1
|
Homola M, Büttner CR, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Sci Adv 2024; 10:eadk1954. [PMID: 38598627 PMCID: PMC11006232 DOI: 10.1126/sciadv.adk1954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth's climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus' inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis.
Collapse
Affiliation(s)
- Miroslav Homola
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Carina R. Büttner
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavel Křepelka
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Radka Holbová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Marten L. Chaillet
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jakub Žák
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Danyil Grybchuk
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Friedrich Förster
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - William H. Wilson
- Marine Biological Association, Plymouth, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | | | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| |
Collapse
|
2
|
Lievens EJP, Agarkova IV, Dunigan DD, Van Etten JL, Becks L. Efficient assays to quantify the life history traits of algal viruses. Appl Environ Microbiol 2023; 89:e0165923. [PMID: 38092674 PMCID: PMC10734466 DOI: 10.1128/aem.01659-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 12/22/2023] Open
Abstract
IMPORTANCE Viruses play a crucial role in microbial ecosystems by liberating nutrients and regulating the growth of their hosts. These effects are governed by viral life history traits, i.e., by the traits determining viral reproduction and survival. Understanding these traits is essential to predicting viral effects, but measuring them is generally labor intensive. In this study, we present efficient methods to quantify the full life cycle of lytic viruses. We developed these methods for viruses infecting unicellular Chlorella algae but expect them to be applicable to other lytic viruses that can be quantified by flow cytometry. By making viral phenotypes accessible, our methods will support research into the diversity and ecological effects of microbial viruses.
Collapse
Affiliation(s)
- Eva J. P. Lievens
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Irina V. Agarkova
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - David D. Dunigan
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - James L. Van Etten
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Lutz Becks
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Konstanz, Germany
| |
Collapse
|
3
|
Ruiz Martínez E, Mckeown DA, Schroeder DC, Thuestad G, Sjøtun K, Sandaa RA, Larsen A, Hoell IA. Phaeoviruses Present in Cultured and Natural Kelp Species, Saccharina latissima and Laminaria hyperborea (Phaeophyceae, Laminariales) , in Norway. Viruses 2023; 15:2331. [PMID: 38140573 PMCID: PMC10747701 DOI: 10.3390/v15122331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Phaeoviruses (Phycodnaviridae) are large icosahedral viruses in the phylum Nucleocytoviricota with dsDNA genomes ranging from 160 to 560 kb, infecting multicellular brown algae (Phaeophyceae). The phaeoviral host range is broader than expected, not only infecting algae from the Ectocarpales but also from the Laminariales order. However, despite phaeoviral infections being reported globally, Norwegian kelp species have not been screened. A molecular analysis of cultured and wild samples of two economically important kelp species in Norway (Saccharina latissima and Laminaria hyperborea) revealed that phaeoviruses are recurrently present along the Norwegian coast. We found the viral prevalence in S. latissima to be significantly higher at the present time compared to four years ago. We also observed regional differences within older samples, in which infections were significantly lower in northern areas than in the south or the fjords. Moreover, up to three different viral sequences were found in the same algal individual, one of which does not belong to the Phaeovirus genus and has never been reported before. This master variant therefore represents a putative new member of an unclassified phycodnavirus genus.
Collapse
Affiliation(s)
- Eliana Ruiz Martínez
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, 5528 Haugesund, Norway; (G.T.); (I.A.H.)
| | - Dean A. Mckeown
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, MN 55108, USA; (D.A.M.); (D.C.S.)
| | - Declan C. Schroeder
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, MN 55108, USA; (D.A.M.); (D.C.S.)
| | - Gunnar Thuestad
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, 5528 Haugesund, Norway; (G.T.); (I.A.H.)
| | - Kjersti Sjøtun
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway; (K.S.); (R.-A.S.)
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway; (K.S.); (R.-A.S.)
| | - Aud Larsen
- NORCE Norwegian Research Centre, 5008 Bergen, Norway;
| | - Ingunn Alne Hoell
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, 5528 Haugesund, Norway; (G.T.); (I.A.H.)
| |
Collapse
|
4
|
Zhang E, Zhang S, Li G, Zhang Z, Liu J. Identification and Verification of Candidate miRNA Biomarkers with Application to Infection with Emiliania huxleyi Virus. Genes (Basel) 2023; 14:1716. [PMID: 37761856 PMCID: PMC10531489 DOI: 10.3390/genes14091716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The interactions of Emiliania huxleyi and its specific lytic virus (EhV) have a profound influence on marine biogeochemical carbon-sulfur cycles and play a prominent role in global climate change. MicroRNAs (miRNAs) have emerged as promising candidates with extensive diagnostic potential due to their role in virus-host interactions. However, the application of miRNA signatures as diagnostic markers in marine viral infection has made limited progress. Based on our previous small-RNA sequencing data, one host miRNA biomarker that is upregulated in early infection and seven viral miRNA biomarkers that are upregulated in late infection were identified and verified using qRT-PCR and a receiver operating characteristic curve analysis in pure culture, mixed culture, and natural seawater culture. The host ehx-miR20-5p was able to significantly differentiate infection groups from the control in the middle (24 h post-infection, hpi) and late infection (48 hpi) phases, while seven virus-derived miRNA biomarkers could diagnose the early and late stages of EhV infection. Functional enrichment analysis showed that these miRNAs participated in numerous essential metabolic pathways, including gene transcription and translation, cell division-related pathways, protein-degradation-related processes, and lipid metabolism. Additionally, a dual-luciferase reporter assay confirmed the targeted relationship between a viral ehv-miR7-5p and the host dihydroceramide desaturase gene (hDCD). This finding suggests that the virus-derived miRNA has the ability to inhibit the host sphingolipid metabolism, which is a specific characteristic of EhV infection during the late stage. Our data revealed a cluster of potential miRNA biomarkers with significant regulatory functions that could be used to diagnose EhV infection, which has implications for assessing the infectious activity of EhV in a natural marine environment.
Collapse
Affiliation(s)
| | | | | | | | - Jingwen Liu
- College of Ocean Food and Biological Engineering, Jimei University, No. 43, Jiyuan Road, Xiamen 361021, China; (E.Z.); (S.Z.); (G.L.); (Z.Z.)
| |
Collapse
|
5
|
Roitman S, Rozenberg A, Lavy T, Brussaard CPD, Kleifeld O, Béjà O. Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga. Nat Microbiol 2023; 8:332-346. [PMID: 36702941 DOI: 10.1038/s41564-022-01305-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/13/2022] [Indexed: 01/27/2023]
Abstract
Virophages are small double stranded DNA (dsDNA) viruses that can only replicate in a host by co-infecting with another virus. Marine algae are commonly associated with virophage-like elements such as Polinton-like viruses (PLVs) that remain largely uncharacterized. Here we isolated a PLV that co-infects the alga Phaeocystis globosa with the Phaeocystis globosa virus-14T (PgV-14T), a close relative of the "Phaeocystis globosa virus-virophage" genomic sequence. We name this PLV 'Gezel-14T. Gezel is phylogenetically distinct from the Lavidaviridae family where all known virophages belong. Gezel-14T co-infection decreases the fitness of its viral host by reducing burst sizes of PgV-14T, yet insufficiently to spare the cellular host population. Genomic screens show Gezel-14T-like PLVs integrated into Phaeocystis genomes, suggesting that these widespread viruses are capable of integration into cellular host genomes. This system presents an opportunity to better understand the evolution of eukaryotic dsDNA viruses as well as the complex dynamics and implications of viral parasitism.
Collapse
Affiliation(s)
- Sheila Roitman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Andrey Rozenberg
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Tali Lavy
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Oded Kleifeld
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
| |
Collapse
|
6
|
Shao Q, Agarkova IV, Noel EA, Dunigan DD, Liu Y, Wang A, Guo M, Xie L, Zhao X, Rossmann MG, Van Etten JL, Klose T, Fang Q. Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1. Nat Commun 2022; 13:6476. [PMID: 36309542 PMCID: PMC9617893 DOI: 10.1038/s41467-022-34218-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/18/2022] [Indexed: 12/25/2022] Open
Abstract
Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play critical roles in the viral life cycles, identities and high-resolution structures of these components remain unknown. Here, by determining a near-atomic-resolution, five-fold averaged structure of Paramecium bursaria chlorella virus 1, we unexpectedly found the viral capsid possesses up to five major capsid protein variants and a penton protein variant. These variants create varied capsid microenvironments for the associations of fibers, a vesicle, and previously unresolved minor capsid proteins. Our structure reveals the identities and atomic models of the capsid components that do not obey the overall icosahedral symmetry and leads to a model for how these components are assembled and initiate capsid assembly, and this model might be applicable to many other giant viruses.
Collapse
Affiliation(s)
- Qianqian Shao
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Irina V Agarkova
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - Eric A Noel
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - David D Dunigan
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - Yunshu Liu
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Aohan Wang
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Mingcheng Guo
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Linlin Xie
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Xinyue Zhao
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA.
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| | - Qianglin Fang
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China.
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| |
Collapse
|
7
|
Asrani P, Seebohm G, Stoll R. Potassium viroporins as model systems for understanding eukaryotic ion channel behaviour. Virus Res 2022; 320:198903. [PMID: 36037849 DOI: 10.1016/j.virusres.2022.198903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022]
Abstract
Ion channels are membrane proteins essential for a plethora of cellular functions including maintaining cell shape, ion homeostasis, cardiac rhythm and action potential in neurons. The complexity and often extensive structure of eukaryotic membrane proteins makes it difficult to understand their basic biological regulation. Therefore, this article suggests, viroporins - the miniature versions of eukaryotic protein homologs from viruses - might serve as model systems to provide insights into behaviour of eukaryotic ion channels in general. The structural requirements for correct assembly of the channel along with the basic functional properties of a K+ channel exist in the minimal design of the viral K+ channels from two viruses, Chlorella virus (Kcv) and Ectocarpus siliculosus virus (Kesv). These small viral proteins readily assemble into tetramers and they sort in cells to distinct target membranes. When these viruses-encoded channels are expressed into the mammalian cells, they utilise their protein machinery and hence can serve as excellent tools to study the cells protein sorting machinery. This combination of small size and robust function makes viral K+ channels a valuable model system for detection of basic structure-function correlations. It is believed that molecular and physiochemical analyses of these viroporins may serve as basis for the development of inhibitors or modulators to ion channel activity for targeting ion channel diseases - so called channelopathies. Therefore, it may provide a potential different scope for molecular pharmacology studies aiming at novel and innovative therapeutics associated with channel related diseases. This article reviews the structural and functional properties of Kcv and Kesv upon expression in mammalian cells and Xenopus oocytes. The mechanisms behind differential protein sorting in Kcv and Kesv are also thoroughly discussed.
