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Yau S, Krasovec M, Benites LF, Rombauts S, Groussin M, Vancaester E, Aury JM, Derelle E, Desdevises Y, Escande ML, Grimsley N, Guy J, Moreau H, Sanchez-Brosseau S, van de Peer Y, Vandepoele K, Gourbiere S, Piganeau G. Virus-host coexistence in phytoplankton through the genomic lens. SCIENCE ADVANCES 2020; 6:eaay2587. [PMID: 32270031 PMCID: PMC7112755 DOI: 10.1126/sciadv.aay2587] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/09/2020] [Indexed: 05/02/2023]
Abstract
Virus-microbe interactions in the ocean are commonly described by "boom and bust" dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this "accordion" chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions.
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Affiliation(s)
- Sheree Yau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Corresponding author. (G.P.); (S.Y.)
| | - Marc Krasovec
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - L. Felipe Benites
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Stephane Rombauts
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Mathieu Groussin
- Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square NE47-378, Cambridge, MA 02139, USA
| | - Emmelien Vancaester
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Evelyne Derelle
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Univ. Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | - Yves Desdevises
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marie-Line Escande
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Julie Guy
- Genoscope, Institut de biologie François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Hervé Moreau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Yves van de Peer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Sebastien Gourbiere
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, UMR 5096, 52 Avenue Paul Alduy, 66860 Perpignan, France
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Corresponding author. (G.P.); (S.Y.)
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Kelley DS, Lennon CW, Li Z, Miller MR, Banavali NK, Li H, Belfort M. Mycobacterial DnaB helicase intein as oxidative stress sensor. Nat Commun 2018; 9:4363. [PMID: 30341292 PMCID: PMC6195587 DOI: 10.1038/s41467-018-06554-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/10/2018] [Indexed: 11/09/2022] Open
Abstract
Inteins are widespread self-splicing protein elements emerging as potential post-translational environmental sensors. Here, we describe two inteins within one protein, the Mycobacterium smegmatis replicative helicase DnaB. These inteins, DnaBi1 and DnaBi2, have homology to inteins in pathogens, splice with vastly varied rates, and are differentially responsive to environmental stressors. Whereas DnaBi1 splicing is reversibly inhibited by oxidative and nitrosative insults, DnaBi2 is not. Using a reporter that measures splicing in a native intein-containing organism and western blotting, we show that H2O2 inhibits DnaBi1 splicing in M. smegmatis. Intriguingly, upon oxidation, the catalytic cysteine of DnaBi1 forms an intramolecular disulfide bond. We report a crystal structure of the class 3 DnaBi1 intein at 1.95 Å, supporting our findings and providing insight into this splicing mechanism. We propose that this cysteine toggle allows DnaBi1 to sense stress, pausing replication to maintain genome integrity, and then allowing splicing immediately when permissive conditions return.
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Affiliation(s)
- Danielle S Kelley
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA
| | - Christopher W Lennon
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, 12222, USA
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA
| | - Michael R Miller
- Department of Chemistry, University at Albany, Albany, NY, 12222, USA
| | - Nilesh K Banavali
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA
| | - Hongmin Li
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA.
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA.
| | - Marlene Belfort
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA.
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, 12222, USA.
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Green CM, Novikova O, Belfort M. The dynamic intein landscape of eukaryotes. Mob DNA 2018; 9:4. [PMID: 29416568 PMCID: PMC5784728 DOI: 10.1186/s13100-018-0111-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/18/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Inteins are mobile, self-splicing sequences that interrupt proteins and occur across all three domains of life. Scrutiny of the intein landscape in prokaryotes led to the hypothesis that some inteins are functionally important. Our focus shifts to eukaryotic inteins to assess their diversity, distribution, and dissemination, with the aim to comprehensively evaluate the eukaryotic intein landscape, understand intein maintenance, and dissect evolutionary relationships. RESULTS This bioinformatics study reveals that eukaryotic inteins are scarce, but present in nuclear genomes of fungi, chloroplast genomes of algae, and within some eukaryotic viruses. There is a preponderance of inteins in several fungal pathogens of humans and plants. Inteins are pervasive in certain proteins, including the nuclear RNA splicing factor, Prp8, and the chloroplast DNA helicase, DnaB. We find that eukaryotic inteins frequently localize to unstructured loops of the host protein, often at highly conserved sites. More broadly, a sequence similarity network analysis of all eukaryotic inteins uncovered several routes of intein mobility. Some eukaryotic inteins appear to have been acquired through horizontal transfer with dsDNA viruses, yet other inteins are spread through intragenomic transfer. Remarkably, endosymbiosis can explain patterns of DnaB intein inheritance across several algal phyla, a novel mechanism for intein acquisition and distribution. CONCLUSIONS Overall, an intriguing picture emerges for how the eukaryotic intein landscape arose, with many evolutionary forces having contributed to its current state. Our collective results provide a framework for exploring inteins as novel regulatory elements and innovative drug targets.
