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Yutin N, Mutz P, Krupovic M, Koonin EV. Mriyaviruses: small relatives of giant viruses. mBio 2024; 15:e0103524. [PMID: 38832788 PMCID: PMC11253617 DOI: 10.1128/mbio.01035-24] [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: 04/06/2024] [Accepted: 05/01/2024] [Indexed: 06/05/2024] Open
Abstract
The phylum Nucleocytoviricota consists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein structure comparison, we delineate a distinct group of viruses with double-stranded (ds) DNA genomes in the range of 35-45 kb that appear to be related to the Nucleocytoviricota. In phylogenetic trees of the conserved double jelly-roll major capsid proteins (MCPs) and DNA packaging ATPases, these viruses do not show affinity to any particular branch of the Nucleocytoviricota and accordingly would comprise a class which we propose to name "Mriyaviricetes" (after Ukrainian "mriya," dream). Structural comparison of the MCP suggests that, among the extant virus lineages, mriyaviruses are the closest one to the ancestor of the Nucleocytoviricota. In the phylogenetic trees, mriyaviruses split into two well-separated branches, the family Yaraviridae and proposed new family "Gamadviridae." The previously characterized members of these families, yaravirus and Pleurochrysis sp. endemic viruses, infect amoeba and haptophytes, respectively. The genomes of the rest of the mriyaviruses were assembled from metagenomes from diverse environments, suggesting that mriyaviruses infect various unicellular eukaryotes. Mriyaviruses lack DNA polymerase, which is encoded by all other members of the Nucleocytoviricota, and RNA polymerase subunits encoded by all cytoplasmic viruses among the Nucleocytoviricota, suggesting that they replicate in the host cell nuclei. All mriyaviruses encode a HUH superfamily endonuclease that is likely to be essential for the initiation of virus DNA replication via the rolling circle mechanism. IMPORTANCE The origin of giant viruses of eukaryotes that belong to the phylum Nucleocytoviricota is not thoroughly understood and remains a matter of major interest and debate. Here, we combine metagenome database searches with extensive protein sequence and structure analysis to describe a distinct group of viruses with comparatively small genomes of 35-45 kilobases that appear to comprise a distinct class within the phylum Nucleocytoviricota that we provisionally named "Mriyaviricetes." Mriyaviruses appear to be the closest identified relatives of the ancestors of the Nucleocytoviricota. Analysis of proteins encoded in mriyavirus genomes suggests that they replicate their genome via the rolling circle mechanism that is unusual among viruses with double-stranded DNA genomes and so far not described for members of Nucleocytoviricota.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
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Caetano-Anollés G. Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment. Viruses 2024; 16:1061. [PMID: 39066224 DOI: 10.3390/v16071061] [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: 06/05/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. Virus species are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by the phylogenetic analysis of aligned genomic or metagenomic sequences. Taxonomic units are assumed to be independent organizational, functional and evolutionary units that follow a 'natural history' rationale. Here, I use phylogenomic and other arguments to show that viruses are not self-standing genetically-driven systems acting as evolutionary units. Instead, they are crucial components of holobionts, which are units of biological organization that dynamically integrate the genetics, epigenetic, physiological and functional properties of their co-evolving members. Remarkably, phylogenomic analyses show that viruses share protein domains and loops with cells throughout history via massive processes of reticulate evolution, helping spread evolutionary innovations across a wider taxonomic spectrum. Thus, viruses are not merely MGEs or microbes. Instead, their genomes and proteomes conduct cellularly integrated processes akin to those cataloged by the GO Consortium. This prompts the generation of compositional hierarchies that replace the 'is-a-kind-of' by a 'is-a-part-of' logic to better describe the mereology of integrated cellular and viral makeup. My analysis demands a new paradigm that integrates virus taxonomy into a modern evolutionarily centered taxonomy of organisms.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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3
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Gontier N. Situating physiology within evolutionary theory. J Physiol 2024; 602:2401-2415. [PMID: 37755322 DOI: 10.1113/jp284410] [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: 07/20/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
Traditionally defined as the science of the living, or as the field that beyond anatomical structure and bodily form studies functional organization and behaviour, physiology has long been excluded from evolutionary research. The main reason for this exclusion is that physiology has a presential and futuristic outlook on life, while evolutionary theory is traditionally defined as the study of natural history. In this paper, I re-evaluate these classic science divisions and situate physiology within the history of the evolutionary sciences, as well as within debates on the Extended Evolutionary Synthesis and the need for a Third Way of Evolution. I then briefly point out how evolutionary physiology in particular contributes to research on function, causation, teleonomy, agency and cognition.
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Affiliation(s)
- Nathalie Gontier
- Applied Evolutionary Epistemology Lab & Centro de Filosofia das Ciências, Departamento de História e Filosofia das Ciências, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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4
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Yutin N, Mutz P, Krupovic M, Koonin EV. Mriyaviruses: Small Relatives of Giant Viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582850. [PMID: 38529486 PMCID: PMC10962738 DOI: 10.1101/2024.02.29.582850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The phylum Nucleocytoviricota consists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein structure comparison, we delineate a distinct group of viruses with double-stranded (ds) DNA genomes in the range of 35-45 kb that appear to be related to the Nucleocytoviricota. In phylogenetic trees of the conserved double jelly-roll major capsid proteins (MCP) and DNA packaging ATPases, these viruses do not show affinity to any particular branch of the Nucleocytoviricota and accordingly would comprise a class which we propose to name "Mriyaviricetes" (after Ukrainian Mriya, dream). Structural comparison of the MCP suggests that, among the extant virus lineages, mriyaviruses are the closest one to the ancestor of the Nucleocytoviricota. In the phylogenetic trees, mriyaviruses split into two well-separated branches, the family Yaraviridae and proposed new family "Gamadviridae". The previously characterized members of these families, Yaravirus and Pleurochrysis sp. endemic viruses, infect amoeba and haptophytes, respectively. The genomes of the rest of the mriyaviruses were assembled from metagenomes from diverse environments, suggesting that mriyaviruses infect various unicellular eukaryotes. Mriyaviruses lack DNA polymerase, which is encoded by all other members of the Nucleocytoviricota, and RNA polymerase subunits encoded by all cytoplasmic viruses among the Nucleocytoviricota, suggesting that they replicate in the host cell nuclei. All mriyaviruses encode a HUH superfamily endonuclease that is likely to be essential for the initiation of virus DNA replication via the rolling circle mechanism.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris 75015, France
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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5
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Prosdocimi F, Cortines JR, José MV, Farias ST. Decoding viruses: An alternative perspective on their history, origins and role in nature. Biosystems 2023; 231:104960. [PMID: 37437771 DOI: 10.1016/j.biosystems.2023.104960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/14/2023]
Abstract
This article provides an alternative perspective on viruses, exploring their origins, ecology, and evolution. Viruses are recognized as the most prevalent biological entities on Earth, permeating nearly all environments and forming the virosphere-a significant biological layer. They play a crucial role in regulating bacterial populations within ecosystems and holobionts, influencing microbial communities and nutrient recycling. Viruses are also key drivers of molecular evolution, actively participating in the maintenance and regulation of ecosystems and cellular organisms. Many eukaryotic genomes contain genomic elements with viral origins, which contribute to organismal equilibrium and fitness. Viruses are involved in the generation of species-specific orphan genes, facilitating adaptation and the development of unique traits in biological lineages. They have been implicated in the formation of vital structures like the eukaryotic nucleus and the mammalian placenta. The presence of virus-specific genes absent in cellular organisms suggests that viruses may pre-date cellular life. Like progenotes, viruses are ribonucleoprotein entities with simpler capsid architectures compared to proteolipidic membranes. This article presents a comprehensive scenario describing major transitions in prebiotic evolution and proposes that viruses emerged prior to the Last Universal Common Ancestor (LUCA) during the progenote era. However, it is important to note that viruses do not form a monophyletic clade, and many viral taxonomic groups originated more recently as reductions of cellular structures. Thus, viral architecture should be seen as an ancient and evolutionarily stable strategy adopted by biological systems. The goal of this article is to reshape perceptions of viruses, highlighting their multifaceted significance in the complex tapestry of life and fostering a deeper understanding of their origins, ecological impact, and evolutionary dynamics.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Juliana Reis Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, CDMX, Mexico
| | - Sávio Torres Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK
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6
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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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Tekle YI, Tran H, Wang F, Singla M, Udu I. Omics of an Enigmatic Marine Amoeba Uncovers Unprecedented Gene Trafficking from Giant Viruses and Provides Insights into Its Complex Life Cycle. MICROBIOLOGY RESEARCH 2023; 14:656-672. [PMID: 37752971 PMCID: PMC10521059 DOI: 10.3390/microbiolres14020047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Amoebozoa include lineages of diverse ecology, behavior, and morphology. They are assumed to encompass members with the largest genome sizes of all living things, yet genomic studies in the group are limited. Trichosphaerium, a polymorphic, multinucleate, marine amoeba with a complicated life cycle, has puzzled experts for over a century. In an effort to explore the genomic diversity and investigate extraordinary behavior observed among the Amoebozoa, we used integrated omics approaches to study this enigmatic marine amoeba. Omics data, including single-cell transcriptomics and cytological data, demonstrate that Trichosphaerium sp. possesses the complete meiosis toolkit genes. These genes are expressed in life stages of the amoeba including medium and large cells. The life cycle of Trichosphaerium sp. involves asexual processes via binary fission and multiple fragmentation of giant cells, as well as sexual-like processes involving genes implicated in sexual reproduction and polyploidization. These findings are in stark contrast to a life cycle previously reported for this amoeba. Despite the extreme morphological plasticity observed in Trichosphaerium, our genomic data showed that populations maintain a species-level intragenomic variation. A draft genome of Trichosphaerium indicates elevated lateral gene transfer (LGT) from bacteria and giant viruses. Gene trafficking in Trichosphaerium is the highest within Amoebozoa and among the highest in microbial eukaryotes.
