d by cloning the 59UTR of the laboratory adapted HIV-1 infectious recombinant proviral clone NL4.3 into the intercistronic region of a dual luciferase reporter construct. The dl reporter construct contained the Renilla luciferase gene upstream and the firefly luciferase gene downstream. To ensure that the two cistrons were independently translated, a defective encephalomyocarditis virus IRES, known to inhibit ribosome reinitiation and read-through, was inserted upstream of the HIV-1 59UTR. In this experimental setting the translational activity of the HIV-1 59UTR was monitored using FLuc activity as the readout, while the RLuc reporter gene served as an upstream translational control. This approach demonstrated that, when in the context of a bicistronic mRNA the HIV-1 59UTR of pNL4.3 was capable of driving efficient translation initiation. Most recently, the presence of a competent IRES was also reported within the 59UTR of the CXCR4 tropic primary isolate HIV-LAI. Since the discovery of the HIV-1 IRES element, a number of additional studies have focused on understanding the mechanisms underlying its function. However, to date all studies regarding the HIV1 IRES have been limited to the 59UTR of pNL4.3 or pLAI, raising the question as to the significance and validity of these findings in the context of naturally circulating viral variants. Here we provide evidence that HIV-1 59UTR sequences recovered from clinically sourced RNA isolates do indeed harbor an IRES, suggesting that the ability of HIV-1 mRNA to drive capindependent translation initiation is likely to be widespread if not ubiquitous and is not MedChemExpress Ki-8751 restricted to the laboratory adapted HIV-1 clone pNL4.3 or to the single primary HIV-1 isolate, pLAI. The full length mRNAs of the HIV-1 clone pNL4.3 and pLAI can initiate translation through a canonical cap-dependent mechanism, or by an alternative IRES-dependent mechanism. In this new study the translational activity of the 59UTR of viral RNA isolated from HIV-1 infected individuals was evaluated in the context of a bicistronic mRNA. Cap-independent translation initiation from the VAR 59UTRs was demonstrated in HeLa cells and in Xenopus laevis oocytes. The notion that expression of the second cistron in the 
bicistronic constructs may be PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/22187495 the result of alternative splicing or due to cryptic promoter activity was also ruled out. Together, data suggest that the 59UTR of the HIV-1 mRNAs isolated from clinical samples enables IRES-mediated translation initiation. Additionally, data presented in figures 1 and 2, confirm previous observations that active translation from the HIV-1 IRES in both HeLa cells and in Xenopus laevis oocytes does not rely on additional viral proteins. The 59UTR recovered from natural viral variants exhibited extensive sequence diversity when compared to the control sequence. Furthermore, translational activity from some of the HIV-1 VAR 59UTRs was enhanced substantially when compared to the control pNL4.3 59UTR and yet these presented a number of nucleotide variations within the PBSstem loop, a structural element known to be required for IRES-mediated translation initiation. These observations prompted us to evaluate possible structural differences between the pNL4.3 59UTR, and the VAR 59UTRs recovered from clinical samples. In summary, data showed that the only differences between the VAR 59UTRs and the pNL4.3 59UTR lied within single stranded RNA regions, being the only exception the U5 region lying in between the