TITLE:
Structural Analysis of Predicted HIV-1 Secis Elements
AUTHORS:
Paushali Roy, Sayak Ganguli, Pooja Sharma, Protip Basu, Abhijit Datta
KEYWORDS:
Selenocysteine, Selenium, SECIS Element, Selenoprotein, Human Sec tRNAsec, UGA Codon
JOURNAL NAME:
World Journal of AIDS,
Vol.1 No.4,
December
5,
2011
ABSTRACT: Incorporation of Selenocysteine into protein requires an RNA structural motif, SECIS (Selenocysteine insertion sequence) element that, along with other factors, demarcates UGA-Sec from the UGA termination codon, for expression of Selenoproteins (in case of eukaryotes). It has been predicted that during HIV infection, several functional viral selenoproteins are expressed and synthesis of these viral selenoproteins deplete the selenium level of the host. It might be that even the viral genome has the SECIS elements in their Selenoprotein mRNA, and during infection, the host cellular machinery is transformed in such a way that the human Sec tRNA binds to the viral Selenoprotein mRNA, instead of binding to its own Selenoprotein mRNA, thus leading to expression of viral selenoproteins. This hypothesis was tested in this study by identifying the SECIS elements in the HIV-1 genome and further predicting their secondary and tertiary structures. We then tried to dock these tertiary structures with human Sec tRNA. Here we report putatively the presence of 3215 SECIS elements in the HIV-1 genome and that the human Sec tRNAsec binds to the viral SECIS elements present in the viral selenoprotein mRNA. Based on an earlier finding, it was observed that atoms of A8 and U9, which present in human Sec tRNA, are the possible key sites for binding.