The central nutrients, used by eukaryotic cells to generate energy in the form of ATP, are carbohydrates, amino acids, and fatty acids (FAs) (15). In the presence of oxygen, non-proliferating cells take up the carbohydrate glucose and metabolize it in the cytoplasm to pyruvate through a process called glycolysis (Figure 1). This results in a net production of two ATPs and the reduction of two nicotinamide adenine dinucleotide (NAD) molecules to NADH. Pyruvate can be transported into the mitochondria, where it is oxidized into acetyl coenzyme A (acetyl-CoA) with the production of one molecule of carbon dioxide and one more NADH. Acetyl-CoA acts as fuel for the tricarboxylic acid (TCA) cycle (also known as citric acid or Krebs cycle), through which it is completely oxidized to carbon dioxide with the net production of three molecules of NADH, one molecule of ATP (or guanosine triphosphate GTP), and one molecule of the reduced form of flavin adenine dinucleotide (FADH₂) (15). The molecules of NADH and FADH₂, generated until this point, are the inputs for the electron transport chain. They are used to establish a proton gradient at the inner mitochondrial membrane, which finally generates ATP from adenosine diphosphate in a process called oxidative phosphorylation (16) (Figure 1). In summary, from one molecule of glucose, theoretically, 36 equivalents of ATP can be generated in eukaryotes, although due to proton leakage and inefficiencies of the ATPase, the observed yield is about 30 ATPs (17). Importantly, glucose is not the only energy source, which can be used by eukaryotic cells. The amino acid glutamine is a second carbon source that can be converted to α-ketoglutarate (αKG) as oxidative substrate to fuel the TCA cycle (16, 18). Moreover, fatty acid oxidation (FAO) in the mitochondria generates acetyl-CoA, NADH, and FADH₂, which are further used to generate ATP (19). FAs are the most energetic nutrients, yielding the highest levels of ATP on an energy per gram basis. Hence, glycolysis and the TCA cycle are the central cellular respiratory systems of eukaryotic cells (15).

When cells start to proliferate, there is increasing demand of nutrients for energy production as well as biosynthesis of novel molecules (20). Therefore, proliferating cells increase glucose uptake and glycolysis, but do not oxidize all of the additional glucose-derived pyruvate in the TCA cycle. Instead, the pyruvate is reduced to lactate despite the presence of oxygen, which is therefore called aerobic glycolysis (21) (Figure 1). This effect was first described in tumor cells by Otto Warburg and is now called the Warburg effect (22). It is important to note that TCA flux is reduced but maintained during aerobic glycolysis in proliferating cells. Although aerobic glycolysis generates only two molecules of ATP, it is thought to generate cellular building blocks for rapidly proliferating cells (15). However, also amino acids are important contributors to increased cell mass in proliferating cells (23). Many glycolytic intermediates provide backbone carbons for multiple non-essential amino acids or function as substrates for the biosynthesis of phospholipids and triacylglycerols. In addition, the glycolytic intermediate glucose-6-phosphate (G6P) can feed into the pentose phosphate pathway to generate ribose-5-phosphate, which is important for nucleotide biosynthesis as well as the conversion of nicotinamide adenine dinucleotide phosphate to its reduced form NADPH (Figure 1). NADPH is used as reducing agent in lipid or nucleic acid synthesis and protects against cellular oxidative stress by generating reduced glutathione that inactivates reactive oxygen species (ROS) (e.g., H₂O₂) and free radicals (16). αKG, derived from glutamine, can be metabolized to malate and then to pyruvate to support NADPH generation in a process called glutaminolysis (16). Furthermore, glutamine is used as nitrogen donor for the biosynthesis of nucleotides, non-essential amino acids, and hexosamines. The hexosamine pathway requires fructose-6-phosphate (F6P) from glycolysis and acetyl-CoA, in addition to glutamine to produce uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), which is important for N-glycosylation of proteins (24). Therefore, N-glycosylation represents a nutrient-sensitive protein modification, which regulates the glycosylation of IFNs and viral glycoproteins (25). This modification is involved in protein trafficking, in viral entry, and in evading the immune system’s detection by some viruses (26).

