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Aquino ILM, Reis ES, Moreira ROAM, Arias NEC, Barcelos MG, Queiroz VF, Arifa RDDN, Lucas LMB, Tatara JM, Souza DG, Costa A, Rosa L, Almeida GMF, Kroon EG, Abrahão JS. Giant viruses inhibit superinfection by downregulating phagocytosis in Acanthamoeba. J Virol 2024:e0104524. [PMID: 39225468 DOI: 10.1128/jvi.01045-24] [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: 06/13/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
In the context of the virosphere, viral particles can compete for host cells. In this scenario, some viruses block the entry of exogenous virions upon infecting a cell, a phenomenon known as superinfection inhibition. The molecular mechanisms associated with superinfection inhibition vary depending on the viral species and the host, but generally, blocking superinfection ensures the genetic supremacy of the virus's progeny that first infects the cell. Giant amoeba-infecting viruses have attracted the scientific community's attention due to the complexity of their particles and genomes. However, there are no studies on the occurrence of superinfection and its inhibition induced by giant viruses. This study shows that mimivirus, moumouvirus, and megavirus, exhibit different strategies related to the infection of Acanthamoeba. For the first time, we have reported that mimivirus and moumouvirus induce superinfection inhibition in amoebas. Interestingly, megaviruses do not exhibit this ability, allowing continuous entry of exogenous virions into infected amoebas. Our investigation into the mechanisms behind superinfection blockage reveals that mimivirus and moumouvirus inhibit amoebic phagocytosis, leading to significant changes in the morphology and activity of the host cells. In contrast, megavirus-infected amoebas continue incorporating newly formed virions, negatively affecting the available viral progeny. This effect, however, is reversible with chemical inhibition of phagocytosis. This work contributes to the understanding of superinfection and its inhibition in mimivirus, moumouvirus, and megavirus, demonstrating that despite their evolutionary relatedness, these viruses exhibit profound differences in their interactions with their hosts.IMPORTANCESome viruses block the entry of new virions upon infecting a cell, a phenomenon known as superinfection inhibition. Superinfection inhibition in giant viruses has yet to be studied. This study reveals that even closely related viruses, such as mimivirus, moumouvirus, and megavirus, have different infection strategies for Acanthamoeba. For the first time, we have reported that mimivirus and moumouvirus induce superinfection inhibition in amoebas. In contrast, megaviruses do not exhibit this ability, allowing continuous entry of exogenous virions into infected amoebas. Our investigation shows that mimivirus and moumouvirus inhibit amoebic phagocytosis, causing significant changes in host cell morphology and activity. Megavirus-infected amoebas, however, continue incorporating newly formed viruses, affecting viral progeny. This research enhances our understanding of superinfection inhibition in these viruses, highlighting their differences in host interactions.
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Affiliation(s)
- Isabella L M Aquino
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Erik Sousa Reis
- Laboratório de Virologia Básica e Aplicada (LVBA), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rafaella Oliveira Almeida Mattos Moreira
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Nídia Esther Colquehuanca Arias
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Matheus Gomes Barcelos
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Victória Fulgêncio Queiroz
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Raquel Duque do Nascimento Arifa
- Laboratory of Microorganism-Host Interaction, Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Larissa Mendes Barbosa Lucas
- Laboratory of Microorganism-Host Interaction, Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana Miranda Tatara
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Daniele G Souza
- Laboratory of Microorganism-Host Interaction, Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Adriana Costa
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Luiz Rosa
- Laboratório de Microbiologia Polar e Conexões Tropicais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel M F Almeida
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Erna Geessien Kroon
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jônatas S Abrahão
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Yi X, Liang JL, Wen P, Jia P, Feng SW, Liu SY, Zhuang YY, Guo YQ, Lu JL, Zhong SJ, Liao B, Wang Z, Shu WS, Li JT. Giant viruses as reservoirs of antibiotic resistance genes. Nat Commun 2024; 15:7536. [PMID: 39214976 PMCID: PMC11364636 DOI: 10.1038/s41467-024-51936-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.
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Affiliation(s)
- Xinzhu Yi
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Ping Wen
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Shi-Wei Feng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Shen-Yan Liu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Yuan-Yue Zhuang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Yu-Qian Guo
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Jing-Li Lu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Sheng-Ji Zhong
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Zhang Wang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, PR China.
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Witt ASA, Carvalho JVRP, Serafim MSM, Arias NEC, Rodrigues RAL, Abrahão JS. The GC% landscape of the Nucleocytoviricota. Braz J Microbiol 2024:10.1007/s42770-024-01496-7. [PMID: 39180708 DOI: 10.1007/s42770-024-01496-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/14/2024] [Indexed: 08/26/2024] Open
Abstract
Genomic studies on sequence composition employ various approaches, such as calculating the proportion of guanine and cytosine within a given sequence (GC% content), which can shed light on various aspects of the organism's biology. In this context, GC% can provide insights into virus-host relationships and evolution. Here, we present a comprehensive gene-by-gene analysis of 61 representatives belonging to the phylum Nucleocytoviricota, which comprises viruses with the largest genomes known in the virosphere. Parameters were evaluated not only based on the average GC% of a given viral species compared to the entire phylum but also considering gene position and phylogenetic history. Our results reveal that while some families exhibit similar GC% among their representatives (e.g., Marseilleviridae), others such as Poxviridae, Phycodnaviridae, and Mimiviridae have members with discrepant GC% values, likely reflecting adaptation to specific biological cycles and hosts. Interestingly, certain genes located at terminal regions or within specific genomic clusters show GC% values distinct from the average, suggesting recent acquisition or unique evolutionary pressures. Horizontal gene transfer and the presence of potential paralogs were also assessed in genes with the most discrepant GC% values, indicating multiple evolutionary histories. Taken together, to the best of our knowledge, this study represents the first global and gene-by-gene analysis of GC% distribution and profiles within genomes of Nucleocytoviricota members, highlighting their diversity and identifying potential new targets for future studies.
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Affiliation(s)
- Amanda Stéphanie Arantes Witt
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Mateus Sá Magalhães Serafim
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Nidia Esther Colquehuanca Arias
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jônatas Santos Abrahão
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Langley CA, Dietzen PA, Emerman M, Tenthorey JL, Malik HS. Antiviral Mx proteins have an ancient origin and widespread distribution among eukaryotes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606855. [PMID: 39149278 PMCID: PMC11326297 DOI: 10.1101/2024.08.06.606855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
First identified in mammals, Mx proteins are potent antivirals against a broad swathe of viruses. Mx proteins arose within the Dynamin superfamily of proteins (DSP), mediating critical cellular processes, such as endocytosis and mitochondrial, plastid, and peroxisomal dynamics. And yet, the evolutionary origins of Mx proteins are poorly understood. Using a series of phylogenomic analyses with stepwise increments in taxonomic coverage, we show that Mx proteins predate the interferon signaling system in vertebrates. Our analyses find an ancient monophyletic DSP lineage in eukaryotes that groups vertebrate and invertebrate Mx proteins with previously undescribed fungal MxF proteins, the relatively uncharacterized plant and algal Dynamin 4A/4C proteins, and representatives from several early-branching eukaryotic lineages. Thus, Mx-like proteins date back close to the origin of Eukarya. Our phylogenetic analyses also reveal that host-encoded and NCLDV (nucleocytoplasmic large DNA viruses)-encoded DSPs are interspersed in four distinct DSP lineages, indicating recurrent viral theft of host DSPs. Our analyses thus reveal an ancient history of viral and antiviral functions encoded by the Dynamin superfamily in eukaryotes.
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Affiliation(s)
- Caroline A. Langley
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
| | - Peter A. Dietzen
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jeannette L. Tenthorey
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
- Cellular Molecular Pharmacology, University of California San Francisco, San Francisco, CA
| | - Harmit S. Malik
- Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA
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5
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Price CTD, Hanford HE, Al-Quadan T, Santic M, Shin CJ, Da'as MSJ, Abu Kwaik Y. Amoebae as training grounds for microbial pathogens. mBio 2024; 15:e0082724. [PMID: 38975782 PMCID: PMC11323580 DOI: 10.1128/mbio.00827-24] [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] [Indexed: 07/09/2024] Open
Abstract
Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.
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Affiliation(s)
- Christopher T. D. Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Hannah E. Hanford
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Tasneem Al-Quadan
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | | | - Cheon J. Shin
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Manal S. J. Da'as
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, Kentucky, USA
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Laperriere SM, Minch B, Weissman JL, Hou S, Yeh YC, Ignacio-Espinoza JC, Ahlgren NA, Moniruzzaman M, Fuhrman JA. Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.12.607631. [PMID: 39185240 PMCID: PMC11343133 DOI: 10.1101/2024.08.12.607631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Nucleocytoplasmic Large DNA Viruses (NCLDVs, also called giant viruses) are widespread in marine systems and infect a broad range of microbial eukaryotes (protists). Recent biogeographic work has provided global snapshots of NCLDV diversity and community composition across the world's oceans, yet little information exists about the guiding 'rules' underpinning their community dynamics over time. We leveraged a five-year monthly metagenomic time-series to quantify the community composition of NCLDVs off the coast of Southern California and characterize these populations' temporal dynamics. NCLDVs were dominated by Algavirales (Phycodnaviruses, 59%) and Imitervirales (Mimiviruses, 36%). We identified clusters of NCLDVs with distinct classes of seasonal and non-seasonal temporal dynamics. Overall, NCLDV population abundances were often highly dynamic with a strong seasonal signal. The Imitervirales group had highest relative abundance in the more oligotrophic late summer and fall, while Algavirales did so in winter. Generally, closely related strains had similar temporal dynamics, suggesting that evolutionary history is a key driver of the temporal niche of marine NCLDVs. However, a few closely-related strains had drastically different seasonal dynamics, suggesting that while phylogenetic proximity often indicates ecological similarity, occasionally phenology can shift rapidly, possibly due to host-switching. Finally, we identified distinct functional content and possible host interactions of two major NCLDV orders-including connections of Imitervirales with primary producers like the diatom Chaetoceros and widespread marine grazers like Paraphysomonas and Spirotrichea ciliates. Together, our results reveal key insights on season-specific effect of phylogenetically distinct giant virus communities on marine protist metabolism, biogeochemical fluxes and carbon cycling.
