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Homo sapiens

ABSTRACT: RNAseq of A549 cells expressing SARS-CoV-2 accessory proteins

PROVIDER: PRJNA946640 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23986815_1.fastq.gz	Fastqsanger.gz
	SRR23986815_2.fastq.gz	Fastqsanger.gz
	SRR23986816_1.fastq.gz	Fastqsanger.gz
	SRR23986816_2.fastq.gz	Fastqsanger.gz
	SRR23986817_1.fastq.gz	Fastqsanger.gz

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13C-glucose tracing analysis of IFN-treated A549 cells expressing wild-type SARS-CoV-2 Nsp3-4 or a deISGylation-defective Nsp3-4 mutant protein

Project description:<p>Interferon (IFN)-stimulated gene 15 (ISG15) regulates diverse cellular processes, including antiviral immunity, through its conjugation to target proteins (ISGylation). Increasing evidence suggests that ISGylation can also reshape cellular metabolism; however, how viruses counteract ISGylation-mediated metabolic rewiring remains poorly understood. This analysis investigated the impact of the deISGylation activity of the SARS-CoV-2 papain-like protease, which is part of the Nsp3 protein, on type I IFN-driven modulation of cellular glucose metabolism. A549 cells expressing empty vector, wild-type (WT) Nsp3-4 from SARS-CoV-2, or a mutant Nsp3-4 protein that is deficient in PLpro deISGylation activity, were treated with IFNα (or mock-treated) and then subjected to 13C-glucose tracing analysis. Following isotope labeling, intracellular metabolites were extracted and analyzed by LC-MS to assess 13C incorporation into intermediates of glycolysis and the pentose phosphate pathway (PPP). Comparative analysis of the results revealed distinct labeling patterns in glycolytic and PPP metabolites under IFN-stimulated conditions, supporting a role for PLpro deISGylation activity in modulating cellular glucose metabolism. These data provide insight into how SARS-CoV-2 Nsp3 counteracts IFN-induced metabolic rewiring through its deISGylation activity.</p>

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Project description:<p>SARS-CoV-2 reprograms host metabolism to promote viral replication and evade immune responses. While infection is known to impair mitochondrial function and enhance glycolysis, the role of viral accessory proteins in these alterations remains unclear. Here, we investigate the metabolic impact of the accessory protein ORF7a. Lentiviral expression of ORF7a in human lung epithelial (A549) and monocytic (THP1) cells, coupled with integrated transcriptomic, proteomic, and metabolomic analyses, revealed profound dysregulation of glucose and lipid metabolism. ORF7a impaired oxidative phosphorylation, reducing basal and maximal respiration, inducing mitochondrial depolarization, and increasing reactive oxygen species. Mechanistically, ORF7a upregulated pyruvate dehydrogenase kinase 4 (PDK4), promoting pyruvate dehydrogenase (PDH) complex phosphorylation and suppressing pyruvate oxidation. However, pharmacological PDK4 inhibition did not restore respiration. High-resolution respirometry in frozen samples revealed impaired complex I function, while Blue Native-PAGE demonstrated defective respiratory supercomplex assembly. By linking enzymatic inhibition with structural destabilization, our study uncovers a functional vulnerability of the mitochondrial respiratory chain to viral manipulation. These findings establish ORF7a as a key modulator of host metabolic reprogramming and highlight mitochondrial pathways as potential therapeutic targets in COVID-19.</p>

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