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Langley CA, Dietzen PA, Emerman M, Tenthorey JL, Malik HS. Antiviral Mx proteins have an ancient origin and widespread distribution among eukaryotes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606855. [PMID: 39149278 PMCID: PMC11326297 DOI: 10.1101/2024.08.06.606855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
First identified in mammals, Mx proteins are potent antivirals against a broad swathe of viruses. Mx proteins arose within the Dynamin superfamily of proteins (DSP), mediating critical cellular processes, such as endocytosis and mitochondrial, plastid, and peroxisomal dynamics. And yet, the evolutionary origins of Mx proteins are poorly understood. Using a series of phylogenomic analyses with stepwise increments in taxonomic coverage, we show that Mx proteins predate the interferon signaling system in vertebrates. Our analyses find an ancient monophyletic DSP lineage in eukaryotes that groups vertebrate and invertebrate Mx proteins with previously undescribed fungal MxF proteins, the relatively uncharacterized plant and algal Dynamin 4A/4C proteins, and representatives from several early-branching eukaryotic lineages. Thus, Mx-like proteins date back close to the origin of Eukarya. Our phylogenetic analyses also reveal that host-encoded and NCLDV (nucleocytoplasmic large DNA viruses)-encoded DSPs are interspersed in four distinct DSP lineages, indicating recurrent viral theft of host DSPs. Our analyses thus reveal an ancient history of viral and antiviral functions encoded by the Dynamin superfamily in eukaryotes.
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Affiliation(s)
- Caroline A. Langley
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
| | - Peter A. Dietzen
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jeannette L. Tenthorey
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
- Cellular Molecular Pharmacology, University of California San Francisco, San Francisco, CA
| | - Harmit S. Malik
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA
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Kawato S, Nozaki R, Kondo H, Hirono I. Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans. Microbiol Spectr 2024; 12:e0055923. [PMID: 38063384 PMCID: PMC10871703 DOI: 10.1128/spectrum.00559-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Crustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities. Our results point to a novel survival strategy of endogenous large DNA viruses colonizing the host genomes. These findings may clarify the evolution and spread of nimaviruses in crustaceans and lead to measures to control and prevent the spread of pathogenic nimaviruses in aquaculture settings.
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Affiliation(s)
- Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
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3
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Minch B, Chakraborty M, Purkis S, Rodrigue M, Moniruzzaman M. Active prokaryotic and eukaryotic viral ecology across spatial scale in a deep-sea brine pool. ISME COMMUNICATIONS 2024; 4:ycae084. [PMID: 39021441 PMCID: PMC11252502 DOI: 10.1093/ismeco/ycae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/03/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024]
Abstract
Deep-sea brine pools represent rare, extreme environments, providing unique insight into the limits of life on Earth, and by analogy, the plausibility of life beyond it. A distinguishing feature of many brine pools is presence of thick microbial mats that develop at the brine-seawater interface. While these bacterial and archaeal communities have received moderate attention, viruses and their host interactions in these environments remain underexplored. To bridge this knowledge gap, we leveraged metagenomic and metatranscriptomic data from three distinct zones within the NEOM brine pool system (Gulf of Aqaba) to reveal the active viral ecology around the pools. We report a remarkable diversity and activity of viruses infecting microbial hosts in this environment, including giant viruses, RNA viruses, jumbo phages, and Polinton-like viruses. Many of these form distinct clades-suggesting presence of untapped viral diversity in this ecosystem. Brine pool viral communities exhibit zone-specific differences in infection strategy-with lysogeny dominating the bacterial mat further away from the pool's center. We linked viruses to metabolically important prokaryotes-including association between a jumbo phage and a key manganese-oxidizing and arsenic-metabolizing bacterium. These foundational results illuminate the role of viruses in modulating brine pool microbial communities and biogeochemistry through revealing novel viral diversity, host associations, and spatial heterogeneity in viral dynamics.
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Affiliation(s)
- Benjamin Minch
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, United States
| | - Morgan Chakraborty
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, United States
| | - Sam Purkis
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, United States
| | | | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, United States
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Collier JL, Rest JS, Gallot-Lavallée L, Lavington E, Kuo A, Jenkins J, Plott C, Pangilinan J, Daum C, Grigoriev IV, Filloramo GV, Novák Vanclová AMG, Archibald JM. The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses. Curr Biol 2023; 33:5199-5207.e4. [PMID: 37913769 DOI: 10.1016/j.cub.2023.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/08/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
Viruses are the most abundant biological entities in the world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these are the recently described mirusviruses, which share some similarities with herpesviruses.1 50 years ago, "herpes-type" viral particles2 were found in a thraustochytrid member of the labyrinthulomycetes, a diverse group of abundant and ecologically important marine eukaryotes,3,4 but could not be further characterized by methods then available. Long-read sequencing has allowed us to connect the biology of mirusviruses and thraustochytrids. We sequenced the genome of the genetically tractable model thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381 and found that its 26 linear chromosomes have an extraordinary configuration. Subtelomeric ribosomal DNAs (rDNAs) found at all chromosome ends are interspersed with long repeated sequence elements denoted as long repeated-telomere and rDNA spacers (LORE-TEARS). We identified two genomic elements that are related to mirusvirus genomes. The first is a ∼300-kbp episome (circular element 1 [CE1]) present at a high copy number. Strikingly, the second, distinct, mirusvirus-like element is integrated between two sets of rDNAs and LORE-TEARS at the left end of chromosome 15 (LE-Chr15). Similar to metagenomically derived mirusviruses, these putative A. limacinum mirusviruses have a virion module related to that of herpesviruses along with an informational module related to nucleocytoplasmic large DNA viruses (NCLDVs). CE1 and LE-Chr15 bear striking similarities to episomal and endogenous latent forms of herpesviruses, respectively, and open new avenues of research into marine virus-host interactions.
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Affiliation(s)
- Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Nicolls Road, Stony Brook, NY 11794, USA.
