Draft Genome Sequence of Gluconobacter oxydans WSH-003, a Strain That Is Extremely Tolerant of Saccharides and Alditols

Abstract

Gluconobacter oxydans is known for its incomplete oxidation of a wide range of alcohols, sugars, and acids in a bioprocess. The corresponding oxidation products are secreted almost completely into the medium. Here, we present the high-quality draft genome sequence of G. oxydans WSH-003, an industrial strain with both high l-sorbose productivity and extreme tolerance to saccharides and alditols.

GENOME ANNOUNCEMENT

Gluconobacter oxydans WSH-003 is an l-sorbose-accumulating strain of industrial interest due to its powerful ability to oxidize d-sorbitol into l-sorbose with a high quantitative yield of over 98% on an industrial scale (4). G. oxydans WSH-003 and its relative derivative strains are widely used for the industrial production of vitamin C in China, which occupies more than 90% of the global vitamin C market. G. oxydans WSH-003 was mutated by different methods from a wild-type strain at least 90 times with reliable records to improve the production of l-sorbose and the tolerance to saccharides and alditols, such as l-sorbose and d-sorbitol. Here, we present the draft genome of G. oxydans WSH-003, the industrial strain with both high l-sorbose productivity and extreme tolerance to saccharides and alditols. The elucidation of the genome sequence might provide a basis for both evolutionary analysis and improvement of the biotechnological usage of the bacterium.

Whole-genome sequencing of G. oxydans WSH-003 was performed using a combination of Illumina Hiseq2000 technology (8) (500-bp single-end shotgun sequencing, 3,728,170 sequencing reads, 85.6-fold coverage) and the Roche Genome Sequencer FLX system (paired ends with an insert size of 2 kb, 1,864,135 reads, 42.8-fold coverage). Assembly of the Illumina sequencing reads was performed with SOAPdenovo 1.05 (7). One hundred seventy-nine contigs were generated using Newbler Assembler (454 Life Sciences, Branford, CT) and assembled into 50 scaffolds using paired-end reads. Physical gaps, repeats, and assembly ambiguities were corrected by multiplex PCR and Sanger sequencing. Protein-coding genes were predicted by using Glimmer 3.02 (3) and Genemark 2.5 (1). Artemis was used for final verification of the annotation results (10). rRNAs and tRNAs were predicted using rRNAmmer (6) and tRNAscan-SE (11), respectively. Each gene was annotated through BLASTP searches against the databases NR, Swiss-Prot, TrEMBL, COG, and KEGG (2, 5, 12).

The complete genome of G. oxydans WSH-003 contains a single circular chromosome of 3,364,884 bp. The overall GC content of the chromosome is 56.77%. The draft genome harbors 3,705 predicted protein-coding sequences (CDSs); a total of 48 tRNA genes and one 16S-23S-5S rRNA were identified. The genome sequences of G. oxydans 621H (2.7Mbp) (GenBank accession no. CP000009) (9) were used as the reference, and the number of reads mapped to the reference gene was 95. The most significant feature of G. oxydans WSH-003 is the ability to produce high-yield l-sorbose. The gene clusters encoding d-sorbitol dehydrogenase (sldhAB, 2,670 bp) and responsible for synthesis of the cofactor pyrroloquinoline quinone (pqqABCDE, 2,979 bp) were identified from the draft genome sequence. The comparison of these two sequences with those of G. oxydans 621H indicated that the homology was 74.8% and 45.8%, respectively. In addition, several genes encoding aldehyde dehydrogenase, alcohol dehydrogenase, glucose dehydrogenase, formaldehyde dehydrogenase, etc., were annotated.

In summary, the genome sequence will facilitate additional bioinformatics and experimental investigations to further improve the vitamin C production. Furthermore, comparative genomics analysis and functional genomics analysis could also be performed to trace the origin and evolution of this organism.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AHKI00000000. The version described in this paper is the first version, AHKI01000000.