Determining the Structural Basis of -1 PRF in the HTLV-1 Retrovirus:
Overview. Human T-cell leukemia virus type 1 (HTLV-1) is a human carcinogenic retrovirus that infects an estimated five to ten million people worldwide. Viral integration into host T lymphocytes, typically mature CD4+ T-cells, results in adult T-cell leukemia/lymphoma and HTLV-1-associated myelopathy/tropical spastic paraparesis in ~5% and ~1% of individuals, respectively. New HTLV-1 infections are established when the viral positive-sense, single-stranded RNA genome is reverse transcribed and the resulting double-stranded DNA is integrated into the host genome. Both processes require viral enzymes that are expressed by way of two independent -1 PRFs (Figure 3A). Therefore, -1 PRFs are essential to HTLV-1 infection. Although the mechanisms of -1 PRF has been extensively studied in a number of other viruses, the equivalent mechanisms in HTLV-1 are less well studied. At the time we started our research, what was clear was that HTLV-1’s two frameshift sites were located at the gag-pro and pro-pol open reading frame junctions (Figure 3A), their slippery sequences were identified, and the frameshift site secondary structures were predicted (Figure 3B and 3C). No direct data validating these structures was published, nor had the frameshift efficiencies been quantitatively measured in vivo. Additionally, how either of HTLV-1’s frameshift site structures stimulated -1 PRF was unclear
Relevant Publication:
Thulson, E.; Hartwick, E.W.; Cooper-Sansone, A.; Williams, M.A.C.; Soliman, M.E., Robinson, L.K.; Kieft, J.S.; Mouzakis,K.D. An RNA Pseudoknot Stimulates HTLV-1 pro-pol Programmed -1 Ribosomal Frameshifting. RNA 2020, 26(4), 512-528.
Article Highlights: We conclusively defined the HTLV-1 pro-pol frameshift site RNA structure and its 3’ boundary. Our results indicated that the HTLV-1 pro-pol frameshift site structure is that of a classic H-type pseudoknot. This pseudoknot acts in cis with the slippery sequence to stimulate -1 PRF to 19.4(±0.3)%. This was the first quantitative measurement of the HTLV-1 pro-pol -1 frameshift efficiency for a frameshift site that includes the pseudoknot structure. These results were significant because, for the first time, they demonstrated that a pseudoknot is important to HTLV-1 pro-pol -1 PRF and defined the frameshift site’s 3’ boundary.
Impact: This published work fills a significant gap in the knowledge base of HTLV-1 -1 PRF by conclusively defining the RNA structure within and the 3′ boundary of the HTLV-1 pro-pol frameshift site.
Learn more about our work on the HTLV-1 pro-pol frameshift site by watching Dr. Mouzakis’ recent presentation at the 2020 CSHL Retroviruses meeting:
“An RNA Pseudoknot Stimulates HTLV-1 pro-pol Programmed -1 Ribosomal Frameshifting.” Presented at the “Cold Spring Harbor Laboratory Virtual Conference: Retroviruses”, Los Angeles, CA, USA, May 20, 2020.
Ongoing projects:
- Investigating the relationship between HTLV-1 gag-pro stem-loop thermodynamic stability and -1 PRF efficiency.
- Determining the impact of the HTLV-1 gag-pro frameshift site stem-loop length on -1 PRF efficiency.
- Exploring structural tools to identify potential base-triples forming in the HTLV-1 pro-pol frameshift site pseudoknot.
