1
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Obanda V, Akinyi M, King'ori E, Nyakundi R, Ochola G, Oreng P, Mugambi K, Waiguchu GM, Chege M, Rosenbaum W, Ylitalo EB, Bäck AT, Pettersson L, Mukunzi OS, Agwanda B, Stenberg-Lewerin S, Lwande OW. Epidemiology and ecology of the sylvatic cycle of African Swine Fever Virus in Kenya. Virus Res 2024; 348:199434. [PMID: 39004284 DOI: 10.1016/j.virusres.2024.199434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/07/2024] [Accepted: 07/07/2024] [Indexed: 07/16/2024]
Abstract
African Swine Fever (ASF) is caused by a DNA virus (AFSV) maintained and transmitted by the Argasid ticks. The re-emergence of the disease in Africa coupled with its rapid spread globally is a threat to the pig industry, food security and livelihoods. The ecology and epidemiology of the ASFV sylvatic cycle, especially in the face of changing land use and land cover, further compounds the menace and impacts of this disease in Kenya. The study aimed to determine the occurrence and distribution of ASFV seroprevalence in warthog populations, the tick vectors and extent of tick infestation of warthog burrows, and the genotypes of ASFV in soft ticks in Kenya. Warthogs from different parts of Kenya were captured and venous blood was centrifuged to harvest sera. Warthog burrows were examined for their conditions and to extract ticks. Sera were analyzed for antibodies against ASFV using a commercial ELISA kit coated with p32 ASFV recombinant protein. Ticks were pooled, DNA extracted and the p72 gene of the ASFV was amplified by qPCR and conventional PCR. The overall seroprevalence of ASFV in warthogs was 87.5 %. A total of 228 warthog burrows were examined and 2154 argasid ticks were extracted from the burrows. Tick pools from Kigio Farm and Lewa Wildlife Conservancies were ASFV-positive by qPCR and conventional PCR. ASFV was further confirmed by the Twist Comprehensive Viral Research Panel (TCVRP), which also identified the argasid ticks as Ornithodoros porcinus. The ticks were infected with virus genotype IX, and their occurrence overlaps with regions of previous ASF outbreaks in domestic pigs. Further, Viruses that could be tick endosymbionts/commensals or due to bloodmeal were detected in ticks by TCVRP; Porcine type-C oncovirus; Pandoravirus neocaledonia; Choristoneura fumiferana granulovirus; Enterobacteria phage p7; Leporid herpesvirus 4 isolate; 5; Human Lymphotropic virus; Human herpesvirus 5. In conclusion, our results suggest that infected Ornithodoros spp. seems to have a rich virome, which has not been explored but could be exploited to inform ASF control in Kenya. Further, the ecology of Ornithodoros spp. and burrow-use dynamics are complex and more studies are needed to understand these dynamics, specifically in the spread of ASFV at the interface of wild and domestic pigs. Further, our results provide evidence of genotype IX ASFV sylvatic cycle which through O. porcinus tick transmission has resulted in high exposure of adult common warthogs. Finally, the co-circulation of ASFV genotype IX in the same location with past ASF outbreaks in domestic pigs and presently in ticks brings to focus the role of the interface and ticks on virus transmission to pigs and warthogs.
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Affiliation(s)
- Vincent Obanda
- Veterinary Science and Laboratories Department, Wildlife Research and Training Institute, P.O Box 842-20117, Naivasha, Kenya
| | - Mercy Akinyi
- Institute of Primate Research, P.O. Box 24481 Karen 00502, Nairobi, Kenya
| | - Edward King'ori
- Veterinary Services Department, Kenya Wildlife Service, P.O. Box 54582 00200, Nairobi, Kenya
| | - Ruth Nyakundi
- Institute of Primate Research, P.O. Box 24481 Karen 00502, Nairobi, Kenya
| | - Griphin Ochola
- Institute of Primate Research, P.O. Box 24481 Karen 00502, Nairobi, Kenya
| | - Purity Oreng
- Institute of Primate Research, P.O. Box 24481 Karen 00502, Nairobi, Kenya
| | - Kevin Mugambi
- Institute of Primate Research, P.O. Box 24481 Karen 00502, Nairobi, Kenya
| | - Grace Mwihaki Waiguchu
- Center for Savannah, Arid and Semi-Arid Ecosystems, Wildlife Research and Training Institute, Tsavo, P.O Box 842-20117, Naivasha, Kenya
| | - Mary Chege
- Institute of Primate Research, P.O. Box 24481 Karen 00502, Nairobi, Kenya
| | - William Rosenbaum
- Department of Medical Biosciences, Clinical Genomics, 901 87, Umeå University, Umeå, Sweden
| | | | | | - Lisa Pettersson
- Department of Clinical Microbiology, Umeå University, 901 85, Umeå, Sweden
| | - Opanda Silvanos Mukunzi
- Centre for Virus Research, Kenya Medical Research Training Institute, P.O. BOX 54628-00200, Nairobi, Kenya
| | - Bernard Agwanda
- Zoology Department, National Museums of Kenya, P.O. BOX 40658- 00100, Nairobi, Kenya
| | - Susanna Stenberg-Lewerin
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, P.O Box 7023 75007, Uppsala, Sweden
| | - Olivia Wesula Lwande
- Department of Clinical Microbiology, Umeå University, 901 85, Umeå, Sweden; Umeå Centre for Microbiology Research, Umeå University, 901 87, Umeå, Sweden.