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Affiliation(s)
- Yonas I. Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Hanh Tran
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Fang Wang
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Mandakini Singla
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Isimeme Udu
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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8
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Hu Z, Liang J, Su T, Zhang D, Li H, Gao X, Yao W, Song X. Minimizing the Anticodon-Recognized Loop of Methanococcus jannaschii Tyrosyl-tRNA Synthetase to Improve the Efficiency of Incorporating Noncanonical Amino Acids. Biomolecules 2023; 13:biom13040610. [PMID: 37189358 DOI: 10.3390/biom13040610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023] Open
Abstract
In the field of genetic code expansion (GCE), improvements in the efficiency of noncanonical amino acid (ncAA) incorporation have received continuous attention. By analyzing the reported gene sequences of giant virus species, we noticed some sequence differences at the tRNA binding interface. On the basis of the structural and activity differences between Methanococcus jannaschii Tyrosyl-tRNA Synthetase (MjTyrRS) and mimivirus Tyrosyl-tRNA Synthetase (MVTyrRS), we found that the size of the anticodon-recognized loop of MjTyrRS influences its suppression activity regarding triplet and specific quadruplet codons. Therefore, three MjTyrRS mutants with loop minimization were designed. The suppression of wild-type MjTyrRS loop-minimized mutants increased by 1.8–4.3-fold, and the MjTyrRS variants enhanced the activity of the incorporation of ncAAs by 15–150% through loop minimization. In addition, for specific quadruplet codons, the loop minimization of MjTyrRS also improves the suppression efficiency. These results suggest that loop minimization of MjTyrRS may provide a general strategy for the efficient synthesis of ncAAs-containing proteins.
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9
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ZeinEldin RA, Ahmed MM, Hassanein WS, Elshafey N, Sofy AR, Hamedo HA, Elnosary ME. Diversity and Distribution Characteristics of Viruses from Soda Lakes. Genes (Basel) 2023; 14:genes14020323. [PMID: 36833250 PMCID: PMC9957498 DOI: 10.3390/genes14020323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/14/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Viruses are the most abundant living things and a source of genetic variation. Despite recent research, we know little about their biodiversity and geographic distribution. We used different bioinformatics tools, MG-RAST, genome detective web tools, and GenomeVx, to describe the first metagenomic examination of haloviruses in Wadi Al-Natrun. The discovered viromes had remarkably different taxonomic compositions. Most sequences were derived from double-stranded DNA viruses, especially from Myoviridae, Podoviridae, Siphoviridae, Herpesviridae, Bicaudaviridae, and Phycodnaviridae families; single-stranded DNA viruses, especially from the family Microviridae; and positive-strand RNA viruses, especially from the family Potyviridae. Additionally, our results showed that Myohalovirus chaoS9 has eight Contigs and is annotated to 18 proteins as follows: tail sheath protein, tco, nep, five uncharacterized proteins, HCO, major capsid protein, putative pro head protease protein, putative head assembly protein, CxxC motive protein, terl, HTH domain protein, and terS Exon 2. Additionally, Halorubrum phage CGphi46 has 19 proteins in the brine sample as follows: portal protein, 17 hypothetical proteins, major capsid protein, etc. This study reveals viral lineages, suggesting the Virus's global dispersal more than other microorganisms. Our study clarifies how viral communities are connected and how the global environment changes.
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Affiliation(s)
- Ramadan A. ZeinEldin
- Deanship of Scientific Research, King AbdulAziz University, Jeddah 21589, Saudi Arabia
- Faculty of Graduate Studies for Statistical Research, Cairo University, Giza 12613, Egypt
- Correspondence: (R.A.Z.); (M.E.E.)
| | - Marwa M. Ahmed
- Department of Electrical and Computer Engineering, Faculty of Engineering-Girls Campus, King Abdulaziz University, Jeddah 80204, Saudi Arabia
| | - Wael S. Hassanein
- Department of Industrial Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah 80204, Saudi Arabia
| | - Naglaa Elshafey
- Botany and Microbiology Department, Faculty of Science, Arish University, Al-Arish 45511, Egypt
| | - Ahmed R. Sofy
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Hend A. Hamedo
- Botany and Microbiology Department, Faculty of Science, Arish University, Al-Arish 45511, Egypt
| | - Mohamed E. Elnosary
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
- Correspondence: (R.A.Z.); (M.E.E.)
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10
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Queiroz VF, Rodrigues RAL, Boratto PVDM, La Scola B, Andreani J, Abrahão JS. Amoebae: Hiding in Plain Sight: Unappreciated Hosts for the Very Large Viruses. Annu Rev Virol 2022; 9:79-98. [DOI: 10.1146/annurev-virology-100520-125832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For decades, viruses have been isolated primarily from humans and other organisms. Interestingly, one of the most complex sides of the virosphere was discovered using free-living amoebae as hosts. The discovery of giant viruses in the early twenty-first century opened a new chapter in the field of virology. Giant viruses are included in the phylum Nucleocytoviricota and harbor large and complex DNA genomes (up to 2.7 Mb) encoding genes never before seen in the virosphere and presenting gigantic particles (up to 1.5 μm). Different amoebae have been used to isolate and characterize a plethora of new viruses with exciting details about novel viral biology. Through distinct isolation techniques and metagenomics, the diversity and complexity of giant viruses have astonished the scientific community. Here, we discuss the latest findings on amoeba viruses and how using these single-celled organisms as hosts has revealed entities that have remained hidden in plain sight for ages. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Victória Fulgêncio Queiroz
- Laboratório de Vírus, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Bernard La Scola
- Department of Microbes, Evolution, Phylogeny and Infection, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Julien Andreani
- Department of Microbes, Evolution, Phylogeny and Infection, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Laboratoire de Virologie, Centre Hospitalier Universitaire Grenoble-Alpes, Grenoble, France
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Battaglia R, Alonzo R, Pennisi C, Caponnetto A, Ferrara C, Stella M, Barbagallo C, Barbagallo D, Ragusa M, Purrello M, Di Pietro C. MicroRNA-Mediated Regulation of the Virus Cycle and Pathogenesis in the SARS-CoV-2 Disease. Int J Mol Sci 2021; 22:ijms222413192. [PMID: 34947989 PMCID: PMC8715670 DOI: 10.3390/ijms222413192] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 12/24/2022] Open
Abstract
In the last few years, microRNA-mediated regulation has been shown to be important in viral infections. In fact, viral microRNAs can alter cell physiology and act on the immune system; moreover, cellular microRNAs can regulate the virus cycle, influencing positively or negatively viral replication. Accordingly, microRNAs can represent diagnostic and prognostic biomarkers of infectious processes and a promising approach for designing targeted therapies. In the past 18 months, the COVID-19 infection from SARS-CoV-2 has engaged many researchers in the search for diagnostic and prognostic markers and the development of therapies. Although some research suggests that the SARS-CoV-2 genome can produce microRNAs and that host microRNAs may be involved in the cellular response to the virus, to date, not enough evidence has been provided. In this paper, using a focused bioinformatic approach exploring the SARS-CoV-2 genome, we propose that SARS-CoV-2 is able to produce microRNAs sharing a strong sequence homology with the human ones and also that human microRNAs may target viral RNA regulating the virus life cycle inside human cells. Interestingly, all viral miRNA sequences and some human miRNA target sites are conserved in more recent SARS-CoV-2 variants of concern (VOCs). Even if experimental evidence will be needed, in silico analysis represents a valuable source of information useful to understand the sophisticated molecular mechanisms of disease and to sustain biomedical applications.
