The Potential Roles of Host Cell miRNAs in Fine-Tuning Bovine Coronavirus (BCoV) Molecular Pathogenesis, Tissue Tropism, and Immune Regulation
Abstract
:1. Introduction
2. Materials and Methods
2.1. BCoV Genome Sequences
2.2. Multiple Sequence Alignment and Comparison of Genomes of BCoV (Enteric and Respiratory) Isolates
2.3. Identification of Bovine miRNAs Targeting Host Genes and miRNAs Targeting Host Transcription Factors in Specific Tissues
2.4. Host miRNAs Potentially Targeting BCoV Genome Sequences at Various Locations
2.5. Functional Enrichment Analysis of Genes Targeted by the Relevant miRNA Candidates
3. Results
3.1. Bovine miRNAs Targeting the BCoV Genome at Various Locations
3.2. Bovine Host Cellular miRNAs Targeting the BCoV-S Protein
3.3. Differential Targeting of Some Bovine Host Cell miRNA Candidates to the Genomes of BCoV (Enteric/Respiratory) Isolates
3.4. Potential Impacts of Host Cell miRNAs on Viral Replication through Targeting Some Host Signal Transduction Pathways in the Context of BCoV Infection
3.5. Bovine Host Cell miRNAs Targeting Some Immune Suppressor Genes
3.6. BCoV Infection Induces Differential Display of the Host Cell miRNAs to Fine-Tune the Viral Tropism and Viral Replication
3.7. Bovine miRNAs Regulating Some Host Transcription Factors That Control the Expression of Some Key Host Genes
3.8. The Putative Regulation of Some Critical Host Signal Transduction Pathways by Bovine miRNAs
4. Discussion
4.1. Host miRNA Targeting BCoV Spike Protein at Various Locations
4.2. Impacts of Host miRNA Targeting Various BCoV Genome Regions Related to the Virus’s Infectivity and Pathogenesis
4.3. Impacts of Host miRNA Targeting Various Immune Regulatory Genes in the Context of BCoV Infection
4.4. Potential Role of miRNAs as Biological Markers for BCoV Infection
5. Limitations of the Current Study
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Accession No. | Strain/Isolate | Country | Year |
---|---|---|---|
Enteric | |||
U00735 | Mebus | USA | 1972 |
AB354579 | Kakegawa | Japan | 1976 |
AF391541 | BCoV-ENT | USA | 1998 |
DQ915164 | Alpaca | USA | 1998 |
EF424615 | Bovine coronavirus E-AH65 | USA | 2007 |
EF424619 | Bovine coronavirus E-AH187 | USA | 2007 |
KX982264 | BCoV_2014_13 | France | 2014 |
KU886219 | BCV-AKS-1 | China | 2015 |
MG518518 | Water deer coronavirus isolate W17-18 | Korea | 2018 |
LC642814 | strain GF2020 | Japan | 2021 |
Respiratory | |||
FJ938066 | Bovine/US/OH-440-TC/1996 | USA | 1996 |
AF391542 | BCoV-LUN | USA | 1998 |
EF424617 | Bovine coronavirus R-AH65 | USA | 2007 |
EF424620 | Bovine coronavirus R-AH187 | USA | 2007 |
MG757140 | BCoV/France/11-ICSA16-LBA/2014 | France | 2014 |
MG757138 | BCoV/France/ICSA21L3/LBA/2014 | France | 2014 |
KX432213 | Canine respiratory coronavirus strain BJ232 | China | 2016 |
ON146444 | Bovine coronavirus strain MARC/BRCV_2014 | USA | 2022 |
Domain | Location (bp) | Sequence (aa) | Sequence (bp) | Gene |
---|---|---|---|---|
S1-NTD Sugar Binding Sites | 24124–24198 | YTMCEYPHTICHPNLGNKRVELWHW | UAUACUAUGUGCGAGUACCCACAUACGAUUUGUCAUCCUAAUCUGGGUAAUAAACGCGUAGAACUAUGGCAUUGG | S1 |
S1/S2 Furin Cleavage Site | 25930–25944 | RRSRR | AGACGAAGUCGUAGA | S1/S2 |
GxCx Motif | 25903–25914 | GYCV | GGUUACUGUGUG | S1 |
Conserved S2 Nonamers | 26044–26070 | IPSEFTIGN | AUACCUUCAGAGUUUACUAUAGGUAAU | S2 |
miRNAs | Left-Most Position of Target Site | Binding Sites | Folding Energy (in Kcal/mol) | Heteroduplex |
---|---|---|---|---|
bta-miR-193a-3p | 24103 | S1-NTD Sugar Binding Sites Tyr-162 Residue | −12.80 | TTAGAGATCTCTGTTTGCCAGTA || || ||| |||||| TGACCCT-GAAACATCCGGTCAA |
bta-miR-494 | 24196 | S1-NTD Sugar Binding Sites His-185 Residue | −13.30 | TGGGATACAGGTGT-TGTTTCC |||| |||||| CTCCAAAGGGCACATACAAAGT |
bta-miR-2375 | 25938 | S1/S2 Furin Cleavage Site | −13.30 | TCGTAGAGCGATT-ACCACTGGT :||| | |: |||||| CTAGTCTGGAGAGGTAGTGACCC |
bta-miR-12059 | 26061 | Conserved S2 Nonamers | −16.30 | TATAGGTA-ATATGGAGGAGT |||:| ||||||| TCCTCCGTCCCACCCTCCTCT |
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Shah, A.U.; Hemida, M.G. The Potential Roles of Host Cell miRNAs in Fine-Tuning Bovine Coronavirus (BCoV) Molecular Pathogenesis, Tissue Tropism, and Immune Regulation. Microorganisms 2024, 12, 897. https://doi.org/10.3390/microorganisms12050897
Shah AU, Hemida MG. The Potential Roles of Host Cell miRNAs in Fine-Tuning Bovine Coronavirus (BCoV) Molecular Pathogenesis, Tissue Tropism, and Immune Regulation. Microorganisms. 2024; 12(5):897. https://doi.org/10.3390/microorganisms12050897
Chicago/Turabian StyleShah, Abid Ullah, and Maged Gomaa Hemida. 2024. "The Potential Roles of Host Cell miRNAs in Fine-Tuning Bovine Coronavirus (BCoV) Molecular Pathogenesis, Tissue Tropism, and Immune Regulation" Microorganisms 12, no. 5: 897. https://doi.org/10.3390/microorganisms12050897