Representing virus-host interactions and other multi-organism processes in the Gene Ontology

Foulger, Rebecca E.; Osumi-Sutherland, David; McIntosh, Brenley K.; Hulo, Chantal; Masson, Patrick; Poux, Sylvain; Mercier, Philippe Le; Lomax, Jane

doi:10.1186/s12866-015-0481-x

Cited by 20 publications

(17 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Other immune genes that were differentially expressed in infected mussels (Figure a) were either annotated by host–virus interaction according to the UniProt database (BUB1, SAMDH, importin subunit alpha‐1) (Foulger et al., ; Masson et al., ; The UniProt Consortium, ), or were related to response to microorganisms. Intestinal parasites have indeed been shown to alter microbial gut homeostasis (e.g., Berrilli, Di Cave, Cavallero, & D'Amelio, ; Cariveau, Elijah Powell, Koch, Winfree, & Moran, ; Kreisinger, Bastien, Hauffe, Marchesi, & Perkins, ).…”

Section: Discussionmentioning

confidence: 99%

Dual transcriptomics reveals co‐evolutionary mechanisms of intestinal parasite infections in blue mussels Mytilus edulis

et al. 2018

View full text Add to dashboard Cite

On theoretical grounds, antagonistic co-evolution between hosts and their parasites should be a widespread phenomenon but only received little empirical support so far. Consequently, the underlying molecular mechanisms and evolutionary steps remain elusive, especially in nonmodel systems. Here, we utilized the natural history of invasive parasites to document the molecular underpinnings of co-evolutionary trajectories. We applied a dual-species transcriptomics approach to experimental cross-infections of blue mussel Mytilus edulis hosts and their invasive parasitic copepods Mytilicola intestinalis from two invasion fronts in the Wadden Sea. We identified differentially regulated genes from an experimental infection contrast for hosts (infected vs. control) and a sympatry contrast (sympatric vs. allopatric combinations) for both hosts and parasites. The damage incurred by Mytilicola infection and the following immune response of the host were mainly reflected in cell division processes, wound healing, apoptosis and the production of reactive oxygen species (ROS). Furthermore, the functional coupling of host and parasite sympatry contrasts revealed the concerted regulation of chitin digestion by a Chitotriosidase 1 homolog in hosts with several cuticle proteins in the parasite. Together with the coupled regulation of ROS producers and antagonists, these genes represent candidates that mediate the different evolutionary trajectories within the parasite's invasion. The host-parasite combination-specific coupling of these effector mechanisms suggests that underlying recognition mechanisms create specificity and local adaptation. In this way, our study demonstrates the use of invasive species' natural history to elucidate molecular mechanisms of host-parasite co-evolution in the wild.

show abstract

Section: Discussionmentioning

confidence: 99%

Dual transcriptomics reveals co‐evolutionary mechanisms of intestinal parasite infections in blue mussels Mytilus edulis

et al. 2018

View full text Add to dashboard Cite

show abstract

“…A bridge that links literature reports to GO term annotation, ViralZone is an online knowledge base that contains 'textbook' information about viral taxonomy, replication, genome organization, and virion structure, and provides links to viral sequence data [62,63]. Importantly, ViralZone staff collaborate with the GO Consortium to define entries for virus-specific molecular functions [63][64][65][66]. ViralZone cross-references its keywords with GO Consortium terms and UniProt [67] identifiers.…”

Section: Box 1 the Viralzone Ontology Outlines Viral Protein Functionmentioning

confidence: 99%

“…ViralZone staff have developed GO concepts specifically for viruses, to represent the diversity of viral replication and processes involved with viral entry, replication, and egress [66]. ViralZone staff have also developed a detailed listing of virus-host interactions, with entries for 65 functions and 57 GO terms [64,65]. Each entry ('keyword') has a unique identifier.…”

Section: Box 1 the Viralzone Ontology Outlines Viral Protein Functionmentioning

confidence: 99%

Resources to Discover and Use Short Linear Motifs in Viral Proteins

Hraber

O’Maille

Silberfarb

et al. 2020

Trends in Biotechnology

View full text Add to dashboard Cite

Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Motif mimicry tolerates mutations, evolves quickly to modify interactions with the host, and enables modular interactions with protein complexes. Host cells cannot easily coordinate changes to conserved motif recognition and binding interfaces under selective pressure to maintain critical signaling pathways. SLiMs offer potential for use in synthetic biology, such as better immunogens and therapies, but may also present biosecurity challenges. We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery. As the number of examples continues to grow, knowledge management tools are essential to help organize and compare new findings.

show abstract

“…As the human disease-gene association is lacking for SARS-CoV-2 infection, gene sets related to SARS-CoV was used to relate various symptoms. A clinical outcome of other gene sets of viral entry and viral life cycle was included from the amigo gene ontology database (41). This comprehensive gene set was compared with the pairwise intersection method by using the Jaccard index.…”

Section: Identification Of Common Genes For Covid-19mentioning

confidence: 99%

COVID-19: A Drug Repurposing and Biomarker Identification by Using Comprehensive Gene-Disease Associations through Protein-Protein Interaction Network Analysis

Kumar¹

2020

Preprint

View full text Add to dashboard Cite

COVID-19 (2019-nCoV) is a pandemic disease with an estimated mortality rate of 3.4% (estimated by the WHO as of March 3, 2020). Until now there is no antiviral drug and vaccine for COVID-19. The current overwhelming situation by COVID-19 patients in hospitals is likely to increase in the next few months. About 15 percent of patients with serious disease in COVID-19 require immediate health services. Rather than waiting for new anti-viral drugs or vaccines that take a few months to years to develop and test, several researchers and public health agencies are attempting to repurpose medicines that are already approved for another similar disease and have proved to be fairly effective. This study aims to identify FDA approved drugs that can be used for drug repurposing and identify biomarkers among high- risk and asymptomatic groups. In this study gene-disease association related to COVID-19 reported mild, severe symptoms and clinical outcomes were determined. The high-risk group was studied related to SARS-CoV-2 viral entry and life cycle by using Disgenet and compared with curated COVID-19 gene data sets from the CTD database. The overlapped gene sets were enriched and the selected genes were constructed for protein-protein interaction networks. Through interactome, key genes were identified for COVID-19 and also for high risk and asymptomatic groups. The key hub genes involved in COVID-19 were VEGFA, TNF, IL-6, CXCL8, IL10, CCL2, IL1B, TLR4, ICAM1, MMP9. The identified key genes were used for drug-gene interaction for drug repurposing. The chloroquine, lenalidomide, pentoxifylline, thalidome, sorafenib, pacitaxel, rapamycin, cortisol, statins were proposed to be probable drug repurposing candidates for the treatment of COVID-19. However, these predicted drug candidates need to be validated through randomized clinical trials. Also, a key gene involved in high risk and the asymptomatic group were identified, which can be used as probable biomarkers for early identification.

show abstract

Representing virus-host interactions and other multi-organism processes in the Gene Ontology

Cited by 20 publications

References 44 publications

Dual transcriptomics reveals co‐evolutionary mechanisms of intestinal parasite infections in blue mussels Mytilus edulis

Dual transcriptomics reveals co‐evolutionary mechanisms of intestinal parasite infections in blue mussels Mytilus edulis

Resources to Discover and Use Short Linear Motifs in Viral Proteins

COVID-19: A Drug Repurposing and Biomarker Identification by Using Comprehensive Gene-Disease Associations through Protein-Protein Interaction Network Analysis

Contact Info

Product

Resources

About