1
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Lievens EJP, Kühn S, Horas EL, Le Pennec G, Peter S, Petrosky AD, Künzel S, Feulner PGD, Becks L. High parasite diversity maintained after an alga-virus coevolutionary arms race. J Evol Biol 2024; 37:795-806. [PMID: 38699979 DOI: 10.1093/jeb/voae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/27/2024] [Accepted: 05/02/2024] [Indexed: 05/05/2024]
Abstract
Arms race dynamics are a common outcome of host-parasite coevolution. While they can theoretically be maintained indefinitely, realistic arms races are expected to be finite. Once an arms race has ended, for example due to the evolution of a generalist-resistant host, the system may transition into coevolutionary dynamics that favour long-term diversity. In microbial experiments, host-parasite arms races often transition into a stable coexistence of generalist-resistant hosts, (semi-)susceptible hosts, and parasites. While long-term host diversity is implicit in these cases, parasite diversity is usually overlooked. In this study, we examined parasite diversity after the end of an experimental arms race between a unicellular alga (Chlorella variabilis) and its lytic virus (PBCV-1). First, we isolated virus genotypes from multiple time points from two replicate microcosms. A time-shift experiment confirmed that the virus isolates had escalating host ranges, i.e., that arms races had occurred. We then examined the phenotypic and genetic diversity of virus isolates from the post-arms race phase. Post-arms race virus isolates had diverse host ranges, survival probabilities, and growth rates; they also clustered into distinct genetic groups. Importantly, host range diversity was maintained throughout the post-arms race phase, and the frequency of host range phenotypes fluctuated over time. We hypothesize that this dynamic polymorphism was maintained by a combination of fluctuating selection and demographic stochasticity. Together with previous work in prokaryotic systems, our results link experimental observations of arms races to natural observations of long-term host and parasite diversity.
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Affiliation(s)
- Eva J P Lievens
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Samuel Kühn
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Elena L Horas
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Guénolé Le Pennec
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Sarah Peter
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Azade D Petrosky
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Department of Biology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Lutz Becks
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
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2
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Lievens EJP, Agarkova IV, Dunigan DD, Van Etten JL, Becks L. Efficient assays to quantify the life history traits of algal viruses. Appl Environ Microbiol 2023; 89:e0165923. [PMID: 38092674 PMCID: PMC10734466 DOI: 10.1128/aem.01659-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 12/22/2023] Open
Abstract
IMPORTANCE Viruses play a crucial role in microbial ecosystems by liberating nutrients and regulating the growth of their hosts. These effects are governed by viral life history traits, i.e., by the traits determining viral reproduction and survival. Understanding these traits is essential to predicting viral effects, but measuring them is generally labor intensive. In this study, we present efficient methods to quantify the full life cycle of lytic viruses. We developed these methods for viruses infecting unicellular Chlorella algae but expect them to be applicable to other lytic viruses that can be quantified by flow cytometry. By making viral phenotypes accessible, our methods will support research into the diversity and ecological effects of microbial viruses.
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Affiliation(s)
- Eva J. P. Lievens
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Irina V. Agarkova
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - David D. Dunigan
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - James L. Van Etten
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Lutz Becks
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Konstanz, Germany
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3
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Cutolo EA, Caferri R, Campitiello R, Cutolo M. The Clinical Promise of Microalgae in Rheumatoid Arthritis: From Natural Compounds to Recombinant Therapeutics. Mar Drugs 2023; 21:630. [PMID: 38132951 PMCID: PMC10745133 DOI: 10.3390/md21120630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Rheumatoid arthritis (RA) is an invalidating chronic autoimmune disorder characterized by joint inflammation and progressive bone damage. Dietary intervention is an important component in the treatment of RA to mitigate oxidative stress, a major pathogenic driver of the disease. Alongside traditional sources of antioxidants, microalgae-a diverse group of photosynthetic prokaryotes and eukaryotes-are emerging as anti-inflammatory and immunomodulatory food supplements. Several species accumulate therapeutic metabolites-mainly lipids and pigments-which interfere in the pro-inflammatory pathways involved in RA and other chronic inflammatory conditions. The advancement of the clinical uses of microalgae requires the continuous exploration of phytoplankton biodiversity and chemodiversity, followed by the domestication of wild strains into reliable producers of said metabolites. In addition, the tractability of microalgal genomes offers unprecedented possibilities to establish photosynthetic microbes as light-driven biofactories of heterologous immunotherapeutics. Here, we review the evidence-based anti-inflammatory mechanisms of microalgal metabolites and provide a detailed coverage of the genetic engineering strategies to enhance the yields of endogenous compounds and to develop innovative bioproducts.
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Affiliation(s)
- Edoardo Andrea Cutolo
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy;
| | - Roberto Caferri
- Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy;
| | - Rosanna Campitiello
- Research Laboratory and Academic Division of Clinical Rheumatology, Department of Internal Medicine, IRCCS San Martino Polyclinic Hospital, University of Genoa, Viale Benedetto XV, 6, 16132 Genoa, Italy; (R.C.)
| | - Maurizio Cutolo
- Research Laboratory and Academic Division of Clinical Rheumatology, Department of Internal Medicine, IRCCS San Martino Polyclinic Hospital, University of Genoa, Viale Benedetto XV, 6, 16132 Genoa, Italy; (R.C.)
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4
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Truchon AR, Chase EE, Gann ER, Moniruzzaman M, Creasey BA, Aylward FO, Xiao C, Gobler CJ, Wilhelm SW. Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research. Front Microbiol 2023; 14:1284617. [PMID: 38098665 PMCID: PMC10720644 DOI: 10.3389/fmicb.2023.1284617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023] Open
Abstract
Since the discovery of the first "giant virus," particular attention has been paid toward isolating and culturing these large DNA viruses through Acanthamoeba spp. bait systems. While this method has allowed for the discovery of plenty novel viruses in the Nucleocytoviricota, environmental -omics-based analyses have shown that there is a wealth of diversity among this phylum, particularly in marine datasets. The prevalence of these viruses in metatranscriptomes points toward their ecological importance in nutrient turnover in our oceans and as such, in depth study into non-amoebal Nucleocytoviricota should be considered a focal point in viral ecology. In this review, we report on Kratosvirus quantuckense (née Aureococcus anophagefferens Virus), an algae-infecting virus of the Imitervirales. Current systems for study in the Nucleocytoviricota differ significantly from this virus and its relatives, and a litany of trade-offs within physiology, coding potential, and ecology compared to these other viruses reveal the importance of K. quantuckense. Herein, we review the research that has been performed on this virus as well as its potential as a model system for algal-virus interactions.
