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

A gapped genome sequence of the biomining bacterium Thiobacillus ferrooxida ns strain ATCC23270 was assembled from sheared DNA fragments (3.2-times cov erage) into 1,912 contigs. A total of 2,712 potential genes (ORFs) were ide ntified in 2.6 Mbp (megabase pairs) of Thiobacillus genomic sequence. Of th ese genes, 2,159 could be assigned functions by using the WIT-Pro/EMP genom e analysis system, most with a high degree of certainty. Nine hundred of th e genes have been assigned roles in metabolic pathways, producing an overvi ew of cellular biosynthesis, bioenergetics, and catabolism. sequence simila rities, relative gene positions on the chromosome, and metabolic reconstruc tion (placement of gene products in metabolic pathways) were all used to ai d 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 involve d in the biosynthesis of all 20 amino acids, are currently unassigned in th e Thiobacillus genome. This result compares favorably with 10 missing genes for amino acid biosynthesis in the complete Escherichia coli genome. Gappe d genome analysis can therefore give a decent picture of the central metabo lism of a microorganism, equivalent to that of a complete sequence, at sign ificantly lower cost.