Conserved determinants of lentiviral genome dimerization

Area of Science:

• Virology
• Molecular Biology
• RNA Structure and Function

Background:

• Retroviruses package two genomic RNA copies via dimerization-dependent mechanisms.
• Human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) genome dimerization involves specific RNA structures like the DIS and U5:AUG pairing.
• Phylogenetic conservation suggests functional importance, but conflicting data exists regarding HIV-2 and SIV dimerization roles.

Purpose of the Study:

• To investigate the roles of the dimer-specific (DIS) stem-loop and U5:AUG base pairing in the dimerization of HIV-1, HIV-2, and SIV 5' leader RNAs.
• To compare intrinsic and NC protein-dependent dimerization properties across different retroviral strains.
• To elucidate the conserved RNA structural switch mechanism underlying retroviral genome packaging.

Main Methods:

• Preparation of native and mutant 5' leader RNAs from HIV-1, HIV-2, and SIV strains.
• Analysis of RNA dimerization using gel electrophoresis and NMR spectroscopy.
• Mutagenesis to alter DIS loop sequences and U5:AUG pairing potential.

Main Results:

• HIV-2 and SIV dimers are more labile than HIV-1 dimers, requiring Mg(2+) for detection.
• Mutations promoting U5:AUG pairing enhanced dimerization in HIV-2 and SIV, while disrupting it inhibited dimerization.
• Chimeric RNAs demonstrated that DIS loop composition dictates HIV-1-like or SIV-like dimerization properties.

Conclusions:

• A common RNA structural switch mechanism involving U5:AUG formation promotes dimerization across HIV-1, HIV-2, and SIV.
• Variations in DIS loop residues, not other leader sequences, account for differences in dimerization propensity and lability.
• The NC protein's role in dimerization resembles that of a classical riboswitch.