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Affiliation(s)
- Alexander R Truchon
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Emily E Chase
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric R Gann
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Surgical Critical Care Initiative (SC2i), Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, United States
| | - Brooke A Creasey
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Chuan Xiao
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
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5
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Qin S, Wang K, Gao F, Ge B, Cui H, Li W. Biotechnologies for bulk production of microalgal biomass: from mass cultivation to dried biomass acquisition. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:131. [PMID: 37644516 PMCID: PMC10466707 DOI: 10.1186/s13068-023-02382-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
Microalgal biomass represents a sustainable bioresource for various applications, such as food, nutraceuticals, pharmaceuticals, feed, and other bio-based products. For decades, its mass production has attracted widespread attention and interest. The process of microalgal biomass production involves several techniques, mainly cultivation, harvesting, drying, and pollution control. These techniques are often designed and optimized to meet optimal growth conditions for microalgae and to produce high-quality biomass at acceptable cost. Importantly, mass production techniques are important for producing a commercial product in sufficient amounts. However, it should not be overlooked that microalgal biotechnology still faces challenges, in particular the high cost of production, the lack of knowledge about biological contaminants and the challenge of loss of active ingredients during biomass production. These issues involve the research and development of low-cost, standardized, industrial-scale production equipment and the optimization of production processes, as well as the urgent need to increase the research on biological contaminants and microalgal active ingredients. This review systematically examines the global development of microalgal biotechnology for biomass production, with emphasis on the techniques of cultivation, harvesting, drying and control of biological contaminants, and discusses the challenges and strategies to further improve quality and reduce costs. Moreover, the current status of biomass production of some biotechnologically important species has been summarized, and the importance of improving microalgae-related standards for their commercial applications is noted.
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Affiliation(s)
- Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, No. 19, Chunhui Road, Laishan District, Yantai, 264003, Shandong, China.
| | - Kang Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, No. 19, Chunhui Road, Laishan District, Yantai, 264003, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengzheng Gao
- Bioprocess Engineering, AlgaePARC, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, Netherlands
- Laboratory of Sustainable Food Processing, ETH Zürich, 8092, Zurich, Switzerland
- Laboratory of Nutrition and Metabolic Epigenetics, ETH Zürich, 8603, Schwerzenbach, Switzerland
| | - Baosheng Ge
- College of Chemical Engineering and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Hongli Cui
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, No. 19, Chunhui Road, Laishan District, Yantai, 264003, Shandong, China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, No. 19, Chunhui Road, Laishan District, Yantai, 264003, Shandong, China
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6
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Esmael A, Agarkova IV, Dunigan DD, Zhou Y, Van Etten JL. Viral DNA Accumulation Regulates Replication Efficiency of Chlorovirus OSy-NE5 in Two Closely Related Chlorella variabilis Strains. Viruses 2023; 15:1341. [PMID: 37376640 DOI: 10.3390/v15061341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Many chloroviruses replicate in Chlorella variabilis algal strains that are ex-endosymbionts isolated from the protozoan Paramecium bursaria, including the NC64A and Syngen 2-3 strains. We noticed that indigenous water samples produced a higher number of plaque-forming viruses on C. variabilis Syngen 2-3 lawns than on C. variabilis NC64A lawns. These observed differences led to the discovery of viruses that replicate exclusively in Syngen 2-3 cells, named Only Syngen (OSy) viruses. Here, we demonstrate that OSy viruses initiate infection in the restricted host NC64A by synthesizing some early virus gene products and that approximately 20% of the cells produce a small number of empty virus capsids. However, the infected cells did not produce infectious viruses because the cells were unable to replicate the viral genome. This is interesting because all previous attempts to isolate host cells resistant to chlorovirus infection were due to changes in the host receptor for the virus.
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Affiliation(s)
- Ahmed Esmael
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583, USA
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Irina V Agarkova
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, USA
| | - David D Dunigan
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, USA
| | - You Zhou
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, USA
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7
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Horas EL, Metzger SM, Platzer B, Kelly JB, Becks L. Context-dependent costs and benefits of endosymbiotic interactions in a ciliate-algae system. Environ Microbiol 2022; 24:5924-5935. [PMID: 35799468 DOI: 10.1111/1462-2920.16112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/20/2022] [Indexed: 01/12/2023]
Abstract
Endosymbiosis, an interaction between two species where one lives within the other, has evolved multiple times independently, but the underlying mechanisms remain unclear. Evolutionary theory suggests that for an endosymbiotic interaction to remain stable over time, births of both partners should be higher than their deaths in symbiosis and deaths of both partners should be higher than their births when living independently. However, experimentally measuring this can be difficult and conclusions tend to focus on the host. Using a ciliate-algal system (Paramecium bursaria host and Chlorella endosymbionts), we estimated the benefits and costs of endosymbiosis for both organisms using fitness measurements in different biotic environments to test under which environmental conditions the net effects of the interaction were positive for both partners. We found that the net effects of harbouring endosymbionts were positive for the ciliate hosts as it allowed them to survive in conditions of low-quality bacteria food. The algae benefitted by being endosymbiotic when predators such as the hosts were present, but the net effects were dependent on the total density of hosts, decreasing as hosts densities increased. Overall, we show that including context-dependency of endosymbiosis is essential in understanding how these interactions have evolved.
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Affiliation(s)
- Elena L Horas
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Sarah M Metzger
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Konstanz, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Barbara Platzer
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Joseph B Kelly
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Lutz Becks
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Konstanz, Germany
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8
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Giant Viruses as a Source of Novel Enzymes for Biotechnological Application. Pathogens 2022; 11:pathogens11121453. [PMID: 36558786 PMCID: PMC9787589 DOI: 10.3390/pathogens11121453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application.
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9
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Speciale I, Notaro A, Abergel C, Lanzetta R, Lowary TL, Molinaro A, Tonetti M, Van Etten JL, De Castro C. The Astounding World of Glycans from Giant Viruses. Chem Rev 2022; 122:15717-15766. [PMID: 35820164 PMCID: PMC9614988 DOI: 10.1021/acs.chemrev.2c00118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Viruses are a heterogeneous ensemble of entities, all
sharing the
need for a suitable host to replicate. They are extremely diverse,
varying in morphology, size, nature, and complexity of their genomic
content. Typically, viruses use host-encoded glycosyltransferases
and glycosidases to add and remove sugar residues from their glycoproteins.
Thus, the structure of the glycans on the viral proteins have, to
date, typically been considered to mimick those of the host. However,
the more recently discovered large and giant viruses differ from this
paradigm. At least some of these viruses code for an (almost) autonomous
glycosylation pathway. These viral genes include those that encode
the production of activated sugars, glycosyltransferases, and other
enzymes able to manipulate sugars at various levels. This review focuses
on large and giant viruses that produce carbohydrate-processing enzymes.
A brief description of those harboring these features at the genomic
level will be discussed, followed by the achievements reached with
regard to the elucidation of the glycan structures, the activity of
the proteins able to manipulate sugars, and the organic synthesis
of some of these virus-encoded glycans. During this progression, we
will also comment on many of the challenging questions on this subject
that remain to be addressed.
