SARS-CoV-2 Infections Can Be Controlled By Inhibiting Human Host SIRT5

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A new study by researchers from Buck Institute for Research on Aging-California, Gladstone Institute-California, University of California-San Francisco and the QBI COVID-19 Research Group (QCRG)-California has revealed that the SARS-CoV-2 coronavirus can be inhibited and controlled by downregulating human host SIRT5.

The study findings showed that SIRT5 is a proviral factor and that SARS-CoV-2 levels decrease when SIRT5 is deleted or inhibited in cell-culture experiments. The study findings also show that SIRT5 inhibitors such as Suramin, Quercetin etc could possibly be used as potential COVID-19 Drugs.

SIRT5 also known as Sirtuin (silent mating type information regulation 2 homolog) is a protein which in humans in encoded by the SIRT5 gene. Members of the sirtuin family are characterized by a sirtuin core domain and belong to the class III of the [histone deacetylase] superfamily, and are dependent on NAD+ as co-factor of enzymatic activities.

SIRT5 is one of the three sirtuins localized primarily to the mitochondrion.

The study findings were published on a preprint server and are currently being peer reviewed. https://www.biorxiv.org/content/10.1101/2022.01.04.474979v1

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a pathogen of global concern that needs no further introduction. After cellular entry, SARS-CoV-2 hijacks the cellular machinery, and the viral proteins physically interact with hundreds of human proteins (1–4). In most cases, however, the exact nature of the interactions and their functions and relevance during viral infection remain unknown.

SARS-CoV-2 encodes two large open reading frames, ORF1a and ORF1b, that are processed into 16 non-structural proteins after proteolytic cleavage by viral proteases.

The 16 non-structural proteins, Nsp1 to Nsp16, are involved in every aspect of viral replication and are highly conserved in coronaviruses. Coronavirus Nsp14 protein is part of the replication-transcription complex and has two conserved domains with distinct functions.

The N-terminal domain acts as a 3’ to 5’ exoribonuclease (ExoN), and the C-terminal domain displays RNA cap guanine N7-methyltransferase (MTase) activity (Fig. 1A) (5–8). The N-terminal ExoN domain provides proofreading activity during RNA replication, allowing the removal of mismatched nucleotides introduced by the viral RNA polymerase (9–11). This proofreading activity ensures a high level of fidelity during RNA replication and is unique among RNA viruses (12, 13).

Coronaviruses and related viruses in the order nidovirales have some of the largest genomes (26–32 kb) among known RNA viruses (14), and the acquisition of ExoN activity is thought to have allowed nidoviruses to evolve these large genomes (9, 15).

The C-terminal MTase domain of Nsp14 is an S-adenosyl methionine (SAM)-dependent methyltransferase critical for viral RNA capping that methylates the 5′ guanine of the Gppp-RNA cap at the N7 position (6, 7). The 5′ cap is important for viral mRNA stability and translation and for escaping host innate antiviral responses.

Importantly, Nsp14 forms a stable complex with the non-structural protein Nsp10, a small zinc-binding co-factor with no reported enzymatic activity on its own (7, 10). Nsp10 binds and stabilizes the N-terminal ExoN domain of Nsp14 and is necessary for ExoN activity, but not for MTase activity.

Interestingly, mutations that abolish ExoN activity cause a lethal phenotype in SARS-CoV-2 and MERS-CoV, but not in SARS-CoV or other coronaviruses (16), suggesting that ExoN has additional functions beyond its proofreading activity. Indeed, Nsp14 triggers translational shutdown, participates in evasion of innate immunity, activates proinflammatory signals, and mediates viral recombination (17–20).

SARS-CoV-2 Nsp14 interacts with human SIRT5A. Cartoon representation of the protein structure of Nsp14/Nsp10 (PDB 7N0B) and SIRT5 (PDB 3YIR) shows the Nsp14 N-terminal ExoN domain and C-terminal MTase domain. B. Affinity-purification of Nsp14-strep and co-purification of endogenous SIRT5 after transfection in HEK293T cells, as shown by western blot. C. Immunofluorescence of transfected Nsp14-Strep and endogenous SIRT5 in A549 cells. D. CETSA in HEK293T cells transfected with Nsp14-step and/or SIRT5, showing an increase in the stability of SIRT5 and Nsp14 by western blot. E. Western blot showing the absence of SIRT5 in Sirt5-KD HEK293T cells. F. Strep-tag affinity-purification or Flag-tag immunoprecipitation, followed by western blot, after transfection with Nsp14-strep, Nsp10-flag and SIRT5 expression constructs. SIRT5 does not interact with Nsp10. 0.5 μg of each construct or of empty control plasmids were transfected in Sirt5-KD HEK293T cells in a six-well plate. G. Strep-tag affinity-purification and western blot after transfection of Nsp14-strep, SIRT5 and increasing concentrations of Nsp10-tag indicates competitive binding of SIRT5 and Nsp10. 0.5 μg of Nsp14-strep and SIRT5 plasmid were used in a 6-well plate, with 0, 0.5, 1 or 2 μg of Nsp10-Flag.

Large-scale protein-protein interaction analyses of SARS-CoV-2 and human proteins revealed putative interacting partners for all of the SARS-CoV-2 proteins. Several independent studies, from us and from others, suggested that SARS-CoV-2 Nsp14 protein interacts with human sirtuin 5 (SIRT5) (1–4).

Sirtuins are a family of conserved protein deacylases and mono-ADP-ribosyltransferases found in organisms ranging from bacteria to humans. Sirtuins use nicotinamide adenine dinucleotide (NAD) as a co-substrate and are important regulators of cellular metabolism and aging (21, 22).

Most sirtuins act as NAD-dependent protein deacetylases, removing acetyl groups from lysine residues and, as such, tightly connect post-translational protein regulation with cellular metabolism. The seven mammalian sirtuins (SIRT1–7) are found in different cellular compartments.

They deacylate histones and transcriptional regulators in the nucleus and also specific proteins in the cytoplasm and in mitochondria. Sirtuins are crucial regulators of cellular metabolism and energy homeostasis and have emerged as key regulators of aging and age-related diseases.

SIRT5 is unique among the seven mammalian sirtuins. It is only a weak protein deacetylase, but it efficiently removes longer-chain acyl groups from proteins, such as succinyl, malonyl or glutaryl groups (23, 24). By preferentially catalyzing the removal of these negatively charged acidic modifications, SIRT5 functions as the main cellular desuccinylase, demalonylase, and deglutarylase (24–26).

SIRT5 is predominantly found in the mitochondria, but also exerts regulatory activity in the cytoplasm in several important metabolic processes, such as glycolysis, fatty acid oxidation and ketone body production f(27). Despite elevated succinylation or malonylation levels in several tissues, no obvious phenotype or abnormalities are observed in Sirt5 knockout mice under basal conditions (28). The roles of SIRT5 in disease, infection, and aging, are unclear.

Here we investigated the role of SIRT5 during infection with SARS-CoV-2. We showed that SIRT5 stably interacts with Nsp14, but not with its cofactor Nsp10, and that SIRT5 catalytic activity is necessary for the interaction. Furthermore, knock-out or inhibition of SIRT5 reduced viral levels in cell-culture experiments, revealing that SIRT5 is a proviral factor necessary for efficient viral replication.

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