Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components
Abstract
:1. Introduction
1.1. Interaction of SARS-CoV-2 with Host Cellular Components
1.2. Interaction of SARS-CoV-2 with the Host Immune System
1.2.1. Interaction of SARS-CoV-2 with Host Effector Cell Components
1.2.2. Interaction of SARS-CoV-2 with Host Intracellular Components
1.3. Interaction of SARS-CoV-2 with Host RNA Binding Proteins and miRNAs
1.4. Impact of Mutations on SARS-CoV-2 Proteins
1.5. Databases and Software Resources for the SARS-CoV-2 Genome
2. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Interactions between SARS-CoV-2, Human RBPs, and miRNAs | Technique Used | References |
---|---|---|
332 SARS-CoV2–host protein–protein interaction | AP-MS | [90] |
309 host proteins interaction with SARS-CoV-2 RNA | ChIRP-MS | [129] |
Host RAB2A, RAB7A, and RAB10 interaction with both viral RNA and protein | CRISPR Cas-9-based perturbation | [130] |
25 human RBPs targeting SARS-CoV-2 viral RNA | RBP motif-based in silico prediction | [133] |
104 human proteins directly and specifically bind to SARS-CoV-2 RNAs | RAP-MS | [87] |
288 host miRNAs predicted to bind SARS-CoV-2 (ORF1ab, N, S, 5′-UTR, and 3′-UTR) | Bioinformatic prediction algorithms and miRNA profiling | [142] |
479 human miRNAs could target various SARS-CoV-2 genes (S, E, M, N, Orf 1ab, 3a, 6, 7, 8, and 10) | Machine learning-based miRNA prediction | [140] |
22 miRNAs could bind throughout the length of the SARS-CoV-2 viral genome | Computational approach using FIMO | [133] |
Database | Interaction(s) | URL | Description |
---|---|---|---|
SARS-3D | Protein–protein | http://sars3d.com (accessed on 30 June 2021) | 3D protein models predicted using genome data |
VirHostNet | Protein–protein | http://virhostnet.prabi.fr (accessed on 30 June 2021) | Interactions between SARS-CoV-2 and human proteins |
BioGRID (curated dataset) | Protein–protein | https://thebiogrid.org/project/3 (accessed on 30 June 2021) | Curated coronavirus dataset with 22,223 interactions over 110 proteins |
IntAct | Protein–protein and protein–RNA | https://www.ebi.ac.uk/intact/query/annot:%22dataset:coronavirus%22 (accessed on 30 June 2021) | Over 4400 binarized SARS-CoV-2–human molecular interactions |
Human Proteome Atlas | Protein–protein | https://www.proteinatlas.org (accessed on 30 June 2021) | Summary of tissue and cell expression patterns of human proteins interacting with SARS-CoV-2 |
Intomics | Protein–protein | https://www.intomics.com/covid19/?utm_source=intomics&utm_medium=linkedin&utm_campaign=covid19 (accessed on 30 June 2021) | PPI network based on transcriptional response in human SARS-CoV-2-infected cells |
Protein Data Bank | Protein–protein | https://www.rcsb.org/news?year=2020&article=5e74d55d2d410731e9944f52&feature=true (accessed on 30 June 2021) | Protein–protein complex crystal structures (i.e., S—ACE2 complex) |
STRING-DB | Protein–protein | https://string-db.org/cgi/covid.pl (accessed on 30 June 2021) | Protein–protein interaction network with 332 virus-interacting human proteins |
Database | Interaction Type(s) | URL | Description |
---|---|---|---|
Viruses.STRING | Protein–protein | http://viruses.string-db.org/ (accessed on 30 June 2021) | Catalog of virus–host PPI |
HVIDB | Protein–protein | http://zzdlab.com/hvidb/ (accessed on 30 June 2021) | Annotated human–virus PPI |
P-HIPSTer | Protein–protein | http://phipster.org/ (accessed on 30 June 2021) | PPI predicted from PDB structure data |
VirusMentha | Protein–protein | https://virusmentha.uniroma2.it/ (accessed on 30 June 2021) | Regularly updated PPI |
Virus MINT | Protein–protein | https://maayanlab.cloud/Harmonizome/resource/Virus+MINT (accessed on 30 June 2021) | 5000 PPI covering 110 viral strains |
HPIDB 3.0 | RNA–RNA, protein–protein | https://hpidb.igbb.msstate.edu/ (accessed on 30 June 2021) | 69,787 annotated and predicted interactions |
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Srivastava, M.; Hall, D.; Omoru, O.B.; Gill, H.M.; Smith, S.; Janga, S.C. Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components. Microorganisms 2021, 9, 1794. https://doi.org/10.3390/microorganisms9091794
Srivastava M, Hall D, Omoru OB, Gill HM, Smith S, Janga SC. Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components. Microorganisms. 2021; 9(9):1794. https://doi.org/10.3390/microorganisms9091794
Chicago/Turabian StyleSrivastava, Mansi, Dwight Hall, Okiemute Beatrice Omoru, Hunter Mathias Gill, Sarah Smith, and Sarath Chandra Janga. 2021. "Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components" Microorganisms 9, no. 9: 1794. https://doi.org/10.3390/microorganisms9091794
APA StyleSrivastava, M., Hall, D., Omoru, O. B., Gill, H. M., Smith, S., & Janga, S. C. (2021). Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components. Microorganisms, 9(9), 1794. https://doi.org/10.3390/microorganisms9091794