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12
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Caetano-Anollés G, Aziz MF, Mughal F, Caetano-Anollés D. Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution. Expert Rev Proteomics 2021; 18:863-880. [PMID: 34628994 DOI: 10.1080/14789450.2021.1992277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chronologies are series of time events describing the history of biological systems and subsystems and the rise of biological innovations. Together with time-varying networks, these chronologies provide a window into the past. AREAS COVERED Here, we review molecular chronologies and networks built with modern methods of phylogeny reconstruction. We discuss how chronologies of structural domain families uncover the explosive emergence of metabolism, the late rise of translation, the co-evolution of ribosomal proteins and rRNA, and the late development of the ribosomal exit tunnel; events that coincided with a tendency to shorten folding time. Evolving networks described the early emergence of domains and a late 'big bang' of domain combinations. EXPERT OPINION Two processes, folding and recruitment appear central to the evolutionary progression. The former increases protein persistence. The later fosters diversity. Chronologically, protein evolution mirrors folding by combining supersecondary structures into domains, developing translation machinery to facilitate folding speed and stability, and enhancing structural complexity by establishing long-distance interactions in novel structural and architectural designs.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA.,C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Derek Caetano-Anollés
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Patil S, Kondabagil K. Coevolutionary and Phylogenetic Analysis of Mimiviral Replication Machinery Suggest the Cellular Origin of Mimiviruses. Mol Biol Evol 2021; 38:2014-2029. [PMID: 33570580 PMCID: PMC8097291 DOI: 10.1093/molbev/msab003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mimivirus is one of the most complex and largest viruses known. The origin and evolution of Mimivirus and other giant viruses have been a subject of intense study in the last two decades. The two prevailing hypotheses on the origin of Mimivirus and other viruses are the reduction hypothesis, which posits that viruses emerged from modern unicellular organisms; whereas the virus-first hypothesis proposes viruses as relics of precellular forms of life. In this study, to gain insights into the origin of Mimivirus, we have carried out extensive phylogenetic, correlation, and multidimensional scaling analyses of the putative proteins involved in the replication of its 1.2-Mb large genome. Correlation analysis and multidimensional scaling methods were validated using bacteriophage, bacteria, archaea, and eukaryotic replication proteins before applying to Mimivirus. We show that a large fraction of mimiviral replication proteins, including polymerase B, clamp, and clamp loaders are of eukaryotic origin and are coevolving. Although phylogenetic analysis places some components along the lineages of phage and bacteria, we show that all the replication-related genes have been homogenized and are under purifying selection. Collectively our analysis supports the idea that Mimivirus originated from a complex cellular ancestor. We hypothesize that Mimivirus has largely retained complex replication machinery reminiscent of its progenitor while losing most of the other genes related to processes such as metabolism and translation.
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Affiliation(s)
- Supriya Patil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India
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14
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Nasir A, Mughal F, Caetano-Anollés G. The tree of life describes a tripartite cellular world. Bioessays 2021; 43:e2000343. [PMID: 33837594 DOI: 10.1002/bies.202000343] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/28/2022]
Abstract
The canonical view of a 3-domain (3D) tree of life was recently challenged by the discovery of Asgardarchaeota encoding eukaryote signature proteins (ESPs), which were treated as missing links of a 2-domain (2D) tree. Here we revisit the debate. We discuss methodological limitations of building trees with alignment-dependent approaches, which often fail to satisfactorily address the problem of ''gaps.'' In addition, most phylogenies are reconstructed unrooted, neglecting the power of direct rooting methods. Alignment-free methodologies lift most difficulties but require employing realistic evolutionary models. We argue that the discoveries of Asgards and ESPs, by themselves, do not rule out the 3D tree, which is strongly supported by comparative and evolutionary genomic analyses and vast genomic and biochemical superkingdom distinctions. Given uncertainties of retrodiction and interpretation difficulties, we conclude that the 3D view has not been falsified but instead has been strengthened by genomic analyses. In turn, the objections to the 2D model have not been lifted. The debate remains open. Also see the video abstract here: https://youtu.be/-6TBN0bubI8.
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Affiliation(s)
- Arshan Nasir
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Fizza Mughal
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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15
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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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16
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Kirschning A. The coenzyme/protein pair and the molecular evolution of life. Nat Prod Rep 2020; 38:993-1010. [PMID: 33206101 DOI: 10.1039/d0np00037j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2020What was first? Coenzymes or proteins? These questions are archetypal examples of causal circularity in living systems. Classically, this "chicken-and-egg" problem was discussed for the macromolecules RNA, DNA and proteins. This report focuses on coenzymes and cofactors and discusses the coenzyme/protein pair as another example of causal circularity in life. Reflections on the origin of life and hypotheses on possible prebiotic worlds led to the current notion that RNA was the first macromolecule, long before functional proteins and hence DNA. So these causal circularities of living systems were solved by a time travel into the past. To tackle the "chicken-and-egg" problem of the protein-coenzyme pair, this report addresses this problem by looking for clues (a) in the first hypothetical biotic life forms such as protoviroids and the last unified common ancestor (LUCA) and (b) in considerations and evidence of the possible prebiotic production of amino acids and coenzymes before life arose. According to these considerations, coenzymes and cofactors can be regarded as very old molecular players in the origin and evolution of life, and at least some of them developed independently of α-amino acids, which here are evolutionarily synonymous with proteins. Discussions on "chicken-and-egg" problems open further doors to the understanding of evolution.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Zentrum für Biomolekulare Wirkstoffchemie (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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17
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Pereira-Santana A, Gamboa-Tuz SD, Zhao T, Schranz ME, Vinuesa P, Bayona A, Rodríguez-Zapata LC, Castano E. Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin. PLoS Comput Biol 2020; 16:e1008318. [PMID: 33075080 PMCID: PMC7608942 DOI: 10.1371/journal.pcbi.1008318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 11/03/2020] [Accepted: 09/07/2020] [Indexed: 12/26/2022] Open
Abstract
Fibrillarin (FIB), a methyltransferase essential for life in the vast majority of eukaryotes, is involved in methylation of rRNA required for proper ribosome assembly, as well as methylation of histone H2A of promoter regions of rRNA genes. RNA viral progression that affects both plants and animals requires FIB proteins. Despite the importance and high conservation of fibrillarins, there little is known about the evolutionary dynamics of this small gene family. We applied a phylogenomic microsynteny-network approach to elucidate the evolutionary history of FIB proteins across the Tree of Life. We identified 1063 non-redundant FIB sequences across 1049 completely sequenced genomes from Viruses, Bacteria, Archaea, and Eukarya. FIB is a highly conserved single-copy gene through Archaea and Eukarya lineages, except for plants, which have a gene family expansion due to paleopolyploidy and tandem duplications. We found a high conservation of the FIB genomic context during plant evolution. Surprisingly, FIB in mammals duplicated after the Eutheria split (e.g., ruminants, felines, primates) from therian mammals (e.g., marsupials) to form two main groups of sequences, the FIB and FIB-like groups. The FIB-like group transposed to another genomic context and remained syntenic in all the eutherian mammals. This transposition correlates with differences in the expression patterns of FIB-like proteins and with elevated Ks values potentially due to reduced evolutionary constraints of the duplicated copy. Our results point to a unique evolutionary event in mammals, between FIB and FIB-like genes, that led to non-redundant roles of the vital processes in which this protein is involved.
