Juan Fontana

The Orthobunyavirus genus of arthropod-borne segmented RNA viruses comprises important pathogens including the human-infecting Oropouche virus and ruminant-infecting Schmallenberg virus (SBV). The prototypical Bunyamwera orthobunyavirus (BUNV) possesses envelope-embedded glycoprotein Gn-Gc tripodal spikes, of which the ectodomains mediate virus entry, while endodomains interact with nucleoprotein (NP) enwrapped genome segments driving virion assembly. Interestingly, BUNV Gc head/stalk domains are redundant for virus growth in mammalian cells, consistent with isolations of SBV from ruminants bearing head/stalk deletions. However, these domains appear strictly maintained in orthobunyavirus isolations from arthropods in nature. To investigate the molecular mechanism that underlines this discrepancy, we compared the multiplication characteristics of wildtype BUNV (BUNV-WT) with a Gc head/stalk deleted BUNV (BUNV-∆7). In mammalian cells BUNV-WT and BUNV-∆7 grew to equivalent titres, whereas in insect cells BUNV-∆7 titres were 1000-fold lower and strikingly produced no virions following blood meal infection of Aedes mosquitoes. To understand this insect-specific restriction in virion production, we showed the intracellular abundance of BUNV-WT and BUNV-∆7 Gc and NP components were equivalent, suggesting the deletion impacted post-translational stages of the infection cycle. To explore this, we investigated Gc and ∆7-Gc interactions during BUNV-WT and BUNV-∆7 infections of both insect and mammalian cells by co-immunoprecipitation and multiplex mass spectrometry, revealing ∆7-Gc exhibited markedly reduced NP interactions in insect cells, potentially indicating reduced segment interactions during assembly. We hypothesize that the Gc head/stalk performs an insect cell-specific role in segment recruitment during virion formation, and that maintenance in nature of full-length Gc is due to this essential role in the insect host.

Bunyamwera virus (BUNV) is the prototypical member of the Peribunyaviridae family of arthropod-borne viruses and possesses a genome comprising three segments of negative-sense RNA, named small, medium and large. The medium segment encodes a polyprotein that is processed to form Gn and Gc spikes and a non-structural protein, NSm. The role of NSm during replication in mammalian cells is poorly characterized, although it associates with a Golgi-derived structure called the virus factory (VF), the site of BUNV genome replication and virion assembly. To further define NSm function, we generated an epitope-tagged BUNV and used co-immunoprecipitation and quantitative proteomics to identify host interacting partners. NSm interacted with BCL-2 interacting protein 1 (BNIP1), a SNARE protein involved in COPI vesicle trafficking, with the importance of this interaction demonstrated by siRNA-mediated knockdown of BNIP1 expression, which significantly reduced BUNV gene expression and virion production. Interestingly, NSm also interacted with components of the NRZ complex, involved in COPI vesicle tethering in association with BNIP1, and inhibition of COPI complex formation resulted in loss of NSm expression. Taken together, our results identify BNIP1 as a host cell factor necessary for efficient BUNV replication and suggest the cellular localization of NSm at the VF is COPI-dependent.

Throughout eukaryotic evolution, the structure of the ribosome has been highly conserved, featuring 80 common protein gene families. However, in many eukaryotes, paralogs of these proteins are present. Specialised ribosomes have been documented across diverse groups of eukaryotes where they play an important role in the regulation of translation of specific mRNAs. In the case of specialised ribosomes it has been documented that assembled ribosomes that contain specific paralogs can directly affect translational output. This has been proposed to contribute to the regulation of complex responses to environmental change and to coordinate cell-type specific physiology. This poses the question of whether ribosome specialisation principally emerges under an adaptive or neutral model of evolution. Using gene tree-species tree reconciliation, we test competing hypotheses regarding the evolutionary drivers of ribosome specialisation. We determine that examples of specialisation tend to emerge by independent duplication of the same ribosomal proteins in different lineages. We show that pathways to specialisation through paralog formation have arisen independent of: (i) paralog location within the 3D ribosome complex, and (ii) positive selection in these paralogs. We determine that the generalisable model of best fit for the evolution of paralog-mediated eukaryotic ribosomal specialisation is one of constructive neutral evolution. In lineages with small effective population sizes and increased complexity, the emergence and retention of ribosomal protein paralogs has provided the raw material for ratcheting and the emergence of translational regulation at the level of the ribosome.

