bims-mevinf Biomed News
on Metabolism in viral infections
Issue of 2023–07–16
twelve papers selected by
Alexander Ivanov, Engelhardt Institute of Molecular Biology



  1. Cancers (Basel). 2023 Jun 29. pii: 3412. [Epub ahead of print]15(13):
      The metabolism of cancer cells and Epstein-Barr virus (EBV) infected cells have remarkable similarities. Cancer cells frequently reprogram metabolic pathways to augment their ability to support abnormal rates of proliferation and promote intra-organismal spread through metastatic invasion. On the other hand, EBV is also capable of manipulating host cell metabolism to enable sustained growth and division during latency as well as intra- and inter-individual transmission during lytic replication. It comes as no surprise that EBV, the first oncogenic virus to be described in humans, is a key driver for a significant fraction of human malignancies in the world (~1% of all cancers), both in terms of new diagnoses and attributable deaths each year. Understanding the contributions of metabolic pathways that underpin transformation and virus replication will be important for delineating new therapeutic targets and designing nutritional interventions to reduce disease burden. In this review, we summarise research hitherto conducted on the means and impact of various metabolic changes induced by EBV and discuss existing and potential treatment options targeting metabolic vulnerabilities in EBV-associated diseases.
    Keywords:  EBV; Epstein–Barr virus; cancer biology; cancer metabolism; latency; lytic infection; oncometabolic pathways
    DOI:  https://doi.org/10.3390/cancers15133412
  2. Anal Bioanal Chem. 2023 Jul 13.
      Emerging and re-emerging zoonotic viral diseases continue to significantly impact public health. Of particular interest are enveloped viruses (e.g., SARS-CoV-2, the causative pathogen of COVID-19), which include emerging pathogens of highest concern. Enveloped viruses contain a viral envelope that encapsulates the genetic material and nucleocapsid, providing structural protection and functional bioactivity. The viral envelope is composed of a coordinated network of glycoproteins and lipids. The lipid composition of the envelope consists of lipids preferentially appropriated from host cell membranes. Subsequently, changes to the host cell lipid metabolism and an accounting of what lipids are changed during viral infection provide an opportunity to fingerprint the host cell's response to the infecting virus. To address this issue, we comprehensively characterized the lipid composition of VeroE6-TMPRSS2 cells infected with SARS-CoV-2. Our approach involved using an innovative solid-phase extraction technique to efficiently extract cellular lipids combined with liquid chromatography coupled to high-resolution tandem mass spectrometry. We identified lipid changes in cells exposed to SARS-CoV-2, of which the ceramide to sphingomyelin ratio was most prominent. The identification of a lipid profile (i.e., lipid fingerprint) that is characteristic of cellular SARS-CoV-2 infection lays the foundation for targeting lipid metabolism pathways to further understand how enveloped viruses infect cells, identifying opportunities to aid antiviral and vaccine development.
    Keywords:  Mass spectrometry; SARS-CoV-2; SPE lipid extraction; Sphingolipids
    DOI:  https://doi.org/10.1007/s00216-023-04825-1
  3. PLoS Pathog. 2023 Jul;19(7): e1010986
      Influenza A virus (IAV), like any other virus, provokes considerable modifications of its host cell's metabolism. This includes a substantial increase in the uptake as well as the metabolization of glucose. Although it is known for quite some time that suppression of glucose metabolism restricts virus replication, the exact molecular impact on the viral life cycle remained enigmatic so far. Using 2-deoxy-d-glucose (2-DG) we examined how well inhibition of glycolysis is tolerated by host cells and which step of the IAV life cycle is affected. We observed that effects induced by 2-DG are reversible and that cells can cope with relatively high concentrations of the inhibitor by compensating the loss of glycolytic activity by upregulating other metabolic pathways. Moreover, mass spectrometry data provided information on various metabolic modifications induced by either the virus or agents interfering with glycolysis. In the presence of 2-DG viral titers were significantly reduced in a dose-dependent manner. The supplementation of direct or indirect glycolysis metabolites led to a partial or almost complete reversion of the inhibitory effect of 2-DG on viral growth and demonstrated that indeed the inhibition of glycolysis and not of N-linked glycosylation was responsible for the observed phenotype. Importantly, we could show via conventional and strand-specific qPCR that the treatment with 2-DG led to a prolonged phase of viral mRNA synthesis while the accumulation of genomic vRNA was strongly reduced. At the same time, minigenome assays showed no signs of a general reduction of replicative capacity of the viral polymerase. Therefore, our data suggest that the significant reduction in IAV replication by glycolytic interference occurs mainly due to an impairment of the dynamic regulation of the viral polymerase which conveys the transition of the enzyme's function from transcription to replication.
