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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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2
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Zhu D, Cao D, Zhang X. Virus structures revealed by advanced cryoelectron microscopy methods. Structure 2023; 31:1348-1359. [PMID: 37797619 DOI: 10.1016/j.str.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions.
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Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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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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4
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Zhao Z, Huang Y, Liu C, Zhu D, Gao S, Liu S, Peng R, Zhang Y, Huang X, Qi J, Wong CCL, Zhang X, Wang P, Qin Q, Gao GF. Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly. Nat Commun 2023; 14:2050. [PMID: 37041173 PMCID: PMC10090177 DOI: 10.1038/s41467-023-37681-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
Singapore grouper iridovirus (SGIV), one of the nucleocytoviricota viruses (NCVs), is a highly pathogenic iridovirid. SGIV infection results in massive economic losses to the aquaculture industry and significantly threatens global biodiversity. In recent years, high morbidity and mortality in aquatic animals have been caused by iridovirid infections worldwide. Effective control and prevention strategies are urgently needed. Here, we present a near-atomic architecture of the SGIV capsid and identify eight types of capsid proteins. The viral inner membrane-integrated anchor protein colocalizes with the endoplasmic reticulum (ER), supporting the hypothesis that the biogenesis of the inner membrane is associated with the ER. Additionally, immunofluorescence assays indicate minor capsid proteins (mCPs) could form various building blocks with major capsid proteins (MCPs) before the formation of a viral factory (VF). These results expand our understanding of the capsid assembly of NCVs and provide more targets for vaccine and drug design to fight iridovirid infections.
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Affiliation(s)
- Zhennan Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Youhua Huang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Congcong Liu
- Cryo-EM Center, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China
| | - Dongjie Zhu
- School of Life Science, University of Science and Technology of China, Hefei, 230026, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuaixin Gao
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
- Department of Human Sciences & James Comprehensive Cancer Center, The Ohio State University, Columbus, 43210, USA
| | - Sheng Liu
- Cryo-EM Center, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ruchao Peng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
| | - Ya Zhang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Xiaohong Huang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Life Science Academy, Beijing, 102209, China.
| | - Catherine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China.
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peiyi Wang
- Cryo-EM Center, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Qiwei Qin
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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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.
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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.
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6
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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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [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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7
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Rochal SB, Konevtsova OV, Roshal DS, Božič A, Golushko IY, Podgornik R. Packing and trimer-to-dimer protein reconstruction in icosahedral viral shells with a single type of symmetrical structural unit. NANOSCALE ADVANCES 2022; 4:4677-4688. [PMID: 36341291 PMCID: PMC9595183 DOI: 10.1039/d2na00461e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Understanding the principles of protein packing and the mechanisms driving morphological transformations in virus shells (capsids) during their maturation can be pivotal for the development of new antiviral strategies. Here, we study how these principles and mechanisms manifest themselves in icosahedral viral capsids assembled from identical symmetric structural units (capsomeres). To rationalize such shells, we model capsomers as symmetrical groups of identical particles interacting with a short-range potential typical of the classic Tammes problem. The capsomere particles are assumed to retain their relative positions on the vertices of planar polygons placed on the spherical shell and to interact only with the particles from other capsomeres. Minimization of the interaction energy enforces equal distances between the nearest particles belonging to neighboring capsomeres and minimizes the number of different local environments. Thus, our model implements the Caspar and Klug quasi-equivalence principle and leads to packings strikingly similar to real capsids. We then study a reconstruction of protein trimers into dimers in a Flavivirus shell during its maturation, connecting the relevant structural changes with the modifications of the electrostatic charges of proteins, wrought by the oxidative switch in the bathing solution that is essential for the process. We highlight the key role of pr peptides in the shell reconstruction and show that the highly ordered arrangement of these subunits in the dimeric state is energetically favored at a low pH level. We also discuss the electrostatic mechanisms controlling the release of pr peptides in the last irreversible step of the maturation process.
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Affiliation(s)
- Sergei B Rochal
- Physics Faculty, Southern Federal University Rostov-on-Don Russia
| | | | - Daria S Roshal
- Physics Faculty, Southern Federal University Rostov-on-Don Russia
| | - Anže Božič
- Department of Theoretical Physics, Jožef Stefan Institute SI-1000 Ljubljana Slovenia
| | - Ivan Yu Golushko
- Physics Faculty, Southern Federal University Rostov-on-Don Russia
| | - Rudolf Podgornik
- Department of Theoretical Physics, Jožef Stefan Institute SI-1000 Ljubljana Slovenia
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana SI-1000 Ljubljana Slovenia
- School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences Beijing 100049 China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences Beijing 100190 China
- Wenzhou Institute of the University of Chinese Academy of Sciences Wenzhou Zhejiang 325000 China
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8
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Asrani P, Seebohm G, Stoll R. Potassium viroporins as model systems for understanding eukaryotic ion channel behaviour. Virus Res 2022; 320:198903. [PMID: 36037849 DOI: 10.1016/j.virusres.2022.198903] [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: 03/14/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022]
Abstract
Ion channels are membrane proteins essential for a plethora of cellular functions including maintaining cell shape, ion homeostasis, cardiac rhythm and action potential in neurons. The complexity and often extensive structure of eukaryotic membrane proteins makes it difficult to understand their basic biological regulation. Therefore, this article suggests, viroporins - the miniature versions of eukaryotic protein homologs from viruses - might serve as model systems to provide insights into behaviour of eukaryotic ion channels in general. The structural requirements for correct assembly of the channel along with the basic functional properties of a K+ channel exist in the minimal design of the viral K+ channels from two viruses, Chlorella virus (Kcv) and Ectocarpus siliculosus virus (Kesv). These small viral proteins readily assemble into tetramers and they sort in cells to distinct target membranes. When these viruses-encoded channels are expressed into the mammalian cells, they utilise their protein machinery and hence can serve as excellent tools to study the cells protein sorting machinery. This combination of small size and robust function makes viral K+ channels a valuable model system for detection of basic structure-function correlations. It is believed that molecular and physiochemical analyses of these viroporins may serve as basis for the development of inhibitors or modulators to ion channel activity for targeting ion channel diseases - so called channelopathies. Therefore, it may provide a potential different scope for molecular pharmacology studies aiming at novel and innovative therapeutics associated with channel related diseases. This article reviews the structural and functional properties of Kcv and Kesv upon expression in mammalian cells and Xenopus oocytes. The mechanisms behind differential protein sorting in Kcv and Kesv are also thoroughly discussed.
