Translation of human immunodeficiency virus type 1 (HIV-1) mRNAs is entirely dependent on the host translation machinery. There are two prevailing hypotheses regarding the translation initiation mechanism in HIV-1; conventional cap-dependent ribosomal scanning mechanism (CDRSM) and cap-independent entry of the ribosome, usually through an internal ribosome entry site (IRES). The first mechanism makes use of the Kozak consensus sequence in locating the translation initiation codon, similar to the mechanism observed in human mRNAs. Therefore, a thorough understanding of the Kozak consensus and translation initiation in human would also shed light on the mechanism of translation initiation in HIV-1. The role of Kozak +4G site in translation initiation has been controversial, with the alternative hypothesis explaining the prevalence of +4G by invoking the observation that small amino acids, coded by G-starting codons, which are efficient for N-terminal methionine excision (NME), are preferred at the penultimate (second) position. Using two bioinformatics approaches we provide strong support for this alternative hypothesis and provide evidence contradicting the involvement of +4G in translation initiation.
One of the predictions of the CDRSM hypothesis is a high conservation of Kozak consensus sequence in different HIV-1 sequences. Our results presented here validate this prediction. The CDRSM hypothesis also predicts that there should be a selective pressure against ATG usage in optimal context in the HIV-1 5'-UTR to avoid their erroneous detection by the scanning ribosome, whereas the IRES-dependent mechanism in the presence of stable secondary structures, predicts no such selective pressure because these ATGs would be embedded in the secondary structures. Here we demonstrate this selective pressure in the HIV-1 5'-UTR which further supports the CDRSM hypothesis. Finally, we present evidence for strong site conservation in the 5'-UTR of HIV-1 sequences, which not only point to as yet unknown mechanisms of translation initiation, but also provide a mean to separate HIV-1 and human mRNAs. This implies that it is theoretically possible to design HIV-1-specific translation inhibition drugs.
| Identifer | oai:union.ndltd.org:uottawa.ca/oai:ruor.uottawa.ca:10393/27866 |
| Date | January 2007 |
| Creators | Khalouei, Sam |
| Publisher | University of Ottawa (Canada) |
| Source Sets | Université d’Ottawa |
| Language | English |
| Detected Language | English |
| Type | Thesis |
| Format | 109 p. |
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