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Nicolls Road, Stony Brook, NY 11794, USA.
| | - Lucie Gallot-Lavallée
- Department of Biochemistry & Molecular Biology, Dalhousie University, College Street, Halifax, NS B3H 4R2, Canada
| | - Erik Lavington
- Department of Ecology and Evolution, Stony Brook University, Nicolls Road, Stony Brook, NY 11794, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA
| | - Jerry Jenkins
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA; HudsonAlpha Institute for Biotechnology, Genome Way Northwest, Huntsville, AL 35806, USA
| | - Chris Plott
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA; HudsonAlpha Institute for Biotechnology, Genome Way Northwest, Huntsville, AL 35806, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, University Avenue, Berkeley, CA 94720, USA
| | - Gina V Filloramo
- Department of Biochemistry & Molecular Biology, Dalhousie University, College Street, Halifax, NS B3H 4R2, Canada
| | | | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, College Street, Halifax, NS B3H 4R2, Canada
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Bellas C, Hackl T, Plakolb MS, Koslová A, Fischer MG, Sommaruga R. Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses. Proc Natl Acad Sci U S A 2023; 120:e2300465120. [PMID: 37036967 PMCID: PMC10120064 DOI: 10.1073/pnas.2300465120] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/20/2023] [Indexed: 04/12/2023] Open
Abstract
Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that are no longer functional and are considered to be "genomic fossils." Genomic surveys of EVEs, however, are strongly biased toward animals and plants, whereas protists, which represent the majority of eukaryotic diversity, remain poorly represented. Here, we show that protist genomes harbor tens to thousands of diverse, ~14 to 40 kbp long dsDNA viruses. These EVEs, composed of virophages, Polinton-like viruses, and related entities, have remained hitherto hidden owing to poor sequence conservation between virus groups and their repetitive nature that precluded accurate short-read assembly. We show that long-read sequencing technology is ideal for resolving virus insertions. Many protist EVEs appear intact, and most encode integrases, which suggests that they have actively colonized hosts across the tree of eukaryotes. We also found evidence for gene expression in host transcriptomes and that closely related virophage and Polinton-like virus genomes are abundant in viral metagenomes, indicating that many EVEs are probably functional viruses.
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Affiliation(s)
| | - Thomas Hackl
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747AGGroningen, The Netherlands
| | | | - Anna Koslová
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120Heidelberg, Germany
| | - Matthias G. Fischer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120Heidelberg, Germany
| | - Ruben Sommaruga
- Department of Ecology, Universität Innsbruck, 6020Innsbruck, Austria
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6
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Benites LF, Stephens TG, Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evol 2022; 8:veac101. [PMID: 36381231 PMCID: PMC9651163 DOI: 10.1093/ve/veac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/29/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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7
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Guglielmini J, Gaia M, Da Cunha V, Criscuolo A, Krupovic M, Forterre P. Viral origin of eukaryotic type IIA DNA topoisomerases. Virus Evol 2022; 8:veac097. [PMID: 36533149 PMCID: PMC9752973 DOI: 10.1093/ve/veac097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/07/2022] [Indexed: 08/24/2023] Open
Abstract
Type II DNA topoisomerases of the family A (Topo IIAs) are present in all Bacteria (DNA gyrase) and eukaryotes. In eukaryotes, they play a major role in transcription, DNA replication, chromosome segregation, and modulation of chromosome architecture. The origin of eukaryotic Topo IIA remains mysterious since they are very divergent from their bacterial homologs and have no orthologs in Archaea. Interestingly, eukaryotic Topo IIAs have close homologs in viruses of the phylum Nucleocytoviricota, an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasmic large DNA viruses. Topo IIAs are also encoded by some bacterioviruses of the class Caudoviricetes (tailed bacteriophages). To elucidate the origin of the eukaryotic Topo IIA, we performed in-depth phylogenetic analyses on a dataset combining viral and cellular Topo IIA homologs. Topo IIAs encoded by Bacteria and eukaryotes form two monophyletic groups nested within Topo IIA encoded by Caudoviricetes and Nucleocytoviricota, respectively. Importantly, Nucleocytoviricota remained well separated from eukaryotes after removing both Bacteria and Caudoviricetes from the data set, indicating that the separation of Nucleocytoviricota and eukaryotes is probably not due to long-branch attraction artifact. The topologies of our trees suggest that the eukaryotic Topo IIA was probably acquired from an ancestral member of the Nucleocytoviricota of the class Megaviricetes, before the emergence of the last eukaryotic common ancestor (LECA). This result further highlights a key role of these viruses in eukaryogenesis and suggests that early proto-eukaryotes used a Topo IIB instead of a Topo IIA for solving their DNA topological problems.
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Affiliation(s)
| | - Morgan Gaia
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, 91000 Evry, France
| | - Violette Da Cunha
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Alexis Criscuolo
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Archaeal Virology Unit, 75015 Paris, France
| | - Patrick Forterre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Archaeal Virology Unit, 75015 Paris, France
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
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Xu Y, Wang H, Sahu SK, Li L, Liang H, Günther G, Wong GKS, Melkonian B, Melkonian M, Liu H, Wang S. Chromosome-level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment. THE NEW PHYTOLOGIST 2022; 235:1409-1425. [PMID: 35560066 DOI: 10.1111/nph.18220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the 'core chlorophytes'. We present a chromosome-level genome assembly of the freshwater type species of the class, Pedinomonas minor. We sequenced the genome using Pacbio, Illumina and Hi-C technologies, performed comparative analyses of genome and gene family evolution, and analyzed the transcriptome under various abiotic stresses. Although the genome is relatively small (55 Mb), it shares many traits with core chlorophytes including number of introns and protein-coding genes, messenger RNA (mRNA) lengths, and abundance of transposable elements. Pedinomonas minor is only bounded by the plasma membrane, thriving in temporary habitats that frequently dry out. Gene family innovations and expansions and transcriptomic responses to abiotic stresses have shed light on adaptations of P. minor to its fluctuating environment. Horizontal gene transfers from bacteria and fungi have possibly contributed to the evolution of some of these traits. We identified a putative endogenization site of a nucleocytoplasmic large DNA virus and hypothesized that endogenous viral elements donated foreign genes to the host genome, their spread enhanced by transposable elements, located at gene boundaries in several of the expanded gene families.
