The Adeno-Associated Virus Replication Protein Rep78 Contains a Strictly C-Terminal Sequence Motif Conserved Across Dependoparvoviruses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Protein Sequence Analysis
2.2. Sequence Motif Searches
2.3. D Structure Prediction and Visualization
3. Results
3.1. The C-Terminal Region of Rep78 Contains 3 Predicted Zinc Fingers and Flexible Regions
- (1)
- (2)
- aa 587–612 are composed of a third zinc finger, also of the CHCC type, followed by a predicted α-helix (Figure 2A, right).
3.2. The C-Terminal Region of Dependoparvoviral Rep78 and Rep52 Contains a Conserved Motif, DDx3EQ, Not Similar to a Known Motif
3.3. The Motif Contains Three Strictly Conserved aa, Is Highly Negatively Charged, and Is Devoid of Prolines
3.4. A Conserved DDx3EQ Motif Is Found in One Protein from a Eukaryotic Virus and in One Human Protein
4. Discussion
4.1. The DDx3EQ Motif Should Have a High Binding Specificity Despite Its Short Length, and Is Probably Essential for AAV Replication
4.2. Hypothesis: The DDx3EQ Motif May Bind the DNA-Binding Interface of the Origin-Binding Domain of Rep78
4.3. The DDx3EQ Motif Might Not Be Necessary for Recombinant AAV Production, but Substitutions Within It Improve Production
4.4. Sequence Motifs Can Be Identified Even Within Highly Variable Protein Regions by Examining Alignment of Orthologs
Supplementary Materials
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Common Name | Species or Taxon | Genbank Accession Number |
---|---|---|
AAV2 | Dependoparvovirus primate1 | YP_680423.1 |
AAV3 | Dependoparvovirus primate1 | NP_043940 |
AAV5 | Dependoparvovirus mammalian1 | YP_068408.1 |
AAV12 | Dependoparvovirus primate1 | DQ813647 |
AAV (isolate Croatia cul1_12) | Unclassified | QHY93489 |
AAV (isolate MHH-05-2015) | Unclassified | YP_009552823.1 |
AAV—Po1 [porcine AAV1] | Unclassified | ACN42943.1 |
Anser anser dependoparvovirus | Unclassified | QTE04020.1 |
Avian AAV (strain DA-1) | Dependoparvovirus avian1 | YP_077182.1 |
Bat AAV (strain YNM) | Dependoparvovirus chiropteran1 | YP_003858571.1 |
Bearded dragon parvovirus | Dependoparvovirus squamate2 | YP_009154712.1 |
California sea lion AAV1 | Dependoparvovirus pinniped1 | YP_009507366.1 |
Canine parvovirus (isolate ParvoviridaeDogfe340C1) | Unclassified (1) | WDW25820.1 |
Dependoparvovirus (isolate cfw059par1) | Unclassified | QKN88755.1 |
Marsupial AAV1 | Unclassified | AZP54391.1 |
Muscovy duck parvovirus | Dependoparvovirus anseriform1 | YP_068410.1 |
Parvoviridae (isolate swa134par3) | Unclassified | QKE54950.1 |
Psittacidae dependoparvovirus | Unclassified | QTE03943.1 |
Rhinolophus pusillus AAV (isolate BtAAV-CXC1) | Unclassified | QDX47269.1 |
Rhinolophus pusillus AAV1 (isolate Rp-BtAAV1_34C_MJ_YN_2012) | Unclassified | ATV81500.1 |
Serpentine AAV2 | Unclassified | ACJ66590.1 |
Snake parvovirus 1 | Dependoparvovirus squamate1 | YP_068093.1 |
Tadarida brasiliensis associated dependoparvovirus | Unclassified | UJO02142.1 |
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Karlin, D.G. The Adeno-Associated Virus Replication Protein Rep78 Contains a Strictly C-Terminal Sequence Motif Conserved Across Dependoparvoviruses. Viruses 2024, 16, 1760. https://doi.org/10.3390/v16111760
Karlin DG. The Adeno-Associated Virus Replication Protein Rep78 Contains a Strictly C-Terminal Sequence Motif Conserved Across Dependoparvoviruses. Viruses. 2024; 16(11):1760. https://doi.org/10.3390/v16111760
Chicago/Turabian StyleKarlin, David G. 2024. "The Adeno-Associated Virus Replication Protein Rep78 Contains a Strictly C-Terminal Sequence Motif Conserved Across Dependoparvoviruses" Viruses 16, no. 11: 1760. https://doi.org/10.3390/v16111760
APA StyleKarlin, D. G. (2024). The Adeno-Associated Virus Replication Protein Rep78 Contains a Strictly C-Terminal Sequence Motif Conserved Across Dependoparvoviruses. Viruses, 16(11), 1760. https://doi.org/10.3390/v16111760