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Affiliation(s)
- Cathleen M. Green
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
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Weynberg KD, Allen MJ, Wilson WH. Marine Prasinoviruses and Their Tiny Plankton Hosts: A Review. Viruses 2017; 9:E43. [PMID: 28294997 PMCID: PMC5371798 DOI: 10.3390/v9030043] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/04/2017] [Accepted: 03/08/2017] [Indexed: 12/29/2022] Open
Abstract
Viruses play a crucial role in the marine environment, promoting nutrient recycling and biogeochemical cycling and driving evolutionary processes. Tiny marine phytoplankton called prasinophytes are ubiquitous and significant contributors to global primary production and biomass. A number of viruses (known as prasinoviruses) that infect these important primary producers have been isolated and characterised over the past decade. Here we review the current body of knowledge about prasinoviruses and their interactions with their algal hosts. Several genes, including those encoding for glycosyltransferases, methyltransferases and amino acid synthesis enzymes, which have never been identified in viruses of eukaryotes previously, have been detected in prasinovirus genomes. The host organisms are also intriguing; most recently, an immunity chromosome used by a prasinophyte in response to viral infection was discovered. In light of such recent, novel discoveries, we discuss why the cellular simplicity of prasinophytes makes for appealing model host organism-virus systems to facilitate focused and detailed investigations into the dynamics of marine viruses and their intimate associations with host species. We encourage the adoption of the prasinophyte Ostreococcus and its associated viruses as a model host-virus system for examination of cellular and molecular processes in the marine environment.
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Affiliation(s)
- Karen D Weynberg
- Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia.
| | - Michael J Allen
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK.
| | - William H Wilson
- Sir Alister Hardy Foundation for Ocean Science, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.
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5
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Abstract
Inteins are self-splicing protein elements that are mobile at the DNA level and are sporadically distributed across microbial genomes. Inteins appear to be horizontally transferred, and it has been speculated that phages may play a role in intein distribution. Our attention turns to mycobacteriophages, which infect mycobacteria, where both phage and host harbor inteins. Using bioinformatics, mycobacteriophage genomes were mined for inteins. This study reveals that these mobile elements are present across multiple mycobacteriophage clusters and are pervasive in certain genes, like the large terminase subunit TerL and a RecB-like nuclease, with the majority of intein-containing genes being phage specific. Strikingly, despite this phage specificity, inteins localize to functional motifs shared with bacteria, such that intein-containing genes have similar roles, like hydrolase activity and nucleic acid binding, indicating a global commonality among intein-hosting proteins. Additionally, there are multiple insertion points within active centers, implying independent invasion events, with regulatory implications. Several phage inteins were shown to be splicing competent and to encode functional homing endonucleases, important for mobility. Further, bioinformatic analysis supports the potential for phages as facilitators of intein movement among mycobacteria and related genera. Analysis of catalytic intein residues finds the highly conserved penultimate histidine inconsistently maintained among mycobacteriophages. Biochemical characterization of a noncanonical phage intein shows that this residue influences precursor accumulation, suggesting that splicing has been tuned in phages to modulate generation of important proteins. Together, this work expands our understanding of phage-based intein dissemination and evolution and implies that phages provide a context for evolution of splicing-based regulation. Inteins are mobile protein splicing elements found in critical genes across all domains of life. Mycobacterial inteins are of particular interest because of their occurrence in pathogenic species, such as Mycobacterium tuberculosis and Mycobacterium leprae, which harbor inteins in important proteins. We have discovered a similarity in activities of intein-containing proteins among mycobacteriophages and their intein-rich actinobacterial hosts, with implications for both posttranslational regulation by inteins and phages participating in horizontal intein transfer. Our demonstration of multiple insertion points within active centers of phage proteins implies independent invasion events, indicating the importance of intein maintenance at specific functional sites. The variable conservation of a catalytic splicing residue, leading to profoundly altered splicing rates, points to the regulatory potential of inteins and to mycobacteriophages playing a role in intein evolution. Collectively, these results suggest inteins as posttranslational regulators and mycobacteriophages as both vehicles for intein distribution and incubators for intein evolution.