As described above, during aerobic glycolysis, the TCA cycle is sustained in proliferating cells by glucose-derived pyruvate, as well as by replenishing depleted intermediates in the form of, e.g., glutamine in a process called anaplerosis (27, 28). The TCA cycle contributes many intermediates that act as biosynthetic substrates. For example, mitochondrial citrate can feed into de novo FA and cholesterol synthesis upon its export to the cytoplasm, where it is converted to acetyl-CoA and oxaloacetate by ATP citrate lyase (ACLY). Cytoplasmic acetyl-CoA is then the substrate for FAs, cholesterol, and isoprenoid synthesis (Figure 1). Phospholipids are generated from FAs and, together with cholesterol, form the majority of the lipid bilayers of the cellular membranes. Oxaloacetate is further metabolized to yield αKG and NADPH (29). Alternatively, oxaloacetate can be transaminated to aspartate, which acts as a carbon source in nucleotide biosynthesis. In addition, ACLY-derived acetyl-CoA and oxaloacetate can serve as precursors for nitric oxide (NO) and ROS production (30, 31).

In light of these functional prerequisites, it comes as no surprise that most viral infections enhance FA and cholesterol synthesis to support generation of membranes and ATP production (53) (Figure 2). For example, human cytomegalovirus (HCMV) upregulates most metabolic pathways in infected fibroblasts and drives flux from glycolysis through the TCA cycle to FAS (59). Inhibition of FAS suppresses replication of HCMV (59). Mechanisms of HCMV-induced metabolic reprograming include the activation of the glucose transporter Glut4 and inductions of ACLY and acetyl coenzyme A carboxylase (ACC) (53, 60). After ACLY-dependent generation of acetyl-CoA in the cytoplasm, ACC carboxylates acetyl-CoA to malonyl-CoA, which is a critical rate-limiting step in FAS (19). ACLY and ACC are currently evaluated as therapeutic targets for cancer, obesity, diabetes, and viral infections (61, 62). Similarly, influenza A, flaviviridae family members including hepatitis C virus (HCV) and West Nile virus (WNV), enteroviruses including poliovirus and coxsackievirus B3, rotavirus, rift valley fever virus, and respiratory syncytial virus depend on FAS for viral replication, making its modulation an attractive therapeutic target (63–65). 5′-adenosine monophosphate-activated protein kinase gets activated after certain virus infections, such as rift valley fever virus or coxsackievirus B3, and potently inhibits FAS (66, 67). Some viruses, such as influenza A, use FAS to induce the production of prostaglandin E2, which inhibits IFN expression and promotes apoptosis in macrophages (68). Viral replication is a highly energy-demanding process. Therefore, utilizing all available energy is critical and rate-limiting for some viral infections. Hence, some viruses depend on FAS and their degradation by FAO to produce ATP. In this respect, Vaccinia virion assembly is dependent on ATP synthesis fueled by FAS and FAO (69). Dengue virus, on the other hand, induces FAO by an autophagy-dependent processing of lipid droplets and triglycerides to generate ATP for efficient replication (70). Nevertheless, dengue virus also induces FAS to support virus replication (71). Hence, channeling the FAs from biosynthesis to catabolism by the induction of FAO, as seen in pDCs (40), could represent a novel powerful antiviral mechanism of IFN. However, further work is required to elucidate whether this represents a general antiviral mechanism.

Many viruses do not only modulate FAs, but also cholesterol homeostasis to enhance their replication efficiency. For example, WNV upregulates biosynthesis of cholesterol, redistributing it to viral membranes in the phase of replication (72). Moreover, HCV, hepatitis B virus (HBV), measles, human immunodeficiency virus (HIV), and dengue virus also change cholesterol pathway gene expression in a variety of cellular systems (73–76). Pharmacological disruption of cholesterol synthesis, e.g., by statins, often results in the inhibition of viral replication (77–82). Recent evidence has shown that an important antiviral mechanism of type I IFN seems to be inhibition of cholesterol and fatty acid biosynthesis derived from glucose (83, 84). Type I IFN reduces cholesterol synthesis upon CMV, herpes simplex (HSV1), semliki forest virus, vaccinia virus (VV), and adenovirus (ADV) infection in bone marrow-derived macrophages, which is dependent on IFNAR1 and TYK2 (83). Similarly, infection with murine gammaherpesvirus-68 (MHV-68) reduces cholesterol and long chain FAS in macrophages (84). It is important to note that total cholesterol levels are not strongly affected upon inhibition of cholesterol synthesis by IFN due to an enhancement of cholesterol import (84) (Figure 2). Similarly, WNV infection enhances cholesterol synthesis, but total cholesterol levels do not change (72). Inhibition of cholesterol biosynthesis has a direct antiviral effect. The sterol regulatory binding protein 2 (SREBP2), together with SREBP1, are the main transcription factors involved in coordinating the regulation of the sterol biosynthesis pathway (85). IFNs potently inhibit the transcription and expression of SREBP2 via IFNAR1 (83). On the other hand, WNV-induced redistribution of cellular cholesterol downregulates the IFN-stimulated JAK–STAT antiviral signaling response to infection potentially by influencing lipid raft signaling (72).