Collapse
Affiliation(s)
- Purva Asrani
- Biomolecular Spectroscopy and RUBiospec|NMR, Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Bochum D-44780, Germany
| | - Guiscard Seebohm
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, Münster D-48149, Germany
| | - Raphael Stoll
- Biomolecular Spectroscopy and RUBiospec|NMR, Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Bochum D-44780, Germany.
| |
Collapse
|
8
|
Abstract
Genetic and molecular modifications of the large dsDNA chloroviruses, with genomes of 290 to 370 kb, would expedite studies to elucidate the functions of both identified and unidentified virus-encoded proteins. These plaque-forming viruses replicate in certain unicellular, eukaryotic chlorella-like green algae. However, to date, only a few of these algal species and virtually none of their viruses have been genetically manipulated due to lack of practical methods for genetic transformation and genome editing. Attempts at using Agrobacterium-mediated transfection of chlorovirus host Chlorella variabilis NC64A with a specially-designed binary vector resulted in successful transgenic cell selection based on expression of a hygromycin-resistance gene, initial expression of a green fluorescence gene and demonstration of integration of Agrobacterium T-DNA. However, expression of the integrated genes was soon lost. To develop gene editing tools for modifying specific chlorovirus CA-4B genes using preassembled Cas9 protein-sgRNA ribonucleoproteins (RNPs), we tested multiple methods for delivery of Cas9/sgRNA RNP complexes into infected cells including cell wall-degrading enzymes, electroporation, silicon carbide (SiC) whiskers, and cell-penetrating peptides (CPPs). In one experiment two independent virus mutants were isolated from macerozyme-treated NC64A cells incubated with Cas9/sgRNA RNPs targeting virus CA-4B-encoded gene 034r, which encodes a glycosyltransferase. Analysis of DNA sequences from the two mutant viruses showed highly targeted nucleotide sequence modifications in the 034r gene of each virus that were fully consistent with Cas9/RNP-directed gene editing. However, in ten subsequent experiments, we were unable to duplicate these results and therefore unable to achieve a reliable system to genetically edit chloroviruses. Nonetheless, these observations provide strong initial suggestions that Cas9/RNPs may function to promote editing of the chlorovirus genome, and that further experimentation is warranted and worthwhile.
Collapse
Affiliation(s)
- Eric A. Noel
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Donald P. Weeks
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, United States of America
| | - James L. Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
| |
Collapse
|
9
|
Zhou H, Chen P, Zhang M, Chen J, Fang J, Li X. Revealing the Viral Community in the Hadal Sediment of the New Britain Trench. Genes (Basel) 2021; 12:genes12070990. [PMID: 34209474 PMCID: PMC8306916 DOI: 10.3390/genes12070990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022] Open
Abstract
Marine viruses are widely distributed and influence matter and energy transformation in ecosystems by modulating hosts’ metabolism. The hadal trenches represent the deepest marine habitat on Earth, for which the viral communities and related biogeochemical functions are least explored and poorly understood. Here, using the sediment samples (8720 m below sea level) collected from the New Britain Trench (NBT), we investigated the viral community, diversity, and genetic potentials in the hadal sediment habitat for the first time by deep shotgun metagenomic sequencing. We found the NBT sediment viral community was dominated by Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, and Phycodnaviridae, which belong to the dsDNA viruses. However, the large majority of them remained uncharacterized. We found the hadal sediment virome had some common components by comparing the hadal sediment viruses with those of hadal aquatic habitats and those of bathypelagic and terrestrial habitats. It was also distinctive in community structure and had many novel viral clusters not associated with the other habitual virome included in our analyses. Further phylogenetic analysis on its Caudovirales showed novel diversities, including new clades specially evolved in the hadal sediment habitat. Annotation of the NBT sediment viruses indicated the viruses might influence microbial hydrocarbon biodegradation and carbon and sulfur cycling via metabolic augmentation through auxiliary metabolic genes (AMGs). Our study filled in the knowledge gaps on the virome of the hadal sediment habitats and provided insight into the evolution and the potential metabolic functions of the hadal sediment virome.
Collapse
Affiliation(s)
- Hui Zhou
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
| | - Mengjie Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawang Chen
- Ocean College, Zhejiang University, Zhoushan 316021, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| |
Collapse
|
10
|
Duncan GA, Dunigan DD, Van Etten JL. Diversity of tRNA Clusters in the Chloroviruses. Viruses 2020; 12:v12101173. [PMID: 33081353 PMCID: PMC7589089 DOI: 10.3390/v12101173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 11/25/2022] Open
Abstract
Viruses rely on their host’s translation machinery for the synthesis of their own proteins. Problems belie viral translation when the host has a codon usage bias (CUB) that is different from an infecting virus due to differences in the GC content between the host and virus genomes. Here, we examine the hypothesis that chloroviruses adapted to host CUB by acquisition and selection of tRNAs that at least partially favor their own CUB. The genomes of 41 chloroviruses comprising three clades, each infecting a different algal host, have been sequenced, assembled and annotated. All 41 viruses not only encode tRNAs, but their tRNA genes are located in clusters. While differences were observed between clades and even within clades, seven tRNA genes were common to all three clades of chloroviruses, including the tRNAArg gene, which was found in all 41 chloroviruses. By comparing the codon usage of one chlorovirus algal host, in which the genome has been sequenced and annotated (67% GC content), to that of two of its viruses (40% GC content), we found that the viruses were able to at least partially overcome the host’s CUB by encoding tRNAs that recognize AU-rich codons. Evidence presented herein supports the hypothesis that a chlorovirus tRNA cluster was present in the most recent common ancestor (MRCA) prior to divergence into three clades. In addition, the MRCA encoded a putative isoleucine lysidine synthase (TilS) that remains in 39/41 chloroviruses examined herein, suggesting a strong evolutionary pressure to retain the gene. TilS alters the anticodon of tRNAMet that normally recognizes AUG to then recognize AUA, a codon for isoleucine. This is advantageous to the chloroviruses because the AUA codon is 12–13 times more common in the chloroviruses than their host, further helping the chloroviruses to overcome CUB. Among large DNA viruses infecting eukaryotes, the presence of tRNA genes and tRNA clusters appear to be most common in the Phycodnaviridae and, to a lesser extent, in the Mimiviridae.
Collapse
Affiliation(s)
- Garry A. Duncan
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA; (G.A.D.); (D.D.D.)
| | - David D. Dunigan
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA; (G.A.D.); (D.D.D.)
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0833, USA
| | - James L. Van Etten
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA; (G.A.D.); (D.D.D.)
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0833, USA
- Correspondence: ; Tel.: +1-402-472-3168
| |
Collapse
|
11
|
Ku C, Sheyn U, Sebé-Pedrós A, Ben-Dor S, Schatz D, Tanay A, Rosenwasser S, Vardi A. A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. Sci Adv 2020; 6:eaba4137. [PMID: 32490206 PMCID: PMC7239649 DOI: 10.1126/sciadv.aba4137] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/10/2020] [Indexed: 05/12/2023]
Abstract
The discovery of giant viruses infecting eukaryotes from diverse ecosystems has revolutionized our understanding of the evolution of viruses and their impact on protist biology, yet knowledge on their replication strategies and transcriptome regulation remains limited. Here, we profile single-cell transcriptomes of the globally distributed microalga Emiliania huxleyi and its specific giant virus during infection. We detected profound heterogeneity in viral transcript levels among individual cells. Clustering single cells based on viral expression profiles enabled reconstruction of the viral transcriptional trajectory. Reordering cells along this path unfolded highly resolved viral genetic programs composed of genes with distinct promoter elements that orchestrate sequential expression. Exploring host transcriptome dynamics across the viral infection states revealed rapid and selective shutdown of protein-encoding nuclear transcripts, while the plastid and mitochondrial transcriptomes persisted into later stages. Single-cell RNA-seq opens a new avenue to unravel the life cycle of giant viruses and their unique hijacking strategies.
Collapse
Affiliation(s)
- Chuan Ku
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Sheyn
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Arnau Sebé-Pedrós
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shilo Rosenwasser
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
12
|
Gran-Stadniczeñko S, Krabberød AK, Sandaa RA, Yau S, Egge E, Edvardsen B. Seasonal Dynamics of Algae-Infecting Viruses and Their Inferred Interactions with Protists. Viruses 2019; 11:v11111043. [PMID: 31717498 PMCID: PMC6893440 DOI: 10.3390/v11111043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 11/28/2022] Open
Abstract
Viruses are a highly abundant, dynamic, and diverse component of planktonic communities that have key roles in marine ecosystems. We aimed to reveal the diversity and dynamics of marine large dsDNA viruses infecting algae in the Northern Skagerrak, South Norway through the year by metabarcoding, targeting the major capsid protein (MCP) and its correlation to protist diversity and dynamics. Metabarcoding results demonstrated a high diversity of algal viruses compared to previous metabarcoding surveys in Norwegian coastal waters. We obtained 313 putative algal virus operational taxonomic units (vOTUs), all classified by phylogenetic analyses to either the Phycodnaviridae or Mimiviridae families, most of them in clades without any cultured or environmental reference sequences. The viral community showed a clear temporal variation, with some vOTUs persisting for several months. The results indicate co-occurrences between abundant viruses and potential hosts during long periods. This study gives new insights into the virus-algal host dynamics and provides a baseline for future studies of algal virus diversity and temporal dynamics.
Collapse
Affiliation(s)
- Sandra Gran-Stadniczeñko
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway; (A.K.K.); (E.E.); (B.E.)
- Correspondence: ; Tel.: +47-22-85-70-38
| | - Anders K. Krabberød
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway; (A.K.K.); (E.E.); (B.E.)
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway;
| | - Sheree Yau
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), 08003 Barcelona, Spain;
| | - Elianne Egge
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway; (A.K.K.); (E.E.); (B.E.)
