Globally defining the effects of mutations in a picornavirus capsid

Mattenberger, Florian; Latorre, Víctor; Tirosh, Omer; Stern, Adi; Geller, Ron

doi:10.7554/elife.64256

“…Vesicular stomatitis virus (VSV) encoding mCherry was kindly provided by Dr. Rafael Sanjuan (University of Valencia). CVB3 was generated as previously described ( Mattenberger et al, 2021 ). The VCP/p97 inhibitor CB-5083 (CAS: 1542705-92-9; Cayman Chemicals, United States) and the hsp90 inhibitor 17-DMAG (CA 467214-20-6; LC Laboratories) were dissolved in DMSO and resazurin (CAS: 62758-13-8; Sigma-Aldrich, United States) was dissolved in water.…”

Section: Methodsmentioning

confidence: 99%

Identification of Cytoplasmic Chaperone Networks Relevant for Respiratory Syncytial Virus Replication

Latorre

¹

,

Geller

²

2022

Self Cite

View full text Add to dashboard Cite

RNA viruses have limited coding capacity and must therefore successfully subvert cellular processes to facilitate their replication. A fundamental challenge faced by both viruses and their hosts is the ability to achieve the correct folding and assembly of their proteome while avoiding misfolding and aggregation. In cells, this process is facilitated by numerous chaperone systems together with a large number of co-chaperones. In this work, we set out to define the chaperones and co-chaperones involved in the replication of respiratory syncytial virus (RSV). Using an RNAi screen, we identify multiple members of cellular protein folding networks whose knockdown alters RSV replication. The reduced number of chaperones and co-chaperones identified in this work can facilitate the unmasking of specific chaperone subnetworks required for distinct steps of the RSV life cycle and identifies new potential targets for antiviral therapy. Indeed, we show that the pharmacological inhibition of one of the genes identified in the RNAi screen, valosin-containing protein (VCP/p97), can impede the replication of RSV by interfering with the infection cycle at multiple steps.

show abstract

“…Vesicular stomatitis virus (VSV) encoding mCherrry was kindly provided by Dr. Rafael Sanjuan (University of Valencia). CVB3 was generated as previously described (Mattenberger et al ., 2021). The VCP/p97 inhibitor CB-5083 (CAS: 1542705-92-9; Cayman Chemicals) and the hsp90 inhibitor 17-DMAG (CA 467214-20-6; LC Laboratories) were dissolved in DMSO and resazurin (CAS: 62758-13-8; Sigma-Aldrich) was dissolved in water.…”

Section: Methodsmentioning

confidence: 99%

Identification of cytoplasmic chaperone networks relevant for respiratory syncytial virus replication

Latorre

¹

,

Geller

²

2022

Preprint

Self Cite

0

View full text Add to dashboard Cite

RNA viruses have limited coding capacity and must therefore successfully subvert cellular processes to facilitate their replication. A fundamental challenge faced by both viruses and their hosts is the ability to achieve the correct folding and assembly of their proteome while avoiding misfolding and aggregation. In cells, this process is facilitated by numerous chaperone systems together with a large number of co-chaperones. In this work, we set out to define the chaperones and co-chaperones involved in the replication of respiratory syncytial virus (RSV). Using an RNAi screen, we identify multiple members of cellular protein folding networks whose knockdown alters RSV replication. The reduced number of chaperones and co-chaperones identified in this work can facilitate the unmasking of specific chaperone subnetworks required for distinct steps of the RSV life cycle and identifies new potential targets for antiviral therapy. Indeed, we show that the pharmacological inhibition of one of the genes identified in the RNAi screen, valosin-containing protein (VCP/p97), can impede the replication of RSV by interfering with the infection cycle at multiple steps.

show abstract

“…It is Random forest algorithms (RFA) are a type of decision tree-based analysis, providing a relatively hypothesis-free approach to interrogating complex data sets. The method has been applied widely, including in host tropism studies in influenza (13), to identify molecules inhibiting flaviviruses (14), to analyse mutational fitness effects in picornaviruses (15), and in the identification of genes related to immunogenicity and pathogenicity in Streptococcus pneumoniae infection (16,17).…”

Section: Methodsmentioning

confidence: 99%

Polymorphisms Predicting Phylogeny in Hepatitis B Virus (HBV)

Lourenço

¹

,

McNaughton

²

,

Pley

³

et al. 2022

Preprint

0

View full text Add to dashboard Cite

Hepatitis B viruses (HBV) are compact viruses with circular genomes of ∼3.2kb in length. Four genes (HBx, Core, Surface and Polymerase) generating seven products are encoded on overlapping reading frames. Ten HBV genotypes have been characterised (A-J), which may account for differences in transmission, outcomes of infection, and treatment response. However, HBV genotyping is rarely undertaken, and sequencing remains inaccessible in many settings. We used a machine learning approach based on random forest algorithms (RFA) to assess which amino acid (aa) sites in the genome are most informative for determining genotype. We downloaded 5496 genome-length HBV sequences from a public database, excluding recombinant sequences, regions with conserved indels, and genotypes I/J. Each gene was separately translated into aa, and the proteins concatenated into a single sequence (length 1614aa). Using RFA, we searched for aa sites predictive of genotype, and assessed co-variation among the sites with a Mutual Information (MI)-based method. We were able to discriminate confidently between genotypes A-H using 10 aa sites. 5/10 sites were identified in Polymerase (Pol), of which 4/5 were in the spacer domain, and a single site in reverse transcriptase. A further 4/10 sites were located in Surface protein, and a single site in HBx. There were no informative sites in Core. Properties of the aa were generally not conserved between genotypes at informative sites. Co-variation analysis identified 55 pairs of highly-linked sites. Three RFA-identified sites were represented across all pairs (two sites in spacer, and one in HBx). Residues that co-vary with these sites are concentrated in the small HBV surface gene. We also observe a cluster of sites adjacent to the Surface promoter region that co-vary with a spacer residue. Overall, we have shown that RFA analysis is a powerful tool for identifying aa sites that predict HBV lineage, with an unexpectedly high number of such sites in the spacer domain, which has conventionally been viewed as unimportant for structure or function. Our results improve ease of genotype prediction from limited regions of HBV sequence, and may have implications for understanding HBV evolution and the role of the spacer domain.

show abstract

Globally defining the effects of mutations in a picornavirus capsid

Cited by 14 publications

References 65 publications

Identification of Cytoplasmic Chaperone Networks Relevant for Respiratory Syncytial Virus Replication

Identification of Cytoplasmic Chaperone Networks Relevant for Respiratory Syncytial Virus Replication

Identification of cytoplasmic chaperone networks relevant for respiratory syncytial virus replication

Polymorphisms Predicting Phylogeny in Hepatitis B Virus (HBV)

Contact Info

Product

Resources

About