1
|
Shao Q, Agarkova IV, Noel EA, Dunigan DD, Liu Y, Wang A, Guo M, Xie L, Zhao X, Rossmann MG, Van Etten JL, Klose T, Fang Q. Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1. Nat Commun 2022; 13:6476. [PMID: 36309542 PMCID: PMC9617893 DOI: 10.1038/s41467-022-34218-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/18/2022] [Indexed: 12/25/2022] Open
Abstract
Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play critical roles in the viral life cycles, identities and high-resolution structures of these components remain unknown. Here, by determining a near-atomic-resolution, five-fold averaged structure of Paramecium bursaria chlorella virus 1, we unexpectedly found the viral capsid possesses up to five major capsid protein variants and a penton protein variant. These variants create varied capsid microenvironments for the associations of fibers, a vesicle, and previously unresolved minor capsid proteins. Our structure reveals the identities and atomic models of the capsid components that do not obey the overall icosahedral symmetry and leads to a model for how these components are assembled and initiate capsid assembly, and this model might be applicable to many other giant viruses.
Collapse
Affiliation(s)
- Qianqian Shao
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Irina V Agarkova
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - Eric A Noel
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - David D Dunigan
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - Yunshu Liu
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Aohan Wang
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Mingcheng Guo
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Linlin Xie
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Xinyue Zhao
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA.
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| | - Qianglin Fang
- Scholl of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 518107, China.
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| |
Collapse
|
2
|
Retel C, Kowallik V, Becks L, Feulner PGD. Strong Selection and High Mutation Supply Characterize Experimental Chlorovirus Evolution. Virus Evol 2022; 8:veac003. [PMID: 35169490 PMCID: PMC8838748 DOI: 10.1093/ve/veac003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
Characterizing how viruses evolve expands our understanding of the underlying fundamental processes, such as mutation, selection and drift. One group of viruses whose evolution has not yet been extensively studied is the Phycodnaviridae, a globally abundant family of aquatic large double-stranded (ds) DNA viruses. Here we studied the evolutionary change of Paramecium bursaria chlorella virus 1 during experimental coevolution with its algal host. We used pooled genome sequencing of six independently evolved populations to characterize genomic change over five time points. Across six experimental replicates involving either strong or weak demographic fluctuations, we found single nucleotide polymorphisms (SNPs) at sixty-seven sites. The occurrence of genetic variants was highly repeatable, with just two of the SNPs found in only a single experimental replicate. Three genes A122/123R, A140/145R and A540L showed an excess of variable sites, providing new information about potential targets of selection during Chlorella–Chlorovirus coevolution. Our data indicated that the studied populations were not mutation-limited and experienced strong positive selection. Our investigation highlighted relevant processes governing the evolution of aquatic large dsDNA viruses, which ultimately contributes to a better understanding of the functioning of natural aquatic ecosystems.
Collapse
Affiliation(s)
- Cas Retel
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Bio-geochemistry, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, Kastanienbaum 6047, Switzerland
- Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
| | | | | | | |
Collapse
|
3
|
Mönttinen HAM, Bicep C, Williams TA, Hirt RP. The genomes of nucleocytoplasmic large DNA viruses: viral evolution writ large. Microb Genom 2021; 7. [PMID: 34542398 PMCID: PMC8715426 DOI: 10.1099/mgen.0.000649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The nucleocytoplasmic large DNA viruses (NCLDVs) are a diverse group that currently contain the largest known virions and genomes, also called giant viruses. The first giant virus was isolated and described nearly 20 years ago. Their genome sizes were larger than for any other known virus at the time and it contained a number of genes that had not been previously described in any virus. The origin and evolution of these unusually complex viruses has been puzzling, and various mechanisms have been put forward to explain how some NCLDVs could have reached genome sizes and coding capacity overlapping with those of cellular microbes. Here we critically discuss the evidence and arguments on this topic. We have also updated and systematically reanalysed protein families of the NCLDVs to further study their origin and evolution. Our analyses further highlight the small number of widely shared genes and extreme genomic plasticity among NCLDVs that are shaped via combinations of gene duplications, deletions, lateral gene transfers and de novo creation of protein-coding genes. The dramatic expansions of the genome size and protein-coding gene capacity characteristic of some NCLDVs is now increasingly understood to be driven by environmental factors rather than reflecting relationships to an ancient common ancestor among a hypothetical cellular lineage. Thus, the evolution of NCLDVs is writ large viral, and their origin, like all other viral lineages, remains unknown.
