Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sequence Collection
2.2. Nucleotide Sequence Alignment and Analysis
2.3. Detection of Regions with Lower Synonymous Substitution Rate
2.4. Protein Sequence Alignment and Domain Identification
2.5. Prediction of Protein Structural Features
3. Results
3.1. The VP1 Gene of B19V Contains 3 Regions with Significantly Increased Synonymous Conservation, among Which the X ORF
3.2. The VP1 Gene of PARV4 Contains 2 Regions with Significantly Reduced Synonymous Variability, Corresponding to ARF1 and ARF2
3.3. The B19V X Protein and PARV4 ARF1 Protein Have Similar Sequence Features
3.4. Conserved Features of the X and ARF1 Proteins Mostly but Not Exclusively Correspond to Conserved Motifs of the PLA2 Domain of VP1
3.5. The VP1 Gene of Bovine Parvovirus 3 and Porcine Parvovirus 2 Differs from That of Other Erythro- and Tetraparvoviruses
3.5.1. Bovine Parvovirus 3 VP1 Gene Encodes an X-like ORF, despite Not Encoding a PLA2 Domain
3.5.2. Porcine Parvovirus 2 Does Not Encode an X ORF, but Encodes a “Z ORF” Overlapping VP1
4. Discussion
4.1. Sequence Analyses Provide Compelling Evidence That the X Protein Must Be Expressed and Have a Crucial Function
4.2. The X Protein Could Be Translated Either by a Non-Conventional Mechanism or from an Overlooked mRNA
4.2.1. Translation of the X ORF through a Non-Canonical Mechanism
4.2.2. Translation of the X ORF from a Currently Unmapped mRNA
4.3. Are X, ARF1, and the Dependoparvovirus MAAP Protein Likely to Have a Similar Function?
4.4. Neither ARF1 nor the X Protein Are Homologous to the Protoparvovirus SAT Protein
5. Conclusions
Supplementary Materials
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
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Genus | Species | Common Name(s) [Abbreviation] | Genbank Genome Accession Number | Boundaries of the X ORF in the Genome Sequence (in Nucleotides) |
---|---|---|---|---|
Erythroparvovirus | Primate erythroparvovirus 1 | Parvovirus B19 [B19V] | NC_000883 | 2874–3119 |
Erythroparvovirus | Primate erythroparvovirus 2 | Simian parvovirus | U26342.1 | 2718–2963 |
Erythroparvovirus | Primate erythroparvovirus 3 | Rhesus macaque parvovirus | AF221122.1 | 2841–3080 |
Erythroparvovirus | Primate erythroparvovirus 4 | Pig-tailed macaque parvovirus | AF221123.1 | 2563–2802 |
Erythroparvovirus | Rodent erythroparvovirus 1 | Chipmunk parvovirus | GQ200736.1 | 3031–3228 |
Erythroparvovirus | Pinniped erythroparvovirus 1 | Seal parvovirus | KF373759.1 | 2789–3100 |
Erythroparvovirus (*) | Ungulate erythroparvovirus 1 | Bovine parvovirus 3 [bPARV3] | NC_037053 | 2627–2926 |
Tetraparvovirus | Chiropteran tetraparvovirus 1 | Eidolon helvum parvovirus | NC_016744.1 | 2829–3062 |
Tetraparvovirus | Primate tetraparvovirus 1 | Human parvovirus 4 [PARV4] | NC_007018.1 | 2937–3140 |
Tetraparvovirus | Ungulate tetraparvovirus 1 | Bovine hokovirus 1 | NC_028136 | 2857–3111 |
Tetraparvovirus | Ungulate tetraparvovirus 2 | Porcine hokovirus | EU200677.1 | 2808–3062 |
Tetraparvovirus | Ungulate tetraparvovirus 5 | Deer tetraparvovirus | NC_031670.1 | 2766–3020 |
Tetraparvovirus (*) | Ungulate tetraparvovirus 3 | Porcine parvovirus 2 [pPARV2]; Porcine cnvirus; Parvovirus YX | NC_035180 | No X ORF; boundaries of the Z ORF are 2817–3098 |
Tetraparvovirus | Ungulate tetraparvovirus 4 | Ovine hokovirus | JF504699.1 | 2855–3112 |
Tetraparvovirus | - | Opossum parvovirus | MG745671.1 | 2862–3092 |
Tetraparvovirus | - | Rodent parvovirus | MG745669.1 | 2960–3217 |
Virus Name | Region | Boundaries of the Region with Lower Synonymous Codon Variability in the VP1 CDS | Boundaries of the Corresponding ORF in the VP1 CDS |
---|---|---|---|
Parvovirus B19 | X ORF | Codons 58–163 (nucleotides 172–489) | Codons 84–166 (Nucleotides 251–496) |
Parvovirus B19 | Y region (*) | Codons 185–239 (nucleotides 553–715) | Codons 185–230 (*) (nucleotides 553–688) |
Human parvovirus 4 | ARF1 ORF (=X ORF) | Codons 180–263 (nucleotides 538–789) | Codons 187–255 (nucleotides 560–763) |
Human parvovirus 4 | ARF2 ORF | Codons 294–397 (nucleotides 880–1189) | Codons 295–379 (nucleotides 884–1135) |
Bovine parvovirus 3 | X-like ORF | Codons 205–306 (nucleotides 614–916) | Codons 215–315 (nucleotides 644–943) |
Porcine parvovirus 2 | Z ORF | Codons 193–309 (nucleotides 577–927) | Codons 193–285 (nucleotides 578–854) |
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Karlin, D.G. Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene. Viruses 2024, 16, 191. https://doi.org/10.3390/v16020191
Karlin DG. Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene. Viruses. 2024; 16(2):191. https://doi.org/10.3390/v16020191
Chicago/Turabian StyleKarlin, David G. 2024. "Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene" Viruses 16, no. 2: 191. https://doi.org/10.3390/v16020191