Ribosomes can slide over and beyond "hungry" codons, resuming protein chain elongation many nucleotides downstream

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• Cells require a constant supply of aminoacyl-tRNAs for efficient protein synthesis.
• Ribosomes can stall at "hungry" codons when specific aminoacyl-tRNAs are limited.
• Stalled ribosomes may exhibit alternative translocation or release mechanisms.

Purpose of the Study:

• To investigate the behavior of the peptidyl-tRNA-ribosome complex stalled at "hungry" codons.
• To determine if ribosomes can resume translation at downstream sites after bypassing a stalled codon.
• To characterize the factors influencing this downstream translation resumption.

Main Methods:

• Analysis of amino acid sequences of synthesized proteins to identify bypassed regions.
• Experimental manipulation of aminoacyl-tRNA levels to induce "hungry" codon stalling.
• Introduction of "trap" sites to assess the translocation process.

Main Results:

• The peptidyl-tRNA-ribosome complex can slide beyond a stalled "hungry" codon and resume translation downstream.
• Protein sequence analysis confirmed the absence of sequences encoded between the stalled codon and downstream landing sites.
• The efficiency of this sliding ranges from 10-20% and decreases with slide length.
• "Trap" sites reduced the frequency of successful slides, supporting ribosome translocation through the bypassed region.
• This phenomenon is general, occurring with different hungry codons, tRNAs, peptide sequences, and resume sites.

Conclusions:

• Ribosome-mediated mRNA sliding is a mechanism cells employ to overcome aminoacyl-tRNA limitation.
• This process allows for the synthesis of truncated proteins by bypassing specific codons.
• The generality of this mechanism suggests its significance in cellular translational regulation.