One Run - Done: 454 Sequencing Quickly Reveals Detailed Insights Into the Physiology of <i>Corynebacterium kroppenstedtii</i>
12 Jun 2008454 Life Sciences, a company of Roche, announces that researchers from Bielefeld University in Germany have used a single sequencing run, generated during the installation of their new Genome Sequencer FLX System, to completely assemble and characterize the genome of Corynebacterium kroppenstedtii. The whole genome analysis, led by Andreas Tauch, revealed that lipophilism is the dominant feature involved in pathogenicity of the corynebacterium. The study1, entitled “Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids” appears in the Journal of Biotechnology.
The single run with the Genome Sequencer FLX System yielded 560,248 shotgun reads with 110,018,974 detected bases that were assembled into a contiguous genomic sequence with a total size of 2,446,804bp. Automatic annotation of the complete genome sequence and the comparative content analysis of the data revealed a large repertoire of genes involved in sugar uptake and central carbohydrate metabolism.
The study was based on a single run from the Genome Sequencer FLX System. The platform generates 100 million bases, from 400,000 individual sequence reads of 250 bases in length, per 7.5 hour run. These characteristics, along with high single read accuracy and paired-end reads, make the technology of 454 Sequencing the clear choice for many applications such as whole genome sequencing, as seen in this study.
The analysis corroborates the lack of corynomycolic acids as well as the lipid-requiring phenotype as the key features of C. kroppenstedtii from the taxonomical viewpoint. The lack of mycolic acids is apparently caused by the loss of a condensase gene cluster and a mycolate reductase gene, whereas the lipophilic phenotype is due the absence of a microbial type I fatty acid synthase gene.
Corynebacterium kroppenstedtii is a lipophilic corynebacterial species that lacks in the cell envelope the characteristic alpha-alkyl-beta-hydroxy long-chain fatty acids, designated mycolic acids. C. kroppenstedtii is rarely recognized in human clinical samples, but it was recovered in research samples from respiratory specimens as well as from breast tissue, pus or deep wound swaps of patients with mastitis.2
1 Tauch A et al.: Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. J Biotechnol 2008 Mar 20 [Epub ahead of print]
2 Paviour S et al: Corynebacterium species isolated from patients with mastitis. Clin Infect Dis 2002; 35: 1434-1440