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Affiliation(s)
- Sarah M. Laperriere
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Benjamin Minch
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Sciences, University of Miami, Miami, FL, USA
| | - JL Weissman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, NY, USA
| | - Shengwei Hou
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yi-Chun Yeh
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | | | | | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Sciences, University of Miami, Miami, FL, USA
| | - Jed A. Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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7
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Nunes GHP, Oliveira JDS, Essus VA, Guimarães AJ, Pontes B, Cortines JR. Cytopathic effects in Mimivirus infection: understanding the kinetics of virus-cell interaction. Mem Inst Oswaldo Cruz 2024; 119:e230186. [PMID: 39045993 DOI: 10.1590/0074-02760230186] [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: 09/09/2023] [Accepted: 05/10/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Giant viruses have brought new insights into different aspects of virus-cell interactions. The resulting cytopathic effects from these interactions are one of the main aspects of infection assessment in a laboratory routine, mainly reflecting on the morphological features of an infected cell. OBJECTIVES In this work, we follow the entire kinetics of the cytopathic effect in cells infected by viruses of the Mimiviridae family, spatiotemporally quantifying typical features such as cell roundness, loss of motility, decrease in cell area and cell lysis. METHODS Infections by Acanthamoeba polyphaga mimivirus (APMV), Tupanvirus (TPV) and M4 were carried out at multiplicity of infection (MOI) 1 and MOI 10 in Acanthamoeba castellanii. Monitoring of infections was carried out using time lapse microscopy for up to 72 hours. The images were analyzed using ImageJ software. FINDINGS The data obtained indicate that APMV is the slowest virus in inducing the cytopathic effects of rounding, decrease in cell area, mobility and cell lysis. However, it is the only virus whose MOI increase accelerates the lysis process of infected cells. In turn, TPV and M4 rapidly induce morphological and behavioral changes. MAIN CONCLUSIONS Our results indicate that mimiviruses induce different temporal responses within the host cell and that it is possible to use these kinetic data to facilitate the understanding of infection by these viruses.
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Affiliation(s)
- Gabriel Henrique Pereira Nunes
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Laboratório de Virologia e Espectrometria de Massas, Rio de Janeiro, RJ, Brasil
| | - Juliana Dos Santos Oliveira
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Laboratório de Virologia e Espectrometria de Massas, Rio de Janeiro, RJ, Brasil
| | - Victor Alejandro Essus
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Laboratório de Virologia e Espectrometria de Massas, Rio de Janeiro, RJ, Brasil
| | - Allan J Guimarães
- Universidade Federal Fluminense, Instituto Biomédico, Departamento de Microbiologia e Parasitologia, Niterói, RJ, Brasil
| | - Bruno Pontes
- Universidade Federal do Rio de Janeiro, Instituto de Ciências Biomédicas & Centro Nacional de Biologia Estrutural e Bioimagem, Rio de Janeiro, RJ, Brasil
| | - Juliana Reis Cortines
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Laboratório de Virologia e Espectrometria de Massas, Rio de Janeiro, RJ, Brasil
- University of Connecticut, Department of Chemistry, Storrs, CT, USA
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8
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Wen Q, Yin X, Moming A, Liu G, Jiang B, Wang J, Fan Z, Sajjad W, Ge Y, Kang S, Shen S, Deng F. Viral communities locked in high elevation permafrost up to 100 m in depth on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172829. [PMID: 38692332 DOI: 10.1016/j.scitotenv.2024.172829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/03/2024]
Abstract
Permafrost serves as a natural cold reservoir for viral communities. However, little is known about the viromes in deep permafrost soil, as most studies of permafrost were restricted to shallow areas. Here, permafrost soil samples of up to 100 m in depth were collected from two sites in the Tuotuo River permafrost area on the Tibetan Plateau. We investigated the viral composition in these permafrost soil samples and analyzed the relationship of viral composition and diversity along with depths. Our study revealed that greater permafrost thickness corresponds to higher diversity within the viral community. Bacteriophages were found to be the dominant viral communities, with "kill the winner" dynamics observed within the Siphoviridae and Myoviridae. The abundance and diversity of viral communities may follow a potential pattern along soil layers and depths, influenced by pH, trace elements, and permafrost thickness. Notably, strong correlations were discovered between the content of inorganic elements, including B, Mg, Cr, Bi, Ti, Na, Ni, and Cu, and the viral composition. Moreover, we discovered highly conserved sequences of giant viruses at depth of 10, 20, and 50 m in permafrost, which play a crucial role in evolutionary processes. These findings provide valuable insights into the viral community patterns from shallow to 100-m-depth in high-elevation permafrost, offering crucial data support for the formulation of strategies for permafrost thaw caused by climate change and anthropogenic activities.
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Affiliation(s)
- Qian Wen
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xiufeng Yin
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 730000 Lanzhou, China
| | - Abulimiti Moming
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Guanyue Liu
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 730000 Lanzhou, China
| | - Boyong Jiang
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Jun Wang
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Zhaojun Fan
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 730000 Lanzhou, China
| | - Yingying Ge
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 730000 Lanzhou, China; University of Chinese Academy of Sciences, 100049 Beijing, China.
| | - Shu Shen
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China; Hubei Jiangxia Laboratory, 430200 Wuhan, China.
| | - Fei Deng
- Key Laboratory of Virology and Biosafety and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China.
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9
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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 PMCID: PMC11281659 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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10
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de Azevedo BL, Queiroz VF, de Aquino ILM, Machado TB, de Assis FL, Reis E, Araújo Júnior JP, Ullmann LS, Colson P, Greub G, Aylward F, Rodrigues RAL, Abrahão JS. The genomic and phylogenetic analysis of Marseillevirus cajuinensis raises questions about the evolution of Marseilleviridae lineages and their taxonomical organization. J Virol 2024; 98:e0051324. [PMID: 38752754 PMCID: PMC11237802 DOI: 10.1128/jvi.00513-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 06/14/2024] Open
Abstract
Marseilleviruses (MsV) are a group of viruses that compose the Marseilleviridae family within the Nucleocytoviricota phylum. They have been found in different samples, mainly in freshwater. MsV are classically organized into five phylogenetic lineages (A/B/C/D/E), but the current taxonomy does not fully represent all the diversity of the MsV lineages. Here, we describe a novel strain isolated from a Brazilian saltwater sample named Marseillevirus cajuinensis. Based on genomics and phylogenetic analyses, M. cajuinensis exhibits a 380,653-bp genome that encodes 515 open reading frames. Additionally, M. cajuinensis encodes a transfer RNA, a feature that is rarely described for Marseilleviridae. Phylogeny suggests that M. cajuinensis forms a divergent branch within the MsV lineage A. Furthermore, our analysis suggests that the common ancestor for the five classical lineages of MsV diversified into three major groups. The organization of MsV into three main groups is reinforced by a comprehensive analysis of clusters of orthologous groups, sequence identities, and evolutionary distances considering several MsV isolates. Taken together, our results highlight the importance of discovering new viruses to expand the knowledge about known viruses that belong to the same lineages or families. This work proposes a new perspective on the Marseilleviridae lineages organization that could be helpful to a future update in the taxonomy of the Marseilleviridae family. IMPORTANCE Marseilleviridae is a family of viruses whose members were mostly isolated from freshwater samples. In this work, we describe the first Marseillevirus isolated from saltwater samples, which we called Marseillevirus cajuinensis. Most of M. cajuinensis genomic features are comparable to other Marseilleviridae members, such as its high number of unknown proteins. On the other hand, M. cajuinensis encodes a transfer RNA, which is a gene category involved in protein translation that is rarely described in this viral family. Additionally, our phylogenetic analyses suggested the existence of, at least, three major Marseilleviridae groups. These observations provide a new perspective on Marseilleviridae lineages organization, which will be valuable in future updates to the taxonomy of the family since the current official classification does not capture all the Marseilleviridae known diversity.
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Affiliation(s)
- Bruna Luiza de Azevedo
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Victória Fulgêncio Queiroz
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Isabella Luiza Martins de Aquino
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Talita Bastos Machado
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Lopes de Assis
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Erik Reis
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - João Pessoa Araújo Júnior
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Alameda das Tecomarias s/n, Chácara Capão Bonito, Botucatu, Brazil
| | - Leila Sabrina Ullmann
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Alameda das Tecomarias s/n, Chácara Capão Bonito, Botucatu, Brazil
| | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille University, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Gilbert Greub
- Centre for Research on Intracellular Bacteria and Giant Viruses, Institute of Microbiology, University Hospital Centre and University of Lausanne, Lausanne, Switzerland
| | - Frank Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease Virginia Tech, Blacksburg, Virginia, USA
| | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
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11
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Machado TB, de Aquino ILM, Azevedo BL, Serafim MS, Barcelos MG, Andrade ACSP, Reis E, Ullmann LS, Pessoa J, Costa AO, Rosa LH, Abrahão JS. A long-term prospecting study on giant viruses in terrestrial and marine Brazilian biomes. Virol J 2024; 21:135. [PMID: 38858684 PMCID: PMC11165748 DOI: 10.1186/s12985-024-02404-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
The discovery of mimivirus in 2003 prompted the search for novel giant viruses worldwide. Despite increasing interest, the diversity and distribution of giant viruses is barely known. Here, we present data from a 2012-2022 study aimed at prospecting for amoebal viruses in water, soil, mud, and sewage samples across Brazilian biomes, using Acanthamoeba castellanii for isolation. A total of 881 aliquots from 187 samples covering terrestrial and marine Brazilian biomes were processed. Electron microscopy and PCR were used to identify the obtained isolates. Sixty-seven amoebal viruses were isolated, including mimiviruses, marseilleviruses, pandoraviruses, cedratviruses, and yaraviruses. Viruses were isolated from all tested sample types and almost all biomes. In comparison to other similar studies, our work isolated a substantial number of Marseillevirus and cedratvirus representatives. Taken together, our results used a combination of isolation techniques with microscopy, PCR, and sequencing and put highlight on richness of giant virus present in different terrestrial and marine Brazilian biomes.
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Affiliation(s)
- Talita B Machado
- Laboratório de vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte city, Minas Gerais, Brazil
| | - Isabella L M de Aquino
- Laboratório de vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte city, Minas Gerais, Brazil
| | - Bruna L Azevedo
- Laboratório de vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte city, Minas Gerais, Brazil
| | - Mateus S Serafim
- Laboratório de vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte city, Minas Gerais, Brazil
| | - Matheus G Barcelos
- Laboratório de vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte city, Minas Gerais, Brazil
| | - Ana Cláudia S P Andrade
- Centre de Recherche du Centre Hospitalier Universitaire de Québec, Université Laval, Laval city, Québec, Canada
| | - Erik Reis
- Laboratório de virologia básica e aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte city, Minas Gerais, Brazil
| | - Leila Sabrina Ullmann
- Laboratório de Virologia Veterinária, Faculdade de Medicina Veterinária e Zootecnia (FAMEZ), Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande city, Mato Grosso do Sul, Brazil
| | - João Pessoa
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista (UNESP), Botucatu city, São Paulo, Brazil
| | - Adriana O Costa
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte city, Minas Gerais, Brazil
| | - Luiz H Rosa
- Laboratório de Microbiologia Polar e Conexões Tropicais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte city, Minas Gerais, Brazil
| | - Jônatas S Abrahão
- Laboratório de vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte city, Minas Gerais, Brazil.
