Impact of IRES sequence insertrion in the HIV-1 genome

The HIV-1 genome contains several RNA structures involved with viral genomic RNA packaging; which is directly related with viral maturation . Thus, mutations leading to structural alterations in the viral genomic RNA have the potential to impact these processes and consequently impair viral infectivity. The insertion of a highly structured RNA element at the 3’-end of the HIV-1 genome may cause deleterious alterations or hide signalling sequences important for viral replication. To characterise this further, we took advantage of an HIV-1 infectious clone harbouring a ECMV Internal Ribosome Entry Site (IRES) sequence followed by the gfp reporter gene introduced downstream of the nef gene (NL4-3-IRES). In cells, NL4-3-IRES was 2.5-fold less infectious than the wild type NL4-3 and had a 2-fold reduction in Gag processing. Mature particles showed less incorporation of p24-Capsid, Reverse Transcriptase, and Integrase proteins within NL4-3-IRES viral particles. In silico molecular modeling analysis revealed that the genomic RNA of NL4-3-IRES had several conformational changes compared with the wild type NL4-3 sequence, especially in regions related to viral maturation, demonstrating that the presence of an IRES element within the 3’ end of the HIV-1 genome has profound impacts on virus assembly and maturation and consequently reduced viral infectivity. This dataset consists in Western blot, RT-qPCR, ELISA and infectivity assay results. Also, results from a iodixanol gradiente, in which each fraction was measured by optical density, can be found. The data can be interpreted by comparing the values of the measuring units from each assay or experiment. The secondary structure of the genome of wild type HIV-1, depleted of not fo Nef gene and with or without IRES sequence, was solved. It can be interpreted by comparing the differences, both local and global, in their structures.