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Affiliation(s)
- Immacolata Speciale
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy
| | - Anna Notaro
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy.,Centre National de la Recherche Scientifique, Information Génomique & Structurale, Aix-Marseille University, Unité Mixte de Recherche 7256, IMM, IM2B, 13288 Marseille, Cedex 9, France
| | - Chantal Abergel
- Centre National de la Recherche Scientifique, Information Génomique & Structurale, Aix-Marseille University, Unité Mixte de Recherche 7256, IMM, IM2B, 13288 Marseille, Cedex 9, France
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Napoli, Via Cintia 4, 80126 Napoli, Italy
| | - Todd L Lowary
- Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, Nangang 11529, Taipei, Taiwan
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli, Via Cintia 4, 80126 Napoli, Italy
| | - Michela Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900, United States.,Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722, United States
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli, Via Università 100, 80055 Portici, Italy
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10
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Bolaños-Martínez OC, Mahendran G, Rosales-Mendoza S, Vimolmangkang S. Current Status and Perspective on the Use of Viral-Based Vectors in Eukaryotic Microalgae. Mar Drugs 2022; 20:md20070434. [PMID: 35877728 PMCID: PMC9318342 DOI: 10.3390/md20070434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022] Open
Abstract
During the last two decades, microalgae have attracted increasing interest, both commercially and scientifically. Commercial potential involves utilizing valuable natural compounds, including carotenoids, polysaccharides, and polyunsaturated fatty acids, which are widely applicable in food, biofuel, and pharmaceutical industries. Conversely, scientific potential focuses on bioreactors for producing recombinant proteins and developing viable technologies to significantly increase the yield and harvest periods. Here, viral-based vectors and transient expression strategies have significantly contributed to improving plant biotechnology. We present an updated outlook covering microalgal biotechnology for pharmaceutical application, transformation techniques for generating recombinant proteins, and genetic engineering tactics for viral-based vector construction. Challenges in industrial application are also discussed.
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Affiliation(s)
- Omayra C. Bolaños-Martínez
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (O.C.B.-M.); (G.M.)
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ganesan Mahendran
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (O.C.B.-M.); (G.M.)
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sergio Rosales-Mendoza
- Laboratorio de Biofarmacéuticos Recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, San Luis Potosí 78210, Mexico;
- Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2a Sección, San Luis Potosí 78210, Mexico
| | - Sornkanok Vimolmangkang
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (O.C.B.-M.); (G.M.)
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: ; Tel.: +662-218-8358
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11
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Xia Y, Cheng H, Zhong J. Hybrid Sequencing Resolved Inverted Terminal Repeats in the Genome of Megavirus Baoshan. Front Microbiol 2022; 13:831659. [PMID: 35620092 PMCID: PMC9127612 DOI: 10.3389/fmicb.2022.831659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
Mimivirus is a group of amoeba-infecting DNA viruses with linear double-strand genome. It is found to be ubiquitous in nature worldwide. Here, we reported the complete genome of a new member of Mimivirus lineage C isolated from a fresh water pond in Shanghai, China. Its 1,224,839-bp genome encoded 1,062 predicted ORFs. Combining the results of Nanopore, Illumina, and Sanger sequencing technologies, two identical 23,919 bp inverted terminal repeats (ITRs) were identified at both extremities of the viral linear genome, one of which was missing in the draft assembly based on Illumina data only. The discovery of ITRs of Mimivirus provided a new insight into Mimivirus genome structure.
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Affiliation(s)
- Yucheng Xia
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Department of Microbiology and Immunology, School of Life Sciences, Fudan University, Shanghai, China
| | - Huanyu Cheng
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Department of Microbiology and Immunology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiang Zhong
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Department of Microbiology and Immunology, School of Life Sciences, Fudan University, Shanghai, China
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12
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Veale CGL, Talukdar A, Vauzeilles B. ICBS 2021: Looking Toward the Next Decade of Chemical Biology. ACS Chem Biol 2022; 17:728-743. [PMID: 35293726 DOI: 10.1021/acschembio.2c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clinton G. L. Veale
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Boris Vauzeilles
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
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13
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Petro TM, Agarkova IV, Esmael A, Dunigan DD, Van Etten JL, Pattee GL. Chlorovirus ATCV-1 Accelerates Motor Deterioration in SOD1-G93A Transgenic Mice and Its SOD1 Augments Induction of Inflammatory Factors From Murine Macrophages. Front Neurol 2022; 13:821166. [PMID: 35280283 PMCID: PMC8908019 DOI: 10.3389/fneur.2022.821166] [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: 11/23/2021] [Accepted: 01/31/2022] [Indexed: 11/25/2022] Open
Abstract
Background Genetically polymorphic Superoxide Dismutase 1 G93A (SOD1-G93A) underlies one form of familial Amyotrophic Lateral Sclerosis (ALS). Exposures from viruses may also contribute to ALS, possibly by stimulating immune factors, such as IL-6, Interferon Stimulated Genes, and Nitric Oxide. Recently, chlorovirus ATCV-1, which encodes a SOD1, was shown to replicate in macrophages and induce inflammatory factors. Objective This study aimed to determine if ATCV-1 influences development of motor degeneration in an ALS mouse model and to assess whether SOD1 of ATCV-1 influences production of inflammatory factors from macrophages. Methods Sera from sporadic ALS patients were screened for antibody to ATCV-1. Active or inactivated ATCV-1, saline, or a viral mimetic, polyinosinic:polycytidylic acid (poly I:C) were injected intracranially into transgenic mice expressing human SOD1-G93A- or C57Bl/6 mice. RAW264.7 mouse macrophage cells were transfected with a plasmid vector expressing ATCV-1 SOD1 or an empty vector prior to stimulation with poly I:C with or without Interferon-gamma (IFN-γ). Results Serum from sporadic ALS patients had significantly more IgG1 antibody directed against ATCV-1 than healthy controls. Infection of SOD1-G93A mice with active ATCV-1 significantly accelerated onset of motor loss, as measured by tail paralysis, hind limb tucking, righting reflex, and latency to fall in a hanging cage-lid test, but did not significantly affect mortality when compared to saline-treated transgenics. By contrast, poly I:C treatment significantly lengthened survival time but only minimally slowed onset of motor loss, while heat-inactivated ATCV-1 did not affect motor loss or survival. ATCV-1 SOD1 significantly increased expression of IL-6, IL-10, ISG promoter activity, and production of Nitric Oxide from RAW264.7 cells. Conclusion ATCV-1 chlorovirus encoding an endogenous SOD1 accelerates pathogenesis but not mortality, while poly I:C that stimulates antiviral immune responses delays mortality in an ALS mouse model. ATCV-1 SOD1 enhances induction of inflammatory factors from macrophages.
