Biopolym. Cell. 2014; 30(1):29-36.
http://dx.doi.org/10.7124/bc.000879
Structure and Function of Biopolymers
Phylogenetic study on structural elements of HIV-1 poly(A) region. 2. USE domain and TAR hairpin
1Zarudnaya M. I., 1Potyahaylo A. L., 1Kolomiets I. M., 1Hovorun D. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

Aim Phylogenetic study on structural elements in the poly(A) region of human immunodeficiency virus type 1 (HIV-1), in particular the major upstream sequence element (USE), which stimulates polyadenylation of HIV-1 transcript, and the TAR (trans-activation response) hairpin, which juxtaposes spatially the AAUAAA and USE signals. Methods. The secondary structure of these elements has been predicted by UNA Fold program. Results. The structure of USE domain and TAR hairpin has been analysed in 1679 HIV-1 genomes and 17 genomes of simian immunodeficiency virus SIVcpzPtt. We found 376 and 588 different sequences for these elements, respectively, and revealed the most frequent base changes and subtypeand country-specific mutations. Only 43 % of HIV-1 isolates contain variants of the USE domain which occur with a frequency 5 % (the main variants) and 35 % of isolates contain main variants of the TAR hairpin. We found that the SIV USE domain and TAR hairpin most closely resemble those found in HIV-1 genomes of A/G-containing subtypes. Conclusions. The results of our large-scale phylogenetic study support a hypothesis on the interaction between tRNA3Lys and the 3' end of HIV-1 genomic RNA and a controversial supposition of HIV-1 genome dimerization by the TAR-TAR kissing mechanism. Since the TAR hairpin is a target for developing antiviral drugs based on the inhibition of signal elements, the data on specific structural features of this hairpin may be useful for new antivirals design.
Keywords: HIV-1, SIVcpzPtt, poly(A) region, secondary structure, USE domain, TAR hairpin
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Supplementary data

References

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