1
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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. SCIENCE ADVANCES 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] [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.
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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
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2
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Zheng S, Lee V, Meza-Padilla I, Nissimov JI. Antiviral discovery in toxic cyanobacteria: Low hanging fruit in the age of pandemics. JOURNAL OF PHYCOLOGY 2024; 60:574-580. [PMID: 38174634 DOI: 10.1111/jpy.13425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/15/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
The power of novel vaccination technologies and their rapid development were elucidated clearly during the COVID-19 pandemic. At the same time, it also became clear that there is an urgent need to discover and manufacture new antivirals that target emerging viral threats. Toxic species of cyanobacteria produce a range of bioactive compounds that makes them good candidates for drug discovery. Nevertheless, few studies demonstrate the antiviral potential of cyanobacteria. This is partly due to the lack of specific and simple protocols designed for the rapid detection of antiviral activity in cyanobacteria and partly because specialized facilities for work with pathogenic viruses are few and far between. We therefore developed an easy method for the screening of cyanobacterial cultures for antiviral activity and used our private culture collection of non-pathogenic virus isolates to show that antiviral activity is a prominent feature in the cyanobacterium Microcystis aeruginosa. In this proof-of-concept study, we show that M. aeruginosa extracts from three different cyanobacterial strains delay infection of diatom-infecting single-stranded DNA and single-stranded RNA viruses by up to 2 days. Our work shows the ease with which cyanobacteria from culture collections can be screened for antiviral activity and highlights the potential of cyanobacteria as an excellent source for the discovery of novel antiviral compounds, warranting further investigation.
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Affiliation(s)
- Sally Zheng
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Victoria Lee
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Isaac Meza-Padilla
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Jozef I Nissimov
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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3
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Hososhima S, Mizutori R, Abe-Yoshizumi R, Rozenberg A, Shigemura S, Pushkarev A, Konno M, Katayama K, Inoue K, Tsunoda SP, Béjà O, Kandori H. Proton-transporting heliorhodopsins from marine giant viruses. eLife 2022; 11:78416. [PMID: 36065640 PMCID: PMC9448325 DOI: 10.7554/elife.78416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/07/2022] [Indexed: 12/02/2022] Open
Abstract
Rhodopsins convert light into signals and energy in animals and microbes. Heliorhodopsins (HeRs), a recently discovered new rhodopsin family, are widely present in archaea, bacteria, unicellular eukaryotes, and giant viruses, but their function remains unknown. Here, we report that a viral HeR from Emiliania huxleyi virus 202 (V2HeR3) is a light-activated proton transporter. V2HeR3 absorbs blue-green light, and the active intermediate contains the deprotonated retinal Schiff base. Site-directed mutagenesis study revealed that E191 in TM6 constitutes the gate together with the retinal Schiff base. E205 and E215 form a PAG of the Schiff base, and mutations at these positions converted the protein into an outward proton pump. Three environmental viral HeRs from the same group as well as a more distantly related HeR exhibited similar proton-transport activity, indicating that HeR functions might be diverse similarly to type-1 microbial rhodopsins. Some strains of E. huxleyi contain one HeR that is related to the viral HeRs, while its viruses EhV-201 and EhV-202 contain two and three HeRs, respectively. Except for V2HeR3 from EhV-202, none of these proteins exhibit ion transport activity. Thus, when expressed in the E. huxleyi cell membranes, only V2HeR3 has the potential to depolarize the host cells by light, possibly to overcome the host defense mechanisms or to prevent superinfection. The neuronal activity generated by V2HeR3 suggests that it can potentially be used as an optogenetic tool, similarly to type-1 microbial rhodopsins.
