Cotranslational Folding Stimulates Programmed Ribosomal Frameshifting in the Alphavirus Structural Polyprotein

Haley R. Harrington; Matthew H. Zimmer; Laura M. Chamness; Veronica Nash; Wesley D. Penn; Thomas F. Miller; Suchetana Mukhopadhyay; Jonathan P. Schlebach

Our model suggests that the hydrophobicity of TM2 and its distance from the slip site are the key determinants of the -1PRF efficiency within the SINV structural polyprotein. To assess whether this mechanism is likely to be operative within other alphaviruses, we surveyed six related structural polyproteins for similar sequence elements. Sequence scans carried out with the ΔG predictor reveal that each form of the alphavirus structural polyprotein contains a marginally hydrophobic TM domain upstream from the ribosomal slip site. Predicted transfer free energies associated with the translocon-mediated membrane integration of these putative TM domains range from +1.4 to +2.7 kcal/ mol (Table 1) , which suggests the translocon-mediated membrane integration of these segments is likely to be inefficient. Consistent with this notion, CGMD simulations of the translation of these polyproteins indicate that the membrane integration efficiency of these segments ranges from 33-64% (Table 1) . Furthermore, these marginally hydrophobic TM domains reside 44-52 residues upstream of their corresponding -1PRF sites . CC-BY 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/790444 doi: bioRxiv preprint (Table 1) , which suggests that the tension generated by their translocon-mediated membrane integration is likely to be propagated back to the slip site. 40, 41 Force measurements derived from CGMD simulations of polyprotein synthesis suggest that the tension in the nascent chain when the slip-site occupies the ribosome is comparable to or greater than the tension generated during translation of the SINV variants characterized herein (Table 1) . Taken together, these findings suggest that this -1PRF mechanism is likely to be conserved across the alphavirus genus.