1
|
Fromm A, Hevroni G, Vincent F, Schatz D, Martinez-Gutierrez CA, Aylward FO, Vardi A. Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment. Nat Microbiol 2024; 9:1619-1629. [PMID: 38605173 DOI: 10.1038/s41564-024-01669-y] [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: 07/14/2023] [Accepted: 03/07/2024] [Indexed: 04/13/2024]
Abstract
Giant viruses (phylum Nucleocytoviricota) are globally distributed in aquatic ecosystems. They play fundamental roles as evolutionary drivers of eukaryotic plankton and regulators of global biogeochemical cycles. However, we lack knowledge about their native hosts, hindering our understanding of their life cycle and ecological importance. In the present study, we applied a single-cell RNA sequencing (scRNA-seq) approach to samples collected during an induced algal bloom, which enabled pairing active giant viruses with their native protist hosts. We detected hundreds of single cells from multiple host lineages infected by diverse giant viruses. These host cells included members of the algal groups Chrysophycae and Prymnesiophycae, as well as heterotrophic flagellates in the class Katablepharidaceae. Katablepharids were infected with a rare Imitervirales-07 giant virus lineage expressing a large repertoire of cell-fate regulation genes. Analysis of the temporal dynamics of these host-virus interactions revealed an important role for the Imitervirales-07 in controlling the population size of the host Katablepharid population. Our results demonstrate that scRNA-seq can be used to identify previously undescribed host-virus interactions and study their ecological importance and impact.
Collapse
Affiliation(s)
- Amir Fromm
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gur Hevroni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Google Geo, Tel Aviv, Israel
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Developmental Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, VA, USA.
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Siddiqui R, El-Gamal MI, Sajeev S, Zaraei SO, Khan NA. Novel anti-Acanthamoebic properties of raloxifene sulfonate/sulfamate derivatives. Mol Biochem Parasitol 2023; 256:111582. [PMID: 37562558 DOI: 10.1016/j.molbiopara.2023.111582] [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: 03/20/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Acanthamoeba are known to cause a vision threatening eye infection typically due to contact lens wear, and an infection of the central nervous system. The ability of these amoebae to switch phenotypes, from an active trophozoite to a resistant cyst form is not well understood; the cyst stage is often resistant to chemotherapy, which is of concern given the rise of contact lens use and the ineffective disinfectants available, versus the cyst stage. Herein, for the first time, a range of raloxifene sulfonate/sulfamate derivatives which target nucleotide pyrophosphatase/phosphodiesterase enzymes, were assessed using amoebicidal and excystation tests versus the trophozoite and cyst stage of Acanthamoeba. Moreover, the potential for cytopathogenicity inhibition in amoebae was assessed. Each of the derivatives showed considerable anti-amoebic activity as well as the ability to suppress phenotypic switching (except for compound 1a). Selected raloxifene derivatives reduced Acanthamoeba-mediated host cell damage using lactate dehydrogenase assay. These findings suggest that pyrophosphatase/phosphodiesterase enzymes may be valuable targets against Acanthamoeba infections.
Collapse
Affiliation(s)
- Ruqaiyyah Siddiqui
- College of Arts and Sciences, American University of Sharjah, Sharjah 26666, United Arab Emirates; Microbiota Research Center, Istinye University, Istanbul 34010, Turkey
| | - Mohammed I El-Gamal
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Sreedevi Sajeev
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, 27272, Unites Arab Emirates
| | - Seyed-Omar Zaraei
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Naveed Ahmed Khan
- Microbiota Research Center, Istinye University, Istanbul 34010, Turkey; Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates.
| |
Collapse
|
5
|
Fromm A, Hevroni G, Vincent F, Schatz D, Martinez-Gutierrez CA, Aylward FO, Vardi A. Homing in on the rare virosphere reveals the native host of giant viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546645. [PMID: 37425953 PMCID: PMC10327091 DOI: 10.1101/2023.06.27.546645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Giant viruses (phylum Nucleocytoviricota) are globally distributed in aquatic ecosystems1,2. They play major roles as evolutionary drivers of eukaryotic plankton3 and regulators of global biogeochemical cycles4. Recent metagenomic studies have significantly expanded the known diversity of marine giant viruses1,5-7, but we still lack fundamental knowledge about their native hosts, thereby hindering our understanding of their lifecycle and ecological importance. Here, we aim to discover the native hosts of giant viruses using a novel, sensitive single-cell metatranscriptomic approach. By applying this approach to natural plankton communities, we unraveled an active viral infection of several giant viruses, from multiple lineages, and identified their native hosts. We identify a rare lineage of giant virus (Imitervirales-07) infecting a minute population of protists (class Katablepharidaceae) and revealed the prevalence of highly expressed viral-encoded cell-fate regulation genes in infected cells. Further examination of this host-virus dynamics in a temporal resolution suggested this giant virus controls its host population demise. Our results demonstrate how single-cell metatranscriptomics is a sensitive approach for pairing viruses with their authentic hosts and studying their ecological significance in a culture-independent manner in the marine environment.
Collapse
Affiliation(s)
- Amir Fromm
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Gur Hevroni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
- Current address: Google Geo, Israel
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
- Current address: Developmental Biology Unit, European Molecular Biological Laboratory, 69117, Heidelberg, Germany
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA 24061
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| |
Collapse
|
6
|
Bisio H, Legendre M, Giry C, Philippe N, Alempic JM, Jeudy S, Abergel C. Evolution of giant pandoravirus revealed by CRISPR/Cas9. Nat Commun 2023; 14:428. [PMID: 36702819 PMCID: PMC9879987 DOI: 10.1038/s41467-023-36145-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
Giant viruses (GVs) are a hotspot of unresolved controversies since their discovery, including the definition of "Virus" and their origin. While increasing knowledge of genome diversity has accumulated, GV functional genomics was largely neglected. Here, we describe an experimental framework to genetically modify nuclear GVs and their host Acanthamoeba castellanii using CRISPR/Cas9, shedding light on the evolution from small icosahedral viruses to amphora-shaped GVs. Ablation of the icosahedral major capsid protein in the phylogenetically-related mollivirus highlights a transition in virion shape and size. We additionally demonstrate the existence of a reduced core essential genome in pandoravirus, reminiscent of their proposed smaller ancestors. This proposed genetic expansion led to increased genome robustness, indicating selective pressures for adaptation to uncertain environments. Overall, we introduce new tools for manipulation of the unexplored genome of nuclear GVs and provide experimental evidence suggesting that viral gigantism has aroused as an emerging trait.
Collapse
Affiliation(s)
- Hugo Bisio
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France.
| | - Matthieu Legendre
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France
| | - Claire Giry
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France
| | - Nadege Philippe
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France
| | - Jean-Marie Alempic
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France
| | - Sandra Jeudy
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France
| | - Chantal Abergel
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Genomique & Structurale, Unite Mixte de Recherche 7256 (Institut de Microbiologie de la Mediterranee, FR3479, IM2B), 13288, Marseille, Cedex 9, France.
| |
Collapse
|
7
|
Giant Viruses as a Source of Novel Enzymes for Biotechnological Application. Pathogens 2022; 11:pathogens11121453. [PMID: 36558786 PMCID: PMC9787589 DOI: 10.3390/pathogens11121453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application.
Collapse
|