HIV-1 matrix-tRNA complex structure reveals basis for host control of Gag localization

Abstract

The HIV-1 virion structural polyprotein, Gag, is directed to particle assembly sites at the plasma membrane by its N-terminal matrix (MA) domain. MA also binds to host tRNAs. To understand the molecular basis of MA-tRNA interaction and its potential function, we present a co-crystal structure of HIV-1 MA-tRNA Lys3 complex. The structure reveals a specialized group of MA basic and aromatic residues preconfigured to recognize the distinctive structure of the tRNA elbow. Mutational, cross-linking, fluorescence, and NMR analyses show that the crystallographically defined interface drives MA-tRNA binding in solution and living cells. The structure indicates that MA is unlikely to bind tRNA and membrane simultaneously. Accordingly, single-amino-acid substitutions that abolish MA-tRNA binding caused striking redistribution of Gag to the plasma membrane and reduced HIV-1 replication. Thus, HIV-1 exploits host tRNAs to occlude a membrane localization signal and control the subcellular distribution of its major structural protein.

Interplay between Host tRNAs and HIV-1: A Structural Perspective

“…Consistent with this role of tRNA Lys3 in RT maturation, knocking down Lysyl-tRNA synthetase (LysRS) in cells led to a pronounced reduction in viral particle production [65]. Given recent findings that tRNA Lys3 also controls virus assembly by regulating Gag membrane localization [59,63,66], the observed replication defect was likely attributable to several tRNA functionalities.…”

“…Finally, viral particles assemble and bud from the infected cell and mature into infectious virions [54][55][56]. This review highlights three interfaces and complexes formed between host tRNAs and HIV-1 (highlighted in red): namely, the reverse transcription complex [57], tRNA-packaging complex [58], and tRNA-Gag complex [59].…”

“…While most of our current knowledge on tRNA-HIV-1 interactions is limited to the cytoplasm, it is conceptually conceivable that tRNAs and pre-tRNAs may engage in presently unidentified, functionally important interplay with HIV-1 components in the nucleus and in virions. In the following three sections, the molecular structures and biological functions of three significant tRNA-HIV-1 complexes will be discussed, namely the reverse transcription initiation complex (RTIC) responsible for genome replication [57], the tRNA-packaging complex that captures and encapsulates tRNA primers for reverse transcription [58,63,64], and the tRNA-Gag complex that regulates Gag membrane localization and virus assembly [59,63].…”

“…Interestingly, tRNAs are not only hijacked and removed to serve as essential structural components of functional virions, they are also exploited in the cytosol as regulatory molecules to control Gag localization and the timing of virion biogenesis (Figure 4) [59,65,91]. This second tRNA parasitism is mediated by a specific interaction between the N-terminal MA domain of Gag and a set of host tRNAs, as revealed by a co-crystal structure of the MA-tRNA Lys3 complex and in-cell crosslinking analyses [59].…”

“…HBR-plasma membrane interactions involve both nonspecific electrostatic interactions and specific contacts between the HBR residues and phosphatidylinositol-4,5-bisphosphate (PIP 2 ), which is a plasma membrane resident phospholipid [94,104,105]. Remarkably, the globular head of MA has evolved a specific structural determinant, consisting primarily of three basic (R22, K27, K32) and one aromatic (W36) residues, that acts to recognize the "elbow" structure of host tRNAs (Figure 4) [59]. The tRNA binding site overlaps significantly with the PIP 2 -binding site on MA [91], which readily explains the observed competition between tRNAs and membranes for MA binding [68,91,93,106].…”