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Affiliation(s)
- Purva Asrani
- Biomolecular Spectroscopy and RUBiospec|NMR, Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Bochum D-44780, Germany
| | - Guiscard Seebohm
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, Münster D-48149, Germany
| | - Raphael Stoll
- Biomolecular Spectroscopy and RUBiospec|NMR, Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Bochum D-44780, Germany.
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9
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Schulz F, Abergel C, Woyke T. Giant virus biology and diversity in the era of genome-resolved metagenomics. Nat Rev Microbiol 2022; 20:721-736. [PMID: 35902763 DOI: 10.1038/s41579-022-00754-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/09/2022]
Abstract
The discovery of giant viruses, with capsids as large as some bacteria, megabase-range genomes and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. Until recently, most of our knowledge of giant viruses came from ~100 species-level isolates for which genome sequences were available. However, these isolates were primarily derived from laboratory-based co-cultivation with few cultured protists and algae and, thus, did not reflect the true diversity of giant viruses. Although virus co-cultures enabled valuable insights into giant virus biology, many questions regarding their origin, evolution and ecological importance remain unanswered. With advances in sequencing technologies and bioinformatics, our understanding of giant viruses has drastically expanded. In this Review, we summarize our understanding of giant virus diversity and biology based on viral isolates as laboratory cultivation has enabled extensive insights into viral morphology and infection strategies. We then explore how cultivation-independent approaches have heightened our understanding of the coding potential and diversity of the Nucleocytoviricota. We discuss how metagenomics has revolutionized our perspective of giant viruses by revealing their distribution across our planet's biomes, where they impact the biology and ecology of a wide range of eukaryotic hosts and ultimately affect global nutrient cycles.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Chantal Abergel
- Aix Marseille University, CNRS, IGS UMR7256, IMM FR3479, IM2B, IO, Marseille, France
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California Merced, Merced, CA, USA.
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10
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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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11
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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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13
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Sun Z, Fu J, Li X, Blatchley ER, Zhou Z. Using Algal Virus Paramecium bursaria Chlorella Virus as a Human Adenovirus Surrogate for Validation of UV Treatment Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15507-15515. [PMID: 33166135 DOI: 10.1021/acs.est.0c06354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Adenovirus is among the most UV-resistant waterborne human pathogens. There is a need to identify nonpathogenic surrogates for adenovirus for the water treatment industry. In this study, the feasibility of using the algal virus Paramecium bursaria chlorella virus (PBCV-1) as an adenovirus surrogate for validation of UV reactors was evaluated. The UV dose-response behavior of PBCV-1 to monochromatic UV radiation at 254 nm and action spectrum for wavelengths ranging from 214 to 289 nm were measured. A culture-based infectivity assay was used to evaluate viral inactivation, and a quantitative PCR assay was used to quantify DNA damage. A UV254 dose of 150 mJ/cm2 resulted in roughly 5-log10 units of reduction of PBCV-1, which is similar to that of adenovirus. Furthermore, the inactivation action spectrum of PBCV-1 was similar to that of adenovirus between 214 and 289 nm. A simplified and inexpensive prepurification method was also developed to prepare PBCV-1 viral suspensions with similar inactivation behavior to purified PBCV-1. Overall, PBCV-1 appears to represent an appropriate adenovirus surrogate for UV system performance evaluation and illustrates the potential of using algal viruses as nonpathogenic, easy to culture, and readily available surrogates for human pathogens.
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Affiliation(s)
- Zhe Sun
- Lyles School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jianing Fu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xing Li
- Lyles School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ernest R Blatchley
- Lyles School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhi Zhou
- Lyles School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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14
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Xian Y, Avila R, Pant A, Yang Z, Xiao C. The Role of Tape Measure Protein in Nucleocytoplasmic Large DNA Virus Capsid Assembly. Viral Immunol 2020; 34:41-48. [PMID: 33074779 DOI: 10.1089/vim.2020.0038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nucleocytoplasmic large DNA viruses (NCLDVs) are a group of large viruses that infect a wide range of hosts, from animals to protists. These viruses are grouped together in NCLDV based on genomic sequence analyses. They share a set of essential genes for virion morphogenesis and replication. Most NCLDVs generally have large physical sizes while their morphologies vary in different families, such as icosahedral, brick, or oval shape, raising the question of the possible regulatory factor on their morphogenesis. The capsids of icosahedral NCLDVs are assembled from small building blocks, named capsomers, which are the trimeric form of the major capsid proteins. Note that the capsids of immature poxvirus are spherical even though they are assembled from capsomers that share high structural conservation with those icosahedral NCLDVs. The recently published high resolution structure of NCLDVs, Paramecium bursaria Chlorella virus 1 and African swine fever virus, described the intensive network of minor capsid proteins that are located underneath the capsomers. Among these minor proteins is the elongated tape measure protein (TmP) that spans from one icosahedral fivefold vertex to another. In this study, we focused on the critical roles that TmP plays in the assembly of icosahedral NCLDV capsids, answering a question raised in a previously proposed spiral mechanism. Interestingly, basic local alignment search on the TmPs showed no significant hits in poxviruses, which might be the factor that differentiates poxviruses and icosahedral NCLDVs in their morphogenesis.