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12
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Piast RW. The bubble theory: exploring the transition from first replicators to cells and viruses in a landscape-based scenario. Theory Biosci 2024; 143:153-160. [PMID: 38722466 PMCID: PMC11127830 DOI: 10.1007/s12064-024-00417-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/07/2024] [Indexed: 05/27/2024]
Abstract
This study proposes a landscape-based scenario for the origin of viruses and cells, focusing on the adaptability of preexisting replicons from the RNP (ribonucleoprotein) world. The scenario postulates that life emerged in a subterranean "warm little pond" where organic matter accumulated, resulting in a prebiotic soup rich in nucleotides, amino acids, and lipids, which served as nutrients for the first self-replicating entities. Over time, the RNA world, followed by the RNP world, came into existence. Replicators/replicons, along with the nutritious soup from the pond, were washed out into the river and diluted. Lipid bubbles, enclosing organic matter, provided the last suitable environment for replicons to replicate. Two survival strategies emerged under these conditions: cell-like structures that obtained nutrients by merging with new bubbles, and virus-like entities that developed various techniques to transmit themselves to fresh bubbles. The presented hypothesis provides the possibility for the common origin of cells and viruses on rocky worlds hosting liquid water, like Earth.
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Affiliation(s)
- Radoslaw W Piast
- Chemistry Department, Warsaw University, Pasteura 1, Warsaw, Poland.
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13
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Maio N, Heffner AL, Rouault TA. Iron‑sulfur clusters in viral proteins: Exploring their elusive nature, roles and new avenues for targeting infections. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119723. [PMID: 38599324 PMCID: PMC11139609 DOI: 10.1016/j.bbamcr.2024.119723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Viruses have evolved complex mechanisms to exploit host factors for replication and assembly. In response, host cells have developed strategies to block viruses, engaging in a continuous co-evolutionary battle. This dynamic interaction often revolves around the competition for essential resources necessary for both host cell and virus replication. Notably, iron, required for the biosynthesis of several cofactors, including iron‑sulfur (FeS) clusters, represents a critical element in the ongoing competition for resources between infectious agents and host. Although several recent studies have identified FeS cofactors at the core of virus replication machineries, our understanding of their specific roles and the cellular processes responsible for their incorporation into viral proteins remains limited. This review aims to consolidate our current knowledge of viral components that have been characterized as FeS proteins and elucidate how viruses harness these versatile cofactors to their benefit. Its objective is also to propose that viruses may depend on incorporation of FeS cofactors more extensively than is currently known. This has the potential to revolutionize our understanding of viral replication, thereby carrying significant implications for the development of strategies to target infections.
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Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
| | - Audrey L Heffner
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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14
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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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15
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Akashi M, Takemura M, Suzuki S. Continuous year-round isolation of giant viruses from brackish shoreline soils. Front Microbiol 2024; 15:1402690. [PMID: 38756730 PMCID: PMC11096492 DOI: 10.3389/fmicb.2024.1402690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
Giant viruses, categorized under Nucleocytoviricota, are believed to exist ubiquitously in natural environments. However, comprehensive reports on isolated giant viruses remain scarce, with limited information available on unrecoverable strains, viral proliferation sites, and natural hosts. Previously, the author highlighted Pandoravirus hades, Pandoravirus persephone, and Mimivirus sp. styx, isolated from brackish water soil, as potential hotspots for giant virus multiplication. This study presents findings from nearly a year of monthly sampling within the same brackish water region after isolating the three aforementioned strains. This report details the recurrent isolation of a wide range of giant viruses. Each month, four soil samples were randomly collected from an approximately 5 × 10 m plot, comprising three soil samples and one water sample containing sediment from the riverbed. Acanthamoeba castellanii was used as a host for virus isolation. These efforts consistently yielded at least one viral species per month, culminating in a total of 55 giant virus isolates. The most frequently isolated species was Mimiviridae (24 isolates), followed by Marseilleviridae (23 isolates), Pandoravirus (6 isolates), and singular isolates of Pithovirus and Cedratvirus. Notably, viruses were not consistently isolated from any of the four samples every month, with certain sites yielding no viruses. Cluster analysis based on isolate numbers revealed that soil samples from May and water and sediment samples from January produced the highest number of viral strains. These findings underscore brackish coastal soil as a significant site for isolating numerous giant viruses, highlighting the non-uniform distribution along coastlines.
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Affiliation(s)
- Motohiro Akashi
- Department of Science and Technology, Faculty of Science and Technology, Seikei University, Tokyo, Japan
| | - Masaharu Takemura
- Institute of Arts and Sciences, Tokyo University of Science, Tokyo, Japan
| | - Seiichi Suzuki
- Department of Science and Technology, Faculty of Science and Technology, Seikei University, Tokyo, Japan
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16
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Malaterre C. Is Life Binary or Gradual? Life (Basel) 2024; 14:564. [PMID: 38792586 PMCID: PMC11121977 DOI: 10.3390/life14050564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
The binary nature of life is deeply ingrained in daily experiences, evident in the stark distinctions between life and death and the living and the inert. While this binary perspective aligns with disciplines like medicine and much of biology, uncertainties emerge in fields such as microbiology, virology, synthetic biology, and systems chemistry, where intermediate entities challenge straightforward classification as living or non-living. This contribution explores the motivations behind both binary and non-binary conceptualizations of life. Despite the perceived necessity to unequivocally define life, especially in the context of origin of life research and astrobiology, mounting evidence indicates a gray area between what is intuitively clearly alive and what is distinctly not alive. This prompts consideration of a gradualist perspective, depicting life as a spectrum with varying degrees of "lifeness". Given the current state of science, the existence or not of a definite threshold remains open. Nevertheless, shifts in epistemic granularity and epistemic perspective influence the framing of the question, and scientific advancements narrow down possible answers: if a threshold exists, it can only be at a finer level than what is intuitively taken as living or non-living. This underscores the need for a more refined distinction between the inanimate and the living.
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Affiliation(s)
- Christophe Malaterre
- Département de Philosophie, Université du Québec à Montréal, Montreal, QC H3C 3P8, Canada;
- Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Montreal, QC H3C 3P8, Canada
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17
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Arthofer P, Panhölzl F, Delafont V, Hay A, Reipert S, Cyran N, Wienkoop S, Willemsen A, Sifaoui I, Arberas-Jiménez I, Schulz F, Lorenzo-Morales J, Horn M. A giant virus infecting the amoeboflagellate Naegleria. Nat Commun 2024; 15:3307. [PMID: 38658525 PMCID: PMC11043551 DOI: 10.1038/s41467-024-47308-2] [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: 08/02/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Giant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.
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Affiliation(s)
- Patrick Arthofer
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Florian Panhölzl
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Vincent Delafont
- Ecologie et Biologie des Interactions Laboratory (EBI), Microorganisms, hosts & environments team, Université de Poitiers, UMR CNRS, Poitiers, France
| | - Alban Hay
- Ecologie et Biologie des Interactions Laboratory (EBI), Microorganisms, hosts & environments team, Université de Poitiers, UMR CNRS, Poitiers, France
| | - Siegfried Reipert
- University of Vienna, Research Support Facilities UBB, Vienna, Austria
| | - Norbert Cyran
- University of Vienna, Research Support Facilities UBB, Vienna, Austria
| | - Stefanie Wienkoop
- University of Vienna, Department of Functional and Evolutionary Ecology, Division of Molecular Systems Biology, Vienna, Austria
| | - Anouk Willemsen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Ines Sifaoui
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, and Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Tenerife, Islas Canarias, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Iñigo Arberas-Jiménez
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, and Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Tenerife, Islas Canarias, Spain
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Jacob Lorenzo-Morales
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, and Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Tenerife, Islas Canarias, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Matthias Horn
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.
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18
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Upadhyay M, Nair D, Moseley GW, Srivastava S, Kondabagil K. Giant Virus Global Proteomics Innovation: Comparative Evaluation of In-Gel and In-Solution Digestion Methods. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:170-181. [PMID: 38621149 DOI: 10.1089/omi.2024.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
With their unusually large genome and particle sizes, giant viruses (GVs) defy the conventional definition of viruses. Although most GVs isolated infect unicellular protozoans, such as amoeba, studies in the last decade have established their much wider prevalence infecting most eukaryotic supergroups and some giant viral families with the potential to be human pathogens. Their complexity, almost autonomous life cycle, and enigmatic evolution necessitate the study of GVs. The accurate assessment of GV proteome is a veritable challenge. We have compared the coverage of global protein identification using different methods for GVs isolated in Mumbai, Mimivirus Bombay (MVB), Powai Lake Megavirus (PLMV), and Kurlavirus (KV), along with two previously studied GVs, Acanthamoeba polyphaga Mimivirus (APMV) and Marseillevirus (MV). Our study shows that the simultaneous use of in-gel and in-solution digestion methods can significantly increase the coverage of protein identification in the global proteome analysis of purified GV particles. Combining the two methods of analyses, we identified an additional 72 proteins in APMV and 114 in MV compared with what have been previously reported. Similarly, proteomes of MVB, PLMV, and KV were analyzed, and a total of 242 proteins in MVB, 287 proteins in PLMV, and 174 proteins in KV were identified. Our results suggest that a combined methodology of in-gel and in-solution methods is more efficient and opens up new avenues for innovation in global proteome analysis of GVs. Future planetary health research on GVs can benefit from consideration of a broader range of proteomics methodologies as illustrated by the present study.
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Affiliation(s)
- Monica Upadhyay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Gregory W Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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19
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Cho A, Lax G, Livingston SJ, Masukagami Y, Naumova M, Millar O, Husnik F, Keeling PJ. Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses. PLoS Genet 2024; 20:e1011218. [PMID: 38557755 PMCID: PMC11008856 DOI: 10.1371/journal.pgen.1011218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/11/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Symbiomonas scintillans Guillou et Chrétiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC257, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.
