Translation, the process that peptides are synthesized by ribosomes using mRNA as the template, is a critical step in the central dogma of molecular biology. The elongation rate of ribosomes along the mRNA is fine-tuned and is known to regulate the subcellular localization of nascent peptides, mRNA stability, and protein homeostasis.
Ribo-seq, which sequences the mRNA fragments protected by single ribosomes, has emerged as a powerful approach to study the translational dynamics at the genomic scale. However, ribo-seq misses larger mRNA fragments protected by two stacked ribosomes (disomes). Disomes are generated from ribosome collisions between the 5′-elongating ribosome and the 3′-paused one, and are the crucial signals for translational pauses.
Researchers from QIAN Wenfeng Lab at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences, and GAO Ning Lab at Peking University collaborated to tackle this problem.
They performed disome-seq in the budding yeast to precisely captured mRNA fragments resulting from ribosome collisions. They detected widespread ribosome collisions and found such collisions were associated with slow ribosome release when stop codons are at the A-site. Slow peptide bond formation from proline, glycine, asparagine, and cysteine when they are at the P-site were also found, as well as slow leaving of polylysine from the exit tunnel of ribosomes.
The structure of disomes obtained by cryo-electron microscopy suggests a different conformation from the substrate of the ribosome-associated protein quality control pathway. Collided ribosomes occurred more frequently in the gap regions between α-helices and were associated with specific chaperones.
These results suggest that ribosome collisions can aid in the cotranslational folding of the nascent peptides. This study has completed a critical but previously neglected part of the translatome and spurs a more comprehensive understanding of the translational pauses.
The work was supported by the Ministry of Science and Technology, the National Natural Science Foundation of China, the Youth Innovation Promotion Association of the Chinese Academy of Sciences, and the State Key Laboratory of Plant Genomics.
Ribosomes on the same mRNA can collide with each other, which aids in cotranslational protein folding (Image by IGDB)