Fascinatingly, limiting cholesterol synthesis alone induces spontaneous type I IFN production and enhances antiviral immunity (84). Deletion of SREBP2 or the ER chaperone SCAP, which regulates SREBP2, reduces synthesis but enhances the uptake of cholesterol. This shift induces spontaneous IFN signaling that is strongly enhanced upon viral infection in bone marrow-derived macrophages or mouse embryonic fibroblasts. The IFN response in these cells is dependent on the cGAS–STING–TBK1–IRF3 pathway (84). The stimulator of interferon gene (STING) protein is anchored on the ER and Golgi apparatus, suggesting that cholesterol levels and potentially lipid rafts in these membranes may modulate STING signaling. Moreover, it is interesting to note that cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS), which senses DNA from viral infections, is evolutionarily conserved with OAS, another important antiviral protein that is induced by IFNs (86). In summary, many viruses increase cholesterol and FAS. This is counteracted by type I IFN signaling, which limits FA and cholesterol synthesis. Reducing cholesterol synthesis alone induces IFN production establishing an inflammatory circuit, which links the regulation of the sterol pathway with the antiviral IFN defense responses. However, one report noted enhanced cholesterol synthesis derived from acetate in IFNβ-treated HeLa cells (87).

Cholesterol-derived metabolites such as oxysterols are important systemic mediators that regulate many immunological functions (88). IFNs or viral infections lead to the induction and secretion of one oxysterol in macrophages: 25-hydroxycholesterol (25-HC) (89) (Figure 2). 25-HC is a soluble antiviral factor, generated from cholesterol by IFN-dependent activation of cholesterol-25-hydroxylase via STAT1 (89). 25-HC broadly inhibits growth of many enveloped viruses, such as vesicular stomatitis virus, HSV, HIV, MHV68, and Ebola virus, by suppressing membrane fusion between the virus and the host cell (90, 91). Mechanistically, 25-HC seems to incorporate into the membrane and/or modify the membrane composition (91). Indeed, an IFN-dependent increase in plasma membrane rigidity has long been observed in several previous studies (92–94). IFNβ augments membrane rigidity already after 30 min, and this is maintained for 2 days making it a powerful antiviral mechanism to prevent viral infection and spreading (93, 95). Nevertheless, type I IFNs decrease membrane contents of saturated FAs and increase unsaturated FAs (92). In patients with chronic hepatitis C infection, treatment with IFNα2 reduces the deformability and membrane fluidity of red blood cells, which may result in hemolytic anemia, a frequent side effect of IFN therapy (96). Another downside of IFN-induced 25-HC expression is its capacity to inhibit SREBP1, which not only drives FAS but also stimulates transcription of interleukin-1, a secreted inflammatory protein with wide-ranging antibacterial functions (97). This may explain why IFNs, produced during viral infections, enhance the subsequent susceptibility to bacterial or fungal infections (98–100). Generally, there is increasing awareness of a close relationship between membrane lipid dynamics and innate immune responses (101).