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Affiliation(s)
- Alejandro Pereira-Santana
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan, Jalisco, México
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Samuel David Gamboa-Tuz
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Tao Zhao
- Bioinformatics and Evolutionary Genomics, VIB-UGent Center for Plant Systems Biology, Gent, Belgium
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Andrea Bayona
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | | | - Enrique Castano
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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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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Rodrigues RAL, da Silva LCF, Abrahão JS. Translating the language of giants: translation-related genes as a major contribution of giant viruses to the virosphere. Arch Virol 2020; 165:1267-1278. [DOI: 10.1007/s00705-020-04626-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/25/2020] [Indexed: 12/21/2022]
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20
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A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder. Genes (Basel) 2020; 11:genes11040407. [PMID: 32283633 PMCID: PMC7230257 DOI: 10.3390/genes11040407] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 12/31/2022] Open
Abstract
Protein tandem repeats (TRs) are often associated with immunity-related functions and diseases. Since that last census of protein TRs in 1999, the number of curated proteins increased more than seven-fold and new TR prediction methods were published. TRs appear to be enriched with intrinsic disorder and vice versa. The significance and the biological reasons for this association are unknown. Here, we characterize protein TRs across all kingdoms of life and their overlap with intrinsic disorder in unprecedented detail. Using state-of-the-art prediction methods, we estimate that 50.9% of proteins contain at least one TR, often located at the sequence flanks. Positive linear correlation between the proportion of TRs and the protein length was observed universally, with Eukaryotes in general having more TRs, but when the difference in length is taken into account the difference is quite small. TRs were enriched with disorder-promoting amino acids and were inside intrinsically disordered regions. Many such TRs were homorepeats. Our results support that TRs mostly originate by duplication and are involved in essential functions such as transcription processes, structural organization, electron transport and iron-binding. In viruses, TRs are found in proteins essential for virulence.
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21
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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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22
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Dos Santos Silva LK, Rodrigues RAL, Dos Santos Pereira Andrade AC, Hikida H, Andreani J, Levasseur A, La Scola B, Abrahão JS. Isolation and genomic characterization of a new mimivirus of lineage B from a Brazilian river. Arch Virol 2020; 165:853-863. [PMID: 32052196 DOI: 10.1007/s00705-020-04542-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/08/2020] [Indexed: 11/25/2022]
Abstract
Since its discovery, the first identified giant virus associated with amoebae, Acanthamoeba polyphaga mimivirus (APMV), has been rigorously studied to understand the structural and genomic complexity of this virus. In this work, we report the isolation and genomic characterization of a new mimivirus of lineage B, named "Borely moumouvirus". This new virus exhibits a structure and replicative cycle similar to those of other members of the family Mimiviridae. The genome of the new isolate is a linear double-strand DNA molecule of ~1.0 Mb, containing over 900 open reading frames. Genome annotation highlighted different translation system components encoded in the DNA of Borely moumouvirus, including aminoacyl-tRNA synthetases, translation factors, and tRNA molecules, in a distribution similar to that in other lineage B mimiviruses. Pan-genome analysis indicated an increase in the genetic arsenal of this group of viruses, showing that the family Mimiviridae is still expanding. Furthermore, phylogenetic analysis has shown that Borely moumouvirus is closely related to moumouvirus australiensis. This is the first mimivirus lineage B isolated from Brazilian territory to be characterized. Further prospecting studies are necessary for us to better understand the diversity of these viruses so a better classification system can be established.
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Affiliation(s)
- Ludmila Karen Dos Santos Silva
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | | | - Hiroyuki Hikida
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Julien Andreani
- Microbes, Evolution, Phylogeny and Infection (MEPHI), Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, 19-21 boulevard Jean moulin, 13005, Marseille, France
| | - Anthony Levasseur
- Microbes, Evolution, Phylogeny and Infection (MEPHI), Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, 19-21 boulevard Jean moulin, 13005, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France.
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, 19-21 boulevard Jean moulin, 13005, Marseille, France.
| | - Jônatas Santos Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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Abstract
Viruses are diverse parasites of cells and extremely abundant. They might have arisen during an early phase of the evolution of life on Earth dominated by ribonucleic acid or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present-day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate; viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via the lateral transfer of genes. These two models have a bearing on viruses being considered predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms.
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24
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Mughal F, Caetano-Anollés G. MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PLoS One 2019; 14:e0224201. [PMID: 31648227 PMCID: PMC6812854 DOI: 10.1371/journal.pone.0224201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/08/2019] [Indexed: 11/30/2022] Open
Abstract
Enzyme recruitment is a fundamental evolutionary driver of modern metabolism. We see evidence of recruitment at work in the metabolic Molecular Ancestry Networks (MANET) database, an online resource that integrates data from KEGG, SCOP and structural phylogenomic reconstruction. The database, which was introduced in 2006, traces the deep history of the structural domains of enzymes in metabolic pathways. Here we release version 3.0 of MANET, which updates data from KEGG and SCOP, links enzyme and PDB information with PDBsum, and traces evolutionary information of domains defined at fold family level of SCOP classification in metabolic subnetwork diagrams. Compared to SCOP folds used in the previous versions, fold families are cohesive units of functional similarity that are highly conserved at sequence level and offer a 10-fold increase of data entries. We surveyed enzymatic, functional and catalytic site distributions among superkingdoms showing that ancient enzymatic innovations followed a biphasic temporal pattern of diversification typical of module innovation. We grouped enzymatic activities of MANET into a hierarchical system of subnetworks and mesonetworks matching KEGG classification. The evolutionary growth of these modules of metabolic activity was studied using bipartite networks and their one-mode projections at enzyme, subnetwork and mesonetwork levels of organization. Evolving metabolic networks revealed patterns of enzyme sharing that transcended mesonetwork boundaries and supported the patchwork model of metabolic evolution. We also explored the scale-freeness, randomness and small-world properties of evolving networks as possible organizing principles of network growth and diversification. The network structure shows an increase in hierarchical modularity and scale-free behavior as metabolic networks unfold in evolutionary time. Remarkably, this evolutionary constraint on structure was stronger at lower levels of metabolic organization. Evolving metabolic structure reveals a 'principle of granularity', an evolutionary increase of the cohesiveness of lower-level parts of a hierarchical system. MANET is available at http://manet.illinois.edu.
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Affiliation(s)
- Fizza Mughal
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gustavo Caetano-Anollés
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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25
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Protozoal giant viruses: agents potentially infectious to humans and animals. Virus Genes 2019; 55:574-591. [PMID: 31290063 PMCID: PMC6746690 DOI: 10.1007/s11262-019-01684-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
The discovery of giant viruses has revolutionised the knowledge on viruses and transformed the idea of three domains of life. Here, we discuss the known protozoal giant viruses and their potential to infect also humans and animals.
