Abstract
Streptomyces auratus strain AGR0001 produces neophoslactomycin A, a novel analog of phoslactomycin that possesses potent activity against some phytopathogenic fungi. Here, the draft genome sequence of S. auratus strain AGR0001 is presented, which would provide insight into the biosynthetic mechanism of neophoslactomycin A.
GENOME ANNOUNCEMENT
Streptomyces auratus strain AGR0001, isolated from the soil samples collected from Yunnan Province, China, produces a series of structurally related phoslactomycins, which have attracted considerable interest in recent years due to their intriguing structures and strong bioactivities against various fungi and/or tumors (5, 13, 17, 18). Among the phoslactomycins produced by S. auratus strain AGR0001, a novel compound named neophoslactomycin A was shown to possess potent activity against some phytopathogenic fungi, such as Alternaria alternata, Botrytis cinerea, and Magnaporthe grisea (our unpublished observation). However, low yield and multiple analogs in the fermentation products have hampered the further development of neophoslactomycin A. The availability of the genome sequence of S. auratus strain AGR0001 would provide an entry point to study the biosynthesis of neophoslactomycin A and thereby facilitate the genetic engineering of its biosynthetic pathway to increase the production of neophoslactomycin A. Herein, we report the draft genome sequence of S. auratus strain AGR0001.
The whole genome sequence was determined by paired-end sequencing with high-throughput Illumina sequencing technology (2). A total of 1,050 Mbp of sequence data was generated, which represents approximately 133-fold coverage of the genome. For the assembly of short reads, SOAPdenovo 1.05 (10) was used, and the assembly was validated with Consed (6). Putative protein-coding sequences were predicted using Glimmer 3.0 (4). The functional annotation was accomplished by BLASTP analyses of sequences in the Swiss-Prot (1), KEGG (8), and COG (16) databases and by manual curation of the outputs. Nontranslating genes were predicted using tRNAscan-SE (15), rRNAmmer (9), and Rfam (7).
The genome of S. auratus strain AGR0001 is composed of one linear chromosome with a size of 7,885,420 bp (71.45% G+C), distributed in 19 scaffolds that include 238 contigs. It is shorter than the other sequenced genomes of model streptomycetes, such as S. coelicolor A3 (2) (8.7 Mbp) (3), S. avermitilis ATCC 31267 (8.7 Mbp) (12), and S. griseus IFO13350 (8.5 Mbp) (11). Analysis of the genome revealed that its chromosome contains 8 rRNA operons, 66 tRNA genes, and 7,102 protein-coding genes, which encode at least 3,935 proteins that have assigned putative functions. There are at least 33 putative gene clusters for the biosynthesis of polyketide, nonribosomal peptide, or terpene.
The putative gene cluster for the biosynthesis of phoslactomycins, localized on the chromosome (scaffolds 1, 4, 7, and 8), has a similar organization to the one described from Streptomyces sp. strain HK-803 (14). It contains all of the open reading frames (ORFs) reported in Streptomyces sp. strain HK-803, including 7 polyketide synthase genes, 11 posttailoring genes, 5 regulatory genes, and 5 cyclohexanecarboxylic acid-coenzyme A (CoA) synthesis genes. All of the putative proteins show extremely high similarity (most of them >96%) to their counterparts in Streptomyces sp. strain HK-803, suggesting that the two may share the same biosynthetic mechanisms. The information provided by the genome sequence is of great importance for guiding the further development of neophoslactomycin A.
Nucleotide sequence accession numbers.
The genome sequence has been deposited in DDBJ/EMBL/GenBank under accession no. AJGV00000000. The version described in this paper is the first version, AJGV01000000.
ACKNOWLEDGMENTS
We thank Xiaoyang Zhi for helping us analyze rRNA and tRNA genes and Min Yin for critical comments on the manuscript.
This work was funded by the National Science Foundation of China (21162039) and National Key Technologies R&D Program (2011BAE06B04-17, 2010GB2F300435), supporting M.W., the Yunnan Provincial Science and Technology Department (W8011303), supporting M.L., and the National Science Foundation of China (30760096) and the Yunnan Provincial Science and Technology Department (2011FA005), supporting T.L.
REFERENCES
- 1. Bairoch A, Apweiler R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28:45–48 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Bentley DR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Bentley SD, et al. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147 [DOI] [PubMed] [Google Scholar]
- 4. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Fushimi S, Nishikawa S, Shimazu A, Seto H. 1989. Studies on new phosphate ester antifungal antibiotics phoslactomycins. I. Taxonomy, fermentation, purification and biological activities. J. Antibiot. (Tokyo) 42:1019–1025 [DOI] [PubMed] [Google Scholar]
- 6. Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195–202 [DOI] [PubMed] [Google Scholar]
- 7. Griffiths-Jones S, et al. 2005. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33:D121–D124 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. 2010. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38:D355–D360 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Lagesen K, et al. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100–3108 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Li R, et al. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265–272 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Ohnishi Y, et al. 2008. Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J. Bacteriol. 190:4050–4060 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Omura S, et al. 2001. Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc. Natl. Acad. Sci. U. S. A. 98:12215–12220 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Ozasa T, et al. 1989. Novel antitumor antibiotic phospholine. 1. Production, isolation and characterization. J. Antibiot. (Tokyo) 42:1331–1338 [DOI] [PubMed] [Google Scholar]
- 14. Palaniappan N, Kim BS, Sekiyama Y, Osada H, Reynolds KA. 2003. Enhancement and selective production of phoslactomycin B, a protein phosphatase IIa inhibitor, through identification and engineering of the corresponding biosynthetic gene cluster. J. Biol. Chem. 278:35552–35557 [DOI] [PubMed] [Google Scholar]
- 15. Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33:W686–W689 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33–36 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17. Tomiya T, Uramoto M, Isono K. 1990. Isolation and structure of phosphazomycin C. J. Antibiot. (Tokyo) 43:118–121 [DOI] [PubMed] [Google Scholar]
- 18. Uramoto M, Shen YC, Takizawa N, Kusakabe H, Isono K. 1985. A new antifungal antibiotic, phosphazomycin A. J. Antibiot. (Tokyo) 38:665–668 [DOI] [PubMed] [Google Scholar]