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Affiliation(s)
- Yan Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongli Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Hongping Liang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Gerd Günther
- Private Laboratory, Knittkuhler Str. 61, Düsseldorf, 40629, Germany
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Barbara Melkonian
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Michael Melkonian
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Huan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
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Schulz F, Abergel C, Woyke T. Giant virus biology and diversity in the era of genome-resolved metagenomics. Nat Rev Microbiol 2022; 20:721-736. [PMID: 35902763 DOI: 10.1038/s41579-022-00754-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/09/2022]
Abstract
The discovery of giant viruses, with capsids as large as some bacteria, megabase-range genomes and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. Until recently, most of our knowledge of giant viruses came from ~100 species-level isolates for which genome sequences were available. However, these isolates were primarily derived from laboratory-based co-cultivation with few cultured protists and algae and, thus, did not reflect the true diversity of giant viruses. Although virus co-cultures enabled valuable insights into giant virus biology, many questions regarding their origin, evolution and ecological importance remain unanswered. With advances in sequencing technologies and bioinformatics, our understanding of giant viruses has drastically expanded. In this Review, we summarize our understanding of giant virus diversity and biology based on viral isolates as laboratory cultivation has enabled extensive insights into viral morphology and infection strategies. We then explore how cultivation-independent approaches have heightened our understanding of the coding potential and diversity of the Nucleocytoviricota. We discuss how metagenomics has revolutionized our perspective of giant viruses by revealing their distribution across our planet's biomes, where they impact the biology and ecology of a wide range of eukaryotic hosts and ultimately affect global nutrient cycles.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Chantal Abergel
- Aix Marseille University, CNRS, IGS UMR7256, IMM FR3479, IM2B, IO, Marseille, France
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California Merced, Merced, CA, USA.
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10
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Park SH, Kyndt JA, Brown JK. Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer. Life (Basel) 2022; 12:life12030458. [PMID: 35330209 PMCID: PMC8955559 DOI: 10.3390/life12030458] [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] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/02/2022] Open
Abstract
Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.
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Affiliation(s)
- Sang-Hyuck Park
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA; (S.-H.P.); (J.K.B.)
- Institute of Cannabis Research, Colorado State University-Pueblo, Pueblo, CO 81001, USA
| | - John A. Kyndt
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA
- Correspondence:
| | - Judith K. Brown
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA; (S.-H.P.); (J.K.B.)
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Hongo Y, Kimura K, Takaki Y, Yoshida Y, Baba S, Kobayashi G, Nagasaki K, Hano T, Tomaru Y. The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus. Sci Rep 2021; 11:22877. [PMID: 34819553 PMCID: PMC8613185 DOI: 10.1038/s41598-021-00565-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
Diatoms are one of the most prominent oceanic primary producers and are now recognized to be distributed throughout the world. They maintain their population despite predators, infections, and unfavourable environmental conditions. One of the smallest diatoms, Chaetoceros tenuissimus, can coexist with infectious viruses during blooms. To further understand this relationship, we sequenced the C. tenuissimus strain NIES-3715 genome. A gene fragment of a replication-associated gene from the infectious ssDNA virus (designated endogenous virus-like fragment, EVLF) was found to be integrated into each 41 Mb of haploid assembly. In addition, the EVLF was transcriptionally active and conserved in nine other C. tenuissimus strains from different geographical areas, although the primary structures of their proteins varied. The phylogenetic tree further suggested that the EVLF was acquired by the ancestor of C. tenuissimus. Additionally, retrotransposon genes possessing a reverse transcriptase function were more abundant in C. tenuissimus than in Thalassiosira pseudonana and Phaeodactylum tricornutum. Moreover, a target site duplication, a hallmark for long interspersed nuclear element retrotransposons, flanked the EVLF. Therefore, the EVLF was likely integrated by a retrotransposon during viral infection. The present study provides further insights into the diatom-virus evolutionary relationship.
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Affiliation(s)
- Yuki Hongo
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan.
| | - Kei Kimura
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, 840-8502, Japan
| | - Yoshihiro Takaki
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yukari Yoshida
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Shuichiro Baba
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, 890-0065, Japan
| | - Genta Kobayashi
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, 840-8502, Japan
| | - Keizo Nagasaki
- Faculty of Science and Technology, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Takeshi Hano
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739-0452, Japan
| | - Yuji Tomaru
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739-0452, Japan.
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12
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Mönttinen HAM, Bicep C, Williams TA, Hirt RP. The genomes of nucleocytoplasmic large DNA viruses: viral evolution writ large. Microb Genom 2021; 7. [PMID: 34542398 PMCID: PMC8715426 DOI: 10.1099/mgen.0.000649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The nucleocytoplasmic large DNA viruses (NCLDVs) are a diverse group that currently contain the largest known virions and genomes, also called giant viruses. The first giant virus was isolated and described nearly 20 years ago. Their genome sizes were larger than for any other known virus at the time and it contained a number of genes that had not been previously described in any virus. The origin and evolution of these unusually complex viruses has been puzzling, and various mechanisms have been put forward to explain how some NCLDVs could have reached genome sizes and coding capacity overlapping with those of cellular microbes. Here we critically discuss the evidence and arguments on this topic. We have also updated and systematically reanalysed protein families of the NCLDVs to further study their origin and evolution. Our analyses further highlight the small number of widely shared genes and extreme genomic plasticity among NCLDVs that are shaped via combinations of gene duplications, deletions, lateral gene transfers and de novo creation of protein-coding genes. The dramatic expansions of the genome size and protein-coding gene capacity characteristic of some NCLDVs is now increasingly understood to be driven by environmental factors rather than reflecting relationships to an ancient common ancestor among a hypothetical cellular lineage. Thus, the evolution of NCLDVs is writ large viral, and their origin, like all other viral lineages, remains unknown.