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26
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Mendler K, Chen H, Parks DH, Lobb B, Hug LA, Doxey AC. AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Res 2019; 47:4442-4448. [PMID: 31081040 PMCID: PMC6511854 DOI: 10.1093/nar/gkz246] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 11/14/2022] Open
Abstract
Bacterial genomics has revolutionized our understanding of the microbial tree of life; however, mapping and visualizing the distribution of functional traits across bacteria remains a challenge. Here, we introduce AnnoTree-an interactive, functionally annotated bacterial tree of life that integrates taxonomic, phylogenetic and functional annotation data from over 27 000 bacterial and 1500 archaeal genomes. AnnoTree enables visualization of millions of precomputed genome annotations across the bacterial and archaeal phylogenies, thereby allowing users to explore gene distributions as well as patterns of gene gain and loss in prokaryotes. Using AnnoTree, we examined the phylogenomic distributions of 28 311 gene/protein families, and measured their phylogenetic conservation, patchiness, and lineage-specificity within bacteria. Our analyses revealed widespread phylogenetic patchiness among bacterial gene families, reflecting the dynamic evolution of prokaryotic genomes. Genes involved in phage infection/defense, mobile elements, and antibiotic resistance dominated the list of most patchy traits, as well as numerous intriguing metabolic enzymes that appear to have undergone frequent horizontal transfer. We anticipate that AnnoTree will be a valuable resource for exploring prokaryotic gene histories, and will act as a catalyst for biological and evolutionary hypothesis generation. AnnoTree is freely available at http://annotree.uwaterloo.ca.
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Affiliation(s)
- Kerrin Mendler
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Han Chen
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, Australia
| | - Briallen Lobb
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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27
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Brandes N, Linial M. Giant Viruses-Big Surprises. Viruses 2019; 11:v11050404. [PMID: 31052218 PMCID: PMC6563228 DOI: 10.3390/v11050404] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Viruses are the most prevalent infectious agents, populating almost every ecosystem on earth. Most viruses carry only a handful of genes supporting their replication and the production of capsids. It came as a great surprise in 2003 when the first giant virus was discovered and found to have a >1 Mbp genome encoding almost a thousand proteins. Following this first discovery, dozens of giant virus strains across several viral families have been reported. Here, we provide an updated quantitative and qualitative view on giant viruses and elaborate on their shared and variable features. We review the complexity of giant viral proteomes, which include functions traditionally associated only with cellular organisms. These unprecedented functions include components of the translation machinery, DNA maintenance, and metabolic enzymes. We discuss the possible underlying evolutionary processes and mechanisms that might have shaped the diversity of giant viruses and their genomes, highlighting their remarkable capacity to hijack genes and genomic sequences from their hosts and environments. This leads us to examine prominent theories regarding the origin of giant viruses. Finally, we present the emerging ecological view of giant viruses, found across widespread habitats and ecological systems, with respect to the environment and human health.
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Affiliation(s)
- Nadav Brandes
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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Seligmann H. Giant viruses: spore‐like missing links betweenRickettsiaand mitochondria? Ann N Y Acad Sci 2019; 1447:69-79. [DOI: 10.1111/nyas.14022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/10/2019] [Accepted: 01/16/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Hervé Seligmann
- The National Natural History Collectionsthe Hebrew University of Jerusalem Jerusalem Israel
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29
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Shapiro JA. No genome is an island: toward a 21st century agenda for evolution. Ann N Y Acad Sci 2019; 1447:21-52. [DOI: 10.1111/nyas.14044] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/17/2019] [Accepted: 02/02/2019] [Indexed: 12/21/2022]
Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular BiologyUniversity of Chicago Chicago Illinois
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Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism. mBio 2019; 10:mBio.02497-18. [PMID: 30837339 PMCID: PMC6401483 DOI: 10.1128/mbio.02497-18] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches. The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, “Megavirales”) include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki’s Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki’s Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae. Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.
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Rodrigues RAL, Arantes TS, Oliveira GP, dos Santos Silva LK, Abrahão JS. The Complex Nature of Tupanviruses. Adv Virus Res 2019; 103:135-166. [PMID: 30635075 DOI: 10.1016/bs.aivir.2018.09.001] [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] [Indexed: 12/24/2022]
Abstract
The discovery of giant viruses revealed a new level of complexity in the virosphere, raising important questions about the diversity, ecology, and evolution of these viruses. The family Mimiviridae was the first group of amoebal giant viruses to be discovered (by Bernard La Scola and Didier Raoult team), containing viruses with structural and genetic features that challenged many concepts of classic virology. The tupanviruses are among the newest members of this family and exhibit structural, biological, and genetic features never previously observed in other giant viruses. The complexity of these viruses has put us one step forward toward the comprehension of giant virus biology and evolution, but also has raised important questions that still need to be addressed. In this chapter, we tell the history behind the discovery of one of the most complex viruses isolated to date, highlighting the unique features exhibited by tupanviruses, and discuss how these giant viruses have contributed to redefining limits for the virosphere.
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32
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Koonin EV, Yutin N. Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism. Adv Virus Res 2019; 103:167-202. [PMID: 30635076 DOI: 10.1016/bs.aivir.2018.09.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Nucleocytoplasmic Large DNA Viruses (NCLDV) of eukaryotes (proposed order "Megavirales") comprise an expansive group of eukaryotic viruses that consists of the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, Pithoviridae, and Mimiviridae, as well as Pandoraviruses, Molliviruses, and Faustoviruses that so far remain unaccounted by the official virus taxonomy. All these viruses have double-stranded DNA genomes that range in size from about 100 kilobases (kb) to more than 2.5 megabases. The viruses with genomes larger than 500kb are informally considered "giant," and the largest giant viruses surpass numerous bacteria and archaea in both particle and genome size. The discovery of giant viruses has been highly unexpected and has changed the perception of viral size and complexity, and even, arguably, the entire concept of a virus. Given that giant viruses encode multiple proteins that are universal among cellular life forms and are components of the translation system, the quintessential cellular molecular machinery, attempts have been made to incorporate these viruses in the evolutionary tree of cellular life. Moreover, evolutionary scenarios of the origin of giant viruses from a fourth, supposedly extinct domain of cellular life have been proposed. However, despite all the differences in the genome size and gene repertoire, the NCLDV can be confidently defined as monophyletic group, on the strength of the presence of about 40 genes that can be traced back to their last common ancestor. Using several most strongly conserved genes from this ancestral set, a well-resolved phylogenetic tree of the NCLDV was built and employed as the scaffold to reconstruct the history of gene gain and loss throughout the course of the evolution of this group of viruses. This reconstruction reveals extremely dynamic evolution that involved extensive gene gain and loss in many groups of viruses and indicates that giant viruses emerged independently in several clades of the NCLDV. Thus, these giants of the virus world evolved repeatedly from smaller and simpler viruses, rather than from a fourth domain of cellular life, and captured numerous genes, including those for translation system components, from eukaryotes, along with some bacterial genes. Even deeper evolutionary reconstructions reveal apparent links between the NCLDV and smaller viruses of eukaryotes, such as adenoviruses, and ultimately, derive all these viruses from tailless bacteriophages.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
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Colson P, Levasseur A, La Scola B, Sharma V, Nasir A, Pontarotti P, Caetano-Anollés G, Raoult D. Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes. Front Microbiol 2018; 9:2668. [PMID: 30538677 PMCID: PMC6277510 DOI: 10.3389/fmicb.2018.02668] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/18/2018] [Indexed: 12/20/2022] Open
Abstract
Giant viruses of amoebae were discovered in 2003. Since then, their diversity has greatly expanded. They were suggested to form a fourth branch of life, collectively named ‘TRUC’ (for “Things Resisting Uncompleted Classifications”) alongside Bacteria, Archaea, and Eukarya. Their origin and ancestrality remain controversial. Here, we specify the evolution and definition of giant viruses. Phylogenetic and phenetic analyses of informational gene repertoires of giant viruses and selected bacteria, archaea and eukaryota were performed, including structural phylogenomics based on protein structural domains grouped into 289 universal fold superfamilies (FSFs). Hierarchical clustering analysis was performed based on a binary presence/absence matrix constructed using 727 informational COGs from cellular organisms. The presence/absence of ‘universal’ FSF domains was used to generate an unrooted maximum parsimony phylogenomic tree. Comparison of the gene content of a giant virus with those of a bacterium, an archaeon, and a eukaryote with small genomes was also performed. Overall, both cladistic analyses based on gene sequences of very central and ancient proteins and on highly conserved protein fold structures as well as phenetic analyses were congruent regarding the delineation of a fourth branch of microbes comprised by giant viruses. Giant viruses appeared as a basal group in the tree of all proteomes. A pangenome and core genome determined for Rickettsia bellii (bacteria), Methanomassiliicoccus luminyensis (archaeon), Encephalitozoon intestinalis (eukaryote), and Tupanvirus (giant virus) showed a substantial proportion of Tupanvirus genes that overlap with those of the cellular microbes. In addition, a substantial genome mosaicism was observed, with 51, 11, 8, and 0.2% of Tupanvirus genes best matching with viruses, eukaryota, bacteria, and archaea, respectively. Finally, we found that genes themselves may be subject to lateral sequence transfers. In summary, our data highlight the quantum leap between classical and giant viruses. Phylogenetic and phyletic analyses and the study of protein fold superfamilies confirm previous evidence of the existence of a fourth TRUC of life that includes giant viruses, and highlight its ancestrality and mosaicism. They also point out that best evolutionary representations for giant viruses and cellular microorganisms are rhizomes, and that sequence transfers rather than gene transfers have to be considered.
