Chu J

Guo M

Herron PR

Hoskisson PA

Hunter IS

Kirby R

Kosec G

Liu T-T

MacFadyen AC

Pethick FE

Petkovic H

Sangal V

Tang Z

We report the draft genome of Streptomyces rimosus (ATCC 10970), a soil isolate that produces oxytetracycline, a commercially important and clinically useful antibiotic

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              This work is licensed under a Creative Commons Attribution 3.0 Unported License   Newcastle University ePrints - eprint.ncl.ac.uk  Pethick FE, MacFadyen AC, Tang Z, Sangal V, Liu T-T, Chu J, Kosec G, Petkovic H, Guo M, Kirby R, Hoskisson PA, Herron PR, Hunter IS. Draft genome sequence of the oxytetracycline-producing bacterium Streptomyces rimosus ATCC 10970. Genome Announcements 2013, 1(2), e00063-13.   Copyright: © 2013 Pethick et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.  DOI link to article: http://dx.doi.org/10.1128/genomeA.00063-13  Date deposited:   16/12/2015 Draft Genome Sequence of the Oxytetracycline-Producing BacteriumStreptomyces rimosus ATCC 10970Florence E. Pethick,a Alison C. MacFadyen,a Zhenyu Tang,a,b Vartul Sangal,a Tze-Tze Liu,c Ju Chu,b Gregor Kosec,d Hrvoje Petkovic,dMeijin Guo,b Ralph Kirby,e Paul A. Hoskisson,a Paul R. Herron,a Iain S. HunteraStrathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdoma; State Key Laboratory of Bioreactor Engineering, EastChina University of Science and Technology, Shanghai, Chinab; Genome Research Center, National Yang-Ming University, Taipei, Taiwanc; Acies Bio, Ltd., Ljubljana,Sloveniad; Department of Life Sciences, Institute of Genome Science, National Yang-Ming University, Taipei, TaiwaneWe report the draft genome of Streptomyces rimosus (ATCC 10970), a soil isolate that produces oxytetracycline, a commerciallyimportant and clinically useful antibiotic.Received 28 January 2013 Accepted 6 February 2013 Published 7 March 2013Citation Pethick FE, MacFadyen AC, Tang Z, Sangal V, Liu T-T, Chu J, Kosec G, Petkovic H, Guo M, Kirby R, Hoskisson PA, Herron PR, Hunter IS. 2013. Draft genome sequence ofthe oxytetracycline-producing bacterium Streptomyces rimosus ATCC 10970. Genome Announc. 1(2):e00063-13. doi:10.1128/genomeA.00063-13.Copyright © 2013 Pethick et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Iain S. Hunter, i.s.hunter@strath.ac.uk.Streptomyces rimosus is a Gram-positive, aerobic, filamentousactinobacterium. It was reported in 1950 and was patented (1)as the founder strain for the production of the antibiotic oxytet-racycline (OTC) (2). Recombination was recognized (3) and arudimentary genetic map was deduced (4). The pharmaceuticalindustry set out to improve the commercial productivity of OTC,deriving higher-titer genealogies that led to the contemporary in-dustrial strains that are now responsible for the production of108 kg of OTC annually. Stimulated by commercial interest overthe years, a sophisticated genetics and molecular biology has beendeveloped for S. rimosus (5). This announcement reports the der-ivation of data to enable the generation of a scaffold genome se-quence for this important industrial species.Genome sequencing of the S. rimosus type strain ATCC 10970was carried out using a whole-genome shotgun sequencing ap-proach performed on a Roche 454 GS Junior apparatus. Usingthree single-ended runs, we obtained 440,253 reads. The readswere assembled using Genome Sequencer de novo Assembler (ver-sion 2.7, Roche), which led to a final assembly of 453 contigs of500 bp. The total size of the assembly was 9.5 Mbp, with a meancontig size of 21 kbp (average, 17 coverage) and a GC contentof 71.88%. Automatic functional annotation results were ob-tained using the NCBI Prokaryotic Genome Annotation Pipeline(http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).The draft genome of S. rimosus is estimated to have a total of8,416 protein-coding genes, along with 66 tRNAs. The overall ge-nome size is consistent with the physical map of