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway; (A.K.K.); (E.E.); (B.E.)
| |
Collapse
|
13
|
Seitzer P, Jeanniard A, Ma F, Van Etten JL, Facciotti MT, Dunigan DD. Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes. Viruses 2018; 10:E576. [PMID: 30347809 PMCID: PMC6213493 DOI: 10.3390/v10100576] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/12/2018] [Accepted: 10/17/2018] [Indexed: 01/16/2023] Open
Abstract
Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world's inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 ± 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic "contexts", the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed "gene gangs". Unlike previously described local genomic contexts, the definition of gene gangs requires only that member genes be consistently co-localized and are not constrained by strand, regulatory sites, or intervening sequences (and therefore represent a new type of conserved structural genomic element). An analysis of functional annotations and transcriptomic data suggests that some of the gene gangs may organize genes involved in specific biochemical processes, but that this organization does not involve their coordinated expression.
Collapse
Affiliation(s)
- Phillip Seitzer
- Department of Biomedical Engineering, One Shields Ave, University of California, Davis, CA 95616, USA;
- Genome Center, One Shields Ave, University of California, Davis, CA 95616, USA
- Proteome Software, Portland, OR 97219, USA
| | - Adrien Jeanniard
- Nebraska Center for Virology, Morrison Research Center, University of Nebraska, Lincoln, NE 68583-0900, USA; (F.M.); (J.L.V.E.)
| | - Fangrui Ma
- Nebraska Center for Virology, Morrison Research Center, University of Nebraska, Lincoln, NE 68583-0900, USA; (F.M.); (J.L.V.E.)
| | - James L. Van Etten
- Nebraska Center for Virology, Morrison Research Center, University of Nebraska, Lincoln, NE 68583-0900, USA; (F.M.); (J.L.V.E.)
- Department of Plant Pathology, Plant Science Hall, University of Nebraska, Lincoln, NE 68583-0722, USA
| | - Marc T. Facciotti
- Department of Biomedical Engineering, One Shields Ave, University of California, Davis, CA 95616, USA;
- Genome Center, One Shields Ave, University of California, Davis, CA 95616, USA
| | - David D. Dunigan
- Nebraska Center for Virology, Morrison Research Center, University of Nebraska, Lincoln, NE 68583-0900, USA; (F.M.); (J.L.V.E.)
- Department of Plant Pathology, Plant Science Hall, University of Nebraska, Lincoln, NE 68583-0722, USA
| |
Collapse
|
14
|
Maat DS, Biggs T, Evans C, van Bleijswijk JDL, van der Wel NN, Dutilh BE, Brussaard CPD. Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses. Viruses 2017; 9:v9060134. [PMID: 28574420 PMCID: PMC5490811 DOI: 10.3390/v9060134] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 11/16/2022] Open
Abstract
Global climate change-induced warming of the Artic seas is predicted to shift the phytoplankton community towards dominance of smaller-sized species due to global warming. Yet, little is known about their viral mortality agents despite the ecological importance of viruses regulating phytoplankton host dynamics and diversity. Here we report the isolation and basic characterization of four prasinoviruses infectious to the common Arctic picophytoplankter Micromonas. We furthermore assessed how temperature influenced viral infectivity and production. Phylogenetic analysis indicated that the putative double-stranded DNA (dsDNA) Micromonas polaris viruses (MpoVs) are prasinoviruses (Phycodnaviridae) of approximately 120 nm in particle size. One MpoV showed intrinsic differences to the other three viruses, i.e., larger genome size (205 ± 2 vs. 191 ± 3 Kb), broader host range, and longer latent period (39 vs. 18 h). Temperature increase shortened the latent periods (up to 50%), increased the burst size (up to 40%), and affected viral infectivity. However, the variability in response to temperature was high for the different viruses and host strains assessed, likely affecting the Arctic picoeukaryote community structure both in the short term (seasonal cycles) and long term (global warming).
Collapse
Affiliation(s)
- Douwe S Maat
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| | - Tristan Biggs
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| | - Claire Evans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
- Ocean Biogeochemistry & Ecosystems Research Group, National Oceanography Centre, Southampton, European Way, Southampton SO14 3ZH, UK.
| | - Judith D L van Bleijswijk
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| | - Nicole N van der Wel
- Electron Microscopy Center Amsterdam, Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands.
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| |
Collapse
|
15
|
López JL, Golemba M, Hernández E, Lozada M, Dionisi H, Jansson JK, Carroll J, Lundgren L, Sjöling S, Mac Cormack WP. Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions. FEMS Microbiol Ecol 2017; 93:fiw216. [PMID: 27815287 DOI: 10.1093/femsec/fiw216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2016] [Indexed: 11/14/2022] Open
Abstract
Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 6224 bacterial rhodopsin sequences according to COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment, 123 viral (51) and non-viral (72) sequences (>50 amino acids) were finally included in further analysis. Viral rhodopsin genes were homologs of Phaeocystis globosa virus and Organic lake Phycodnavirus. Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus and Cryptophyta and Fungi. A rescreening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 amino acids). Phylogeographic analysis revealed a geographical clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsin genes related to Actinobacteria and Chloroflexi. This is the first report about the existence of a phylogeographic association of the viral rhodopsin sequences from marine sediments.
Collapse
Affiliation(s)
- José L López
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Floor 4, C1113AAD CABA, Argentina
| | - Marcelo Golemba
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría 'Juan P. Garrahan', Combate de los Pozos 1881, C1245AAM CABA, Argentina
| | - Edgardo Hernández
- Instituto Antártico Argentino, UNSAM Campus Miguelete, 25 de Mayo y Francia, B1650HMJ San Martín, Buenos Aires, Argentina
- Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología e Instituto de Nanobiotecnología UBA-CONICET, Universidad de Buenos Aires, Junin 956 Floor 6, C1113AAD CABA, Argentina
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Chubut, Argentina
| | - Hebe Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Chubut, Argentina
| | - Janet K Jansson
- Pacific Northwest National Laboratory, MSIN: J4-18, Richland, WA 99352, USA
| | - Jolynn Carroll
- CAGE-Centre for Arctic Gas Hydrate, Environment and Climate, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
- Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, NO-9296, Tromsø, Norway
| | - Leif Lundgren
- Department of Systems Ecology, Stockholm University, SE-10691, Sweden
| | - Sara Sjöling
- School of Natural Sciences, Technology and Environmental Studies, Sodertorn University, 14189 Huddinge, Sweden
| | - Walter P Mac Cormack
- Instituto Antártico Argentino, UNSAM Campus Miguelete, 25 de Mayo y Francia, B1650HMJ San Martín, Buenos Aires, Argentina
- Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología e Instituto de Nanobiotecnología UBA-CONICET, Universidad de Buenos Aires, Junin 956 Floor 6, C1113AAD CABA, Argentina
| |
Collapse
|
16
|
Van Etten JL, Agarkova I, Dunigan DD, Tonetti M, De Castro C, Duncan GA. Chloroviruses Have a Sweet Tooth. Viruses 2017; 9:E88. [PMID: 28441734 PMCID: PMC5408694 DOI: 10.3390/v9040088] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/13/2017] [Accepted: 04/14/2017] [Indexed: 01/16/2023] Open
Abstract
Chloroviruses are large double-stranded DNA (dsDNA) viruses that infect certain isolates of chlorella-like green algae. They contain up to approximately 400 protein-encoding genes and 16 transfer RNA (tRNA) genes. This review summarizes the unexpected finding that many of the chlorovirus genes encode proteins involved in manipulating carbohydrates. These include enzymes involved in making extracellular polysaccharides, such as hyaluronan and chitin, enzymes that make nucleotide sugars, such as GDP-L-fucose and GDP-D-rhamnose and enzymes involved in the synthesis of glycans attached to the virus major capsid proteins. This latter process differs from that of all other glycoprotein containing viruses that traditionally use the host endoplasmic reticulum and Golgi machinery to synthesize and transfer the glycans.
Collapse
Affiliation(s)
- James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA.
| | - Irina Agarkova
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA.
| | - David D Dunigan
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA.
| | - Michela Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova Viale Benedetto XV/1, 16132 Genova, Italy.
| | - Christina De Castro
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, NA, Italy.
| | - Garry A Duncan
- Department of Biology, Nebraska Wesleyan University, Lincoln, NE 68504-2796, USA.
| |
Collapse
|
17
|
Nissimov JI, Pagarete A, Ma F, Cody S, Dunigan DD, Kimmance SA, Allen MJ. Coccolithoviruses: A Review of Cross-Kingdom Genomic Thievery and Metabolic Thuggery. Viruses 2017; 9:v9030052. [PMID: 28335474 PMCID: PMC5371807 DOI: 10.3390/v9030052] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 11/24/2022] Open
Abstract
Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses—EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis. The viruses clustered into distinct clades, based on their DNA polymerase gene as well as full genome comparisons. We discuss the use of such clustering and suggest that a gene-by-gene investigation approach may be more useful when the goal is to reveal differences related to functionally important genes. A multi domain “Best BLAST hit” analysis revealed that 84% of the EhV genes have closer similarities to the domain Eukarya. However, 16% of the EhV CDSs were very similar to bacterial genes, contributing to the idea that a significant portion of the gene flow in the planktonic world inter-crosses the domains of life.
Collapse
Affiliation(s)
- Jozef I Nissimov
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, UK.
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA.
| | - António Pagarete
- Department of Biology, University of Bergen, Bergen, 7803, Norway.
| | - Fangrui Ma
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583, USA.
| | - Sean Cody
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583, USA.
| | - David D Dunigan
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583, USA.
| | - Susan A Kimmance
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, UK.
| | - Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, UK.
| |
Collapse
|
18
|
Mordecai GJ, Verret F, Highfield A, Schroeder DC. Schrödinger's Cheshire Cat: Are Haploid Emiliania huxleyi Cells Resistant to Viral Infection or Not? Viruses 2017; 9:v9030051. [PMID: 28335465 PMCID: PMC5371806 DOI: 10.3390/v9030051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/10/2017] [Accepted: 03/14/2017] [Indexed: 11/16/2022] Open
Abstract
Emiliania huxleyi is the main calcite producer on Earth and is routinely infected by a virus (EhV); a double stranded DNA (dsDNA) virus belonging to the family Phycodnaviridae. E. huxleyi exhibits a haplodiploid life cycle; the calcified diploid stage is non-motile and forms extensive blooms. The haploid phase is a non-calcified biflagellated cell bearing organic scales. Haploid cells are thought to resist infection, through a process deemed the “Cheshire Cat” escape strategy; however, a recent study detected the presence of viral lipids in the same haploid strain. Here we report on the application of an E. huxleyi CCMP1516 EhV-86 combined tiling array (TA) that further confirms an EhV infection in the RCC1217 haploid strain, which grew without any signs of cell lysis. Reverse transcription polymerase chain reaction (RT-PCR) and PCR verified the presence of viral RNA in the haploid cells, yet indicated an absence of viral DNA, respectively. These infected cells are an alternative stage of the virus life cycle deemed the haplococcolithovirocell. In this instance, the host is both resistant to and infected by EhV, i.e., the viral transcriptome is present in haploid cells whilst there is no evidence of viral lysis. This superimposed state is reminiscent of Schrödinger’s cat; of being simultaneously both dead and alive.