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Affiliation(s)
- Philippe Colson
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Vikas Sharma
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique, Marseille, France
| | - Arshan Nasir
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States.,Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Pierre Pontarotti
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique, Marseille, France
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
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Abstract
The nucleocytoplasmic large DNA viruses (NCLDVs) are a monophyletic group of diverse eukaryotic viruses that reproduce primarily in the cytoplasm of the infected cells and include the largest viruses currently known: the giant mimiviruses, pandoraviruses, and pithoviruses. With virions measuring up to 1.5 μm and genomes of up to 2.5 Mb, the giant viruses break the now-outdated definition of a virus and extend deep into the genome size range typical of bacteria and archaea. Additionally, giant viruses encode multiple proteins that are universal among cellular life forms, particularly components of the translation system, the signature cellular molecular machinery. These findings triggered hypotheses on the origin of giant viruses from cells, likely of an extinct fourth domain of cellular life, via reductive evolution. However, phylogenomic analyses reveal a different picture, namely multiple origins of giant viruses from smaller NCLDVs via acquisition of multiple genes from the eukaryotic hosts and bacteria, along with gene duplication. Thus, with regard to their origin, the giant viruses do not appear to qualitatively differ from the rest of the virosphere. However, the evolutionary forces that led to the emergence of virus gigantism remain enigmatic.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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35
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Mimiviridae: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes. Viruses 2018; 10:v10090506. [PMID: 30231528 PMCID: PMC6163669 DOI: 10.3390/v10090506] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 01/22/2023] Open
Abstract
Since 1998, when Jim van Etten’s team initiated its characterization, Paramecium bursaria Chlorella virus 1 (PBCV-1) had been the largest known DNA virus, both in terms of particle size and genome complexity. In 2003, the Acanthamoeba-infecting Mimivirus unexpectedly superseded PBCV-1, opening the era of giant viruses, i.e., with virions large enough to be visible by light microscopy and genomes encoding more proteins than many bacteria. During the following 15 years, the isolation of many Mimivirus relatives has made Mimiviridae one of the largest and most diverse families of eukaryotic viruses, most of which have been isolated from aquatic environments. Metagenomic studies of various ecosystems (including soils) suggest that many more remain to be isolated. As Mimiviridae members are found to infect an increasing range of phytoplankton species, their taxonomic position compared to the traditional Phycodnaviridae (i.e., etymologically “algal viruses”) became a source of confusion in the literature. Following a quick historical review of the key discoveries that established the Mimiviridae family, we describe its current taxonomic structure and propose a set of operational criteria to help in the classification of future isolates.
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36
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Mihara T, Koyano H, Hingamp P, Grimsley N, Goto S, Ogata H. Taxon Richness of "Megaviridae" Exceeds those of Bacteria and Archaea in the Ocean. Microbes Environ 2018; 33:162-171. [PMID: 29806626 PMCID: PMC6031395 DOI: 10.1264/jsme2.me17203] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family “Megaviridae”, suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene. By leveraging existing microbial metagenomic data, we found higher richness and phylogenetic diversity in this single viral family than in the two prokaryotic domains. We also obtained results showing that the evolutionary rate alone cannot account for the observed high diversity of Megaviridae lineages. These results suggest that the Megaviridae family has a deep co-evolutionary history with diverse marine protists since the early “Big-Bang” radiation of the eukaryotic tree of life.
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Affiliation(s)
- Tomoko Mihara
- Bioinformatics Center, Institute for Chemical Research, Kyoto University
| | - Hitoshi Koyano
- School of Life Science and Technology, Laboratory of Genome Informatics, Tokyo Institute of Technology
| | | | - Nigel Grimsley
- Integrative Marine Biology Laboratory (BIOM), CNRS UMR7232, Sorbonne Universities
| | - Susumu Goto
- Database Center for Life Science, Joint-Support Center for Data Science Research, Research Organization of Information and Systems
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University
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37
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Carrara G, Parsons M, Saraiva N, Smith GL. Golgi anti-apoptotic protein: a tale of camels, calcium, channels and cancer. Open Biol 2018; 7:rsob.170045. [PMID: 28469007 PMCID: PMC5451544 DOI: 10.1098/rsob.170045] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022] Open
Abstract
Golgi anti-apoptotic protein (GAAP), also known as transmembrane Bax inhibitor-1 motif-containing 4 (TMBIM4) or Lifeguard 4 (Lfg4), shares remarkable amino acid conservation with orthologues throughout eukaryotes, prokaryotes and some orthopoxviruses, suggesting a highly conserved function. GAAPs regulate Ca2+ levels and fluxes from the Golgi and endoplasmic reticulum, confer resistance to a broad range of apoptotic stimuli, promote cell adhesion and migration via the activation of store-operated Ca2+ entry, are essential for the viability of human cells, and affect orthopoxvirus virulence. GAAPs are oligomeric, multi-transmembrane proteins that are resident in Golgi membranes and form cation-selective ion channels that may explain the multiple functions of these proteins. Residues contributing to the ion-conducting pore have been defined and provide the first clues about the mechanistic link between these very different functions of GAAP. Although GAAPs are naturally oligomeric, they can also function as monomers, a feature that distinguishes them from other virus-encoded ion channels that must oligomerize for function. This review summarizes the known functions of GAAPs and discusses their potential importance in disease.
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Affiliation(s)
- Guia Carrara
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Maddy Parsons
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Nuno Saraiva
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK .,CBIOS, Universidade Lusófona Research Centre for Biosciences and Health Technologies, Campo Grande 376, Lisbon 1749-024, Portugal
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
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Malik SS, Azem-E-Zahra S, Kim KM, Caetano-Anollés G, Nasir A. Do Viruses Exchange Genes across Superkingdoms of Life? Front Microbiol 2017; 8:2110. [PMID: 29163404 PMCID: PMC5671483 DOI: 10.3389/fmicb.2017.02110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/16/2017] [Indexed: 12/13/2022] Open
Abstract
Viruses can be classified into archaeoviruses, bacterioviruses, and eukaryoviruses according to the taxonomy of the infected host. The host-constrained perception of viruses implies preference of genetic exchange between viruses and cellular organisms of their host superkingdoms and viral origins from host cells either via escape or reduction. However, viruses frequently establish non-lytic interactions with organisms and endogenize into the genomes of bacterial endosymbionts that reside in eukaryotic cells. Such interactions create opportunities for genetic exchange between viruses and organisms of non-host superkingdoms. Here, we take an atypical approach to revisit virus-cell interactions by first identifying protein fold structures in the proteomes of archaeoviruses, bacterioviruses, and eukaryoviruses and second by tracing their spread in the proteomes of superkingdoms Archaea, Bacteria, and Eukarya. The exercise quantified protein structural homologies between viruses and organisms of their host and non-host superkingdoms and revealed likely candidates for virus-to-cell and cell-to-virus gene transfers. Unexpected lifestyle-driven genetic affiliations between bacterioviruses and Eukarya and eukaryoviruses and Bacteria were also predicted in addition to a large cohort of protein folds that were universally shared by viral and cellular proteomes and virus-specific protein folds not detected in cellular proteomes. These protein folds provide unique insights into viral origins and evolution that are generally difficult to recover with traditional sequence alignment-dependent evolutionary analyses owing to the fast mutation rates of viral gene sequences.