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Affiliation(s)
- Shoko Hososhima
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | - Ritsu Mizutori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | | | - Shunta Shigemura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | | | - Masae Konno
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
- OptoBioTechnology Research Center, Nagoya Institute of Technology
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
- OptoBioTechnology Research Center, Nagoya Institute of Technology
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology
- OptoBioTechnology Research Center, Nagoya Institute of Technology
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4
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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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5
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Nissimov JI, Talmy D, Haramaty L, Fredricks HF, Zelzion E, Knowles B, Eren AM, Vandzura R, Laber CP, Schieler BM, Johns CT, More KD, Coolen MJL, Follows MJ, Bhattacharya D, Van Mooy BAS, Bidle KD. Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology. Environ Microbiol 2019; 21:2182-2197. [PMID: 31001863 DOI: 10.1111/1462-2920.14633] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/15/2019] [Indexed: 11/29/2022]
Abstract
Coccolithoviruses (EhVs) are large, double-stranded DNA-containing viruses that infect the single-celled, marine coccolithophore Emiliania huxleyi. Given the cosmopolitan nature and global importance of E. huxleyi as a bloom-forming, calcifying, photoautotroph, E. huxleyi-EhV interactions play a key role in oceanic carbon biogeochemistry. Virally-encoded glycosphingolipids (vGSLs) are virulence factors that are produced by the activity of virus-encoded serine palmitoyltransferase (SPT). Here, we characterize the dynamics, diversity and catalytic production of vGSLs in an array of EhV strains in relation to their SPT sequence composition and explore the hypothesis that they are a determinant of infectivity and host demise. vGSL production and diversity was positively correlated with increased virulence, virus replication rate and lytic infection dynamics in laboratory experiments, but they do not explain the success of less-virulent EhVs in natural EhV communities. The majority of EhV-derived SPT amplicon sequences associated with infected cells in the North Atlantic derived from slower infecting, less virulent EhVs. Our lab-, field- and mathematical model-based data and simulations support ecological scenarios whereby slow-infecting, less-virulent EhVs successfully compete in North Atlantic populations of E. huxleyi, through either the preferential removal of fast-infecting, virulent EhVs during active infection or by having access to a broader host range.
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Affiliation(s)
- Jozef I Nissimov
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.,Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, Scotland, UK
| | - David Talmy
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Liti Haramaty
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Helen F Fredricks
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Ehud Zelzion
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ben Knowles
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - A Murat Eren
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Massachusetts, 02543, USA.,Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Rebecca Vandzura
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Christien P Laber
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Brittany M Schieler
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Christopher T Johns
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Kuldeep D More
- WA-Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Marco J L Coolen
- WA-Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Michael J Follows
- Department of Earth, Atmosphere and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
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6
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Thamatrakoln K, Talmy D, Haramaty L, Maniscalco C, Latham JR, Knowles B, Natale F, Coolen MJL, Follows MJ, Bidle KD. Light regulation of coccolithophore host-virus interactions. THE NEW PHYTOLOGIST 2019; 221:1289-1302. [PMID: 30368816 DOI: 10.1111/nph.15459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/20/2018] [Indexed: 06/08/2023]
Abstract
Viruses that infect photoautotrophs have a fundamental relationship with light, given the need for host resources. We investigated the role of light on Coccolithovirus (EhV) infection of the globally distributed coccolithophore, Emiliania huxleyi. Light was required for EhV adsorption, and viral production was highest when host cultures were maintained in continuous light or at irradiance levels of 150-300 μmol m-2 s-1 . During the early stages of infection, photosynthetic electron transport remained high, while RuBisCO expression decreased concomitant with an induction of the pentose phosphate pathway, the primary source of de novo nucleotides. A mathematical model developed and fitted to the laboratory data supported the hypothesis that EhV replication was controlled by a trade-off between host nucleotide recycling and de novo synthesis, and that photoperiod and photon flux could toggle this switch. Laboratory results supported field observations that light was the most robust driver of EhV replication within E. huxleyi populations collected across a 2000 nautical mile transect in the North Atlantic. Collectively, these findings demonstrate that light can drive host-virus interactions through a mechanistic interplay between host metabolic processes, which serve to structure infection and phytoplankton mortality in the upper ocean.