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Affiliation(s)
- Yuejiao Xian
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas, USA
| | - Ricardo Avila
- Bioinformatics Program, University of Texas at El Paso, El Paso, Texas, USA
| | - Anil Pant
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Zhilong Yang
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Chuan Xiao
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas, USA
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15
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Xian Y, Xiao C. Current capsid assembly models of icosahedral nucleocytoviricota viruses. Adv Virus Res 2020; 108:275-313. [PMID: 33837719 PMCID: PMC8328511 DOI: 10.1016/bs.aivir.2020.09.006] [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] [Indexed: 10/23/2022]
Abstract
Nucleocytoviricota viruses (NCVs) belong to a newly established phylum originally grouped as Nucleocytoplasmic large DNA viruses. NCVs are unique because of their large and complicated genomes that contain cellular genes with homologs from all kingdoms of life, raising intensive debates on their evolutional origins. Many NCVs pack their genomes inside massive icosahedral capsids assembled from thousands of proteins. Studying the assembly mechanism of such capsids has been challenging until breakthroughs from structural studies. Subsequently, several models of the capsid assembly were proposed, which provided some interesting insights on this elaborate process. In this review, we discuss three of the most recent assembly models as well as supporting experimental observations. Furthermore, we propose a new model that combines research developments from multiple sources. Investigation of the assembly process of these vast NCV capsids will facilitate future deciphering of the molecular mechanisms driving the formation of similar supramolecular complexes.
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Affiliation(s)
- Yuejiao Xian
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas, United States
| | - Chuan Xiao
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas, United States.
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16
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Gann ER, Xian Y, Abraham PE, Hettich RL, Reynolds TB, Xiao C, Wilhelm SW. Structural and Proteomic Studies of the Aureococcus anophagefferens Virus Demonstrate a Global Distribution of Virus-Encoded Carbohydrate Processing. Front Microbiol 2020; 11:2047. [PMID: 33013751 PMCID: PMC7507832 DOI: 10.3389/fmicb.2020.02047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/04/2020] [Indexed: 01/28/2023] Open
Abstract
Viruses modulate the function(s) of environmentally relevant microbial populations, yet considerations of the metabolic capabilities of individual virus particles themselves are rare. We used shotgun proteomics to quantitatively identify 43 virus-encoded proteins packaged within purified Aureococcus anophagefferens Virus (AaV) particles, normalizing data to the per-virion level using a 9.5-Å-resolution molecular reconstruction of the 1900-Å (AaV) particle that we generated with cryogenic electron microscopy. This packaged proteome was used to determine similarities and differences between members of different giant virus families. We noted that proteins involved in sugar degradation and binding (e.g., carbohydrate lyases) were unique to AaV among characterized giant viruses. To determine the extent to which this virally encoded metabolic capability was ecologically relevant, we examined the TARA Oceans dataset and identified genes and transcripts of viral origin. Our analyses demonstrated that putative giant virus carbohydrate lyases represented up to 17% of the marine pool for this function. In total, our observations suggest that the AaV particle has potential prepackaged metabolic capabilities and that these may be found in other giant viruses that are widespread and abundant in global oceans.
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Affiliation(s)
- Eric R. Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Yuejiao Xian
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Paul E. Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Todd B. Reynolds
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, 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, The University of Tennessee, Knoxville, Knoxville, TN, United States
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17
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Genetic Diversity of Potassium Ion Channel Proteins Encoded by Chloroviruses That Infect Chlorella heliozoae. Viruses 2020; 12:v12060678. [PMID: 32585987 PMCID: PMC7354518 DOI: 10.3390/v12060678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/17/2022] Open
Abstract
Chloroviruses are large, plaque-forming, dsDNA viruses that infect chlorella-like green algae that live in a symbiotic relationship with protists. Chloroviruses have genomes from 290 to 370 kb, and they encode as many as 400 proteins. One interesting feature of chloroviruses is that they encode a potassium ion (K+) channel protein named Kcv. The Kcv protein encoded by SAG chlorovirus ATCV-1 is one of the smallest known functional K+ channel proteins consisting of 82 amino acids. The KcvATCV-1 protein has similarities to the family of two transmembrane domain K+ channel proteins; it consists of two transmembrane α-helixes with a pore region in the middle, making it an ideal model for studying K+ channels. To assess their genetic diversity, kcv genes were sequenced from 103 geographically distinct SAG chlorovirus isolates. Of the 103 kcv genes, there were 42 unique DNA sequences that translated into 26 new Kcv channels. The new predicted Kcv proteins differed from KcvATCV-1 by 1 to 55 amino acids. The most conserved region of the Kcv protein was the filter, the turret and the pore helix were fairly well conserved, and the outer and the inner transmembrane domains of the protein were the most variable. Two of the new predicted channels were shown to be functional K+ channels.
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18
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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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19
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Xian Y, Karki CB, Silva SM, Li L, Xiao C. The Roles of Electrostatic Interactions in Capsid Assembly Mechanisms of Giant Viruses. Int J Mol Sci 2019; 20:ijms20081876. [PMID: 30995716 PMCID: PMC6514965 DOI: 10.3390/ijms20081876] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 11/16/2022] Open
Abstract
In the last three decades, many giant DNA viruses have been discovered. Giant viruses present a unique and essential research frontier for studies of self-assembly and regulation of supramolecular assemblies. The question on how these giant DNA viruses assemble thousands of proteins so accurately to form their protein shells, the capsids, remains largely unanswered. Revealing the mechanisms of giant virus assembly will help to discover the mysteries of many self-assembly biology problems. Paramecium bursaria Chlorella virus-1 (PBCV-1) is one of the most intensively studied giant viruses. Here, we implemented a multi-scale approach to investigate the interactions among PBCV-1 capsid building units called capsomers. Three binding modes with different strengths are found between capsomers around the relatively flat area of the virion surface at the icosahedral 2-fold axis. Furthermore, a capsomer structure manipulation package is developed to simulate the capsid assembly process. Using these tools, binding forces among capsomers were investigated and binding funnels were observed that were consistent with the final assembled capsid. In addition, total binding free energies of each binding mode were calculated. The results helped to explain previous experimental observations. Results and tools generated in this work established an initial computational approach to answer current unresolved questions regarding giant virus assembly mechanisms. Results will pave the way for studying more complicated process in other biomolecular structures.