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Affiliation(s)
- Heli A M Mönttinen
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Present address: Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Viikki Biocenter 2, Helsinki 00014, Finland
| | - Cedric Bicep
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Present address: Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont Ferrand, France
| | - Tom A Williams
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,School of Biological Sciences, University of Bristol, 24 Tyndall Ave., Bristol, BS8 1TH, UK
| | - Robert P Hirt
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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13
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Hannat S, Pontarotti P, Colson P, Kuhn ML, Galiana E, La Scola B, Aherfi S, Panabières F. Diverse Trajectories Drive the Expression of a Giant Virus in the Oomycete Plant Pathogen Phytophthora parasitica. Front Microbiol 2021; 12:662762. [PMID: 34140938 PMCID: PMC8204020 DOI: 10.3389/fmicb.2021.662762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Giant viruses of amoebas, recently classified in the class Megaviricetes, are a group of viruses that can infect major eukaryotic lineages. We previously identified a set of giant virus sequences in the genome of Phytophthora parasitica, an oomycete and a devastating major plant pathogen. How viral insertions shape the structure and evolution of the invaded genomes is unclear, but it is known that the unprecedented functional potential of giant viruses is the result of an intense genetic interplay with their hosts. We previously identified a set of giant virus sequences in the genome of P. parasitica, an oomycete and a devastating major plant pathogen. Here, we show that viral pieces are found in a 550-kb locus and are organized in three main clusters. Viral sequences, namely RNA polymerases I and II and a major capsid protein, were identified, along with orphan sequences, as a hallmark of giant viruses insertions. Mining of public databases and phylogenetic reconstructions suggest an ancient association of oomycetes and giant viruses of amoeba, including faustoviruses, African swine fever virus (ASFV) and pandoraviruses, and that a single viral insertion occurred early in the evolutionary history of oomycetes prior to the Phytophthora–Pythium radiation, estimated at ∼80 million years ago. Functional annotation reveals that the viral insertions are located in a gene sparse region of the Phytophthora genome, characterized by a plethora of transposable elements (TEs), effectors and other genes potentially involved in virulence. Transcription of viral genes was investigated through analysis of RNA-Seq data and qPCR experiments. We show that most viral genes are not expressed, and that a variety of mechanisms, including deletions, TEs insertions and RNA interference may contribute to transcriptional repression. However, a gene coding a truncated copy of RNA polymerase II along a set of neighboring sequences have been shown to be expressed in a wide range of physiological conditions, including responses to stress. These results, which describe for the first time the endogenization of a giant virus in an oomycete, contribute to challenge our view of Phytophthora evolution.
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Affiliation(s)
- Sihem Hannat
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,MEPHI, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Pierre Pontarotti
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,MEPHI, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France.,CNRS SNC5039, Marseille, France
| | - Philippe Colson
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,MEPHI, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France.,Assistance Publique - Hôpitaux de Marseille, Marseille, France
| | - Marie-Line Kuhn
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, France
| | - Eric Galiana
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, France
| | - Bernard La Scola
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,MEPHI, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Sarah Aherfi
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,MEPHI, Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France.,Assistance Publique - Hôpitaux de Marseille, Marseille, France
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14
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Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes. Proc Natl Acad Sci U S A 2021; 118:2009974118. [PMID: 33419955 DOI: 10.1073/pnas.2009974118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.
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15
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Moniruzzaman M, Weinheimer AR, Martinez-Gutierrez CA, Aylward FO. Widespread endogenization of giant viruses shapes genomes of green algae. Nature 2020; 588:141-145. [PMID: 33208937 DOI: 10.1038/s41586-020-2924-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/01/2020] [Indexed: 12/21/2022]
Abstract
Endogenous viral elements (EVEs)-viruses that have integrated their genomes into those of their hosts-are prevalent in eukaryotes and have an important role in genome evolution1,2. The vast majority of EVEs that have been identified to date are small genomic regions comprising a few genes2, but recent evidence suggests that some large double-stranded DNA viruses may also endogenize into the genome of the host1. Nucleocytoplasmic large DNA viruses (NCLDVs) have recently become of great interest owing to their large genomes and complex evolutionary origins3-6, but it is not yet known whether they are a prominent component of eukaryotic EVEs. Here we report the widespread endogenization of NCLDVs in diverse green algae; these giant EVEs reached sizes greater than 1 million base pairs and contained as many as around 10% of the total open reading frames in some genomes, substantially increasing the scale of known viral genes in eukaryotic genomes. These endogenized elements often shared genes with host genomic loci and contained numerous spliceosomal introns and large duplications, suggesting tight assimilation into host genomes. NCLDVs contain large and mosaic genomes with genes derived from multiple sources, and their endogenization represents an underappreciated conduit of new genetic material into eukaryotic lineages that can substantially impact genome composition.
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Affiliation(s)
| | | | | | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
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16
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Gong Z, Zhang Y, Han GZ. Molecular fossils reveal ancient associations of dsDNA viruses with several phyla of fungi. Virus Evol 2020; 6:veaa008. [PMID: 32071765 PMCID: PMC7017919 DOI: 10.1093/ve/veaa008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Little is known about the infections of double-stranded DNA (dsDNA) viruses in fungi. Here, we use a paleovirological method to systematically identify the footprints of past dsDNA virus infections within the fungal genomes. We uncover two distinct groups of endogenous nucleocytoplasmic large DNA viruses (NCLDVs) in at least seven fungal phyla (accounting for about a third of known fungal phyla), revealing an unprecedented diversity of dsDNA viruses in fungi. Interestingly, one fungal dsDNA virus lineage infecting six fungal phyla is closely related to the giant virus Pithovirus, suggesting giant virus relatives might widely infect fungi. Co-speciation analyses indicate fungal NCLDVs mainly evolved through cross-species transmission. Taken together, our findings provide novel insights into the diversity and evolution of NCLDVs in fungi.