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Affiliation(s)
- Thomas M. Petro
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, United States
- Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE, United States
- *Correspondence: Thomas M. Petro
| | - Irina V. Agarkova
- Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE, United States
- Department Plant Pathology, University of Nebraska Lincoln, Lincoln, NE, United States
| | - Ahmed Esmael
- Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE, United States
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, Egypt
| | - David D. Dunigan
- Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE, United States
- Department Plant Pathology, University of Nebraska Lincoln, Lincoln, NE, United States
| | - James L. Van Etten
- Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE, United States
- Department Plant Pathology, University of Nebraska Lincoln, Lincoln, NE, United States
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14
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Speciale I, Di Lorenzo F, Notaro A, Noel E, Agarkova I, Molinaro A, Van Etten JL, De Castro C. N-glycans from Paramecium bursaria chlorella virus MA-1D: Re-evaluation of the oligosaccharide common core structure. Glycobiology 2021; 32:260-273. [DOI: 10.1093/glycob/cwab113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 11/12/2022] Open
Abstract
Abstract
Paramecium bursaria chlorella virus MA-1D is a chlorovirus that infects Chlorella variabilis strain NC64A, a symbiont of the protozoan Paramecium bursaria. MA-1D has a 339-kb genome encoding ca. 366 proteins and 11 tRNAs. Like other chloroviruses, its major capsid protein (MCP) is decorated with N-glycans, whose structures have been solved in this work by using nuclear magnetic (NMR) spectroscopy and MALDI-TOF mass spectrometry along with MS/MS experiments. This analysis identified three N-linked oligosaccharides that differ in the non-stoichiometric presence of three monosaccharides, with the largest oligosaccharide composed of eight residues organized in a highly branched fashion. The N-glycans described here share several features with those of the other chloroviruses except that they lack a distal xylose unit that was believed to be part of a conserved core region for all the chloroviruses. Examination of the MA-1D genome detected a gene with strong homology to the putative xylosyltransferase in the reference chlorovirus PBCV-1 and in virus NY-2A, albeit mutated with a premature stop codon. This discovery means that we need to reconsider the essential features of the common core glycan region in the chloroviruses.
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Affiliation(s)
- Immacolata Speciale
- Department of Agricultural Sciences, University of Napoli Federico II, Via Università 100, 80055, Portici, Italy
| | - Flaviana Di Lorenzo
- Department of Agricultural Sciences, University of Napoli Federico II, Via Università 100, 80055, Portici, Italy
| | - Anna Notaro
- Department of Agricultural Sciences, University of Napoli Federico II, Via Università 100, 80055, Portici, Italy
| | - Eric Noel
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583-0900, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0118, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Irina Agarkova
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583-0900, USA
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, 68583-0722, USA
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia 26, 80126, Napoli, Italy
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583-0900, USA
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, 68583-0722, USA
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli Federico II, Via Università 100, 80055, Portici, Italy
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15
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Functional genomic analyses reveal an open pan-genome for the chloroviruses and a potential for genetic innovation in new isolates. J Virol 2021; 96:e0136721. [PMID: 34669449 DOI: 10.1128/jvi.01367-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chloroviruses (family Phycodnaviridae) are large dsDNA viruses that infect unicellular green algae present in inland waters. These viruses have been isolated using three main chlorella-like green algal host cells, traditionally called NC64A, SAG and Pbi, revealing extensive genetic diversity. In this study, we performed a functional genomic analysis on 36 chloroviruses that infected the three different hosts. Phylogenetic reconstruction based on the DNA polymerase B family gene clustered the chloroviruses into three distinct clades. The viral pan-genome consists of 1,345 clusters of orthologous groups of genes (COGs), with 126 COGs conserved in all viruses. 368, 268 and 265 COGs are found exclusively in viruses that infect NC64A, SAG, and Pbi algal hosts, respectively. Two-thirds of the COGs have no known function, constituting the "dark pan-genome" of chloroviruses, and further studies focusing on these genes may identify important novelties. The proportion of functionally characterized COGs composing the pan- and the core-genome are similar, but those related to transcription and RNA processing, protein metabolism, and virion morphogenesis are at least 4-fold more represented in the core-genome. Bipartite network construction evidencing the COG-sharing among host-specific viruses identified 270 COGs shared by at least one virus from each of the different host groups. Finally, our results reveal an open pan-genome for chloroviruses and a well-established core-genome, indicating that the isolation of new chloroviruses can be a valuable source of genetic discovery. Importance Chloroviruses are large dsDNA viruses that infect unicellular green algae distributed worldwide in freshwater environments. They comprise a genetically diverse group of viruses; however, a comprehensive investigation of the genomic evolution of these viruses is still missing. Here we performed a functional pan-genome analysis comprising 36 chloroviruses associated with three different algal hosts in the family Chlorellaceae, referred to as zoochlorellae because of their endosymbiotic lifestyle. We identified a set of 126 highly conserved genes, most of which are related to essential functions in the viral replicative cycle. Several genes are unique to distinct isolates, resulting in an open pan-genome for chloroviruses. This profile is associated with generalist organisms, and new insights into the evolution and ecology of chloroviruses are presented. Ultimately, our results highlight the potential for genetic diversity in new isolates.
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16
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Notaro A, Couté Y, Belmudes L, Laugeri ME, Salis A, Damonte G, Molinaro A, Tonetti MG, Abergel C, De Castro C. Expanding the Occurrence of Polysaccharides to the Viral World: The Case of Mimivirus. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Anna Notaro
- Department of Chemical Sciences University of Naples Federico II Via Cinthia 21 80126 Naples Italy
- Information Génomique & Structurale Unité Mixte de Recherche 7256 Aix-Marseille University Centre National de la Recherche Scientifique, IMM, IM2B 13288 Marseille Cedex 9 France
| | - Yohann Couté
- INSERM, CEA, UMR BioSanté U1292 Univ. Grenoble Alpes CNRS, CEA, FR2048 38000 Grenoble France
| | - Lucid Belmudes
- INSERM, CEA, UMR BioSanté U1292 Univ. Grenoble Alpes CNRS, CEA, FR2048 38000 Grenoble France
| | - Maria Elena Laugeri
- Department of Experimental Medicine and Center of Excellence for Biomedical Research University of Genova Genova Italy
| | - Annalisa Salis
- Department of Experimental Medicine and Center of Excellence for Biomedical Research University of Genova Genova Italy
| | - Gianluca Damonte
- Department of Experimental Medicine and Center of Excellence for Biomedical Research University of Genova Genova Italy
| | - Antonio Molinaro
- Department of Chemical Sciences University of Naples Federico II Via Cinthia 21 80126 Naples Italy
| | - Michela G. Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research University of Genova Genova Italy
| | - Chantal Abergel
- Information Génomique & Structurale Unité Mixte de Recherche 7256 Aix-Marseille University Centre National de la Recherche Scientifique, IMM, IM2B 13288 Marseille Cedex 9 France
| | - Cristina De Castro
- Department of Agricultural Sciences University of Naples Federico II Via Università, 100 80055 Portici (NA) Italy
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17
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Notaro A, Couté Y, Belmudes L, Laugeri ME, Salis A, Damonte G, Molinaro A, Tonetti MG, Abergel C, De Castro C. Expanding the Occurrence of Polysaccharides to the Viral World: The Case of Mimivirus. Angew Chem Int Ed Engl 2021; 60:19897-19904. [PMID: 34241943 PMCID: PMC8456856 DOI: 10.1002/anie.202106671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Indexed: 11/05/2022]
Abstract
The general perception of viruses is that they are small in terms of size and genome, and that they hijack the host machinery to glycosylate their capsid. Giant viruses subvert all these concepts: their particles are not small, and their genome is more complex than that of some bacteria. Regarding glycosylation, this concept has been already challenged by the finding that Chloroviruses have an autonomous glycosylation machinery that produces oligosaccharides similar in size to those of small viruses (6-12 units), albeit different in structure compared to the viral counterparts. We report herein that Mimivirus possesses a glycocalyx made of two different polysaccharides, now challenging the concept that all viruses coat their capsids with oligosaccharides of discrete size. This discovery contradicts the paradigm that such macromolecules are absent in viruses, blurring the boundaries between giant viruses and the cellular world and opening new avenues in the field of viral glycobiology.
