Structure and expression of the puf operon messenger RNA in rhodospirillum rubrum

Abstract

In Rhodospirillum rubrum, the genes coding for the alpha and beta polypeptides of the B880 antenna (pufA,B) and the L and M polypeptides of the photoreaction center (pufL,M) are clustered on operon puf. In oxygen-limited cells, the puf mRNA is present as species of 2561, 640, and 617 nucleotides. Aerated cells contain only traces of these mRNAs. The large mRNA encodes the alpha,beta, L, and M polypeptides, whereas the small mRNAs encode only alpha and beta. S1 nuclease protection mapping showed these transcripts to have a common 5' end, immediately downstream of a region of dyad symmetry and at 166 nucleotides upstream of the initiation codon of pufB. The 3' termini of the small transcripts are located in the intercistronic region between pufA and pufL, downstream of another region of dyad symmetry. This region is highly conserved in Rhodospirillum rubrum, Rhodobacter capsulatus, and Rhodobacter sphaeroides and shares 61% sequence similarity with the repetitive extragenic palindromic sequences of Escherichia coli. The slightly heterogeneous 3' termini of the large transcript are downstream of a region of dyad symmetry characteristic of rho-independent transcription termination. Following a shift from oxygen-limited to aerated conditions, the pufL,M and the pufA,B mRNAs decayed with respective half-lives of 9 and 20 min. These high relative stabilities, attributed to secondary structure, are in accord with the mole ratio (2:1) of the pufA,B/pufL,M messages. While the differential expression of alpha,beta/L,M congruent to 15 is thought to be due, in part, to this relative stability, the main factor may be a more efficient translation initiation for pufA,B than for pufL,M.