TY - JOUR
T1 - Determining How Stem-loop Structure Thermodynamic Stability Influences Frameshift Efficiency at the HTLV-1 gag-proFrameshift Site
AU - Soliman, Mary
AU - Robinson, Leila
AU - Maille, Madison
AU - Egekeze, Carolyn
AU - Salamon, Rebecca
AU - Mouzakis, Kathryn D.
PY - 2022/5
Y1 - 2022/5
N2 - The human T-lymphotropic virus type 1 (HTLV-1) RNA genome includes two programmed -1 ribosomal frameshift (-1 PRF) sites. These sites allow ribosomes access to alternate reading frames encoding critical viral enzymes. The gag-proframeshift site includes a slippery sequence, spacer, and stem-loop structure. How the stem-loop acts to promote frameshifting is unclear. Previous HTLV-2 research showed that changes to the gag-pro frameshift site stem-loop thermodynamic stability influenced its frameshift efficiency to a modest degree. There is substantial conservation between the HTLV-1 and HTLV-2 gag-pro frameshift site sequences (86%) and structures. We hypothesized that the HTLV-1 gag-pro frameshift efficiency would be similarly influenced by its stem-loop thermodynamic stability. To test this hypothesis, we designed 15 stem-loop mutants (SLMs) with varied base-pair composition. These mutations decoupled changes in overall thermodynamic stability from those localized to the stem-loop base. The SLM thermodynamic stabilities were calculated using nearest neighbor parameters and the in vitro frameshift efficiencies were measured with a dual-luciferase assay. Correlations between frameshift efficiency and thermodynamic stability were subsequently assessed. Preliminarily results reveal a moderate correlation between the SLM stem-loop overall thermodynamic stability and frameshifting efficiency. No correlation was observed between the thermodynamic stability of the stem-loop base and frameshifting efficiency. While the overall thermodynamic stability does impact the frameshift efficiency, it cannot be used exclusively to predict it. This reflects a complex interplay between the frameshift site elements. Overall, our preliminary results suggest a conserved function for the gag-pro frameshift site stem-loop between the HTLV-1 and HTLV-2 retroviruses.
AB - The human T-lymphotropic virus type 1 (HTLV-1) RNA genome includes two programmed -1 ribosomal frameshift (-1 PRF) sites. These sites allow ribosomes access to alternate reading frames encoding critical viral enzymes. The gag-proframeshift site includes a slippery sequence, spacer, and stem-loop structure. How the stem-loop acts to promote frameshifting is unclear. Previous HTLV-2 research showed that changes to the gag-pro frameshift site stem-loop thermodynamic stability influenced its frameshift efficiency to a modest degree. There is substantial conservation between the HTLV-1 and HTLV-2 gag-pro frameshift site sequences (86%) and structures. We hypothesized that the HTLV-1 gag-pro frameshift efficiency would be similarly influenced by its stem-loop thermodynamic stability. To test this hypothesis, we designed 15 stem-loop mutants (SLMs) with varied base-pair composition. These mutations decoupled changes in overall thermodynamic stability from those localized to the stem-loop base. The SLM thermodynamic stabilities were calculated using nearest neighbor parameters and the in vitro frameshift efficiencies were measured with a dual-luciferase assay. Correlations between frameshift efficiency and thermodynamic stability were subsequently assessed. Preliminarily results reveal a moderate correlation between the SLM stem-loop overall thermodynamic stability and frameshifting efficiency. No correlation was observed between the thermodynamic stability of the stem-loop base and frameshifting efficiency. While the overall thermodynamic stability does impact the frameshift efficiency, it cannot be used exclusively to predict it. This reflects a complex interplay between the frameshift site elements. Overall, our preliminary results suggest a conserved function for the gag-pro frameshift site stem-loop between the HTLV-1 and HTLV-2 retroviruses.
UR - https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=lmupure2024&SrcAuth=WosAPI&KeyUT=WOS:000878430600703&DestLinkType=FullRecord&DestApp=WOS_CPL
U2 - 10.1096/fasebj.2022.36.S1.L6403
DO - 10.1096/fasebj.2022.36.S1.L6403
M3 - Meeting abstract
C2 - 35555441
SN - 0892-6638
VL - 36
JO - Faseb Journal
JF - Faseb Journal
ER -