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2
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Haltom J, Trovao NS, Guarnieri J, Vincent P, Singh U, Tsoy S, O'Leary CA, Bram Y, Widjaja GA, Cen Z, Meller R, Baylin SB, Moss WN, Nikolau BJ, Enguita FJ, Wallace DC, Beheshti A, Schwartz R, Wurtele ES. SARS-CoV-2 Orphan Gene ORF10 Contributes to More Severe COVID-19 Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.27.23298847. [PMID: 38076862 PMCID: PMC10705665 DOI: 10.1101/2023.11.27.23298847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The orphan gene of SARS-CoV-2, ORF10, is the least studied gene in the virus responsible for the COVID-19 pandemic. Recent experimentation indicated ORF10 expression moderates innate immunity in vitro. However, whether ORF10 affects COVID-19 in humans remained unknown. We determine that the ORF10 sequence is identical to the Wuhan-Hu-1 ancestral haplotype in 95% of genomes across five variants of concern (VOC). Four ORF10 variants are associated with less virulent clinical outcomes in the human host: three of these affect ORF10 protein structure, one affects ORF10 RNA structural dynamics. RNA-Seq data from 2070 samples from diverse human cells and tissues reveals ORF10 accumulation is conditionally discordant from that of other SARS-CoV-2 transcripts. Expression of ORF10 in A549 and HEK293 cells perturbs immune-related gene expression networks, alters expression of the majority of mitochondrially-encoded genes of oxidative respiration, and leads to large shifts in levels of 14 newly-identified transcripts. We conclude ORF10 contributes to more severe COVID-19 clinical outcomes in the human host.
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Affiliation(s)
- Jeffrey Haltom
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Nidia S Trovao
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Pan Vincent
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
| | - Sergey Tsoy
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Collin A O'Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Gabrielle A Widjaja
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zimu Cen
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert Meller
- Morehouse School of Medicine, Atlanta, GA , 30310-1495, USA
| | - Stephen B Baylin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231
- Van Andel Research Institute, Grand Rapids, MI 49503
| | - Walter N Moss
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Basil J Nikolau
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Blue Marble Space Institute of Science, Seattle, WA, 98104 USA
| | - Robert Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
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3
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Ha AD, Aylward FO. Automated classification of giant virus genomes using a random forest model built on trademark protein families. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566645. [PMID: 38014039 PMCID: PMC10680617 DOI: 10.1101/2023.11.10.566645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Viruses of the phylum Nucleocytoviricota , often referred to as "giant viruses," are prevalent in various environments around the globe and play significant roles in shaping eukaryotic diversity and activities in global ecosystems. Given the extensive phylogenetic diversity within this viral group and the highly complex composition of their genomes, taxonomic classification of giant viruses, particularly incomplete metagenome-assembled genomes (MAGs) can present a considerable challenge. Here we developed TIGTOG ( T axonomic Information of G iant viruses using T rademark O rthologous G roups), a machine learning-based approach to predict the taxonomic classification of novel giant virus MAGs based on profiles of protein family content. We applied a random forest algorithm to a training set of 1,531 quality-checked, phylogenetically diverse Nucleocytoviricota genomes using pre-selected sets of giant virus orthologous groups (GVOGs). The classification models were predictive of viral taxonomic assignments with a cross-validation accuracy of 99.6% to the order level and 97.3% to the family level. We found that no individual GVOGs or genome features significantly influenced the algorithm's performance or the models' predictions, indicating that classification predictions were based on a comprehensive genomic signature, which reduced the necessity of a fixed set of marker genes for taxonomic assigning purposes. Our classification models were validated with an independent test set of 823 giant virus genomes with varied genomic completeness and taxonomy and demonstrated an accuracy of 98.6% and 95.9% to the order and family level, respectively. Our results indicate that protein family profiles can be used to accurately classify large DNA viruses at different taxonomic levels and provide a fast and accurate method for the classification of giant viruses. This approach could easily be adapted to other viral groups.
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4
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Moniruzzaman M, Erazo Garcia MP, Farzad R, Ha AD, Jivaji A, Karki S, Sheyn U, Stanton J, Minch B, Stephens D, Hancks DC, Rodrigues RAL, Abrahao JS, Vardi A, Aylward FO. Virologs, viral mimicry, and virocell metabolism: the expanding scale of cellular functions encoded in the complex genomes of giant viruses. FEMS Microbiol Rev 2023; 47:fuad053. [PMID: 37740576 PMCID: PMC10583209 DOI: 10.1093/femsre/fuad053] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023] Open
Abstract
The phylum Nucleocytoviricota includes the largest and most complex viruses known. These "giant viruses" have a long evolutionary history that dates back to the early diversification of eukaryotes, and over time they have evolved elaborate strategies for manipulating the physiology of their hosts during infection. One of the most captivating of these mechanisms involves the use of genes acquired from the host-referred to here as viral homologs or "virologs"-as a means of promoting viral propagation. The best-known examples of these are involved in mimicry, in which viral machinery "imitates" immunomodulatory elements in the vertebrate defense system. But recent findings have highlighted a vast and rapidly expanding array of other virologs that include many genes not typically found in viruses, such as those involved in translation, central carbon metabolism, cytoskeletal structure, nutrient transport, vesicular trafficking, and light harvesting. Unraveling the roles of virologs during infection as well as the evolutionary pathways through which complex functional repertoires are acquired by viruses are important frontiers at the forefront of giant virus research.
