Draft Genome Sequence of Marine-Derived Streptomyces sp. Strain AA0539, Isolated from the Yellow Sea, China

Abstract

Here, we report the draft genome sequence of Streptomyces sp. strain AA0539, isolated from marine sediment of the Yellow Sea, China. Its small genome (∼5.8 Mb) contains large, unique genes and gene clusters for diverse secondary metabolites, suggesting great potential as a source for the discovery of novel natural products.

GENOME ANNOUNCEMENT

Streptomyces spp. are remarkably rich sources of natural products and still produce a larger number and variety of novel bioactive compounds than any other genus (13). Recent trends in drug discovery from natural sources emphasize investigation of marine Streptomyces spp., which have great potential to increase the number of natural products in clinical trials (12). Streptomyces sp. strain AA0539 was isolated from a marine sediment sample taken at a water depth of 50 m in the Yellow Sea (latitude, 35°12′125′′N; longitude, 119°41′881′′E). Its metabolites showed specific antitumor activity on a human ovarian carcinoma cell line, NIH:OVCAR-3. In the interest of the above-described information, we herein reported the draft genome sequence of Streptomyces sp. AA0539.

Raw data of the genome were generated by a Roche 454 Genome Sequencer FLX and assembled using Newbler 2.3. Putative protein-encoding sequences were identified by Glimmer 3.02 (2) and GeneMark (5). Functional annotation was based on BLASTP results with NR and KEGG databases. tRNA and rRNA genes were predicted with tRNAscan-SE (11) and RNAmmer (4), respectively. A total of 374,828 reads including up to 159.5 Mb were obtained, which represented a 27.2-fold coverage of the Streptomyces sp. AA0539 genome. The draft genome distributed in 57 contigs totaling 5,768,564 bp with an average GC content of 72.92% was significantly smaller than the genome size (8 to 12 Mb) of other reported Streptomycetes spp. (7), suggesting that the AA0539 genome is highly strain specific. This draft genome consisted of one linear chromosome with 3 rRNA operons, 55 tRNA genes, and 5,149 coding sequences (CDSs). For the CDSs, 3,814 proteins could be assigned to COG families (10), and 1,335 CDSs encode proteins with no match to any known proteins in the public databases. Additionally, the signal peptide cleavage sites, transmembrane topologies, and lipoproteins were predicted using SignalP 4.0 (8), TMHMM 2.0 (3), and LipoP 1.0 (9), respectively. We identified 433 proteins as secreted proteins, 1,184 proteins as transmembrane proteins, 1,055 lipoproteins, and 295 proteins as the transporter.

Twenty biosynthetic gene clusters for secondary metabolites (2 siderophores, 4 terpenes, 1 lantibiotic, 2 polyketide synthases [PKS], 3 nonribosomal peptide synthetases [NRPS], 2 nucleosides, 1 ectoine, and 5 hybrid NRPS/PKS) were identified by antiSMASH (6). For example, the predicted ectoine cluster is responsible for the biosynthesis of ectoine and 5-hydroxyectoine, which act as protectants against osmotic and heat stress in the cell (1). More than 168 diverse genes located in these secondary metabolic gene clusters were predicted using genome analysis, indicating high genomic synteny to those of various Streptomyces species. More importantly, many putative genes in these gene clusters showed low identity with the known ones, suggesting that AA0539 may be a potential producer of novel natural products. Hence, the unique genome information of Streptomyces sp. AA0539 will further promote the elucidation of chemical and genetic diversity of this strain for the discovery of novel gene clusters and natural products.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ALNP00000000. The version described in this paper is the first version, ALNP01000000.