Aromatic residue mutations reveal direct correlation between HIV-1 nucleocapsid protein's nucleic acid chaperone activity and retroviral replication

Wu, Hao; Mitra, Mithun; McCauley, Micah J.; Thomas, James A.; Rouzina, Ioulia; Musier‐Forsyth, Karin; Williams, Mark C.; Gorelick, Robert J.

doi:10.1016/j.virusres.2012.07.008

Cited by 42 publications

(72 citation statements)

References 107 publications

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“…In contrast, NC binding to stem-loops with lower affinities than SL2 and SL3 induces destabilization of the adjacent stems (Johnson et al 2000;Bourbigot et al 2008). Consistent with these findings, the sequential processing of Gag by protease enhances the nucleic acid chaperone activity of the resulting polypeptides (NCp15, NCp9, NCp7), and this improvement is associated with a lower affinity and faster binding/dissociation kinetics with nucleic acids (Cruceanu et al 2006b;Rein 2010;Wu et al 2013;Wang et al 2014). TAR destabilization by HIV-1 nucleocapsid protein www.rnajournal.org 511…”

Section: Discussionmentioning

confidence: 66%

Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

Belfetmi¹,

Zargarian²,

Tisné³

et al. 2016

RNA

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The mature HIV-1 nucleocapsid protein NCp7 (NC) plays a key role in reverse transcription facilitating the two obligatory strand transfers. Several properties contribute to its efficient chaperon activity: preferential binding to single-stranded regions, nucleic acid aggregation, helix destabilization, and rapid dissociation from nucleic acids. However, little is known about the relationships between these different properties, which are complicated by the ability of the protein to recognize particular HIV-1 stem-loops, such as SL1, SL2, and SL3, with high affinity and without destabilizing them. These latter properties are important in the context of genome packaging, during which NC is part of the Gag precursor. We used NMR to investigate destabilization of the full-length TAR (trans activating response element) RNA by NC, which is involved in the first strand transfer step of reverse transcription. NC was used at a low protein:nucleotide (nt) ratio of 1:59 in these experiments. NMR data for the imino protons of TAR identified most of the base pairs destabilized by NC. These base pairs were adjacent to the loops in the upper part of the TAR hairpin rather than randomly distributed. Gel retardation assays showed that conversion from the initial TAR-cTAR complex to the fully annealed form occurred much more slowly at the 1:59 ratio than at the higher ratios classically used. Nevertheless, NC significantly accelerated the formation of the initial complex at a ratio of 1:59.

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Section: Discussionmentioning

confidence: 66%

Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

Belfetmi¹,

Zargarian²,

Tisné³

et al. 2016

RNA

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“…Previous studies have shown that NC binds RNAs in a largely nonspecific manner via electrostatic interactions between the nucleic acid backbone and the basic residues in the protein (Levin et al 2005;Fisher et al 2006;Vo et al 2009a;Darlix et al 2011;Wu et al 2012). However, binding to certain RNA motifs, especially single-stranded UG sequences (Fisher et al 1998), or exposed G residues in loop regions such as SL3 (De Guzman et al 1998), involves high-affinity binding in which the zinc finger (ZF) aromatic residues stack with the G base in a hydrophobic pocket formed between the two ZFs (De Guzman et al 1998;Darlix et al 2011).…”

Section: The Zinc Fingers In Gag Are Required For High-affinity Psi Rmentioning

confidence: 99%

Distinct binding interactions of HIV-1 Gag to Psi and non-Psi RNAs: Implications for viral genomic RNA packaging

Webb

Jones

Parent

et al. 2013

RNA

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144

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Despite the vast excess of cellular RNAs, precisely two copies of viral genomic RNA (gRNA) are selectively packaged into new human immunodeficiency type 1 (HIV-1) particles via specific interactions between the HIV-1 Gag and the gRNA psi (ψ) packaging signal. Gag consists of the matrix (MA), capsid, nucleocapsid (NC), and p6 domains. Binding of the Gag NC domain to ψ is necessary for gRNA packaging, but the mechanism by which Gag selectively interacts with ψ is unclear. Here, we investigate the binding of NC and Gag variants to an RNA derived from ψ (Psi RNA), as well as to a non-ψ region (TARPolyA). Binding was measured as a function of salt to obtain the effective charge (Z eff ) and nonelectrostatic (i.e., specific) component of binding, K d(1M) . Gag binds to Psi RNA with a dramatically reduced K d(1M) and lower Z eff relative to TARPolyA. NC, GagΔMA, and a dimerization mutant of Gag bind TARPolyA with reduced Z eff relative to WT Gag. Mutations involving the NC zinc finger motifs of Gag or changes to the G-rich NC-binding regions of Psi RNA significantly reduce the nonelectrostatic component of binding, leading to an increase in Z eff . These results show that Gag interacts with gRNA using different binding modes; both the NC and MA domains are bound to RNA in the case of TARPolyA, whereas binding to Psi RNA involves only the NC domain. Taken together, these results suggest a novel mechanism for selective gRNA encapsidation.

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“…The highly basic nature of HIV-1 NC stems primarily from its a-helical N-terminal domain, and is the driving force behind NC's strong NA aggregation activity [4][5][6][7]. The Zn fingers each contain one or two aromatic residues that can interact with nucleobases via stacking interactions, and have been shown to promote duplex destabilization [8][9][10][11][12][13][14]. However, prominent structural differences exist between NCs of different retroviruses, and often produce differences in function.…”

Section: Introductionmentioning

confidence: 99%

Bovine leukemia virus nucleocapsid protein is an efficient nucleic acid chaperone

Qualley

Sokolove

2015

Biochemical and Biophysical Research Communications

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Aromatic residue mutations reveal direct correlation between HIV-1 nucleocapsid protein's nucleic acid chaperone activity and retroviral replication

Cited by 42 publications

References 107 publications

Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

Distinct binding interactions of HIV-1 Gag to Psi and non-Psi RNAs: Implications for viral genomic RNA packaging

Bovine leukemia virus nucleocapsid protein is an efficient nucleic acid chaperone

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