Researchers explore vulnerabilities within SARS-CoV-2 replication ‘foci’

Electron micrograph of transmission of SARS-CoV-2 virus particles, isolated from a patient. The image was captured and enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID

It lies beneath the SARS-CoV-2 membrane and its spikes of genetic material, or RNA, are enveloped by a protein that acts like a bubble wrap to protect the genetic material. This protein also serves as a “hot spot” for multiple interactions to control the affected cell.

Through atomic precision studies by University of Colorado Anschutz Medical Campus researchers and others, how this protein interacts with its targets to regulate multiple functions, such as viral replication, is now more clear.

Identifying the root of SARS-CoV-2 infection — and searching for vulnerabilities to exploit them, possibly to limit infection from further coronaviruses — is one of the research interests of Elan Eisenmesser, PhD, associate professor in the Department of Biochemistry and Molecular Genetics at the University of Medicine School of Medicine. Colorado.

This ‘hot center’ of the interactions is located on the nucleocapsid, which is one of the four structural proteins encoded by SARS-CoV-2. The other three proteins are spike, membrane and envelope proteins.

The nucleocapsid consists of 419 residues with distinct domains that include a well-folded N- and C-terminal domain. However, more than half of the nucleoprotein (N-protein) is largely composed of dynamic, or flexible, regions made of spaghetti-like sections, referred to as “intrinsically disordered regions”.

Eisenmer’s team has been studying all regions of the nucleocapsid protein to better understand how N-proteins play a role in viral RNA packaging and manipulation of host cell machinery.

Part of the nucleocapsid’s manipulative behavior, Eisenmer said, could be preventing the host cell’s ability to mount an immune response, primarily by preventing the proteins from carrying out their virus-fighting functions.

Study expands to include complete protein

Eisenmers co-authored a study led by Jasmina S. Journal of Molecular Biology (July 2021), which elucidated the interactions of the N-terminal domain of the SARS-CoV-2 N protein with several biological targets. The researchers determined that the N-terminal folded domain was able to bind to segments of small host RNA and DNA.

Recently, their studies have expanded to the flexible and highly dynamic regions of protein N that extend from the folded domains and also link the folded domains together.

“We are now expanding our studies to look at larger molecular interactions, not only interactions with the host enzyme cyclophilin A, but with larger RNA directly from the COVID genome as well,” Eisenmer said.

“We’re also identifying which parts of the protein are really flexible and can be used as a candidate vaccine,” he said. “At the same time, we really go to the regions of the nucleocapsid that interact with host RNA and proteins first.”

Drops are parts of replication

Eisenmer and other scientists have learned that the N-terminal region of the protein initially binds RNA, and recent data indicate that the C-terminal portion binds thereafter. While the host cell’s RNA interacts with the N protein by wrapping around it, essentially forming the bubble envelope, the nucleocapsid plug is now known to cleave the discrete droplets that form membraneless compartments, which is the focus of his team’s current study.

Eisenmiser describes the nucleocapsid encapsulation reaction as “a fascinating dance that controls multiple activities during viral replication.”

And what would organize this dance to form these parts? It’s an enzyme called cyclophilin A, which is found in large amounts within normal cells and has long been known to play a role in viral infections.

“While host cell cyclophilin-A has been known to regulate viral replication through unknown mechanisms, our results now indicate that cyclophilin-A does this by binding to the same regions of the nucleocapsid known to form these fragments,” Eisenmer said.

“An elegant dance of devastating viral productions”

“Those two things — RNA/DNA interactions and host (cyclophilin-A) interactions — are coupled in this double packing process. It’s not like one thing is happening at once,” Eisenmeier said. “It all happens at the same time and in concert. It’s an elegant dance of host cell regulation, replication, and finally destructive viral production.”

“Then the question is: How is it wrapped around the RNA? How does this[bubble wrap activity]happen with atomic precision?” He said. “Of course, if we can figure that out, maybe we can design drugs that target those spots in the package.”

Eisenmer said his team’s goal is to use data from the study published in 2021 and “go further and discover how they actually bind to specific regions of the genome using larger RNAs, as well as how other host proteins can be targeted to modulate host response and RNA packaging.”

Ways to change spots on a nucleocapsid?

Eisenmers’ team uses nuclear magnetic resonance to identify these molecular interactions. “Now that we’ve identified the spots on the nucleocapsid that cyclophilin-A binds to — and potentially modulates viral replication — what do we want to do? We want to change these spots, change those spots to determine how they modify the compartments.”

Biochemists are collaborating with colleagues in the departments of Biochemistry, Molecular Genetics, Immunology and Microbiology at CU Anschutz with the goal of developing a treatment that can prevent infection with the coronavirus after it occurs, or at least slow its devastating dance within host cells.

“The goal is to advance an understanding of the atomic precision of coronavirus interactions that will aid in the development of drugs that may impede specific steps in the viral life cycle,” Eisenmer said.


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more information:
Jasmina S. Redzic et al, Inherent dynamics and interaction sites of the SARS-CoV-2 Nucleocapsid N-Terminal region, Journal of Molecular Biology (2021). DOI: 10.1016 / j.jmb.2021.167108

Provided by CU Anschutz Campus

the quote: Researchers explore vulnerabilities within SARS-CoV-2 replication ‘hots’ (2022, Jan 18), retrieved Jan 18, 2022 from https://phys.org/news/2022-01-explore-vulnerabilities-sars -cov-hotbeds-replication.html

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