Abstract
Ketogulonicigenium vulgare is characterized by the efficient production of 2KGA from l-sorbose. Ketogulonicigenium vulgare Y25 is known as a 2-keto-l-gulonic acid-producing strain in the vitamin C industry. Here we report the finished, annotated genome sequence of Ketogulonicigenium vulgare Y25.
Ketogulonicigenium vulgare Y25 is used in the production of vitamin C, which is responsible for the conversion reaction of l-sorbose to l-ketogulonic acid in mixed culture fermentation with Bacillus species 8. The entire genome of Ketogulonicigenium vulgare Y25 was sequenced to elucidate the metabolic pathway of sorbose and to obtained detailed insights into the growth potential of the organism.
The complete genome sequence of Ketogulonicigenium vulgare Y25 was determined by the Beijing Genome Institute (Shenjun, China) using Solexa technology. A total of 221 million high-quality base pairs, giving 67.2-fold coverage of the genome, were assembled into 36 contigs using by SOAP software (http://soap.genomics.org.cn) 7. Then, the contigs were joined into 14 scaffolds using paired-end information. Gaps between contigs were closed by custom primer walks or by PCR amplification followed by DNA sequencing.
The genome of Ketogulonicigenium vulgare Y25 consists of a circular chromosome and two plasmids. The chromosome is composed of 2,776,084 bp, with a G+C content of 61.72%. One plasmid contains 268,675 bp, with a G+C content of 61.35%, and the other contains 243,645 bp, with a G+C content of 62.63%. Hence, the total size of the genome is 3,288,404 bp and the average G+C content is 61.76%. There are a total of 3,290 putative open reading frames (2,807 [chromosome], 256 [pYP1], and 227 [pYP2]) using Glimmer, giving a coding intensity of 91.05%. A total of 59 tRNA genes for all 20 amino acids but tyrosine and five 16S-23S-5S rRNA operons were identified.
Four genes encoding sorbose dehydrogenase were found in the chromosome. All of them were cloned and characterized. The result indicated that every one could transform l-sorbose into 2-keto-gulonic acid and required pyrroloquinoline quinine for the prosthetic groups in vitro (unpublished data). Sequence alignment analysis showed that they hadhigh homology in nucleic acid and amino acid sequences 1, 4, 9, and 10. It is estimated that multiple copies of the sorbose dehydrogenase gene can be attributed to highly efficient conversion of sorbose to 2-keto-gulonic acid. A pqqABCDE cluster of coenzyme PQQ biosynthesis has also been isolated. It shows the same arrangement of pqq genes as that in other species: a small pqqA gene with its own promoter followed by an operon with the other four genes2, 3, 5, 6. In addition, several genes encoding sorbitol dehydrogenase, sorbose reductase, sorbsone dehydrogenase, etc., were annotated in the genome.
The Y25 genome sequence and its curated annotation are important assets to better understand the physiology and metabolic potential of Ketogulonicigenium vulgare and will open up new opportunities in the functional genomics of this species.
Nucleotide sequence accession numbers.
The nucleotide sequence comprising the Ketogulonicigenium vulgare Y25 genome was deposited in the GenBank database with the accession numbers CP002224, CP002225, and CP002226.
Acknowledgments
This work was funded by the National Programs for High Technology Research and Development of China (2006AA020303) and the National Key Technology R&D Program(2007BAI46B01).
We acknowledge the Beijing Genome Institute for Solexa shotgun sequencing and the analysis and annotation of the genome.
Footnotes
Published ahead of print on 29 October 2010.
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