EFFECT OF THE PUFQ-PUFB INTERCISTRONIC REGION ON PUF MESSENGER-RNA STABILITY IN RHODOBACTER-CAPSULATUS

Differential expression of genes localized within the polycistronic pu f operon of Rhodobacter capsulatus is partly due to altered stabilitie s of individual mRNA segments. We show that the 5' untranslated region (UTR) of pufB contributes to the unusual longevity of the 0.5 kb ligh t-harvesting (LH) 1 specific pufBA mRNA and of the 2.7 kb pufBALMX mRN A. Three stem-loop structures have been identified within the pufQ-puf B intercistronic region by means of RNA secondary-structure analysis i n vitro and in vivo. Deletion analysis of the pufB 5' UTR indicates th at the complete set of secondary structures is required to maintain wi ldtype levels of pufBA mRNA stability. A phylogenetic comparison of pu fB 5' UTRs of other photosynthetic bacteria reveals an evolutionary co nservation of the base-pairing potential despite sequence divergence. Comparison of puf mRNA decay in Escherichia coli strains with or witho ut endoribonuclease E (RNase E) activity suggests that the pufB 5' sec ondary structures protect the downstream mRNA segment against degradat ion by RNase E. Removal of the 117-nucleotide pufQ-pufB intercistronic region results in loss of stability for the pufBA and pufBALMX mRNAs with concomitant stabilization of the full-length puf primary transcri pt (QBALMX). We therefore conclude that the deleted sequence functions both as a stabilizing element for pufBALMX and pufBA segments and as a target site for initial rate-limiting decay of the unstable pufQBALM X mRNA.