Draft Genome Sequence of Acetobacter tropicalis Type Strain NBRC16470, a Producer of Optically Pure d-Glyceric Acid.

Here we report the 3.7-Mb draft genome sequence of Acetobacter tropicalis NBRC16470(T), which can produce optically pure d-glyceric acid (d-GA; 99% enantiomeric excess) from raw glycerol feedstock derived from biodiesel fuel production processes.

GENOME ANNOUNCEMENT

Acetic acid bacteria (Acetobacteriaceae) are obligate aerobes that show efficient oxidation of a wide range of substrates, such as alcohols, sugars, sugar acids, and sugar alcohols. These bacteria have numerous membrane-bound dehydrogenases and oxidoreductases to accomplish such oxidative reactions; therefore, energy-consuming transport of substrates into the cell and products out of the cell is not required (1). Among acetic acid bacteria, Acetobacter sp. have been used for industrial vinegar production due to their strong ethanol-oxidizing ability, and their complete or draft genome sequences were reported previously (e.g., 2, 3).

We previously reported a biotechnological method for producing optically pure d-glyceric acid (d-GA) with a 99% enantiomeric excess (ee) from glycerol using Acetobacter tropicalis NBRC16470T. The maximal 101-g/liter·day GA productivity under optimized conditions was achieved using this strain (4, 5). d-GA is a promising compound that likely exerts biological activities, such as d-GA-promoted acceleration of ethanol metabolism in rats (6) and d-GA-promoted proliferation of human dermal fibroblasts (7).

The A. tropicalis NBRC 16470T draft genome was generated using the next-generation sequence platform, Illumina MiSeq (Illumina, San Diego, CA). A paired-end DNA library (insert size, ~500 bp) was prepared using an NEBNext Ultra DNA library prep kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced using the MiSeq reagent kit v2. Sequence data were generated, totalling 2.2 M paired-end reads, each 250 bp in length. Genomic sequence assembly using the SOAPdenovo2 assembler (8) generated 453 scaffolds composed of 654 contigs and a 3.7-Mb draft genome sequence at 151-fold coverage from the paired-end library. The length of the longest scaffold was 394,032 bp, and the N50 length was 97,875 bp with 11 scaffolds. Protein-coding genes were predicted using the Microbial Genome Annotation Pipeline (MiGAP) system (9), which identified a total of 3,347 coding sequences. A total of 42 tRNA-encoding genes and three rRNA-encoding genes were also identified.

Previously, a draft genome sequence of a thermotolerant strain, Acetobacter tropicalis SKU1100 (NBRC101654), isolated from fruit in Thailand, was reported (10). However, that of the A. tropicalis type strain (NBRC16470) has not yet been analyzed. In A. tropicalis, we demonstrated that the membrane-bound alcohol dehydrogenase (mADH) subunit I-encoding gene (adhA) was involved in d-GA production from glycerol (11). Another two genes encoding mADH subunits were also identified in the A. tropicalis NBRC16470 genome: the cytochrome c subunit II and an AdhS-like subunit III (12). Several other membrane-bound dehydrogenases were annotated from the genome information, including membrane-bound aldehyde dehydrogenase and pyrroquinoline quinone-dependent glucose dehydrogenase. The draft genome sequence of A. tropicalis NBRC16470 may provide novel molecular information and increase our understanding of the production mechanism of high optical pure d-GA from glycerol.

Nucleotide sequence accession numbers.

The A. tropicalis NBRC16470 genome sequence (accession number BBMU00000000) was deposited as 654 contigs (accession numbers BBMU01000001 to BBMU01000654) and 453 scaffolds (accession numbers DF850035 to DF850487) at DDBJ/EMBL/GenBank. The version described in this study is the first version.