Computer aided identification of a potential 5'-3' exonuclease gene encoded by Escherichia coli

The predicted amino acid sequence of a previously overlooked open reading frame (ORF) from E. coli has been subjected to sequence analysis. The ORF, sequenced independently by two research groups, appears to encode a protein of 251 amino acids residues (25 kDa). The protein sequence shares a high degree of similarity with the amino acid termini of E. coli DNA polymerase I and other bacterial DNA polymerases (and phage-encoded enzymes) known to possess 5'-3' exonuclease activity. The newly identified E. coli gene, designated exo, is positioned downstream of signals characteristic of an efficient translation initiation sequence. Codon bias analysis indicates that the ORF has good protein coding potential. These observations indicate that the gene is likely to be expressed. The gene is 60% identical with the 5'-region of the E. coli DNA PolI gene (polA) over a 260 base-pair region. These two genes may have arisen by duplication of an ancestral gene or polA may have arisen by a recombination event involving exo. A comparison of the predicted secondary structures of 5'-3' exonucleases revealed the presence of several conserved regions of secondary structure, including a potential helix-turn-helix motif.