Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling

Abstract

Viruses must effectively remodel host cellular pathways to replicate and evade immune defenses, and they must do so with limited genomic coding capacity. Targeting posttranslational modification (PTM) pathways provides a mechanism by which viruses can broadly and rapidly transform a hostile host environment into a hospitable one. We used quantitative proteomics to measure changes in two PTM types -phosphorylation and ubiquitination -in response to HIV-1 infection with viruses harboring targeted deletions of a subset of HIV-1 genes. PTM analysis revealed a requirement for Aurora kinase A activity in HIV-1 infection and furthermore revealed that AMP-activated kinase activity is modulated during infection via HIV-1 Vif-mediated degradation of B56-containing protein phosphatase 2A (PP2A). Finally, we demonstrated that the Cullin4A-DDB1-DCAF1 E3 ubiquitin ligase ubiquitinates histone H1 somatic variants and that HIV-1 Vpr inhibits this process, leading to defects in DNA repair. Thus, global PTM profiling of infected cells serves as an effective tool for uncovering specific mechanisms of host pathway modulation.

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

“…Proteomics approaches that globally quantify changes in protein abundance and phosphorylation are powerful tools to elucidate mechanisms of viral pathogenesis by providing a snapshot of how cellular pathways and processes are rewired upon infection (Johnson et al, 2020). Importantly, the functional outcomes of many phosphorylation events are well annotated, especially for kinases where phosphorylation directly regulates their activity.…”

Directing HIV-1 for degradation by non-target cells, using bi-specific single-chain llama antibodies

“…In general however, since earlier controverses about the fate of HIV-1 in endosomal vesicles, much evidence indicated that HIV-1 is degraded in lysosomes [53][54][55] and generally requires CD4 and a coreceptor for productive infection [56][57][58] . In addition, not all cell types will provide all the gene products required to support viral propagation [59][60][61] . Note that also the natural Fc-mediated degradation of HIV-1 bound by conventional antibodies was recently indicated to occur by endocytosis (into liver sinusoidal endothelial cells) and subsequent degradation in lysosomes 62 .…”

Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology

“…This approach has been applied to HIV to study phosphorylation and ubiquitin signaling associated with accessory proteins Vif, Vpr, and Vpu. 120 , 122 , 160 Given its DUB activity, Nsp3 represents a promising target to apply this type of study to SARS-CoV-2. PTM and abundance changes identified during infection with wild type SARS-CoV-2 but not with a ΔNsp3 virus may represent proteins and PTMs regulated by Nsp3.…”

“…To better understand the mechanism of how SARS-CoV-2 rewires signaling pathways, PTM and abundance analysis can be performed after infection with gene deletion mutant viruses to identify which viral proteins are responsible for rewiring a given pathway. This approach has been applied to HIV to study phosphorylation and ubiquitin signaling associated with accessory proteins Vif, Vpr, and Vpu. ,, Given its DUB activity, Nsp3 represents a promising target to apply this type of study to SARS-CoV-2. PTM and abundance changes identified during infection with wild type SARS-CoV-2 but not with a ΔNsp3 virus may represent proteins and PTMs regulated by Nsp3.…”