Foot-and-mouth disease virus (FMDV) remains an ever-present threat to the economic stability of the livestock industry and global trade. Despite this, questions remain regarding the fundamental biology underpinning the replication of this virus. Here, we examine components of the FMDV replication machinery (focussing on the viral 2C protein) and investigate the conditions under which they interact. Using a novel 2C antibody in co-immunoprecipitation experiments under different conditions followed by MS, we identify membrane-associated proteins (such as the viral proteins 2B and precursors of 3A, which are poorly characterized proteins involved in viral replication) along with endoplasmic reticulum (ER)-associated host proteins. In addition, our analysis shows that a number of nuclear factors interact with 2C in a membrane-independent manner, potentially being co-opted to support RNA replication of the virus. Furthermore, we demonstrate that the membrane-mediated interaction of 2C with several viral proteins (including key members of the replication machinery and viral RNA) is maintained following ultracentrifugation, suggesting that these co-sediment as part of a complex. Our data suggest that the replication complex is ER-derived and highlight several new avenues of investigation for the disruption of the FMDV lifecycle.

The Nairoviridae family of segmented negative-sense RNA viruses includes the serious human pathogen Crimean-Congo haemorrhagic fever virus (CCHFV), associated with a case/fatality rate of up to 40% for which no approved vaccines or treatments exist. Nairoviruses internalize via endocytosis and pass through the endolysosomal network, exploiting the changing ionic environment to promote envelope fusion. Fusion is influenced by hydrogen (H ⁺ ) and potassium ions (K ⁺ ), which increase in concentration as endosomes mature, regulated by host ion channels. Using the model nairovirus Hazara virus (HAZV) of the CCHFV serogroup, we performed an siRNA screen to identify cellular ion channels involved in nairovirus infection. Most high-ranking hits belonged to K ⁺ and calcium (Ca ²⁺ ) channel families. Consistent with this, we showed that clinically-approved K ⁺ channel blockers quinidine, quinine and dronedarone and clinically-approved Ca ²⁺ channel blockers tetrandrine and nifedipine significantly reduced HAZV activities. To further probe the role of K ⁺ in HAZV infection, we used time-of-addition studies, showing K ⁺ was required during entry. Biochemical experiments showed K ⁺ expanded the pH range that promoted entry, potentially allowing endosome escape deeper within the endolysosomal network. These results show clinically-approved channel blockers effectively inhibit HAZV replication, suggesting repurposing existing therapies may represent promising avenues to block nairovirus infection.

Adhirons are small, antibody-like proteins expressed in bacteria that bind to biological targets with high affinity. Since their discovery, Adhirons have been isolated against over 350 targets, and they can be used for many research applications. However, their therapeutic application is at present in its early stages, hence the interest in developing novel small molecules to mimic their effect. We develop a pipeline for small molecule discovery where Adhirons act as starting templates in a ligand-based virtual screening workflow. For proof of concept, we use Adhirons against two viral systems: Crimean-Congo Haemorrhagic Fever Virus and Influenza A Virus. In both cases, a hit was identified from the mimics using biophysical and cell-based assays, highlighting how Adhirons, commercial libraries and structural approaches can be combined to accelerate small molecule inhibitor discovery of viruses.

