Extended Data Fig. 5: Working model of Vms1 function at stalled ribosomes. | Nature

Extended Data Fig. 5: Working model of Vms1 function at stalled ribosomes.

From: Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes

Extended Data Fig. 5

In non-stop decay of mRNAs lacking a stop codon, ribosomes translate the poly(A) tail and stall after translating several lysines4, 19. The A site as a consequence is occupied by an AAA codon. Our data suggest that Vms1 can potentially hydrolyse peptidyl-tRNA chains on this leading stalled ribosome without prior splitting by Dom34–Hbs1–Rli1. One of the known responses to stalling is endonucleolytic cleavage of the mRNA by an as-yet unidentified endonuclease. The cleavage reaction generates a truncated transcript. Lagging ribosomes that translate up to the cleavage site stall with an empty A site. Such stalls are recognized by Dom34–Hbs1 that together with Rli1 dissociate the 80S ribosome into the 40S subunit and the 60S subunit, which contains the nascent peptidyl-tRNA1. Dissociation allows for stable association of the RQC complex members Rqc1–Rqc2 and the E3 ubiquitin ligase Ltn19. Rqc2 adds non-templated alanine and threonine residues to the C-terminal end of the nascent chain to extrude sequences in the exit tunnel past the active site of Ltn1, which ubiquitylates lysine residues in the emerging nascent chain10 and with the aid of Cdc48, optimizes the conformation of Vms1 at the PTC such that it can hydrolyse the tRNA. The ubiquitylated nascent chain is engaged by Ufd1–Npl4 bound to Cdc48 that together unfold and extract the nascent chain. Dissociation of Rqc2 allows Vms1 to access the 60S subunit29, resulting in hydrolysis of the peptidyl-tRNA. Recruitment of Cdc48–Ufd1–Npl4 to the ubiquitylated nascent chain7 ensures its efficient extraction from the 60S subunit. It is unclear whether the action of Vms1 on 80S ribosomes is coupled in some manner to ribosome splitting.