Complete Genome Sequence of Sphingorhabdus sp. YGSMI21, Exhibiting High Enantioselective Epoxide Hydrolase Activity.

Sphingorhabdus sp. YGSMI21 is a novel strain exhibiting high enantioselective hydrolysis activity for styrene oxide. Here, we present its complete genome sequence, consisting of one circular chromosome (3.86 Mb) and one plasmid (0.196 Mb).

GENOME ANNOUNCEMENT

Epoxide hydrolases (EHase) (EC 3.3.2.3) hydrolyze epoxides to their corresponding vicinal diols (1–3). EHase was recently reported as a potential biocatalyst for the production of chiral epoxides (4). In chiral compounds, it is common for biological activities to occur in one enantiomer, while other enantiomers have no activity or adverse side effects (4). Since pharmaceuticals with a chiral carbon should be developed as a single enantiomer (5, 6), there is a need for continuous study to find microbial sources of enantioselective EHase that preferably hydrolyze only one enantiomer in racemic substrates (1). EHase with a desired enantioselectivity has been screened from polycyclic aromatic hydrocarbon-degrading bacteria, resulting in the isolation of the novel strain Sphingorhabdus sp. YGSMI21 (7, 8). It was reported that Sphingorhabdus sp. YGSMI21 itself preferentially hydrolyzed the (R)-enantiomer of styrene oxide, yielding the (S)-enantiomer at greater than 99.9% efficiency (7, 8).

The extracted DNA from Sphingorhabdus sp. YGSMI21 was used to construct 20-kb SMRTbell template libraries. Whole-genome sequencing was conducted using the PacBio RS Ⅱ platform (Pacific Biosciences) (9), yielding 75,245 long reads totaling 770,716,593 bp after filtering of the subreads. De novo assembly was conducted using the Hierarchical Genome Assembly Process (HGAP) version 2.3 (10). The estimated genome size was 4,129,946 bp with an average coverage of 162×. The genome annotation was conducted using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP).

The sizes of the chromosome and plasmid were 3,864,176 bp and 196,579 bp, respectively. The genome of Sphingorhabdus sp. YGSMI21 contained 3,993 protein-coding genes, 47 tRNAs, and 6 rRNAs with a G+C content of 56.0%. Our analysis confirmed the presence of three epoxide hydrolases and one limonene-1,2-epoxide hydrolase in this genome.

Accession number(s).

The complete genome sequence of Sphingorhabdus sp. strain YGSMI21 was deposited at GenBank under the accession numbers CP022548 and CP022549. Sphingorhabdus sp. YGSMI21 is currently available from the Korean Culture Center of Microorganisms with the accession number KCCM 12136P.