Modeling research sheds light on SARS-CoV-2 genome packaging

Researcher University of North Carolina at Chapel Hill A study investigating how the spatial patterning of specific genomic RNA regions of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) promotes compression, packaging, and cyclization of the viral genome. Was carried out.

The new SARS-CoV-2 virus is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, which continues to pose an unprecedented threat to global health and the global economy.

An important challenge for viruses such as SARS-CoV-2 is to specifically and efficiently package large genomes into relatively small capsids, while eliminating viral subgenome fragments and cellular nucleic acids.

It is not yet clear how these viruses select the genome from subgenomic RNA produced by the virus and the host transcriptome and compress it into virions.

Now, using a coarse-grained polymer model, Amy Gladfelter et al. Have shown that a process called phase separation promotes favorable conditions for a single packaging. However, the placement of phase separation-promoting sequences at the ends of the genome is essential for genome compression. Elements must also be placed at both ends of the genome for cyclization to occur.

The team says the model presented here may be applicable to other viruses and cellular systems, including long nucleotide chains and proteins.

The preprinted version of the paper bioRxiv* Servers and articles have been peer reviewed.

FERNA containing 5 ¢ terminal and N protein behaves in opposite phase. A) The N protein is represented as two bead chains, the first bead is involved in isotropic isomorphic interactions and the second bead is involved in anisotropic isomorphic interactions. Both the 5 ¢ end and the FERNA segment are about three times as large as the N protein and are each represented by 6 beads. The N protein interacts with all 5 ¢ terminal RNA beads via isotropic binding with the first bead and with all FERNA beads via anisotropic binding with the second bead. .. This interaction with FE competes with N protein dimerization. B) The N protein phase separates (PS) by itself over a narrow concentration and temperature range. C) N protein with 5 ¢ terminal RNA in the 1 au phase at temperature separates in a wider concentration range than itself. D) N protein containing FERNA at a temperature of 1 au is solubilized at a sufficiently high FERNA concentration.

Understand coronavirus replication

The COVID-19 pandemic has influenced a great deal of research effort to understand the underlying mechanisms of coronavirus replication.

The virus must selectively package the large genome into relatively small capsids, excluding host nucleic acids and viral subgenome fragments.

Recent studies have shown that viral proteins required for genome packaging may undergo a process called liquid-liquid phase separation (LLPS), with one or two proteins binding to the virus. Nucleic acid Condenses with the genome.

In the case of SARS-CoV-2, genomic RNA can condense with the nucleocapsid (N) protein, a protein essential for genomic packaging of many viruses.

Importantly, some regions of genomic RNA promote the condensation of N proteins, while others solubilize it.

A previous study by Gladfelter and colleagues found that the N protein undergoes LLPS in an RNA sequence-specific manner within various regions of the genome.

“Surprisingly, RNAs of the same length can promote or limit phase separation depending on their sequence,” the researchers say.

They found that the LLPS-promoting sequences were at the 5 ¢ and 3 ¢ ends of the genome. This led the team to hypothesize that phase separation may be involved in packaging, as these sequences occur specifically throughout the genome and not together in subgenomes or host nucleic acids.

What was included in the current study?

Researchers used a coarse-grained polymer model to investigate how spatial patterning of LLPS-promoting or LLPS-inhibiting RNA regions within the genome facilitates specific packaging of a single genome. ..

First, the team analyzed parts of the SARS-CoV-2 genome that behaved in reverse phase when mixed with N protein.

Researchers have shown that the 5 ¢ and 3 ¢ ends of the genome promote phase separation, while frameshift elements (FEs) and central regions solubilize N proteins.

The team then investigated the spatial pattern of these opposite elements in the entire genome model and the effect of this pattern on phase separation and single-genome packaging, compression, and cyclization.

The model reveals that optimal placement for genome packaging and compression is the localization of LLPS-promoting elements to the 5 ¢ and 3 ¢ ends of the genome, which is required for cyclization. Did.

Future application of the model

Researchers say the model can inform future studies investigating spatial patterns of ly cumbersome genomic features due to their large genome size.

“We assume that this model should be generalized to multiple viruses as well as organelles,” they write.

“Several viral components have been shown to undergo phase separation, and the spatial patterning of RNA or DNA sequences that promote certain LLPS has evolved to allow SARS-CoV-2 as well as other viruses. May have facilitated optimal genomic packaging in the virus. ” team.

*Important Notices

bioRxiv Publish preliminary scientific reports that should not be considered definitive as they are not peer-reviewed, guide clinical practice / health-related behaviors, and should not be treated as established information.