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Yakubovskaya E, Zaliznyak T, Martínez JM, Taylor GT. Raman Microspectroscopy Goes Viral: Infection Dynamics in the Cosmopolitan Microalga, Emiliania huxleyi. Front Microbiol 2021; 12:686287. [PMID: 34795644 PMCID: PMC8593419 DOI: 10.3389/fmicb.2021.686287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022] Open
Abstract
Emiliania huxleyi is a cosmopolitan member of the marine phytoplankton. This species’ capacities for carbon sequestration and sulfur mobilization make it a key player in oceanic biogeochemical cycles that influence climate on a planetary scale. Seasonal E. huxleyi blooms are abruptly terminated by viral epidemics caused by a clade of large DNA viruses collectively known as coccolithoviruses (EhVs). EhVs thereby mediate a significant part of material and energy fluxes associated with E. huxleyi population dynamics. In this study, we use spontaneous Raman microspectroscopy to perform label-free and non-invasive measurements of the macromolecular composition of individual virions and E. huxleyi host cells. Our novel autofluorescence suppression protocol enabled spectroscopic visualization of evolving macromolecular redistributions in individual E. huxleyi cells at different stages of EhV infection. Material transfer from E. huxleyi hosts to single EhV-163 virions was confirmed by combining stable isotope probing (SIP) experiments with Raman microspectroscopy. Inheritance of the host cells’ 13C-enriched isotopic signature was quantified based on red shifts of Raman peaks characteristic of phenylalanine’s phenyl ring. Two-dimensional Raman mapping of EhV-infected E. huxleyi cells revealed that the compact region producing an intense Raman DNA signal (i.e., the nucleus) in healthy E. huxleyi cells becomes diffuse during the first hours of infection. Raman DNA emissions integrated throughout individual cells decreased during the infection cycle. Our observations are consistent with EhV-163 degrading the host’s nuclear DNA, scavenging released nucleotides for its own genome replication, and shedding newly-produced virions prior to host lysis via budding.
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Affiliation(s)
- Elena Yakubovskaya
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Tatiana Zaliznyak
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | | | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
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2
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Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol 2019; 18:21-34. [PMID: 31690825 DOI: 10.1038/s41579-019-0270-x] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2019] [Indexed: 12/23/2022]
Abstract
Ecosystems are controlled by 'bottom-up' (resources) and 'top-down' (predation) forces. Viral infection is now recognized as a ubiquitous top-down control of microbial growth across ecosystems but, at the same time, cell death by viral predation influences, and is influenced by, resource availability. In this Review, we discuss recent advances in understanding the biogeochemical impact of viruses, focusing on how metabolic reprogramming of host cells during lytic viral infection alters the flow of energy and nutrients in aquatic ecosystems. Our synthesis revealed several emerging themes. First, viral infection transforms host metabolism, in part through virus-encoded metabolic genes; the functions performed by these genes appear to alleviate energetic and biosynthetic bottlenecks to viral production. Second, viral infection depends on the physiological state of the host cell and on environmental conditions, which are challenging to replicate in the laboratory. Last, metabolic reprogramming of infected cells and viral lysis alter nutrient cycling and carbon export in the oceans, although the net impacts remain uncertain. This Review highlights the need for understanding viral infection dynamics in realistic physiological and environmental contexts to better predict their biogeochemical consequences.
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Affiliation(s)
- Amy E Zimmerman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | | | - David M Needham
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Seth G John
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.
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3
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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] [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.
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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.
