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Infection cycle and phylogeny of the Polinton-like virus Phaeocystis globosa virus virophage-14T
Open accessPreprint — published as 10.1038/s41564-022-01305-7
Abstract
Virophages are small dsDNA viruses dependent on a nucleocytoplasmic large-DNA virus infection of a cellular host for replication. Putative virophages infecting algal hosts are classified together with polinton-like viruses, transposable elements widely found in algal genomes, yet the lack of isolated strains raises questions about their existence as independent entities. In this work we isolated and characterized a virophage (PgVV-14T) co-infecting Phaeocystis globosa with the Phaeocystis globosa virus-14T (PgV-14T). PgVV-14T decreases the fitness of its PgV-14T viral host, yet it does not salvage the cellular host population. We found viral-like elements resembling PgVV-14T in Phaeocystis genomes, suggesting that these virophages are capable of integrating to the cellular host genome, bridging the gap between Polinton-like viruses and virophages. This system, with a giant virus, a virophage and endogenous viral elements preying on an algal host, presents an opportunity to gain a better understanding on the evolution of eukaryotes and their viruses.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Research works printed but not linked: 85
- 2014, Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements, Microbiol. Mol. Biol. Rev. MMBR, 78, 278, 10.1128/MMBR.00049-13 · DOI
- 10.1016/j.gene.2006.08.008 · DOI
- 10.1073/pnas.0600833103 · DOI
- 10.1038/nrmicro3389 · DOI
- 10.1111/nyas.12728 · DOI
- Yutin, N. , Raoult, D. & Koonin, E. V . Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies. Virol. J. 10, 158 (2013). · DOI
- Krupovic, M. , Bamford, D. H. & Koonin, E. V . Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses. Biol. Direct 9, 6 (2014). · DOI
- Yutin, N. , Shevchenko, S. , Kapitonov, V. , Krupovic, M. & Koonin, E. V . A novel group of diverse Polinton-like viruses discovered by metagenome analysis. BMC Biol. 13, 95 (2015). · DOI
- Bellas, C. M. & Sommaruga, R . Polinton-like viruses are abundant in aquatic ecosystems. Microbiome 9, 13 (2021). · DOI
- 10.3390/v7072806 · DOI
- Bekliz, M. , Colson, P. & La Scola, B . The Expanding Family of Virophages. Viruses 8, 317 (2016). · DOI
- 10.21775/cimb.040.001 · DOI
- 10.1073/pnas.1208835109 · DOI
- Campos, R. K. et al. Samba virus: a novel mimivirus from a giant rain forest, the Brazilian Amazon. Virol. J. 11, 95 (2014). · DOI
- Gaia, M. et al. Broad spectrum of mimiviridae virophage allows its isolation using a mimivirus reporter. PLoS One 8, e61912 (2013). · DOI
- Hackl, T. , Duponchel, S. , Barenhoff, K. , Weinmann, A. & Fischer, M. G . Virophages and retrotransposons colonize the genomes of a heterotrophic flagellate. Elife 10, e72674 (2021). · DOI
- 10.1073/pnas.1018221108 · DOI
- Gong, C. et al. Novel Virophages Discovered in a Freshwater Lake in China. Front. Microbiol. 7, 5 (2016). · DOI
- 2014, Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes, J. Virol, 89, 1278
- Yutin, N. , Kapitonov, V. V. & Koonin, E. V . A new family of hybrid virophages from an animal gut metagenome. Biol. Direct 10, 19 (2015). · DOI
- Stough, J. M. A. et al. Genome and Environmental Activity of a Chrysochromulina parva Virus and Its Virophages. Front. Microbiol. 10, 703 (2019). · DOI
- 10.1038/nature07218 · DOI
- 10.1126/science.1199412 · DOI
- Gaia, M. et al. Zamilon, a Novel Virophage with Mimiviridae Host Specificity. PLoS One 9, e94923 (2014). · DOI
- Mougari, S. et al. Guarani Virophage, a New Sputnik-Like Isolate From a Brazilian Lake. Front. Microbiol. 10, (2019). · DOI
- 2022, Isolation and Identification of a Large Green Alga Virus (Chlorella Virus XW01) of Mimiviridae and Its Virophage (Chlorella Virus Virophage SW01) by Using Unicellular Green Algal Cultures, J. Virol, 96, e02114
- 10.1073/pnas.1303251110 · DOI
- 10.1016/j.hal.2004.12.015 · DOI
- 10.3354/ame044207 · DOI
- 10.1016/j.virol.2005.07.002 · DOI
- 2006, Virus adsorption process determines virus susceptibility in Heterosigma akashiwo (Raphidophyceae), Aquat. Microb. Ecol, 42, 209, 10.3354/ame042209 · DOI
- Gann, E. R. , Gainer, P. J. , Reynolds, T. B. & Wilhelm, S. W . Influence of light on the infection of Aureococcus anophagefferens CCMP 1984 by a “giant virus”. PLoS ONE 15, (2020). · DOI
- 10.1016/0042-6822(83)90466-X · DOI
- 10.1073/pnas.1101118108 · DOI
- 10.1159/000312914 · DOI
- Sobhy, H. , Scola, B. L. , Pagnier, I. , Raoult, D. & Colson, P . Identification of giant Mimivirus protein functions using RNA interference. Front. Microbiol. 6, (2015). · DOI
- 10.1038/nature20593 · DOI
- 10.1002/ece3.600 · DOI
- 10.1073/pnas.0508477102 · DOI
- 10.1073/pnas.0506465102 · DOI
- 10.1101/gr.102582.109 · DOI
- 10.1016/j.ympev.2013.10.018 · DOI
