Peptidase D gene (pepD) of Escherichia coli K-12: nucleotide sequence, transcript mapping, and comparison with other peptidase genes

Abstract

The nucleotide sequence of a 2.3-kilobase-pair DNA fragment of Escherichia coli that contains the transcription signals and the coding region of the pepD gene specifying aminopeptidase D was determined. The location and extent of the open reading frame were verified by partial amino acid sequencing of the purified pepD product. By use of a promoter-screening vector, initiation signals for pepD transcription were located in the 5'-flanking region of the open reading frame. Analysis of pepD transcripts by S1 mapping, primer extension, and Northern (RNA) hybridization revealed two species of monocistronic mRNA with different 5' ends and a common 3' end. Calculation of the degree of codon usage bias in the coding region suggested that the efficiency of pepD translation is relatively low. As deduced from the predicted amino acid sequence, peptidase D is a slightly hydrophilic protein of 485 amino acid residues that contains no extended domains of marked hydrophobicity. Structural and functional features of the pepD gene are discussed and compared with other already sequenced peptidase genes of E. coli.