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4
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Maruyama F, Ueki S. Evolution and Phylogeny of Large DNA Viruses, Mimiviridae and Phycodnaviridae Including Newly Characterized Heterosigma akashiwo Virus. Front Microbiol 2016; 7:1942. [PMID: 27965659 PMCID: PMC5127864 DOI: 10.3389/fmicb.2016.01942] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 11/18/2016] [Indexed: 11/13/2022] Open
Abstract
Nucleocytoplasmic DNA viruses are a large group of viruses that harbor double-stranded DNA genomes with sizes of several 100 kbp, challenging the traditional concept of viruses as small, simple ‘organisms at the edge of life.’ The most intriguing questions about them may be their origin and evolution, which have yielded the variety we see today. Specifically, the phyletic relationship between two giant dsDNA virus families that are presumed to be close, Mimiviridae, which infect Acanthamoeba, and Phycodnaviridae, which infect algae, is still obscure and needs to be clarified by in-depth analysis. Here, we studied Mimiviridae–Phycodnaviridae phylogeny including the newly identified Heterosigma akashiwo virus strain HaV53. Gene-to-gene comparison of HaV53 with other giant dsDNA viruses showed that only a small proportion of HaV53 genes show similarities with the others, revealing its uniqueness among Phycodnaviridae. Phylogenetic/genomic analysis of Phycodnaviridae including HaV53 revealed that the family can be classified into four distinctive subfamilies, namely, Megaviridae (Mimivirus-like), Chlorovirus-type, and Coccolitho/Phaeovirus-type groups, and HaV53 independent of the other three groups. Several orthologs found in specific subfamilies while absent from the others were identified, providing potential family marker genes. Finally, reconstruction of the evolutionary history of Phycodnaviridae and Mimiviridae revealed that these viruses are descended from a common ancestor with a small set of genes and reached their current diversity by differentially acquiring gene sets during the course of evolution. Our study illustrates the phylogeny and evolution of Mimiviridae–Phycodnaviridae and proposes classifications that better represent phyletic relationships among the family members.
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Affiliation(s)
- Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Shoko Ueki
- Institute of Plant Science and Resources, Okayama University Kurashiki, Japan
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5
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Nissimov JI, Napier JA, Allen MJ, Kimmance SA. Intragenus competition between coccolithoviruses: an insight on how a select few can come to dominate many. Environ Microbiol 2015; 18:133-45. [PMID: 25970076 DOI: 10.1111/1462-2920.12902] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 03/20/2015] [Accepted: 05/04/2015] [Indexed: 11/27/2022]
Abstract
Viruses are a major cause of coccolithophore bloom demise in both temperate and sub-temperate oceanic regions. Most infection studies on coccolithoviruses have been conducted with a single virus strain, and the effect of intragenus competition by closely related coccolithoviruses has been ignored. Here we conducted combined infection experiments, infecting Emiliania huxleyi CCMP 2090 with two coccolithoviruses: EhV-86 and EhV-207 both simultaneously and independently. EhV-207 displayed a shorter lytic cycle and increased production potential than EhV-86 and was remarkably superior under competitive conditions. Although the viruses displayed identical adsorption kinetics in the first 2 h post infection, EhV-207 gained a numerical advantage as early as 8 h post infection. Quantitative polymerase chain reaction (PCR) revealed that when infecting in combination, EhV-207 was not affected by the presence of EhV-86, whereas EhV-86 was quickly out-competed, and a significant reduction in free and cell-associated EhV-86 was seen as early as 2 days after the initial infection. The observation of such clear phenotypic differences between genetically distinct, yet similar, coccolithovirus strains, by flow cytometry and quantitative real-time PCR allowed tentative links to the burgeoning genomic, transcriptomic and metabolic data to be made and the factors driving their selection, in particular to the de novo coccolithovirus-encoded sphingolipid biosynthesis pathway. This work illustrates that, even within a family, not all viruses are created equally, and the potential exists for relatively small genetic changes to infer disproportionately large competitive advantages for one coccolithovirus over another, ultimately leading to a few viruses dominating the many.
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Affiliation(s)
- Jozef I Nissimov
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Johnathan A Napier
- Department of Biological Chemistry, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Susan A Kimmance
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
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6
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Rosenwasser S, Mausz MA, Schatz D, Sheyn U, Malitsky S, Aharoni A, Weinstock E, Tzfadia O, Ben-Dor S, Feldmesser E, Pohnert G, Vardi A. Rewiring Host Lipid Metabolism by Large Viruses Determines the Fate of Emiliania huxleyi, a Bloom-Forming Alga in the Ocean. THE PLANT CELL 2014; 26:2689-2707. [PMID: 24920329 PMCID: PMC4114960 DOI: 10.1105/tpc.114.125641] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/07/2014] [Accepted: 05/26/2014] [Indexed: 05/21/2023]
Abstract
Marine viruses are major ecological and evolutionary drivers of microbial food webs regulating the fate of carbon in the ocean. We combined transcriptomic and metabolomic analyses to explore the cellular pathways mediating the interaction between the bloom-forming coccolithophore Emiliania huxleyi and its specific coccolithoviruses (E. huxleyi virus [EhV]). We show that EhV induces profound transcriptome remodeling targeted toward fatty acid synthesis to support viral assembly. A metabolic shift toward production of viral-derived sphingolipids was detected during infection and coincided with downregulation of host de novo sphingolipid genes and induction of the viral-encoded homologous pathway. The depletion of host-specific sterols during lytic infection and their detection in purified virions revealed their novel role in viral life cycle. We identify an essential function of the mevalonate-isoprenoid branch of sterol biosynthesis during infection and propose its downregulation as an antiviral mechanism. We demonstrate how viral replication depends on the hijacking of host lipid metabolism during the chemical "arms race" in the ocean.
