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2012 | 59 | 4 | 619-626

Article title

Low recombination activity of R region located at both ends of the HIV-1 genome

Content

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EN

Abstracts

EN
Although two strand transfer events are indispensable for the synthesis of double-stranded DNA and establishing HIV-1 infection, the molecular basis of these phenomena is still unclear. The first obligatory template switching event occurs just at the beginning of the virus replication cycle and involves two copies of the 97-nucleotide long R region, located one each at the both ends of the HIV-1 genome (HIV-1 R). Thus, one can expect that the molecular mechanism of this process is similar to the mechanism of homologous recombination which operates in RNA viruses. To verify the above-mentioned hypothesis, we attempted to assess the recombination activity of HIV-1 R. To this end, we tested in vitro, how effectively it induces template switching by HIV-1 RT in comparison with another well-characterized sequence supporting frequent homologous crossovers in an unrelated virus (R region derived from Brome mosaic virus - BMV R). We also examined if the RNA sequences neighboring HIV-1 R influence its recombination activity. Finally, we tested if HIV-1 R could cause BMV polymerase complex to switch between RNA templates in vivo. Overall, our results have revealed a relatively low recombination activity of HIV-1 R as compared to BMV R. This observation suggests that different factors modulate the efficiency of the first obligatory strand transfer in HIV-1 and the homology-driven recombination in RNA viruses.

Year

Volume

59

Issue

4

Pages

619-626

Physical description

Dates

published
2012
received
2012-05-23
revised
2012-09-24
accepted
2012-10-24
(unknown)
2012-11-06

Contributors

  • Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
  • Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
  • Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
  • Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
  • Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland and Institute of Computing Science, Poznań University of Technology, Poznań, Poland