Collapse
Affiliation(s)
- Gideon J Mordecai
- Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UK.
| | - Frederic Verret
- Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UK.
| | - Andrea Highfield
- Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UK.
| | - Declan C Schroeder
- Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UK.
| |
Collapse
|
19
|
Abstract
Viruses play a crucial role in the marine environment, promoting nutrient recycling and biogeochemical cycling and driving evolutionary processes. Tiny marine phytoplankton called prasinophytes are ubiquitous and significant contributors to global primary production and biomass. A number of viruses (known as prasinoviruses) that infect these important primary producers have been isolated and characterised over the past decade. Here we review the current body of knowledge about prasinoviruses and their interactions with their algal hosts. Several genes, including those encoding for glycosyltransferases, methyltransferases and amino acid synthesis enzymes, which have never been identified in viruses of eukaryotes previously, have been detected in prasinovirus genomes. The host organisms are also intriguing; most recently, an immunity chromosome used by a prasinophyte in response to viral infection was discovered. In light of such recent, novel discoveries, we discuss why the cellular simplicity of prasinophytes makes for appealing model host organism-virus systems to facilitate focused and detailed investigations into the dynamics of marine viruses and their intimate associations with host species. We encourage the adoption of the prasinophyte Ostreococcus and its associated viruses as a model host-virus system for examination of cellular and molecular processes in the marine environment.
Collapse
Affiliation(s)
- Karen D Weynberg
- Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia.
| | - Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - William H Wilson
- Sir Alister Hardy Foundation for Ocean Science, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.
| |
Collapse
|
20
|
Highfield A, Joint I, Gilbert JA, Crawfurd KJ, Schroeder DC. Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment. Viruses 2017; 9:v9030041. [PMID: 28282890 PMCID: PMC5371796 DOI: 10.3390/v9030041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 11/16/2022] Open
Abstract
Effects of elevated pCO₂ on Emiliania huxleyi genetic diversity and the viruses that infect E. huxleyi (EhVs) have been investigated in large volume enclosures in a Norwegian fjord. Triplicate enclosures were bubbled with air enriched with CO₂ to 760 ppmv whilst the other three enclosures were bubbled with air at ambient pCO₂; phytoplankton growth was initiated by the addition of nitrate and phosphate. E. huxleyi was the dominant coccolithophore in all enclosures, but no difference in genetic diversity, based on DGGE analysis using primers specific to the calcium binding protein gene (gpa) were detected in any of the treatments. Chlorophyll concentrations and primary production were lower in the three elevated pCO₂ treatments than in the ambient treatments. However, although coccolithophores numbers were reduced in two of the high-pCO₂ treatments; in the third, there was no suppression of coccolithophores numbers, which were very similar to the three ambient treatments. In contrast, there was considerable variation in genetic diversity in the EhVs, as determined by analysis of the major capsid protein (mcp) gene. EhV diversity was much lower in the high-pCO₂ treatment enclosure that did not show inhibition of E. huxleyi growth. Since virus infection is generally implicated as a major factor in terminating phytoplankton blooms, it is suggested that no study of the effect of ocean acidification in phytoplankton can be complete if it does not include an assessment of viruses.
Collapse
Affiliation(s)
- Andrea Highfield
- The Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.
| | - Ian Joint
- The Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.
| | - Jack A Gilbert
- The Microbiome Centre, Department of Surgery, University of Chicago, Chicago, IL 60637, USA.
- Division of Bioscience, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA.
| | - Katharine J Crawfurd
- Department of Biological Oceanography, NIOZ-Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| | - Declan C Schroeder
- The Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.
| |
Collapse
|
21
|
Quispe CF, Sonderman O, Seng A, Rasmussen B, Weber G, Mueller C, Dunigan DD, Van Etten JL. Three-year survey of abundance, prevalence and genetic diversity of chlorovirus populations in a small urban lake. Arch Virol 2016; 161:1839-47. [PMID: 27068168 DOI: 10.1007/s00705-016-2853-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/30/2016] [Indexed: 11/28/2022]
Abstract
Inland water environments cover about 2.5 percent of our planet and harbor huge numbers of known and still unknown microorganisms. In this report, we examined water samples for the abundance, prevalence, and genetic diversity of a group of infectious viruses (chloroviruses) that infect symbiotic chlorella-like green algae. Samples were collected on a weekly basis for a period of 24 to 36 months from a recreational freshwater lake in Lincoln, Nebraska, and assayed for infectious viruses by plaque assay. The numbers of infectious virus particles were both host- and site-dependent. The consistent fluctuations in numbers of viruses suggest their impact as key factors in shaping microbial community structures in the water surface. Even in low-viral-abundance months, infectious chlorovirus populations were maintained, suggesting either that the viruses are very stable or that there is ongoing viral production in natural hosts.
Collapse
Affiliation(s)
- Cristian F Quispe
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
- School of Biological Science, Manter Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
| | - Olivia Sonderman
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Anya Seng
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Brenna Rasmussen
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Garrett Weber
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Claire Mueller
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - David D Dunigan
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - James L Van Etten
- Department of Plant Pathology, Plant Science Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| |
Collapse
|
22
|
Clerissi C, Desdevises Y, Romac S, Audic S, de Vargas C, Acinas SG, Casotti R, Poulain J, Wincker P, Hingamp P, Ogata H, Grimsley N. Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes. Environ Microbiol Rep 2015; 7:979-989. [PMID: 26472079 DOI: 10.1111/1758-2229.12345] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 10/08/2015] [Accepted: 10/08/2015] [Indexed: 06/05/2023]
Abstract
High-throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution. Nevertheless, analysis of single environmental variables showed that eutrophic conditions strongly influence the distributions of both hosts and viruses. Moreover, these communities were not correlated, in their composition or specific richness. These observations could result from antagonistic dynamics, such as that illustrated in a prey-predator model, and/or because hosts might be under a complex set of selective pressures. Both of these reasons must be considered to interpret environmental surveys of viruses and hosts, because covariation does not always imply interaction.
Collapse
Affiliation(s)
- Camille Clerissi
- Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
- Biologie Intégrative des Organismes Marins, CNRS, UMR 7232, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
| | - Yves Desdevises
- Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
- Biologie Intégrative des Organismes Marins, CNRS, UMR 7232, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
| | - Sarah Romac
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Equipe Evolution du Plancton et Paleo-Ocean, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Stéphane Audic
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Equipe Evolution du Plancton et Paleo-Ocean, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Colomban de Vargas
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Equipe Evolution du Plancton et Paleo-Ocean, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Science (ICM), CSIC, Pg Marítim de la Barceloneta 37-49, Barcelona, Spain
| | - Raffaella Casotti
- Stazione Zoologica, Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Julie Poulain
- CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, BP5706, Evry, 91057, France
| | - Patrick Wincker
- CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, BP5706, Evry, 91057, France
| | - Pascal Hingamp
- CNRS, Université Aix-Marseille, Laboratoire Information Génomique et Structurale (UMR 7256), Mediterranean Institute of Microbiology (FR 3479), 13288, Marseille, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
| | - Nigel Grimsley
- Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
- Biologie Intégrative des Organismes Marins, CNRS, UMR 7232, Avenue du Fontaulé, 66650, Banyuls-sur-Mer, France
| |
Collapse
|
23
|
Baudoux AC, Lebredonchel H, Dehmer H, Latimier M, Edern R, Rigaut-Jalabert F, Ge P, Guillou L, Foulon E, Bozec Y, Cariou T, Desdevises Y, Derelle E, Grimsley N, Moreau H, Simon N. Interplay between the genetic clades of Micromonas and their viruses in the Western English Channel. Environ Microbiol Rep 2015; 7:765-773. [PMID: 26081716 DOI: 10.1111/1758-2229.12309] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/13/2015] [Accepted: 06/04/2015] [Indexed: 06/04/2023]
Abstract
The genus Micromonas comprises distinct genetic clades that commonly dominate eukaryotic phytoplankton community from polar to tropical waters. This phytoplankter is also recurrently infected by abundant and genetically diverse prasinoviruses. Here we report on the interplay between prasinoviruses and Micromonas with regard to the genetic diversity of this host. For 1 year, we monitored the abundance of three clades of Micromonas and their viruses in the Western English Channel, both in the environment using clade-specific probes and flow cytometry, and in the laboratory using clonal strains of Micromonas clades to assay for their viruses by plaque-forming units. We showed that the seasonal fluctuations of Micromonas clades were closely mirrored by the abundance of their corresponding viruses, indicating that the members of Micromonas genus are susceptible to viral infection, regardless of their genetic affiliation. The characterization of 45 viral isolates revealed that Micromonas clades are attacked by specific virus populations, which exhibit distinctive clade specificity, life strategies and genetic diversity. However, some viruses can also cross-infect different host clades, suggesting a mechanism of horizontal gene transfer within the Micromonas genus. This study provides novel insights into the impact of viral infection for the ecology and evolution of the prominent phytoplankter Micromonas.
