Super-resolution proximity labeling reveals anti-viral protein network and its structural changes against SARS-CoV-2 viral proteins

Proximity Proteome Analysis Reveals Novel TREM2 Interactors in the ER-Mitochondria Interface of Human Microglia

“…The samples were subjected to streptavidin pull-down to enrich biotin-conjugated proteins. We then performed on-bead trypsin digestion, allowing direct mass spectrometry analysis of the peptide harboring biotin-conjugated lysine (K+226) (Lee et al, 2023). This approach removes the bulk of unlabeled peptides, therefore drastically improving detection sensitivity and reducing false positive results.…”

“…This approach removes the bulk of unlabeled peptides, therefore drastically improving detection sensitivity and reducing false positive results. After verifying the biotin labeling, biotin-labeled peptides were analyzed by mass spectrometry as previously described (Lee et al, 2019; 2023; Kwak et al, 2020). By statistically assessing the relative enrichment of the biotinylated peptides from TREM2-V5-TurboID relative to the control (V5-TurboID-NES), we identified 47 proteins as components of a TREM2 interactome (Fig.…”

“…We established stable IM-HM transfectants expressing TREM2-V5-TurboID and performed 'super resolution PL' (Fig. 1A; Lee at al. 2023).…”

“…TurboID, an engineered biotin ligase, uses ATP to convert biotin into biotin-AMP, a reactive intermediate that covalently labels biotin to the proximal proteins (Doerr, 2018; Brandon et al, 2018). Recently, we improved the TurboID-based PL further and performed ‘super resolution PL’, which involves the highly selective capture of biotinylated peptides, allowing the detection the TurboID-mediated biotinylation event at the single amino acid level (Lee et al, 2023).…”

RNF5: inhibiting antiviral immunity and shaping virus life cycle

“…The RNF5 activator Analog-1 has been shown to significantly inhibit SARS-CoV-2 replication in infection models, making it a potential candidate for treating infections caused by related viruses. The levels of both RNF5 mRNA and protein are higher in adolescents than in older populations, and interestingly, the mRNA levels in mild SARS-CoV-2 patients exceed those in patients with severe symptoms, suggesting a potential role for RNF5 in reflecting the prognosis of SARS-CoV-2 patients (56). Due to the critical role of STING in chronic inflammation and functional decline during aging, the decrease of RNF5 in older populations, which leads to the declined degradation of STING, may also be involved in neurodegenerative processes in the elderly (16).…”