Origin of the mRNA stoichiometry of the puf operon in Rhodobacter sphaeroides.

The LH-I structural genes are located 5' of the RC-L and -M structural genes on what has been designated as the puf operon of Rhodobacter sphaeroides. Analysis of puf operon expression in R. sphaeroides by Northern hybridization with probes specific for individual structural gene has identified two transcripts encoded by this operon. The large (2.6 kilobase pairs (kb] transcript contains sequences for all four polypeptides of the puf operon, whereas the small (0.5 kb) transcript, which is more abundant (10-15-fold) than the large transcript under photosynthetic growth, is homologous only to the two LH-I structural genes. Transcription of the puf operon during photosynthetic growth under saturating light conditions is increased approximately 3-fold relative to growth in the presence of oxygen while the relative ratio of these two transcripts is independent of the incident light intensity. Analysis of the turnover of the two transcripts (t1/2 of 9 and 20 min for the large and small transcripts, respectively) indicates that 5' processing is the initial step in the degradation of the large transcript and that the molar excess of the small transcript cannot be accounted for by differences in the rates of turnover of these two mRNA species. Analysis of the 5' ends of the 2.6- and 0.5-kb transcripts, their relative abundance, and stabilities indicates that these two transcripts have different 5'-ends corresponding to 75 and 104 base pairs upstream from the start of the LH-I beta structural gene, respectively. Northern hybridization analysis with specific synthetic deoxyoligonucleotide probes confirmed that the two transcripts differ by 29 bases at their 5'-ends, suggesting that differential transcript initiation may be involved in regulating the relative levels of these two mRNA species in vivo, although we cannot rule out complex mechanisms of post-transcriptional processing.