Collapse
Affiliation(s)
- Heli A M Mönttinen
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Present address: Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Viikki Biocenter 2, Helsinki 00014, Finland
| | - Cedric Bicep
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Present address: Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont Ferrand, France
| | - Tom A Williams
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,School of Biological Sciences, University of Bristol, 24 Tyndall Ave., Bristol, BS8 1TH, UK
| | - Robert P Hirt
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| |
Collapse
|
4
|
Van Etten JL, Agarkova I, Dunigan DD, Tonetti M, De Castro C, Duncan GA. Chloroviruses Have a Sweet Tooth. Viruses 2017; 9:E88. [PMID: 28441734 PMCID: PMC5408694 DOI: 10.3390/v9040088] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/13/2017] [Accepted: 04/14/2017] [Indexed: 01/16/2023] Open
Abstract
Chloroviruses are large double-stranded DNA (dsDNA) viruses that infect certain isolates of chlorella-like green algae. They contain up to approximately 400 protein-encoding genes and 16 transfer RNA (tRNA) genes. This review summarizes the unexpected finding that many of the chlorovirus genes encode proteins involved in manipulating carbohydrates. These include enzymes involved in making extracellular polysaccharides, such as hyaluronan and chitin, enzymes that make nucleotide sugars, such as GDP-L-fucose and GDP-D-rhamnose and enzymes involved in the synthesis of glycans attached to the virus major capsid proteins. This latter process differs from that of all other glycoprotein containing viruses that traditionally use the host endoplasmic reticulum and Golgi machinery to synthesize and transfer the glycans.
Collapse
Affiliation(s)
- James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA.
| | - Irina Agarkova
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA.
| | - David D Dunigan
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA.
| | - Michela Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova Viale Benedetto XV/1, 16132 Genova, Italy.
| | - Christina De Castro
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, NA, Italy.
| | - Garry A Duncan
- Department of Biology, Nebraska Wesleyan University, Lincoln, NE 68504-2796, USA.
| |
Collapse
|
5
|
Oliveira GP, Andrade ACDSP, Rodrigues RAL, Arantes TS, Boratto PVM, Silva LKDS, Dornas FP, Trindade GDS, Drumond BP, La Scola B, Kroon EG, Abrahão JS. Promoter Motifs in NCLDVs: An Evolutionary Perspective. Viruses 2017; 9:v9010016. [PMID: 28117683 PMCID: PMC5294985 DOI: 10.3390/v9010016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/30/2016] [Accepted: 01/05/2017] [Indexed: 01/18/2023] Open
Abstract
For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations.
Collapse
Affiliation(s)
- Graziele Pereira Oliveira
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Ana Cláudia Dos Santos Pereira Andrade
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Thalita Souza Arantes
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Paulo Victor Miranda Boratto
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Ludmila Karen Dos Santos Silva
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Fábio Pio Dornas
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Giliane de Souza Trindade
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Betânia Paiva Drumond
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Université., 27 Boulevard Jean Moulin, Faculté de Médecine, 13385 Marseille Cedex 05, France.
| | - Erna Geessien Kroon
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil.
