ThepheA/tyrA/aroF region fromErwinia herbicola: An emerging comparative basis for analysis of gene organization and regulation in enteric bacteria

Summary

Extensive knowledge exists inEscherichia coli about the contiguouspheA andaroF-tyrA operons which have opposite transcription orientations and are separated by a bidirectional transcription terminator. The corresponding structural genes and individual components of the terminator and attenuator fromErwinia herbicola have been analyzed from an evolutionary vantage point. A 7.5-kb DNA fragment fromE. herbicola carrying the linkedpheA, tyrA, andaroF genes was cloned by functional complementation ofE. coli auxotrophic requirements. A 3,433-bp segment of DNA consisting of more than half ofaroF, all oftyrA, and the entire phenylalanine operon (promoter, leader region encoding the leader peptide and containing thephe attenuator, andpheA) was sequenced. A bidirectional transcription terminator was positioned between the divergently transcribedpheA andtyrA. The adjacentaroF andtyrA genes share a common transcription orientation, consistent with their probable coexistence within an operon. However,tyrA can be expressed efficiently from an internal promoter which appears to lie within the 3′ portion ofaroF. The gene order ispheA tyrA aroF inE. herbicola, with the same tail-to-tail arrangement of transcription known to exist inE. coli. ThepheL coding region of the phe operon was dominated by phenylalanine codons, seven of the 15 amino acid residues of the leader peptide beingl-phenylalanine. TheE. herbicola pheA andtyrA genes were 1,161 by and 1,119 by in length, respectively, and corresponded to deduced gene products having subunit molecular weights of 43,182 and 41,847. The deduced amino acid sequences ofPheA andTyrA were homologous at their N-termini, consistent with a common evolutionary origin of the chorismate mutase domains present at the amino terminus of bothPheA andTyrA. A detailed comparison of theE. coli andE. herbicola sequences was made. ThepheA, tyrA, andaroF genes ofE. herbicola exhibited high overall identity with the counterpartE. coli genes. Within the leader region of thephe operon, the leader peptide coding region was highly conserved. Although the 1:2 and 2′:3′ stems defining the pause structure and the antiterminator, respectively, were also highly conserved, RNA segment 4 of the attenuator terminator exhibited considerable divergence, as did the distal portion of the attenuator region. Within the span of attenuator region encoding the three stern-loop structures of mRNA secondary configuration, hot spots of base-residue divergence were localized to looped-out regions. No changes occurred which would simultaneously disrupt alternative pairing relationships of secondary configuration. The bidirectional terminator betweenpheA andtyrA has diverged very substantially. Much of the promoter region and the untranslated region between the promoter and thepheL coding region also differed considerably between the two organisms.