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Affiliation(s)
- Anna Cho
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel J. Livingston
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yumiko Masukagami
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Mariia Naumova
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Olivia Millar
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Filip Husnik
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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20
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Morimoto D, Tateishi N, Takahashi M, Nagasaki K. Isolation of viruses, including mollivirus, with the potential to infect Acanthamoeba from a Japanese warm temperate zone. PLoS One 2024; 19:e0301185. [PMID: 38547190 PMCID: PMC10977731 DOI: 10.1371/journal.pone.0301185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
Acanthamoeba castellanii is infected with diverse nucleocytoplasmic large DNA viruses. Here, we report the co-isolation of 12 viral strains from marine sediments in Uranouchi Inlet, Kochi, Japan. Based on the morphological features revealed by electron microscopy, these isolates were classified into four viral groups including Megamimiviridae, Molliviridae, Pandoraviridae, and Pithoviridae. Genomic analyses indicated that these isolates showed high similarities to the known viral genomes with which they are taxonomically clustered, and their phylogenetic relationships were also supported by core gene similarities. It is noteworthy that Molliviridae was isolated from the marine sediments in the Japanese warm temperate zone because other strains have only been found in the subarctic region. Furthermore, this strain has 19 and 4 strain-specific genes found in Mollivirus sibericum and Mollivirus kamchatka, respectively. This study extends our knowledge about the habitat and genomic diversity of Molliviridae.
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Affiliation(s)
- Daichi Morimoto
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
| | - Naohisa Tateishi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | | | - Keizo Nagasaki
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
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21
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Queiroz VF, Tatara JM, Botelho BB, Rodrigues RAL, Almeida GMDF, Abrahao JS. The consequences of viral infection on protists. Commun Biol 2024; 7:306. [PMID: 38462656 PMCID: PMC10925606 DOI: 10.1038/s42003-024-06001-2] [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: 10/28/2023] [Accepted: 02/29/2024] [Indexed: 03/12/2024] Open
Abstract
Protists encompass a vast widely distributed group of organisms, surpassing the diversity observed in metazoans. Their diverse ecological niches and life forms are intriguing characteristics that render them valuable subjects for in-depth cell biology studies. Throughout history, viruses have played a pivotal role in elucidating complex cellular processes, particularly in the context of cellular responses to viral infections. In this comprehensive review, we provide an overview of the cellular alterations that are triggered in specific hosts following different viral infections and explore intricate biological interactions observed in experimental conditions using different host-pathogen groups.
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Affiliation(s)
- Victoria Fulgencio Queiroz
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana Miranda Tatara
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Bruna Barbosa Botelho
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Magno de Freitas Almeida
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway.
| | - Jonatas Santos Abrahao
- Federal University of Minas Gerais, Institute of Biological Sciences, Department of Microbiology, Belo Horizonte, Minas Gerais, Brazil
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22
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Crispim APC, Serafim MSM, Costa AO, Abrahão JS. Could giant viruses be considered as a biotechnological tool for preventing and controlling Acanthamoeba infections? J Appl Microbiol 2024; 135:lxae044. [PMID: 38373822 DOI: 10.1093/jambio/lxae044] [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: 12/28/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
AIM The aim of the study was to evaluate the efficiency of mimivirus as a potential therapeutic and prophylactic tool against Acanthamoeba castellanii, the etiological agent of Acanthamoeba keratitis, a progressive corneal infection, that is commonly associated with the use of contact lenses and can lead to blindness if not properly treated. METHODS AND RESULTS Mimivirus particles were tested in different multiplicity of infection, along with commercial multipurpose contact lenses' solutions, aiming to assess their ability to prevent encystment and excystment of A. castellanii. Solutions were evaluated for their amoebicidal potential and cytotoxicity in MDCK cells, as well as their effectiveness in preventing A. castellanii damage in Madin-Darby canine kidney (MDCK) cells. Results indicated that mimivirus was able to inhibit the formation of A. castellanii cysts, even in the presence of Neff encystment solution. Mimivirus also showed greater effectiveness in controlling A. castellanii excystment compared to commercial solutions. Additionally, mimivirus solution was more effective in preventing damage caused by A. castellanii, presented greater amoebicidal activity, and were less cytotoxic to MDCK cells than commercial MPS. CONCLUSIONS Mimivirus demonstrates a greater ability to inhibit A. castellanii encystment and excystment compared to commercial multipurpose contact lens solutions. Additionally, mimivirus is less toxic to MDCK cells than those commercial solutions. New studies utilizing in vivo models will be crucial for confirming safety and efficacy parameters.
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Affiliation(s)
- Ana Paula Correia Crispim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Adriana Oliveira Costa
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Jônatas Santos Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil
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23
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Simón D, Ramos N, Lamolle G, Musto H. Two decades ago, giant viruses were discovered: the fall of an old paradigm. Front Microbiol 2024; 15:1356711. [PMID: 38463488 PMCID: PMC10920292 DOI: 10.3389/fmicb.2024.1356711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024] Open
Affiliation(s)
- Diego Simón
- Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Montevideo, Uruguay
- Laboratorio de Virología Molecular, Facultad de Ciencias, Centro de Investigaciones Nucleares, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Natalia Ramos
- Sección Virología, Departamento de Biología Celular y Molecular, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Guillermo Lamolle
- Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Montevideo, Uruguay
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24
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Zong G, Desfougères Y, Portela-Torres P, Kwon YU, Saiardi A, Shears SB, Wang H. Biochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus. EMBO J 2024; 43:462-480. [PMID: 38216735 PMCID: PMC10897400 DOI: 10.1038/s44318-023-00005-0] [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: 07/13/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 01/14/2024] Open
Abstract
Kinases that synthesize inositol phosphates (IPs) and pyrophosphates (PP-IPs) control numerous biological processes in eukaryotic cells. Herein, we extend this cellular signaling repertoire to viruses. We have biochemically and structurally characterized a minimalist inositol phosphate kinase (i.e., TvIPK) encoded by Terrestrivirus, a nucleocytoplasmic large ("giant") DNA virus (NCLDV). We show that TvIPK can synthesize inositol pyrophosphates from a range of scyllo- and myo-IPs, both in vitro and when expressed in yeast cells. We present multiple crystal structures of enzyme/substrate/nucleotide complexes with individual resolutions from 1.95 to 2.6 Å. We find a heart-shaped ligand binding pocket comprising an array of positively charged and flexible side chains, underlying the observed substrate diversity. A crucial arginine residue in a conserved "G-loop" orients the γ-phosphate of ATP to allow substrate pyrophosphorylation. We highlight additional conserved catalytic and architectural features in TvIPK, and support their importance through site-directed mutagenesis. We propose that NCLDV inositol phosphate kinases may have assisted evolution of inositol pyrophosphate signaling, and we discuss the potential biogeochemical significance of TvIPK in soil niches.
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Affiliation(s)
- Guangning Zong
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Yann Desfougères
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Paloma Portela-Torres
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Yong-Uk Kwon
- Department of Chemistry and Nanoscience, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK.
| | - Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
| | - Huanchen Wang
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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25
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Nishimura L, Tanino A, Ajimoto M, Katsumura T, Ogawa M, Koganebuchi K, Waku D, Kumagai M, Sugimoto R, Nakaoka H, Oota H, Inoue I. Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. PLoS One 2024; 19:e0295924. [PMID: 38265980 PMCID: PMC10807776 DOI: 10.1371/journal.pone.0295924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 12/03/2023] [Indexed: 01/26/2024] Open
Abstract
Coprolites contain various kinds of ancient DNAs derived from gut micro-organisms, viruses, and foods, which can help to determine the gut environment of ancient peoples. Their genomic information should be helpful in elucidating the interaction between hosts and microbes for thousands of years, as well as characterizing the dietary behaviors of ancient people. We performed shotgun metagenomic sequencing on four coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. The coprolites were found in the layers of the Early Jomon period, corresponding stratigraphically to 7000 to 5500 years ago. After shotgun sequencing, we found that a significant number of reads showed homology with known gut microbe, viruses, and food genomes typically found in the feces of modern humans. We detected reads derived from several types of phages and their host bacteria simultaneously, suggesting the coexistence of viruses and their hosts. The food genomes provide biological evidence for the dietary behavior of the Jomon people, consistent with previous archaeological findings. These results indicate that ancient genomic analysis of coprolites is useful for understanding the gut environment and lifestyle of ancient peoples.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Akio Tanino
- Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan
| | | | - Takafumi Katsumura
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Motoyuki Ogawa
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Kae Koganebuchi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Daisuke Waku
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Masahiko Kumagai
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Ryota Sugimoto
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
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26
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Vieira HH, Bulzu PA, Kasalický V, Haber M, Znachor P, Piwosz K, Ghai R. Isolation of a widespread giant virus implicated in cryptophyte bloom collapse. THE ISME JOURNAL 2024; 18:wrae029. [PMID: 38401169 PMCID: PMC10960955 DOI: 10.1093/ismejo/wrae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/29/2024] [Accepted: 02/22/2024] [Indexed: 02/26/2024]
Abstract
Photosynthetic cryptophytes are ubiquitous protists that are major participants in the freshwater phytoplankton bloom at the onset of spring. Mortality due to change in environmental conditions and grazing have been recognized as key factors contributing to bloom collapse. In contrast, the role of viral outbreaks as factors terminating phytoplankton blooms remains unknown from freshwaters. Here, we isolated and characterized a cryptophyte virus contributing to the annual collapse of a natural cryptophyte spring bloom population. This viral isolate is also representative for a clade of abundant giant viruses (phylum Nucleocytoviricota) found in freshwaters all over the world.
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Affiliation(s)
- Helena H Vieira
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Vojtěch Kasalický
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Markus Haber
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Petr Znachor
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, 81-332 Gdynia, Poland
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
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27
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Balestreri C, Schroeder DC, Sampedro F, Marqués G, Palowski A, Urriola PE, van de Ligt JLG, Yancy HF, Shurson GC. Unexpected thermal stability of two enveloped megaviruses, Emiliania huxleyi virus and African swine fever virus, as measured by viability PCR. Virol J 2024; 21:1. [PMID: 38172919 PMCID: PMC10765680 DOI: 10.1186/s12985-023-02272-z] [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: 04/20/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The particle structure of Emiliania huxleyi virus (EhV), an algal infecting member of nucleocytoplasmic large DNA viruses (NCLDVs), contains an outer lipid membrane envelope similar to that found in animal viruses such as African swine fever virus (ASFV). Despite both being enveloped NCLDVs, EhV and ASFV are known for their stability outside their host environment. METHOD Here we report for the first time, the application of a viability qPCR (V-qPCR) method to describe the unprecedented and similar virion thermal stability of both EhV and ASFV. This result contradicts the cell culture-based assay method that suggests that virus "infectivity" is lost in a matter of seconds (for EhV) and minutes (for ASFV) at temperature greater than 50 °C. Confocal microscopy and analytical flow cytometry methods was used to validate the V-qPCR data for EhV. RESULTS We observed that both EhV and ASFV particles has unprecedented thermal tolerances. These two NCLDVs are exceptions to the rule that having an enveloped virion anatomy is a predicted weakness, as is often observed in enveloped RNA viruses (i.e., the viruses causing Porcine Reproductive and Respiratory Syndrome (PRRS), COVID-19, Ebola, or seasonal influenza). Using the V-qPCR method, we confirm that no PRRSV particles were detectable after 20 min of exposure to temperatures up to 100 °C. We also show that the EhV particles that remain after 50 °C 20 min exposure was in fact still infectious only after the three blind passages in bioassay experiments. CONCLUSIONS This study raises the possibility that ASFV is not always eliminated or contained after applying time and temperature inactivation treatments in current decontamination or biosecurity protocols. This observation has practical implications for industries involved in animal health and food security. Finally, we propose that EhV could be used as a surrogate for ASFV under certain circumstances.