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Affiliation(s)
- Yuejiao Xian
- Department of Chemistry, University of Texas, 500 West University Ave, El Paso, TX 79902, USA.
| | - Chitra B Karki
- Department of Physics, University of Texas, 500 West University Ave, El Paso, TX 79902, USA.
| | - Sebastian Miki Silva
- Department of Physics, University of Texas, 500 West University Ave, El Paso, TX 79902, USA.
| | - Lin Li
- Department of Physics, University of Texas, 500 West University Ave, El Paso, TX 79902, USA.
| | - Chuan Xiao
- Department of Chemistry, University of Texas, 500 West University Ave, El Paso, TX 79902, USA.
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20
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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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21
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Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly. Virology 2018; 516:239-245. [PMID: 29407382 DOI: 10.1016/j.virol.2018.01.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 02/07/2023]
Abstract
Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron cryo-microscopy structure of the MelV particle, with the large triangulation number T = 309 constructed by 3080 pseudo-hexagonal capsomers. The most distinct feature of the particle is a large and dense body (LDB) consistently found inside all particles. Electron cryo-tomography of 147 particles shows that the LDB is preferentially located in proximity to the probable lipid bilayer. The LDB is 30 nm in size and its density matches that of a genome/protein complex. The observed LDB reinforces the structural complexity of MelV, setting it apart from other NCLDVs.
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22
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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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23
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Abstract
Large icosahedral viruses that infect bacteria represent an extreme of the coevolution of capsids and the genomes they accommodate. One subset of these large viruses is the jumbophages, tailed phages with double-stranded DNA genomes of at least 200,000 bp. We explored the mechanism leading to increased capsid and genome sizes by characterizing structures of several jumbophage capsids and the DNA packaged within them. Capsid structures determined for six jumbophages were consistent with the canonical phage HK97 fold, and three had capsid geometries with novel triangulation numbers (T=25, T=28, and T=52). Packaged DNA (chromosome) sizes were larger than the genome sizes, indicating that all jumbophages use a head-full DNA packaging mechanism. For two phages (PAU and G), the sizes appeared very much larger than their genome length. We used two-dimensional DNA gel electrophoresis to show that these two DNAs migrated abnormally due to base modifications and to allow us to calculate their actual chromosome sizes. Our results support a ratchet model of capsid and genome coevolution whereby mutations lead to increased capsid volume and allow the acquisition of additional genes. Once the added genes and larger capsid are established, mutations that restore the smaller size are disfavored. A large family of viruses share the same fold of the capsid protein as bacteriophage HK97, a virus that infects bacteria. Members of this family use different numbers of the capsid protein to build capsids of different sizes. Here, we examined the structures of extremely large capsids and measured their DNA content relative to the sequenced genome lengths, aiming to understand the process that increases size. We concluded that mutational changes leading to larger capsids become locked in by subsequent changes to the genome organization.
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24
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Milrot E, Shimoni E, Dadosh T, Rechav K, Unger T, Van Etten JL, Minsky A. Structural studies demonstrating a bacteriophage-like replication cycle of the eukaryote-infecting Paramecium bursaria chlorella virus-1. PLoS Pathog 2017; 13:e1006562. [PMID: 28850602 PMCID: PMC5593192 DOI: 10.1371/journal.ppat.1006562] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 09/11/2017] [Accepted: 07/31/2017] [Indexed: 11/18/2022] Open
Abstract
A fundamental stage in viral infection is the internalization of viral genomes in host cells. Although extensively studied, the mechanisms and factors responsible for the genome internalization process remain poorly understood. Here we report our observations, derived from diverse imaging methods on genome internalization of the large dsDNA Paramecium bursaria chlorella virus-1 (PBCV-1). Our studies reveal that early infection stages of this eukaryotic-infecting virus occurs by a bacteriophage-like pathway, whereby PBCV-1 generates a hole in the host cell wall and ejects its dsDNA genome in a linear, base-pair-by-base-pair process, through a membrane tunnel generated by the fusion of the virus internal membrane with the host membrane. Furthermore, our results imply that PBCV-1 DNA condensation that occurs shortly after infection probably plays a role in genome internalization, as hypothesized for the infection of some bacteriophages. The subsequent perforation of the host photosynthetic membranes presumably enables trafficking of viral genomes towards host nuclei. Previous studies established that at late infection stages PBCV-1 generates cytoplasmic organelles, termed viral factories, where viral assembly takes place, a feature characteristic of many large dsDNA viruses that infect eukaryotic organisms. PBCV-1 thus appears to combine a bacteriophage-like mechanism during early infection stages with a eukaryotic-like infection pathway in its late replication cycle. Although extensively studied, the mechanisms responsible for internalization of viral genomes into their host cells remain unclear. A particularly interesting case of genome release and internalization is provided by the large Paramecium bursaria chlorella virus-1 (PBCV-1), which infects unicellular eukaryotic photosynthetic chlorella cells. In order to release its long dsDNA genome and to enable its translocation to the host nucleus, PBCV-1 must overcome multiple hurdles, including a thick host cell wall and multilayered chloroplast membranes that surround the host cytoplasm. Our observations indicate that these obstacles are dealt with perforations of the host wall, the host cellular membrane, and the host photosynthetic membranes by viral-encoded proteins. Furthermore, our results highlight a bacteriophage-like nature of early PBCV-1 infection stages, thus implying that this virus uniquely combines bacteriophage-like and eukaryotic-like pathways to accomplish its replication cycle.
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Affiliation(s)
- Elad Milrot
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (EM); (AM)
| | - Eyal Shimoni
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Tali Dadosh
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Proteomics, The Weizmann Institute of Science, Rehovot, Israel
| | - James L. Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States of America
| | - Abraham Minsky
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (EM); (AM)
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25
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Abstract
Recently, dozens of virus structures have been solved to resolutions between 2.5 and 5.0 Å by means of electron cryomicroscopy. With these structures we are now firmly within the "atomic age" of electron cryomicroscopy, as these studies can reveal atomic details of protein and nucleic acid topology and interactions between specific residues. This improvement in resolution has been the result of direct electron detectors and image processing advances. Although enforcing symmetry facilitates reaching near-atomic resolution with fewer particle images, it unfortunately obscures some biologically interesting components of a virus. New approaches on relaxing symmetry and exploring structure dynamics and heterogeneity of viral assemblies have revealed important insights into genome packaging, virion assembly, cell entry, and other stages of the viral life cycle. In the future, novel methods will be required to reveal yet-unknown structural conformations of viruses, relevant to their biological activities. Ultimately, these results hold the promise of answering many unresolved questions linking structural diversity of viruses to their biological functions.
