SARS‐CoV‐2 infection remodels the host protein thermal stability landscape

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health and has compromised economic stability. In addition to the development of an effective vaccine, it is imperative to understand how SARS-CoV-2 hijacks host cellular machineries on a system-wide scale so that potential host-directed therapies can be developed. In situ proteome-wide abundance and thermal stability measurements using thermal proteome profiling (TPP) can inform on global changes in protein activity. Here we adapted TPP to high biosafety conditions amenable to SARS-CoV-2 handling. We discovered pronounced temporal alterations in host protein thermostability during infection, which converged on cellular processes including cell cycle, microtubule and RNA splicing regulation. Pharmacological inhibition of host proteins displaying altered thermal stability or abundance during infection suppressed SARS-CoV-2 replication. Overall, this work serves as a framework for expanding TPP workflows to globally important human pathogens that require high biosafety containment and provides deeper resolution into the molecular changes induced by SARS-CoV-2 infection.

Role of Heat Shock Proteins (HSP70 and HSP90) in Viral Infection

“…In studies by Joel Selkrig et al [126] attempts were made to disturb the SARS-CoV-2induced destabilization of HSP90 by the use of tanespimycin-an HSP90 inhibitor. The resulting inhibition of viral proliferation provided convincing evidence that SARS-CoV-2 requires the presence of HSP90 for proliferation during infection.…”

Decoding the Role of Temperature in RNA Virus Infections

“…One new technique to probe the RNA-protein and protein-protein interactions as a function of temperature is thermal proteome profiling (TPP). It can reveal molecular interaction networks and the stability of the interactions in these networks ( 130 ) and can be used to study which links in the interaction network change upon RNA virus infections or between different infections ( 131 ). For instance, TPP revealed that during SARS-CoV-2 infection, the virus induces changes in the cell cycle and microtubule and spliceosome complexes ( 131 ), highlighting the role of endogenous host protein machinery being utilized by the virus for its survival.…”

Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

“…48 An MS-based approach defined phosphoribosylated peptides alongside phosphopeptides on distinct proteoforms in lipopolysaccharide (LPS)-stimulated macrophages, pointing to possible functional cross-talk between PTMs. 49 Thermal proximity coaggregation (TPCA) and thermal proteome profiling have characterized overall impacts, both pro-and antiviral, on protein−protein interactions of human cytomegalovirus, 50 SARS-CoV-2, 51 and herpes simplex virus type 1. 52 The TPCA method captured dynamic enzyme−substrate interactions, leading to discovery of a functional link between the viral DNA interferon inducible protein 16 (IFI16) and the DNA-dependent protein kinase (DNA-PK), 52 enhanced computationally.…”