References

  • Alejska M, Figlerowicz M, Malinowska N, Urbanowicz A, Figlerowicz M (2005) A universal BMV-based RNA recombination system - how to search for general rules in RNA recombination. Nucl Acids Res 33: e105. doi:10.1093/nar/gni106.
  • Alejska M, Kurzynska-Kokorniak A, Broda M, Kierzek R, Figlerowicz M (2001) How RNA viruses exchange their genetic material. Acta Biochim Pol 48: 391-407.
  • Berkhout B, Ooms M, Beerens N, Huthoff H, Southern E, Verhoef K (2002) In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes. J Biol Chem 277: 19967-19975.
  • Berkhout B, Vastenhouw NL, Klasens BI, Huthoff H (2001) Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription. RNA 7: 1097-1114.
  • Borja M, Rubio T, Scholthof HB, Jackson AO (1999) Restoration of wild-type virus by double recombination of tombusvirus mutants with a host transgene. Mol Plant Microbe Interact 12: 153-162.
  • Bruyere A, Wantroba M, Flasinski S, Dzianott A, Bujarski JJ (2000) Frequent homologous recombination events between molecules of one RNA component in a multipartite RNA virus. J Virol 74: 4214-4219.
  • Chare ER, Holmes EC (2006) A phylogenetic survey of recombination frequency in plant RNA viruses. Arch Virol 151: 933-946.
  • Chen Y, Balakrishnan M, Roques BP, Bambara RA (2005) Acceptor RNA cleavage profile supports an invasion mechanism for HIV-1 minus strand transfer. J Biol Chem 280: 14443-14452.
  • Cheng C, Nagy PD (2003) Mechanism of RNA recombination in carmo - and tombusviruses: evidence for template switching by the RNA - dependent RNA polymenrase in vitro. J Virol 77: 12033-12047.
  • Cornelissen M, van den Burg R, Zorgdrager F, Lukashov V, Goudsmit J (1997) pol gene diversity of five human immunodeficiency virus type 1 subtypes: evidence for naturally occurring mutations that contribute to drug resistance, limited recombination patterns, and common ancestry for subtypes B and D. J Virol 71: 6348-6358.
  • Driscoll MD, Hughes SH (2000) Human immunodeficiency virus type 1 nucleocapsid protein can prevent self-priming of minus-strand strong stop DNA by promoting the annealing of short oligonucleotides to hairpin sequences. J Virol 74: 8785-8792.
  • Figlerowicz M, Alejska M, Kurzyńska-Kokorniak A, Figlerowicz M (2003) Genetic variability: the key problem in the prevention and therapy of RNA-based virus infections. Med Res Rev 23: 488-518.
  • Figlerowicz M, Bujarski JJ (1998) RNA recombination in brome mosaic virus, a model plus stranded RNA virus. Acta Biochim Pol 45: 847-868.
  • Figlerowicz M, Nagy PD, Bujarski JJ (1997) A mutation in the putative RNA polymerase gene inhibits nonhomologous, but not homologous, genetic recombination in an RNA virus. Proc Natl Acad Sci USA 94: 2073-2078.
  • Figlerowicz M, Nagy PD, Tang N, Kao CC, Bujarski JJ (1998) Mutations in the N terminus of the brome mosaic virus polymerase affect genetic RNA-RNA recombination. J Virol 72: 9192-9200.
  • Fisher W, Ganusov VV, Giorgi EE, Hraber PT, Keele BF et al. (2010) Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLOSone: 5: e12303.
  • Greene AE, Allison RF (1994) Recombination between viral RNA and transgenic plant transcripts. Science 263: 1423-1425.
  • Greene AE, Allison RF (1996) Deletions in the 3' untranslated region of cowpea chlorotic mottle virus transgene reduce recovery of recombinant viruses in transgenic plants. Virology 225: 231-234.
  • Guo JH, Henderson LE, Bess J, Kane B, Levin JR (1997) Human immunodeficiency virus type 1 nucleocapsid protein promotes efficient strand transfer and specific viral DNA synthesis by inhibiting TAR-dependent self-priming from minus-strand strong-stop DNA. J Virol 71: 5178-5188.
  • Hanson MN, Balakrishnan M, Roques BP, Bambara RA (2005) Effects of donor and acceptor RNA structures on the mechanism of strand transfer by HIV-1 reverse transcriptase. J Mol Biol 353: 772-787.
  • Holland JJ, De La Torre JC, Steinhauer DA (1992) RNA virus populations as quasispecies. Curr Top Microbiol Immunol 176: 1-20.
  • Huthoff H, Berkhout B (2001) Two alternating structures of the HIV-1 leader. RNA 7: 143-157.
  • Kati WM, Johnson KA, Jerva LF, Anderson KS (1992) Mechanism and fidelity of HIV-1 Reverse transcriptase. J Biol Chem 267: 25988-25997.
  • Klaver B, Berkhout B (1994) Premature strand transfer by the HIV-1 reverse transcriptase during strong-stop DNA synthesis. Nucleic Acids Res 22: 137-144.
  • Kurzyńska-Kokorniak A, Jaskólski M, Figlerowicz M (2002) Reverse transcriptase - an enzyme generating the genetic variability of human immunodeficiency virus Biotechnologia 1: 24-34.
  • Lai MM (1992) RNA recombination in animal and plant viruses. Microbiol Rev 56: 61-79.
  • Lahser FC, Marsh LE, Hall TC (1993) Contributions of the brome mosaic virus RNA-3 3'-nontranslated region to replication and translation. J Virol 67: 3295-3303.
  • Marque R, Isel C, Ehresmann C, Ehresmann B (1995) tRNAs as primer of reverse transcriptases. Biochimie 77: 113-124.
  • Moumen A, Polomack L, Roques B, Buc H, Negroni M (2001) The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination. Nucleic Acids Res 29: 3814-3821.
  • Muchiri JM, Rigby ST, Nguyen LA, Kim B, Bambara RA (2011) HIV-1 Reverse transcriptase dissociates during strand transfer. J Mol Biol 412: 354-364.
  • Nagy PD, Bujarski JJ. (1992) Genetic recombination in brome mosaic virus: effect of sequence and replication of RNA on accumulation of recombinants. J Virol 66: 6824-6828.
  • Nagy PD, Bujarski JJ (1995) Efficient system of homologous RNA recombination in brome mosaic virus: sequence and structure requirements and accuracy of crossovers. J Virol 69: 131-140.
  • Nagy PD, Bujarski JJ (1997) Engineering of homologous recombination hotspots with AU-rich sequences in brome mosaic virus. J Virol 71: 3799-3810.
  • Nagy PD, Bujarski JJ (1998) Silencing homologous RNA recombination hot spots with GC-rich sequences in brome mosaic virus. J Virol 72: 1122-1130.
  • Nagy PD, Simon AE (1997) New insights into the mechanisms of RNA recombination. Virology 235: 1-9.
  • Olsthoorn RC, Bruyere A, Dzianott A, Bujarski JJ (2002) RNA recombination in brome mosaic virus: effects of strand-specific stem-loop inserts. J Virol 76: 12654-12662.
  • Powell RL, Lezeau L, Kinge T, Nyambi PN (2010) Longitudinal quasispecies analysis of viral variants in HIV type 1 dually infected individuals highlights the importance of sequence identity in viral recombination. AIDS Res Hum Retroviruses 26: 253-264.
  • Purohit V, Balakrishnan M, Kim B, Bambara RA (2005) Evidence that HIV-1 reverse transcriptase employs the DNA 3' end-directed primary/secondary RNase H cleavage mechanism during synthesis and strand transfer. J Biol Chem 280: 40534-40543.
  • Shapka N, Nagy PD (2004) The AU-rich RNA recombination hot spot sequence of brome mosaic virus is functional in tombusviruses: implications for the mechanism of RNA recombination. J Virol 78: 2288-2300.
  • Smyth RP, Davenport MP, Mak J (2012) The origin of genetic diversity in HIV-1. Virus Res http://dx.doi.org/10.1016/j.virusres.2012.06.015.
  • Strauss JH, Strauss EG (1988) Evolution of RNA viruses. Annu Rev Microbiol 42: 657-683.
  • Urbanowicz A, Alejska M, Formanowicz P, Błażewicz J, Figlerowicz M, Bujarski JJ (2005) Homologous crossovers among molecules of brome mosaic bromovirus RNA1 or RNA2 segments in vivo. J Virol 79: 5732-5742.
  • Warrilow D, Warren K, Harrich D (2010) Strand transfer and elongation of HIV-1 reverse transcription is facilitated by cell factors in vitro. PLoS One 5: e13229.
  • Worobey M, Holmes E (1999) Evolutionary aspects of recombination in RNA viruses. J Gen Virol 80: 2535-2543.

Document Type

Publication order reference

Identifiers

YADDA identifier

bwmeta1.element.bwnjournal-article-abpv59p619kz
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