Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria

• Published in: eLife Vol. 6
• Main Authors: Ferrin, Michael A, Subramaniam, Arvind R
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 12-05-2017; eLife Sciences Publications, Ltd
• Subjects: amino acid starvation; Amino acids; Codons; Computational and Systems Biology; Computer applications; Computer Simulation; E coli; Escherichia coli - metabolism; kinetic modeling; Kinetics; premature termination; Protein Biosynthesis; Protein expression; Protein synthesis; Proteins; Quality control; ribosome collisions; ribosome stalling; Ribosomes; Ribosomes - metabolism; Simulation; Traffic congestion; Translation initiation; computational biology; systems biology; amino acid starvation; premature termination; quality control; ribosome stalling; ribosome collisions; E. coli; kinetic modeling
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.23629

Ribosome stalling on mRNAs can decrease protein expression. To decipher ribosome kinetics at stall sites, we induced ribosome stalling at specific codons by starving the bacterium
for the cognate amino acid. We measured protein synthesis rates from a reporter library of over 100 variants that encoded systematic perturbations of translation initiation rate, the number of stall sites, and the distance between stall sites. Our measurements are quantitatively inconsistent with two widely-used kinetic models for stalled ribosomes: ribosome traffic jams that block initiation, and abortive (premature) termination of stalled ribosomes. Rather, our measurements support a model in which collision with a trailing ribosome causes abortive termination of the stalled ribosome. In our computational analysis, ribosome collisions selectively stimulate abortive termination without fine-tuning of kinetic rate parameters at ribosome stall sites. We propose that ribosome collisions serve as a robust timer for translational quality control pathways to recognize stalled ribosomes.