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Andam CP, Carver SM, Berthrong ST. Horizontal Gene Flow in Managed Ecosystems. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054126] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cheryl P. Andam
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115;
| | - Sarah M. Carver
- Central Research, The Kraft Heinz Company, Glenview, Illinois 60025;
| | - Sean T. Berthrong
- Department of Biological Sciences, Butler University, Indianapolis, Indiana 46208;
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Baudoux AC, Lebredonchel H, Dehmer H, Latimier M, Edern R, Rigaut-Jalabert F, Ge P, Guillou L, Foulon E, Bozec Y, Cariou T, Desdevises Y, Derelle E, Grimsley N, Moreau H, Simon N. Interplay between the genetic clades of Micromonas and their viruses in the Western English Channel. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:765-773. [PMID: 26081716 DOI: 10.1111/1758-2229.12309] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/13/2015] [Accepted: 06/04/2015] [Indexed: 06/04/2023]
Abstract
The genus Micromonas comprises distinct genetic clades that commonly dominate eukaryotic phytoplankton community from polar to tropical waters. This phytoplankter is also recurrently infected by abundant and genetically diverse prasinoviruses. Here we report on the interplay between prasinoviruses and Micromonas with regard to the genetic diversity of this host. For 1 year, we monitored the abundance of three clades of Micromonas and their viruses in the Western English Channel, both in the environment using clade-specific probes and flow cytometry, and in the laboratory using clonal strains of Micromonas clades to assay for their viruses by plaque-forming units. We showed that the seasonal fluctuations of Micromonas clades were closely mirrored by the abundance of their corresponding viruses, indicating that the members of Micromonas genus are susceptible to viral infection, regardless of their genetic affiliation. The characterization of 45 viral isolates revealed that Micromonas clades are attacked by specific virus populations, which exhibit distinctive clade specificity, life strategies and genetic diversity. However, some viruses can also cross-infect different host clades, suggesting a mechanism of horizontal gene transfer within the Micromonas genus. This study provides novel insights into the impact of viral infection for the ecology and evolution of the prominent phytoplankter Micromonas.
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Affiliation(s)
- A-C Baudoux
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - H Lebredonchel
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls sur Mer, France
| | - H Dehmer
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - M Latimier
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - R Edern
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - F Rigaut-Jalabert
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Fédération de Recherche (FR2424), Station Biologique de Roscoff, 29680, Roscoff, France
| | - P Ge
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - L Guillou
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - E Foulon
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - Y Bozec
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
| | - T Cariou
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Fédération de Recherche (FR2424), Station Biologique de Roscoff, 29680, Roscoff, France
| | - Y Desdevises
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls sur Mer, France
| | - E Derelle
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls sur Mer, France
| | - N Grimsley
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls sur Mer, France
| | - H Moreau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650, Banyuls sur Mer, France
| | - N Simon
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Adaptation et Diversité en Milieu Marin (AD2M UMR7144), Station Biologique de Roscoff, 29680, Roscoff, France
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Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus. J Virol 2015; 89:5812-21. [PMID: 25787287 DOI: 10.1128/jvi.00246-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/06/2015] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED The functional diversity of eukaryotic viruses infecting a single host strain from seawater samples originating from distant marine locations is unknown. To estimate this diversity, we used lysis plaque assays to detect viruses that infect the widespread species Ostreococcus lucimarinus, which is found in coastal and mesotrophic systems, and O. tauri, which was isolated from coastal and lagoon sites from the northwest Mediterranean Sea. Detection of viral lytic activities against O. tauri was not observed using seawater from most sites, except those close to the area where the host strain was isolated. In contrast, the more cosmopolitan O. lucimarinus species recovered viruses from locations in the Atlantic and Pacific Oceans and the Mediterranean Sea. Six new O. lucimarinus viruses (OlVs) then were characterized and their genomes sequenced. Two subgroups of OlVs were distinguished based on their genetic distances and on the inversion of a central 32-kb-long DNA fragment, but overall their genomes displayed a high level of synteny. The two groups did not correspond to proximity of isolation sites, and the phylogenetic distance between these subgroups was higher than the distances observed among viruses infecting O. tauri. Our study demonstrates that viruses originating from very distant sites are able to infect the same algal host strain and can be more diverse than those infecting different species of the same genus. Finally, distinctive features and evolutionary distances between these different viral subgroups does not appear to be linked to biogeography of the viral isolates. IMPORTANCE Marine eukaryotic phytoplankton virus diversity has yet to be addressed, and more specifically, it is unclear whether diversity is connected to geographical distance and whether differential infection and lysis patterns exist among such viruses that infect the same host strain. Here, we assessed the genetic distance of geographically segregated viruses that infect the ubiquitous green microalga Ostreococcus. This study provides the first glimpse into the diversity of predicted gene functions in Ostreococcus viruses originating from distant sites and provides new insights into potential host distributions and restrictions in the world oceans.
