Individual segments of the polycistronic puf mRNA of Rhodobacter capsulatus exhibit extremely different half-lives contributing to the stoichiometry of light-harvesting and reaction centre complexes of this facultative phototrophic bacterium. While earlier investigations shed light on the processes leading to the degradation of the 2.7 kb pufBALMX mRNA and, consequently, to the formation of the highly stable 0.5 kb pufBA mRNA processing product, we have now investigated the initial events in the degradation of the highly unstable 3.2 kb pufQBALMX primary transcript. Sequence modifications of two putative RNase E recognition sites within the pufQ coding region provide strong evidence that RNase E-mediated cleavage of a sequence at the 3' end of pufQ is involved in rate-limiting cleavage of the primary pufQBALMX transcript in vivo. The putative RNase E recognition sequence at the 5' end of pufQ is cleaved in vitro but does not contribute to rate-limiting cleavage in vivo. Analysis of the decay of puf mRNA segments transcribed from wild-type and mutated puf DNA sequences in R. capsulatus and Escherichia coli reveal that RNase E-mediated cleavage within the pufQ mRNA sequence also affects the stability of the 0.5 kb pufBA processing product. These findings demonstrate that the stability of a certain mRNA segment depends on the pathway of processing of its precursor molecule.