Polyamines are a family of small polycationic molecules, derived from decarboxylation of the amino acid ornithine, that classically comprise three molecules: putrescine, spermidine, and spermine (102). Spermine is generated from spermidine, which itself is produced from putrescine (Figure 3). Ornithine, which generates putrescine, is produced from l-arginine by arginase (103). Polyamines bind DNA, RNA, and proteins and are implicated in supporting transcription, translation, and deacetylation to influence a plethora of different cellular functions, including proliferation, apoptosis, autophagy, and gene regulation (103). Spermidine–spermine acetyltransferase (SAT1 or SSAT) acetylates spermidine and spermine, which promotes either their conversion back to putrescine or their export from the cell (102, 103). Interestingly, type I IFNs induce the expression of SAT1 and, therefore, deplete spermidine and spermine levels (104). The depletion of these two polyamines has a strong antiviral effect and inhibits replication of the RNA viruses, Zika virus and Chikungunya virus (104). Mechanistically, polyamines seem to be important for transcription and translation of viral RNA and proteins. Limiting polyamine synthesis, therefore, emerges as a novel antiviral strategy and SAT1 constitutes an important ISG.

NO is a gaseous and inorganic free radical best known for its vasodilatory and microbicidal effects (105). However, NO is also an important mediator in intracellular inhibition of viral replication, which results in lower viral yields and more efficient host clearance of the infection (106). NO is produced by the enzymatic modification of l-arginine to l-citrulline by NO synthases (NOS) (Figure 3). NOS type 2 (NOS2, iNOS) is an IFNγ-inducible protein in macrophages and requires IRF1 as a transcription factor, which itself is regulated by STAT1 (106, 107). Molecularly, the antiviral activities of NO are poorly described, but one demonstrated mechanism is nitrosylation of viral molecules (108). For example, NO S-nitrosylates the cysteine residue in the active site of Coxsackievirus protease 3C, thus inhibiting protease activity and interrupting the viral life cycle (109). In addition, the generation of NO by NOS2 depletes the common substrate l-arginine and, subsequently reduces polyamine levels, as described above. Moreover, this relieves a feedback inhibition mechanism, because polyamines can directly inhibit NOS2 (110). Hence, IFN-induced NOS2 and SAT1 induction have antiviral effects due to a coordinated shift from polyamine synthesis to NO production.

Viral or bacterial infections often cause immunopathology and tissue damage, not only because of the pathogens destroying the tissue but because of an overactivation of the immune system, which promotes tissue destruction. For example, excessive type I and II IFN production can drive tissue damage by proinflammatory actions on innate and adaptive immune cells, as well as the induction of apoptosis (111–113). IFNγ can cause the production of ROS, which induces apoptosis (114). NO contributes to tissue damage, especially if substantial numbers of IFN-activated macrophages produce large micromolar quantities of NO (115). First, NO can have proinflammatory effects on other cells of the immune system causing hyperactivation and immunopathology (105). Moreover, NO can rapidly react with hydrogen peroxide (H₂O₂) to form peroxynitrite (ONOO⁻), which nitrates proteins and is highly toxic, leading to the accumulation of injurious intracellular oxidants and to DNA damage (116). This NO-induced oxidative stress causes cytotoxicity, which promotes cellular and organ dysfunction (115). Currently, there is no clear-cut way of predicting whether NO has a more important role in viral clearance or in tissue pathology for a particular viral pathogen.

There are additional metabolic mechanisms explaining how IFN signaling can promote immunopathology. Infection of mice with LCMV causes a dysregulation of the redox system in the liver. In this infection model, the early production of type I IFN causes tissue pathology due to the downregulation of superoxide dismutase 1 (Sod1) in the liver (117). Sod1 is a ubiquitously expressed antioxidative molecule, which can protect cells from oxidative stress by scavenging O2− radicals (118) (Figure 3). Hence, type I IFN-mediated oxidative stress may be a key mediator of virus-induced liver damage, and this suggests that early antioxidant treatment may be therapeutically helpful in ameliorating tissue damage. On the other hand, this oxidative stress, induced by the downregulation of Sod1, may also be part of an immediate antioxidant host defense system against pathogens (117).

