Complete Genome Sequence of the Proteorhodopsin-Containing Marine Bacterium Sediminicola sp. YIK13.

Sediminicola sp. YIK13 is a marine flavobacterium, isolated from tidal flat sediment. Here, we present the first complete genome sequence of this genus, which consists of 3,569,807 bp with 39.4% GC content. This strain contains proteorhodopsin, as well as retinal biosynthesis genes, allowing it to utilize sunlight as an energy source.

GENOME ANNOUNCEMENT

Proteorhodopsin (PR) is a retinal-binding membrane protein belonging to the largest family of microbial rhodopsins, which function as light-driven proton pumps (1). PR genes are abundant in various ecosystems, particularly within the open ocean and are widely distributed among numerous bacterial groups, including Gammaproteobacteria, Alphaproteobacteria, and Flavobacteria (2–11). However, PR-containing sediment bacteria have not yet been studied. Here, we report the first complete genome for Sediminicola sp. YIK13, which was isolated from tidal flat sediment. The light-driven pumping activity of PR in this strain was directly measured using native cell suspensions and reported previously (12).

The strain YIK13 was isolated from a sample of tidal flat sediment collected at Yeongheung Island, Korea (E126°26′, N37°16′) in January 2009. Analysis of the 16S rRNA gene sequence indicates that the strain is a member of the family Flavobacteriaceae and shows the highest similarity to Sediminicola luteus CNI-3T (99.5%).

Genomic sequencing was performed using PacBio RS II single-molecule real-time (SMRT) sequencing technology (Pacific Biosciences, USA). A 10-kb insert library was constructed and sequenced, yielding >189.9× average genome coverage. De novo assembly of the 131,118 reads (677,903,501-bp total) was conducted using the hierarchical genome-assembly process (HGAP) pipeline in SMRT Analysis version 2.2.0 (Pacific Biosciences). Open reading frames were predicted by NCBI Prokaryotic Genomes Annotation Pipeline (PGAAP) version 2.6 (http://www.ncbi.nlm.nih.gov/genome/annotation_prok). The complete genome of Sediminicola sp. YIK13 consists of 3,569,807 bp with 39.4% GC content as a circular chromosome without any plasmid DNA. The genome contained 3,113 protein-coding sequences, 9 rRNAs (5S, 16S, and 23S), and 41 tRNAs with a single rRNA operon.

Genomic analysis of YIK13 revealed the presence of a green light-absorbing PR, 242 amino acids in length, with features typical of proton-pumping rhodopsins, including the DTE (corresponding positions of D85, T89, and D96 positions in bacteriorhodopsin) motif, which acts as proton acceptor and donor (2, 13, 14). The blh gene encoding a 15,15′-β-carotene dioxygenase was located adjacent to the PR gene, as seen in other PR-containing genomes of Bacteriodetes (7). The genome also contains the genes required for β-carotene biosynthesis, including those encoding crtB (phytoene synthase), crtI (phytoene desaturase), crtY (lycopene cyclase), and crtA (spheroidene monooxygenase) (15). Furthermore, it also contained a putative transcriptional regulator (MerR family) in front of the crtI, dxs (1-deoxy-d-xylulose-5-phosphate synthase), and idi (isopentenyl pyrophosphate d-isomerase) genes involved in FPP (farnesyl diphosphate) and IPP (isopentenyl diphosphate) precursor synthesis. Similar to other PR-containing genomes of Bacteriodetes (7), this genome also contained the crtZ (β-carotene hydroxylase) gene involved in the synthesis of zeaxanthin (a carotenoid pigment). This sequence may provide further information necessary to understand the physiological and ecological functions of PR-mediated light utilization in sediment-dwelling microorganisms.

Nucleotide sequence accession numbers.

The complete genome sequence of Sediminicola sp. YIK13 has been deposited at DDBJ/EMBL/GenBank under the accession number CP010535. The partial sequence of the 16S rRNA gene of Sediminicola sp. YIK13 has been deposited into the GenBank database under the accession number JX312334.