Genome Sequence of Streptomyces sp. Strain Tü6071

Abstract

Streptomyces sp. Tü6071 is a soil-dwelling bacterium which has a highly active isoprenoid biosynthesis. Isoprenoids are important precursors for biopharmaceutical molecules such as antibiotics or anticancer agents, e.g., landomycin. Streptomyces sp. Tü6071 produces the industrially important terpene glycosides phenalinolactones, which have antibacterial activity against several Gram-positive bacteria. The availability of the genome sequence of Streptomyces sp. Tü6071 allows for understanding the biosynthesis of these pharmaceutical molecules and will facilitate rational genome modification to improve industrial use.

GENOME ANNOUNCEMENT

Streptomyces sp. Tü6071 was isolated from a soil sample collected in Cape Coast, Ghana. Today, this strain is the most important bacterium in producing natural drugs, such as phenalinolactones and landomycin (3, 4). Considering the fertility of the secondary metabolites produced by Tü6071, its genome sequence will provide fundamental understanding of the biosynthesis of these compounds and facilitate the bioengineering efforts of this species.

The whole genome shotgun sequence was determined by Roche/454 pyrosequencing (9) and Sanger paired-end sequencing (5) on cosmids. A cosmid library of Tü6071 was constructed in pWeb (Epicentre, Madison WI), with an average insert size of 35 kb. A 3-fold physical coverage of cosmids was chosen to order most of the Roche/454 contigs. Using standard primers and BigDye version 3.1 on the ABI3730xl genome analyzer, 672 clones were end sequenced from both sides. A total number of 1,298 reads with an average read length of 793 bases (Phred20/30) were generated. 454 contigs and paired-end cosmid reads were coassembled using GAP4 (Staden Package) to determine cosmids spanning gaps in the Newbler assembly. Gap closure was performed by sequencing on combinatorial PCR products generated from genomic DNA.

Putative protein-coding sequences were predicted using Glimmer3 (2) trained on annotated open reading frames of Streptomyces coelicolor A3(2) (1) and Streptomyces avermitilis (6). The annotation was accomplished by BlastP analyses of sequences in UniProt databases and by manual curation of the outputs of a variety of similarity searches. Nontranslating genes were predicted using tRNAscan-SE (8) and ARAGORN (7).

The genome of Streptomyces sp. Tü6071 consists of one linear chromosome composed of 7,359,294 bp (contig 1, contig 2) with 73.1% G+C content, as well as one linear plasmid (147,347 bp, 70.9% G+C content). It is shorter than the other streptomycete linear chromosomes of S. coelicolor A3(2) (8.7 Mbp), S. avermitilis MA-4680 (9.0 Mbp), and S. griseus IFO13350 (8.5 Mbp) (10).

Analysis of the Streptomyces Tü6071 genome revealed that its chromosome contains 6,466 protein-coding genes with at least 4,887 proteins with assigned putative functions based on 70% sequence identity and an amino acid alignment length of at least 100 residues. On the plasmid, from 176 predicted coding sequences, 73 have been functionally annotated. Furthermore, at least six rRNA operons and 74 tRNAs on the linear chromosome were predicted.

Isoprenoid-derived antibiotics, such as phenalinolactone A, produced by Tü6071 are synthesized by the condensation of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate. The IPP units required for isoprene biosynthesis are generated by two distinct pathways. In eukaryotes, the mevalonate pathway is very common, while in prokaryotes, the 2-C-methyl-d-erylthritol 4-phosphate (MEP) pathway is mainly used. The phenalinolactone biosynthetic gene cluster (3) is located on the linear chromosome at megabase positions 1.69 to 1.73. In Tü6071, members of the MEP pathway are located upstream of the phenalinolactone biosynthetic gene cluster.

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AFHJ00000000. The version described in this paper is the first version, AFHJ01000000.