| |
Collapse
|
6
|
Quispe CF, Esmael A, Sonderman O, McQuinn M, Agarkova I, Battah M, Duncan GA, Dunigan DD, Smith TPL, De Castro C, Speciale I, Ma F, Van Etten JL. Characterization of a new chlorovirus type with permissive and non-permissive features on phylogenetically related algal strains. Virology 2016; 500:103-113. [PMID: 27816636 DOI: 10.1016/j.virol.2016.10.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/13/2016] [Accepted: 10/15/2016] [Indexed: 11/26/2022]
Abstract
A previous report indicated that prototype chlorovirus PBCV-1 replicated in two Chlorella variabilis algal strains, NC64A and Syngen 2-3, that are ex-endosymbionts isolated from the protozoan Paramecium bursaria. Surprisingly, plaque-forming viruses on Syngen 2-3 lawns were often higher than on NC64A lawns from indigenous water samples. These differences led to the discovery of viruses that exclusively replicate in Syngen 2-3 cells, named Only Syngen (OSy) viruses. OSy-NE5, the prototype virus for the proposed new species, had a linear dsDNA genome of 327kb with 44-nucleotide-long, incompletely base-paired, covalently closed hairpin ends. Each hairpin structure was followed by an identical 2612 base-paired inverted sequence after which the DNA sequence diverged. OSy-NE5 encoded 357 predicted CDSs and 13 tRNAs. Interestingly, OSy-NE5 attached to and initiated infection in NC64A cells but infectious progeny viruses were not produced; thus OSy-NE5 replication in NC64A is blocked at some later stage of replication.
Collapse
Affiliation(s)
- Cristian F Quispe
- Nebraska Center for Virology, University of Nebraska-Lincoln, NE 68583-0900, USA; School of Biological Science, University of Nebraska-Lincoln, NE 68588-0118, USA
| | - Ahmed Esmael
- Nebraska Center for Virology, University of Nebraska-Lincoln, NE 68583-0900, USA; Botany Department, Faculty of Science, Benha University, Qalubiya Governorate, 13511, Egypt
| | - Olivia Sonderman
- Nebraska Center for Virology, University of Nebraska-Lincoln, NE 68583-0900, USA; School of Biological Science, University of Nebraska-Lincoln, NE 68588-0118, USA
| | - Michelle McQuinn
- Nebraska Center for Virology, University of Nebraska-Lincoln, NE 68583-0900, USA
| | - Irina Agarkova
- Nebraska Center for Virology, University of Nebraska-Lincoln, NE 68583-0900, USA; Department of Plant Pathology and University of Nebraska-Lincoln, NE 68583-0722, USA
| | - Mohammed Battah
- Botany Department, Faculty of Science, Benha University, Qalubiya Governorate, 13511, Egypt
| | - Garry A Duncan
- Department of Biology, Nebraska Wesleyan University, Lincoln, NE 68504-2794, USA
| | - David D Dunigan
- Nebraska Center for Virology, University of Nebraska-Lincoln, NE 68583-0900, USA; Department of Plant Pathology and University of Nebraska-Lincoln, NE 68583-0722, USA
| | - Timothy P L Smith
- Agricultural Research Service, United States Department of Agriculture, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, USA
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli, Via Universita 100, 80055 Portici, NA, Italy
| | | | - Fangrui Ma
- Center for Biotechnology, University of Nebraska, Lincoln, NE 68583-0900, USA
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska-Lincoln, NE 68583-0900, USA; Department of Plant Pathology and University of Nebraska-Lincoln, NE 68583-0722, USA.
| |
Collapse
|
7
|
Paramecium bursaria chlorella virus 1 proteome reveals novel architectural and regulatory features of a giant virus. J Virol 2012; 86:8821-34. [PMID: 22696644 DOI: 10.1128/jvi.00907-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 331-kbp chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) genome was resequenced and annotated to correct errors in the original 15-year-old sequence; 40 codons was considered the minimum protein size of an open reading frame. PBCV-1 has 416 predicted protein-encoding sequences and 11 tRNAs. A proteome analysis was also conducted on highly purified PBCV-1 virions using two mass spectrometry-based protocols. The mass spectrometry-derived data were compared to PBCV-1 and its host Chlorella variabilis NC64A predicted proteomes. Combined, these analyses revealed 148 unique virus-encoded proteins associated with the virion (about 35% of the coding capacity of the virus) and 1 host protein. Some of these proteins appear to be structural/architectural, whereas others have enzymatic, chromatin modification, and signal transduction functions. Most (106) of the proteins have no known function or homologs in the existing gene databases except as orthologs with proteins of other chloroviruses, phycodnaviruses, and nuclear-cytoplasmic large DNA viruses. The genes encoding these proteins are dispersed throughout the virus genome, and most are transcribed late or early-late in the infection cycle, which is consistent with virion morphogenesis.
