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Rousvoal S, Bouyer B, López-Cristoffanini C, Boyen C, Collén J. Mutant swarms of a totivirus-like entities are present in the red macroalga Chondrus crispus and have been partially transferred to the nuclear genome. JOURNAL OF PHYCOLOGY 2016; 52:493-504. [PMID: 27151076 DOI: 10.1111/jpy.12427] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
Chondrus crispus Stackhouse (Gigartinales) is a red seaweed found on North Atlantic rocky shores. Electrophoresis of RNA extracts showed a prominent band with a size of around 6,000 bp. Sequencing of the band revealed several sequences with similarity to totiviruses, double-stranded RNA viruses that normally infect fungi. This virus-like entity was named C. crispus virus (CcV). It should probably be regarded as an extreme viral quasispecies or a mutant swarm since low identity (<65%) was found between sequences. Totiviruses typically code for two genes: one capsid gene (gag) and one RNA-dependent RNA polymerase gene (pol) with a pseudoknot structure between the genes. Both the genes and the intergenic structures were found in the CcV sequences. A nonidentical gag gene was also found in the nuclear genome of C. crispus, with associated expressed sequence tags (EST) and upstream regulatory features. The gene was presumably horizontally transferred from the virus to the alga. Similar dsRNA bands were seen in extracts from different life cycle stages of C. crispus and from all geographic locations tested. In addition, similar bands were also observed in RNA extractions from other red algae; however, the significance of this apparently widespread phenomenon is unknown. Neither phenotype caused by the infection nor any virus particles or capsid proteins were identified; thus, the presence of viral particles has not been validated. These findings increase the known host range of totiviruses to include marine red algae.
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Affiliation(s)
- Sylvie Rousvoal
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Betty Bouyer
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Camilo López-Cristoffanini
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Catherine Boyen
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
| | - Jonas Collén
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, CS 90074, 29688, Roscoff Cedex, France
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Stevens K, Weynberg K, Bellas C, Brown S, Brownlee C, Brown MT, Schroeder DC. A novel evolutionary strategy revealed in the phaeoviruses. PLoS One 2014; 9:e86040. [PMID: 24465858 PMCID: PMC3897601 DOI: 10.1371/journal.pone.0086040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/04/2013] [Indexed: 11/18/2022] Open
Abstract
Phaeoviruses infect the brown algae, which are major contributors to primary production of coastal waters and estuaries. They exploit a Persistent evolutionary strategy akin to a K- selected life strategy via genome integration and are the only known representatives to do so within the giant algal viruses that are typified by r- selected Acute lytic viruses. In screening the genomes of five species within the filamentous brown algal lineage, here we show an unprecedented diversity of viral gene sequence variants especially amongst the smaller phaeoviral genomes. Moreover, one variant shares features from both the two major sub-groups within the phaeoviruses. These phaeoviruses have exploited the reduction of their giant dsDNA genomes and accompanying loss of DNA proofreading capability, typical of an Acute life strategist, but uniquely retain a Persistent life strategy.
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Affiliation(s)
- Kim Stevens
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Karen Weynberg
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Christopher Bellas
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Sonja Brown
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Colin Brownlee
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Murray T. Brown
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Declan C. Schroeder
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- * E-mail:
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Schroeder DC, Park Y, Yoon HM, Lee YS, Kang SW, Meints RH, Ivey RG, Choi TJ. Genomic analysis of the smallest giant virus--Feldmannia sp. virus 158. Virology 2009; 384:223-32. [PMID: 19054537 DOI: 10.1016/j.virol.2008.10.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 10/08/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
Genomic analysis of Feldmannia sp. virus 158, the second phaeovirus to be sequenced in its entirety, provides further evidence that large double-stranded DNA viruses share similar evolutionary pressures as cellular organisms. Reductive evolution is clearly evident within the phaeoviruses which occurred via several routes: the loss of genes from an ancestral virus core genome most likely through genetic drift; and as a result of relatively large recombination events that caused wholesale loss of genes. The entire genome is 154,641 bp in length and has 150 predicted coding sequences of which 87% have amino acid sequence similarities to other algal virus coding sequences within the family Phycodnaviridae. Significant similarities were found, for thirty eight coding sequences (25%), to genes in gene databanks that are known to be involved in processes that include DNA replication, DNA methylation, signal transduction, viral integration and transposition, and protein-protein interactions. Unsurprisingly, the greatest similarity was observed between the two known viruses that infect Feldmannia, indicating the taxonomic linkage of these two viruses with their hosts. Moreover, comparative analysis of phycodnaviral genomic sequences revealed the smallest set of core genes (10 out of a possible 31) required to make a functional nucleocytoplasmic large dsDNA virus.
