Journal Article

A Tiny Viral Protein, SARS-CoV-2-ORF7b: Functional Molecular Mechanisms

Colonna, Giovanni, Mansueto, Gelsomina, Fusco, Giovanna

2024

Overview

This study presents the interaction with the human host metabolism of SARS-CoV-2 ORF7b protein (43 aa), using a protein–protein interaction network analysis. After pruning, we selected from BioGRID the 51 most significant proteins among 2753 proven interactions and 1708 interactors specific to ORF7b. We used these proteins as functional seeds, and we obtained a significant network of 551 nodes via STRING. We performed topological analysis and calculated topological distributions by Cytoscape. By following a hub-and-spoke network architectural model, we were able to identify seven proteins that ranked high as hubs and an additional seven as bottlenecks. Through this interaction model, we identified significant GO-processes (5057 terms in 15 categories) induced in human metabolism by ORF7b. We discovered high statistical significance processes of dysregulated molecular cell mechanisms caused by acting ORF7b. We detected disease-related human proteins and their involvement in metabolic roles, how they relate in a distorted way to signaling and/or functional systems, in particular intra- and inter-cellular signaling systems, and the molecular mechanisms that supervise programmed cell death, with mechanisms similar to that of cancer metastasis diffusion. A cluster analysis showed 10 compact and significant functional clusters, where two of them overlap in a Giant Connected Component core of 206 total nodes. These two clusters contain most of the high-rank nodes. ORF7b acts through these two clusters, inducing most of the metabolic dysregulation. We conducted a co-regulation and transcriptional analysis by hub and bottleneck proteins. This analysis allowed us to define the transcription factors and miRNAs that control the high-ranking proteins and the dysregulated processes within the limits of the poor knowledge that these sectors still impose.

• Publisher: MDPI AG
• Subject: Algorithms / Analysis / Apoptosis / Cell death / Cluster analysis / Clustering / co-regulation network / Coronaviruses / COVID-19 / COVID-19 - genetics / COVID-19 - metabolism / COVID-19 - virology / Gene regulation / Genes / Humans / Interactomes / interactomics / Metabolism / Metastases / MicroRNAs / Molecular biology / Molecular modelling / Nodes / Physiological aspects / Protein Interaction Maps - genetics / Protein turnover / Proteins / SARS-CoV-2 - genetics / SARS-CoV-2 - metabolism / SARS-CoV-2-ORF7b / Severe acute respiratory syndrome coronavirus 2 / topological analysis / Transcription factors / Viral proteins / Viral Proteins - genetics / Viral Proteins - metabolism / Viruses