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Affiliation(s)
- Jason T Kaelber
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030.,National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Corey F Hryc
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030;
| | - Wah Chiu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030.,National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030;
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26
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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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27
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28
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Veesler D, Kearney BM, Johnson JE. Integration of X-ray crystallography and electron cryo-microscopy in the analysis of virus structure and function. CRYSTALLOGR REV 2015. [DOI: 10.1080/0889311x.2015.1038530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Poon HC, Saldin DK. Use of triple correlations for the sign determinations of expansion coefficients of symmetric approximations to the diffraction volumes of regular viruses. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041716. [PMID: 26798815 PMCID: PMC4711643 DOI: 10.1063/1.4922476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/02/2015] [Indexed: 05/16/2023]
Abstract
An X-ray free electron laser is a new source of x-rays some 10 × 10(9) times brighter than any previous X-ray source, giving rise to the possibility of structure determination of individual biological particles without crystallization. Some of the earliest samples used in the X-ray free electron laser are viruses because they are about the largest of reproducible bioparticles. We show how common virus near-symmetries can be exploited to find a first approximation to their structures to give a starting point for a perturbation approach to determine their structures.
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Affiliation(s)
- H C Poon
- Department of Physics and Laboratory for Surface Studies, University of Wisconsin Milwaukee , P.O. Box 413, Milwaukee, Wisconsin 53201, USA
| | - D K Saldin
- Department of Physics and Laboratory for Surface Studies, University of Wisconsin Milwaukee , P.O. Box 413, Milwaukee, Wisconsin 53201, USA
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Large dsDNA chloroviruses encode diverse membrane transport proteins. Virology 2015; 479-480:38-45. [PMID: 25766639 DOI: 10.1016/j.virol.2015.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/20/2015] [Accepted: 02/07/2015] [Indexed: 10/23/2022]
Abstract
Many large DNA viruses that infect certain isolates of chlorella-like green algae (chloroviruses) are unusual because they often encode a diverse set of membrane transport proteins, including functional K(+) channels and aquaglyceroporins as well as K(+) transporters and calcium transporting ATPases. Some chloroviruses also encode putative ligand-gated-like channel proteins. No one protein is present in all of the chloroviruses that have been sequenced, but the K(+) channel is the most common as only two chloroviruses have been isolated that lack this complete protein. This review describes the properties of these membrane-transporting proteins and suggests possible physiological functions and evolutionary histories for some of them.
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Yolken RH, Jones-Brando L, Dunigan DD, Kannan G, Dickerson F, Severance E, Sabunciyan S, Talbot CC, Prandovszky E, Gurnon JR, Agarkova IV, Leister F, Gressitt KL, Chen O, Deuber B, Ma F, Pletnikov MV, Van Etten JL. Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice. Proc Natl Acad Sci U S A 2014; 111:16106-11. [PMID: 25349393 PMCID: PMC4234575 DOI: 10.1073/pnas.1418895111] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chloroviruses (family Phycodnaviridae) are large DNA viruses known to infect certain eukaryotic green algae and have not been previously shown to infect humans or to be part of the human virome. We unexpectedly found sequences homologous to the chlorovirus Acanthocystis turfacea chlorella virus 1 (ATCV-1) in a metagenomic analysis of DNA extracted from human oropharyngeal samples. These samples were obtained by throat swabs of adults without a psychiatric disorder or serious physical illness who were participating in a study that included measures of cognitive functioning. The presence of ATCV-1 DNA was confirmed by quantitative PCR with ATCV-1 DNA being documented in oropharyngeal samples obtained from 40 (43.5%) of 92 individuals. The presence of ATCV-1 DNA was not associated with demographic variables but was associated with a modest but statistically significant decrease in the performance on cognitive assessments of visual processing and visual motor speed. We further explored the effects of ATCV-1 in a mouse model. The inoculation of ATCV-1 into the intestinal tract of 9-11-wk-old mice resulted in a subsequent decrease in performance in several cognitive domains, including ones involving recognition memory and sensory-motor gating. ATCV-1 exposure in mice also resulted in the altered expression of genes within the hippocampus. These genes comprised pathways related to synaptic plasticity, learning, memory formation, and the immune response to viral exposure.
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Affiliation(s)
- Robert H Yolken
- Stanley Division of Developmental Neurovirology, Department of Pediatrics,
| | | | - David D Dunigan
- Nebraska Center for Virology and Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0900; and
| | - Geetha Kannan
- Department of Psychiatry and Behavioral Sciences, and
| | - Faith Dickerson
- Department of Psychology, Sheppard Pratt Health System, Baltimore, MD 21205
| | - Emily Severance
- Stanley Division of Developmental Neurovirology, Department of Pediatrics
| | - Sarven Sabunciyan
- Stanley Division of Developmental Neurovirology, Department of Pediatrics
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205
| | - Emese Prandovszky
- Stanley Division of Developmental Neurovirology, Department of Pediatrics
| | - James R Gurnon
- Nebraska Center for Virology and Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0900; and
| | - Irina V Agarkova
- Nebraska Center for Virology and Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0900; and
| | - Flora Leister
- Stanley Division of Developmental Neurovirology, Department of Pediatrics
| | - Kristin L Gressitt
- Stanley Division of Developmental Neurovirology, Department of Pediatrics
| | - Ou Chen
- Stanley Division of Developmental Neurovirology, Department of Pediatrics
| | - Bryan Deuber
- Stanley Division of Developmental Neurovirology, Department of Pediatrics
| | - Fangrui Ma
- Nebraska Center for Virology and Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0900; and
| | | | - James L Van Etten
- Nebraska Center for Virology and Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0900; and
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Agarkova I, Hertel B, Zhang X, Lane L, Tchourbanov A, Dunigan DD, Thiel G, Rossmann MG, Van Etten JL. Dynamic attachment of Chlorovirus PBCV-1 to Chlorella variabilis. Virology 2014; 466-467:95-102. [PMID: 25240455 PMCID: PMC4254200 DOI: 10.1016/j.virol.2014.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 05/29/2014] [Accepted: 07/01/2014] [Indexed: 11/27/2022]
Abstract
Chloroviruses infect their hosts by specifically binding to and degrading the cell wall of their algal hosts at the site of attachment, using an intrinsic digesting enzyme(s). Chlorovirus PBCV-1 stored as a lysate survived longer than virus alone, suggesting virus attachment to cellular debris may be reversible. Ghost cells (algal cells extracted with methanol) were used as a model to study reversibility of PBCV-1 attachment because ghost cells are as susceptible to attachment and wall digestion as are live cells. Reversibility of attachment to ghost cells was examined by releasing attached virions with a cell wall degrading enzyme extract. The majority of the released virions retained infectivity even after re-incubating the released virions with ghost cells two times. Thus the chloroviruses appear to have a dynamic attachment strategy that may be beneficial in indigenous environments where cell wall debris can act as a refuge until appropriate host cells are available.
