Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate
bioinformatics molecular biology virology
Authors: Iserman et al.,
Link to paper: https://doi.org/10.1101/2020.06.11.147199
Journal/ Pre-Print:BioRxiv
Tags; Bioinformatics, Virology, Molecular Biology
Research Highlights
-
SARS-CoV-2 N-protein undergoes temperature-dependent phase separation in physiological buffer with or without viral genomic RNA.
-
Association with viral RNA fragment can either reduce or promote phase separation of N-protein, which is hypothesized to depend on RNA concentration, length, sequence and structure.
-
Small molecules can decrease N-protein phase separation in cells.
Summary
Using in vitro reconstituted purified N-protein, the authors visualised under microscopethe liquid-liquid phase separation (LLPS) of SARS-CoV-2 N-protein with and without viral genomic RNA (gRNA). They found that the level of LLPS is temperature- and RNA-concentration-dependent. Through comparing the levels of LLPS between different segments of SARS-CoV-2 genome, the authors also discovered that viral RNA fragments of different sequence and length can either promote or decrease the level of phase separation. Using in silico reconstruction of local RNA structure, the study also showed that RNA structure affect N-protein binding sites, hence LLPS. Lastly, the study showed N-protein phase separation in HEK293 cells and identified small molecules that disrupt this LLPS in cells.
Impact for SARS-CoV2/COVID19 research efforts
Understand the virology and/or cell biology of SARS-CoV2/COVID19
Clinical symptoms and pathogenesis of SARS-Cov2/COVID19
Inhibit of SARS-CoV2/COVID19 transmission
Treat of SARS-CoV2/COVID19 positive individuals
Study Type
-
In silico study / bioinformatics study
-
In vitro study (and cell culture)
Strengths and limitations of the paper
Novelty: The first to study RNA-related factors that affect the phase separation of N-protein and the first proposed the effect of LLPS on SARS-CoV-2 genome packaging.
Standing in the field: The role of phase separation in SARS-CoV-2 viral packaging suggested in the paper agrees with multiple other recent BioRxiv publications. High affinity N-protein binding sites on SARs-CoV-2 gRNA have also been suggested in other recent models.
Appropriate statistics:
Viral model used: SARS-CoV-2 （strain unspecified）
Translatability:Very early start point of drug development/repurposing. Suggested that condensate of SARS-CoV-2 N-protein could be a new potential antiviral target for inhibiting viral packaging process.
Main limitations:
-
Did not draw parallel comparison with other coronaviruses or other RNA viruses
-
Did not discuss any other potential function of N-protein LLPS other than aiding viral packaging, which is hypothesized before experimental design.
-
Many hypothesises are drawn from comparison between limited number of RNA fragments, that are artificially fragmented. More experiments, with synthetic RNA with specific length, sequence features or structure, are needed to test the hypothesises.
-
Did not investigate the effect of disrupted LLPS on viral growth (in the context of infection).