Abstract
A draft genome sequence of Streptomyces zinciresistens K42, a novel Streptomyces species displaying a high level of resistance to zinc and cadmium, is presented here. The genome contains a large number of genes encoding proteins predicted to be involved in conferring metal resistance. Many of these genes appear to have been acquired through horizontal gene transfer.
GENOME ANNOUNCEMENT
The Gram-positive, high-G+C-content, filamentous bacteria of genus Streptomyces have mainly been studied and characterized due to their ability to produce a wide variety of secondary metabolites, such as antibiotics (11, 17). The complete genome sequences of five Streptomyces species have been reported in recent years. In addition, there are numerous ongoing projects to sequence isolates from different Streptomyces species (4, 6, 11, 12, 15).
To this point, there has been no report of a genome sequence for a metal-resistant Streptomyces species. The ability of some strains to tolerate high levels of metals and metalloids has been reported (1, 7, 13). Streptomyces zinciresistens K42 (CCNWNQ 0016T), a novel species of the genus Streptomyces, was selected from a copper-zinc mine tailing (8).
Sequencing reads were generated with a 454 GS FLX sequencer (10) and assembled using GS De Novo Assembler (Newbler) version 2.5.3. The assembled contigs were submitted to the RAST annotation server for subsystem classification and functional annotation (3). The coding sequences (CDSs) were assigned using BLASTp with KEGG Orthology (KO). The GC content was analyzed using seqool (http://www.biossc.de/seqool/index.html). The NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) was employed for gene annotation in preparation for submission to GenBank (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).
The draft genome sequence of Streptomyces zinciresistens strain K42 comprises 8,228,741 bases representing a 43-fold coverage of the genome. Since some contigs appear to be present in multiple copies, this should be considered a lower bound for the size of the strain K42 genome, which is about 4% smaller than the genome size reported for Streptomyces griseus (11) and 5% smaller than that for Streptomyces coelicolor (4). The assembled genome consists of 488 large contigs (>500 bp) and has a high G+C content of 72.46%. Seventeen of these contigs showed extremely high coverage (∼2,000-fold) and were subsequently joined into a single plasmid of 30,979 bp using the assembly editor Consed (5). The 5S, 16S, and 23S rRNAs (probably present in several copies), 69 tRNA genes, and 7,307 protein-coding genes (CDSs) were annotated in RAST. For the CDSs, 4,943 proteins could be assigned to COG (Cluster of Orthologous Groups) families (14). The genome has 2,019 proteins with orthologs in Streptomyces coelicolor, Streptomyces avermitilis, Streptomyces griseus, and Streptomyces scabiei in KEGG (bit score of >60) (http://www.genome.jp/kegg). It has 2,520 hypothetical proteins with no match to any known proteins in the databases, which may be a reflection of a high degree of strain specificity of the K42 genome. Sixty-one diverse secondary metabolic genes could be identified, with a total of 31 genes predicted to be involved in biosynthesis of antibiotics.
Furthermore, a number of genes were predicted to encode proteins conferring resistance to metals and metalloids. Comparison to orthologs in other related species suggests that at least 8 out of 13 genes encoding heavy and transition metal-translocating P1B-type ATPase were likely acquired by horizontal gene transfer. A subset of three putative P-type ATPases transporting divalent cations show unusual features in their conserved metal binding domains and are all regulated by a CadC-type repressor, indicating that they confer cadmium and zinc resistance (2, 9, 16).
Nucleotide sequence accession numbers.
This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under accession number AGBF00000000. The version described in this paper is the first version, AGBF01000000.
Acknowledgments
This work was supported by the National Natural Science Foundation of China (grants 31070444, 30970003, 30900215, and 30630054), 973 Project of China (grant 2010CB126502), International Science & Technology Cooperation Program of China (grant 2010DFA91930), and Chinese Universities Scientific Fund (grant QN2011025).
Sequencing was performed at the University of Arizona Genetics Core.
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