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Affiliation(s)
- Zhen Gong
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Yu Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
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17
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Kabbara S, Bidon B, Kilani J, Dugé de Bernonville T, Clastre M, Courdavault V, Cock JM, Papon N. Megaviruses: An involvement in phytohormone receptor gene transfer in brown algae? Gene 2019; 704:149-151. [PMID: 31009683 DOI: 10.1016/j.gene.2019.04.055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/18/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Samar Kabbara
- Groupe d'Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Univ Angers, SFR 4208 ICAT, Angers, France
| | - Baptiste Bidon
- Groupe d'Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Univ Angers, SFR 4208 ICAT, Angers, France
| | - Jaafar Kilani
- Groupe d'Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Univ Angers, SFR 4208 ICAT, Angers, France
| | | | - Marc Clastre
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - J Mark Cock
- Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Université Paris 06, CNRS, Roscoff, France
| | - Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Univ Angers, SFR 4208 ICAT, Angers, France.
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18
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Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, Sebé-Pedrós A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. Comparative genomic analysis of the 'pseudofungus' Hyphochytrium catenoides. Open Biol 2019; 8:rsob.170184. [PMID: 29321239 PMCID: PMC5795050 DOI: 10.1098/rsob.170184] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/01/2017] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete ‘pseudofungus’; Hyphochytrium catenoides. Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.
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Affiliation(s)
- Guy Leonard
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Aurélie Labarre
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - David S Milner
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Adam Monier
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Darren Soanes
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Jeremy G Wideman
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Finlay Maguire
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sam Stevens
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Divya Sain
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92506, USA
| | - Xavier Grau-Bové
- Institute of Evolutionary Biology, CSIC-UPF, Barcelona, Catalonia, Spain
| | | | - Jason E Stajich
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92506, USA
| | - Konrad Paszkiewicz
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Neil Hall
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Thomas A Richards
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
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19
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Kabbara S, Hérivaux A, Dugé de Bernonville T, Courdavault V, Clastre M, Gastebois A, Osman M, Hamze M, Cock JM, Schaap P, Papon N. Diversity and Evolution of Sensor Histidine Kinases in Eukaryotes. Genome Biol Evol 2019; 11:86-108. [PMID: 30252070 PMCID: PMC6324907 DOI: 10.1093/gbe/evy213] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2018] [Indexed: 12/20/2022] Open
Abstract
Histidine kinases (HKs) are primary sensor proteins that act in cell signaling pathways generically referred to as "two-component systems" (TCSs). TCSs are among the most widely distributed transduction systems used by both prokaryotic and eukaryotic organisms to detect and respond to a broad range of environmental cues. The structure and distribution of HK proteins are now well documented in prokaryotes, but information is still fragmentary for eukaryotes. Here, we have taken advantage of recent genomic resources to explore the structural diversity and the phylogenetic distribution of HKs in the prominent eukaryotic supergroups. Searches of the genomes of 67 eukaryotic species spread evenly throughout the phylogenetic tree of life identified 748 predicted HK proteins. Independent phylogenetic analyses of predicted HK proteins were carried out for each of the major eukaryotic supergroups. This allowed most of the compiled sequences to be categorized into previously described HK groups. Beyond the phylogenetic analysis of eukaryotic HKs, this study revealed some interesting findings: 1) characterization of some previously undescribed eukaryotic HK groups with predicted functions putatively related to physiological traits; 2) discovery of HK groups that were previously believed to be restricted to a single kingdom in additional supergroups, and 3) indications that some evolutionary paths have led to the appearance, transfer, duplication, and loss of HK genes in some phylogenetic lineages. This study provides an unprecedented overview of the structure and distribution of HKs in the Eukaryota and represents a first step toward deciphering the evolution of TCS signaling in living organisms.
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Affiliation(s)
- Samar Kabbara
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
| | - Anaïs Hérivaux
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
| | | | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université François Rabelais de Tours, France
| | - Marc Clastre
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université François Rabelais de Tours, France
| | - Amandine Gastebois
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - J Mark Cock
- Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Université Paris 06, CNRS, Roscoff, France
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, United Kingdom
| | - Nicolas Papon
- Groupe d’Etude des Interactions Hôte-Pathogène, GEIHP, EA3142, Université d’Angers, SFR 4208 ICAT, France
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20
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Filée J. Giant viruses and their mobile genetic elements: the molecular symbiosis hypothesis. Curr Opin Virol 2018; 33:81-88. [DOI: 10.1016/j.coviro.2018.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 01/28/2023]
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21
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Zhang QY, Gui JF. Diversity, evolutionary contribution and ecological roles of aquatic viruses. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1486-1502. [DOI: 10.1007/s11427-018-9414-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 01/21/2023]
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22
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Bzhalava Z, Hultin E, Dillner J. Extension of the viral ecology in humans using viral profile hidden Markov models. PLoS One 2018; 13:e0190938. [PMID: 29351302 PMCID: PMC5774701 DOI: 10.1371/journal.pone.0190938] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/23/2017] [Indexed: 11/18/2022] Open
Abstract
When human samples are sequenced, many assembled contigs are "unknown", as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, "vFam". We used HMMER3 analysis of "unknown" human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family). In summary, we find that analysis using the HMMER3 algorithm and the "vFam" database greatly extended the detection of viruses in biospecimens from humans.