- 10.1007/s00705-015-2622-9 · DOI
- 10.1093/protein/gzs068 · DOI
- 10.1016/j.gde.2004.09.010 · DOI
- 10.1101/2022.05.02.489867 · DOI
- 2017, Disentangling the origins of virophages and polintons, Curr. Opin. Virol, 25, 59, 10.1016/j.coviro.2017.07.011 · DOI
- Koonin, E. V. , Senkevich, T. G. & Dolja, V. V . The ancient Virus World and evolution of cells. Biol. Direct 1, 29 (2006). · DOI
- 10.1007/978-1-4615-8714-9 · DOI
- 10.3354/meps078001 · DOI
- 10.1093/bioinformatics/btw038 · DOI
- 10.1089/cmb.2012.0021 · DOI
- Deng, Z. & Delwart, E . ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data. BMC Bioinformatics 22, 119 (2021). · DOI
- 10.1038/nmeth.2089 · DOI · Paper page
- 10.1038/nprot.2007.6 · DOI
- 10.1111/j.1365-2818.2006.01706.x · DOI
- 10.1128/AEM.70.3.1506-1513.2004 · DOI
- 10.1111/1758-2229.12409 · DOI
- 2011, A Perturbed Ubiquitin Landscape Distinguishes Between Ubiquitin in Trafficking and in Proteolysis, Mol. Cell. Proteomics MCP, 10, M111.009753, 10.1074/mcp.M111.009753 · DOI
- 10.1021/acs.jproteome.8b00505 · DOI
- 10.1038/nprot.2007.261 · DOI · Paper page
- 2017, MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics, Nat. Methods, 14, 513, 10.1038/nmeth.4256 · DOI
- 10.1093/bioinformatics/btl158 · DOI
- Lechner, M. et al. Proteinortho: Detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 12, 124 (2011). · DOI
- 10.1038/s41592-021-01101-x · DOI · Paper page
- Mirdita, M. et al. ColabFold - Making protein folding accessible to all. 2021.08.15.456425 Preprint at https://doi.org/10.1101/2021.08.15.456425 (2022). · DOI · Paper page
- 10.1093/bioinformatics/btv057 · DOI
- 10.1093/bioinformatics/btv033 · DOI
- Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1, 2047-217X-1–18 (2012). · DOI
- Chevreux, B. , Wetter, T. & Suhai, S . Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. in Proceedings of the German Conference on Bioinformatics, GCB 1999, October 4-6, 1999, Hannover, Germany 45–56 (1999).
- Walker, B. J. et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS One 9, e112963 (2014). · DOI
- Eddy, S. R . Accelerated Profile HMM Searches. PLoS Comput. Biol. 7, e1002195 (2011). · DOI · Paper page
- 10.1093/molbev/msaa015 · DOI · Paper page
- 10.1093/molbev/msx281 · DOI · Paper page
- 2019, RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference, Bioinformatics, 35, 4453, 10.1093/bioinformatics/btz305 · DOI
- 10.1038/nbt.3988 · DOI · Paper page
- Steinegger, M. et al. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20, 473 (2019). · DOI · Paper page
- 10.1093/nar/30.7.1575 · DOI
- 10.1016/j.jmb.2017.12.007 · DOI · Paper page
- 2000, Rapid automatic detection and alignment of repeats in protein sequences, Proteins Struct. Funct. Bioinforma, 41, 224, 10.1002/1097-0134(20001101)41:2<224::AID-PROT70>3.0.CO;2-Z · DOI
- 2015, Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing, J. Eukaryot. Microbiol, 62, 121, 10.1111/jeu.12157 · DOI
- 2019, Chrysochromulina: Genomic assessment and taxonomic diagnosis of the type species for an oleaginous algal clade, Algal Res, 37, 307, 10.1016/j.algal.2018.11.023 · DOI
- 2015, Phaeocystis rex sp. nov. (Phaeocystales, Prymnesiophyceae): a new solitary species that produces a multilayered scale cell covering. Eur. J. Phycol, 50, 207
- 2016, Black Sea algal viruses. Russ, J. Mar. Biol, 42, 123
- 2019, Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula, Front. Microbiol, 10, 1014, 10.3389/fmicb.2019.01014 · DOI
Metadata
- Authors
- Roitman, S., Rozenberg, A., Lavy, T., Brussaard, C. P. D., Kleifeld, O., & Béjà, O.
- Affiliations
- Technion – Israel Institute of Technology (IL)
- Royal Netherlands Institute for Sea Research (NL)
- Corresponding author
- Roitman, Sheila
- Béjà, Oded
- Venue
- Nature Microbiology
- Publisher
- openRxiv
- Published
- 2022-07-28
- Volume
- 8
- Issue
- 2
- Pages
- 332-346
- ISSN
- 2058-5276 (ISSN-L)
- OpenAlex
- W4318071672
- Cited by
- 53
- References
- 1
- Citations by year
- 2026: 11 · 2025: 14 · 2024: 14 · 2023: 14
- FWCI
- 8.56
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature Microbiology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- UvA-DARE (University of Amsterdam) (publishedVersion)
- Flanders Marine Institute (Flanders Marine Institute) (submittedVersion, other-oa)
- Funders
- European Commission (321647)
- Israel Science Foundation (2167/17, 1623/17, 143/18)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
- Life Sciences › Immunology and Microbiology › Virology › Plant and Fungal Interactions Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- virophages, Polinton-like viruses, Phaeocystis globosa, co-infection, viral integration into host genome, burst size, marine algae, virus isolation
- MeSH terms
- Virophages, Phylogeny, Viruses, Genome, Viral, Phycodnaviridae, Haptophyta
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