S. rimosus, de-rived by pulsed-field gel electrophoresis (6). It is also within therange of other published streptomycete genome sequences. Threegene clusters associated with the production of previously re-ported secondary metabolites [OTC (7), rimocidin (8), and des-ferrioxamine C (9)] are readily identified within the sequence, inaddition to around 45 other putative secondary metabolite bio-synthetic clusters whose functions remain to be elucidated (10).The strain is lysogenic for phages RP2 and RP3, with the DNAsequences corresponding to the restriction maps published previ-ously (11). The genome sequence is also likely to include at leastone giant (387 kb) linear plasmid known to be present in S. rimo-sus (12).Sequencing of S. rimosus ATCC 10970 provides a scaffold fromwhich to investigate and understand how mutation results inhigher titers of OTC.Nucleotide sequence accession numbers. The S. rimosusATCC 10970 Whole Genome Shotgun project has beendeposited at DDBJ/EMBL/GenBank under the accession no.ANSJ00000000. The version described in this paper is the firstversion, ANSJ01000000.ACKNOWLEDGMENTSWe acknowledge financial support from the National Yang-Ming Univer-sity, Taiwan, for the sequencing project (R.K.), a British Council for Re-search Projects Network grant (P.A.H. and H.P.), and the British Council/CUC for a Scotland-China Higher Education Research Partnership forPhD Studies (Z.T.).REFERENCES1. Sobin BA, Finlay AC. 1950. Terramycin and its production. US patent2,516,080.2. Finlay AC, Hobby GL, P’an SY, Regna PP, Routien JB, Seeley DB, ShullGM, Sobin BA, Solomons IA, Vinson JW, Kane JH. 1950. Terramycin,a new antibiotic. Science 111:85.3. Alikhanian SI, Mindlin SZ. 1957. Recombinations in Streptomyces rimo-sus. Nature 180:1208 –1209.4. Friend EJ, Hopwood DA. 1971. The linkage map of Streptomyces rimosus.J. Gen. Microbiol. 68:187–197.5. Petković H, Cullum J, Hranueli D, Hunter IS, Perić-Concha N, Pigac J,Thamchaipenet A, Vujaklija D, Long PF. 2006. Genetics of Streptomycesrimosus, the oxytetracycline producer. Microbiol. Mol. Biol. Rev. 70:704 –728.6. Pandza K, Pfalzer G, Cullum J, Hranueli D. 1997. Physical mappingshows that the unstable oxytetracycline gene cluster of Streptomyces rimo-sus lies close to one end of the linear chromosome. Microbiology 143:1493–1501.7. Zhang W, Ames BD, Tsai SC, Tang Y. 2006. Engineered biosynthesis ofa novel amidated polyketide, using the malonamyl-specific initiationmodule from the oxytetracycline polyketide synthase. Appl. Environ. Mi-crobiol. 72:2573–2580.8. Seco EM, Perez-Zuniga FJ, Rolon MS, Malpartida F. 2004. Starter unitGenome AnnouncementsMarch/April 2013 Volume 1 Issue 2 e00063-13 genomea.asm.org 1choice determines the production of two tetraene macrolides, rimocidinand CE-108, in Streptomyces diastaticus var. Chem. Biol. 11:357–366.9. Barona-Gómez F, Wong U, Giannakopulos AE, Derrick PJ, Challis GL.2004. Identification of a cluster of genes that directs desferrioxamine bio-synthesis in Streptomyces coelicolor M145. J. Am. Chem. Soc. 126:16282–16283.10. 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 bio-synthesis gene clusters. Nucleic Acids Res. 29:W339 –W346.11. Rausch H, Vesligaj M, Pocta D, Biuković G, Pigac J, Cullum J,Schmieger H, Hranueli D. 1993. The temperate phages RP2 and RP3 ofStreptomyces rimosus. J. Gen. Microbiol. 139:2517–2524.12. Gravius B, Glocker D, Pigac J, Pandza K, Hranueli D, Cullum J. 1994.The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its inter-actions with the chromosome. Microbiology 140:2271–2277.Pethick et al.Genome Announcements2 genomea.asm.org March/April 2013 Volume 1 Issue 2 e00063-13

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Draft genome sequence of the oxytetracycline-producing bacterium <em>Streptomyces rimosus</em> ATCC 10970

Draft genome sequence of the oxytetracycline-producing bacterium <em>Streptomyces rimosus</em> ATCC 10970

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