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Affiliation(s)
- Shahana S Malik
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Syeda Azem-E-Zahra
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Arshan Nasir
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan.,Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Jeong H, Nasir A. A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation. Front Genet 2017; 8:112. [PMID: 28894459 PMCID: PMC5581361 DOI: 10.3389/fgene.2017.00112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/14/2017] [Indexed: 12/03/2022] Open
Abstract
Genome-wide global detection of genes involved in horizontal gene transfer (HGT) remains an active area of research in medical microbiology and evolutionary genomics. Utilizing the explicit evolutionary method of comparing topologies of a total of 154,805 orthologous gene trees against corresponding 16S rRNA “reference” trees, we previously detected a total of 660,894 candidate HGT events in 2,472 completely-sequenced prokaryotic genomes. Here, we report an HGT-index for each individual gene-reference tree pair reconciliation, representing the total number of detected HGT events on the gene tree divided by the total number of genomes (taxa) member of that tree. HGT-index is thus a simple measure indicating the sensitivity of prokaryotic genes to participate (or not participate) in HGT. Our preliminary list provides HGT-indices for a total of 69,365 genes (detected in >10 and <50% available prokaryotic genomes) that are involved in a wide range of biological processes such as metabolism, information, and bacterial response to environment. Identification of horizontally-derived genes is important to combat antibiotic resistance and is a step forward toward reconstructions of improved phylogenies describing the history of life. Our effort is thus expected to benefit ongoing research in the fields of clinical microbiology and evolutionary biology.
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Affiliation(s)
- Hyeonsoo Jeong
- Department of Animal Sciences, University of Illinois at Urbana-ChampaignUrbana, IL, United States
| | - Arshan Nasir
- Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan.,Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-ChampaignUrbana, IL, United States
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40
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Colson P, La Scola B, Raoult D. Giant Viruses of Amoebae: A Journey Through Innovative Research and Paradigm Changes. Annu Rev Virol 2017; 4:61-85. [PMID: 28759330 DOI: 10.1146/annurev-virology-101416-041816] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Giant viruses of amoebae were discovered serendipitously in 2003; they are visible via optical microscopy, making them bona fide microbes. Their lifestyle, structure, and genomes break the mold of classical viruses. Giant viruses of amoebae are complex microorganisms. Their genomes harbor between 444 and 2,544 genes, including many that are unique to viruses, and encode translation components; their virions contain >100 proteins as well as mRNAs. Mimiviruses have a specific mobilome, including virophages, provirophages, and transpovirons, and can resist virophages through a system known as MIMIVIRE (mimivirus virophage resistance element). Giant viruses of amoebae bring upheaval to the definition of viruses and tend to separate the current virosphere into two categories: very simple viruses and viruses with complexity similar to that of other microbes. This new paradigm is propitious for enhanced detection and characterization of giant viruses of amoebae, and a particular focus on their role in humans is warranted.
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Affiliation(s)
- Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France;
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France;
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France;
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Harish A, Kurland CG. Empirical genome evolution models root the tree of life. Biochimie 2017; 138:137-155. [DOI: 10.1016/j.biochi.2017.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 04/25/2017] [Indexed: 01/05/2023]
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Nasir A, Kim KM, Caetano-Anollés G. Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells. Front Microbiol 2017; 8:1178. [PMID: 28690608 PMCID: PMC5481351 DOI: 10.3389/fmicb.2017.01178] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/09/2017] [Indexed: 01/05/2023] Open
Abstract
Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors. However, it was recently argued that the rooting of our trees and the basal placement of viruses was artifactually induced by small genome (proteome) size. Here we show that these claims arise from misunderstanding and misinterpretations of cladistic methodology. Trees are reconstructed unrooted, and thus, their topologies cannot be distorted a posteriori by the rooting methodology. Tracing proteome size in trees and multidimensional views of evolutionary relationships as well as tests of leaf stability and exclusion/inclusion of taxa demonstrated that the smallest proteomes were neither attracted toward the root nor caused any topological distortions of the trees. Simulations confirmed that taxa clustering patterns were independent of proteome size and were determined by the presence of known evolutionary relatives in data matrices, highlighting the need for broader taxon sampling in phylogeny reconstruction. Instead, phylogenetic tracings of proteome size revealed a slowdown in innovation of the structural domain vocabulary and four regimes of allometric scaling that reflected a Heaps law. These regimes explained increasing economies of scale in the evolutionary growth and accretion of kernel proteome repertoires of viruses and cellular organisms that resemble growth of human languages with limited vocabulary sizes. Results reconcile dynamic and static views of domain frequency distributions that are consistent with the axiom of spatiotemporal continuity that is tenet of evolutionary thinking.
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Affiliation(s)
- Arshan Nasir
- Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-ChampaignUrbana, IL, United States
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research InstituteIncheon, South Korea
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-ChampaignUrbana, IL, United States
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Koç I, Caetano-Anollés G. The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data. PLoS One 2017; 12:e0176129. [PMID: 28467492 PMCID: PMC5414959 DOI: 10.1371/journal.pone.0176129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 04/05/2017] [Indexed: 11/18/2022] Open
Abstract
The origin and natural history of molecular functions hold the key to the emergence of cellular organization and modern biochemistry. Here we use a genomic census of Gene Ontology (GO) terms to reconstruct phylogenies at the three highest (1, 2 and 3) and the lowest (terminal) levels of the hierarchy of molecular functions, which reflect the broadest and the most specific GO definitions, respectively. These phylogenies define evolutionary timelines of functional innovation. We analyzed 249 free-living organisms comprising the three superkingdoms of life, Archaea, Bacteria, and Eukarya. Phylogenies indicate catalytic, binding and transport functions were the oldest, suggesting a 'metabolism-first' origin scenario for biochemistry. Metabolism made use of increasingly complicated organic chemistry. Primordial features of ancient molecular functions and functional recruitments were further distilled by studying the oldest child terms of the oldest level 1 GO definitions. Network analyses showed the existence of an hourglass pattern of enzyme recruitment in the molecular functions of the directed acyclic graph of molecular functions. Older high-level molecular functions were thoroughly recruited at younger lower levels, while very young high-level functions were used throughout the timeline. This pattern repeated in every one of the three mappings, which gave a criss-cross pattern. The timelines and their mappings were remarkable. They revealed the progressive evolutionary development of functional toolkits, starting with the early rise of metabolic activities, followed chronologically by the rise of macromolecular biosynthesis, the establishment of controlled interactions with the environment and self, adaptation to oxygen, and enzyme coordinated regulation, and ending with the rise of structural and cellular complexity. This historical account holds important clues for dissection of the emergence of biomcomplexity and life.
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Affiliation(s)
- Ibrahim Koç
- Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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Harish A, Kurland CG. Akaryotes and Eukaryotes are independent descendants of a universal common ancestor. Biochimie 2017; 138:168-183. [PMID: 28461155 DOI: 10.1016/j.biochi.2017.04.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/25/2017] [Indexed: 11/29/2022]
Abstract
We reconstructed a global tree of life (ToL) with non-reversible and non-stationary models of genome evolution that root trees intrinsically. We implemented Bayesian model selection tests and compared the statistical support for four conflicting ToL hypotheses. We show that reconstructions obtained with a Bayesian implementation (Klopfstein et al., 2015) are consistent with reconstructions obtained with an empirical Sankoff parsimony (ESP) implementation (Harish et al., 2013). Both are based on the genome contents of coding sequences for protein domains (superfamilies) from hundreds of genomes. Thus, we conclude that the independent descent of Eukaryotes and Akaryotes (archaea and bacteria) from the universal common ancestor (UCA) is the most probable as well as the most parsimonious hypothesis for the evolutionary origins of extant genomes. Reconstructions of ancestral proteomes by both Bayesian and ESP methods suggest that at least 70% of unique domain-superfamilies known in extant species were present in the UCA. In addition, identification of a vast majority (96%) of the mitochondrial superfamilies in the UCA proteome precludes a symbiotic hypothesis for the origin of eukaryotes. Accordingly, neither the archaeal origin of eukaryotes nor the bacterial origin of mitochondria is supported by the data. The proteomic complexity of the UCA suggests that the evolution of cellular phenotypes in the two primordial lineages, Akaryotes and Eukaryotes, was driven largely by duplication of common superfamilies as well as by loss of unique superfamilies. Finally, innovation of novel superfamilies has played a surprisingly small role in the evolution of Akaryotes and only a marginal role in the evolution of Eukaryotes.