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Affiliation(s)
- Mohammad Moniruzzaman
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Maria Paula Erazo Garcia
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Roxanna Farzad
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Anh D Ha
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Abdeali Jivaji
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Sangita Karki
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Uri Sheyn
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Joshua Stanton
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
| | - Benjamin Minch
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Danae Stephens
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables, FL 33149, United States
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, United States
| | - Rodrigo A L Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Jonatas S Abrahao
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, United States
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg, VA 24061, United States
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5
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Caetano-Anollés G, Claverie JM, Nasir A. A critical analysis of the current state of virus taxonomy. Front Microbiol 2023; 14:1240993. [PMID: 37601376 PMCID: PMC10435761 DOI: 10.3389/fmicb.2023.1240993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and a priorism. Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification. We emphasize that viruses are crucial contributors to the genomic and functional makeup of holobionts, organismal communities that behave as units of biological organization. Consequently, viruses cannot be considered taxonomic units because they challenge crucial concepts of organismality and individuality. Instead, they should be considered processes that integrate virions and their hosts into life cycles. Viruses harbor phylogenetic signatures of genetic transfer that compromise monophyly and the validity of deep taxonomic ranks. A focus on building phylogenetic networks using alignment-free methodologies and molecular structure can help mitigate the impasse, at least in part. Finally, structural phylogenomic analysis challenges the polyphyletic scenario of multiple viral origins adopted by virus taxonomy, defeating a polyphyletic origin and supporting instead an ancient cellular origin of viruses. We therefore, prompt abandoning deep ranks and urgently reevaluating the validity of taxonomic units and principles of virus classification.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and C.R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jean-Michel Claverie
- Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), IM2B, IOM, Aix Marseille University, CNRS, Marseille, France
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6
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Alempic JM, Lartigue A, Goncharov AE, Grosse G, Strauss J, Tikhonov AN, Fedorov AN, Poirot O, Legendre M, Santini S, Abergel C, Claverie JM. An Update on Eukaryotic Viruses Revived from Ancient Permafrost. Viruses 2023; 15:v15020564. [PMID: 36851778 PMCID: PMC9958942 DOI: 10.3390/v15020564] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
One quarter of the Northern hemisphere is underlain by permanently frozen ground, referred to as permafrost. Due to climate warming, irreversibly thawing permafrost is releasing organic matter frozen for up to a million years, most of which decomposes into carbon dioxide and methane, further enhancing the greenhouse effect. Part of this organic matter also consists of revived cellular microbes (prokaryotes, unicellular eukaryotes) as well as viruses that have remained dormant since prehistorical times. While the literature abounds on descriptions of the rich and diverse prokaryotic microbiomes found in permafrost, no additional report about "live" viruses have been published since the two original studies describing pithovirus (in 2014) and mollivirus (in 2015). This wrongly suggests that such occurrences are rare and that "zombie viruses" are not a public health threat. To restore an appreciation closer to reality, we report the preliminary characterizations of 13 new viruses isolated from seven different ancient Siberian permafrost samples, one from the Lena river and one from Kamchatka cryosol. As expected from the host specificity imposed by our protocol, these viruses belong to five different clades infecting Acanthamoeba spp. but not previously revived from permafrost: Pandoravirus, Cedratvirus, Megavirus, and Pacmanvirus, in addition to a new Pithovirus strain.
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Affiliation(s)
- Jean-Marie Alempic
- IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Institut Microbiologie, Bioénergies et Biotechnologie, and Institut Origines, CNRS, Aix Marseille University, 13288 Marseille, France
| | - Audrey Lartigue
- IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Institut Microbiologie, Bioénergies et Biotechnologie, and Institut Origines, CNRS, Aix Marseille University, 13288 Marseille, France
| | - Artemiy E. Goncharov
- Department of Molecular Microbiology, Institute of Experimental Medicine, Department of Epidemiology, Parasitology and Disinfectology, Northwestern State Medical Mechnikov University, Saint Petersburg 195067, Russia
| | - Guido Grosse
- Permafrost Research Section, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 14473 Potsdam, Germany
- Institute of Geosciences, University of Potsdam, 14478 Potsdam, Germany
| | - Jens Strauss
- Permafrost Research Section, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 14473 Potsdam, Germany
| | - Alexey N. Tikhonov
- Laboratory of Theriology, Zoological Institute of Russian Academy of Science, Saint Petersburg 199034, Russia
| | | | - Olivier Poirot
- IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Institut Microbiologie, Bioénergies et Biotechnologie, and Institut Origines, CNRS, Aix Marseille University, 13288 Marseille, France
| | - Matthieu Legendre
- IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Institut Microbiologie, Bioénergies et Biotechnologie, and Institut Origines, CNRS, Aix Marseille University, 13288 Marseille, France
| | - Sébastien Santini
- IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Institut Microbiologie, Bioénergies et Biotechnologie, and Institut Origines, CNRS, Aix Marseille University, 13288 Marseille, France
| | - Chantal Abergel
- IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Institut Microbiologie, Bioénergies et Biotechnologie, and Institut Origines, CNRS, Aix Marseille University, 13288 Marseille, France
| | - Jean-Michel Claverie
- IGS, Information Génomique & Structurale (UMR7256), Institut de Microbiologie de la Méditerranée (FR 3489), Institut Microbiologie, Bioénergies et Biotechnologie, and Institut Origines, CNRS, Aix Marseille University, 13288 Marseille, France
- Correspondence: ; Tel.: +33-413-946-777
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7
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Past and present giant viruses diversity explored through permafrost metagenomics. Nat Commun 2022; 13:5853. [PMID: 36207343 PMCID: PMC9546926 DOI: 10.1038/s41467-022-33633-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
Giant viruses are abundant in aquatic environments and ecologically important through the metabolic reprogramming of their hosts. Less is known about giant viruses from soil even though two of them, belonging to two different viral families, were reactivated from 30,000-y-old permafrost samples. This suggests an untapped diversity of Nucleocytoviricota in this environment. Through permafrost metagenomics we reveal a unique diversity pattern and a high heterogeneity in the abundance of giant viruses, representing up to 12% of the sum of sequence coverage in one sample. Pithoviridae and Orpheoviridae-like viruses were the most important contributors. A complete 1.6 Mb Pithoviridae-like circular genome was also assembled from a 42,000-y-old sample. The annotation of the permafrost viral sequences revealed a patchwork of predicted functions amidst a larger reservoir of genes of unknown functions. Finally, the phylogenetic reconstructions not only revealed gene transfers between cells and viruses, but also between viruses from different families. Although giant viruses are abundant in aquatic environments, less is known about giant viruses in soil. Here, the authors use permafrost metagenomics to reveal giant virus diversity and heterogeneity, as well as gene transfers between viruses from different families.
