Abstract
Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 Å cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two α-helices connected by an α-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50-55 Å of the exit tunnel. The structure reveals how α-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome.
Highlights
Many diverse nascent chain sequences have been identified that act as cis-regulatory polypeptides to promote ribosome stalling and thereby regulate gene expression
Our results suggest that residues beyond the previously characterized 19-aa stalling window of Vibrio export monitoring polypeptide (VemP) contribute to the efficiency of VemP-mediated translation arrest
VemP adopts an extremely compacted conformation within the ribosomal exit tunnel, comprising an upper and a lower a-helix connected by an aturn and a loop
Summary
Many diverse nascent chain sequences have been identified that act as cis-regulatory polypeptides to promote ribosome stalling and thereby regulate gene expression. One of the most recently discovered examples is the Vibrio export monitoring polypeptide (VemP) that allows Vibrio alginolyticus to adapt to changes in salinity by modulating expression of components of the protein targeting machinery (Ishii et al, 2015). In Na+-rich environments, VemP is targeted by its signal sequence (SS) to the SecDF1-SecYEG translocon (Ishii et al, 2015). The force applied to VemP during protein translocation prevents VemP-dependent ribosome stalling, thereby enabling the complete VemP to be translated and released from the ribosome. Under such conditions, SecDF2 expression is repressed due to sequestration of the ribosome-binding site (RBS) of secDF2
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