A tandem active site model for the ribosomal helicase

Abstract

During protein synthesis, the messenger RNA (mRNA) helicase activity of the ribosome ensures that codons are made single stranded before decoding. Here, based on recent structural and functional findings, a quantitative model is presented for a tandem arrangement of two helicase active sites on the ribosome. A distal site encounters mRNA structures first, one elongation cycle earlier than a proximal site. Although unwinding of encountered mRNA structures past the proximal site is required for translocation, two routes exist for translocation past the distal site: sliding, which requires unwinding, and stick‐slip, which does not. The model accounts in detail for a number of findings related to the ribosomal helicase and provides a testable framework to further study mRNA unwinding.

The energy landscape of −1 ribosomal frameshifting

“…2, C and D). The rotated-state lifetimes for the subsequent 9th and 10th codons were not substantially longer, suggesting either (i) the whole 19 base pairs in the mRNA structure have melted during translocation from the eighth codon or (ii) only the initial encounter of the mRNA structure induces translocation pause on the ribosome, and unfolding of the rest of RNA structure involves a different mechanism ( 24 ).…”

Modulation of Viral Programmed Ribosomal Frameshifting and Stop Codon Readthrough by the Host Restriction Factor Shiftless

“…Central to –1 PRF is the interaction of the ribosome with a stimulatory mRNA structure (a stem-loop or pseudoknot) that promotes frameshifting at the slippery sequence ( Figure 1 ). How these RNA structures act is incompletely understood, but by presenting an unusual topology [ 3 , 4 , 23 , 24 , 25 ], they likely confound an intrinsic unwinding activity of the ribosome with consequent effects on the elongation cycle and frame maintenance [ 26 , 27 , 28 ]. Indeed, kinetic analyses in bacterial systems indicate that stimulatory RNAs can impair movements of the ribosomal small subunit (30S) head, delaying the dissociation of EF-G, and the release of tRNA from the ribosome [ 29 , 30 , 31 ].…”

Programmed −1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes

“…While uS3 and mRNA move together and their interaction is relatively unchanged, uS4 slides in the opposite direction from +12 to +15 (from the red to the yellow regions in Fig. 2 E) [67] , [75] . This countermovement between the head and body of the 30S subunit effectively stretches the mRNA tunnel by one codon.…”

“…Structural, biochemical, and computational studies have located potential ribosomal helicase in the positively charged residues that line up the mRNA entrance site at positions between +11 and +14 (the first nucleotide of mRNA at the P site is denoted by +1), including R131, R132, and K135 in ribosomal protein uS3, and K44 and R46 in uS4 [38] , [67] , [73] , [75] , [76] ( Fig. 2 E).…”

“…2 E). A high-resolution X-ray structure [67] revealed that the residues in uS3 interact with and stabilize the single-stranded form of mRNA at +12 to +14 with a binding energy of approximately 9 kcal·mol −1 per codon [75] . Because uS3 is at the head and uS4 is at the body of the 30S subunit, uS3 and uS4 are pulled away from each other when the head rotates during translocation ( Fig.…”