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Delaroque N, Boland W. The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses. BMC Evol Biol 2008; 8:110. [PMID: 18405387 PMCID: PMC2373305 DOI: 10.1186/1471-2148-8-110] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 04/12/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ectocarpus siliculosus virus-1 (EsV-1) is a lysogenic dsDNA virus belonging to the super family of nucleocytoplasmic large DNA viruses (NCLDV) that infect Ectocarpus siliculosus, a marine filamentous brown alga. Previous studies indicated that the viral genome is integrated into the host DNA. In order to find the integration sites of the viral genome, a genomic library from EsV-1-infected algae was screened using labelled EsV-1 DNA. Several fragments were isolated and some of them were sequenced and analyzed in detail. RESULTS Analysis revealed that the algal genome is split by a copy of viral sequences that have a high identity to EsV-1 DNA sequences. These fragments are interspersed with DNA repeats, pseudogenes and genes coding for products involved in DNA replication, integration and transposition. Some of these gene products are not encoded by EsV-1 but are present in the genome of other members of the NCLDV family. Further analysis suggests that the Ectocarpus algal genome contains traces of the integration of a large dsDNA viral genome; this genome could be the ancestor of the extant NCLDV genomes. Furthermore, several lines of evidence indicate that the EsV-1 genome might have originated in these viral DNA pieces, implying the existence of a complex integration and recombination system. A protein similar to a new class of tyrosine recombinases might be a key enzyme of this system. CONCLUSION Our results support the hypothesis that some dsDNA viruses are monophyletic and evolved principally through genome reduction. Moreover, we hypothesize that phaeoviruses have probably developed an original replication system.
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Affiliation(s)
- Nicolas Delaroque
- Max-Planck-Institut für Chemische Ökologie, Beutenberg Campus, Hans Knöll Str. 8, D - 07745 Jena, Germany
| | - Wilhelm Boland
- Max-Planck-Institut für Chemische Ökologie, Beutenberg Campus, Hans Knöll Str. 8, D - 07745 Jena, Germany
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Meints RH, Ivey RG, Lee AM, Choi TJ. Identification of two virus integration sites in the brown alga Feldmannia chromosome. J Virol 2008; 82:1407-13. [PMID: 18032486 PMCID: PMC2224422 DOI: 10.1128/jvi.01983-07] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Accepted: 11/12/2007] [Indexed: 11/20/2022] Open
Abstract
Two similar, large double-stranded DNA viruses, Feldmannia species virus 158 (FsV-158) and FsV-178, replicate only in the unilocular reproductive cells (sporangia) of a brown filamentous alga in the genus Feldmannia. Virus particles are not present in vegetative cells but they are produced in the sporangia formed on vegetative filaments that have been transferred newly into culture. Thus, we proposed that these viruses exist in the vegetative cells in a latent form (R. G. Ivey, E. C. Henry, A. M. Lee, L. Klepper, S. K. Krueger, and R. H. Meints, Virology 220:267-273, 1996). In this article we present evidence that the two FsV genomes are integrated into the host genome during vegetative growth. The FsV genome integration sites were identified by cloning the regions where the FsV genome is linked to the host DNA. FsV-158 and FsV-178 are integrated into two distinct locations in the algal genome. In contrast, the integration sites in the two viral genomes are identical. Notably, the integration sites in the host and viruses contain GC and CG dinucleotide sequences, respectively, from which the GC sequences are recovered at both host-virus junctions. The splice sites in the two FsV genomes are predicted to form a stem-loop structure with the CG dinucleotide in the loop portion.