Collapse
|
8
|
Wilson WH, Van Etten JL, Allen MJ. The Phycodnaviridae: the story of how tiny giants rule the world. Curr Top Microbiol Immunol 2009; 328:1-42. [PMID: 19216434 DOI: 10.1007/978-3-540-68618-7_1] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The family Phycodnaviridae encompasses a diverse and rapidly expanding collection of large icosahedral, dsDNA viruses that infect algae. These lytic and lysogenic viruses have genomes ranging from 160 to 560 kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect them with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV). The phycodnaviruses have diverse genome structures, some with large regions of noncoding sequence and others with regions of ssDNA. The genomes of members in three genera in the Phycodnaviridae have been sequenced. The genome analyses have revealed more than 1000 unique genes, with only 14 homologous genes in common among the three genera of phycodnaviruses sequenced to date. Thus, their gene diversity far exceeds the number of so-called core genes. Not much is known about the replication of these viruses, but the consequences of these infections on phytoplankton have global affects, including influencing geochemical cycling and weather patterns.
Collapse
Affiliation(s)
- W H Wilson
- Bigelow Laboratory for Ocean Sciences, 180 McKown Point, P.O. Box 475, West Boothbay Harbor, ME 04575-0475, USA.
| | | | | |
Collapse
|
9
|
Dunigan DD, Fitzgerald LA, Van Etten JL. Phycodnaviruses: a peek at genetic diversity. Virus Res 2006; 117:119-32. [PMID: 16516998 DOI: 10.1016/j.virusres.2006.01.024] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Revised: 01/18/2006] [Accepted: 01/23/2006] [Indexed: 10/24/2022]
Abstract
The family Phycodnaviridae encompasses a diverse collection of large icosahedral, dsDNA viruses infecting algae. These viruses have genomes ranging from 160 to 560kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV). The genomes of members in three genera in the Phycodnaviridae have recently been sequenced and the purpose of this manuscript is to summarize these data. The viruses have diverse genome structures, some with large regions of non-coding sequence and others with regions of single-stranded DNA. Typically, phycodnaviruses have the coding capacity for hundreds of genes. The genome analyses have revealed in excess of 1000 unique genes, with only 14 homologous genes held in common among the three genera of the phycodnavirses sequenced to date. Thus, the gene diversity far exceeds the number of so-called "core" genes. Little is known about the replication of these viruses, but the consequences of these infections of the phytoplankton have global affects, including altered geochemical cycling and weather patterns.
Collapse
Affiliation(s)
- David D Dunigan
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, USA.
| | | | | |
Collapse
|
10
|
Abstract
Chlorella viruses or chloroviruses are large, icosahedral, plaque-forming, double-stranded-DNA-containing viruses that replicate in certain strains of the unicellular green alga Chlorella. DNA sequence analysis of the 330-kbp genome of Paramecium bursaria chlorella virus 1 (PBCV-1), the prototype of this virus family (Phycodnaviridae), predict approximately 366 protein-encoding genes and 11 tRNA genes. The predicted gene products of approximately 50% of these genes resemble proteins of known function, including many that are completely unexpected for a virus. In addition, the chlorella viruses have several features and encode many gene products that distinguish them from most viruses. These products include: (1) multiple DNA methyltransferases and DNA site-specific endonucleases, (2) the enzymes required to glycosylate their proteins and synthesize polysaccharides such as hyaluronan and chitin, (3) a virus-encoded K(+) channel (called Kcv) located in the internal membrane of the virions, (4) a SET domain containing protein (referred to as vSET) that dimethylates Lys27 in histone 3, and (5) PBCV-1 has three types of introns; a self-splicing intron, a spliceosomal processed intron, and a small tRNA intron. Accumulating evidence indicates that the chlorella viruses have a very long evolutionary history. This review mainly deals with research on the virion structure, genome rearrangements, gene expression, cell wall degradation, polysaccharide synthesis, and evolution of PBCV-1 as well as other related viruses.