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Affiliation(s)
- Shilo Rosenwasser
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michaela A Mausz
- Institute of Inorganic and Analytical Chemistry/Bioorganic Analytics, Friedrich Schiller University Jena, 07743 Jena, Germany Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Daniella Schatz
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uri Sheyn
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal Weinstock
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Oren Tzfadia
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ester Feldmesser
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry/Bioorganic Analytics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Assaf Vardi
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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7
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Permanent draft genomes of four new coccolithoviruses: EhV-18, EhV-145, EhV-156 and EhV-164. Mar Genomics 2014; 15:7-8. [PMID: 24631268 DOI: 10.1016/j.margen.2014.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 02/18/2014] [Accepted: 02/26/2014] [Indexed: 11/21/2022]
Abstract
Coccolithoviruses infect the marine coccolithophorid microalga Emiliania huxleyi. Here, we describe the genomes of four new coccolithoviruses isolated from UK coastal locations. Of particular interest, EhV-18 and EhV-145 encode serine palmitoyltransferase function via two distinct genes, whereas all other coccolithoviruses have SPT as a gene fusion of LCB1/LCB2 domains.
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8
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Nissimov JI, Jones M, Napier JA, Munn CB, Kimmance SA, Allen MJ. Functional inferences of environmental coccolithovirus biodiversity. Virol Sin 2013; 28:291-302. [PMID: 24006045 DOI: 10.1007/s12250-013-3362-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/12/2013] [Indexed: 11/25/2022] Open
Abstract
The cosmopolitan calcifying alga Emiliania huxleyi is one of the most abundant bloom forming coccolithophore species in the oceans and plays an important role in global biogeochemical cycling. Coccolithoviruses are a major cause of coccolithophore bloom termination and have been studied in laboratory, mesocosm and open ocean studies. However, little is known about the dynamic interactions between the host and its viruses, and less is known about the natural diversity and role of functionally important genes within natural coccolithovirus communities. Here, we investigate the temporal and spatial distribution of coccolithoviruses by the use of molecular fingerprinting techniques PCR, DGGE and genomic sequencing. The natural biodiversity of the virus genes encoding the major capsid protein (MCP) and serine palmitoyltransferase (SPT) were analysed in samples obtained from the Atlantic Meridional Transect (AMT), the North Sea and the L4 site in the Western Channel Observatory. We discovered nine new coccolithovirus genotypes across the AMT and L4 site, with the majority of MCP sequences observed at the deep chlorophyll maximum layer of the sampled sites on the transect. We also found four new SPT gene variations in the North Sea and at L4. Their translated fragments and the full protein sequence of SPT from laboratory strains EhV-86 and EhV-99B1 were modelled and revealed that the theoretical fold differs among strains. Variation identified in the structural distance between the two domains of the SPT protein may have an impact on the catalytic capabilities of its active site. In summary, the combined use of 'standard' markers (i.e. MCP), in combination with metabolically relevant markers (i.e. SPT) are useful in the study of the phylogeny and functional biodiversity of coccolithoviruses, and can provide an interesting intracellular insight into the evolution of these viruses and their ability to infect and replicate within their algal hosts.