Collapse
Affiliation(s)
- A-C Baudoux
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - H Lebredonchel
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls sur Mer, France
| | - H Dehmer
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - M Latimier
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - R Edern
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - F Rigaut-Jalabert
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Fédération de Recherche (FR2424), Station Biologique de Roscoff, 29680, Roscoff, France
| | - P Ge
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - L Guillou
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - E Foulon
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - Y Bozec
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - T Cariou
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Fédération de Recherche (FR2424), Station Biologique de Roscoff, 29680, Roscoff, France
| | - Y Desdevises
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls sur Mer, France
| | - E Derelle
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls sur Mer, France
| | - N Grimsley
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls sur Mer, France
| | - H Moreau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls sur Mer, France
| | - N Simon
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| |
Collapse
|
24
|
Bihmidine S, Cao M, Kang M, Awada T, Van Etten JL, Dunigan DD, Clemente TE. Expression of Chlorovirus MT325 aquaglyceroporin (aqpv1) in tobacco and its role in mitigating drought stress. Planta 2014; 240:209-21. [PMID: 24797278 PMCID: PMC4148780 DOI: 10.1007/s00425-014-2075-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/08/2014] [Indexed: 06/03/2023]
Abstract
MAIN CONCLUSIONS A Chlorovirus aquaglyceroporin expressed in tobacco is localized to the plastid and plasma membranes. Transgenic events display improved response to water deficit. Necrosis in adult stage plants is observed. Aquaglyceroporins are a subclass of the water channel aquaporin proteins (AQPs) that transport glycerol along with other small molecules transcellular in addition to water. In the studies communicated herein, we analyzed the expression of the aquaglyceroporin gene designated, aqpv1, from Chlorovirus MT325, in tobacco (Nicotiana tabacum), along with phenotypic changes induced by aqpv1 expression in planta. Interestingly, aqpv1 expression under control of either a constitutive or a root-preferred promoter, triggered local lesion formation in older leaves, which progressed significantly after induction of flowering. Fusion of aqpv1 with GFP suggests that the protein localized to the plasmalemma, and potentially with plastid and endoplasmic reticulum membranes. Physiological characterizations of transgenic plants during juvenile stage growth were monitored for potential mitigation to water dry-down (i.e., drought) and recovery. Phenotypic analyses on drought mimic/recovery of juvenile transgenic plants that expressed a functional aqpv1 transgene had higher photosynthetic rates, stomatal conductance, and water use efficiency, along with maximum carboxylation and electron transport rates when compared to control plants. These physiological attributes permitted the juvenile aqpv1 transgenic plants to perform better under drought-mimicked conditions and hastened recovery following re-watering. This drought mitigation effect is linked to the ability of the transgenic plants to maintain cell turgor.
Collapse
Affiliation(s)
- Saadia Bihmidine
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE
68583-0968, USA
| | - Mingxia Cao
- Department of A gronomy and Horticulture, Center for Plant Science
Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588-0660, USA
| | - Ming Kang
- Department of Plant Pathology, Nebraska Center for Virology, University of
Nebraska-Lincoln, Lincoln, NE 68583-0900, USA
| | - Tala Awada
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE
68583-0968, USA
| | - James L. Van Etten
- Department of Plant Pathology, Nebraska Center for Virology, University of
Nebraska-Lincoln, Lincoln, NE 68583-0900, USA
| | - David D. Dunigan
- Department of Plant Pathology, Nebraska Center for Virology, University of
Nebraska-Lincoln, Lincoln, NE 68583-0900, USA
| | - Tom E. Clemente
- Department of A gronomy and Horticulture, Center for Plant Science
Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588-0660, USA,
| |
Collapse
|
25
|
Blanc G, Mozar M, Agarkova IV, Gurnon JR, Yanai-Balser G, Rowe JM, Xia Y, Riethoven JJ, Dunigan DD, Van Etten JL. Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1. PLoS One 2014; 9:e90989. [PMID: 24608750 PMCID: PMC3946568 DOI: 10.1371/journal.pone.0090989] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/05/2014] [Indexed: 11/18/2022] Open
Abstract
Paramecium bursaria chlorella virus 1 (PBCV-1) is the prototype of the genus Chlorovirus (family Phycodnaviridae) that infects the unicellular, eukaryotic green alga Chlorella variabilis NC64A. The 331-kb PBCV-1 genome contains 416 major open reading frames. A mRNA-seq approach was used to analyze PBCV-1 transcriptomes at 6 progressive times during the first hour of infection. The alignment of 17 million reads to the PBCV-1 genome allowed the construction of single-base transcriptome maps. Significant transcription was detected for a subset of 50 viral genes as soon as 7 min after infection. By 20 min post infection (p.i.), transcripts were detected for most PBCV-1 genes and transcript levels continued to increase globally up to 60 min p.i., at which time 41% or the poly (A+)-containing RNAs in the infected cells mapped to the PBCV-1 genome. For some viral genes, the number of transcripts in the latter time points (20 to 60 min p.i.) was much higher than that of the most highly expressed host genes. RNA-seq data revealed putative polyadenylation signal sequences in PBCV-1 genes that were identical to the polyadenylation signal AAUAAA of green algae. Several transcripts have an RNA fragment excised. However, the frequency of excision and the resulting putative shortened protein products suggest that most of these excision events have no functional role but are probably the result of the activity of misled splicesomes.
Collapse
Affiliation(s)
- Guillaume Blanc
- Laboratoire Information Structurale and Génomique UMR7256 CNRS, Aix-Marseille Université, Marseille, France
- * E-mail:
| | - Michael Mozar
- Laboratoire Information Structurale and Génomique UMR7256 CNRS, Aix-Marseille Université, Marseille, France
| | - Irina V. Agarkova
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - James R. Gurnon
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Giane Yanai-Balser
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Janet M. Rowe
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Yuannan Xia
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Jean-Jack Riethoven
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - David D. Dunigan
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - James L. Van Etten
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| |
Collapse
|
26
|
Stevens K, Weynberg K, Bellas C, Brown S, Brownlee C, Brown MT, Schroeder DC. A novel evolutionary strategy revealed in the phaeoviruses. PLoS One 2014; 9:e86040. [PMID: 24465858 PMCID: PMC3897601 DOI: 10.1371/journal.pone.0086040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/04/2013] [Indexed: 11/18/2022] Open
Abstract
Phaeoviruses infect the brown algae, which are major contributors to primary production of coastal waters and estuaries. They exploit a Persistent evolutionary strategy akin to a K- selected life strategy via genome integration and are the only known representatives to do so within the giant algal viruses that are typified by r- selected Acute lytic viruses. In screening the genomes of five species within the filamentous brown algal lineage, here we show an unprecedented diversity of viral gene sequence variants especially amongst the smaller phaeoviral genomes. Moreover, one variant shares features from both the two major sub-groups within the phaeoviruses. These phaeoviruses have exploited the reduction of their giant dsDNA genomes and accompanying loss of DNA proofreading capability, typical of an Acute life strategist, but uniquely retain a Persistent life strategy.
Collapse
Affiliation(s)
- Kim Stevens
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Karen Weynberg
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Christopher Bellas
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Sonja Brown
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Colin Brownlee
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Murray T. Brown
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Declan C. Schroeder
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- * E-mail:
| |
Collapse
|
27
|
Stepanova OA, Boĭko AL, Shcherbatenko IS. [Computational genome analysis of three marine algoviruses]. Mikrobiol Z 2013; 75:76-81. [PMID: 24479317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Computational analysis of genomic sequences of three new marine algoviruses: Tetraselmis viridis virus (TvV-S20 and TvV-SI1 strains) and Dunaliella viridis virus (DvV-SI2 strain) was conducted. Both considerable similarity and essential distinctions between studied strains and the most studied marine algoviruses of Phycodnaviridae family were revealed. Our data show that the tested strains are new viruses with the following features: only they were isolated from marine eukaryotic microalgae T. viridis and D. viridis, coding sequences (CDSs) of their genomes are localized mainly on one of the DNA strands and form several clusters with short intergenic spaces; there are considerable variations in genome structure within viruses and their strains; viral genomic DNA has a high GC-content (55.5 - 67.4%); their genes contain no well-known optimal contexts of translation start codones, and the contexts of terminal codons read-through; the vast majority of viral genes and proteins do not have any matches in gene banks.
Collapse
|
28
|
Philosof A, Béjà O. Bacterial, archaeal and viral-like rhodopsins from the Red Sea. Environ Microbiol Rep 2013; 5:475-482. [PMID: 23754728 DOI: 10.1111/1758-2229.12037] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/13/2013] [Accepted: 01/14/2013] [Indexed: 06/02/2023]
Abstract
The Gulf of Aqaba, extending north to the Red Sea, is an oligotrophic basin with typical open ocean gyre characteristics. Here we report on the existence of diverse microbial rhodopsins in the Gulf of Aqaba, based on 454-pyrosequencing-generated metagenome and metatranscriptome data sets, obtained from the microbial fraction smaller than 1.6 μm. Bacterial SAR11, SAR86 and archaeal proteorhodopsins as well as viral-like rhodopsins were detected on the DNA level. On the RNA level, only SAR11 and SAR86 proteorhodopsin transcripts were detected. Our results add to the growing evidence that microbial rhodopsins are a diverse, abundant and widespread protein family.
Collapse
Affiliation(s)
- Alon Philosof
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | | |
Collapse
|
29
|
Hamacher K, Greiner T, Ogata H, Van Etten JL, Gebhardt M, Villarreal LP, Cosentino C, Moroni A, Thiel G. Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis. PLoS One 2012; 7:e38826. [PMID: 22685610 PMCID: PMC3369850 DOI: 10.1371/journal.pone.0038826] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 05/11/2012] [Indexed: 11/26/2022] Open
Abstract
Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K(+) channels. To determine if these viral K(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the K(+) channel pore modules from seven phycodnaviruses to the K(+) channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K(+) channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K(+) channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K(+) channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K(+) channels in algae and perhaps even all cellular organisms.
Collapse
Affiliation(s)
- Kay Hamacher
- Computational Biology Group, Technische Universität Darmstadt, Darmstadt, Germany
| | - Timo Greiner
- Membrane Biophysics Group, Technische Universität Darmstadt, Darmstadt, Germany
| | - Hiroyuki Ogata
- Structural and Genomic Information Laboratory, Aix-Marseille University, Marseille, France
| | - James L. Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Manuela Gebhardt
- Membrane Biophysics Group, Technische Universität Darmstadt, Darmstadt, Germany
| | - Luis P. Villarreal
- Center of Virus Research, University of California Irvine, Irvine, California, United States of America
| | | | - Anna Moroni
- Department of Biology, Università degli Studi di Milano, Milan, Italy
| | - Gerhard Thiel
- Membrane Biophysics Group, Technische Universität Darmstadt, Darmstadt, Germany
| |
Collapse
|
30
|
Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden AZ. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environ Microbiol 2012; 14:162-76. [PMID: 21914098 PMCID: PMC3429862 DOI: 10.1111/j.1462-2920.2011.02576.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 07/27/2011] [Indexed: 11/28/2022]
Abstract
Phosphate (PO(4)) is an important limiting nutrient in marine environments. Marine cyanobacteria scavenge PO(4) using the high-affinity periplasmic phosphate binding protein PstS. The pstS gene has recently been identified in genomes of cyanobacterial viruses as well. Here, we analyse genes encoding transporters in genomes from viruses that infect eukaryotic phytoplankton. We identified inorganic PO(4) transporter-encoding genes from the PHO4 superfamily in several virus genomes, along with other transporter-encoding genes. Homologues of the viral pho4 genes were also identified in genome sequences from the genera that these viruses infect. Genome sequences were available from host genera of all the phytoplankton viruses analysed except the host genus Bathycoccus. Pho4 was recovered from Bathycoccus by sequencing a targeted metagenome from an uncultured Atlantic Ocean population. Phylogenetic reconstruction showed that pho4 genes from pelagophytes, haptophytes and infecting viruses were more closely related to homologues in prasinophytes than to those in what, at the species level, are considered to be closer relatives (e.g. diatoms). We also identified PHO4 superfamily members in ocean metagenomes, including new metagenomes from the Pacific Ocean. The environmental sequences grouped with pelagophytes, haptophytes, prasinophytes and viruses as well as bacteria. The analyses suggest that multiple independent pho4 gene transfer events have occurred between marine viruses and both eukaryotic and bacterial hosts. Additionally, pho4 genes were identified in available genomes from viruses that infect marine eukaryotes but not those that infect terrestrial hosts. Commonalities in marine host-virus gene exchanges indicate that manipulation of host-PO(4) uptake is an important adaptation for viral proliferation in marine systems. Our findings suggest that PO(4) -availability may not serve as a simple bottom-up control of marine phytoplankton.