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Affiliation(s)
- Ajith Harish
- Department of Cell and Molecular Biology, Structural and Molecular Biology Program, Uppsala University, Uppsala, Sweden.
| | - Charles G Kurland
- Department of Biology, Microbial Ecology Program, Lund University, Lund, Sweden.
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Abrahão JS, Araújo R, Colson P, La Scola B. The analysis of translation-related gene set boosts debates around origin and evolution of mimiviruses. PLoS Genet 2017; 13:e1006532. [PMID: 28207761 PMCID: PMC5313130 DOI: 10.1371/journal.pgen.1006532] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The giant mimiviruses challenged the well-established concept of viruses, blurring the roots of the tree of life, mainly due to their genetic content. Along with other nucleo-cytoplasmic large DNA viruses, they compose a new proposed order-named Megavirales-whose origin and evolution generate heated debate in the scientific community. The presence of an arsenal of genes not widespread in the virosphere related to important steps of the translational process, including transfer RNAs, aminoacyl-tRNA synthetases, and translation factors for peptide synthesis, constitutes an important element of this debate. In this review, we highlight the main findings to date about the translational machinery of the mimiviruses and compare their distribution along the distinct members of the family Mimiviridae. Furthermore, we discuss how the presence and/or absence of the translation-related genes among mimiviruses raises important insights to boost the debate on their origin and evolutionary history.
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Affiliation(s)
- Jônatas Santos Abrahão
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille, France.,Instituto de Ciências Biológicas, Departamento de Microbiologia, Laboratório de Vírus, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Araújo
- Instituto de Ciências Biológicas, Departamento de Microbiologia, Laboratório de Vírus, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille, France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille, France
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Oliveira GP, Andrade ACDSP, Rodrigues RAL, Arantes TS, Boratto PVM, Silva LKDS, Dornas FP, Trindade GDS, Drumond BP, La Scola B, Kroon EG, Abrahão JS. Promoter Motifs in NCLDVs: An Evolutionary Perspective. Viruses 2017; 9:v9010016. [PMID: 28117683 PMCID: PMC5294985 DOI: 10.3390/v9010016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/30/2016] [Accepted: 01/05/2017] [Indexed: 01/18/2023] Open
Abstract
For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations.
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Affiliation(s)
- Graziele Pereira Oliveira
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Ana Cláudia Dos Santos Pereira Andrade
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Thalita Souza Arantes
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Paulo Victor Miranda Boratto
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Ludmila Karen Dos Santos Silva
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Fábio Pio Dornas
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Giliane de Souza Trindade
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Betânia Paiva Drumond
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Université., 27 Boulevard Jean Moulin, Faculté de Médecine, 13385 Marseille Cedex 05, France.
| | - Erna Geessien Kroon
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
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Claverie JM, Abergel C. Giant viruses: The difficult breaking of multiple epistemological barriers. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 59:89-99. [PMID: 26972873 DOI: 10.1016/j.shpsc.2016.02.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/27/2016] [Indexed: 06/05/2023]
Abstract
The discovery of the first "giant virus", Mimivirus, in 2003 could solely have been that of an exceptional freak, a blind alley of evolution as occasionally encountered in biology, albeit without conceptual significance. On the contrary, once broken this epistemological barrier, additional unrelated families of giant viruses such as the Pandoraviruses, the Pithoviruses and most recently Mollivirus, were quickly unraveled, suggesting that an entire chapter of microbiology had been ignored since Pasteur and Ivanovski. In this article, we examine to what extent the giant viruses challenge previous definitions of viruses, the diversity of forms they could take, and how they might have evolved from extinct ancestral cellular lineages. Inspired by the epistemology of Gaston Bachelard, we will also suggest the reasons for which giant viruses laid hidden in plain sight for more than a century. Finally, we propose a new definition for "viruses" that paradoxically emphasize the fact that they do not encode a single universally shared macromolecule or biochemical function.
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Affiliation(s)
- Jean-Michel Claverie
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) CNRS Aix-Marseille Université, Luminy Campus, Marseille, France; Assistance Publique des Hôpitaux de Marseille, La Timone, 13005, Marseille, France.
| | - Chantal Abergel
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) CNRS Aix-Marseille Université, Luminy Campus, Marseille, France
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Harish A, Abroi A, Gough J, Kurland C. Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells? Genome Biol Evol 2016; 8:2474-81. [PMID: 27497315 PMCID: PMC5010908 DOI: 10.1093/gbe/evw175] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The evolutionary origins of viruses according to marker gene phylogenies, as well as their relationships to the ancestors of host cells remains unclear. In a recent article Nasir and Caetano-Anollés reported that their genome-scale phylogenetic analyses based on genomic composition of protein structural-domains identify an ancient origin of the “viral supergroup” (Nasir et al. 2015. A phylogenomic data-driven exploration of viral origins and evolution. Sci Adv. 1(8):e1500527.). It suggests that viruses and host cells evolved independently from a universal common ancestor. Examination of their data and phylogenetic methods indicates that systematic errors likely affected the results. Reanalysis of the data with additional tests shows that small-genome attraction artifacts distort their phylogenomic analyses, particularly the location of the root of the phylogenetic tree of life that is central to their conclusions. These new results indicate that their suggestion of a distinct ancestry of the viral supergroup is not well supported by the evidence.
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Affiliation(s)
- Ajith Harish
- Structural and Molecular Biology Group, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Sweden
| | - Aare Abroi
- Estonian Biocentre, Riia 23, Tartu 51010, Estonia
| | - Julian Gough
- Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, UK
| | - Charles Kurland
- Microbial Ecology, Department of Biology, Lund University, Sweden
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Giant viruses come of age. Curr Opin Microbiol 2016; 31:50-57. [DOI: 10.1016/j.mib.2016.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 12/18/2022]
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50
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Rodrigues RAL, Abrahão JS, Drumond BP, Kroon EG. Giants among larges: how gigantism impacts giant virus entry into amoebae. Curr Opin Microbiol 2016; 31:88-93. [PMID: 27039270 DOI: 10.1016/j.mib.2016.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 11/29/2022]
Abstract
The proposed order Megavirales comprises the nucleocytoplasmic large DNA viruses (NCLDV), infecting a wide range of hosts. Over time, they co-evolved with different host cells, developing various strategies to penetrate them. Mimiviruses and other giant viruses enter cells through phagocytosis, while Marseillevirus and other large viruses explore endocytosis and macropinocytosis. These differing strategies might reflect the evolution of those viruses. Various scenarios have been proposed for the origin and evolution of these viruses, presenting one of the most enigmatic issues to surround these microorganisms. In this context, we believe that giant viruses evolved independently by massive gene/size gain, exploring the phagocytic pathway of entry into amoebas. In response to gigantism, hosts developed mechanisms to evade these parasites.
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Affiliation(s)
- Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Brasil (UFMG), Postal code 486, Belo Horizonte, Minas Gerais, Brazil
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Brasil (UFMG), Postal code 486, Belo Horizonte, Minas Gerais, Brazil
| | - Betânia Paiva Drumond
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Brasil (UFMG), Postal code 486, Belo Horizonte, Minas Gerais, Brazil
| | - Erna Geessien Kroon
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Brasil (UFMG), Postal code 486, Belo Horizonte, Minas Gerais, Brazil.
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