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Affiliation(s)
- Irina Agarkova
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, United States; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, United States
| | - Brigitte Hertel
- Technische Universität Darmstadt, Department of Biology, Plant Membrane Biophysics, 64287 Darmstadt, Germany
| | - Xinzheng Zhang
- Department of Biological Sciences, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-2032, United States
| | - Les Lane
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, United States
| | - Alexander Tchourbanov
- Genetics Core, University of Arizona, 246B Biological Science West, 1041 East Lowell St, Tucson, AZ 85721-0499, United States
| | - David D Dunigan
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, United States; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, United States
| | - Gerhard Thiel
- Technische Universität Darmstadt, Department of Biology, Plant Membrane Biophysics, 64287 Darmstadt, Germany
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-2032, United States
| | - James L Van Etten
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, United States; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, United States.
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Sirotkin S, Mermet A, Bergoin M, Ward V, Van Etten JL. Viruses as nanoparticles: structure versus collective dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022718. [PMID: 25215769 DOI: 10.1103/physreve.90.022718] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 06/03/2023]
Abstract
In order to test the application of the "nanoparticle" concept to viruses in terms of low-frequency dynamics, large viruses (140-190 nm) were compared to similar-sized polymer colloids using ultra-small-angle x-ray scattering and very-low-frequency Raman or Brillouin scattering. While both viruses and polymer colloids show comparable highly defined morphologies, with comparable abilities of forming self-assembled structures, their respective abilities to confine detectable acoustic vibrations, as expected for such monodisperse systems, differed. Possible reasons for these different behaviors are discussed.
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Affiliation(s)
- S Sirotkin
- Institut Lumière Matière, Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5306, 69622 Villeurbanne, France
| | - A Mermet
- Institut Lumière Matière, Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5306, 69622 Villeurbanne, France
| | - M Bergoin
- Laboratoire de Virologie Comparé des Invertébrés, E.P.H.E., Université Montpellier 2, France
| | - V Ward
- University of Otago, Department of Microbology and Immunology, New Zealand
| | - J L Van Etten
- Department of Plant Pathology and the Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska USA
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Abstract
Nucleocytoplasmic large dsDNA viruses (NCLDVs) encompass an ever-increasing group of large eukaryotic viruses, infecting a wide variety of organisms. The set of core genes shared by all these viruses includes a major capsid protein with a double jelly-roll fold forming an icosahedral capsid, which surrounds a double layer membrane that contains the viral genome. Furthermore, some of these viruses, such as the members of the Mimiviridae and Phycodnaviridae have a unique vertex that is used during infection to transport DNA into the host.
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Affiliation(s)
- Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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Abstract
This review is a partially personal account of the discovery of virus structure and its implication for virus function. Although I have endeavored to cover all aspects of structural virology and to acknowledge relevant individuals, I know that I have favored taking examples from my own experience in telling this story. I am anxious to apologize to all those who I might have unintentionally offended by omitting their work. The first knowledge of virus structure was a result of Stanley's studies of tobacco mosaic virus (TMV) and the subsequent X-ray fiber diffraction analysis by Bernal and Fankuchen in the 1930s. At about the same time it became apparent that crystals of small RNA plant and animal viruses could diffract X-rays, demonstrating that viruses must have distinct and unique structures. More advances were made in the 1950s with the realization by Watson and Crick that viruses might have icosahedral symmetry. With the improvement of experimental and computational techniques in the 1970s, it became possible to determine the three-dimensional, near-atomic resolution structures of some small icosahedral plant and animal RNA viruses. It was a great surprise that the protecting capsids of the first virus structures to be determined had the same architecture. The capsid proteins of these viruses all had a 'jelly-roll' fold and, furthermore, the organization of the capsid protein in the virus were similar, suggesting a common ancestral virus from which many of today's viruses have evolved. By this time a more detailed structure of TMV had also been established, but both the architecture and capsid protein fold were quite different to that of the icosahedral viruses. The small icosahedral RNA virus structures were also informative of how and where cellular receptors, anti-viral compounds, and neutralizing antibodies bound to these viruses. However, larger lipid membrane enveloped viruses did not form sufficiently ordered crystals to obtain good X-ray diffraction. Starting in the 1990s, these enveloped viruses were studied by combining cryo-electron microscopy of the whole virus with X-ray crystallography of their protein components. These structures gave information on virus assembly, virus neutralization by antibodies, and virus fusion with and entry into the host cell. The same techniques were also employed in the study of complex bacteriophages that were too large to crystallize. Nevertheless, there still remained many pleomorphic, highly pathogenic viruses that lacked the icosahedral symmetry and homogeneity that had made the earlier structural investigations possible. Currently some of these viruses are starting to be studied by combining X-ray crystallography with cryo-electron tomography.
