Ribosome stalling, spacing and A-site occupancy impact translation and co-translational mRNA decay in plants

Di-Proline codons that require structural rearrangements for polypeptide bond formation cause stalling without triggering mRNA decay. Hypoxia was used to evaluate relationships between ribosome conformation, disome spacing, and translational efficiency and co-translational decay under contrasting environmental conditions. Newly synthesized hypoxia-response mRNAs display high translational efficiency, codon-separated disomes, and active co-translational turnover.

Co-translational decay under hypoxia is associated with pausing at A-site vacant ribosomes awaiting an Aspartate aa-tRNA. Collision of ribosomes is pronounced for mRNAs encoding cell wall proteins and coupled with co-translational decay. On conserved peptide (CP)uORFs, A-site vacant ribosomes can conditionally pause at the stop codon that coincides with elevated decay.

Examination of maize confirms deep conservation of di-Proline and uORF stall sites, but also highlights differences. In conclusion, ribosome A-site occupancy and disome spacing contribute to mRNA translation and co-translational decay in plants.