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8
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Genome Sequences of Two New Pandoravirus Strains Isolated from Brazil and France. Microbiol Resour Announc 2022; 11:e0013122. [PMID: 35731201 PMCID: PMC9302070 DOI: 10.1128/mra.00131-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Pandoraviruses are giant viruses of amoebas with a wide range of genome sizes (1.5 to 2.5 Mbp) and 1-μm ovoid viral particles. Here, we report the isolation, genome sequencing, and annotation of two new strains from the proposed family Pandoraviridae: Pandoravirus belohorizontensis and Pandoravirus aubagnensis.
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9
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Speciale I, Notaro A, Abergel C, Lanzetta R, Lowary TL, Molinaro A, Tonetti M, Van Etten JL, De Castro C. The Astounding World of Glycans from Giant Viruses. Chem Rev 2022; 122:15717-15766. [PMID: 35820164 PMCID: PMC9614988 DOI: 10.1021/acs.chemrev.2c00118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Viruses are a heterogeneous ensemble of entities, all
sharing the
need for a suitable host to replicate. They are extremely diverse,
varying in morphology, size, nature, and complexity of their genomic
content. Typically, viruses use host-encoded glycosyltransferases
and glycosidases to add and remove sugar residues from their glycoproteins.
Thus, the structure of the glycans on the viral proteins have, to
date, typically been considered to mimick those of the host. However,
the more recently discovered large and giant viruses differ from this
paradigm. At least some of these viruses code for an (almost) autonomous
glycosylation pathway. These viral genes include those that encode
the production of activated sugars, glycosyltransferases, and other
enzymes able to manipulate sugars at various levels. This review focuses
on large and giant viruses that produce carbohydrate-processing enzymes.
A brief description of those harboring these features at the genomic
level will be discussed, followed by the achievements reached with
regard to the elucidation of the glycan structures, the activity of
the proteins able to manipulate sugars, and the organic synthesis
of some of these virus-encoded glycans. During this progression, we
will also comment on many of the challenging questions on this subject
that remain to be addressed.
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Affiliation(s)
- Immacolata Speciale
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy
| | - Anna Notaro
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy.,Centre National de la Recherche Scientifique, Information Génomique & Structurale, Aix-Marseille University, Unité Mixte de Recherche 7256, IMM, IM2B, 13288 Marseille, Cedex 9, France
| | - Chantal Abergel
- Centre National de la Recherche Scientifique, Information Génomique & Structurale, Aix-Marseille University, Unité Mixte de Recherche 7256, IMM, IM2B, 13288 Marseille, Cedex 9, France
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Napoli, Via Cintia 4, 80126 Napoli, Italy
| | - Todd L Lowary
- Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, Nangang 11529, Taipei, Taiwan
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli, Via Cintia 4, 80126 Napoli, Italy
| | - Michela Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900, United States.,Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, United States
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy
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10
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Xia Y, Cheng H, Zhong J. Hybrid Sequencing Resolved Inverted Terminal Repeats in the Genome of Megavirus Baoshan. Front Microbiol 2022; 13:831659. [PMID: 35620092 PMCID: PMC9127612 DOI: 10.3389/fmicb.2022.831659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
Mimivirus is a group of amoeba-infecting DNA viruses with linear double-strand genome. It is found to be ubiquitous in nature worldwide. Here, we reported the complete genome of a new member of Mimivirus lineage C isolated from a fresh water pond in Shanghai, China. Its 1,224,839-bp genome encoded 1,062 predicted ORFs. Combining the results of Nanopore, Illumina, and Sanger sequencing technologies, two identical 23,919 bp inverted terminal repeats (ITRs) were identified at both extremities of the viral linear genome, one of which was missing in the draft assembly based on Illumina data only. The discovery of ITRs of Mimivirus provided a new insight into Mimivirus genome structure.