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Affiliation(s)
- Zurab Bzhalava
- Dept. of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Emilie Hultin
- Dept. of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Dillner
- Dept. of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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23
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Drezen JM, Gauthier J, Josse T, Bézier A, Herniou E, Huguet E. Foreign DNA acquisition by invertebrate genomes. J Invertebr Pathol 2017; 147:157-168. [DOI: 10.1016/j.jip.2016.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/09/2016] [Accepted: 09/14/2016] [Indexed: 12/14/2022]
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24
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A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window. Viruses 2017; 9:v9010017. [PMID: 28117696 PMCID: PMC5294986 DOI: 10.3390/v9010017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/13/2017] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases. A total of 66 eukaryotic genomic or transcriptomic datasets-many of which are from algae and aquatic protists-contained at least one of the five most consistently conserved NCLDV core genes. Phylogenetic study of the eukaryotic NCLDV-like sequences identified putative new members of already recognized viral families, as well as members of as yet unknown viral clades. Genomic evidence suggested that most of these sequences resulted from viral DNA integrations rather than contaminating viruses. Furthermore, the nature of the inserted viral genes helped predicting original functional capacities of the donor viruses. These insights confirm that genomic insertions of NCLDV DNA are common in eukaryotes and can be exploited to delineate the contours of NCLDV biodiversity.
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25
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Maumus F, Blanc G. Study of Gene Trafficking between Acanthamoeba and Giant Viruses Suggests an Undiscovered Family of Amoeba-Infecting Viruses. Genome Biol Evol 2016; 8:3351-3363. [PMID: 27811174 PMCID: PMC5203793 DOI: 10.1093/gbe/evw260] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2016] [Indexed: 01/10/2023] Open
Abstract
The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain unicellular eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. These findings prompted us to search the genome of Acanthamoeba castellanii strain Neff (Neff), one of the most prolific hosts in the discovery of giant NCLDVs, for possible DNA inserts of viral origin. We report the identification of 267 markers of lateral gene transfer with viruses, approximately half of which are clustered in Neff genome regions of viral origins, transcriptionally inactive or exhibit nucleotide-composition signatures suggestive of a foreign origin. The integrated viral genes had diverse origin among relatives of viruses that infect Neff, including Mollivirus, Pandoravirus, Marseillevirus, Pithovirus, and Mimivirus However, phylogenetic analysis suggests the existence of a yet-undiscovered family of amoeba-infecting NCLDV in addition to the five already characterized. The active transcription of some apparently anciently integrated virus-like genes suggests that some viral genes might have been domesticated during the amoeba evolution. These insights confirm that genomic insertion of NCLDV DNA is a common theme in eukaryotes. This gene flow contributed fertilizing the eukaryotic gene repertoire and participated in the occurrence of orphan genes, a long standing issue in genomics. Search for viral inserts in eukaryotic genomes followed by environmental screening of the original viruses should be used to isolate radically new NCLDVs.
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Affiliation(s)
| | - Guillaume Blanc
- Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS UMR (IMM FR 3479), Marseille, France
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Villarreal LP. Persistent virus and addiction modules: an engine of symbiosis. Curr Opin Microbiol 2016; 31:70-79. [PMID: 27039268 DOI: 10.1016/j.mib.2016.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 12/14/2022]
Abstract
The giant DNA viruses are highly prevalent and have a particular affinity for the lytic infection of unicellular eukaryotic host. The giant viruses can also be infected by inhibitory virophage which can provide lysis protection to their host. The combined protective and destructive action of such viruses can define a general model (PD) of virus-mediated host survival. Here, I present a general model for role such viruses play in the evolution of host symbiosis. By considering how virus mixtures can participate in addiction modules, I provide a functional explanation for persistence of virus derived genetic 'junk' in their host genomic habitats.
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Affiliation(s)
- Luis P Villarreal
- Center for Virus Research, University of California, Irvine, Irvine, CA 926197, USA.
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Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses. Proc Natl Acad Sci U S A 2015; 112:E5318-26. [PMID: 26305943 DOI: 10.1073/pnas.1506469112] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Virophages are recently discovered double-stranded DNA virus satellites that prey on giant viruses (nucleocytoplasmic large DNA viruses; NCLDVs), which are themselves parasites of unicellular eukaryotes. This coupled parasitism can result in the indirect control of eukaryotic cell mortality by virophages. However, the details of such tripartite relationships remain largely unexplored. We have discovered ∼300 predicted genes of putative virophage origin in the nuclear genome of the unicellular alga Bigelowiella natans. Physical clustering of these genes indicates that virophage genomes are integrated into the B. natans genome. Virophage inserts show high levels of similarity and synteny between each other, indicating that they are closely related. Virophage genes are transcribed not only in the sequenced B. natans strain but also in other Bigelowiella isolates, suggesting that transcriptionally active virophage inserts are widespread in Bigelowiella populations. Evidence that B. natans is also a host to NCLDV members is provided by the identification of NCLDV inserts in its genome. These putative large DNA viruses may be infected by B. natans virophages. We also identify four repeated elements sharing structural and genetic similarities with transpovirons--a class of mobile elements first discovered in giant viruses--that were probably independently inserted in the B. natans genome. We argue that endogenized provirophages may be beneficial to both the virophage and B. natans by (i) increasing the chances for the virophage to coinfect the host cell with an NCLDV prey and (ii) defending the host cell against fatal NCLDV infections.
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Abstract
ABSTRACT In the past decade knowledge about Megaviruses, also denoted as nucleocytoplasmic large DNA viruses (NCLDVs) has been growing quickly. In the current paper, we present a general description of NCLDVs including their genome size, gene functions and homologies to other forms of life and viruses. Evolution of giant viruses from the fourth domain of life (now extinct) and a genomic complexification from smaller DNA viruses are described. Undeniable is the fact that Megaviruses in terms of their size and genomic capacity belong in between cellular and viral worlds breaking several ‘viral dogmas.’ The host range of NCLDVs goes far beyond unicellular organisms and a major challenge in the future is to establish their pathogenicity in human population.
