Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms.
Recombination is recognized as a primary force in human immunodeficiency virus type 1 (HIV-1) evolution, increasing viral diversity through reshuffling of genomic portions. The strand-switching activity of reverse transcriptase is required to complete HIV-1 replication and can occur randomly throughout the genome, leading to viral recombination. Some recombination hotspots have been identified and found to correlate with RNA structure or sequence features. The aim of this study was to evaluate the presence of recombination hotspots in the pol gene of HIV-1 and to assess their correlation with the underlying RNA structure. Analysis of the recombination pattern and breakpoint distribution in a group of unique recombinant forms (URFs) detected two recombination hotspots in the pol region. Two stable and conserved hairpins were consistently predicted corresponding to the identified hotspots using six different RNA-folding algorithms on the URF parental strains. These findings suggest that such hairpins may play a role in the higher recombination rates detected at these positions.
Galli
Andrea
A
Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
Lai
Alessia
A
Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
Corvasce
Stefano
S
Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
Saladini
Francesco
F
Department of Molecular Biology, University of Siena, Siena, Italy.
Riva
Chiara
C
Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
Dehò
Lorenzo
L
Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
Caramma
Ilaria
I
Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
Franzetti
Marco
M
Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
Romano
Laura
L
Department of Molecular Biology, University of Siena, Siena, Italy.
Galli
Massimo
M
Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
Zazzi
Maurizio
M
Department of Molecular Biology, University of Siena, Siena, Italy.
Balotta
Claudia
C
Department of Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
D015684:Gene Products, pol / Q000737:chemistry / Q000235:genetics*; D015751:Genes, pol; D016333:HIV Protease / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
D015684:Gene Products, pol; D012367:RNA, Viral; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase; D016333:HIV Protease