Structure Unveils Relationships between RNA Virus Polymerases
Abstract
:1. Introduction
2. Materials and Methods
3. Results and Discussion
3.1. Identification of a Common Structural Core for Viral RdRps
3.2. Structure-Based Distance Tree and Overall Grouping of the RdRp Structures
3.3. Stability of the Structure-Based Distance Tree and the Common Structural Core
3.4. RdRps from (+)RNA and dsRNA Viruses with Permutated Catalytic Site Sequence Group Together
3.5. Early Separation of Semi-Conservative and Conservative Mechanism of Viral RNA Transcription
3.6. Branch I: Origin of (−)RNA Virus RdRps and Development of RNA-Primed Initiation
3.7. Branch II: Development of Protein Priming
3.8. Considerations on the RNA Virus Taxonomy
3.9. Evolutionary Implications and Future Directions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Genome | Kingdom | Phylum; Subphylum | Class; Order | Family; Subfamily | Genus | Virus |
---|---|---|---|---|---|---|
(−)RNA | Orthornavirae | Negarnaviricota; Polyploviricotina | Ellioviricetes; Bunyavirales | Arenaviridae | Mammarenavirus | Machupo mammarenavirus |
Peribunyaviridae | Orthobunyavirus | La Crosse orthobunyavirus | ||||
Phenuiviridae | Bandavirus | Huaiyangshan banyangvirus | ||||
Insthoviricetes; Articulavirales | Orthomyxoviridae | Alphainfluenzavirus | influenza A virus | |||
Betainfluenzavirus | influenza B virus | |||||
Gammainfluenzavirus | influenza C virus | |||||
Deltainfluenzavirus | influenza D virus | |||||
Negarnaviricota; Haploviricotina | Monjiviricetes; Mononegavirales | Pneumoviridae | Metapneumovirus | human metapneumovirus | ||
Rhabdoviridae | Lyssavirus | rabies lyssavirus | ||||
Vesiculovirus | vesicular stomatitis Indian virus | |||||
dsRNA | Duplornaviricota | Resentoviricetes; Reovirales | Reoviridae; Sedoreovirinae | Rotavirus | rotavirus A | |
Orbivirus | bluetongue virus | |||||
Reoviridae; Spinareovirinae | Aquareovirus | aquareovirus G | ||||
Cypovirus | Bombyx mori cypovirus 1 | |||||
Orthoreovirus | mammalian orthoreovirus | |||||
Vidaverviricetes; Mindivirales | Cystoviridae | Cystovirus | Pseudomonas phage phi6 | |||
Pseudomonas phage phi12 | ||||||
Not determined (ND) | ND; ND | Birnaviridae | Avibirnavirus | infectious bursal disease virus | ||
Aquabirnavirus | infectious pancreatic necrosis virus | |||||
(+)RNA | Permutotetraviridae | Alphapermutotetravirus | thosean asigna virus | |||
Kitrinoviricota | Flasuviricetes; Amarillovirales | Flaviviridae | Hepacivirus | hepacivirus C | ||
Pestivirus | pestivirus A | |||||
pestivirus C | ||||||
Flavivirus | Dengue virus | |||||
Zika virus | ||||||
West Nile virus | ||||||
Japanese encephalitis virus | ||||||
Yellow fever virus | ||||||
ds | Pisuviricota | Duplopiviricetes; Durnavirales | Picobirnaviridae | Picobirnavirus | human picobirnavirus | |
(+)RNA | Pisoniviricetes; Nidovirales | Coronaviridae; Orthocoronavirinae | Betacoronavirus | SARS-CoV-2 2 | ||
Pisoniviricetes; Picornavirales | Picornaviridae | Kobuvirus | aichivirus C | |||
Cardiovirus | cardiovirus A | |||||
Aphthovirus | foot-and-mouth disease virus | |||||
Enterovirus | enterovirus A71 (enterovirus A) | |||||
coxsackievirus B3 (enterovirus B) | ||||||
poliovirus 1 (enterovirus C) | ||||||
human rhinovirus A | ||||||
Sicinivirus | sicinivirus A | |||||
Caliciviridae | Norovirus | Norwalk virus | ||||
Lagovirus | rabbit hemorrhagic disease virus | |||||
Sapovirus | Sapporo virus | |||||
Lenarviricota | Allassoviricetes; Levivirales | Leviviridae | Allolevivirus | Enterobacteria phage Qβ |
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Mönttinen, H.A.M.; Ravantti, J.J.; Poranen, M.M. Structure Unveils Relationships between RNA Virus Polymerases. Viruses 2021, 13, 313. https://doi.org/10.3390/v13020313
Mönttinen HAM, Ravantti JJ, Poranen MM. Structure Unveils Relationships between RNA Virus Polymerases. Viruses. 2021; 13(2):313. https://doi.org/10.3390/v13020313
Chicago/Turabian StyleMönttinen, Heli A. M., Janne J. Ravantti, and Minna M. Poranen. 2021. "Structure Unveils Relationships between RNA Virus Polymerases" Viruses 13, no. 2: 313. https://doi.org/10.3390/v13020313