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Affiliation(s)
- Anna Notaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 21, 80126, Naples, Italy.,Information Génomique & Structurale, Unité Mixte de Recherche 7256, Aix-Marseille University, Centre National de la Recherche Scientifique, IMM, IM2B, 13288, Marseille Cedex 9, France
| | - Yohann Couté
- INSERM, CEA, UMR BioSanté U1292, Univ. Grenoble Alpes, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - Lucid Belmudes
- INSERM, CEA, UMR BioSanté U1292, Univ. Grenoble Alpes, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - Maria Elena Laugeri
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy
| | - Annalisa Salis
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy
| | - Gianluca Damonte
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 21, 80126, Naples, Italy
| | - Michela G Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy
| | - Chantal Abergel
- Information Génomique & Structurale, Unité Mixte de Recherche 7256, Aix-Marseille University, Centre National de la Recherche Scientifique, IMM, IM2B, 13288, Marseille Cedex 9, France
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, 80055, Portici (NA), Italy
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18
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Mishra B, Manmode S, Walke G, Chakraborty S, Neralkar M, Hotha S. Synthesis of the hyper-branched core tetrasaccharide motif of chloroviruses. Org Biomol Chem 2021; 19:1315-1328. [PMID: 33459320 DOI: 10.1039/d0ob02176h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chemical synthesis of complex oligosaccharides, especially those possessing hyper-branched structures with one or multiple 1,2-cis glycosidic bonds, is a challenging task. Complementary reactivity of glycosyl donors and acceptors and proper tuning of the solvent/temperature/activator coupled with compromised glycosylation yields for sterically congested glycosyl acceptors are among several factors that make such syntheses daunting. Herein, we report the synthesis of a semi-conserved hyper-branched core tetrasaccharide motif from chloroviruses which are associated with reduced cognitive function in humans as well as in mouse models. The target tetrasaccharide contains four different sugar residues in which l-fucose is connected to d-xylose and l-rhamnose via a 1,2-trans glycosidic bond, whereas with the d-galactose residue is connected through a 1,2-cis glycosidic bond. A thorough and comprehensive study of various accountable factors enabled us to install a 1,2-cis galactopyranosidic linkage in a stereoselective fashion under [Au]/[Ag]-catalyzed glycosidation conditions en route to the target tetrasaccharide motif in 14 steps.
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Affiliation(s)
- Bijoyananda Mishra
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
| | - Sujit Manmode
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
| | - Gulab Walke
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
| | - Saptashwa Chakraborty
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
| | - Mahesh Neralkar
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
| | - Srinivas Hotha
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
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19
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Prospects for viruses infecting eukaryotic microalgae in biotechnology. Biotechnol Adv 2021; 54:107790. [PMID: 34182051 DOI: 10.1016/j.biotechadv.2021.107790] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/02/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022]
Abstract
Besides being considered pathogens, viruses are important drivers of evolution and they can shape large ecological and biogeochemical processes, by influencing host fitness, population dynamics, and community structures. Moreover, they are simple systems that can be used and manipulated to be beneficial and useful for biotechnological applications. In this context, microalgae biotechnology is a growing field of research, which investigated the usage of photosynthetic microorganisms for the sustainable production of food, fuel, chemical, and pharmaceutical sectors. Viruses infecting microalgae have become important subject of ecological studies related to marine and aquatic environments only four decades ago when virus-like-particles associated with bloom-forming algae were discovered. These first findings have opened new questions on evolution and identity. To date, 63 viruses that infect eukaryotic microalgae have been isolated and cultured. In this short review we briefly summarize what is known about viruses infecting eukaryotic microalgae, and how acknowledging their importance can shape future research focussed not only on marine ecology and evolutionary biology but also on biotechnological applications related to microalgae cell factories.
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20
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Identification of a Chlorovirus PBCV-1 Protein Involved in Degrading the Host Cell Wall during Virus Infection. Viruses 2021; 13:v13050782. [PMID: 33924931 PMCID: PMC8145301 DOI: 10.3390/v13050782] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 12/22/2022] Open
Abstract
Chloroviruses are unusual among viruses infecting eukaryotic organisms in that they must, like bacteriophages, penetrate a rigid cell wall to initiate infection. Chlorovirus PBCV-1 infects its host, Chlorella variabilis NC64A by specifically binding to and degrading the cell wall of the host at the point of contact by a virus-packaged enzyme(s). However, PBCV-1 does not use any of the five previously characterized virus-encoded polysaccharide degrading enzymes to digest the Chlorella host cell wall during virus entry because none of the enzymes are packaged in the virion. A search for another PBCV-1-encoded and virion-associated protein identified protein A561L. The fourth domain of A561L is a 242 amino acid C-terminal domain, named A561LD4, with cell wall degrading activity. An A561LD4 homolog was present in all 52 genomically sequenced chloroviruses, infecting four different algal hosts. A561LD4 degraded the cell walls of all four chlorovirus hosts, as well as several non-host Chlorella spp. Thus, A561LD4 was not cell-type specific. Finally, we discovered that exposure of highly purified PBCV-1 virions to A561LD4 increased the specific infectivity of PBCV-1 from about 25–30% of the particles forming plaques to almost 50%. We attribute this increase to removal of residual host receptor that attached to newly replicated viruses in the cell lysates.
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21
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Jin T, Yin J. Patterns of virus growth across the diversity of life. Integr Biol (Camb) 2021; 13:44-59. [PMID: 33616184 DOI: 10.1093/intbio/zyab001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/24/2020] [Accepted: 01/04/2021] [Indexed: 01/14/2023]
Abstract
Although viruses in their natural habitats add up to less than 10% of the biomass, they contribute more than 90% of the genome sequences [1]. These viral sequences or 'viromes' encode viruses that populate the Earth's oceans [2, 3] and terrestrial environments [4, 5], where their infections impact life across diverse ecological niches and scales [6, 7], including humans [8-10]. Most viruses have yet to be isolated and cultured [11-13], and surprisingly few efforts have explored what analysis of available data might reveal about their nature. Here, we compiled and analyzed seven decades of one-step growth and other data for viruses from six major families, including their infections of archaeal, bacterial and eukaryotic hosts [14-191]. We found that the use of host cell biomass for virus production was highest for archaea at 10%, followed by bacteria at 1% and eukarya at 0.01%, highlighting the degree to which viruses of archaea and bacteria exploit their host cells. For individual host cells, the yield of virus progeny spanned a relatively narrow range (10-1000 infectious particles per cell) compared with the million-fold difference in size between the smallest and largest cells. Furthermore, healthy and infected host cells were remarkably similar in the time they needed to multiply themselves or their virus progeny. Specifically, the doubling time of healthy cells and the delay time for virus release from infected cells were not only correlated (r = 0.71, p < 10-10, n = 101); they also spanned the same range from tens of minutes to about a week. These results have implications for better understanding the growth, spread and persistence of viruses in complex natural habitats that abound with diverse hosts, including humans and their associated microbes.