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Affiliation(s)
- Jozef I Nissimov
- Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK
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9
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Pagarete A, Lanzén A, Puntervoll P, Sandaa RA, Larsen A, Larsen JB, Allen MJ, Bratbak G. Genomic sequence and analysis of EhV-99B1, a new coccolithovirus from the Norwegian fjords. Intervirology 2012; 56:60-6. [PMID: 22986606 DOI: 10.1159/000341611] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/02/2012] [Indexed: 11/19/2022] Open
Abstract
Coccolithoviruses are giant dsDNA viruses that infect Emiliania huxleyi, the most ubiquitous marine microalga. Here, we present the genome of the latest coccolithovirus strain to be sequenced, EhV-99B1, and compare it with two other coccolithovirus genomes (EhV-86 and EhV-163). EhV-99B1 shares a pairwise nucleotide identity of 98% with EhV-163 (the two strains were isolated from the same Norwegian fjord but in different years), and just 96.5% with EhV-86 (isolated in the same spring as EhV-99B1 but in the English Channel). We confirmed and extended the list of relevant genomic differences between these EhVs from the Norwegian fjord and EhVs from the English Channel, namely the removal/insertions of: a phosphate permease, an endonuclease, a transposase, and two specific tRNAs. As a whole, this study provided new clues and insights into the diversity and mechanisms driving the evolution of these large oceanic viruses, in particular those processes involving selfish genetic elements.
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Affiliation(s)
- A Pagarete
- Department of Biology, University of Bergen, NO–5006 Bergen, Norway.
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10
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Abstract
Emiliania huxleyi virus 202 (EhV-202) is a member of the Coccolithoviridae, a group of viruses that infect the marine coccolithophorid Emiliania huxleyi. EhV-202 has a 160- to 180-nm-diameter icosahedral structure and a genome of approximately 407 kbp, consisting of 485 coding sequences (CDSs). Here we describe the genomic features of EhV-202, together with a draft genome sequence and its annotation, highlighting the homology and heterogeneity of this genome in comparison with the EhV-86 reference genome.
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Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ. Draft genome sequence of the coccolithovirus EhV-84. Stand Genomic Sci 2011; 5:1-11. [PMID: 22180805 PMCID: PMC3236045 DOI: 10.4056/sigs.1884581] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Coccolithoviridae is a recently discovered group of viruses that infect the marine coccolithophorid Emiliania huxleyi. Emiliania huxleyi virus 84 (EhV-84) has a 160 -180 nm diameter icosahedral structure and a genome of approximately 400 kbp. Here we describe the structural and genomic features of this virus, together with a near complete draft genome sequence (~99%) and its annotation. This is the fourth genome sequence of a member of the coccolithovirus family.
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Affiliation(s)
- Jozef I. Nissimov
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Charlotte A. Worthy
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
- Department of Biological Chemistry, Rothamsted Research, Harpenden, Herts AL5
| | - Paul Rooks
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Johnathan A. Napier
- Department of Biological Chemistry, Rothamsted Research, Harpenden, Herts AL5
| | - Susan A. Kimmance
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Matthew R Henn
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
| | - Hiroyuki Ogata
- Structural and Genomic Information Laboratory, CNRS-UPR2589, Mediterranean Institute of Microbiology (IFR-88), Aix-Marseille University, 163 avenue de Luminy Case 934, FR-13288 Marseille, France
| | - Michael J. Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
- Corresponding author: Michael J. Allen ()
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Pagarete A, Corguillé G, Tiwari B, Ogata H, Vargas C, Wilson WH, Allen MJ. Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms. FEMS Microbiol Ecol 2011; 78:555-64. [PMID: 22066669 DOI: 10.1111/j.1574-6941.2011.01191.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 08/01/2011] [Accepted: 08/12/2011] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Gildas Corguillé
- CNRS/UMPC, FR2424; Service Informatique et Génomique; Station Biologique; Roscoff; France
| | - Bela Tiwari
- NERC Environmental Bioinformatics Centre; Centre for Ecology and Hydrology; Wallingford; UK
| | - Hiroyuki Ogata
- Structural and Genomic Information Laboratory; CNRS-UPR2589; Mediterranean Institute of Microbiology (IFR-88); Aix-Marseille University; Marseille; France
| | - Colomban Vargas
- Equipe EPPO-Evolution du Plancton et PaléoOcéans; CNRS-UMR7144; Université Pierre et Marie Curie; Station Biologique; Roscoff; France
| | - William H. Wilson
- Bigelow Laboratory for Ocean Sciences; West Boothbay Harbor; ME; USA
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13
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Allen MJ, Lanzén A, Bratbak G. Characterisation of the coccolithovirus intein. Mar Genomics 2010; 4:1-7. [PMID: 21429459 DOI: 10.1016/j.margen.2010.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 11/17/2022]
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.