    DOI:  https://doi.org/10.1371/journal.ppat.1010986
  4. Vet Microbiol. 2023 Jun 30. pii: S0378-1135(23)00178-5. [Epub ahead of print]284 109826
      Pseudorabies virus (PRV) preferably invades neural tissue and various organs, whereupon may result in multisystemic lesions. Pyroptosis mediated by proteolytic cleavage of gasdermin D (GSDMD) by inflammatory caspases (caspase-1/4/5/11), is closely associated with the activation of inflammasomes, a multiprotein proinflammatory complex. However, further studies on the mechanisms regarding PRV-induced pyroptosis in its natural host are required. Herein, it is demonstrated that PRV infection triggered GSDMD- not GSDME-mediated pyroptosis in porcine alveolar macrophage cells, resulting in increased secretion of IL-1β and LDH. During this process, caspase-1 was activated and participated in the cleaving of GSDMD. Interestingly, we found that the viral replication process or protein production is required to induce pyroptotic cell death. Also, our findings showed that PRV triggered NLRP3 inflammasome activation, which was associated with the production of reactive oxygen species (ROS) and potassium efflux. In addition to the NLRP3 inflammasome, the IFI16 inflammasome was also activated. Importantly, the NLRP3- and IFI16- inflammasomes were both involved in pyroptosis during PRV infection. Finally, we observed that the cleaved GSDMD, activated caspase-1, increased IFI16 levels, and elevated NLRP3 protein in PRV-infected tissues (brain and lung), supporting the occurrence of pyroptosis and the activation of NLRP3- and IFI16- inflammasome in PRV-infected pigs. This research advances our understanding of the PRV-mediated inflammatory response and cell death pathways, providing a deeper knowledge of effective treatments for pseudorabies.
    Keywords:  IFI16 inflammasome; NLRP3 inflammasome; Pseudorabies virus; Pyroptosis
    DOI:  https://doi.org/10.1016/j.vetmic.2023.109826
  5. mBio. 2023 Jul 12. e0102023
      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the causative agent of the recent COVID-19 pandemic, continues representing one of the main health concerns worldwide. Autophagy, in addition to its role in cellular homeostasis and metabolism, plays an important part for the host antiviral immunity. However, viruses including SARS-CoV-2 have evolved diverse mechanisms to not only overcome autophagy's antiviral pressure but also manipulate its machinery in order to enhance viral replication and propagation. Here, we discuss our current knowledge on the impact that autophagy exerts on SARS-CoV-2 replication, as well as the different counteracting measures that this virus has developed to manipulate autophagy's complex machinery. Some of the elements regarding this interplay may become future therapeutic targets in the fight against SARS-CoV-2.
    Keywords:  COVID-19; SARS-CoV-2; autophagy; innate immunity; therapeutic targets
    DOI:  https://doi.org/10.1128/mbio.01020-23
  6. Mol Cell. 2023 Jun 29. pii: S1097-2765(23)00467-7. [Epub ahead of print]
      Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remodels the endoplasmic reticulum (ER) to form replication organelles, leading to ER stress and unfolded protein response (UPR). However, the role of specific UPR pathways in infection remains unclear. Here, we found that SARS-CoV-2 infection causes marginal activation of signaling sensor IRE1α leading to its phosphorylation, clustering in the form of dense ER-membrane rearrangements with embedded membrane openings, and XBP1 splicing. By investigating the factors regulated by IRE1α-XBP1 during SARS-CoV-2 infection, we identified stress-activated kinase NUAK2 as a novel host-dependency factor for SARS-CoV-2, HCoV-229E, and MERS-CoV entry. Reducing NUAK2 abundance or kinase activity impaired SARS-CoV-2 particle binding and internalization by decreasing cell surface levels of viral receptors and viral trafficking likely by modulating the actin cytoskeleton. IRE1α-dependent NUAK2 levels were elevated in SARS-CoV-2-infected and bystander non-infected cells, promoting viral spread by maintaining ACE2 cell surface levels and facilitating virion binding to bystander cells.
    Keywords:  ACE2; CLEM; IRE1a ultrastructure; SARS-CoV-2; TMPRSS2; coronavirus; membrane dynamics; trafficking; unfolded protein response; virus entry
    DOI:  https://doi.org/10.1016/j.molcel.2023.06.020
  7. Virol J. 2023 07 11. 20(1): 145
       BACKGROUND: Cell responses to different stress inducers are efficient mechanisms that prevent and fight the accumulation of harmful macromolecules in the cells and also reinforce the defenses of the host against pathogens. Vaccinia virus (VACV) is an enveloped, DNA virus, belonging to the Poxviridae family. Members of this family have evolved numerous strategies to manipulate host responses to stress controlling cell survival and enhancing their replicative success. In this study, we investigated the activation of the response signaling to malformed proteins (UPR) by the VACV virulent strain-Western Reserve (WR)-or the non-virulent strain-Modified Vaccinia Ankara (MVA).