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Affiliation(s)
- Tianyi Jin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
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22
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Chlorovirus PBCV-1 Multidomain Protein A111/114R Has Three Glycosyltransferase Functions Involved in the Synthesis of Atypical N-Glycans. Viruses 2021; 13:v13010087. [PMID: 33435207 PMCID: PMC7826918 DOI: 10.3390/v13010087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/03/2021] [Accepted: 01/08/2021] [Indexed: 12/04/2022] Open
Abstract
The structures of the four N-linked glycans from the prototype chlorovirus PBCV-1 major capsid protein do not resemble any other glycans in the three domains of life. All known chloroviruses and antigenic variants (or mutants) share a unique conserved central glycan core consisting of five sugars, except for antigenic mutant virus P1L6, which has four of the five sugars. A combination of genetic and structural analyses indicates that the protein coded by PBCV-1 gene a111/114r, conserved in all chloroviruses, is a glycosyltransferase with three putative domains of approximately 300 amino acids each. Here, in addition to in silico sequence analysis and protein modeling, we measured the hydrolytic activity of protein A111/114R. The results suggest that domain 1 is a galactosyltransferase, domain 2 is a xylosyltransferase and domain 3 is a fucosyltransferase. Thus, A111/114R is the protein likely responsible for the attachment of three of the five conserved residues of the core region of this complex glycan, and, if biochemically corroborated, it would be the second three-domain protein coded by PBCV-1 that is involved in glycan synthesis. Importantly, these findings provide additional support that the chloroviruses do not use the canonical host endoplasmic reticulum–Golgi glycosylation pathway to glycosylate their glycoproteins; instead, they perform glycosylation independent of cellular organelles using virus-encoded enzymes.
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23
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Speciale I, Laugieri ME, Noel E, Lin S, Lowary TL, Molinaro A, Duncan GA, Agarkova IV, Garozzo D, Tonetti MG, Van Etten JL, De Castro C. Chlorovirus PBCV-1 protein A064R has three of the transferase activities necessary to synthesize its capsid protein N-linked glycans. Proc Natl Acad Sci U S A 2020; 117:28735-28742. [PMID: 33139538 PMCID: PMC7682578 DOI: 10.1073/pnas.2016626117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Paramecium bursaria chlorella virus-1 (PBCV-1) is a large double-stranded DNA (dsDNA) virus that infects the unicellular green alga Chlorella variabilis NC64A. Unlike many other viruses, PBCV-1 encodes most, if not all, of the enzymes involved in the synthesis of the glycans attached to its major capsid protein. Importantly, these glycans differ from those reported from the three domains of life in terms of structure and asparagine location in the sequon of the protein. Previous data collected from 20 PBCV-1 spontaneous mutants (or antigenic variants) suggested that the a064r gene encodes a glycosyltransferase (GT) with three domains, each with a different function. Here, we demonstrate that: domain 1 is a β-l-rhamnosyltransferase; domain 2 is an α-l-rhamnosyltransferase resembling only bacterial proteins of unknown function, and domain 3 is a methyltransferase that methylates the C-2 hydroxyl group of the terminal α-l-rhamnose (Rha) unit. We also establish that methylation of the C-3 hydroxyl group of the terminal α-l-Rha is achieved by another virus-encoded protein A061L, which requires an O-2 methylated substrate. This study, thus, identifies two of the glycosyltransferase activities involved in the synthesis of the N-glycan of the viral major capsid protein in PBCV-1 and establishes that a single protein A064R possesses the three activities needed to synthetize the 2-OMe-α-l-Rha-(1→2)-β-l-Rha fragment. Remarkably, this fragment can be attached to any xylose unit.
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Affiliation(s)
- Immacolata Speciale
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
- Department of Agricultural Sciences, University of Napoli Federico II, 80055 Portici NA, Italy
| | - Maria Elena Laugieri
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy
| | - Eric Noel
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118
| | - Sicheng Lin
- Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, AB T6G 2G2 , Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, AB T6G 2G2 , Canada
- Institute of Biological Chemistry, Academia Sinica, Nangang, 11529 Taipei, Taiwan
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
| | - Garry A Duncan
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
| | - Irina V Agarkova
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0722
| | - Domenico Garozzo
- CNR, Institute for Polymers, Composites and Biomaterials, 95126 Catania, Italy
| | - Michela G Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy;
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900;
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0722
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli Federico II, 80055 Portici NA, Italy;
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24
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Lin S, Lowary TL. Synthesis of a Highly Branched Nonasaccharide Chlorella Virus N-Glycan Using a "Counterclockwise" Assembly Approach. Org Lett 2020; 22:7645-7649. [PMID: 32940477 DOI: 10.1021/acs.orglett.0c02839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chloroviruses produce a capsid protein containing N-linked glycans differing in structure from those found in all other organisms. These species feature a core "hyper-branched" fucose residue in which every hydroxyl group is glycosylated. We describe the synthesis of a nonasaccharide from Paramecium bursaria chlorella virus 1, one of most complex chlorovirus N-glycans reported, using a "counterclockwise" strategy involving the sequential addition of trisaccharide, disaccharide, and monosaccharide motifs to a trisaccharide containing the core fucose residue.
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Affiliation(s)
- Sicheng Lin
- Department of Chemistry, The University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Todd L Lowary
- Department of Chemistry, The University of Alberta, Edmonton, Alberta, Canada, T6G 2G2.,Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128, Nangang, Taipei 11529, Taiwan
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Coy SR, Gann ER, Papoulis SE, Holder ME, Ajami NJ, Petrosino JF, Zinser ER, Van Etten JL, Wilhelm SW. SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems. Front Microbiol 2020; 11:887. [PMID: 32508769 PMCID: PMC7248222 DOI: 10.3389/fmicb.2020.00887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Chloroviruses (family Phycodnaviridae) infect eukaryotic, freshwater, unicellular green algae. A unique feature of these viruses is an abundance of DNA methyltransferases, with isolates dedicating up to 4.5% of their protein coding potential to these genes. This diversity highlights just one of the long-standing values of the chlorovirus model system; where group-wide epigenomic characterization might begin to elucidate the function(s) of DNA methylation in large dsDNA viruses. We characterized DNA modifications in the prototype chlorovirus, PBCV-1, using single-molecule real time (SMRT) sequencing (aka PacBio). Results were compared to total available sites predicted in silico based on DNA sequence alone. SMRT-software detected N6-methyl-adenine (m6A) at GATC and CATG recognition sites, motifs previously shown to be targeted by PBCV-1 DNA methyltransferases M.CviAI and M. CviAII, respectively. At the same time, PacBio analyses indicated that 10.9% of the PBCV-1 genome had large interpulse duration ratio (ipdRatio) values, the primary metric for DNA modification identification. These events represent 20.6x more sites than can be accounted for by all available adenines in GATC and CATG motifs, suggesting base or backbone modifications other than methylation might be present. To define methylation stability, we cross-compared methylation status of each GATC and CATG sequence in three biological replicates and found ∼81% of sites were stably methylated, while ∼2% consistently lack methylation. The remaining 17% of sites were stochastically methylated. When methylation status was analyzed for both strands of each target, we show that palindromes existed in completely non-methylated states, fully-methylated states, or hemi-methylated states, though GATC sites more often lack methylation than CATG sequences. Given that both sequences are targeted by not just methyltransferases, but by restriction endonucleases that are together encoded by PBCV-1 as virus-originating restriction modification (RM) systems, there is strong selective pressure to modify all target sites. The finding that most instances of non-methylation are associated with hemi-methylation is congruent with observations that hemi-methylated palindromes are resistant to cleavage by restriction endonucleases. However, sites where hemi-methylation is conserved might represent a unique regulatory function for PBCV-1. This study serves as a baseline for future investigation into the epigenomics of chloroviruses and their giant virus relatives.
