Structural Determinants and Mechanism of HIV-1 Genome Packaging

Abstract

Like all retroviruses, the Human Immunodeficiency Virus (HIV) selectively packages two copies of its unspliced RNA genome, both of which are utilized for strand-transfer mediated recombination during reverse transcription – a process that enables rapid evolution under environmental and chemotherapeutic pressures. The viral RNA appears to be selected for packaging as a dimer, and there is evidence that dimerization and packaging are mechanistically coupled. Both processes are mediated by interactions between the nucleocapsid (NC) domains of a small number of assembling viral Gag polyproteins and RNA elements within the 5′-untranslated region (5′-UTR) of the genome. A number of secondary structures have been predicted for regions of the genome that are responsible for packaging, and high-resolution structures have been determined for a few small RNA fragments and protein-RNA complexes. However, major questions remain open regarding the RNA structures, and potentially the structural changes, that are responsible for dimeric genome selection. Here we review efforts that have been made to identify the molecular determinants and mechanism of HIV-1 genome packaging.

Specific recognition of the HIV-1 genomic RNA by the Gag precursor

“…D uring assembly, the HIV-1 must select its genomic RNA (gRNA) from a variety of RNAs, including cellular RNAs as well as more than 100 partially or fully spliced viral RNAs (vRNAs) (for recent reviews, see refs [1][2][3][4][5]. HIV-1 gRNA and spliced vRNAs compete for a common packaging pathway, while cellular RNAs are usually packaged with low efficiency, through a different mechanism 6 .…”

“…It consists of the matrix (MA), capsid (CA), nucleocapsid (NC), and p6 or 'late' domains; the CA and NC domains, and the NC and p6 domains are separated by the linker peptides p2 and p1, respectively (Fig. 1a) [1][2][3][4][5] . During or shortly after budding, Pr55 Gag is cleaved by the viral protease to produce the structural proteins of the mature virions: MA, CA and NC.…”

“…The HIV-1 MA domain binds RNA, and binding of the viral genome may enhance the selectivity of Gag for lipid raft-containing membranes 2 . A mutation in the disordered segment of the carboxy-terminal domain of CA has been shown to reduce RNA packaging 19 .…”

“…The 5 0 -region of the HIV-1 gRNA folds into several secondary structure motifs associated with key functions of the retroviral life cycle (Fig. 1b) 2,3,25 . The trans-activation response element (TAR) stem-loop (SL) is essential for Tat-mediated activation of transcription; the poly(A) hairpin contains the 5 0 -copy of the polyadenylation signal and may also be involved in a long range pseudo-knot 26 ; the PBS domain is crucial for initiation of reverse transcription (RT); SL1 initiates dimerization of the gRNA thanks to the 6-nt self-complementary motif in its loop 2,3,27 ; SL2 contains the major splice donor site; SL3 is involved in RNA packaging (see below); the unstable SL4 involves the initiation codon of gag and may adopt alternative conformations.…”

Conformation and dynamics of the Gag polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy

“…G ag, the primary structural polyprotein of human immunodeficiency virus type 1 (HIV-1), mediates all essential events during the assembly and maturation of HIV-1 (1)(2)(3)(4)(5). Gag is composed of six organizational units, matrix (MA)-capsid (CA)-spacer peptide 1 (SP1)-nucleocapsid (NC)-spacer peptide 2 (SP2)-p6, with an HIV-1 protease cleavage site at each junction.…”