Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Single-particle studies of the effects of RNA-protein interactions on the self-assembly of RNA virus particles

View ORCID ProfileRees F. Garmann, Aaron M. Goldfain, Cheylene R. Tanimoto, Christian E. Beren, Fernando F. Vasquez, View ORCID ProfileCharles M. Knobler, View ORCID ProfileWilliam M. Gelbart, View ORCID ProfileVinothan N. Manoharan
doi: https://doi.org/10.1101/2022.05.09.488235
Rees F. Garmann
aHarvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
bDepartment of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182
cViral Information Institute, San Diego State University, San Diego, CA 92182
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Rees F. Garmann
  • For correspondence: rgarmann@sdsu.edu
Aaron M. Goldfain
aHarvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
dSensor Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Cheylene R. Tanimoto
eDepartment of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christian E. Beren
eDepartment of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
fDepartment of Chemistry, Colorado School of Mines, Golden, CO 80401
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fernando F. Vasquez
cViral Information Institute, San Diego State University, San Diego, CA 92182
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Charles M. Knobler
eDepartment of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Charles M. Knobler
William M. Gelbart
eDepartment of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
gMolecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095
hCalifornia Nanosystems Institute, University of California Los Angeles, Los Angeles, CA 90095
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for William M. Gelbart
Vinothan N. Manoharan
aHarvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
iDepartment of Physics, Harvard University, Cambridge MA 02138
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Vinothan N. Manoharan
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Understanding the pathways by which simple RNA viruses self-assemble from their coat proteins and RNA is of practical and fundamental interest. Although RNA-protein interactions are thought to play a critical role in the assembly, our understanding of their effects is limited because the assembly process is difficult to observe directly. We address this problem by using interferometric scattering microscopy, a sensitive optical technique with high dynamic range, to follow the in vitro assembly kinetics of over 500 individual particles of brome mosaic virus (BMV)—for which RNA-protein interactions can be controlled by varying the ionic strength of the buffer. We find that when RNA-protein interactions are weak, BMV assembles by a nucleation-and-growth pathway in which a small cluster of RNA-bound proteins must exceed a critical size before additional proteins can bind. As the strength of RNA-protein interactions increases, the nucleation time becomes shorter and more narrowly distributed until the assembly kinetics become indistinguishable from diffusion-limited adsorption. In contrast, the time to grow a capsid after nucleation varies weakly with both salt and protein concentration. These results show that the nucleation rate is controlled by RNA-protein interactions, while the growth process is driven less by RNA-protein interactions and more by protein-protein interactions and intra-protein forces. The nucleated pathway observed with the plant virus BMV is strikingly similar to that previously observed with bacteriophage MS2, a phylogenetically distinct virus with a different host kingdom. These results raise the possibility that nucleated assembly pathways might be common to other RNA viruses.

RNA viruses first inspired the term “self-assembly.” Yet much is still not understood about how even the simplest such viruses assemble or if different viruses assemble in similar ways. Theoretical models suggest many possible assembly pathways, with many different roles for the RNA, but until recently measuring these pathways has not been possible. We use a sensitive microscopy technique to follow the assembly of individual particles of BMV, a plant virus. We find evidence of an RNA-mediated nucleation-and-growth pathway that is strikingly similar to that of MS2, a bacterial virus. The last common ancestor of BMV and MS2 existed only in ancient times, suggesting that their assembly pathway might be evolutionarily conserved and other viruses might follow a similar pathway.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted May 10, 2022.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Single-particle studies of the effects of RNA-protein interactions on the self-assembly of RNA virus particles
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Single-particle studies of the effects of RNA-protein interactions on the self-assembly of RNA virus particles
Rees F. Garmann, Aaron M. Goldfain, Cheylene R. Tanimoto, Christian E. Beren, Fernando F. Vasquez, Charles M. Knobler, William M. Gelbart, Vinothan N. Manoharan
bioRxiv 2022.05.09.488235; doi: https://doi.org/10.1101/2022.05.09.488235
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Single-particle studies of the effects of RNA-protein interactions on the self-assembly of RNA virus particles
Rees F. Garmann, Aaron M. Goldfain, Cheylene R. Tanimoto, Christian E. Beren, Fernando F. Vasquez, Charles M. Knobler, William M. Gelbart, Vinothan N. Manoharan
bioRxiv 2022.05.09.488235; doi: https://doi.org/10.1101/2022.05.09.488235

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One
Subject Areas
All Articles
  • Animal Behavior and Cognition (3609)
  • Biochemistry (7590)
  • Bioengineering (5533)
  • Bioinformatics (20833)
  • Biophysics (10347)
  • Cancer Biology (7998)
  • Cell Biology (11663)
  • Clinical Trials (138)
  • Developmental Biology (6619)
  • Ecology (10227)
  • Epidemiology (2065)
  • Evolutionary Biology (13648)
  • Genetics (9557)
  • Genomics (12860)
  • Immunology (7932)
  • Microbiology (19575)
  • Molecular Biology (7678)
  • Neuroscience (42193)
  • Paleontology (309)
  • Pathology (1259)
  • Pharmacology and Toxicology (2208)
  • Physiology (3272)
  • Plant Biology (7064)
  • Scientific Communication and Education (1295)
  • Synthetic Biology (1953)
  • Systems Biology (5435)
  • Zoology (1119)