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Affiliation(s)
- Yucheng Xia
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Department of Microbiology and Immunology, School of Life Sciences, Fudan University, Shanghai, China
| | - Huanyu Cheng
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Department of Microbiology and Immunology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiang Zhong
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Department of Microbiology and Immunology, School of Life Sciences, Fudan University, Shanghai, China
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11
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Talbert PB, Armache KJ, Henikoff S. Viral histones: pickpocket's prize or primordial progenitor? Epigenetics Chromatin 2022; 15:21. [PMID: 35624484 PMCID: PMC9145170 DOI: 10.1186/s13072-022-00454-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
The common histones H2A, H2B, H3, and H4 are the characteristic components of eukaryotic nucleosomes, which function to wrap DNA and compact the genome as well as to regulate access to DNA for transcription and replication in all eukaryotes. In the past two decades, histones have also been found to be encoded in some DNA viruses, where their functions and properties are largely unknown, though recently histones from two related viruses have been shown to form nucleosome-like structures in vitro. Viral histones can be highly similar to eukaryotic histones in primary sequence, suggesting they have been recently picked up from eukaryotic hosts, or they can be radically divergent in primary sequence and may occur as conjoined histone doublets, triplets, or quadruplets, suggesting ancient origins prior to the divergence of modern eukaryotes. Here, we review what is known of viral histones and discuss their possible origins and functions. We consider how the viral life cycle may affect their properties and histories, and reflect on the possible roles of viruses in the origin of the nucleus of modern eukaryotic cells.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute and Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 550 First Ave, New York, NY, 10016, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute and Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
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12
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Boratto PVM, Serafim MSM, Witt ASA, Crispim APC, de Azevedo BL, de Souza GAP, de Aquino ILM, Machado TB, Queiroz VF, Rodrigues RAL, Bergier I, Cortines JR, de Farias ST, dos Santos RN, Campos FS, Franco AC, Abrahão JS. A Brief History of Giant Viruses’ Studies in Brazilian Biomes. Viruses 2022; 14:v14020191. [PMID: 35215784 PMCID: PMC8875882 DOI: 10.3390/v14020191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 02/01/2023] Open
Abstract
Almost two decades after the isolation of the first amoebal giant viruses, indubitably the discovery of these entities has deeply affected the current scientific knowledge on the virosphere. Much has been uncovered since then: viruses can now acknowledge complex genomes and huge particle sizes, integrating remarkable evolutionary relationships that date as early as the emergence of life on the planet. This year, a decade has passed since the first studies on giant viruses in the Brazilian territory, and since then biomes of rare beauty and biodiversity (Amazon, Atlantic forest, Pantanal wetlands, Cerrado savannas) have been explored in the search for giant viruses. From those unique biomes, novel viral entities were found, revealing never before seen genomes and virion structures. To celebrate this, here we bring together the context, inspirations, and the major contributions of independent Brazilian research groups to summarize the accumulated knowledge about the diversity and the exceptionality of some of the giant viruses found in Brazil.
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Affiliation(s)
- Paulo Victor M. Boratto
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Mateus Sá M. Serafim
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Amanda Stéphanie A. Witt
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Ana Paula C. Crispim
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Bruna Luiza de Azevedo
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Gabriel Augusto P. de Souza
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Isabella Luiza M. de Aquino
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Talita B. Machado
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Victória F. Queiroz
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Rodrigo A. L. Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
| | - Ivan Bergier
- Embrapa Pantanal, Corumbá 79320-900, Mato Grosso do Sul, Brazil;
| | - Juliana Reis Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Rio de Janeiro, Brazil;
| | - Savio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa 58050-085, Paraíba, Brazil;
| | - Raíssa Nunes dos Santos
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 90.050-170, Rio Grande do Sul, Brazil; (R.N.d.S.); (F.S.C.); (A.C.F.)
| | - Fabrício Souza Campos
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 90.050-170, Rio Grande do Sul, Brazil; (R.N.d.S.); (F.S.C.); (A.C.F.)
| | - Ana Cláudia Franco
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 90.050-170, Rio Grande do Sul, Brazil; (R.N.d.S.); (F.S.C.); (A.C.F.)
| | - Jônatas S. Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil; (P.V.M.B.); (M.S.M.S.); (A.S.A.W.); (A.P.C.C.); (B.L.d.A.); (G.A.P.d.S.); (I.L.M.d.A.); (T.B.M.); (V.F.Q.); (R.A.L.R.)
- Correspondence:
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13
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Claverie JM, Santini S. Validation of predicted anonymous proteins simply using Fisher's exact test. BIOINFORMATICS ADVANCES 2021; 1:vbab034. [PMID: 36700095 PMCID: PMC9710694 DOI: 10.1093/bioadv/vbab034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 01/28/2023]
Abstract
Motivation Genomes sequencing has become the primary (and often the sole) experimental method to characterize newly discovered organisms, in particular from the microbial world (bacteria, archaea, viruses). This generates an ever increasing number of predicted proteins the existence of which is unwarranted, in particular among those without homolog in model organisms. As a last resort, the computation of the selection pressure from pairwise alignments of the corresponding 'Open Reading Frames' (ORFs) can be used to validate their existences. However, this approach is error-prone, as not usually associated with a significance test. Results We introduce the use of the straightforward Fisher's exact test as a postprocessing of the results provided by the popular CODEML sequence comparison software. The respective rates of nucleotide changes at the nonsynonymous versus synonymous position (as determined by CODEML) are turned into entries into a 2 × 2 contingency table, the probability of which is computed under the Null hypothesis that they should not behave differently if the ORFs do not encode actual proteins. Using the genome sequences of two recently isolated giant viruses, we show that strong negative selection pressures do not always provide a solid argument in favor of the existence of proteins.
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Affiliation(s)
- Jean-Michel Claverie
- Aix-Marseille University, CNRS, IGS (UMR7256), IMM (FR3479), Luminy, Marseille F-13288, France,To whom correspondence should be addressed.
| | - Sébastien Santini
- Aix-Marseille University, CNRS, IGS (UMR7256), IMM (FR3479), Luminy, Marseille F-13288, France
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14
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Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses. mSphere 2021; 6:6/2/e01298-20. [PMID: 33883262 PMCID: PMC8546719 DOI: 10.1128/msphere.01298-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, in silico host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Tara Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships 4-fold compared to random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by 12-fold. Finally, we inferred virophage-NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments.IMPORTANCE NCLDVs can infect a wide range of eukaryotes, although their life cycle is less dependent on hosts compared to other viruses. However, our understanding of NCLDV-host systems is highly limited because few of these viruses have been isolated so far. Co-occurrence information has been assumed to be useful to predict virus-host interactions. In this study, we quantitatively show the effectiveness of co-occurrence inference for NCLDV host prediction. We also improve the prediction performance with a phylogeny-guided method, which leads to a concise list of candidate host lineages for three NCLDV families. Our results underpin the usage of co-occurrence approaches for the metagenomic exploration of the ecology of this diverse group of viruses.
