In eubacteria, ribosome stalling on broken messenger RNA transcripts can lead to cell death. The trans-translation quality control mechanism rescues many of these stalled ribosomes. In this process, tmRNA enters stalled ribosomes by mimicking a transfer RNA, accepting the stalled nascent peptide. The ribosome then releases the broken mRNA and resumes translation on a coding region within tmRNA itself. Translation of tmRNA marks the nascent peptide for destruction by the addition of a short proteolysis tag and the ribosome is released at a stop codon within the tmRNA open reading frame. An intriguing aspect of trans-translation is that the ribosome synthesizes one protein from two RNA templates. How is the proper site chosen on tmRNA to resume translation? Do the conserved pseudoknot structures help set the reading frame? Using a genetic selection to assay libraries of tmRNA mutants, we found that stable hairpin structures can functionally replace pseudoknot 1. We conclude that the role of pseudoknot 1 in tmRNA function is purely structural. Our results demonstrate that the inactivity of an RNA mutant designed to destroy a given structure should not be interpreted as proof that the structure is necessary for RNA function. Such mutations may only destabilize a global fold that could be formed equally well by an entirely different, stable structure. Broken mRNAs are not the only cause of ribosome stalling; stalling can also result from nascent peptide interactions with the ribosomal exit tunnel that inhibit peptidyl-transferase activity. SecM, TnaC, and ErmCL all stall ribosomes to regulate the expression of downstream genes. What other peptide sequences can cause ribosome stalling? We modified our tmRNA-based selection to screen libraries of random peptides and identified a number of novel stalling peptides, including the sequence FxxYxIWPP. This sequence interacts with the exit tunnel differently than SecM and TnaC as seen in studies using mutant ribosomes. Like SecM, stalling occurs on this sequence with the next aminoacyl tRNA trapped in the A site but unable to react with the nascent peptide. These results show that a variety of peptides can interact in the exit tunnel and peptidyl-transferase center to regulate ribosome activity.



College and Department

Physical and Mathematical Sciences; Chemistry and Biochemistry



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ribosome, stalling, tmRNA, trans-translation, exit tunnel, WPP, stalling peptides, pk1, pseudoknot 1, RNA folding, peptidyl-transferase, genetic selection, library selection, SecM, TnaC, ErmCL, FxxYxIWPP