Dissection of specific binding of HIV-1 Gag to the "packaging signal" in viral RNA
- National Cancer Institute, United States
- Xencor Inc., United States
- Leidos Biomedical Research, United States
Abstract
Selective packaging of HIV-1 genomic RNA (gRNA) requires the presence of a cis-acting RNA element called the “packaging signal” (Ψ). However, the mechanism by which Ψ promotes selective packaging of the gRNA is not well understood. We used fluorescence correlation spectroscopy and quenching data to monitor the binding of recombinant HIV-1 Gag protein to Cy5-tagged 190-base RNAs. At physiological ionic strength, Gag binds with very similar, nanomolar affinities to both Ψ-containing and control RNAs. We challenged these interactions by adding excess competing tRNA; introducing mutations in Gag; or raising the ionic strength. These modifications all revealed high specificity for Ψ. This specificity is evidently obscured in physiological salt by non-specific, predominantly electrostatic interactions. This nonspecific activity was attenuated by mutations in the MA, CA, and NC domains, including CA mutations disrupting Gag-Gag interaction. We propose that gRNA is selectively packaged because binding to Ψ nucleates virion assembly with particular efficiency.
Article and author information
Author details
Mauricio Comas-Garcia
Funding
National Cancer Institute
- Mauricio Comas-Garcia
- Siddhartha AK Datta
- Alan Rein
Intramural AIDS Targeted Antiviral Therapy Program
- Mauricio Comas-Garcia
- Alan Rein
National Institutes of Health (Contract HHS N26120080001E)
- Prabhakar R Gudla
National Institute of Allergy and Infectious Diseases
- Rajat Varma
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Stephen P Goff, Howard Hughes Medical Institute, Columbia University, United States
Version history
- Received: March 21, 2017
- Accepted: July 13, 2017
- Accepted Manuscript published: July 20, 2017 (version 1)
- Version of Record published: July 27, 2017 (version 2)
- Version of Record updated: July 28, 2017 (version 3)
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
Metrics
-
- 2,445
- views
-
- 410
- downloads
-
- 54
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Dissection of specific binding of HIV-1 Gag to the "packaging signal" in viral RNA
eLife 6:e27055.
https://doi.org/10.7554/eLife.27055
Further reading
-
- Microbiology and Infectious Disease
- Structural Biology and Molecular Biophysics
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
-
- Microbiology and Infectious Disease
- Structural Biology and Molecular Biophysics
A new study reveals how naturally occurring mutations affect the biophysical properties of nucleocapsid proteins in SARS-CoV-2.