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Affiliation(s)
- Russel H Meints
- Department of Microbiology, Pukyong National University, 599-1, Daeyeon 3-Dong, Nam-Gu, Busan 608-737, South Korea
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Park Y, Kim GD, Choi TJ. Molecular cloning and characterization of the DNA adenine methyltransferase gene in Feldmannia sp. virus. Virus Genes 2007; 34:177-83. [PMID: 17180708 DOI: 10.1007/s11262-006-0059-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 11/16/2006] [Indexed: 11/26/2022]
Abstract
The genome of Feldmannia sp. virus (FsV), a marine brown alga virus, contains a putative DNA adenine methyltransferase (dam) gene of 1,245 bp that encodes a polypeptide of 45.8 kDa. A BLAST search with the FsV dam gene showed high amino acid identity to two putative methyltransferase genes, ORF B29 of Feldmannia irregularis virus (FirrV, 54%) and ORF129 of Ectocarpus siliculosus virus (EsV, 36%); and a PSI BLAST search revealed similarity to the N(6)-adenine methyltransferases (MTases) of other species. Most conserved motifs of beta-class MTases were observed in the FsV dam gene. However, neither of the highly conserved sequences in motifs I (FxGxG) or IV [(S/N/D)PP(Y/F/W)] perfectly matched those in the FsV dam gene. The highly conserved DPPY consensus sequence in motif IV was NTPW in the FsV dam gene, perfectly matching the sequences in ORF B29 of FirrV and ORF129 of EsV. Therefore, the dam genes in brown algae viruses may belong to a yet undiscovered group. The FsV Dam protein expressed from the cloned FsV dam gene methylated E. coli chromosomal DNA. This is the first report showing that a virus infecting marine filamentous brown algae encodes a functional Dam protein.
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Affiliation(s)
- Yunjung Park
- Department of Microbiology, Pukyong National University, 599-1, Daeyeon 3-Dong, Busan, South Korea.
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Claverie JM. Giant viruses in the oceans: the 4th Algal Virus Workshop. Virol J 2005; 2:52. [PMID: 15967028 PMCID: PMC1188081 DOI: 10.1186/1743-422x-2-52] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2005] [Accepted: 06/20/2005] [Indexed: 11/16/2022] Open
Abstract
Giant double-stranded DNA viruses (such as record breaking Acanthamoeba polyphaga Mimivirus), with particle sizes of 0.2 to 0.6 μm, genomes of 300 kbp to 1.200 kbp, and commensurate complex gene contents, constitute an evolutionary mystery. They challenge the common vision of viruses, traditionally seen as highly streamlined genomes optimally fitted to the smallest possible -filterable- package. Such giant viruses are now discovered in increasing numbers through the systematic sampling of ocean waters as well as freshwater aquatic environments, where they play a significant role in controlling phyto- and bacterio- plankton populations. The 4th algal virus workshop showed that the study of these ecologically important viruses is now massively entering the genomic era, promising a better understanding of their diversity and, hopefully, some insights on their origin and the evolutionary forces that shaped their genomes.
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Affiliation(s)
- Jean-Michel Claverie
- Structural & Genomic Information Laboratory, UPR 2589, IBSM, CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
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Delaroque N, Boland W, Müller DG, Knippers R. Comparisons of two large phaeoviral genomes and evolutionary implications. J Mol Evol 2003; 57:613-22. [PMID: 14745530 DOI: 10.1007/s00239-003-2501-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2002] [Accepted: 05/12/2003] [Indexed: 11/26/2022]
Abstract
The evolution of viral genomes has recently attracted considerable attention. We compare the sequences of two large viral genomes, EsV-1 and FirrV-1, belonging to the family of phaeoviruses which infect different species of marine brown algae. Although their genomes differ substantially in size, these viruses share similar morphologies and similar latent infection cycles. In fact, sequence comparisons show that the viruses have more than 60% of their genes in common. However, the order of genes is completely different in the two genomes, suggesting that extensive recombinational events in addition to several large deletions had occurred during the separate evolutionary routes from a common ancestor. We investigated genes encoding components of signal transduction pathways and genes encoding replicative functions in more detail. We found that the two genomes possess different, although overlapping, sets of genes in both classes, suggesting that different genes from each class were lost, perhaps randomly, after the separate evolution from an ancestral genome. Random loss would also account for the fact that more than one-third of the genes in one viral genome has no counterparts in the other genome. We speculate that the ancestral genome belonged to a cellular organism that had once invaded a primordial brown algal host.