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15
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Chaudhari HV, Inamdar MM, Kondabagil K. Scaling relation between genome length and particle size of viruses provides insights into viral life history. iScience 2021; 24:102452. [PMID: 34113814 PMCID: PMC8169800 DOI: 10.1016/j.isci.2021.102452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/23/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
In terms of genome and particle sizes, viruses exhibit great diversity. With the discovery of several nucleocytoplasmic large DNA viruses (NCLDVs) and jumbo phages, the relationship between particle and genome sizes has emerged as an important criterion for understanding virus evolution. We use allometric scaling of capsid volume with the genome length of different groups of viruses to shed light on its relationship with virus life history. The allometric exponents for icosahedral dsDNA bacteriophages and NCDLVs were found to be 1 and 2, respectively, indicating that with increasing capsid size DNA packaging density remains the same in bacteriophages but decreases for NCLDVs. We argue that the exponents are largely shaped by their entry mechanism and capsid mechanical stability. We further show that these allometric size parameters are also intricately linked to the relative energy costs of translation and replication in viruses and can have further implications on viral life history. Capsid and genome size allometric exponent gives insights into viral life history The allometric exponent of NCLDVs is almost twice that of bacteriophages The exponent is largely shaped by the viral entry mechanism and capsid stability The relaxed genome size constraint allows large viruses to evolve greater autonomy
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Affiliation(s)
- Harshali V Chaudhari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Mandar M Inamdar
- Department of Civil Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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16
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Nasir A, Romero-Severson E, Claverie JM. Investigating the Concept and Origin of Viruses. Trends Microbiol 2020; 28:959-967. [PMID: 33158732 PMCID: PMC7609044 DOI: 10.1016/j.tim.2020.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/21/2022]
Abstract
The ongoing COVID-19 pandemic has piqued public interest in the properties, evolution, and emergence of viruses. Here, we discuss how these basic questions have surprisingly remained disputed despite being increasingly within the reach of scientific analysis. We review recent data-driven efforts that shed light into the origin and evolution of viruses and explain factors that resist the widespread acceptance of new views and insights. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We note that the philosophical aspects of virus evolution also impact the way we might prepare for future outbreaks.
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Affiliation(s)
- Arshan Nasir
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Ethan Romero-Severson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jean-Michel Claverie
- Aix Marseille University, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
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17
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Shrinking of repeating unit length in leucine-rich repeats from double-stranded DNA viruses. Arch Virol 2020; 166:43-64. [PMID: 33052487 DOI: 10.1007/s00705-020-04820-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
Leucine-rich repeats (LRRs) are present in over 563,000 proteins from viruses to eukaryotes. LRRs repeat in tandem and have been classified into fifteen classes in which the repeat unit lengths range from 20 to 29 residues. Most LRR proteins are involved in protein-protein or ligand interactions. The amount of genome sequence data from viruses is increasing rapidly, and although viral LRR proteins have been identified, a comprehensive sequence analysis has not yet been done, and their structures, functions, and evolution are still unknown. In the present study, we characterized viral LRRs by sequence analysis and identified over 600 LRR proteins from 89 virus species. Most of these proteins were from double-stranded DNA (dsDNA) viruses, including nucleocytoplasmic large dsDNA viruses (NCLDVs). We found that the repeating unit lengths of 11 types are one to five residues shorter than those of the seven known corresponding LRR classes. The repeating units of six types are 19 residues long and are thus the shortest among all LRRs. In addition, two of the LRR types are unique and have not been observed in bacteria, archae or eukaryotes. Conserved strongly hydrophobic residues such as Leu, Val or Ile in the consensus sequences are replaced by Cys with high frequency. Phylogenetic analysis indicated that horizontal gene transfer of some viral LRR genes had occurred between the virus and its host. We suggest that the shortening might contribute to the survival strategy of viruses. The present findings provide a new perspective on the origin and evolution of LRRs.
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18
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Mughal F, Nasir A, Caetano-Anollés G. The origin and evolution of viruses inferred from fold family structure. Arch Virol 2020; 165:2177-2191. [PMID: 32748179 PMCID: PMC7398281 DOI: 10.1007/s00705-020-04724-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/30/2020] [Indexed: 12/16/2022]
Abstract
The canonical frameworks of viral evolution describe viruses as cellular predecessors, reduced forms of cells, or entities that escaped cellular control. The discovery of giant viruses has changed these standard paradigms. Their genetic, proteomic and structural complexities resemble those of cells, prompting a redefinition and reclassification of viruses. In a previous genome-wide analysis of the evolution of structural domains in proteomes, with domains defined at the fold superfamily level, we found the origins of viruses intertwined with those of ancient cells. Here, we extend these data-driven analyses to the study of fold families confirming the co-evolution of viruses and ancient cells and the genetic ability of viruses to foster molecular innovation. The results support our suggestion that viruses arose by genomic reduction from ancient cells and validate a co-evolutionary ‘symbiogenic’ model of viral origins.
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Affiliation(s)
- Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Arshan Nasir
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Abstract
DNA methylation is an important epigenetic mark that contributes to various regulations in all domains of life. Giant viruses are widespread dsDNA viruses with gene contents overlapping the cellular world that also encode DNA methyltransferases. Yet, virtually nothing is known about the methylation of their DNA. Here, we use single-molecule real-time sequencing to study the complete methylome of a large spectrum of giant viruses. We show that DNA methylation is widespread, affecting 2/3 of the tested families, although unevenly distributed. We also identify the corresponding viral methyltransferases and show that they are subject to intricate gene transfers between bacteria, viruses and their eukaryotic host. Most methyltransferases are conserved, functional and under purifying selection, suggesting that they increase the viruses' fitness. Some virally encoded methyltransferases are also paired with restriction endonucleases forming Restriction-Modification systems. Our data suggest that giant viruses' methyltransferases are involved in diverse forms of virus-pathogens interactions during coinfections.