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Affiliation(s)
- Cecilia Balestreri
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Declan C Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Fernando Sampedro
- Environmental Health Sciences Division, University of Minnesota, St. Paul, MN, 55455, USA
| | - Guillermo Marqués
- Department of Neuroscience, University Imaging Centers, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Amanda Palowski
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Pedro E Urriola
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Haile F Yancy
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD, 20708, USA
| | - Gerald C Shurson
- Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA.
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28
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Pitot TM, Rapp JZ, Schulz F, Girard C, Roux S, Culley AI. Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes. ISME COMMUNICATIONS 2024; 4:ycae048. [PMID: 38800130 PMCID: PMC11128243 DOI: 10.1093/ismeco/ycae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/29/2024] [Accepted: 03/27/2024] [Indexed: 05/29/2024]
Abstract
Giant viruses (GVs) are key players in ecosystem functioning, biogeochemistry, and eukaryotic genome evolution. GV diversity and abundance in aquatic systems can exceed that of prokaryotes, but their diversity and ecology in lakes, especially polar ones, remain poorly understood. We conducted a comprehensive survey and meta-analysis of GV diversity across 20 lakes, spanning polar to temperate regions, combining our extensive lake metagenome database from the Canadian Arctic and subarctic with publicly available datasets. Leveraging a novel GV genome identification tool, we identified 3304 GV metagenome-assembled genomes, revealing lakes as untapped GV reservoirs. Phylogenomic analysis highlighted their dispersion across all Nucleocytoviricota orders. Strong GV population endemism emerged between lakes from similar regions and biomes (Antarctic and Arctic), but a polar/temperate barrier in lacustrine GV populations and differences in their gene content could be observed. Our study establishes a robust genomic reference for future investigations into lacustrine GV ecology in fast changing polar environments.
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Affiliation(s)
- Thomas M Pitot
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, United States
- Center for Northern Studies, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- IBIS Institute of Integrative Biology and Systems, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
| | - Josephine Z Rapp
- Center for Northern Studies, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Department of Biology, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Catherine Girard
- Center for Northern Studies, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi (UQAC), Chicoutimi, QC G7H 2B1, Canada
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Alexander I Culley
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Center for Northern Studies, Université Laval, 2325 rue de l’Université, Québec, QC G1V0A6, Canada
- Pacific Biosciences Research Center, 1800 East-West Road, Honolulu, HI 96822, United States
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29
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Machado TB, Picorelli ACR, de Azevedo BL, de Aquino ILM, Queiroz VF, Rodrigues RAL, Araújo JP, Ullmann LS, dos Santos TM, Marques RE, Guimarães SL, Andrade ACSP, Gularte JS, Demoliner M, Filippi M, Pereira VMAG, Spilki FR, Krupovic M, Aylward FO, Del-Bem LE, Abrahão JS. Gene duplication as a major force driving the genome expansion in some giant viruses. J Virol 2023; 97:e0130923. [PMID: 38092658 PMCID: PMC10734413 DOI: 10.1128/jvi.01309-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/26/2023] [Indexed: 12/22/2023] Open
Abstract
IMPORTANCE Giant viruses are noteworthy not only due to their enormous particles but also because of their gigantic genomes. In this context, a fundamental question has persisted: how did these genomes evolve? Here we present the discovery of cedratvirus pambiensis, featuring the largest genome ever described for a cedratvirus. Our data suggest that the larger size of the genome can be attributed to an unprecedented number of duplicated genes. Further investigation of this phenomenon in other viruses has illuminated gene duplication as a key evolutionary mechanism driving genome expansion in diverse giant viruses. Although gene duplication has been described as a recurrent event in cellular organisms, our data highlights its potential as a pivotal event in the evolution of gigantic viral genomes.
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Affiliation(s)
- Talita B. Machado
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Agnello C. R. Picorelli
- Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Bruna L. de Azevedo
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Isabella L. M. de Aquino
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Victória F. Queiroz
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Rodrigo A. L. Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - João Pessoa Araújo
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista (UNESP), Botucatu, Brazil
| | - Leila S. Ullmann
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista (UNESP), Botucatu, Brazil
| | - Thiago M. dos Santos
- Del-Bem Lab, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Rafael E. Marques
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Samuel L. Guimarães
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Ana Cláudia S. P. Andrade
- Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Laval, Québec, Canada
| | - Juliana S. Gularte
- Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - Micheli Filippi
- Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | | | - Fernando R. Spilki
- Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Brazil
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, Paris, France
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease Virginia Tech, Blacksburg, Virginia, USA
| | - Luiz-Eduardo Del-Bem
- Del-Bem Lab, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Jônatas S. Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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30
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Jung Y, Mitsuhashi T, Sato S, Senda M, Senda T, Fujita M. Function and Structure of a Terpene Synthase Encoded in a Giant Virus Genome. J Am Chem Soc 2023; 145:25966-25970. [PMID: 38010834 DOI: 10.1021/jacs.3c10603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Giant viruses are nonstandard viruses with large particles and genomes. While previous studies have shown that their genomes contain various sequences of interest, their genes related specifically to natural product biosynthesis remain unexplored. Here we analyze the function and structure of a terpene synthase encoded by the gene of a giant virus. The enzyme is phylogenetically separated from the terpene synthases of cellular organisms; however, heterologous gene expression revealed that it still functions as a terpene synthase and produces a cyclic terpene from a farnesyl diphosphate precursor. Crystallographic analysis revealed its protein structure, which is relatively compact but retains essential motifs of the terpene synthases. We thus suggest that like cellular organisms, giant viruses produce and utilize natural products for their ecological strategies.
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Affiliation(s)
- Youngcheol Jung
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Mitsui Link Lab, Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Takaaki Mitsuhashi
- Division of Advanced Molecular Science, Institute for Molecular Science (IMS), Okazaki, Aichi 444-8787, Japan
| | - Sota Sato
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Mitsui Link Lab, Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
- Division of Advanced Molecular Science, Institute for Molecular Science (IMS), Okazaki, Aichi 444-8787, Japan
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Mitsui Link Lab, Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
- Division of Advanced Molecular Science, Institute for Molecular Science (IMS), Okazaki, Aichi 444-8787, Japan
- Tokyo College, Institutes for Advanced Study, The University of Tokyo, Mitsui Link Lab Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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31
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Liang H, Mower JP, Chia CP. Functional Prokaryotic-Like Deoxycytidine Triphosphate Deaminases and Thymidylate Synthase in Eukaryotic Social Amoebae: Vertical, Endosymbiotic, or Horizontal Gene Transfer? Mol Biol Evol 2023; 40:msad268. [PMID: 38064674 PMCID: PMC10733785 DOI: 10.1093/molbev/msad268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/22/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023] Open
Abstract
The de novo synthesis of deoxythymidine triphosphate uses several pathways: gram-negative bacteria use deoxycytidine triphosphate deaminase to convert deoxycytidine triphosphate into deoxyuridine triphosphate, whereas eukaryotes and gram-positive bacteria instead use deoxycytidine monophosphate deaminase to transform deoxycytidine monophosphate to deoxyuridine monophosphate. It is then unusual that in addition to deoxycytidine monophosphate deaminases, the eukaryote Dictyostelium discoideum has 2 deoxycytidine triphosphate deaminases (Dcd1Dicty and Dcd2Dicty). Expression of either DcdDicty can fully rescue the slow growth of an Escherichia coli dcd knockout. Both DcdDicty mitigate the hydroxyurea sensitivity of a Schizosaccharomyces pombe deoxycytidine monophosphate deaminase knockout. Phylogenies show that Dcd1Dicty homologs may have entered the common ancestor of the eukaryotic groups of Amoebozoa, Obazoa, Metamonada, and Discoba through an ancient horizontal gene transfer from a prokaryote or an ancient endosymbiotic gene transfer from a mitochondrion, followed by horizontal gene transfer from Amoebozoa to several other unrelated groups of eukaryotes. In contrast, the Dcd2Dicty homologs were a separate horizontal gene transfer from a prokaryote or a virus into either Amoebozoa or Rhizaria, followed by a horizontal gene transfer between them. ThyXDicty, the D. discoideum thymidylate synthase, another enzyme of the deoxythymidine triphosphate biosynthesis pathway, was suggested previously to be acquired from the ancestral mitochondria or by horizontal gene transfer from alpha-proteobacteria. ThyXDicty can fully rescue the E. coli thymidylate synthase knockout, and we establish that it was obtained by the common ancestor of social amoebae not from mitochondria but from a bacterium. We propose horizontal gene transfer and endosymbiotic gene transfer contributed to the enzyme diversity of the deoxythymidine triphosphate synthesis pathway in most social amoebae, many Amoebozoa, and other eukaryotes.
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Affiliation(s)
- Heng Liang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Catherine P Chia
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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32
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Talbert PB, Henikoff S, Armache KJ. Giant variations in giant virus genome packaging. Trends Biochem Sci 2023; 48:1071-1082. [PMID: 37777391 DOI: 10.1016/j.tibs.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
Giant viruses (Nucleocytoviricota) have a largely conserved lifecycle, yet how they cram their large genomes into viral capsids is mostly unknown. The major capsid protein and the packaging ATPase (pATPase) comprise a highly conserved morphogenesis module in giant viruses, yet some giant viruses dispense with an icosahedral capsid, and others encode multiple versions of pATPases, including conjoined ATPase doublets, or encode none. Some giant viruses have acquired DNA-condensing proteins to compact their genomes, including sheath-like structures encasing folded DNA or densely packed viral nucleosomes that show a resemblance to eukaryotic nucleosomes at the telomeres. Here, we review what is known and unknown about these ATPases and condensing proteins, and place these variations in the context of viral lifecycles.
