Genome Sequence of the Abyssomicin- and Proximicin-Producing Marine Actinomycete Verrucosispora maris AB-18-032

Abstract

Verrucosispora maris AB-18-032 is a marine actinomycete that produces atrop-abyssomicin C and proximicin A, both of which have novel structures and modes of action. In order to understand the biosynthesis of these compounds, to identify further biosynthetic potential, and to facilitate rational improvement of secondary metabolite titers, we have sequenced the complete 6.7-Mb genome of Verrucosispora maris AB-18-032.Verrucosispora maris AB-18-032 was isolated from a deep marine sediment sample collected from the East Sea (Sea of Japan) (3, 9). It produces unique polycyclic type 1 polyketide antibiotics, namely, the abyssomicins, which are the first known natural-product inhibitors of the para-aminobenzoic acid biosynthetic pathway (6, 7). In particular, atrop-abyssomicin C is active against Gram-positive bacteria, including Bacillus subtilis, methicillin-resistant Staphylococcus aureus and vancomycin-resistant S. aureus (6,7,9), and Mycobacterium tuberculosis (5). The strain also produces proximicin A, a furan analogue of netropsin with novel antitumor properties (4, 10). Here, we announce the genome sequence of Verrucosispora maris AB-18-032, the first member of this genus to be sequenced, which should provide fundamental understanding of the biosynthesis of these antibiotics and facilitate bioengineering and biodiscovery efforts involving this strain.The complete genome of Verrucosispora maris AB-18-032 was sequenced using Roche 454 genome sequencer (GS) FLX (9.4-, 9.9-, 6.7-, and 6.8-times coverage of single-end reads and 13.3-times coverage of paired-end reads having 3-kb inserts) and Solexa (Illumina genome analyzer [GA], 43-times coverage with ϳ350-bp inserts and paired-end reads) sequencing technology.To combine the GA library with 454 GS FLX libraries, reads were assembled into 1,730 contigs using the ABySS 1.20 assembler (11), and the contigs were shredded into 15,379 fake reads. The fake reads and 454 GS FLX reads were assembled into 5 scaffolds (116 contigs) by using a combination of Newbler gsAssembler 2.3 (454 Life Sciences, Branford, CT) and CABOG assembler (8). The actual order of the scaffolds was determined by a series of PCRs based on a permutation table, and gaps were filled by primer-walking PCR followed by sequencing using an ABI 3730 system (Applied Biosystems, CA). Finally, Polisher software (Alla Lapidus, unpublished data) was used with the Illumina data to correct for homopolymers in the 454 reads and increase consensus quality. Annotation was performed by the RAST server (2) and the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static /Pipeline.html), and both annotations were scrutinized by manual inspection based on BLAST searches (1).The genome of Verrucosispora maris AB-18-032 has a single circular chromosome of 6,673,976 bp with a GC content of 70.9%. A circular plasmid of 58,295 bp with a GC content of 70.3%, pVMKU, was also identified. The chromosome has 5,947 coding sequences (CDS), 51 tRNA genes, and 9 rRNA genes, and the pla...

Verrucosispora maris sp. nov., a novel deep-sea actinomycete isolated from a marine sediment which produces abyssomicins

“…L. gen. n. maris of the sea, denoting the source of the isolate). The description is based on data taken from this and previous studies Goodfellow and Fiedler 2010;Roh et al 2011). Aerobic, Grampositive, non-acid-fast actinomycete which forms an extensively branched, light to dark orange pigmented substrate mycelium on ISP media.…”

“…This isolate, which has been provisionally labeled ''Verrucosispora maris'' (Goodfellow and Fiedler 2010), produces a family of novel polycyclic polyketides, the abyssomicins Riedlinger et al 2004;Keller et al 2007a, b) and proximicin A, an aminofuran type antibiotic ). In addition, it is known from the whole genome sequence of this organism that it contains around 23 biosynthetic gene clusters encoding for the production of known or predicted secondary metabolites (Roh et al 2011). Partial characterization of the abyssomicin-producing strain showed that it had chemotaxonomic and morphological properties similar to that of the type strain of V. gifhornensis, but could be distinguished from the latter using a combination of genotypic and phenotypic properties .…”

Genome sequences published outside of Standards in Genomic Sciences, January – June 2011

“…JS614, sequence accession CP000509, CP000508 [136] Saccharopolyspora spinosa NRRL 18395, sequence accession AEYC00000000 [137] Streptomyces griseoaurantiacus, sequence accession AEYX01000000 [138] Streptomyces griseus XyelbKG-1, sequence accession ADFC00000000 [139] Streptomyces sp. PP-C42, sequence accession AEWS01000000 [140] Verrucosispora maris AB-18-032, sequence accession CP002638, CP002639 [141] Phylum Chlamydiae Chlamydia pecorum E58, sequence accession CP002608 [142] Chlamydia psittaci 6BC, sequence accession CP002586 (chromosome), CP002587 (plasmid) [143] Chlamydia psittaci Cal10, sequence accession AEZD00000000 [143] Chlamydophila psittaci RD1, sequence accession FQ482149 (chromosome) FQ482150 (plasmid) [144] Standards in Genomic Sciences…”

Biologically active secondary metabolites from Actinomycetes

“…One of these compounds, abyssomicin, is isolated from Verrucosispora maris AB-18-032 [52]. It demonstrates antibacterial properties by inhibiting para-aminobenzoic acid biosynthesis [8,53].…”