Indoleamine-2,3-dioxygenase 1 (IDO1) is an intracellular, non-secreted enzyme, which catalyzes the production of kynurenine (Kyn) derivatives from the essential amino acid tryptophan (Trp) (119). The IDO1 promoter region contains two IFN-stimulated response elements and three IFNγ-activated sites. Hence, IFNγ is the most potent inducer of IDO1 expression in many cells, including macrophages, fibroblasts, and pDCs (120, 121) (Figure 4). Although type I IFNs are able to directly induce IDO1, the maximum IDO1 expression requires co-stimulation with TNF-α or LPS (122, 123). Strong activation of IDO1 by IFNγ decreases serum levels of Trp. Since many microbial organisms rely on Trp, its degradation by IDO1-expressing cells of the innate immune system seems to be a major immune mechanism against bacterial infections (124). In fact, IFNγ-induced IDO1 expression seems to be protective in Toxoplasma gondii, Salmonella enterica serovar Typhi (S. Typhi), or Chlamydia pneumoniae infections (124, 125). For example, IFNγ-primed macrophages effectively contain intracellular replication of S. Typhi depending on the activation of IDO1 (125).

IDO1 expression also plays an important role during viral infections, such as HIV, influenza, Epstein–Barr, HBV, and HCV (124, 126). However, in viral infections, the induction of IDO1 by IFN seems to be generally harmful by the establishment of an immunotolerogenic microenvironment (124). Trp is important for activation and proliferation of T cells. Hence, Trp depletion inhibits T cell immunity and, moreover, the oxidation of Trp by IDO1 generates Kyn derivatives, which promote T cell tolerance by induction of regulatory T cells (121) (Figure 4). Therefore, mice lacking IDO1 exhibit significantly lower morbidity after sub-lethal influenza A infection by generating a stronger influenza-specific effector CD8 T cell response, though viral clearance rates are unaffected by IDO1 ablation (127). Similarly, genetic ablation of IDO1 or chemical inhibition with 1-methyl-d-l-tryptophan suppresses viral replication of murine leukemia virus in vivo and upregulates type I IFN production (128). In conclusion, in various chronic infections, autoimmune diseases, and cancer, an increased expression of IDO1, besides its antiviral effects, may promote an immunosuppressive environment, which potentially contributes to disease (119, 121, 123, 125).

The importance of translational control of many cellular responses, including metabolism, is increasingly appreciated (129, 130). On the one hand, type I IFNs cause massive translational inhibition as antiviral strategy (131), but on the other hand, they do promote the translation of ISGs, including PKR (10). Molecularly, AKT-mTORC1, mTORC2, and MAP kinase-interacting kinases (MNK), as well as eukaryotic initiation factor 4E (eIF4E) signaling are transiently activated by type I IFNs. An increase in ISG mRNA translation follows, which represents the early phase of IFN response (132–135). However, in primary human macrophages, stimulated by TLR2 ligands, IFNγ induces a strikingly different response. It reprograms metabolic pathways toward enhanced mitochondrial pathways and oxidative phosphorylation by inhibition of mTORC1 as well as MNK (136) (Figure 4). IFNγ treatment of patients with sepsis also enhances mitochondrial oxidative phosphorylation in peripheral blood mononuclear cells (137). mTORC1 and mTORC2 are well-known to control a wide array of metabolic pathways, including glycolysis, oxidative phosphorylation, and lipid metabolism (5, 138). Moreover, IFNγ suppresses the translation of repressors of inflammation, including HES1, HEY1, and IκBα, via mTORC1 in human macrophages (136, 139). The translational inhibition of these molecules promotes an inflammatory response and may contribute to the potent proinflammatory effects of this cytokine (140). Similarly, diminishing translation by blocking mTORC1 with rapamycin favors the translation of the more abundant proinflammatory cytokines such as IL-12 and blocks the translation of low abundant mRNAs such as IL-10 (5, 141). Mechanistically, IFNγ induces IDO1 expression (as explained above) by depleting intracellular tryptophan levels, and this suppresses mTORC1 (136). The amino acids leucine, arginine, as well as tryptophan are sensed by mTORC1 at the level of the lysosome. Only if sufficient amino acids are present, full mTORC1 activation by growth factors or PRR ligands occurs (142, 143). Additionally, IFNγ inhibits expression of the macrophage colony-stimulating factor receptor and interferes with the expression of SIRT1, a major deacetylase that influences energy metabolism and longevity (136, 144). Together, these data indicate that both the control of the cellular metabolism and mTORC1 activation by IFNγ may be central mediators of this pleiotropic proinflammatory molecule.