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Affiliation(s)
- Paul B Talbert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
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33
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Truchon AR, Chase EE, Gann ER, Moniruzzaman M, Creasey BA, Aylward FO, Xiao C, Gobler CJ, Wilhelm SW. Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research. Front Microbiol 2023; 14:1284617. [PMID: 38098665 PMCID: PMC10720644 DOI: 10.3389/fmicb.2023.1284617] [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] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023] Open
Abstract
Since the discovery of the first "giant virus," particular attention has been paid toward isolating and culturing these large DNA viruses through Acanthamoeba spp. bait systems. While this method has allowed for the discovery of plenty novel viruses in the Nucleocytoviricota, environmental -omics-based analyses have shown that there is a wealth of diversity among this phylum, particularly in marine datasets. The prevalence of these viruses in metatranscriptomes points toward their ecological importance in nutrient turnover in our oceans and as such, in depth study into non-amoebal Nucleocytoviricota should be considered a focal point in viral ecology. In this review, we report on Kratosvirus quantuckense (née Aureococcus anophagefferens Virus), an algae-infecting virus of the Imitervirales. Current systems for study in the Nucleocytoviricota differ significantly from this virus and its relatives, and a litany of trade-offs within physiology, coding potential, and ecology compared to these other viruses reveal the importance of K. quantuckense. Herein, we review the research that has been performed on this virus as well as its potential as a model system for algal-virus interactions.
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Affiliation(s)
- Alexander R Truchon
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Emily E Chase
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric R Gann
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Surgical Critical Care Initiative (SC2i), Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, United States
| | - Brooke A Creasey
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Chuan Xiao
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
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Hikida H, Okazaki Y, Zhang R, Nguyen TT, Ogata H. A rapid genome-wide analysis of isolated giant viruses using MinION sequencing. Environ Microbiol 2023; 25:2621-2635. [PMID: 37543720 DOI: 10.1111/1462-2920.16476] [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: 03/14/2023] [Accepted: 07/20/2023] [Indexed: 08/07/2023]
Abstract
Following the discovery of Acanthamoeba polyphaga mimivirus, diverse giant viruses have been isolated. However, only a small fraction of these isolates have been completely sequenced, limiting our understanding of the genomic diversity of giant viruses. MinION is a portable and low-cost long-read sequencer that can be readily used in a laboratory. Although MinION provides highly error-prone reads that require correction through additional short-read sequencing, recent studies assembled high-quality microbial genomes only using MinION sequencing. Here, we evaluated the accuracy of MinION-only genome assemblies for giant viruses by re-sequencing a prototype marseillevirus. Assembled genomes presented over 99.98% identity to the reference genome with a few gaps, demonstrating a high accuracy of the MinION-only assembly. As a proof of concept, we de novo assembled five newly isolated viruses. Average nucleotide identities to their closest known relatives suggest that the isolates represent new species of marseillevirus, pithovirus and mimivirus. The assembly of subsampled reads demonstrated that their taxonomy and genomic composition could be analysed at the 50× sequencing coverage. We also identified a pithovirus gene whose homologues were detected only in metagenome-derived relatives. Collectively, we propose that MinION-only assembly is an effective approach to rapidly perform a genome-wide analysis of isolated giant viruses.
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Affiliation(s)
- Hiroyuki Hikida
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Yusuke Okazaki
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Ruixuan Zhang
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Thi Tuyen Nguyen
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
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35
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Malaterre C, Ten Kate IL, Baqué M, Debaille V, Grenfell JL, Javaux EJ, Khawaja N, Klenner F, Lara YJ, McMahon S, Moore K, Noack L, Patty CHL, Postberg F. Is There Such a Thing as a Biosignature? ASTROBIOLOGY 2023; 23:1213-1227. [PMID: 37962841 DOI: 10.1089/ast.2023.0042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The concept of a biosignature is widely used in astrobiology to suggest a link between some observation and a biological cause, given some context. The term itself has been defined and used in several ways in different parts of the scientific community involved in the search for past or present life on Earth and beyond. With the ongoing acceleration in the search for life in distant time and/or deep space, there is a need for clarity and accuracy in the formulation and reporting of claims. Here, we critically review the biosignature concept(s) and the associated nomenclature in light of several problems and ambiguities emphasized by recent works. One worry is that these terms and concepts may imply greater certainty than is usually justified by a rational interpretation of the data. A related worry is that terms such as "biosignature" may be inherently misleading, for example, because the divide between life and non-life-and their observable effects-is fuzzy. Another worry is that different parts of the multidisciplinary community may use non-equivalent or conflicting definitions and conceptions, leading to avoidable confusion. This review leads us to identify a number of pitfalls and to suggest how they can be circumvented. In general, we conclude that astrobiologists should exercise particular caution in deciding whether and how to use the concept of biosignature when thinking and communicating about habitability or life. Concepts and terms should be selected carefully and defined explicitly where appropriate. This would improve clarity and accuracy in the formulation of claims and subsequent technical and public communication about some of the most profound and important questions in science and society. With this objective in mind, we provide a checklist of questions that scientists and other interested parties should ask when assessing any reported detection of a "biosignature" to better understand exactly what is being claimed.
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Affiliation(s)
- Christophe Malaterre
- Département de philosophie, Chaire de recherche du Canada en philosophie des sciences de la vie, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
- Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
| | - Inge Loes Ten Kate
- Department of Earth Sciences, Utrecht University, Utrecht, the Netherlands
| | - Mickael Baqué
- Planetary Laboratories Department, Institute of Planetary Research, German Aerospace Center (DLR), Berlin, Germany
| | - Vinciane Debaille
- Laboratoire G-Time, Université libre de Bruxelles, Brussels, Belgium
| | - John Lee Grenfell
- Department of Extrasolar Planets and Atmospheres, Institute of Planetary Research, German Aerospace Center (DLR), Berlin, Germany
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Nozair Khawaja
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - Fabian Klenner
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Sean McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
- School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Keavin Moore
- Department of Earth & Planetary Sciences, McGill University, Montreal, Québec, Canada
- Trottier Space Institute, McGill University, Montreal, Québec, Canada
| | - Lena Noack
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - C H Lucas Patty
- Physikalisches Institut, Universität Bern, Bern, Switzerland
- Center for Space and Habitability, Universität Bern, Bern, Switzerland
| | - Frank Postberg
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
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36
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de Aquino ILM, Barcelos MG, Machado TB, Serafim MSM, Abrahão JS. Surface fibrils on the particles of nucleocytoviruses: A review. Exp Biol Med (Maywood) 2023; 248:2045-2052. [PMID: 37955170 PMCID: PMC10800130 DOI: 10.1177/15353702231208410] [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] [Indexed: 11/14/2023] Open
Abstract
The capsid has a central role in viruses' life cycle. Although one of its major functions is to protect the viral genome, the capsid may be composed of elements that, at some point, promote interaction with host cells and trigger infection. Considering the scenario of multiple origins of viruses along the viral evolution, a substantial number of capsid shapes, sizes, and symmetries have been described. In this context, capsids of giant viruses (GV) that infect protists have drawn the attention of the scientific community, especially in the last 20 years, specifically for having bacterial-like dimensions with hundreds of different proteins and exclusive features. For instance, the surface fibrils present on the mimivirus capsid are one of the most intriguing features of the known virosphere. They are 150-nm-long structures attached to a 450-nm capsid, resulting in a particle with a hairy appearance. Surface fibrils have also been described in the capsids of other nucleocytoviruses, although they may differ substantially among them. In this mini review for non-experts, we compile the most important available information on surface fibrils of nucleocytoviruses, discussing their putative functions, composition, length, organization, and origins.
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Affiliation(s)
- Isabella Luiza Martins de Aquino
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Matheus Gomes Barcelos
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Talita Bastos Machado
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Mateus Sá Magalhães Serafim
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
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37
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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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38
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Gaïa M, Forterre P. From Mimivirus to Mirusvirus: The Quest for Hidden Giants. Viruses 2023; 15:1758. [PMID: 37632100 PMCID: PMC10458455 DOI: 10.3390/v15081758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Our perception of viruses has been drastically evolving since the inception of the field of virology over a century ago. In particular, the discovery of giant viruses from the Nucleocytoviricota phylum marked a pivotal moment. Their previously concealed diversity and abundance unearthed an unprecedented complexity in the virus world, a complexity that called for new definitions and concepts. These giant viruses underscore the intricate interactions that unfold over time between viruses and their hosts, and are themselves suspected to have played a significant role as a driving force in the evolution of eukaryotes since the dawn of this cellular domain. Whether they possess exceptional relationships with their hosts or whether they unveil the actual depths of evolutionary connections between viruses and cells otherwise hidden in smaller viruses, the attraction giant viruses exert on the scientific community and beyond continues to grow. Yet, they still hold surprises. Indeed, the recent identification of mirusviruses connects giant viruses to herpesviruses, each belonging to distinct viral realms. This discovery substantially broadens the evolutionary landscape of Nucleocytoviricota. Undoubtedly, the years to come will reveal their share of surprises.
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Affiliation(s)
- Morgan Gaïa
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75012 Paris, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- Département de Microbiologie, Institut Pasteur, 75015 Paris, France
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39
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Queiroz VF, Carvalho JVRP, de Souza FG, Lima MT, Santos JD, Rocha KLS, de Oliveira DB, Araújo JP, Ullmann LS, Rodrigues RAL, Abrahão JS. Analysis of the Genomic Features and Evolutionary History of Pithovirus-Like Isolates Reveals Two Major Divergent Groups of Viruses. J Virol 2023; 97:e0041123. [PMID: 37395647 PMCID: PMC10373538 DOI: 10.1128/jvi.00411-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/09/2023] [Indexed: 07/04/2023] Open
Abstract
New representatives of the phylum Nucleocytoviricota have been rapidly described in the last decade. Despite this, not all viruses of this phylum are allocated to recognized taxonomic families, as is the case for orpheovirus, pithovirus, and cedratvirus, which form the proposed family Pithoviridae. In this study, we performed comprehensive comparative genomic analyses of 8 pithovirus-like isolates, aiming to understand their common traits and evolutionary history. Structural and functional genome annotation was performed de novo for all the viruses, which served as a reference for pangenome construction. The synteny analysis showed substantial differences in genome organization between these viruses, with very few and short syntenic blocks shared between orpheovirus and its relatives. It was possible to observe an open pangenome with a significant increase in the slope when orpheovirus was added, alongside a decrease in the core genome. Network analysis placed orpheovirus as a distant and major hub with a large fraction of unique clusters of orthologs, indicating a distant relationship between this virus and its relatives, with only a few shared genes. Additionally, phylogenetic analyses of strict core genes shared with other viruses of the phylum reinforced the divergence of orpheovirus from pithoviruses and cedratviruses. Altogether, our results indicate that although pithovirus-like isolates share common features, this group of ovoid-shaped giant viruses presents substantial differences in gene contents, genomic architectures, and the phylogenetic history of several core genes. Our data indicate that orpheovirus is an evolutionarily divergent viral entity, suggesting its allocation to a different viral family, Orpheoviridae. IMPORTANCE Giant viruses that infect amoebae form a monophyletic group named the phylum Nucleocytoviricota. Despite being genomically and morphologically very diverse, the taxonomic categories of some clades that form this phylum are not yet well established. With advances in isolation techniques, the speed at which new giant viruses are described has increased, escalating the need to establish criteria to define the emerging viral taxa. In this work, we performed a comparative genomic analysis of representatives of the putative family Pithoviridae. Based on the dissimilarity of orpheovirus from the other viruses of this putative family, we propose that orpheovirus be considered a member of an independent family, Orpheoviridae, and suggest criteria to demarcate families consisting of ovoid-shaped giant viruses.