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Affiliation(s)
- Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK.
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14
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Bellec L, Grimsley N, Derelle E, Moreau H, Desdevises Y. Abundance, spatial distribution and genetic diversity of Ostreococcus tauri viruses in two different environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:313-21. [PMID: 23766083 DOI: 10.1111/j.1758-2229.2010.00138.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Although large DNA viruses of eukaryotic algae represent a major force in shaping populations of plankton, knowledge about them is often limited to their overall diversity, abundance, and the flux of their constituent matter between ecosystem compartments. In order to gain insight about the genetics and structure of such populations, we used an easily cultivable model unicellular algal species, Ostreococcus tauri (Prasinophyceae), to monitor and compare populations of viruses in different marine environments. The abundance of O. tauri viruses showed very large temporal fluctuations, but remarkably was more than two orders of magnitude higher in lagoons than in coastal waters. We analysed 161 individual viruses found after plating out for lysis plaques on the host during a time series of water samplings. The haplotypes of viruses infecting our host strain were determined by sequence analysis of the partial DNA polymerase gene, permitting a spatiotemporal analysis of their population structure. We found 48 haplotypes, only the two most abundant ones being shared among all of the three study sites (lagoon, coastal and offshore), supporting the hypothesis that there is great diversity among the viruses infecting one host strain. However, our data suggest that the population structure differ between lagoons and coastal sea.
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Affiliation(s)
- Laure Bellec
- UPMC Univ Paris 06 and CNRS, UMR 7621, Observatoire océanologique, 66650, Banyuls-sur-Mer, France
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15
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Monier A, Pagarete A, de Vargas C, Allen MJ, Read B, Claverie JM, Ogata H. Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res 2009; 19:1441-9. [PMID: 19451591 DOI: 10.1101/gr.091686.109] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Interactions between viruses and phytoplankton, the main primary producers in the oceans, affect global biogeochemical cycles and climate. Recent studies are increasingly revealing possible cases of gene transfers between cyanobacteria and phages, which might have played significant roles in the evolution of cyanobacteria/phage systems. However, little has been documented about the occurrence of horizontal gene transfer in eukaryotic phytoplankton/virus systems. Here we report phylogenetic evidence for the transfer of seven genes involved in the sphingolipid biosynthesis pathway between the cosmopolitan eukaryotic microalga Emiliania huxleyi and its large DNA virus EhV. PCR assays indicate that these genes are prevalent in E. huxleyi and EhV strains isolated from different geographic locations. Patterns of protein and gene sequence conservation support that these genes are functional in both E. huxleyi and EhV. This is the first clear case of horizontal gene transfer of multiple functionally linked enzymes in a eukaryotic phytoplankton-virus system. We examine arguments for the possible direction of the gene transfer. The virus-to-host direction suggests the existence of ancient viruses that controlled the complex metabolic pathway in order to infect primitive eukaryotic cells. In contrast, the host-to-virus direction suggests that the serial acquisition of genes involved in the same metabolic pathway might have been a strategy for the ancestor of EhVs to stay ahead of their closest relatives in the great evolutionary race for survival.
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Affiliation(s)
- Adam Monier
- Structural and Genomic Information Laboratory, CNRS-UPR2589, Mediterranean Institute of Microbiology (IFR-88), Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France
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16
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Bellec L, Grimsley N, Moreau H, Desdevises Y. Phylogenetic analysis of new Prasinoviruses (Phycodnaviridae) that infect the green unicellular algae Ostreococcus, Bathycoccus and Micromonas. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:114-123. [PMID: 23765742 DOI: 10.1111/j.1758-2229.2009.00015.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Viruses play an important role in the regulation of phytoplankton populations. In the Mediterranean Sea, prasinophyte green algae are abundant and widespread, and within this group the genera Bathycoccus, Micromonas and Ostreococcus (Mamiellales) are the most common. Although these organisms constitute a significant part of the marine ecosystem, little is known about the viruses infecting them. We showed that double-stranded DNA viruses, likely members of the Phycodnaviridae family, can infect and grow in different host laboratory prasinophyte strains. Different pairs of degenerate primers were designed to PCR amplify a region of the conserved viral polymerase gene in order to characterize these viral strains. Twenty-seven new viral strains from five different host strains were thus analysed. We established phylogenetic trees for the hosts (18S) and their associated viruses (partial polymerase gene) and discuss the taxonomic significance of Phycodnaviridae. Within eukaryotic double-stranded DNA viruses, we showed that viruses from Bathycoccus, Micromonas and Ostreococcus form a monophyletic group that we refer to as 'Prasinovirus'.