Collapse
Affiliation(s)
- Takashi Yamada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi, Japan
| | | | | |
Collapse
|
11
|
Kawasaki T, Tanaka M, Fujie M, Usami S, Yamada T. Immediate early genes expressed in chlorovirus infections. Virology 2004; 318:214-23. [PMID: 14972549 DOI: 10.1016/j.virol.2003.09.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 09/11/2003] [Accepted: 09/12/2003] [Indexed: 11/17/2022]
Abstract
Twenty-three chlorovirus genes expressed in host cells as early as 5-10 min postinfection (p.i.), or immediate early, were isolated and characterized. Some showed significant homology with those for transcriptional factors and mRNA-processing proteins including TFIIB, helicases, mRNA capping enzyme, nucleolin, and bean transcription factor. Others code for (i) factors influencing translation such as aminoacyl tRNA synthetases and ribosomal protein, and (ii) unknown proteins. Enzymes involved in polysaccharide synthesis were also found. All transcripts of these genes had a poly(A) tail, which decreased in size after 20 min p.i., possibly caused by the shortening by an exonuclease. Often, due to readthrough either from an upstream ORF or into a downstream ORF, a few extra transcripts for each gene appeared after 40 min p.i., suggesting a change in promoter selection and termination accuracy at this point. A typical TATA-box and a common element 5'-ATGACAA were in the promoter region of almost all of the immediate early genes, which may be recognized by host RNA polymerase and transcription factors.
Collapse
Affiliation(s)
- Takeru Kawasaki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima 739-8530, Japan
| | | | | | | | | |
Collapse
|
12
|
Onimatsu H, Sugimoto I, Fujie M, Usami S, Yamada T. Vp130, a chloroviral surface protein that interacts with the host Chlorella cell wall. Virology 2004; 319:71-80. [PMID: 14967489 DOI: 10.1016/j.virol.2003.10.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2003] [Revised: 10/16/2003] [Accepted: 10/16/2003] [Indexed: 11/20/2022]
Abstract
A protein, Vp130, that interacts with the host cell wall was isolated from Chlorovirus CVK2. From its peptide sequence, the gene for Vp130 was identified on the PBCV-1 genomic sequence as an ORF combining A140R and A145R. In Vp130, the N-terminus was somehow modified and the C-terminus was occupied by 23-26 tandem repeats of a PAPK motif. In the internal region, Vp130 contained seven repeats of 70-73 amino acids, each copy of which was separated by PAPK sequences. This protein was well conserved among NC64A viruses. A recombinant rVp130N protein formed in Escherichia coli was shown not only to bind directly to the host cell wall in vitro but also to specifically bind to the host cells, as demonstrated by fluorescence microscopy. Because externally added rVp130N competed with CVK2 to bind to host cells, Vp130 is most likely to be a host-recognizing protein on the virion.
Collapse
Affiliation(s)
- Hideki Onimatsu
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan.
| | | | | | | | | |
Collapse
|
13
|
Abstract
Paramecium bursaria chlorella virus (PBCV-1) is the prototype of a family of large, icosahedral, plaque-forming, dsDNA viruses that replicate in certain unicellular, eukaryotic chlorella-like green algae. Its 330-kb genome contains approximately 373 protein-encoding genes and 11 tRNA genes. The predicted gene products of approximately 50% of these genes resemble proteins of known function, including many that are unexpected for a virus, e.g., ornithine decarboxylase, hyaluronan synthase, GDP-D-mannose 4,6 dehydratase, and a potassium ion channel protein. In addition to their large genome size, the chlorella viruses have other features that distinguish them from most viruses. These features include: (a) The viruses encode multiple DNA methyltransferases and DNA site-specific endonucleases. (b) The viruses encode at least some, if not all, of the enzymes required to glycosylate their proteins. (c) PBCV-1 has at least three types of introns, a self-splicing intron in a transcription factor-like gene, a spliceosomal processed intron in its DNA polymerase gene, and a small intron in one of its tRNA genes. (d) Many chlorella virus-encoded proteins are either the smallest or among the smallest proteins of their class. (e) Accumulating evidence indicates that the chlorella viruses have a very long evolutionary history.
Collapse
Affiliation(s)
- James L Van Etten
- Nebraska Center for Virology and Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, USA.
| |
Collapse
|