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Affiliation(s)
- Victória F. Queiroz
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - João Victor R. P. Carvalho
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda G. de Souza
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Maurício T. Lima
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Juliane D. Santos
- Laboratório de Doenças Infecciosas e Parasitárias, Programa de pós graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil
| | - Kamila L. S. Rocha
- Laboratório de Doenças Infecciosas e Parasitárias, Programa de pós graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil
| | - Danilo B. de Oliveira
- Laboratório de Doenças Infecciosas e Parasitárias, Programa de pós graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil
| | - João Pessoa Araújo
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Leila Sabrina Ullmann
- Laboratório de Virologia, Departamento de Microbiologia e Imunologia, Instituto de Biotecnologia, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- Laboratório de Virologia Veterinária, Faculdade de Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Rodrigo A. L. Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jônatas S. Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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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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López-García P, Moreira D. The symbiotic origin of the eukaryotic cell. C R Biol 2023; 346:55-73. [PMID: 37254790 DOI: 10.5802/crbiol.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 06/01/2023]
Abstract
Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.
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Hannat S, La Scola B, Andreani J, Aherfi S. Asfarviruses and Closely Related Giant Viruses. Viruses 2023; 15:v15041015. [PMID: 37112995 PMCID: PMC10146109 DOI: 10.3390/v15041015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Acanthamoeba polyphaga mimivirus, so called because of its "mimicking microbe", was discovered in 2003 and was the founding member of the first family of giant viruses isolated from amoeba. These giant viruses, present in various environments, have opened up a previously unexplored field of virology. Since 2003, many other giant viruses have been isolated, founding new families and taxonomical groups. These include a new giant virus which was isolated in 2015, the result of the first co-culture on Vermamoeba vermiformis. This new giant virus was named "Faustovirus". Its closest known relative at that time was African Swine Fever Virus. Pacmanvirus and Kaumoebavirus were subsequently discovered, exhibiting phylogenetic clustering with the two previous viruses and forming a new group with a putative common ancestor. In this study, we aimed to summarise the main features of the members of this group of giant viruses, including Abalone Asfarvirus, African Swine Fever Virus, Faustovirus, Pacmanvirus, and Kaumoebavirus.
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Affiliation(s)
- Sihem Hannat
- Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France
- MEPHI, Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, 13005 Marseille, France
| | - Bernard La Scola
- Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France
- MEPHI, Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, 13005 Marseille, France
- Assistance Publique des Hôpitaux de Marseille (AP-HM), 13005 Marseille, France
| | - Julien Andreani
- CHU Grenoble Alpes, 27 Boulevard de la Chantourne, 38700 La Tronche, France
| | - Sarah Aherfi
- Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France
- MEPHI, Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, 13005 Marseille, France
- Assistance Publique des Hôpitaux de Marseille (AP-HM), 13005 Marseille, France
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Weitao T, Grandinetti G, Guo P. Revolving ATPase motors as asymmetrical hexamers in translocating lengthy dsDNA via conformational changes and electrostatic interactions in phi29, T7, herpesvirus, mimivirus, E. coli, and Streptomyces. EXPLORATION (BEIJING, CHINA) 2023; 3:20210056. [PMID: 37324034 PMCID: PMC10191066 DOI: 10.1002/exp.20210056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/28/2022] [Indexed: 06/17/2023]
Abstract
Investigations of the parallel architectures of biomotors in both prokaryotic and eukaryotic systems suggest a similar revolving mechanism in the use of ATP to drive translocation of the lengthy double-stranded (ds)DNA genomes. This mechanism is exemplified by the dsDNA packaging motor of bacteriophage phi29 that operates through revolving but not rotating dsDNA to "Push through a one-way valve". This unique and novel revolving mechanism discovered in phi29 DNA packaging motor was recently reported in other systems including the dsDNA packaging motor of herpesvirus, the dsDNA ejecting motor of bacteriophage T7, the plasmid conjugation machine TraB in Streptomyces, the dsDNA translocase FtsK of gram-negative bacteria, and the genome-packaging motor in mimivirus. These motors exhibit an asymmetrical hexameric structure for transporting the genome via an inch-worm sequential action. This review intends to delineate the revolving mechanism from a perspective of conformational changes and electrostatic interactions. In phi29, the positively charged residues Arg-Lys-Arg in the N-terminus of the connector bind the negatively charged interlocking domain of pRNA. ATP binding to an ATPase subunit induces the closed conformation of the ATPase. The ATPase associates with an adjacent subunit to form a dimer facilitated by the positively charged arginine finger. The ATP-binding induces a positive charging on its DNA binding surface via an allostery mechanism and thus the higher affinity for the negatively charged dsDNA. ATP hydrolysis induces an expanded conformation of the ATPase with a lower affinity for dsDNA due to the change of the surface charge, but the (ADP+Pi)-bound subunit in the dimer undergoes a conformational change that repels dsDNA. The positively charged lysine rings of the connector attract dsDNA stepwise and periodically to keep its revolving motion along the channel wall, thus maintaining the one-way translocation of dsDNA without reversal and sliding out. The finding of the presence of the asymmetrical hexameric architectures of many ATPases that use the revolving mechanism may provide insights into the understanding of translocation of the gigantic genomes including chromosomes in complicated systems without coiling and tangling to speed up dsDNA translocation and save energy.
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Affiliation(s)
- Tao Weitao
- UT Southwestern Medical CenterCenter for the Genetics of Host DefenseDallasTXUSA
- College of Science and MathematicsSouthwest Baptist UniversityBolivarMOUSA
| | - Giovanna Grandinetti
- Center for Electron Microscopy and AnalysisThe Ohio State UniversityColumbusOHUSA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and NanomedicineDivision of Pharmaceutics and Pharmacology, College of PharmacyDorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of MedicineThe Ohio State UniversityColumbusOHUSA
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Siddiqui R, Muhammad JS, Alharbi AM, Alfahemi H, Khan NA. Can Acanthamoeba Harbor Monkeypox Virus? Microorganisms 2023; 11:microorganisms11040855. [PMID: 37110278 PMCID: PMC10146756 DOI: 10.3390/microorganisms11040855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Acanthamoeba is well known to host a variety of microorganisms such as viruses, bacteria, protozoa, and yeast. Given the recent number of cases of monkeypox infection, we speculate that amoebae may be aiding viral transmission to the susceptible hosts. Although there is no confirmatory evidence to suggest that Acanthamoeba is a host to monkeypox (a double-stranded DNA virus), the recent discovery of mimivirus (another double-stranded DNA virus) from Acanthamoeba, suggests that amoebae may shelter monkeypox virus. Furthermore, given the possible spread of monkeypox virus from animals to humans during an earlier outbreak, which came about after patients came in contact with prairie dogs, it is likely that animals may also act as mixing vessel between ubiquitously distributed Acanthamoeba and monkeypox virus, in addition to the environmental habitat that acts as an interface in complex interactions between diverse microorganisms and the host.
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Affiliation(s)
- Ruqaiyyah Siddiqui
- College of Arts and Sciences, American University of Sharjah, Sharjah 26666, United Arab Emirates
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul 34010, Turkey
| | | | - Ahmad M. Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
| | - Hasan Alfahemi
- Department of Medical Microbiology, Faculty of Medicine, Al-Baha University, Al-Baha 65799, Saudi Arabia
| | - Naveed Ahmed Khan
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul 34010, Turkey
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Correspondence: ; Tel.: +971-65057722
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Fukaya S, Masuda L, Takemura M. Analysis of Morphological Changes in the Nucleus and Vacuoles of Acanthamoeba castellanii following Giant Virus Infection. Microbiol Spectr 2023; 11:e0418222. [PMID: 36943052 PMCID: PMC10100661 DOI: 10.1128/spectrum.04182-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
Acanthamoeba castellanii medusavirus is a member of the phylum Nucleocytoviricota, also known as giant viruses, and has a unique strategy of infecting Acanthamoeba castellanii and replicating viral genes in the host nucleus. Here, we show time series changes in the intracellular morphology, including the nucleus, of host cells infected with four types of giant viruses, including medusavirus, using time-lapse phase-contrast microscopy and image analysis. We updated our phase-contrast-based kinetic analysis algorithm for amoebae (PKA3) to use multiple microscopic images with different focus positions to allow a more detailed analysis of their intracellular structures. Image analysis using PKA3 revealed that as medusavirus infection progressed, the host nucleus increased in size and the number of vacuoles decreased. In addition, infected host cells are known to become smaller and rounder at later stages of infection, but here they were found to be larger than uninfected cells at earlier stages. These results suggested that the propagation mechanism of medusavirus includes the formation of empty virus particles in the host cytoplasm, packaging of the viral genome replicated in the host nucleus, and then the release of viral particles. IMPORTANCE In this study, we quantitatively revealed how long the increase in host cell size or the increase in host nucleus size occurs after infection with giant viruses, especially medusavirus. To understand the underlying mechanism, we performed image analysis and determined that the host cell size increased at approximately 6 h postinfection (hpi) and the host nucleus enlarged at approximately 22 hpi, pointing to the importance of biochemical experiments. In addition, we showed that the intracellular structures could be quantitatively analyzed using multiple phase-contrast microscopy images with different focus positions at the same time point. Hence, morphological analyses of intracellular structures using phase-contrast microscopy, which have wide applications in live-cell observations, may be useful in studying various organisms that infect or are symbiotic with A. castellanii.