    METHODS: Through RT-PCR RFLP and qPCR assays, we detected negative regulation of XBP1 mRNA processing in VACV-infected cells. On the other hand, through assays of reporter genes for the ATF6 component, we observed its translocation to the nucleus of infected cells and a robust increase in its transcriptional activity, which seems to be important for virus replication. WR strain single-cycle viral multiplication curves in ATF6α-knockout MEFs showed reduced viral yield.
    RESULTS: We observed that VACV WR and MVA strains modulate the UPR pathway, triggering the expression of endoplasmic reticulum chaperones through ATF6α signaling while preventing IRE1α-XBP1 activation.
    CONCLUSIONS: The ATF6α sensor is robustly activated during infection while the IRE1α-XBP1 branch is down-regulated.
    Keywords:  Cell stress; Endoplasmic reticulum stress; MVA; Unfolded protein response; Vaccinia virus; WR
    DOI:  https://doi.org/10.1186/s12985-023-02122-y
  8. Front Virol. 2021 Sep;pii: 720760. [Epub ahead of print]1
       Background: Multiple studies have shown both induction and inhibition of autophagy during Zika virus (ZIKV) infection. While some have proposed mechanisms by which autophagic dysregulation might facilitate ZIKV vertical transmission, there is a lack of in situ data in human and non-human primate models. This is an especially pertinent question as autophagy-inhibitors, such as hydroxychloroquine, have been proposed as potential therapeutic agents aimed at preventing vertical transmission of ZIKV and other RNA viruses.
    Objectives: Given the paucity of pre-clinical data in support of either autophagic enhancement or inhibition of placental ZIKV viral infection, we sought to assess cellular, spatial, and temporal associations between placental ZIKV infection and measures of autophagy in human primary cell culture and congenital infection cases, as well as an experimental non-human primate (marmoset, Callithrix jacchus) model.
    Study Design: Primary trophoblast cells were isolated from human placentae (n = 10) and infected in vitro with ZIKV. Autophagy-associated gene expression (ULK-1, BECN1, ATG5, ATG7, ATG12, ATG16L1, MAP1LC3A, MAP1LC3B, p62/SQSTM1) was then determined by TaqMan qPCR to determine fold-change with ZIKV-infection. In in vivo validation experiments, autophagy genes LC3B and p62/SQSTM1 were probed using in situ hybridization (ISH) in the placentae of human Congenital Zika Syndrome (CZS) cases (n = 3) and ZIKV-infected marmoset placenta (n = 1) and fetal tissue (n = 1). Infected and uninfected villi were compared for mean density and co-localization of autophagic protein markers.
    Results: Studies of primary cultured human trophoblasts revealed decreased expression of autophagy genes ATG5 and p62/SQSTM1 in ZIKV-infected trophoblasts [ATG5 fold change (±SD) 0.734-fold (±0.722), p = 0.036; p62/SQSTM1 0.661-fold (±0.666), p = 0.029]. Histologic examination by ISH and immunohistochemistry confirmed spatial association of autophagy and ZIKV infection in human congenital infection cases, as well as marmoset placental and fetal tissue samples. When quantified by densitometric data, autophagic protein LC3B, and p62/SQSTM1 expression in marmoset placenta were significantly decreased in in situ ZIKV-infected villi compared to less-infected areas [LC3B mean 0.951 (95% CI, 0.930-0.971), p = 0.018; p62/SQSTM1 mean 0.863 (95% CI, 0.810-0.916), p = 0.024].
    Conclusion: In the current study, we observed that in the non-transformed human and non-human primate placenta, disruption (specifically down-regulation) of autophagy accompanies later ZIKV replication in vitro, in vivo, and in situ. The findings collectively suggest that dysregulated autophagy spatially and temporally accompanies placental ZIKV replication, providing the first in situ evidence in relevant primate pre-clinical and clinical models for the importance of timing of human therapeutic strategies aimed at agonizing/antagonizing autophagy. These studies have likely further implications for other congenitally transmitted viruses, particularly the RNA viruses, given the ubiquitous nature of autophagic disruption and dysregulation in host responses to viral infection during pregnancy.
