Earlier studies have shown that the insertion of sequences able to form mRNA secondary structures into a gene may cause the RNA polymerase to stall or invoke a target for endonucleolytic attacks (19) . Therefore, in our analysis of mRNA pseudoknot-stalled ribosomes, it was important to verify that there was no significant population of mRNAs that ended within the pseudoknot structure. If such truncated transcripts were abundant, it would be difficult to distinguish between protein products from ribosomes stalled within the pseudoknot and protein products originating from ribosomes ending translation at 'non-stop' mRNAs having their 3 0 -ends within the pseudoknot sequence. In the latter case translation would be terminated by tmRNA trans-translation thus rendering the protein products unstable due to the tmRNA-encoded tag (36) . In the following subsections 'Identification of transcripts from the T7gene10-PK-lacZ gene fusions', 'Messenger RNA stability' and 'Coupling between translation and transcription is required for full-length transcripts', we will show that the observed proteins did indeed originate from stalled ribosomes and that they were not caused by other effects.