Abstract
Streptomyces sp. SS produces a series of uridyl peptide antibiotic sansanmycins. Here, we present a draft genome sequence of Streptomyces sp. SS containing the biosynthetic gene cluster for the antibiotics. The identification of the biosynthetic gene cluster of sansanmycins may provide further insight into biosynthetic mechanisms for uridyl peptide antibiotics.
GENOME ANNOUNCEMENT
Streptomyces sp. SS, isolated from Guizhou Province of China, produces a series of sansanmycins with activities against Pseudomonas aeruginosa and, more intriguing, multidrug-resistant Mycobacterium tuberculosis (6–8). Sansanmycins are members of a class of uridyl peptide antibiotics including pacidamycins, mureidomycins, and napsamycins, which target bacterial translocase MraY involved in cell wall biosynthesis (5). These antibiotics share the common structure with a pseudo tetrapeptide attached to 3′-deoxyuridine nucleoside via an exocyclic enamide. The pseudo tetrapeptides of some sansanmycins consist of leucine, which is absent in other uridyl peptide antibiotics. Herein, we report the draft genome sequence of Streptomyces sp. SS.
The nucleotide sequencing was performed by BGI (Shenzhen, China) using an Illumina/Hiseq 2000 sequencer. A total of 838 Mb of raw data was obtained, which represented approximately 100-fold coverage of the genome. Assembly was performed using SOAP de novo software (3). The draft genome sequence of Streptomyces sp. SS contains 8,119,746 bp, with a GC content of 72.41%, distributed over 69 scaffolds containing 87 contigs. The N50 of contig size was 255,986 bp and that of scaffold size was 418,211 bp. Putative protein-coding sequences were predicted using the Glimmer version 3.0 (1), and gene functional annotation was based on BLASTP results determined with the KEGG, COG, Swiss-Port, NT, and NR databases. A total of 7,632 putative protein coding sequences (CDSs) were identified in the draft genome containing 7,211,148 bp, accounting for 88.77% of the genome. A total of 69 tRNA-encoding genes were predicted with tRNAscan-SE (4), and three rRNA operons were found by rRNAmmer software and aligning with an rRNA pool.
The biosynthetic gene cluster of pacidamycin was first characterized in 2010 (10) and contained 22 uninterrupted genes (pacA to pacV), and a digene cassette (pacW and pacX) was identified to be associated with the biosynthesis of pacidamycin separately (9). Based on BLASTP searches, PacA to PacV (except PacU) have homologues with high amino acid sequence similarity (identity of >70%) in the draft genome of Streptomyces sp. SS, and these genes are assigned on scaffold 7 and scaffold 36. The PCR-based method was used for chromosome walking, resulting in the connection of scaffold 7 and scaffold 36. An ORF encoding SsaU, showing 77% identify to PacU, was found within the linking sequence. The genetic organization of the sansanmycin biosynthetic gene cluster resembles the recently characterized napsamycin gene cluster of Streptomyces sp. DSM5940 (2). In contrast to the pacidamycin gene cluster, ssaX (homologues of pacX), encoding a phenylalanine hydroxylase, was not in a digene cassette but was located in the defined gene cluster downstream of ssaT. The study of the biosynthetic genes for these uridyl peptide antibiotics will set the stage for future mechanism studies of their biosynthesis and the generation of new uridyl peptide derivatives by combinatorial biosynthesis.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. AKXV00000000. The version described in this paper is the first version, AKXV01000000.
ACKNOWLEDGMENTS
We thank BGI (Shenzhen, China) for Solexa shotgun sequencing, assembly, and annotation of the genome.
This work was supported by grants from the National Natural Science Foundation of China (31170042, 81273415, and 30973668), the Ministry of Science and Technology of China (2012ZX09301002-001-016, 2009ZX09501-008, and 2010ZX09401-403), and the Beijing Natural Science Foundation (5102032).
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