HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome.
HIV-1 replication can be efficiently inhibited by intracellular expression of an siRNA targeting the viral RNA. However, HIV-1 escape variants emerged after prolonged culturing. These RNAi-resistant viruses contain nucleotide substitutions or deletions in or near the targeted sequence. We observed an inverse correlation between the level of resistance and the stability of the siRNA/target-RNA duplex. However, two escape variants showed a higher level of resistance than expected based on the duplex stability. We demonstrate that these mutations induce alternative folding of the RNA such that the target sequence is occluded from binding to the siRNA, resulting in reduced RNAi efficiency. HIV-1 can thus escape from RNAi-mediated inhibition not only through nucleotide substitutions or deletions in the siRNA target sequence, but also through mutations that alter the local RNA secondary structure. The results highlight the enormous genetic flexibility of HIV-1 and provide detailed molecular insight into the sequence specificity of RNAi and the impact of target RNA secondary structure.
Westerhout
Ellen M
EM
Department of Human Retrovirology, Academic Medical Center, University of Amsterdam Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
Ooms
Marcel
M
Vink
Monique
M
Das
Atze T
AT
Berkhout
Ben
B
D019380:Anti-HIV Agents / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D001483:Base Sequence; D002460:Cell Line; D015693:Gene Products, nef / Q000037:antagonists & inhibitors / Q000235:genetics; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D034622:RNA Interference; D020871:RNA Stability; D034741:RNA, Small Interfering / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D012367:RNA, Viral / Q000737:chemistry* / Q000187:drug effects / Q000235:genetics; D054311:nef Gene Products, Human Immunodeficiency Virus
D019380:Anti-HIV Agents; D015693:Gene Products, nef; D034741:RNA, Small Interfering; D012367:RNA, Viral; D054311:nef Gene Products, Human Immunodeficiency Virus