Biopolym. Cell. 2014; 30(1):29-36.
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


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

Supplementary data


[1] Chan S, Choi EA, Shi Y. Pre-mRNA 3'-end processing complex assembly and function. Wiley Interdiscip. Rev RNA. 2011; 2(3): 321–35.
[2] Ashe MP, Furger A, Proudfoot NJ. Stem-loop 1 of the U1 snRNP plays a critical role in the suppression of HIV-1 polyadenylation. RNA. 2000; 6(2):170–7.
[3] DeZazzo JD, Kilpatrick JE, Imperiale MJ. Involvement of long terminal repeat U3 sequences overlapping the transcription control region in human immunodeficiency virus type 1 mRNA 3' end formation. Mol Cell Biol. 1991; 11(3):1624–30.
[4] Valsamakis A, Zeichner S, Carswell S, Alwine JC. The human immunodeficiency virus type 1 polyadenylylation signal: a 3' long terminal repeat element upstream of the AAUAAA necessary for efficient polyadenylylation. Proc Natl Acad Sci USA. 1991; 88(6):2108–12.
[5] Klasens BI, Thiesen M, Virtanen A, Berkhout B. The ability of the HIV-1 AAUAAA signal to bind polyadenylation factors is controlled by local RNA structure. Nucleic Acids Res. 1999; 27(2): 446–54.
[6] Gilmartin GM, Fleming ES, Oetjen J, Graveley BR. CPSF recognition of an HIV-1 mRNA 3'-processing enhancer: multiple sequence contacts involved in poly(A) site definition. Genes Dev. 1995; 9(1):72–83.
[7] Kaufmann I, Martin G, Friedlein A, Langen H, Keller W. Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase. EMBO J. 2004; 23(3):616–26.
[8] Gilmartin GM, Fleming ES, Oetjen J. Activation of HIV-1 premRNA 3' processing in vitro requires both an upstream element and TAR. EMBO J. 1992; 11(12):4419–28.
[9] Ott M, Geyer M, Zhou Q. The control of HIV transcription: keeping RNA polymerase II on track. Cell Host Microbe. 2011; 10 (5):426–35.
[10] Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DM. Structural model of the complete poly(A) region of HIV-1 premRNA. J Biomol Struct Dyn. 2013; 31(10):1044–56.
[11] Piekna-Przybylska D, Dykes C, Demeter LM, Bambara RA. Sequences in the U3 region of human immunodeficiency virus 1 improve efficiency of minus strand transfer in infected cells. Virology. 2011; 410(2):368–74.
[12] Paillart JC, Skripkin E, Ehresmann B, Ehresmann C, Marquet R. In vitro evidence for a long range pseudoknot in the 5'-untranslated and matrix coding regions of HIV-1 genomic RNA. J Biol Chem. 2002; 277(8):5995–6004.
[13] Abbink TE, Berkhout B. A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon. J Biol Chem. 2003; 278(13):11601–11.
[14] Ooms M, Cupac D, Abbink TE, Huthoff H, Berkhout B. The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation. Nucleic Acids Res. 2007; 35(5):1649–59.
[15] Decorsiere A, Cayrel A, Vagner S, Millevoi S. Essential role for the interaction between hnRNP H/F and a G quadruplex in maintaining p53 pre-mRNA 3'-end processing and function during DNA damage. Genes Dev. 2011; 25(3):220–5.
[16] Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DM. Phylogenetic study on structural elements of HIV-1 poly(A) region. 1. PolyA and DSE hairpins. Biopolym Cell. 2013; 29(6): 454–62.
[17] Markham NR, Zuker M. UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol. 2008; 453:3–31.
[18] Watts JM, Dang KK, Gorelick RJ, Leonard CW, Bess JW, Swanstrom R, Burch CL, Weeks KM. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature. 2009; 460(7256): 711–6.
[19] Ramirez de Arellano E, Soriano V, Alcamil J, Holguin A. New findings on transcription regulation across different HIV-1 subtypes. AIDS Rev. 2006; 8(1):9–16.
[20] Vrolijk MM, Harwig A, Berkhout B, Das AT. Destabilization of the TAR hairpin leads to extension of the polyA hairpin and inhibition of HIV-1 polyadenylation. Retrovirology. 2009; 6:13.
[21] Das AT, Vrolijk MM, Harwig A, Berkhout B. Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging. Retrovirology. 2012; 9:59.
[22] Schopman NC, Willemsen M, Liu YP, Bradley T, van Kampen A, Baas F, Berkhout B, Haasnoot J. Deep sequencing of virus-infected cells reveals HIV-encoded small RNAs. Nucleic Acids Res. 2012; 40(1):414–27.
[23] Jalalirad M, Saadatmand J, Laughrea M. Dominant role of the 5' TAR bulge in dimerization of HIV-1 genomic RNA, but no evidence of TAR-TAR kissing during in vivo virus assembly. Biochemistry. 2012; 51(18):3744–58.
[24] Andersen ES, Contera SA, Knudsen B, Damgaard CK, Besenbacher F, Kjems J. Role of the trans-activation response element in dimerization of HIV-1 RNA. J Biol Chem. 2004; 279(21): 22243–9.
[25] Pallesen J. Structure of the HIV-1 5' untranslated region dimer alone and in complex with gold nanocolloids: support of a TARTAR-containing 5' dimer linkage site (DLS) and a 3' DIS-DIScontaining DLS. Biochemistry. 2011; 50(28):6170–7.
[26] Freisz S, Mezher J, Hafirassou L, Wolff P, Nomine Y, Romier C, Dumas P, Ennifar E. Sequence and structure requirements for specific recognition of HIV-1 TAR and DIS RNA by the HIV-1 Vif protein. RNA Biol. 2012; 9(7):966–77.
[27] Berkhout B. Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis. Nucleic Acids Res. 1992; 20(1):27–31.
[28] Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, AlHashimi HM. Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. Nat Chem Biol. 2011; 7(8):553–9.