    Keywords:  Zika virus; autophagy; autophagy and viral infection; congenital Zika syndrome; placental viral infection; viral transmission
    DOI:  https://doi.org/10.3389/fviro.2021.720760
  9. bioRxiv. 2023 Jun 30. pii: 2023.06.29.546885. [Epub ahead of print]
      G3BP1/2 are paralogous proteins that promote stress granule formation in response to cellular stresses, including viral infection. G3BP1/2 are prominent interactors of the nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the functional consequences of the G3BP1-N interaction in the context of viral infection remain unclear. Here we used structural and biochemical analyses to define the residues required for G3BP1-N interaction, followed by structure-guided mutagenesis of G3BP1 and N to selectively and reciprocally disrupt their interaction. We found that mutation of F17 within the N protein led to selective loss of interaction with G3BP1 and consequent failure of the N protein to disrupt stress granule assembly. Introduction of SARS-CoV-2 bearing an F17A mutation resulted in a significant decrease in viral replication and pathogenesis in vivo, indicating that the G3BP1-N interaction promotes infection by suppressing the ability of G3BP1 to form stress granules.
    DOI:  https://doi.org/10.1101/2023.06.29.546885
  10. Antiviral Res. 2023 Jul 08. pii: S0166-3542(23)00144-4. [Epub ahead of print]216 105666
      Zika virus (ZIKV) has garnered global attention due to its association with severe congenital defects including microcephaly. However, there are no licensed vaccines or drugs against ZIKV infection. Pregnant women have the greatest need for treatment, making drug safety crucial. Alpha-linolenic acid (ALA), a polyunsaturated ω-3 fatty acid, has been used as a health-care product and dietary supplement due to its potential medicinal properties. Here, we demonstrated that ALA inhibits ZIKV infection in cells without loss of cell viability. Time-of-addition assay revealed that ALA interrupts the binding, adsorption, and entry stages of ZIKV replication cycle. The mechanism is probably that ALA disrupts membrane integrity of the virions to release ZIKV RNA, inhibiting viral infectivity. Further examination revealed that ALA inhibited DENV-2, HSV-1, influenza virus and SARS-CoV-2 infection dose-dependently. ALA is a promising broad-spectrum antiviral agent.
    Keywords:  Alpha-linolenic acid; Antiviral; Entry; Membrane integrity; Zika virus
    DOI:  https://doi.org/10.1016/j.antiviral.2023.105666
  11. J Biol Chem. 2023 Jul 07. pii: S0021-9258(23)02056-2. [Epub ahead of print] 105028
      As part of the antiviral response, cells activate the expressions of type I interferons (IFNs) and proinflammatory mediators to control viral spreading. Viral infections can impact DNA integrity, however, how DNA damage-repair coordinates antiviral response remains elusive. Here we report Nei-like DNA glycosylase 2 (NEIL2), a transcription-coupled DNA repair protein, actively recognizes the oxidative DNA substrates induced by respiratory syncytial virus (RSV) infection to set the threshold of IFN-β expression. Our results show that NEIL2 antagonizes nuclear factor κB (NF-κB) acting on the IFN-β promoter early after infection, thus limiting gene expression amplified by type I IFNs. Mice lacking Neil2 are far more susceptible to RSV-induced illness with exuberant expression of proinflammatory genes and tissue damage, and the administration of NEIL2 protein into the airway corrected these defects. These results suggest a safeguarding function of NEIL2 in controlling IFN-β levels against RSV infection. Due to the short and long term side effects of type I IFNs applied in antiviral therapy, NEIL2 may provide an alternative not only for ensuring genome fidelity, but also for controlling immune responses.
    Keywords:  DNA damage; NF-κB; antiviral response; inflammation; innate immunity; oxidative stress; transcription regulation
    DOI:  https://doi.org/10.1016/j.jbc.2023.105028
  12. Nat Commun. 2023 Jul 13. 14(1): 4159
      Ebola virus (EBOV) infection induces the formation of membrane-less, cytoplasmic compartments termed viral factories, in which multiple viral proteins gather and coordinate viral transcription, replication, and assembly. Key to viral factory function is the recruitment of EBOV polymerase, a multifunctional machine that mediates transcription and replication of the viral RNA genome. We show that intracellularly reconstituted EBOV viral factories are biomolecular condensates, with composition-dependent internal exchange dynamics that likely facilitates viral replication. Within the viral factory, we found the EBOV polymerase clusters into foci. The distance between these foci increases when viral replication is enabled. In addition to the typical droplet-like viral factories, we report the formation of network-like viral factories during EBOV infection. Unlike droplet-like viral factories, network-like factories are inactive for EBOV nucleocapsid assembly. This unique view of EBOV propagation suggests a form-to-function relationship that describes how physical properties and internal structures of biomolecular condensates influence viral biogenesis.
    DOI:  https://doi.org/10.1038/s41467-023-39821-7