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Characterization of Mollivirus kamchatka, the First Modern Representative of the Proposed Molliviridae Family of Giant Viruses. J Virol 2020; 94:JVI.01997-19. [PMID: 31996429 DOI: 10.1128/jvi.01997-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
Microbes trapped in permanently frozen paleosoils (permafrost) are the focus of increasing research in the context of global warming. Our previous investigations led to the discovery and reactivation of two Acanthamoeba-infecting giant viruses, Mollivirus sibericum and Pithovirus sibericum, from a 30,000-year old permafrost layer. While several modern pithovirus strains have since been isolated, no contemporary mollivirus relative was found. We now describe Mollivirus kamchatka, a close relative to M. sibericum, isolated from surface soil sampled on the bank of the Kronotsky River in Kamchatka, Russian Federation. This discovery confirms that molliviruses have not gone extinct and are at least present in a distant subarctic continental location. This modern isolate exhibits a nucleocytoplasmic replication cycle identical to that of M. sibericum Its spherical particle (0.6 μm in diameter) encloses a 648-kb GC-rich double-stranded DNA genome coding for 480 proteins, of which 61% are unique to these two molliviruses. The 461 homologous proteins are highly conserved (92% identical residues, on average), despite the presumed stasis of M. sibericum for the last 30,000 years. Selection pressure analyses show that most of these proteins contribute to virus fitness. The comparison of these first two molliviruses clarify their evolutionary relationship with the pandoraviruses, supporting their provisional classification in a distinct family, the Molliviridae, pending the eventual discovery of intermediary missing links better demonstrating their common ancestry.IMPORTANCE Virology has long been viewed through the prism of human, cattle, or plant diseases, leading to a largely incomplete picture of the viral world. The serendipitous discovery of the first giant virus visible under a light microscope (i.e., >0.3 μm in diameter), mimivirus, opened a new era of environmental virology, now incorporating protozoan-infecting viruses. Planet-wide isolation studies and metagenome analyses have shown the presence of giant viruses in most terrestrial and aquatic environments, including upper Pleistocene frozen soils. Those systematic surveys have led authors to propose several new distinct families, including the Mimiviridae, Marseilleviridae, Faustoviridae, Pandoraviridae, and Pithoviridae We now propose to introduce one additional family, the Molliviridae, following the description of M. kamchatka, the first modern relative of M. sibericum, previously isolated from 30,000-year-old arctic permafrost.
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Bokhari RH, Amirjan N, Jeong H, Kim KM, Caetano-Anollés G, Nasir A. Bacterial Origin and Reductive Evolution of the CPR Group. Genome Biol Evol 2020; 12:103-121. [PMID: 32031619 PMCID: PMC7093835 DOI: 10.1093/gbe/evaa024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2020] [Indexed: 12/24/2022] Open
Abstract
The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. These features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial organisms that have probably evolved in an Archaea-like manner via the early loss of metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.
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Affiliation(s)
| | - Nooreen Amirjan
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Hyeonsoo Jeong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana
| | - Arshan Nasir
- Department of Biosciences, COMSATS University Islamabad, Pakistan
- Theoretical Biology & Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
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Brahim Belhaouari D, Baudoin JP, Gnankou F, Di Pinto F, Colson P, Aherfi S, La Scola B. Evidence of a Cellulosic Layer in Pandoravirus massiliensis Tegument and the Mystery of the Genetic Support of Its Biosynthesis. Front Microbiol 2019; 10:2932. [PMID: 31921087 PMCID: PMC6932959 DOI: 10.3389/fmicb.2019.02932] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/05/2019] [Indexed: 11/13/2022] Open
Abstract
Pandoraviruses are giant viruses of ameba with 1 μm-long virions. They have an ovoid morphology and are surrounded by a tegument-like structure lacking any capsid protein nor any gene encoding a capsid protein. In this work, we studied the ultrastructure of the tegument surrounding Pandoravirus massiliensis virions and noticed that this tegument is composed of a peripheral sugar layer, an electron-dense membrane, and a thick electron-dense layer consisting in several tubules arranged in a helicoidal structure resembling that of cellulose. Pandoravirus massiliensis particles were stained by Calcofluor white, a fluorescent dye of cellulose, and the enzymatic treatment of particles by cellulase showed the degradation of the viral tegument. We first hypothesized that the cellulose tegument could be synthesized by enzymes encoded by the virus. Bioinformatic analyses revealed in P. massiliensis, a candidate gene encoding a putative cellulose synthase, with a homology with the BcsA domain, one of the catalytic subunits of the bacterial cellulose synthase, but with a low level of homology. This gene was transcribed during the replicative cycle of P. massiliensis, but several arguments run counter to this hypothesis. Indeed, even if this gene is present in other pandoraviruses, the one of the strain studied is the only one to have this BcsA domain and no other enzymes involved in the synthesis of cellulose could be detected, although we cannot rule out that such genes could have been undetected among the large proportion of Orfans of pandoraviruses. As an alternative, we investigated whether P. massiliensis could divert the cellulose synthesis machinery of the ameba to its own account. Indeed, contrary to what is observed in the case of infections with other giant viruses such as mimiviruses, it appears that the transcription of the ameba, at least for the cellulose synthase gene, continues throughout the growth phase of particles of P. massiliensis. Finally, we believe that this scenario is more plausible. If confirmed, it could be a unique mechanism in the virosphere.