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Affiliation(s)
- Kimberlee Thamatrakoln
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - David Talmy
- Department of Microbiology, The University of Tennessee, Ken and Blaire Mossman Bldg, 1311 Cumberland Ave #307, Knoxville, TN 37996, USA
| | - Liti Haramaty
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Christopher Maniscalco
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Jason R Latham
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Ben Knowles
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Frank Natale
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Marco J L Coolen
- WA Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Michael J Follows
- Department of Earth, Atmosphere and Planetary Sciences, MIT, Cambridge, MA, 02139, USA
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ, 08901, USA
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7
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Johns CT, Grubb AR, Nissimov JI, Natale F, Knapp V, Mui A, Fredricks HF, Van Mooy BAS, Bidle KD. The mutual interplay between calcification and coccolithovirus infection. Environ Microbiol 2018; 21:1896-1915. [PMID: 30043404 PMCID: PMC7379532 DOI: 10.1111/1462-2920.14362] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/15/2018] [Accepted: 07/11/2018] [Indexed: 11/30/2022]
Abstract
Two prominent characteristics of marine coccolithophores are their secretion of coccoliths and their susceptibility to infection by coccolithoviruses (EhVs), both of which display variation among cells in culture and in natural populations. We examined the impact of calcification on infection by challenging a variety of Emiliania huxleyi strains at different calcification states with EhVs of different virulence. Reduced cellular calcification was associated with increased infection and EhV production, even though calcified cells and associated coccoliths had significantly higher adsorption coefficients than non-calcified (naked) cells. Sialic acid glycosphingolipids, molecules thought to mediate EhV infection, were generally more abundant in calcified cells and enriched in purified, sorted coccoliths, suggesting a biochemical link between calcification and adsorption rates. In turn, viable EhVs impacted cellular calcification absent of lysis by inducing dramatic shifts in optical side scatter signals and a massive release of detached coccoliths in a subpopulation of cells, which could be triggered by resuspension of healthy, calcified host cells in an EhV-free, 'induced media'. Our findings show that calcification is a key component of the E. huxleyi-EhV arms race and an aspect that is critical both to the modelling of these host-virus interactions in the ocean and interpreting their impact on the global carbon cycle.
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Affiliation(s)
- Christopher T Johns
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Austin R Grubb
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Jozef I Nissimov
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Frank Natale
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Viki Knapp
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.,University of South Carolina, Honors College, Columbia, SC, 29208, USA
| | - Alwin Mui
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Helen F Fredricks
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
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8
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Nissimov JI, Vandzura R, Johns CT, Natale F, Haramaty L, Bidle KD. Dynamics of transparent exopolymer particle production and aggregation during viral infection of the coccolithophore, Emiliania huxleyi. Environ Microbiol 2018; 20:2880-2897. [PMID: 29921002 DOI: 10.1111/1462-2920.14261] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 11/30/2022]
Abstract
Emiliania huxleyi produces calcium carbonate (CaCO3 ) coccoliths and transparent exopolymer particles (TEP), sticky, acidic carbohydrates that facilitate aggregation. E. huxleyi's extensive oceanic blooms are often terminated by coccolithoviruses (EhVs) with the transport of cellular debris and associated particulate organic carbon (POC) to depth being facilitated by TEP-bound 'marine snow' aggregates. The dynamics of TEP production and particle aggregation in response to EhV infection are poorly understood. Using flow cytometry, spectrophotometry and FlowCam visualization of alcian blue (AB)-stained aggregates, we assessed TEP production and the size spectrum of aggregates for E. huxleyi possessing different degrees of calcification and cellular CaCO3 :POC mass ratios, when challenged with two EhVs (EhV207 and EhV99B1). FlowCam imaging also qualitatively assessed the relative amount of AB-stainable TEP (i.e., blue:red ratio of each particle). We show significant increases in TEP during early phase EhV207-infection (∼ 24 h) of calcifying strains and a shift towards large aggregates following EhV99B1-infection. We also observed the formation of large aggregates with low blue:red ratios, suggesting that other exopolymer substances contribute towards aggregation. Our findings show the potential for virus infection and the associated response of their hosts to impact carbon flux dynamics and provide incentive to explore these dynamics in natural populations.