Collapse
Affiliation(s)
- Adam Monier
- Monterey Bay Aquarium Research Institute7700 Sandholdt Road, Moss Landing, CA 95039, USA
| | - Rory M Welsh
- Monterey Bay Aquarium Research Institute7700 Sandholdt Road, Moss Landing, CA 95039, USA
| | - Chelle Gentemann
- Remote Sensing Systems444 Tenth Street, Suite 200, Santa Rosa, CA, 95401, USA
| | - George Weinstock
- The Genome Center, Washington University School of Medicine4444 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Erica Sodergren
- The Genome Center, Washington University School of Medicine4444 Forest Park Avenue, St. Louis, MO 63108, USA
| | | | - Jonathan A Eisen
- University of California DavisDavis, CA 95616DOE Joint Genome Institute Walnut CreekCA, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute7700 Sandholdt Road, Moss Landing, CA 95039, USA
| |
Collapse
|
31
|
Abstract
Viruses infecting higher plants are among the smallest viruses known and typically have four to ten protein-encoding genes. By contrast, many viruses that infect algae (classified in the virus family Phycodnaviridae) are among the largest viruses found to date and have up to 600 protein-encoding genes. This brief review focuses on one group of plaque-forming phycodnaviruses that infect unicellular chlorella-like green algae. The prototype chlorovirus PBCV-1 has more than 400 protein-encoding genes and 11 tRNA genes. About 40% of the PBCV-1 encoded proteins resemble proteins of known function including many that are completely unexpected for a virus. In many respects, chlorovirus infection resembles bacterial infection by tailed bacteriophages.
Collapse
Affiliation(s)
- James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, USA.
| | | |
Collapse
|
32
|
Yau S, Lauro FM, DeMaere MZ, Brown MV, Thomas T, Raftery MJ, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Gibson JA, Cavicchioli R. Virophage control of antarctic algal host-virus dynamics. Proc Natl Acad Sci U S A 2011; 108:6163-8. [PMID: 21444812 PMCID: PMC3076838 DOI: 10.1073/pnas.1018221108] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Viruses are abundant ubiquitous members of microbial communities and in the marine environment affect population structure and nutrient cycling by infecting and lysing primary producers. Antarctic lakes are microbially dominated ecosystems supporting truncated food webs in which viruses exert a major influence on the microbial loop. Here we report the discovery of a virophage (relative of the recently described Sputnik virophage) that preys on phycodnaviruses that infect prasinophytes (phototrophic algae). By performing metaproteogenomic analysis on samples from Organic Lake, a hypersaline meromictic lake in Antarctica, complete virophage and near-complete phycodnavirus genomes were obtained. By introducing the virophage as an additional predator of a predator-prey dynamic model we determined that the virophage stimulates secondary production through the microbial loop by reducing overall mortality of the host and increasing the frequency of blooms during polar summer light periods. Virophages remained abundant in the lake 2 y later and were represented by populations with a high level of major capsid protein sequence variation (25-100% identity). Virophage signatures were also found in neighboring Ace Lake (in abundance) and in two tropical lakes (hypersaline and fresh), an estuary, and an ocean upwelling site. These findings indicate that virophages regulate host-virus interactions, influence overall carbon flux in Organic Lake, and play previously unrecognized roles in diverse aquatic ecosystems.
Collapse
Affiliation(s)
- Sheree Yau
- School of Biotechnology and Biomolecular Sciences
| | | | | | | | - Torsten Thomas
- School of Biotechnology and Biomolecular Sciences
- Centre for Marine Bio-Innovation, and
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, New South Wales 2052, Australia
| | | | | | | | - John A. Gibson
- Marine Research Laboratories, Tasmanian Aquaculture and Fisheries Institute, University of Tasmania, Hobart, Tasmania 7001, Australia
| | | |
Collapse
|
33
|
Abstract
The identification of inteins in viral genomes is becoming increasingly common. Inteins are selfish DNA elements found within coding regions of host proteins. Following translation, they catalyse their own excision and the formation of a peptide bond between the flanking protein regions. Many inteins also display homing endonuclease function. Here, the newly identified coccolithovirus intein is described and is predicted to have both self-splicing and homing endonuclease activity. The biochemical mechanism of its protein splicing activity is hypothesised, and the prevalence of the intein among natural coccolithovirus isolates is tested.
Collapse
Affiliation(s)
- Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.
| | | | | |
Collapse
|
34
|
Thiel G, Baumeister D, Schroeder I, Kast SM, Van Etten JL, Moroni A. Minimal art: or why small viral K(+) channels are good tools for understanding basic structure and function relations. Biochim Biophys Acta 2010; 1808:580-8. [PMID: 20417613 DOI: 10.1016/j.bbamem.2010.04.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/09/2010] [Accepted: 04/13/2010] [Indexed: 11/17/2022]
Abstract
Some algal viruses contain genes that encode proteins with the hallmarks of K(+) channels. One feature of these proteins is that they are less than 100 amino acids in size, which make them truly minimal for a K(+) channel protein. That is, they consist of only the pore module present in more complex K(+) channels. The combination of miniature size and the functional robustness of the viral K(+) channels make them ideal model systems for studying how K(+) channels work. Here we summarize recent structure/function correlates from these channels, which provide insight into functional properties such as gating, pharmacology and sorting in cells.
Collapse
Affiliation(s)
- Gerhard Thiel
- Institute of Botany, Technische Universität Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany.
| | | | | | | | | | | |
Collapse
|
35
|
Yanai-Balser GM, Duncan GA, Eudy JD, Wang D, Li X, Agarkova IV, Dunigan DD, Van Etten JL. Microarray analysis of Paramecium bursaria chlorella virus 1 transcription. J Virol 2010; 84:532-42. [PMID: 19828609 PMCID: PMC2798440 DOI: 10.1128/jvi.01698-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 10/07/2009] [Indexed: 11/20/2022] Open
Abstract
Paramecium bursaria chlorella virus 1 (PBCV-1), a member of the family Phycodnaviridae, is a large double-stranded DNA, plaque-forming virus that infects the unicellular green alga Chlorella sp. strain NC64A. The 330-kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To monitor global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDSs) was constructed. Competitive hybridization experiments were conducted by using cDNAs from poly(A)-containing RNAs obtained from cells at seven time points after virus infection. The results led to the following conclusions: (i) the PBCV-1 replication cycle is temporally programmed and regulated; (ii) 360 (99%) of the arrayed PBCV-1 CDSs were expressed at some time in the virus life cycle in the laboratory; (iii) 227 (62%) of the CDSs were expressed before virus DNA synthesis begins; (iv) these 227 CDSs were grouped into two classes: 127 transcripts disappeared prior to initiation of virus DNA synthesis (considered early), and 100 transcripts were still detected after virus DNA synthesis begins (considered early/late); (v) 133 (36%) of the CDSs were expressed after virus DNA synthesis begins (considered late); and (vi) expression of most late CDSs is inhibited by adding the DNA replication inhibitor, aphidicolin, prior to virus infection. This study provides the first comprehensive evaluation of virus gene expression during the PBCV-1 life cycle.
