{"doi":"10.1074/jbc.ra120.013961","title":"Visualizing a viral genome with contrast variation small angle X-ray scattering","abstract":"Despite the threat to human health posed by some single-stranded RNA viruses, little is understood about their assembly. The goal of this work is to introduce a new tool for watching an RNA genome direct its own packaging and encapsidation by proteins. Contrast variation small-angle X-ray scattering (CV-SAXS) is a powerful tool with the potential to monitor the changing structure of a viral RNA through this assembly process. The proteins, though present, do not contribute to the measured signal. As a first step in assessing the feasibility of viral genome studies, the structure of encapsidated MS2 RNA was exclusively detected with CV-SAXS and compared with a structure derived from asymmetric cryo-EM reconstructions. Additional comparisons with free RNA highlight the significant structural rearrangements induced by capsid proteins and invite the application of time-resolved CV-SAXS to reveal interactions that result in efficient viral assembly. Despite the threat to human health posed by some single-stranded RNA viruses, little is understood about their assembly. The goal of this work is to introduce a new tool for watching an RNA genome direct its own packaging and encapsidation by proteins. Contrast variation small-angle X-ray scattering (CV-SAXS) is a powerful tool with the potential to monitor the changing structure of a viral RNA through this assembly process. The proteins, though present, do not contribute to the measured signal. As a first step in assessing the feasibility of viral genome studies, the structure of encapsidated MS2 RNA was exclusively detected with CV-SAXS and compared with a structure derived from asymmetric cryo-EM reconstructions. Additional comparisons with free RNA highlight the significant structural rearrangements induced by capsid proteins and invite the application of time-resolved CV-SAXS to reveal interactions that result in efficient viral assembly. Viruses exploit many strategies to encapsidate the genome that codes for its container. The exact packaging process depends on the nature and form of the genetic material as well as the container or capsid. For some dsDNA viruses, there is clear structural separation between container and message; the genome is pumped into the preformed protein capsid by ATP-activated motor proteins (1Aksyuk A.A. Rossmann M.G. Bacteriophage assembly.Viruses. 2011; 3 (21994726): 172-20310.3390/v3030172Crossref PubMed Scopus (74) Google Scholar). The packaged genome, under high pressure, uniformly fills the capsid (2Duda R.L. Ross P.D. Cheng N. Firek B.A. Hendrix R.W. Conway J.F. Steven A.C. Structure and energetics of encapsidated DNA in bacteriophage HK97 studied by scanning calorimetry and cryo-electron microscopy.J. Mol. Biol. 2009; 391 (19540242): 471-48310.1016/j.jmb.2009.06.035Crossref PubMed Scopus (41) Google Scholar). In contrast, viruses with single-stranded RNA genomes appear to exploit RNA–protein interactions to facilitate encapsidation. The few examples of spatially resolved, encapsidated ssRNA genomes suggest that the genetic material is not uniformly distributed, often asymmetric and with higher density at the protein interface (3van den Worm S.H.E. Koning R.I. Warmenhoven H.J. Koerten H.K. van Duin J. Cryo electron microscopy reconstructions of the leviviridae unveil the densest icosahedral RNA packing possible.J. Mol. Biol. 2006; 363 (16989861): 858-86510.1016/j.jmb.2006.08.053Crossref PubMed Scopus (40) Google Scholar, 4Koning R. Van Den Worm S. Plaisier J.R. Van Duin J. Abrahams J.P. Koerten H. Visualization by cryo-electron microscopy of genomic RNA that binds to the protein capsid inside bacteriophage MS2.J. Mol. Biol. 2003; 332 (12948491): 415-42210.1016/S0022-2836(03)00846-5Crossref PubMed Scopus (52) Google Scholar, 5Dai X. Li Z. Lai M. Shu S. Du Y. Zhou Z.H. Sun R. In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus.Nature. 2017; 541 (27992877): 112-11610.1038/nature20589Crossref PubMed Scopus (80) ","journal":"Journal of Biological Chemistry","year":2020,"id":87064,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":12,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9545,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":240542,"name":"Lois Pollack","orcid":"0000-0002-9366-4396","position":1,"is_corresponding":false},{"id":243627,"name":"Josue San Emeterio","orcid":null,"position":0,"is_corresponding":true}],"reference_count":68,"raw_metadata":null,"created_at":"2026-07-18T21:59:31.247492Z","pmid":"32913117","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}