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Affiliation(s)
- Samantha R. Coy
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- BioSciences at Rice, Rice University, Houston, TX, United States
| | - Eric R. Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Spiridon E. Papoulis
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Michael E. Holder
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States
| | - Nadim J. Ajami
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States
| | - Erik R. Zinser
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - James L. Van Etten
- Department of Plant Pathology and the Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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26
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Van Etten JL, Agarkova IV, Dunigan DD. Chloroviruses. Viruses 2019; 12:E20. [PMID: 31878033 PMCID: PMC7019647 DOI: 10.3390/v12010020] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/20/2022] Open
Abstract
Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation.
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Affiliation(s)
- James L. Van Etten
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA; (I.V.A.); (D.D.D.)
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27
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Chloroviruses Lure Hosts through Long-Distance Chemical Signaling. J Virol 2019; 93:JVI.01688-18. [PMID: 30626679 DOI: 10.1128/jvi.01688-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/18/2018] [Indexed: 11/20/2022] Open
Abstract
Chloroviruses exist in aquatic systems around the planet and they infect certain eukaryotic green algae that are mutualistic endosymbionts in a variety of protists and metazoans. Natural chlorovirus populations are seasonally dynamic, but the precise temporal changes in these populations and the mechanisms that underlie them have heretofore been unclear. We recently reported the novel concept that predator/prey-mediated virus activation regulates chlorovirus population dynamics, and in the current study, we demonstrate virus-packaged chemotactic modulation of prey behavior.IMPORTANCE Viruses have not previously been reported to act as chemotactic/chemoattractive agents. Rather, viruses as extracellular entities are generally viewed as non-metabolically active spore-like agents that await further infection events upon collision with appropriate host cells. That a virus might actively contribute to its fate via chemotaxis and change the behavior of an organism independent of infection is unprecedented.
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28
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Speciale I, Duncan GA, Unione L, Agarkova IV, Garozzo D, Jimenez-Barbero J, Lin S, Lowary TL, Molinaro A, Noel E, Laugieri ME, Tonetti MG, Van Etten JL, De Castro C. The N-glycan structures of the antigenic variants of chlorovirus PBCV-1 major capsid protein help to identify the virus-encoded glycosyltransferases. J Biol Chem 2019; 294:5688-5699. [PMID: 30737276 DOI: 10.1074/jbc.ra118.007182] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/07/2019] [Indexed: 11/06/2022] Open
Abstract
The chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) is a large dsDNA virus that infects the microalga Chlorella variabilis NC64A. Unlike most other viruses, PBCV-1 encodes most, if not all, of the machinery required to glycosylate its major capsid protein (MCP). The structures of the four N-linked glycans from the PBCV-1 MCP consist of nonasaccharides, and similar glycans are not found elsewhere in the three domains of life. Here, we identified the roles of three virus-encoded glycosyltransferases (GTs) that have four distinct GT activities in glycan synthesis. Two of the three GTs were previously annotated as GTs, but the third GT was identified in this study. We determined the GT functions by comparing the WT glycan structures from PBCV-1 with those from a set of PBCV-1 spontaneous GT gene mutants resulting in antigenic variants having truncated glycan structures. According to our working model, the virus gene a064r encodes a GT with three domains: domain 1 has a β-l-rhamnosyltransferase activity, domain 2 has an α-l-rhamnosyltransferase activity, and domain 3 is a methyltransferase that decorates two positions in the terminal α-l-rhamnose (Rha) unit. The a075l gene encodes a β-xylosyltransferase that attaches the distal d-xylose (Xyl) unit to the l-fucose (Fuc) that is part of the conserved N-glycan core region. Last, gene a071r encodes a GT that is involved in the attachment of a semiconserved element, α-d-Rha, to the same l-Fuc in the core region. Our results uncover GT activities that assemble four of the nine residues of the PBCV-1 MCP N-glycans.
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Affiliation(s)
- Immacolata Speciale
- From the Department of Agricultural Sciences, University of Napoli Federico II, Via Università 100, 80055 Portici NA, Italy
| | - Garry A Duncan
- the Department of Biology, Nebraska Wesleyan University, Lincoln, Nebraska 68504-2794
| | - Luca Unione
- the Chemical Glycobiology Lab, CIC bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Irina V Agarkova
- the Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900.,the Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722
| | - Domenico Garozzo
- Institute for Polymers, Composites, and Biomaterials, CNR, Via P. Gaifami 18, 95126 Catania, Italy
| | - Jesus Jimenez-Barbero
- the Chemical Glycobiology Lab, CIC bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain.,the Basque Foundation for Science (IKERBASQUE), 48940 Bilbao, Spain.,the Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
| | - Sicheng Lin
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, Alberta T6G 2G2, Canada
| | - Todd L Lowary
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, Alberta T6G 2G2, Canada
| | - Antonio Molinaro
- the Department of Chemical Sciences, Università of Napoli Federico II, 80126 Napoli, Italy
| | - Eric Noel
- the Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900.,the School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0118, and
| | - Maria Elena Laugieri
- the Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV/1, 16132 Genova, Italy
| | - Michela G Tonetti
- the Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV/1, 16132 Genova, Italy
| | - James L Van Etten
- the Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska 68583-0900, .,the Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722
| | - Cristina De Castro
- From the Department of Agricultural Sciences, University of Napoli Federico II, Via Università 100, 80055 Portici NA, Italy,
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Cobaviruses - a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME JOURNAL 2019; 13:1404-1421. [PMID: 30718806 PMCID: PMC6775973 DOI: 10.1038/s41396-019-0362-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 11/13/2022]
Abstract
Bacteriophages are widely considered to influence bacterial communities, however most phages are still unknown or not studied well enough to understand their ecological roles. We have isolated two phages infecting Lentibacter sp. SH36, affiliated with the marine Roseobacter group, and retrieved similar phage genomes from publicly available metagenomics databases. Phylogenetic analysis placed the new phages within the Cobavirus group, in the here newly proposed genus Siovirus and subfamily Riovirinae of the Podoviridae. Gene composition and presence of direct terminal repeats in cultivated cobaviruses point toward a genome replication and packaging strategy similar to the T7 phage. Investigation of the genomes suggests that viral lysis of the cell proceeds via the canonical holin-endolysin pathway. Cobaviral hosts include members of the genera Lentibacter, Sulfitobacter and Celeribacter of the Roseobacter group within the family Rhodobacteraceae (Alphaproteobacteria). Screening more than 5,000 marine metagenomes, we found cobaviruses worldwide from temperate to tropical waters, in the euphotic zone, mainly in bays and estuaries, but also in the open ocean. The presence of cobaviruses in protist metagenomes as well as the phylogenetic neighborhood of cobaviruses in glutaredoxin and ribonucleotide reductase trees suggest that cobaviruses could infect bacteria associated with phototrophic or grazing protists. With this study, we expand the understanding of the phylogeny, classification, genomic organization, biogeography and ecology of this phage group infecting marine Rhodobacteraceae.
