Functional analysis of gapped microbial genomes: Amino acid metabolism of Thiobacillus ferrooxidans

Evgeni Selkov, Ross Overbeek, Yakov Kogan, Lien Chu, Veronika Vonstein, David Holmes, Simon Silver, Robert Haselkorn, Michael Fonstein

Resultado de la investigación: Contribución a una revistaArtículorevisión exhaustiva

51 Citas (Scopus)

Resumen

A gapped genome sequence of the biomining bacterium Thiobacillus ferrooxidans strain ATCC23270 was assembled from sheared DNA fragments (3.2- times coverage) into 1,912 contigs. A total of 2,712 potential genes (ORFs) were identified in 2.6 Mbp (megabase pairs) of Thiobacillus genomic sequence. Of these genes, 2,159 could be assigned functions by using the WIT-Pro/EMP genome analysis system, most with a high degree of certainty. Nine hundred of the genes have been assigned roles in metabolic pathways, producing an overview of cellular biosynthesis, bioenergetics, and catabolism. Sequence similarities, relative gene positions on the chromosome, and metabolic reconstruction (placement of gene products in metabolic pathways) were all used to aid gene assignments and for development of a functional overview. Amino acid biosynthesis was chosen to demonstrate the analytical capabilities of this approach. Only 10 expected enzymatic activities, of the nearly 150 involved in the biosynthesis of all 20 amino acids, are currently unassigned in the Thiobacillus genome. This result compares favorably with 10 missing genes for amino acid biosynthesis in the complete Escherichia coil genome. Gapped genome analysis can therefore give a decent picture of the central metabolism of a microorganism, equivalent to that of a complete sequence, at significantly lower cost.

Idioma originalInglés
Páginas (desde-hasta)3509-3514
Número de páginas6
PublicaciónProceedings of the National Academy of Sciences of the United States of America
Volumen97
N.º7
DOI
EstadoPublicada - 28 mar 2000

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