No abstract

The Coronaviridae are a family of viruses that cause disease in humans ranging from mild respiratory infection to potentially lethal acute respiratory distress syndrome. Finding host factors common to multiple coronaviruses could facilitate the development of therapies to combat current and future coronavirus pandemics. Here, we conducted genome-wide CRISPR screens in cells infected by SARS-CoV-2 as well as two seasonally circulating common cold coronaviruses, OC43 and 229E. This approach correctly identified the distinct viral entry factors ACE2 (for SARS-CoV-2), aminopeptidase N (for 229E) and glycosaminoglycans (for OC43). Additionally, we identified phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis as critical host pathways supporting infection by all three coronaviruses. By contrast, the lysosomal protein TMEM106B appeared unique to SARS-CoV-2 infection. Pharmacological inhibition of phosphatidylinositol kinases and cholesterol homeostasis reduced replication of all three coronaviruses. These findings offer important insights for the understanding of the coronavirus life cycle and the development of host-directed therapies.

No abstract

Gene regulatory networks (GRNs) drive developmental and cellular differentiation, and variation in their architectures gives rise to morphological diversity. Pioneering studies in Aspergillus fungi, coupled with subsequent work in other filamentous fungi, have shown that the GRN governed by the BrlA, AbaA, and WetA proteins controls the development of the asexual fruiting body, or conidiophore. A specific aspect of conidiophore development is the production of phialides, conidiophore structures that are under the developmental control of AbaA and function to repetitively generate spores. Fungal genome sequencing has revealed that some filamentous fungi lack abaA, and also produce asexual structures that lack phialides, raising the hypothesis that abaA loss is functionally linked to diversity in asexual fruiting body morphology. To examine this hypothesis, we carried out an extensive search for the abaA gene across 241 genomes of species from the fungal subphylum Pezizomycotina. We found that abaA was independently lost in four lineages of Eurotiomycetes, including from all sequenced species within the order Onygenales, and that all four lineages that have lost abaA also lack the ability to form phialides. Genetic restoration of abaA from Aspergillus nidulans into Histoplasma capsulatum, a pathogenic species from the order Onygenales that lacks an endogenous copy of abaA, did not alter Histoplasma conidiation morphology but resulted in a marked increase in spore viability. We also discovered that species lacking abaA contain fewer AbaA binding motifs in the regulatory regions of orthologs of some AbaA target genes, suggesting that the asexual fruiting body GRN of organisms that have lost abaA has likely been rewired. Our results provide an illustration of how repeated losses of a key regulatory transcription factor have contributed to the diversity of an iconic fungal morphological trait.

Author Summary 46Fungi exhibit tremendous variation in their asexual fruiting bodies. For example, whereas some 47 fungi form complex fruiting bodies whose tips repeatedly generate and release spores, others 48 produce single spores in the absence of a specialized structure. To gain insights into the 49 molecular differences that underpin fungal asexual fruiting body diversity, we examined the 50 genomes of hundreds of filamentous fungi for the presence of abaA, a master regulatory gene 51 previously shown to control the development of fungal asexual fruiting bodies. We found that 52 abaA was repeatedly lost during fungal evolution, including in a lineage of human pathogenic 53 fungi, and that the loss of the gene was always associated with the loss of specialized structures 54 in fungal asexual fruiting bodies. Reintroduction of abaA into the human pathogenic fungus 55Histoplasma capsulatum, which normally lacks the regulator, did not result in a change in the 56 spore-producing structure but did increase spore outgrowth. Based on these results, we 57 hypothesize that the loss of the master regulatory gene abaA has contributed to the observed 58 diversity of fungal fruiting body morphology. This work advances our understanding of how 59 fungal developmental networks evolve over time and advances our understanding of how 60 infectious spores form in pathogenic fungi. 61