Journal Article

Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2

Myagmarsuren, Dulguun, Nguyen, Ai, Srinivasan, Sanjana, Schuck, Peter, Piszczek, Grzegorz, Chen, Jiji, Zhao, Huaying, Wu, Di

2024

Overview

Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs. Like other types of RNA viruses, the genetic material of SARS-CoV-2 (the agent responsible for COVID-19) is formed of an RNA molecule which is prone to accumulating mutations. This gives SARS-CoV-2 the ability to evolve quickly, and often to remain one step ahead of treatments. Understanding how these mutations shape the behavior of RNA viruses is therefore crucial to keep diseases such as COVID-19 under control. The gene that codes for the protein that ‘packages’ the genetic information inside SARS-CoV-2 is particularly prone to mutations. This nucleocapsid (N) protein participates in many key processes during the life cycle of the virus, including potentially interfering with the immune response. Exactly how the physical properties of the N-Protein are impacted by the mutations in its genetic sequence remains unclear. To investigate this question, Nguyen et al. predicted the various biophysical properties of different regions of the N-protein based on a computer-based analysis of SARS-CoV-2 genetic databases. This allowed them to determine if specific protein regions were positively or negatively charged in different mutants. The analyses showed that some domains exhibited great variability in their charge between protein variants – reflecting the fact that the corresponding genetic sequences showed high levels of plasticity. Other regions remained conserved, however, including across related coronaviruses. Nguyen et al. also conducted biochemical experiments on a range of N-proteins obtained from clinically relevant SARS-CoV-2 variants. Their results highlighted the importance of protein segments with no fixed three-dimensional structure. Mutations in the related sequences created high levels of variation in the physical properties of these ‘intrinsically disordered’ regions, which had wide-ranging consequences. Some of these genetic changes even gave individual N-proteins the ability to interact with each other in a completely new way. These results shed new light on the relationship between genetic mutations and the variable physical properties of RNA virus proteins. Nguyen et al. hope that this knowledge will eventually help to develop more effective treatments for viral infections.

• Publisher: eLife Sciences Publications Ltd
• Subject: Amino acids / biophysical fitness landscape / Coronavirus Nucleocapsid Proteins - chemistry / Coronavirus Nucleocapsid Proteins - genetics / Coronavirus Nucleocapsid Proteins - metabolism / Coronaviruses / COVID-19 - genetics / COVID-19 - virology / Evolution / Functional plasticity / Genetic diversity / genotype-phenotype relationship / Humans / intrinsically disordered protein / Intrinsically Disordered Proteins - chemistry / Intrinsically Disordered Proteins - genetics / Intrinsically Disordered Proteins - metabolism / mutant spectrum / Mutation / Nucleocapsid Proteins - chemistry / Nucleocapsid Proteins - genetics / Nucleocapsid Proteins - metabolism / Nucleocapsids / Phenotypes / Phenotypic plasticity / Phenotypic variations / Phosphoproteins - chemistry / Phosphoproteins - genetics / Phosphoproteins - metabolism / Physicochemical properties / Point mutation / protein evolution / Protein interaction / Protein Stability / Protein structure / Proteins / RNA viruses / SARS-CoV-2 / SARS-CoV-2 - chemistry / SARS-CoV-2 - genetics / SARS-CoV-2 - metabolism / Secondary structure / Severe acute respiratory syndrome coronavirus 2 / Thermodynamics