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Dent KC, Thompson R, Barker AM, Hiscox JA, Barr JN, Stockley PG, Ranson NA. The asymmetric structure of an icosahedral virus bound to its receptor suggests a mechanism for genome release. Structure 2014; 21:1225-34. [PMID: 23810697 PMCID: PMC3701328 DOI: 10.1016/j.str.2013.05.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/23/2013] [Accepted: 05/07/2013] [Indexed: 11/23/2022]
Abstract
Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their genomes, which are vital for infection. Here, we report an asymmetric structure of bacteriophage MS2, attached to its receptor, the F-pilus. Cryo-electron tomography and subtomographic averaging of such complexes result in a structure containing clear density for the packaged genome, implying that the conformation of the genome is the same in each virus particle. The data also suggest that the single-copy viral maturation protein breaks the symmetry of the capsid, occupying a position that would be filled by a coat protein dimer in an icosahedral shell. This capsomere can thus fulfill its known biological roles in receptor and genome binding and suggests an exit route for the genome during infection. The asymmetric structure of a virus receptor complex is described The density for ordered genomic RNA was observed in the structure Viral maturation protein was visualized
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Affiliation(s)
- Kyle C Dent
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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Peralta B, Gil-Carton D, Castaño-Díez D, Bertin A, Boulogne C, Oksanen HM, Bamford DH, Abrescia NGA. Mechanism of membranous tunnelling nanotube formation in viral genome delivery. PLoS Biol 2013; 11:e1001667. [PMID: 24086111 PMCID: PMC3782422 DOI: 10.1371/journal.pbio.1001667] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 08/15/2013] [Indexed: 11/19/2022] Open
Abstract
In internal membrane-containing viruses, a lipid vesicle enclosed by the icosahedral capsid protects the genome. It has been postulated that this internal membrane is the genome delivery device of the virus. Viruses built with this architectural principle infect hosts in all three domains of cellular life. Here, using a combination of electron microscopy techniques, we investigate bacteriophage PRD1, the best understood model for such viruses, to unveil the mechanism behind the genome translocation across the cell envelope. To deliver its double-stranded DNA, the icosahedral protein-rich virus membrane transforms into a tubular structure protruding from one of the 12 vertices of the capsid. We suggest that this viral nanotube exits from the same vertex used for DNA packaging, which is biochemically distinct from the other 11. The tube crosses the capsid through an aperture corresponding to the loss of the peripentonal P3 major capsid protein trimers, penton protein P31 and membrane protein P16. The remodeling of the internal viral membrane is nucleated by changes in osmolarity and loss of capsid-membrane interactions as consequence of the de-capping of the vertices. This engages the polymerization of the tail tube, which is structured by membrane-associated proteins. We have observed that the proteo-lipidic tube in vivo can pierce the gram-negative bacterial cell envelope allowing the viral genome to be shuttled to the host cell. The internal diameter of the tube allows one double-stranded DNA chain to be translocated. We conclude that the assembly principles of the viral tunneling nanotube take advantage of proteo-lipid interactions that confer to the tail tube elastic, mechanical and functional properties employed also in other protein-membrane systems.
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Affiliation(s)
- Bibiana Peralta
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Derio, Spain
| | | | - Daniel Castaño-Díez
- Center for Cellular Imaging and Nano-Analitics (C-CINA) Biozentrum, University of Basel, Basel, Switzerland
| | - Aurelie Bertin
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université de Paris–Sud, Orsay, France
| | - Claire Boulogne
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université de Paris–Sud, Orsay, France
| | - Hanna M. Oksanen
- Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, University of Helsinki, Finland
| | - Dennis H. Bamford
- Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, University of Helsinki, Finland
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- * E-mail:
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A strain-specific epitope of enterovirus 71 identified by cryo-electron microscopy of the complex with fab from neutralizing antibody. J Virol 2013; 87:11363-70. [PMID: 23946455 DOI: 10.1128/jvi.01926-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Enterovirus 71 (EV71) is a picornavirus that causes outbreaks of hand, foot, and mouth disease (HFMD), primarily in the Asia-Pacific area. Unlike coxsackievirus A16, which also causes HFMD, EV71 induces severe neuropathology leading to high fatalities, especially among children under the age of 6 years. Currently, no established vaccines or treatments are available against EV71 infection. The monoclonal antibody MA28-7 neutralizes only specific strains of EV71 that have a conserved glycine at amino acid VP1-145, a surface-exposed residue that maps to the 5-fold vertex and that has been implicated in receptor binding. The cryo-electron microscopy structure of a complex between EV71 and the Fab fragment of MA28-7 shows that only one Fab fragment occupies each 5-fold vertex. A positively charged patch, which has also been implicated in receptor binding, lies within the Fab footprint. We identify the strain-specific epitope of EV71 and discuss the possible neutralization mechanisms of the antibody.
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Thiel G, Moroni A, Blanc G, Van Etten JL. Potassium ion channels: could they have evolved from viruses? PLANT PHYSIOLOGY 2013; 162:1215-24. [PMID: 23719891 PMCID: PMC3707557 DOI: 10.1104/pp.113.219360] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 05/23/2013] [Indexed: 06/01/2023]
Abstract
Phylogenetic analyses of small viral K+ channels suggests that they did not originate from their hosts, but instead could be the source of the postulated pore precursor in the evolution of K+ channels.
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Affiliation(s)
- Gerhard Thiel
- Department of Biology, Technische Universität-Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany.
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Abstract
This chapter discusses the astonishing discovery of the Sputnik virophage, a new virus infecting giant viruses of the genera Mimivirus and Mamavirus. While other virophages have also since been described, this chapter focuses mainly on Sputnik, which is the best described. We detail the general properties of the virophage life cycle, as well as its hosts, genomic characteristics, ecology, and origin. In addition to genetic, phylogenetic, and structural evidence, the existence of virophages has deeply altered our view of the tripartite division of life to include the addition of a fourth domain constituted of the nucleocytoplasmic large DNA viruses, an important point that is discussed.
