| Ribosomal fidelity during translation is crucial for cell viability. However, translational rules are sometimes subverted. Ribosomal frameshifting has been known for two decades to be utilized for expression by a minority of genes. Studying these exceptions to the rules can help our understanding of what defines translational rules in the first place and expand our knowledge of translational mechanisms. Recent advances in genomics and proteomics are producing a vast amount of data, analysis of which by different methods can be helpful in discovering new cases of ribosomal frameshifting.; It is generally believed that frameshift-prone sequences are under-represented in genes unless there is a functional role for them. Analysis of occurrences of four frameshift-prone sequences, CCC_UGA, A_AAA_AAG, AGG_AGG and AGA_AGA, revealed that these sequences are not avoided in Escherichia coli coding sequences. The great majority of those tested in their genomic context cause 1--15% efficient ribosomal frameshifting. Comparative sequence analysis was employed to assess a potential biological role for frameshifting in these genes. Two new candidates for utilized frameshifting, in pheL and ydaY. have been identified in addition to those previously known in dnaX and nine insertion sequence elements. For the majority of the shift-prone sequences no functional role can be attributed to them and frameshifting is likely erroneous. However, none of these frameshift sequences is in the 306 most highly expressed genes. It may well be that there is no strong selection against shift-prone sequences in general in ORFs that are not highly expressed.; Frameshifting at AGA_AGA and AGG_AGG is mRNA concentration dependent and thus it is conceivable that in the very low copy mRNAs, the frameshifting level is lower than detectable by available methods.; Frameshifting at CCC_UGA of pheL, which occurs with about 20% efficiency, was further investigated. The pheL gene encodes a leader peptide of the phenylalanine operon and its translation is crucial for transcription attenuation control of the downstream pheA gene. Analysis of frameshift stimulators revealed that the identity of a few amino acids in the nascent PheL peptide is crucial for efficient frameshifting. A potential role for frameshifting at the end of pheL in transcription attenuation control is investigated. Finally, a refined model of transcription attenuation which explains the role of frameshifting and tmRNA tagging, another nonstandard translational event, is proposed. |