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Affiliation(s)
- Nicolas Delaroque
- Max-Planck-lnstitut für Chemische Okologie, Beutenberg Campus, Hans-Knöll-Strasse 8, D-07745 Jena, Germany.
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Abstract
Paramecium bursaria chlorella virus (PBCV-1) is the prototype of a family of large, icosahedral, plaque-forming, double-stranded-DNA-containing viruses that replicate in certain unicellular, eukaryotic chlorella-like green algae. DNA sequence analysis of its 330, 742-bp genome leads to the prediction that this phycodnavirus has 376 protein-encoding genes and 10 transfer RNA genes. The predicted gene products of approximately 40% of these genes resemble proteins of known function. The chlorella viruses have other features that distinguish them from most viruses, in addition to their large genome size. These features include the following: (a) The viruses encode multiple DNA methyltransferases and DNA site-specific endonucleases; (b) PBCV-1 encodes at least part, if not the entire machinery to glycosylate its proteins; (c) PBCV-1 has at least two types of introns--a self-splicing intron in a transcription factor-like gene and a splicesomal processed type of intron in its DNA polymerase gene. Unlike the chlorella viruses, large double-stranded-DNA-containing viruses that infect marine, filamentous brown algae have a circular genome and a lysogenic phase in their life cycle.
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Affiliation(s)
- J L Van Etten
- Department of Plant Pathology, University of Nebraska, Lincoln 68583-0722, USA.
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Lee AM, Ivey RG, Meints RH. Repetitive DNA insertion in a protein kinase ORF of a latent FSV (Feldmannia sp. virus) genome. Virology 1998; 248:35-45. [PMID: 9705253 DOI: 10.1006/viro.1998.9245] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe the structure of a Feldmannia sp. virus (FsV) genome integrated in the brown alga, Feldmannia. This integrated FsV genome appears to be permanently inactivated and lost its ability to excise and replicate. Unlike the replicated form of FsV, this integrated FsV genome contains a large (>50 kb) repeat region inserted in a protein kinase open reading frame. While related to the 173-bp repeats previously characterized in the FsV genome (Lee et al., 1995), Southern blot analysis indicates that the repeats in the inactive, integrated FsV genome are distinct from those previously characterized. Fine structural analysis of the repeat-insertion sites in the protein kinase gene indicates that there are 8- and 10-bp palindromic sequences present in multiple locations located near the repeat-insertion site. The translated protein kinase contains all of the catalytic motifs conserved in most serine/threonine protein kinases and a potential autophosphorylation site. This protein kinase gene is expressed as RNA in sporophyte plants where virus production is active but not in gametophyte plants where the virus genome is latent. The structure of the integrated virus genome is discussed.
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Affiliation(s)
- A M Lee
- Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon, 97331-2906, USA
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Abstract
Viruses infecting algal hosts possess large double-stranded DNA as genomes. We have recently identified a family of viruses specific for filamentous brown algae. In contrast to the better known Chlorella viruses with their lytic infection cycle, marine brown algal viruses latently occur in their host cells and are induced to multiply in response to a variety of external stimuli such as change in light and temperature. Here, I summarize the known properties of this family of viruses and discuss their taxonomic classification.
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Affiliation(s)
- M Kapp
- Fakultät für Biologie, Universität Konstanz.
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Affiliation(s)
- D G Müller
- Fakultät für Biologie, Universität Konstanz, Germany
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