Selective Packaging of HIV-1 RNA by GAG Proteins

Abstract

It is not understood how the HIV-1 retrovirus selects it genomic RNA (gRNA) for packaging into virions from among the multitude of cellular RNA molecules in the cytoplasm of infected cells. Under in vitro conditions, the Gag proteins of HIV-1 have no specific binding affinity for the RNA Ψ sequence, which has been shown to be the key recognition element of genomic RNA. We propose a search mechanism based on the two-state nature of the Gag proteins in solution. The minimum free energy state is the B (or “bent”) state. In this state, Gag is non-specifically bound to RNA molecules through the NC and MA cationic subdomains and mobile. Next, in the E (or “extended”) state, only the NC domain of Gag binds to the RNA molecule that is being searched, while the MA domain may bind to distant regions of RNA, small RNAs, small molecules such as PIP, or the plasma membrane. In the E state, Gag is immobile and has an enhanced binding affinity for the Ψ sequence (1,2). In addition, unlike the B-state form E-state Gag has a binding interface for other E-state Gags, thereby allowing stabilization of E state by multimerization and eventual capsid assembly. Alternation between B and E state Gag allows for an efficient search mechanism that is similar to that of transcription factor proteins searching DNA (3). (3) Slutsky, et.al. 2004. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophysical journal, 87(6), pp.4021-4035. (1)Webb, et.al. Distinct binding interactions of HIV-1 Gag to Psi and non-Psi RNAs: implications for viral genomic RNA packaging. RNA. 2013 (8):pp.1078-88. (2) Comas-Garcia, et.al. 2017. Dissection of specific binding of HIV-1 Gag to the “packaging signal” in viral RNA. eLife, 6, p.27055.