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9
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Molecular evolution of nitrogen assimilatory enzymes in marine prasinophytes. J Mol Evol 2014; 80:65-80. [PMID: 25504421 DOI: 10.1007/s00239-014-9659-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/22/2014] [Indexed: 01/11/2023]
Abstract
Nitrogen assimilation is a highly regulated process requiring metabolic coordination of enzymes and pathways in the cytosol, chloroplast, and mitochondria. Previous studies of prasinophyte genomes revealed that genes encoding nitrate and ammonium transporters have a complex evolutionary history involving both vertical and horizontal transmission. Here we examine the evolutionary history of well-conserved nitrogen-assimilating enzymes to determine if a similar complex history is observed. Phylogenetic analyses suggest that genes encoding glutamine synthetase (GS) III in the prasinophytes evolved by horizontal gene transfer from a member of the heterokonts. In contrast, genes encoding GSIIE, a canonical vascular plant and green algal enzyme, were found in the Micromonas genomes but have been lost from Ostreococcus. Phylogenetic analyses placed the Micromonas GSIIs in a larger chlorophyte/vascular plant clade; a similar topology was observed for ferredoxin-dependent nitrite reductase (Fd-NiR), indicating the genes encoding GSII and Fd-NiR in these prasinophytes evolved via vertical transmission. Our results show that genes encoding the nitrogen-assimilating enzymes in Micromonas and Ostreococcus have been differentially lost and as well as recruited from different evolutionary lineages, suggesting that the regulation of nitrogen assimilation in prasinophytes will differ from other green algae.
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10
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Clerissi C, Grimsley N, Subirana L, Maria E, Oriol L, Ogata H, Moreau H, Desdevises Y. Prasinovirus distribution in the Northwest Mediterranean Sea is affected by the environment and particularly by phosphate availability. Virology 2014; 466-467:146-57. [PMID: 25109909 DOI: 10.1016/j.virol.2014.07.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/13/2014] [Accepted: 07/08/2014] [Indexed: 10/24/2022]
Abstract
Numerous seawater lagoons punctuate the southern coastline of France. Exchanges of seawater between these lagoons and the open sea are limited by narrow channels connecting them. Lagoon salinities vary according to evaporation and to the volume of freshwater arriving from influent streams, whose nutrients also promote the growth of algae. We compared Prasinovirus communities, whose replication is supported by microscopic green algae, in four lagoons and at a coastal sampling site. Using high-throughput sequencing of DNA from a giant virus-specific marker gene, we show that the environmental conditions significantly affect the types of detectable viruses across samples. In spatial comparisons between 5 different sampling sites, higher levels of phosphates, nitrates, nitrites, ammonium and silicates tend to increase viral community richness independently of geographical distances between the sampling sites. Finally, comparisons of Prasinovirus communities at 2 sampling sites over a period of 10 months highlighted seasonal effects and the preponderant nature of phosphate concentrations in constraining viral distribution.
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Affiliation(s)
- Camille Clerissi
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, Biologie Intégrative des Organismes Marin, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7232, Observatoire Océanologique, Biologie Intégrative des Organismes Marins, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
| | - Nigel Grimsley
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, Biologie Intégrative des Organismes Marin, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7232, Observatoire Océanologique, Biologie Intégrative des Organismes Marins, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France.
| | - Lucie Subirana
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, Biologie Intégrative des Organismes Marin, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7232, Observatoire Océanologique, Biologie Intégrative des Organismes Marins, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
| | - Eric Maria
- Sorbonne Universités, UPMC Univ Paris 06, UMS 2348, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
| | - Louise Oriol
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d׳Océanographie Microbienne, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7621, Observatoire Océanologique, Laboratoire d׳Océanographie Microbienne, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hervé Moreau
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, Biologie Intégrative des Organismes Marin, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7232, Observatoire Océanologique, Biologie Intégrative des Organismes Marins, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
| | - Yves Desdevises
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, Biologie Intégrative des Organismes Marin, Observatoire Océanologique, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France; Sorbonne Universités, CNRS, UMR 7232, Observatoire Océanologique, Biologie Intégrative des Organismes Marins, Avenue du Fontaulé, F-66650 Banyuls-sur-Mer, France
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Unveiling of the diversity of Prasinoviruses (Phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-amplified DNA polymerase and major capsid protein genes. Appl Environ Microbiol 2014; 80:3150-60. [PMID: 24632251 DOI: 10.1128/aem.00123-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.
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Swithers KS, Soucy SM, Lasek-Nesselquist E, Lapierre P, Gogarten JP. Distribution and Evolution of the Mobile vma-1b Intein. Mol Biol Evol 2013; 30:2676-87. [DOI: 10.1093/molbev/mst164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Intermolecular domain swapping induces intein-mediated protein alternative splicing. Nat Chem Biol 2013; 9:616-22. [DOI: 10.1038/nchembio.1320] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 07/17/2013] [Indexed: 11/09/2022]
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