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Affiliation(s)
- Laure Bellec
- UPMC Univ Paris 06 and CNRS, FRE3247, Observatoire océanologique, F-66651, Banyuls-sur-Mer, France
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Wilson WH, Van Etten JL, Allen MJ. The Phycodnaviridae: the story of how tiny giants rule the world. Curr Top Microbiol Immunol 2009; 328:1-42. [PMID: 19216434 DOI: 10.1007/978-3-540-68618-7_1] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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.
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Affiliation(s)
- W H Wilson
- Bigelow Laboratory for Ocean Sciences, 180 McKown Point, P.O. Box 475, West Boothbay Harbor, ME 04575-0475, USA.
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Aquatic virus diversity accessed through omic techniques: a route map to function. Curr Opin Microbiol 2008; 11:226-32. [PMID: 18554975 DOI: 10.1016/j.mib.2008.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 05/07/2008] [Accepted: 05/08/2008] [Indexed: 11/22/2022]
Abstract
Viruses are arguably the simplest form of life yet they play a crucial role in regulating planetary processes. From shuttling genes to 'lubricating' microbial loop dynamics, viruses are integral in shaping microbial ecology. In every environment on Earth the role of viruses goes far beyond the simple infect-replicate-kill cycle. Their enormous abundance and seemingly infinite diversity provide the vital clues to the true function of viruses. New 'omic' approaches are now allowing researchers to gain extraordinary insights into virus diversity and inferred function, particularly within aquatic environments. The development of molecular markers and application of techniques including microarrays, metagenomic sequencing and proteomic analysis are now being applied to virus communities. Despite this shift towards culture-independent approaches it has proved difficult to derive useful information about infection strategies since so much of the sequence information has no database matches. Future advances will involve tools such as microarrays to help determine the functionality of unknown genes. Sequence information should be considered as a starting point for asking questions and developing hypotheses about the role of viruses. It is an exciting new era for virus ecology and when used in combination with more traditional approaches, virus genomics will give us access to their ecological function on an unprecedented scale.
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Derelle E, Ferraz C, Escande ML, Eychenié S, Cooke R, Piganeau G, Desdevises Y, Bellec L, Moreau H, Grimsley N. Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri. PLoS One 2008; 3:e2250. [PMID: 18509524 PMCID: PMC2386258 DOI: 10.1371/journal.pone.0002250] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Accepted: 04/02/2008] [Indexed: 12/22/2022] Open
Abstract
Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon.