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Abstract
Although the nucleocytoplasmic large DNA viruses (NCLDVs) are one of the largest group of viruses that infect many eukaryotic hosts, the near-atomic resolution structures of these viruses have remained unknown. Here we describe a 3.5 Å resolution icosahedrally averaged capsid structure of Paramecium bursaria chlorella virus 1 (PBCV-1). This structure consists of 5040 copies of the major capsid protein, 60 copies of the penton protein and 1800 minor capsid proteins of which there are 13 different types. The minor capsid proteins form a hexagonal network below the outer capsid shell, stabilizing the capsid by binding neighboring capsomers together. The size of the viral capsid is determined by a tape-measure, minor capsid protein of which there are 60 copies in the virion. Homologs of the tape-measure protein and some of the other minor capsid proteins exist in other NCLDVs. Thus, a similar capsid assembly pathway might be used by other NCLDVs.
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31
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Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions. Viruses 2018; 10:v10090487. [PMID: 30208617 PMCID: PMC6165237 DOI: 10.3390/v10090487] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 11/16/2022] Open
Abstract
The scope for ecological studies of eukaryotic algal viruses has greatly improved with the development of molecular and bioinformatic approaches that do not require algal cultures. Here, we review the history and perceived future opportunities for research on eukaryotic algal viruses. We begin with a summary of the 65 eukaryotic algal viruses that are presently in culture collections, with emphasis on shared evolutionary traits (e.g., conserved core genes) of each known viral type. We then describe how core genes have been used to enable molecular detection of viruses in the environment, ranging from PCR-based amplification to community scale "-omics" approaches. Special attention is given to recent studies that have employed network-analyses of -omics data to predict virus-host relationships, from which a general bioinformatics pipeline is described for this type of approach. Finally, we conclude with acknowledgement of how the field of aquatic virology is adapting to these advances, and highlight the need to properly characterize new virus-host systems that may be isolated using preliminary molecular surveys. Researchers can approach this work using lessons learned from the Chlorella virus system, which is not only the best characterized algal-virus system, but is also responsible for much of the foundation in the field of aquatic virology.
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32
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Genes for Membrane Transport Proteins: Not So Rare in Viruses. Viruses 2018; 10:v10090456. [PMID: 30149667 PMCID: PMC6163359 DOI: 10.3390/v10090456] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 12/27/2022] Open
Abstract
Some viruses have genes encoding proteins with membrane transport functions. It is unknown if these types of proteins are rare or are common in viruses. In particular, the evolutionary origin of some of the viral genes is obscure, where other viral proteins have homologs in prokaryotic and eukaryotic organisms. We searched virus genomes in databases looking for transmembrane proteins with possible transport function. This effort led to the detection of 18 different types of putative membrane transport proteins indicating that they are not a rarity in viral genomes. The most abundant proteins are K+ channels. Their predicted structures vary between different viruses. With a few exceptions, the viral proteins differed significantly from homologs in their current hosts. In some cases the data provide evidence for a recent gene transfer between host and virus, but in other cases the evidence indicates a more complex evolutionary history.
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33
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De Castro C, Duncan GA, Garozzo D, Molinaro A, Sturiale L, Tonetti M, Van Etten JL. Biophysical Approaches to Solve the Structures of the Complex Glycan Shield of Chloroviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1104:237-257. [PMID: 30484252 DOI: 10.1007/978-981-13-2158-0_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The capsid of Paramecium bursaria chlorella virus (PBCV-1) contains a heavily glycosylated major capsid protein, Vp54. The capsid protein contains four glycans, each N-linked to Asn. The glycan structures are unusual in many aspects: (1) they are attached by a β-glucose linkage, which is rare in nature; (2) they are highly branched and consist of 8-10 neutral monosaccharides; (3) all four glycoforms contain a dimethylated rhamnose as the capping residue of the main chain, a hyper-branched fucose residue and two rhamnose residues ''with opposite absolute configurations; (4) the four glycoforms differ by the nonstoichiometric presence of two monosaccharides, L-arabinose and D-mannose ; (5) the N-glycans from all of the chloroviruses have a strictly conserved core structure; and (6) these glycans do not resemble any structures previously reported in the three domains of life.The structures of these N-glycoforms remained elusive for years because initial attempts to solve their structures used tools developed for eukaryotic-like systems, which we now know are not suitable for this noncanonical glycosylation pattern. This chapter summarizes the methods used to solve the chlorovirus complex glycan structures with the hope that these methodologies can be used by scientists facing similar problems.
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Affiliation(s)
- Cristina De Castro
- Department of Agricultural Sciences, University of Napoli, Portici, NA, Italy.
| | - Garry A Duncan
- Department of Biology, Nebraska Wesleyan University, Lincoln, NE, USA
| | - Domenico Garozzo
- CNR, Institute for Polymers, Composites and Biomaterials, Catania, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli, Napoli, Italy
| | - Luisa Sturiale
- CNR, Institute for Polymers, Composites and Biomaterials, Catania, Italy
| | - Michela Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
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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.
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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.
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35
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Structure of the N-glycans from the chlorovirus NE-JV-1. Antonie van Leeuwenhoek 2017; 110:1391-1399. [PMID: 28331984 DOI: 10.1007/s10482-017-0861-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
Results from recent studies are breaking the paradigm that all viruses depend on their host machinery to glycosylate their proteins. Chloroviruses encode several genes involved in glycan biosynthesis and some of their capsid proteins are decorated with N-linked oligosaccharides with unique features. Here we describe the elucidation of the N-glycan structure of an unusual chlorovirus, NE-JV-1, that belongs to the Pbi group. The host for NE-JV-1 is the zoochlorella Micractinium conductrix. Spectroscopic analyses established that this N-glycan consists of a core region that is conserved in all of the chloroviruses. The one difference is that the residue 3OMe-L-rhamnose is acetylated at the O-2 position in a non-stoichiometric fashion.
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