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Affiliation(s)
- Sho Fukaya
- Department of Applied Information Engineering, Faculty of Engineering, Suwa University of Science, Chino, Nagano, Japan
- Laboratory of Biology, Institute of Arts and Sciences, Tokyo University of Science, Shinjuku, Tokyo, Japan
| | - Lisa Masuda
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science, Shinjuku, Tokyo, Japan
| | - Masaharu Takemura
- Laboratory of Biology, Institute of Arts and Sciences, Tokyo University of Science, Shinjuku, Tokyo, Japan
- Laboratory of Biology, Graduate School of Mathematics and Science Education, Tokyo University of Science, Shinjuku, Tokyo, Japan
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Behera BK, Patra B, Chakraborty HJ, Rout AK, Dixit S, Rai A, Das BK, Mohapatra T. Bacteriophages diversity in India's major river Ganga: a repository to regulate pathogenic bacteria in the aquatic environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:34101-34114. [PMID: 36508095 DOI: 10.1007/s11356-022-24637-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/03/2022] [Indexed: 06/18/2023]
Abstract
Bacteriophages are key viruses that can kill thousands of harmful microbes generally present at polluted sites. Such bacteriophages are abundantly present in the river Ganga, where millions of people in India and abroad drink its water and take baths every day for spiritual reasons. Besides bacteriophages, several pathogenic and zoonotic microbes are present in the river Ganga. It is interesting to study the diversity and abundance of bacteria and their respective phages present in polluted or non-polluted sites. Thus, the metagenomics study was carried out at the most polluted sites of river Ganga near Kanpur and non-polluted sites at Farakka, which harbors several harmful bacteria and their phages. The results revealed a significantly higher percentage of Microviridae phage family, ssDNA viruses, and Mimiviridae virus family near Kanpur than Farakka. In addition, compared to Kanpur, Farakka has a more significant percentage of Myoviridae, an unidentified phage family, and Retroviridae viral families. Despite heavy drainage of untreated and contaminated effluents from the leather industry, pesticide industry, paper mills, metropolitan cities, and other sources, the vast number of said phages kills several harmful pathogenic microbes in polluted sites to maintain the Ganga water's healing power or natural sterility. In a polluted aquatic environment, the varieties of bacteriophages were identified in the Ganga and their interaction with the microbial host. The taxonomic diversity of several bacteriophages found in pathogenic host systems was investigated to get exceptional knowledge of these small viruses in the aquatic environment.
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Affiliation(s)
- Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India.
| | - Biswanath Patra
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Hirak Jyoti Chakraborty
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Sangita Dixit
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to Be University), Bhubaneswar, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
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Diversity of Surface Fibril Patterns in Mimivirus Isolates. J Virol 2023; 97:e0182422. [PMID: 36728417 PMCID: PMC9972986 DOI: 10.1128/jvi.01824-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Among the most intriguing structural features in the known virosphere are mimivirus surface fibrils, proteinaceous filaments approximately 150 nm long, covering the mimivirus capsid surface. Fibrils are important to promote particle adhesion to host cells, triggering phagocytosis and cell infection. However, although mimiviruses are one of the most abundant viral entities in a plethora of biomes worldwide, there has been no comparative analysis on fibril organization and abundance among distinct mimivirus isolates. Here, we describe the isolation and characterization of Megavirus caiporensis, a novel lineage C mimivirus with surface fibrils organized as "clumps." This intriguing feature led us to expand our analyses to other mimivirus isolates. By employing a combined approach including electron microscopy, image processing, genomic sequencing, and viral prospection, we obtained evidence of at least three main patterns of surface fibrils that can be found in mimiviruses: (i) isolates containing particles with abundant fibrils, distributed homogeneously on the capsid surface; (ii) isolates with particles almost fibrilless; and (iii) isolates with particles containing fibrils in abundance, but organized as clumps, as observed in Megavirus caiporensis. A total of 15 mimivirus isolates were analyzed by microscopy, and their DNA polymerase subunit B genes were sequenced for phylogenetic analysis. We observed a unique match between evolutionarily-related viruses and their fibril profiles. Biological assays suggested that patterns of fibrils can influence viral entry in host cells. Our data contribute to the knowledge of mimivirus fibril organization and abundance, as well as raising questions on the evolution of those intriguing structures. IMPORTANCE Mimivirus fibrils are intriguing structures that have drawn attention since their discovery. Although still under investigation, the function of fibrils may be related to host cell adhesion. In this work, we isolated and characterized a new mimivirus, called Megavirus caiporensis, and we showed that mimivirus isolates can exhibit at least three different patterns related to fibril organization and abundance. In our study, evolutionarily-related viruses presented similar fibril profiles, and such fibrils may affect how those viruses trigger phagocytosis in amoebas. These data shed light on aspects of mimivirus particle morphology, virus-host interactions, and their evolution.
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Multiple Regulations of Parasitic Protozoan Viruses: A Double-Edged Sword for Protozoa. mBio 2023; 14:e0264222. [PMID: 36633419 PMCID: PMC9973342 DOI: 10.1128/mbio.02642-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Parasite infections affect human and animal health significantly and contribute to a major burden on the global economy. Parasitic protozoan viruses (PPVs) affect the protozoan parasites' morphology, phenotypes, pathogenicity, and growth rates. This discovery provides an opportunity to develop a novel preventive and therapeutic strategy for parasitic protozoan diseases (PPDs). Currently, there is greater awareness regarding PPVs; however, knowledge of viruses and their associations with host diseases remains limited. Parasite-host interactions become more complex owing to PPVs; however, few studies have investigated underlying viral regulatory mechanisms in parasites. In this study, we reviewed relevant studies to identify studies that investigated PPV development and life cycles, the triangular association between viruses, parasites, and hosts, and the effects of viruses on protozoan pathogenicity. This study highlights that viruses can alter parasite biology, and viral infection of parasites may exacerbate the adverse effects of virus-containing parasites on hosts or reduce parasite virulence. PPVs should be considered in the prevention of parasitic epidemics and outbreaks, although their effects on the host and the complexity of the triangular association between PPVs, protozoans, and hosts remain unclear. IMPORTANCE PPVs-based regulation of parasitic protozoa can provide a theoretical basis and direction for PPD prevention and control, although PPVs and PPV regulatory mechanisms remain unclear. In this review, we investigated the differences between PPVs and the unique properties of each virus regarding virus discovery, structures, and life cycles, focused on the Trichomonas vaginalis virus, Giardia lamblia virus, Leishmania RNA virus, and the Cryptosporidium parvum virus 1. The triangular association between PPVs, parasitic protozoa, and hosts reveals the "double-edged sword" property of PPVs, which maintains a balance between parasitic protozoa and hosts in both positive and negative respects. These studies discuss the complexity of parasitic protozoa and their co-existence with hosts and suggest novel pathways for using PPVs as tools to gain a deeper understanding of protozoal infection and treatment.
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Villalta A, Srour B, Lartigue A, Clémancey M, Byrne D, Chaspoul F, Loquet A, Guigliarelli B, Blondin G, Abergel C, Burlat B. Evidence for [2Fe-2S] 2+ and Linear [3Fe-4S] 1+ Clusters in a Unique Family of Glycine/Cysteine-Rich Fe-S Proteins from Megavirinae Giant Viruses. J Am Chem Soc 2023; 145:2733-2738. [PMID: 36705935 DOI: 10.1021/jacs.2c10484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have discovered a protein with an amino acid composition exceptionally rich in glycine and cysteine residues in the giant virus mimivirus. This small 6 kDa protein is among the most abundant proteins in the icosahedral 0.75 μm viral particles; it has no predicted function but is probably essential for infection. The aerobically purified red-brownish protein overproduced inEscherichia coli contained both iron and inorganic sulfide. UV/vis, EPR, and Mössbauer studies revealed that the viral protein, coined GciS, accommodated two distinct Fe-S clusters: a diamagnetic S = 0 [2Fe-2S]2+ cluster and a paramagnetic S = 5/2 linear [3Fe-4S]1+ cluster, a geometry rarely stabilized in native proteins. Orthologs of mimivirus GciS were identified within all clades of Megavirinae, a Mimiviridae subfamily infecting Acanthamoeba, including the distantly related tupanviruses, and displayed the same spectroscopic features. Thus, these glycine/cysteine-rich proteins form a new family of viral Fe-S proteins sharing unique Fe-S cluster binding properties.
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Affiliation(s)
- Alejandro Villalta
- Aix-Marseille Université, CNRS, Information Génomique et Structurale (IGS), IMM FR3479, IM2B, IOM, Marseille 13288, France
| | - Batoul Srour
- Aix-Marseille Université, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM FR3479, IM2B, Marseille 13402, France
| | - Audrey Lartigue
- Aix-Marseille Université, CNRS, Information Génomique et Structurale (IGS), IMM FR3479, IM2B, IOM, Marseille 13288, France
| | - Martin Clémancey
- Université Grenoble Alpes, CNRS, CEA, Laboratoire de Chimie et Biologie des Métaux (LCBM), Grenoble 38000, France
| | - Deborah Byrne
- Aix-Marseille Université, CNRS, Expression Facility, Institut de Microbiologie de la Méditerranée (IMM), Marseille 13402, France
| | - Florence Chaspoul
- Aix Marseille Université, Avignon Université, CNRS, IRD, Institut Méditerranéen de la Biodiversité et d'Ecologie Marine et Continentale (IMBE), Marseille 13005, France
| | - Antoine Loquet
- Université of Bordeaux, CNRS, IECB, CBMN, Pessac 33600, France
| | - Bruno Guigliarelli
- Aix-Marseille Université, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM FR3479, IM2B, Marseille 13402, France
| | - Geneviève Blondin
- Université Grenoble Alpes, CNRS, CEA, Laboratoire de Chimie et Biologie des Métaux (LCBM), Grenoble 38000, France
| | - Chantal Abergel
- Aix-Marseille Université, CNRS, Information Génomique et Structurale (IGS), IMM FR3479, IM2B, IOM, Marseille 13288, France
| | - Bénédicte Burlat
- Aix-Marseille Université, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM FR3479, IM2B, Marseille 13402, France
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"Mamonoviridae", a proposed new family of the phylum Nucleocytoviricota. Arch Virol 2023; 168:80. [PMID: 36740641 DOI: 10.1007/s00705-022-05633-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Acanthamoeba castellanii medusavirus J1 is a giant virus that was isolated from a hot spring in Japan in 2019. Recently, a close relative of this virus, named medusavirus stheno T3, was isolated in Japan. Here, we describe their morphological, genomic, and gene content similarities and also propose to create a new family, "Mamonoviridae", a new genus, "Medusavirus", and two species, "Medusavirus medusae" and "Medusavirus sthenus", to classify these two viruses within the phylum Nucleocytoviricota.
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