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Ye N, Zhang X, Miao M, Fan X, Zheng Y, Xu D, Wang J, Zhou L, Wang D, Gao Y, Wang Y, Shi W, Ji P, Li D, Guan Z, Shao C, Zhuang Z, Gao Z, Qi J, Zhao F. Saccharina genomes provide novel insight into kelp biology. Nat Commun 2015; 6:6986. [PMID: 25908475 PMCID: PMC4421812 DOI: 10.1038/ncomms7986] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/20/2015] [Indexed: 01/28/2023] Open
Abstract
Seaweeds are essential for marine ecosystems and have immense economic value. Here we present a comprehensive analysis of the draft genome of Saccharina japonica, one of the most economically important seaweeds. The 537-Mb assembled genomic sequence covered 98.5% of the estimated genome, and 18,733 protein-coding genes are predicted and annotated. Gene families related to cell wall synthesis, halogen concentration, development and defence systems were expanded. Functional diversification of the mannuronan C-5-epimerase and haloperoxidase gene families provides insight into the evolutionary adaptation of polysaccharide biosynthesis and iodine antioxidation. Additional sequencing of seven cultivars and nine wild individuals reveal that the genetic diversity within wild populations is greater than among cultivars. All of the cultivars are descendants of a wild S. japonica accession showing limited admixture with S. longissima. This study represents an important advance toward improving yields and economic traits in Saccharina and provides an invaluable resource for plant genome studies.
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Affiliation(s)
- Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Miao Miao
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Yi Zheng
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Zhou
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongsheng Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Yuan Gao
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yitao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Wenyu Shi
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peifeng Ji
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biosystems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zheng Guan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Changwei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhimeng Zhuang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhengquan Gao
- School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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Billoud B, Jouanno É, Nehr Z, Carton B, Rolland É, Chenivesse S, Charrier B. Localization of causal locus in the genome of the brown macroalga Ectocarpus: NGS-based mapping and positional cloning approaches. FRONTIERS IN PLANT SCIENCE 2015; 6:68. [PMID: 25745426 PMCID: PMC4333798 DOI: 10.3389/fpls.2015.00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/26/2015] [Indexed: 05/12/2023]
Abstract
Mutagenesis is the only process by which unpredicted biological gene function can be identified. Despite that several macroalgal developmental mutants have been generated, their causal mutation was never identified, because experimental conditions were not gathered at that time. Today, progresses in macroalgal genomics and judicious choices of suitable genetic models make mutated gene identification possible. This article presents a comparative study of two methods aiming at identifying a genetic locus in the brown alga Ectocarpus siliculosus: positional cloning and Next-Generation Sequencing (NGS)-based mapping. Once necessary preliminary experimental tools were gathered, we tested both analyses on an Ectocarpus morphogenetic mutant. We show how a narrower localization results from the combination of the two methods. Advantages and drawbacks of these two approaches as well as potential transfer to other macroalgae are discussed.
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Affiliation(s)
- Bernard Billoud
- Sorbonne Université, UPMC University Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de RoscoffCS 90074, F-29688, Roscoff cedex, France
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Forterre P, Krupovic M, Prangishvili D. Cellular domains and viral lineages. Trends Microbiol 2014; 22:554-8. [PMID: 25129822 DOI: 10.1016/j.tim.2014.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/09/2014] [Accepted: 07/16/2014] [Indexed: 11/25/2022]
Abstract
It has been claimed that giant DNA viruses represent a separate, fourth domain of life in addition to the domains of Bacteria, Archaea, and Eukarya. Such classification disregards fundamental differences between the two types of living entities - viruses and cells - and results in confusion and controversies in evolutionary scenarios. We highlight these problems and emphasize the importance of restricting the term 'domain' to the descendants of the last universal cellular ancestor (LUCA), based on the shared ribosome structure. We suggest tracing phylogeny of viruses along evolutionary lineages primarily defined by virion architectures and the structures of the major capsid proteins.
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Affiliation(s)
- Patrick Forterre
- Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France; Institut de Génétique et Microbiologie, University Paris-Sud, Centre National de la Recherche Scientifique (CNRS) UMR 8621, 91405 Orsay CEDEX, France.
| | - Mart Krupovic
- Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
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Filée J. Multiple occurrences of giant virus core genes acquired by eukaryotic genomes: the visible part of the iceberg? Virology 2014; 466-467:53-9. [PMID: 24998348 DOI: 10.1016/j.virol.2014.06.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 12/18/2022]
Abstract
Giant Viruses are a widespread group of viruses, characterized by huge genomes composed of a small subset of ancestral, vertically inherited core genes along with a large body of highly variable genes. In this study, I report the acquisition of 23 core ancestral Giant Virus genes by diverse eukaryotic species including various protists, a moss and a cnidarian. The viral genes are inserted in large scaffolds or chromosomes with intron-rich, eukaryotic-like genomic contexts, refuting the possibility of DNA contaminations. Some of these genes are expressed and in the cryptophyte alga Guillardia theta, a possible non-homologous displacement of the eukaryotic DNA primase by a viral D5 helicase/primase is documented. As core Giant Virus genes represent only a tiny fraction of the total genomic repertoire of these viruses, these results suggest that Giant Viruses represent an underestimated source of new genes and functions for their hosts.
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Affiliation(s)
- Jonathan Filée
- Laboratoire Evolution, Genomes, Spéciation (LEGS), CNRS UPR9034, Université Paris-Sud. Avenue de la Terrasse, 91190 Gif Sur Yvette, France.
