Figure 1. Diagrammatic representation of a polycistronic mRNA. This polycistronic mRNA contains the coding sequences for three different genes that have originated from a single transcription start site upstream of gene 1. Each gene has its own ribosome-binding site (RBS) as well as a translation start and translation stop. The intercistronic spacer region (dotted line) can vary in length from –1 nucleotide to approximately 40 nucleotides in length.

Figure 2. Structural features of an mRNA molecule that can affect its stability. (a) The formation of a stem–loop structure in an mRNA molecule by the pairing of complementary nucleotides. Since the formation of the double-stranded region generates a structure that is energetically more stable than the single-stranded molecule, the stem–loop will rapidly form in vivo. (b) Diagrammatic representation of an mRNA molecule showing possible stability elements at both the 5¢ and 3¢ ends. In addition, upward arrows indicate the presence of endonucleolytic cleavage sites that would lead to the functional inactivation of the mRNA. The relative positions of the ribosome-binding site (RBS), the translation start and the translation stop are also indicated. Since transcription and translation are coupled, the preserved ribosomes (not shown here) will reduce the occurrence of secondary structures between the translation start and stop codons.

Figure 3. Model for mRNA decay in E. coli. For most mRNAs, RNase E will initiate decay by first binding to the 5¢ end of the transcript, probably as part of the multiprotein complex called the degradosome (not shown here for the sake of simplicity). In some cases, it will attack an mRNA at an internal location in the absence of binding to the 5¢ terminus. Once the initial cleavage takes place, RNase E and/or RNase G can continue degrading the mRNA, moving in a 5¢ 3¢ direction. The endonucleolytic cleavage products are subsequently degraded in the 3¢ 5¢ direction by either polynucleotide phosphorylase, RNase II or RNase R. For those species that have secondary structures at their 3¢ termini, poly(A) polymerase adds A residues to enhance the binding of the 3¢ 5¢ exonucleases.