Escherichia coli K-12: a cooperatively developed annotation snapshot--2005

Abstract

The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.

Figure 1

Gene fissions, fusions and an inversion resulting from 1 nt indel corrections. Of 78 frameshift corrections, two 1 nt indels led to fissions (splitting) of genes (A and B), 23 resulted in gene fusions, similar to the example in (C), and 1 led to an inversion (D) (4). (D) The original annotation of the rpiB region showed a gene called phnQ, whose sequence is not conserved. A 1 nt insertion created a CDS for a conserved protein (yjdP) in the opposite orientation. While phnQ was originally thought to be a downstream gene in the large phosphonate (phn) operon (39), mutational studies later revealed no role for it in phosphonate metabolism (40).

Figure 2

Status of annotation of E.coli gene products. The total number of gene products present in both MG1655 and W3110, 4452 excluding oriC, are categorized according to their function assignment. Evidence code and gene type assignments available in the Supplementary Table 1 were used to group the gene products. The annotation groups include gene products whose function is experimentally determined (2403, 54.1%), predicted by computational analysis (1425, 32%), or unknown (616, 13.9%). The gene products of unknown function are further separated into those containing a conserved domain (145, 3.3%), those with (233, 5.3%) or without (238, 5.3%) a detectable homolog in the sequence databases.