Collapse
Affiliation(s)
- Giane M. Yanai-Balser
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, Biology Department, Nebraska Wesleyan University, Lincoln, Nebraska 68504-2794, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198-5455, Statistics Department, University of Nebraska, Lincoln, Nebraska 68583-0963, Biomedical Engineering and Biotechnology, University of Massachusetts, Lowell, Massachusetts 01854, Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900
| | - Garry A. Duncan
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, Biology Department, Nebraska Wesleyan University, Lincoln, Nebraska 68504-2794, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198-5455, Statistics Department, University of Nebraska, Lincoln, Nebraska 68583-0963, Biomedical Engineering and Biotechnology, University of Massachusetts, Lowell, Massachusetts 01854, Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900
| | - James D. Eudy
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, Biology Department, Nebraska Wesleyan University, Lincoln, Nebraska 68504-2794, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198-5455, Statistics Department, University of Nebraska, Lincoln, Nebraska 68583-0963, Biomedical Engineering and Biotechnology, University of Massachusetts, Lowell, Massachusetts 01854, Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900
| | - Dong Wang
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, Biology Department, Nebraska Wesleyan University, Lincoln, Nebraska 68504-2794, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198-5455, Statistics Department, University of Nebraska, Lincoln, Nebraska 68583-0963, Biomedical Engineering and Biotechnology, University of Massachusetts, Lowell, Massachusetts 01854, Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900
| | - Xiao Li
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, Biology Department, Nebraska Wesleyan University, Lincoln, Nebraska 68504-2794, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198-5455, Statistics Department, University of Nebraska, Lincoln, Nebraska 68583-0963, Biomedical Engineering and Biotechnology, University of Massachusetts, Lowell, Massachusetts 01854, Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900
| | - Irina V. Agarkova
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, Biology Department, Nebraska Wesleyan University, Lincoln, Nebraska 68504-2794, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198-5455, Statistics Department, University of Nebraska, Lincoln, Nebraska 68583-0963, Biomedical Engineering and Biotechnology, University of Massachusetts, Lowell, Massachusetts 01854, Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900
| | - David D. Dunigan
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, Biology Department, Nebraska Wesleyan University, Lincoln, Nebraska 68504-2794, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198-5455, Statistics Department, University of Nebraska, Lincoln, Nebraska 68583-0963, Biomedical Engineering and Biotechnology, University of Massachusetts, Lowell, Massachusetts 01854, Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900
| | - James L. Van Etten
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, Biology Department, Nebraska Wesleyan University, Lincoln, Nebraska 68504-2794, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198-5455, Statistics Department, University of Nebraska, Lincoln, Nebraska 68583-0963, Biomedical Engineering and Biotechnology, University of Massachusetts, Lowell, Massachusetts 01854, Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900
| |
Collapse
|
36
|
Pagarete A, Allen MJ, Wilson WH, Kimmance SA, de Vargas C. Host-virus shift of the sphingolipid pathway along anEmiliania huxleyibloom: survival of the fattest. Environ Microbiol 2009; 11:2840-8. [PMID: 19638172 DOI: 10.1111/j.1462-2920.2009.02006.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- António Pagarete
- UPMC Univ. Paris 06, UMR 7144, Equipe EPPO: Evolution du Plancton et PaléoOcéans, Station Biologique de Roscoff, 29682 Roscoff, France
| | | | | | | | | |
Collapse
|
37
|
Weynberg KD, Allen MJ, Ashelford K, Scanlan DJ, Wilson WH. From small hosts come big viruses: the complete genome of a secondOstreococcus taurivirus, OtV-1. Environ Microbiol 2009; 11:2821-39. [PMID: 19650882 DOI: 10.1111/j.1462-2920.2009.01991.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karen D Weynberg
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, UK
| | | | | | | | | |
Collapse
|
38
|
Schroeder DC, Park Y, Yoon HM, Lee YS, Kang SW, Meints RH, Ivey RG, Choi TJ. Genomic analysis of the smallest giant virus--Feldmannia sp. virus 158. Virology 2009; 384:223-32. [PMID: 19054537 DOI: 10.1016/j.virol.2008.10.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 10/08/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
Genomic analysis of Feldmannia sp. virus 158, the second phaeovirus to be sequenced in its entirety, provides further evidence that large double-stranded DNA viruses share similar evolutionary pressures as cellular organisms. Reductive evolution is clearly evident within the phaeoviruses which occurred via several routes: the loss of genes from an ancestral virus core genome most likely through genetic drift; and as a result of relatively large recombination events that caused wholesale loss of genes. The entire genome is 154,641 bp in length and has 150 predicted coding sequences of which 87% have amino acid sequence similarities to other algal virus coding sequences within the family Phycodnaviridae. Significant similarities were found, for thirty eight coding sequences (25%), to genes in gene databanks that are known to be involved in processes that include DNA replication, DNA methylation, signal transduction, viral integration and transposition, and protein-protein interactions. Unsurprisingly, the greatest similarity was observed between the two known viruses that infect Feldmannia, indicating the taxonomic linkage of these two viruses with their hosts. Moreover, comparative analysis of phycodnaviral genomic sequences revealed the smallest set of core genes (10 out of a possible 31) required to make a functional nucleocytoplasmic large dsDNA virus.
Collapse
|
39
|
Abstract
The family Phycodnaviridae encompasses a diverse and rapidly expanding collection of large icosahedral, dsDNA viruses that infect algae. These lytic and lysogenic viruses have genomes ranging from 160 to 560 kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect them with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV). The phycodnaviruses have diverse genome structures, some with large regions of noncoding sequence and others with regions of ssDNA. The genomes of members in three genera in the Phycodnaviridae have been sequenced. The genome analyses have revealed more than 1000 unique genes, with only 14 homologous genes in common among the three genera of phycodnaviruses sequenced to date. Thus, their gene diversity far exceeds the number of so-called core genes. Not much is known about the replication of these viruses, but the consequences of these infections on phytoplankton have global affects, including influencing geochemical cycling and weather patterns.
Collapse
Affiliation(s)
- W H Wilson
- Bigelow Laboratory for Ocean Sciences, 180 McKown Point, P.O. Box 475, West Boothbay Harbor, ME 04575-0475, USA.
| | | | | |
Collapse
|
40
|
Iashchenko VV, Potekhin AA, Migunova AV, Kvitko KV, Rautian MS. [Identification of Chlorella viruses in Paramecium bursaria clones by pulse-field electrophoresis]. Mikrobiologiia 2008; 77:668-674. [PMID: 19004349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The ciliates Paramecium bursaria contain endosymbiotic green algae Chlorella spp. in their cytoplasm. The algae isolated from P. bursaria are sensitive to large DNA-containing viruses of the family Phycodnaviridae. The type virus of this family is PBCV-1 (Paramecium bursaria Chlorella virus). Investigation of the total DNA of P. bursaria clones by pulse-field electrophoresis (PEP) revealed a pronounced band on PEP profiles of some P. bursaria clones; the band was formed by DNA molecules of approx. 300 kb. This band probably contained the DNA of chlorella virus. Two approaches were used in the present work to confirm this hypothesis. Microbiological tests were used to scan a collection of P. bursaria clones for specific types of viruses; the 300-kb band was revealed only in the PEP profiles of virus-containing clones. Blot hybridization of P. bursaria total DNA separated by pulse-field electrophoresis with the virus-specific probe revealed that the band under study contained the DNA of a chlorella virus. Paramecium clones were shown to contain approx. 10(5) copies of nonintegrated viral DNA.
Collapse
|
41
|
Delaroque N, Boland W. The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses. BMC Evol Biol 2008; 8:110. [PMID: 18405387 PMCID: PMC2373305 DOI: 10.1186/1471-2148-8-110] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 04/12/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ectocarpus siliculosus virus-1 (EsV-1) is a lysogenic dsDNA virus belonging to the super family of nucleocytoplasmic large DNA viruses (NCLDV) that infect Ectocarpus siliculosus, a marine filamentous brown alga. Previous studies indicated that the viral genome is integrated into the host DNA. In order to find the integration sites of the viral genome, a genomic library from EsV-1-infected algae was screened using labelled EsV-1 DNA. Several fragments were isolated and some of them were sequenced and analyzed in detail. RESULTS Analysis revealed that the algal genome is split by a copy of viral sequences that have a high identity to EsV-1 DNA sequences. These fragments are interspersed with DNA repeats, pseudogenes and genes coding for products involved in DNA replication, integration and transposition. Some of these gene products are not encoded by EsV-1 but are present in the genome of other members of the NCLDV family. Further analysis suggests that the Ectocarpus algal genome contains traces of the integration of a large dsDNA viral genome; this genome could be the ancestor of the extant NCLDV genomes. Furthermore, several lines of evidence indicate that the EsV-1 genome might have originated in these viral DNA pieces, implying the existence of a complex integration and recombination system. A protein similar to a new class of tyrosine recombinases might be a key enzyme of this system. CONCLUSION Our results support the hypothesis that some dsDNA viruses are monophyletic and evolved principally through genome reduction. Moreover, we hypothesize that phaeoviruses have probably developed an original replication system.
Collapse
Affiliation(s)
- Nicolas Delaroque
- Max-Planck-Institut für Chemische Ökologie, Beutenberg Campus, Hans Knöll Str. 8, D - 07745 Jena, Germany
| | - Wilhelm Boland
- Max-Planck-Institut für Chemische Ökologie, Beutenberg Campus, Hans Knöll Str. 8, D - 07745 Jena, Germany
| |
Collapse
|
42
|
Meints RH, Ivey RG, Lee AM, Choi TJ. Identification of two virus integration sites in the brown alga Feldmannia chromosome. J Virol 2008; 82:1407-13. [PMID: 18032486 PMCID: PMC2224422 DOI: 10.1128/jvi.01983-07] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Accepted: 11/12/2007] [Indexed: 11/20/2022] Open
Abstract
Two similar, large double-stranded DNA viruses, Feldmannia species virus 158 (FsV-158) and FsV-178, replicate only in the unilocular reproductive cells (sporangia) of a brown filamentous alga in the genus Feldmannia. Virus particles are not present in vegetative cells but they are produced in the sporangia formed on vegetative filaments that have been transferred newly into culture. Thus, we proposed that these viruses exist in the vegetative cells in a latent form (R. G. Ivey, E. C. Henry, A. M. Lee, L. Klepper, S. K. Krueger, and R. H. Meints, Virology 220:267-273, 1996). In this article we present evidence that the two FsV genomes are integrated into the host genome during vegetative growth. The FsV genome integration sites were identified by cloning the regions where the FsV genome is linked to the host DNA. FsV-158 and FsV-178 are integrated into two distinct locations in the algal genome. In contrast, the integration sites in the two viral genomes are identical. Notably, the integration sites in the host and viruses contain GC and CG dinucleotide sequences, respectively, from which the GC sequences are recovered at both host-virus junctions. The splice sites in the two FsV genomes are predicted to form a stem-loop structure with the CG dinucleotide in the loop portion.
Collapse
Affiliation(s)
- Russel H Meints
- Department of Microbiology, Pukyong National University, 599-1, Daeyeon 3-Dong, Nam-Gu, Busan 608-737, South Korea
| | | | | | | |
Collapse
|
43
|
Gazzarrini S, Abenavoli A, Gradmann D, Thiel G, Moroni A. Electrokinetics of miniature K+ channel: open-state V sensitivity and inhibition by K+ driving force. J Membr Biol 2007; 214:9-17. [PMID: 17568981 DOI: 10.1007/s00232-006-0024-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2006] [Revised: 10/26/2006] [Indexed: 11/26/2022]
Abstract
Kcv, isolated from a Chlorella virus, is the smallest known K+ channel. When Kcv is expressed in Xenopus oocytes and exposed to 50 mM: [K+](o), its open-state current-voltage relationship (I-V) has the shape of a "tilted S" between -200 and +120 mV. Details of this shape depend on the conditioning voltage (V (c)) immediately before an I-V recording. Unexpectedly, the I-V relationships, recorded in different [K+](o), do intersect. These characteristics are numerically described here by fits of a kinetic model to the experimental data. In this model, the V (c) sensitivity of I-V is mainly assigned to an affinity increase of external K+ association at more positive voltages. The general, tilted-S shape as well as the unexpected intersections of the I-V relationships are kinetically described by a decrease of the cord conductance by the electrochemical driving force for K+ in either direction, like in fast V-dependent blocking by competing ions.