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Affiliation(s)
- Jozef I Nissimov
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road New Brunswick, NJ, USA
| | - Rebecca Vandzura
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road New Brunswick, NJ, USA
| | - Christopher T Johns
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road New Brunswick, NJ, USA
| | - Frank Natale
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road New Brunswick, NJ, USA
| | - Liti Haramaty
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road New Brunswick, NJ, USA
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road New Brunswick, NJ, USA
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9
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Abstract
Viruses infect all kingdoms of marine life from bacteria to whales. Viruses in the world's oceans play important roles in the mortality of phytoplankton, and as drivers of evolution and biogeochemical cycling. They shape host population abundance and distribution and can lead to the termination of algal blooms. As discoveries about this huge reservoir of genetic and biological diversity grow, our understanding of the major influences viruses exert in the global marine environment continues to expand. This chapter discusses the key discoveries that have been made to date about marine viruses and the current direction of this field of research.
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Affiliation(s)
- Karen D Weynberg
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia.
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10
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Laber CP, Hunter JE, Carvalho F, Collins JR, Hunter EJ, Schieler BM, Boss E, More K, Frada M, Thamatrakoln K, Brown CM, Haramaty L, Ossolinski J, Fredricks H, Nissimov JI, Vandzura R, Sheyn U, Lehahn Y, Chant RJ, Martins AM, Coolen MJL, Vardi A, DiTullio GR, Van Mooy BAS, Bidle KD. Coccolithovirus facilitation of carbon export in the North Atlantic. Nat Microbiol 2018. [DOI: 10.1038/s41564-018-0128-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Emerging Interaction Patterns in the Emiliania huxleyi-EhV System. Viruses 2017; 9:v9030061. [PMID: 28327527 PMCID: PMC5371816 DOI: 10.3390/v9030061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 01/25/2023] Open
Abstract
Viruses are thought to be fundamental in driving microbial diversity in the oceanic planktonic realm. That role and associated emerging infection patterns remain particularly elusive for eukaryotic phytoplankton and their viruses. Here we used a vast number of strains from the model system Emiliania huxleyi/Emiliania huxleyi Virus to quantify parameters such as growth rate (µ), resistance (R), and viral production (Vp) capacities. Algal and viral abundances were monitored by flow cytometry during 72-h incubation experiments. The results pointed out higher viral production capacity in generalist EhV strains, and the virus-host infection network showed a strong co-evolution pattern between E. huxleyi and EhV populations. The existence of a trade-off between resistance and growth capacities was not confirmed.
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12
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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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13
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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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14
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How many Coccolithovirus genotypes does it take to terminate an Emiliania huxleyi bloom? Virology 2014; 466-467:138-45. [DOI: 10.1016/j.virol.2014.07.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/08/2014] [Accepted: 07/11/2014] [Indexed: 11/22/2022]
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15
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Pagarete A, Kusonmano K, Petersen K, Kimmance SA, Martínez Martínez J, Wilson WH, Hehemann JH, Allen MJ, Sandaa RA. Dip in the gene pool: metagenomic survey of natural coccolithovirus communities. Virology 2014; 466-467:129-37. [PMID: 24947907 DOI: 10.1016/j.virol.2014.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/23/2014] [Accepted: 05/18/2014] [Indexed: 11/30/2022]
Abstract
Despite the global oceanic distribution and recognised biogeochemical impact of coccolithoviruses (EhV), their diversity remains poorly understood. Here we employed a metagenomic approach to study the occurrence and progression of natural EhV community genomic variability. Analysis of EhV metagenomes from the early and late stages of an induced bloom led to three main discoveries. First, we observed resilient and specific genomic signatures in the EhV community associated with the Norwegian coast, which reinforce the existence of limitations to the capacity of dispersal and genomic exchange among EhV populations. Second, we identified a hyper-variable region (approximately 21kbp long) in the coccolithovirus genome. Third, we observed a clear trend for EhV relative amino-acid diversity to reduce from early to late stages of the bloom. This study validated two new methodological combinations, and proved very useful in the discovery of new genomic features associated with coccolithovirus natural communities.
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Affiliation(s)
| | | | - Kjell Petersen
- Computational Biology Unit, University of Bergen, Norway
| | | | | | - William H Wilson
- Plymouth Marine Laboratory, Plymouth, UK; Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jan-Hendrik Hehemann
- Department of Civil & Environmental Engineering, Massachusetts Institute of Technology, USA
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16
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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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17
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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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18
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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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19
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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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