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Plant genomes enclose footprints of past infections by giant virus relatives. Nat Commun 2014; 5:4268. [PMID: 24969138 PMCID: PMC4083422 DOI: 10.1038/ncomms5268] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/30/2014] [Indexed: 01/04/2023] Open
Abstract
Nucleocytoplasmic large DNA viruses (NCLDVs) are eukaryotic viruses with large genomes (100 kb–2.5 Mb), which include giant Mimivirus, Megavirus and Pandoravirus. NCLDVs are known to infect animals, protists and phytoplankton but were never described as pathogens of land plants. Here, we show that the bryophyte Physcomitrella patens and the lycophyte Selaginella moellendorffii have open reading frames (ORFs) with high phylogenetic affinities to NCLDV homologues. The P. patens genes are clustered in DNA stretches (up to 13 kb) containing up to 16 NCLDV-like ORFs. Molecular evolution analysis suggests that the NCLDV-like regions were acquired by horizontal gene transfer from distinct but closely related viruses that possibly define a new family of NCLDVs. Transcriptomics and DNA methylation data indicate that the NCLDV-like regions are transcriptionally inactive and are highly cytosine methylated through a mechanism not relying on small RNAs. Altogether, our data show that members of NCLDV have infected land plants. Nucleocytoplasmic large DNA viruses, NCLDVs, are eukaryotic viruses with large genomes, known to infect animals and diverse unicellular eukaryotes. Here, Maumus et al. find NCLDV-like sequences in two land plants and show that they are transcriptionally inactive and highly methylated.
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Gilbert C, Cordaux R. Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes. Genome Biol Evol 2013; 5:822-32. [PMID: 23563966 PMCID: PMC3673617 DOI: 10.1093/gbe/evt057] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Horizontal transfer (HT) of transposable elements (TEs) plays a key role in prokaryotic evolution, and mounting evidence suggests that it has also had an important impact on eukaryotic evolution. Although many prokaryote-to-prokaryote and eukaryote-to-eukaryote HTs of TEs have been characterized, only few cases have been reported between prokaryotes and eukaryotes. Here, we carried out a comprehensive search for all major groups of prokaryotic insertion sequences (ISs) in 430 eukaryote genomes. We uncovered a total of 80 sequences, all deriving from the IS607 family, integrated in the genomes of 14 eukaryote species belonging to four distinct phyla (Amoebozoa, Ascomycetes, Basidiomycetes, and Stramenopiles). Given that eukaryote IS607-like sequences are most closely related to cyanobacterial IS607 and that their phylogeny is incongruent with that of their hosts, we conclude that the presence of IS607-like sequences in eukaryotic genomes is the result of several HT events. Selection analyses further suggest that our ability to detect these prokaryote TEs today in eukaryotes is because HT of these sequences occurred recently and/or some IS607 elements were domesticated after HT, giving rise to new eukaryote genes. Supporting the recent age of some of these HTs, we uncovered intact full-length, potentially active IS607 copies in the amoeba Acanthamoeba castellani. Overall, our study shows that prokaryote-to-eukaryote HT of TEs occurred at relatively low frequency during recent eukaryote evolution and it sets IS607 as the most widespread TE (being present in prokaryotes, eukaryotes, and viruses).
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Affiliation(s)
- Clément Gilbert
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France.
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The giant Cafeteria roenbergensis virus that infects a widespread marine phagocytic protist is a new member of the fourth domain of Life. PLoS One 2011; 6:e18935. [PMID: 21559486 PMCID: PMC3084725 DOI: 10.1371/journal.pone.0018935] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 03/13/2011] [Indexed: 12/22/2022] Open
Abstract
Background A recent work has provided strong arguments in favor of a fourth domain of Life composed of nucleo-cytoplasmic large DNA viruses (NCLDVs). This hypothesis was supported by phylogenetic and phyletic analyses based on a common set of proteins conserved in Eukarya, Archaea, Bacteria, and viruses, and implicated in the functions of information storage and processing. Recently, the genome of a new NCLDV, Cafeteria roenbergensis virus (CroV), was released. The present work aimed to determine if CroV supports the fourth domain of Life hypothesis. Methods A consensus phylogenetic tree of NCLDVs including CroV was generated from a concatenated alignment of four universal proteins of NCLDVs. Some features of the gene complement of CroV and its distribution along the genome were further analyzed. Phylogenetic and phyletic analyses were performed using the previously identified common set of informational genes present in Eukarya, Archaea, Bacteria, and NCLDVs, including CroV. Findings Phylogenetic reconstructions indicated that CroV is clearly related to the Mimiviridae family. The comparison between the gene repertoires of CroV and Mimivirus showed similarities regarding the gene contents and genome organization. In addition, the phyletic clustering based on the comparison of informational gene repertoire between Eukarya, Archaea, Bacteria, and NCLDVs unambiguously classified CroV with other NCLDVs and clearly included it in a fourth domain of Life. Taken together, these data suggest that Mimiviridae, including CroV, may have inherited a common gene content probably acquired from a common Mimiviridae ancestor. Conclusions This further analysis of the gene repertoire of CroV consolidated the fourth domain of Life hypothesis and contributed to outline a functional pan-genome for giant viruses infecting phagocytic protistan grazers.
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Schroeder DC, Park Y, Yoon HM, Lee YS, Kang SW, Meints RH, Ivey RG, Choi TJ. Genomic analysis of the smallest giant virus--Feldmannia sp. virus 158. Virology 2009; 384:223-32. [PMID: 19054537 DOI: 10.1016/j.virol.2008.10.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 10/08/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
Genomic analysis of Feldmannia sp. virus 158, the second phaeovirus to be sequenced in its entirety, provides further evidence that large double-stranded DNA viruses share similar evolutionary pressures as cellular organisms. Reductive evolution is clearly evident within the phaeoviruses which occurred via several routes: the loss of genes from an ancestral virus core genome most likely through genetic drift; and as a result of relatively large recombination events that caused wholesale loss of genes. The entire genome is 154,641 bp in length and has 150 predicted coding sequences of which 87% have amino acid sequence similarities to other algal virus coding sequences within the family Phycodnaviridae. Significant similarities were found, for thirty eight coding sequences (25%), to genes in gene databanks that are known to be involved in processes that include DNA replication, DNA methylation, signal transduction, viral integration and transposition, and protein-protein interactions. Unsurprisingly, the greatest similarity was observed between the two known viruses that infect Feldmannia, indicating the taxonomic linkage of these two viruses with their hosts. Moreover, comparative analysis of phycodnaviral genomic sequences revealed the smallest set of core genes (10 out of a possible 31) required to make a functional nucleocytoplasmic large dsDNA virus.
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