Collapse
Affiliation(s)
- Sabrina Gazzarrini
- Department of Biology and IBF-CNR, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | | | | | | | | |
Collapse
|
44
|
Fitzgerald LA, Graves MV, Li X, Hartigan J, Pfitzner AJP, Hoffart E, Van Etten JL. Sequence and annotation of the 288-kb ATCV-1 virus that infects an endosymbiotic chlorella strain of the heliozoon Acanthocystis turfacea. Virology 2007; 362:350-61. [PMID: 17276475 PMCID: PMC2018652 DOI: 10.1016/j.virol.2006.12.028] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 11/16/2006] [Accepted: 12/24/2006] [Indexed: 11/25/2022]
Abstract
Acanthocystis turfacea chlorella virus (ATCV-1), a prospective member of the family Phycodnaviridae, genus Chlorovirus, infects a unicellular, eukaryotic, chlorella-like green alga, Chlorella SAG 3.83, that is a symbiont in the heliozoon A. turfacea. The 288,047-bp ATCV-1 genome is the first virus to be sequenced that infects Chlorella SAG 3.83. ATCV-1 contains 329 putative protein-encoding and 11 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands and intergenic space is minimal. Thirty-four percent of the viral gene products resemble entries in the public databases, including some that are unexpected for a virus. For example, these unique gene products include ribonucleoside-triphosphate reductase, dTDP-d-glucose 4,6 dehydratase, potassium ion transporter, aquaglyceroporin, and mucin-desulfating sulfatase. Comparison of ATCV-1 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that about 80% of the ATCV-1 genes are present in PBCV-1.
Collapse
Affiliation(s)
- Lisa A Fitzgerald
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | | | | | | | | | | | | |
Collapse
|
45
|
Abstract
The diversity among the coccolithovirus strains held in the Plymouth Virus Collection (PVC) was assessed using three complementary techniques: phylogeny based on DNA polymerase and major capsid protein gene sequence; host range; and a new, microarray-based genome-wide approach. The PVC is composed of three groups of strains that are geographically and temporally distinct. Virus strains clustered according to these groups in all three diversity assessments. Furthermore, the microarray approach based on genomic content showed that two strains, previously considered as identical to others in the PVC, are actually distinct. These results show the importance of genome-wide surveys for assessing strain diversity. Not only has the microarray provided an alternative to the phylogeny-derived pattern for virus evolution, it has also begun to provide some clues to the genes that may be responsible for the different phenotypes displayed by these viruses.
Collapse
Affiliation(s)
- Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | | | | | | | | |
Collapse
|
46
|
Park Y, Kim GD, Choi TJ. Molecular cloning and characterization of the DNA adenine methyltransferase gene in Feldmannia sp. virus. Virus Genes 2007; 34:177-83. [PMID: 17180708 DOI: 10.1007/s11262-006-0059-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 11/16/2006] [Indexed: 11/26/2022]
Abstract
The genome of Feldmannia sp. virus (FsV), a marine brown alga virus, contains a putative DNA adenine methyltransferase (dam) gene of 1,245 bp that encodes a polypeptide of 45.8 kDa. A BLAST search with the FsV dam gene showed high amino acid identity to two putative methyltransferase genes, ORF B29 of Feldmannia irregularis virus (FirrV, 54%) and ORF129 of Ectocarpus siliculosus virus (EsV, 36%); and a PSI BLAST search revealed similarity to the N(6)-adenine methyltransferases (MTases) of other species. Most conserved motifs of beta-class MTases were observed in the FsV dam gene. However, neither of the highly conserved sequences in motifs I (FxGxG) or IV [(S/N/D)PP(Y/F/W)] perfectly matched those in the FsV dam gene. The highly conserved DPPY consensus sequence in motif IV was NTPW in the FsV dam gene, perfectly matching the sequences in ORF B29 of FirrV and ORF129 of EsV. Therefore, the dam genes in brown algae viruses may belong to a yet undiscovered group. The FsV Dam protein expressed from the cloned FsV dam gene methylated E. coli chromosomal DNA. This is the first report showing that a virus infecting marine filamentous brown algae encodes a functional Dam protein.
Collapse
Affiliation(s)
- Yunjung Park
- Department of Microbiology, Pukyong National University, 599-1, Daeyeon 3-Dong, Busan, South Korea.
| | | | | |
Collapse
|
47
|
Shim JW, Yang M, Gu LQ. In vitro synthesis, tetramerization and single channel characterization of virus-encoded potassium channel Kcv. FEBS Lett 2007; 581:1027-34. [PMID: 17316630 DOI: 10.1016/j.febslet.2007.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 02/02/2007] [Accepted: 02/02/2007] [Indexed: 10/23/2022]
Abstract
Chlorella virus-encoded membrane protein Kcv represents a new class of potassium channel. This 94-amino acids miniature K(+) channel consists of two trans-membrane alpha-helix domains intermediated by a pore domain that contains a highly conserved K(+) selectivity filter. Therefore, as an archetypal K(+) channel, the study of Kcv may yield valuable insights into the structure-function relationships underlying this important class of ion channel. Here, we report a series of new properties of Kcv. We first verified Kcv can be synthesized in vitro. By co-synthesis and assembly of wild-type and the tagged version of Kcv, we were able to demonstrate a tetrameric stoichiometry, a molecular structure adopted by all known K(+) channels. Most notably, the tetrameric Kcv complex retains its functional integrity in SDS (strong detergent)-containing solutions, a useful feature that allows for direct purification of protein from polyacrylamide gel. Once purified, the tetramer can form single potassium-selective ion channels in a lipid bilayer with functions consistent to the heterologously expressed Kcv. These finding suggest that the synthetic Kcv can serve as a model of virus-encoded K(+) channels; and its newly identified properties can be applied to the future study on structure-determined mechanisms such as K(+) channel functional stoichiometry.
Collapse
Affiliation(s)
- Ji Wook Shim
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA
| | | | | |
Collapse
|
48
|
Abstract
The miniature viral K+ channel Kcv represents the pore module of all K+ channels. A synthetic gene of Kcv with an elevated GC content compared to that of the wild-type gene was expressed heterologously in Pichia pastoris, and the purified protein was functionally reconstituted into liposomes. Biochemical assays reveal a remarkable cation selective stability of the channel tetramer via SDS-PAGE. Only cations, which permeate Kcv, were able to protect the oligomer against disassembly into monomers at high temperatures. Electrophysiological characterization of the single Kcv channel reveals a saturating conductance (lambda(max)) of 360 pS; the single-channel current-voltage relation was strongly rectifying with a negative slope conductance at extreme voltages. The channel was highly selective for K+ and was blocked by Ba2+ and in a side specific manner by Na+ and Cs+ also. The channel conducted Rb+, but as a consequence, the channel was shifted into a hyperactive state. We conclude that specific binding interactions of cations in the conductive pathway are an important determinant of channel stability and function.
Collapse
Affiliation(s)
- Cinzia Pagliuca
- Dipartimento di Biologia e IBF-CNR, Universitá degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | | | | | | | | | | |
Collapse
|
49
|
Baumann S, Sander A, Gurnon JR, Yanai-Balser G, VanEtten JL, Piotrowski M. Chlorella viruses contain genes encoding a complete polyamine biosynthetic pathway. Virology 2006; 360:209-17. [PMID: 17101165 PMCID: PMC1971760 DOI: 10.1016/j.virol.2006.10.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 10/02/2006] [Accepted: 10/04/2006] [Indexed: 11/27/2022]
Abstract
Two genes encoding the putative polyamine biosynthetic enzymes agmatine iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase (CPA) were cloned from the chloroviruses PBCV-1, NY-2A and MT325. They were expressed in Escherichia coli to form C-terminal (His)6-tagged proteins and the recombinant proteins were purified by Ni2+-binding affinity chromatography. The biochemical properties of the two enzymes are similar to AIH and CPA enzymes from Arabidopsis thaliana and Pseudomonas aeruginosa. Together with the previously known virus genes encoding ornithine/arginine decarboxlyase (ODC/ADC) and homospermidine synthase, the chloroviruses have genes that encode a complete set of functional enzymes that synthesize the rare polyamine homospermidine from arginine via agmatine, N-carbamoylputrescine and putrescine. The PBCV-1 aih and cpa genes are expressed early during virus infection together with the odc/adc gene, suggesting that biosynthesis of putrescine is important in early stages of viral replication. The aih and cpa genes are widespread in the chlorella viruses.
Collapse
Affiliation(s)
- Sascha Baumann
- Department of Plant Physiology, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Adrianne Sander
- Department of Plant Physiology, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - James R. Gurnon
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583-0722, USA
| | - Giane Yanai-Balser
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583-0722, USA
| | - James L. VanEtten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583-0722, USA
| | - Markus Piotrowski
- Department of Plant Physiology, Ruhr-Universität Bochum, 44780 Bochum, Germany
| |
Collapse
|
50
|
Han G, Gable K, Yan L, Allen MJ, Wilson WH, Moitra P, Harmon JM, Dunn TM. Expression of a novel marine viral single-chain serine palmitoyltransferase and construction of yeast and mammalian single-chain chimera. J Biol Chem 2006; 281:39935-42. [PMID: 17090526 DOI: 10.1074/jbc.m609365200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The genus Coccolithovirus is a recently discovered group of viruses that infect the globally important marine calcifying microalga Emiliania huxleyi. Surprisingly, the viral genome contains a cluster of putative sphingolipid biosynthetic genes not found in other viral genus. To address the role of these genes in viral pathogenesis, the ehv050 gene predicted to encode a serine palmitoyltransferase (SPT), the first and rate-limiting enzyme of sphingolipid biosynthesis, was expressed and characterized in Saccharomyces cerevisiae. We show that the encoded protein is indeed a fully functional, endoplasmic reticulum-localized, single-chain SPT. In eukaryotes SPT is a heterodimer comprised of long chain base 1 (LCB1) and LCB2 subunits. Sequence alignment and mutational analysis showed that the N-terminal domain of the viral protein most closely resembled the LCB2 subunit and the C-terminal domain most closely resembled the LCB1 subunit. Regardless of whether the viral protein was expressed as a single polypeptide or as two independent domains, it exhibited an unusual preference for myristoyl-CoA rather than palmitoyl-CoA. This preference was reflected by the increased presence of C16-sphingoid bases in yeast cells expressing the viral protein. The occurrence of a single-chain SPT suggested to us that it might be possible to create other fusion SPTs with unique properties. Remarkably, when the two subunits of the yeast SPT were thus expressed, the single-chain chimera was functional and displayed a novel substrate preference. This suggests that expression of other multisubunit membrane proteins as single-chain chimera could provide a powerful approach to the characterization of integral membrane proteins.
Collapse
Affiliation(s)
- Gongshe Han
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20184, USA
| | | | | | | | | | | | | | | |
Collapse
|