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Affiliation(s)
- Djamal Brahim Belhaouari
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
| | - Jean-Pierre Baudoin
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
| | - Franck Gnankou
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
| | - Fabrizio Di Pinto
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France.,IHU Méditerranée Infection, Marseille, France
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Akashi M, Takemura M. Co-Isolation and Characterization of Two Pandoraviruses and a Mimivirus from a Riverbank in Japan. Viruses 2019; 11:v11121123. [PMID: 31817274 PMCID: PMC6950457 DOI: 10.3390/v11121123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/14/2019] [Accepted: 11/19/2019] [Indexed: 11/24/2022] Open
Abstract
Giant viruses, like pandoraviruses and mimiviruses, have been discovered from diverse environments, and their broad global distribution has been established. Here, we report two new isolates of Pandoravirus spp. and one Mimivirus sp., named Pandoravirus hades, Pandoravirus persephone, and Mimivirus sp. isolate styx, co-isolated from riverbank soil in Japan. We obtained nearly complete sequences of the family B DNA polymerase gene (polB) of P. hades and P. persephone; the former carried two known intein regions, while the latter had only one. Phylogenetic analysis revealed that the two new pandoravirus isolates are closely related to Pandoravirus dulcis. Furthermore, random amplified polymorphic DNA analysis revealed that P. hades and P. persephone might harbor different genome structures. Based on phylogenetic analysis of the partial polB sequence, Mimivirus sp. isolate styx belongs to mimivirus lineage A. DNA staining suggested that the Pandoravirus spp. asynchronously replicates in amoeba cells while Mimivirus sp. replicates synchronously. We also observed that P. persephone- or Mimivirus sp. isolate styx-infected amoeba cytoplasm is extruded by the cells. To the best of our knowledge, we are the first to report the isolation of pandoraviruses in Asia. In addition, our results emphasize the importance of virus isolation from soil to reveal the ecology of giant viruses.
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A Puzzling Anomaly in the 4-Mer Composition of the Giant Pandoravirus Genomes Reveals a Stringent New Evolutionary Selection Process. J Virol 2019; 93:JVI.01206-19. [PMID: 31534042 DOI: 10.1128/jvi.01206-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/10/2019] [Indexed: 12/26/2022] Open
Abstract
Pandoraviridae is a rapidly growing family of giant viruses, all of which have been isolated using laboratory strains of Acanthamoeba The genomes of 10 distinct strains have been fully characterized, reaching up to 2.5 Mb in size. These double-stranded DNA genomes encode the largest of all known viral proteomes and are propagated in oblate virions that are among the largest ever described (1.2 μm long and 0.5 μm wide). The evolutionary origin of these atypical viruses is the object of numerous speculations. Applying the chaos game representation to the pandoravirus genome sequences, we discovered that the tetranucleotide (4-mer) "AGCT" is totally absent from the genomes of 2 strains (Pandoravirus dulcis and Pandoravirus quercus) and strongly underrepresented in others. Given the amazingly low probability of such an observation in the corresponding randomized sequences, we investigated its biological significance through a comprehensive study of the 4-mer compositions of all viral genomes. Our results indicate that AGCT was specifically eliminated during the evolution of the Pandoraviridae and that none of the previously proposed host-virus antagonistic relationships could explain this phenomenon. Unlike the three other families of giant viruses (Mimiviridae, Pithoviridae, and Molliviridae) infecting the same Acanthamoeba host, the pandoraviruses exhibit a puzzling genomic anomaly suggesting a highly specific DNA editing in response to a new kind of strong evolutionary pressure.IMPORTANCE Recent years have seen the discovery of several families of giant DNA viruses infecting the ubiquitous amoebozoa of the genus Acanthamoeba With double-stranded DNA (dsDNA) genomes reaching 2.5 Mb in length packaged in oblate particles the size of a bacterium, the pandoraviruses are currently the most complex and largest viruses known. In addition to their spectacular dimensions, the pandoraviruses encode the largest proportion of proteins without homologs in other organisms, which is thought to result from a de novo gene creation process. While using comparative genomics to investigate the evolutionary forces responsible for the emergence of such an unusual giant virus family, we discovered a unique bias in the tetranucleotide composition of the pandoravirus genomes that can result only from an undescribed evolutionary process not encountered in any other microorganism.
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Abstract
Genes encoding cytochrome P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play important roles in metabolism of endogenous regulatory molecules and exogenous chemicals. We now report that genes for multiple and unique P450s occur commonly in giant viruses in the Mimiviridae, Pandoraviridae, and other families in the proposed order Megavirales. P450 genes were also identified in a herpesvirus (Ranid herpesvirus 3) and a phage (Mycobacterium phage Adler). The Adler phage P450 was classified as CYP102L1, and the crystal structure of the open form was solved at 2.5 Å. Genes encoding known redox partners for P450s (cytochrome P450 reductase, ferredoxin and ferredoxin reductase, and flavodoxin and flavodoxin reductase) were not found in any viral genome so far described, implying that host redox partners may drive viral P450 activities. Giant virus P450 proteins share no more than 25% identity with the P450 gene products we identified in Acanthamoeba castellanii, an amoeba host for many giant viruses. Thus, the origin of the unique P450 genes in giant viruses remains unknown. If giant virus P450 genes were acquired from a host, we suggest it could have been from an as yet unknown and possibly ancient host. These studies expand the horizon in the evolution and diversity of the enormously important P450 superfamily. Determining the origin and function of P450s in giant viruses may help to discern the origin of the giant viruses themselves.
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