 [DOI] [PubMed] [Google Scholar]
- 10. 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. 2013. A bacterial source for mollusk pyrone polyketides. Chem. Biol. 20:73–81. 10.1016/j.chembiol.2012.10.019 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. 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. 74:2219–2223. 10.1021/np200597m [DOI] [PubMed] [Google Scholar]
- 12. Kim MC, Kwon OW, Park JS, Kim SY, Kwon HC. 2013. Nocapyrones H-J, 3,6-disubstituted alpha-pyrones from the marine actinomycete Nocardiopsis sp. KMF-001. Chem. Pharm. Bull. (Tokyo) 61:511–515. 10.1248/cpb.c12-00956 [DOI] [PubMed] [Google Scholar]
- 13. Schneemann I, Ohlendorf B, Zinecker H, Nagel K, Wiese J, Imhoff JF. 2010. Nocapyrones A-D, gamma-pyrones from a Nocardiopsis strain isolated from the marine sponge Halichondria panicea. J. Nat. Prod. 73:1444–1447. 10.1021/np100312f [DOI] [PubMed] [Google Scholar]
- 14. Kim Y, Ogura H, Akasaka K, Oikawa T, Matsuura N, Imada C, Yasuda H, Igarashi Y. Nocapyrones: α- and γ-pyrones from a marine-derived Nocardiopsis sp. Mar. Drugs, in press [DOI] [PMC free article] [PubMed] [Google Scholar]