The Orthobunyavirus genus of arthropod-borne segmented RNA viruses comprises several important pathogens including the human-infecting Oropouche virus and animal-infecting Schmallenberg virus (SBV). The prototypical Bunyamwera orthobunyavirus (BUNV) possesses envelope-embedded glycoprotein spikes, with Gc head and stalk domains forming distinctive tripods covering the envelope-proximal Gn. Spike ectodomains mediate virus entry, while endodomains interact with nucleoprotein (NP) enwrapped genome segments to mediate virion assembly. Interestingly, BUNV Gc head/stalk domains are redundant for virus growth in mammalian cells, consistent with isolations of SBV from animals bearing head/stalk deletions. However, orthobunyavirus isolations from arthropods in nature appear to maintain these domains strictly. To investigate this discrepancy, we compared the multiplication characteristics of wildtype BUNV (BUNV-WT) with a Gc head/stalk deleted BUNV (BUNV-Δ7). In mammalian cells BUNV-WT and BUNV-Δ7 grew to equivalent titres, whereas BUNV-Δ7 titres from insect cells were 1000-fold lower than BUNV-WT and strikingly produced no virions following blood meal infection of Aedes mosquitoes. To understand this insect-specific restriction in virion production, we showed the intracellular abundance of BUNV-WT and BUNV-Δ7 Gc and NP components were equivalent, suggesting Δ7-Gc was assembly-deficient. To explore this, we investigated Gc and Δ7-Gc interactions during BUNV-WT and BUNV-Δ7 infections of both insect and mammalian cells by co-immunoprecipitation and multiplex mass spectrometry, revealing Δ7-Gc exhibited markedly reduced NP interactions in insect cells. We propose Gc recruits genome segments during virion assembly and that the complete Gc head/stalk assembly is maintained in nature due to its essential role in the insect host. IMPORTANCE: Orthobunyaviruses are arthropod-borne viruses that cause severe disease in humans and animals, including congenital malformations and abortions. Orthobunyavirus Gn and Gc glycoproteins form spikes, which mediate entry and genome recruitment during assembly. In nature, OBVs bearing large deletions within Gc head/stalk domains have been isolated from animals, yet the head/stalk domains appear to be strictly maintained within insects. To investigate this discrepancy, we compared the multiplication of Bunyamwera orthobunyavirus (BUNV-WT) with head/stalk-deleted variant (BUNV-Δ7). In mammalian cells both viruses reached similar titres, but strikingly BUNV-Δ7 failed to produce virions in both insect cells and Aedes mosquitoes. We showed this was because BUNV-Δ7 failed to assemble new virions, revealing its head/stalk-deleted Gc was deficient in interactions with genome components. We propose that Gc drives species-specific interactions with genome segments during virion assembly, explaining why Gc head/stalk domains are conserved in nature due to their essential role in the insect host.

: The complement cascade is part of the first line of defence against viral infections, and many viruses have evolved to block it. For example, glycoprotein C (gC) from Herpes Simplex Virus 1 and 2 (gC1 and gC2) facilitates infection by modulating the complement cascade through an interaction with C3b. gC is also involved in attachment and other viral processes. However, our understanding of the molecular mechanisms of gC have been limited due to the absence of a structure. AlphaFold predicts that gC contains a disordered N-terminus and three immunoglobulin-like domains. Here, we generated various gC2 constructs and demonstrated that gC2 domains 1 and 2 are necessary and sufficient to interact with C3b and block the alternative pathway. A gC2 construct lacking the N-terminus in complex with C3b was characterised by cryo-EM at 3.6 Å, providing the first structure for gC2, and revealing that the interaction is predominantly driven by gC2 domain 2 and the MG8 domain of C3b. This structure was confirmed by cross-linking mass spectrometry and by using C3b-blocking antibodies that recognised gC2 linear epitopes at the interface with C3b. Overall, the gC-C3b interaction is different from other C3b-interacting partners, providing a novel mechanism to regulate the complement cascade.

Adhirons are small, antibody-like proteins expressed in bacteria that bind to biological targets with high affinity. Since their discovery, Adhirons have been isolated against over 350 targets, and they can be used for many research applications. However, their therapeutic application is at present in its early stages, hence the interest in developing novel small molecules to mimic their effect. We developed a pipeline for small molecule discovery where Adhirons act as starting templates in a ligand-based virtual screening workflow. For proof of concept, we used Adhirons against two viral systems: Crimean-Congo Haemorrhagic Fever Virus and Influenza A Virus. In both cases, a hit was identified from the mimics using biophysical and cell-based assays, highlighting how Adhirons, commercial libraries and structural approaches can be combined to accelerate small molecule inhibitor discovery of viruses.