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Affiliation(s)
- Evelyne Derelle
- Université Pierre et Marie Curie-Paris 06, Laboratoire Arago, Banyuls-sur-Mer, France
- CNRS, UMR7628, Laboratoire Arago, Banyuls-sur-Mer, France
| | - Conchita Ferraz
- Institut de Génétique Humaine, Génopole Montpellier Languedoc-Roussillon, UPR1142, Montpellier, France
| | - Marie-Line Escande
- Université Pierre et Marie Curie-Paris 06, Laboratoire Arago, Banyuls-sur-Mer, France
- CNRS, UMR7628, Laboratoire Arago, Banyuls-sur-Mer, France
| | - Sophie Eychenié
- Institut de Génétique Humaine, Génopole Montpellier Languedoc-Roussillon, UPR1142, Montpellier, France
| | - Richard Cooke
- Génopole Languedoc-Roussillon, Génome et Développement de Plantes, UMR5096, Perpignan, France
| | - Gwenaël Piganeau
- Université Pierre et Marie Curie-Paris 06, Laboratoire Arago, Banyuls-sur-Mer, France
- CNRS, UMR7628, Laboratoire Arago, Banyuls-sur-Mer, France
| | - Yves Desdevises
- Université Pierre et Marie Curie-Paris 06, Laboratoire Arago, Banyuls-sur-Mer, France
| | - Laure Bellec
- Université Pierre et Marie Curie-Paris 06, Laboratoire Arago, Banyuls-sur-Mer, France
| | - Hervé Moreau
- Université Pierre et Marie Curie-Paris 06, Laboratoire Arago, Banyuls-sur-Mer, France
- CNRS, UMR7628, Laboratoire Arago, Banyuls-sur-Mer, France
| | - Nigel Grimsley
- Université Pierre et Marie Curie-Paris 06, Laboratoire Arago, Banyuls-sur-Mer, France
- CNRS, UMR7628, Laboratoire Arago, Banyuls-sur-Mer, France
- * E-mail:
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Abstract
In the last 30 years, the study of virus evolution has undergone a transformation. Originally concerned with disease and its emergence, virus evolution had not been well integrated into the general study of evolution. This chapter reviews the developments that have brought us to this new appreciation for the general significance of virus evolution to all life. We now know that viruses numerically dominate all habitats of life, especially the oceans. Theoretical developments in the 1970s regarding quasispecies, error rates, and error thresholds have yielded many practical insights into virus–host dynamics. The human diseases of HIV-1 and hepatitis C virus cannot be understood without this evolutionary framework. Yet recent developments with poliovirus demonstrate that viral fitness can be the result of a consortia, not one fittest type, a basic Darwinian concept in evolutionary biology. Darwinian principles do apply to viruses, such as with Fisher population genetics, but other features, such as reticulated and quasispecies-based evolution distinguish virus evolution from classical studies. The available phylogenetic tools have greatly aided our analysis of virus evolution, but these methods struggle to characterize the role of virus populations. Missing from many of these considerations has been the major role played by persisting viruses in stable virus evolution and disease emergence. In many cases, extreme stability is seen with persisting RNA viruses. Indeed, examples are known in which it is the persistently infected host that has better survival. We have also recently come to appreciate the vast diversity of phage (DNA viruses) of prokaryotes as a system that evolves by genetic exchanges across vast populations (Chapter 10). This has been proposed to be the “big bang” of biological evolution. In the large DNA viruses of aquatic microbes we see surprisingly large, complex and diverse viruses. With both prokaryotic and eukaryotic DNA viruses, recombination is the main engine of virus evolution, and virus host co-evolution is common, although not uniform. Viral emergence appears to be an unending phenomenon and we can currently witness a selective sweep by retroviruses that infect and become endogenized in koala bears.
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Allen MJ, Martinez-Martinez J, Schroeder DC, Somerfield PJ, Wilson WH. Use of microarrays to assess viral diversity: from genotype to phenotype. Environ Microbiol 2007; 9:971-82. [PMID: 17359269 DOI: 10.1111/j.1462-2920.2006.01219.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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.
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Affiliation(s)
- Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
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Allen MJ, Forster T, Schroeder DC, Hall M, Roy D, Ghazal P, Wilson WH. Locus-specific gene expression pattern suggests a unique propagation strategy for a giant algal virus. J Virol 2006; 80:7699-705. [PMID: 16840348 PMCID: PMC1563701 DOI: 10.1128/jvi.00491-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Emiliania huxleyi virus strain 86 is the largest algal virus sequenced to date and is unique among the Phycodnaviridae since its genome is predicted to contain six RNA polymerase subunit genes. We have used a virus microarray to profile the temporal transcription strategy of this unusual virus during infection. There are two distinct transcription phases to the infection process. The primary phase is dominated by a group of coding sequences (CDSs) expressed by 1 h postinfection that are localized to a subregion of the genome. The CDS of the primary group have no database homologues, and each is associated with a unique promoter element. The remainder of the CDSs are expressed in a secondary phase between 2 and 4 hours postinfection. Compartmentalized transcription of the two distinctive phases is discussed. We hypothesize that immediately after infection the nucleic acid of the virus targets the host nucleus, where primary-phase genes are transcribed by host RNA polymerase which recognizes the viral promoter. Secondary-phase transcription may then be conducted in the cytoplasm.
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Affiliation(s)
- Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, United Kingdom
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