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Affiliation(s)
- Christelle Desnues
- URMITE, Centre National de la Recherche Scientifique UMR IRD 6236, Faculté de Médecine, Aix-Marseille Université, Marseille, France
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The structure of the NTPase that powers DNA packaging into Sulfolobus turreted icosahedral virus 2. J Virol 2013; 87:8388-98. [PMID: 23698307 DOI: 10.1128/jvi.00831-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biochemical reactions powered by ATP hydrolysis are fundamental for the movement of molecules and cellular structures. One such reaction is the encapsidation of the double-stranded DNA (dsDNA) genome of an icosahedrally symmetric virus into a preformed procapsid with the help of a genome-translocating NTPase. Such NTPases have been characterized in detail from both RNA and tailed DNA viruses. We present four crystal structures and the biochemical activity of a thermophilic NTPase, B204, from the nontailed, membrane-containing, hyperthermoacidophilic archaeal dsDNA virus Sulfolobus turreted icosahedral virus 2. These are the first structures of a genome-packaging NTPase from a nontailed, dsDNA virus with an archaeal host. The four structures highlight the catalytic cycle of B204, pinpointing the molecular movement between substrate-bound (open) and empty (closed) active sites. The protein is shown to bind both single-stranded and double-stranded nucleic acids and to have an optimum activity at 80°C and pH 4.5. The overall fold of B204 places it in the FtsK-HerA superfamily of P-loop ATPases, whose cellular and viral members have been suggested to share a DNA-translocating mechanism.
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Abstract
Viral particles consist essentially of a proteinaceous capsid protecting a genome and involved also in many functions during the virus life cycle. In simple viruses, the capsid consists of a number of copies of the same, or a few different proteins organized into a symmetric oligomer. Structurally complex viruses present a larger variety of components in their capsids than simple viruses. They may contain accessory proteins with specific architectural or functional roles; or incorporate non-proteic elements such as lipids. They present a range of geometrical variability, from slight deviations from the icosahedral symmetry to complete asymmetry or even pleomorphism. Putting together the many different elements in the virion requires an extra effort to achieve correct assembly, and thus complex viruses require sophisticated mechanisms to regulate morphogenesis. This chapter provides a general view of the structure and assembly of complex viruses.
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Affiliation(s)
- Mauricio G. Mateu
- "Severo Ochoa" (CSIC_UAM), And Dept. of Molecular Biology, Centro de Biología Molecular, Cantoblanco, Madrid, 28049 Madrid Spain
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Wada K, Kimura K, Hasegawa A, Fukuyama K, Nagasaki K. Establishment of a bacterial expression system and immunoassay platform for the major capsid protein of HcRNAV, a dinoflagellate-infecting RNA virus. Microbes Environ 2012; 27:483-9. [PMID: 23047150 PMCID: PMC4103558 DOI: 10.1264/jsme2.me12046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HcRNAV is a small icosahedral virus that infects the shellfish-killing marine dinoflagellate Heterocapsa circularisquama, which harbors a dicistronic linear single-stranded RNA (ssRNA) genome ca. 4.4 kb in length. Its major capsid protein (MCP) gene sequence is not expressed by various strains of Escherichia coli, possibly because of a codon usage problem. To solve this problem, a chemically modified (i.e., de novo synthesized) gene was designed and cloned into the pCold-GST expression vector, and transformed into E. coli strain C41 (DE3), in which codon usage was universally optimized to efficiently express the polypeptide having the viral MCP amino acid sequence. The bacterially expressed protein, which was purified after a procedure involving denaturation and refolding, successfully formed virus-like particles that significantly resembled native HcRNAV particles. The purified, denatured protein was used as an antigen to immunize rabbits, and the resulting antiserum was shown to be strongly reactive to not only the bacterially expressed recombinant protein, but also to native HcRNAV MCP by Western blotting and dot immunoassays, respectively. These results indicate that an antiserum recognizing native HcRNAV MCP was successfully obtained using bacterially expressed HcRNAV MCP as the antigen.
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Affiliation(s)
- Kei Wada
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560–0043, Japan
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Abstract
In the last twenty years, numerous giant, dsDNA, icosahedral viruses have been discovered and assigned to the nucleocytoplasmic large dsDNA virus (NCLDV) clade. The major capsid proteins of these viruses consist of two consecutive jelly-roll domains, assembled into trimers, with pseudo 6-fold symmetry. The capsomers are assembled into arrays that have either p6 (as in Paramecium bursaria Chlorella virus-1) or p3 symmetry (as in Mimivirus). Most of the NCLDV viruses have a membrane that separates the nucleocapsid from the external capsid.
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Affiliation(s)
- Chuan Xiao
- Department of Chemistry, University of Texas at El Paso, 79968, USA
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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.
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47
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Abstract
Is it possible to meaningfully comprehend the diversity of the viral world? We propose that it is. This is based on the observation that, although there is immense genomic variation, every infective virion is restricted by strict constraints in structure space (i.e., there are a limited number of ways to fold a protein chain, and only a small subset of these have the potential to construct a virion, the hallmark of a virus). We have previously suggested the use of structure for the higher-order classification of viruses, where genomic similarities are no longer observable. Here, we summarize the arguments behind this proposal, describe the current status of structural work, highlighting its power to infer common ancestry, and discuss the limitations and obstacles ahead of us. We also reflect on the future opportunities for a more concerted effort to provide high-throughput methods to facilitate the large-scale sampling of the virosphere.
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Abstract
My undergraduate education in mathematics and physics was a good grounding for graduate studies in crystallographic studies of small organic molecules. As a postdoctoral fellow in Minnesota, I learned how to program an early electronic computer for crystallographic calculations. I then joined Max Perutz, excited to use my skills in the determination of the first protein structures. The results were even more fascinating than the development of techniques and provided inspiration for starting my own laboratory at Purdue University. My first studies on dehydrogenases established the conservation of nucleotide-binding structures. Having thus established myself as an independent scientist, I could start on my most cherished ambition of studying the structure of viruses. About a decade later, my laboratory had produced the structure of a small RNA plant virus and then, in another six years, the first structure of a human common cold virus. Many more virus structures followed, but soon it became essential to supplement crystallography with electron microscopy to investigate viral assembly, viral infection of cells, and neutralization of viruses by antibodies. A major guide in all these studies was the discovery of evolution at the molecular level. The conservation of three-dimensional structure has been a recurring theme, from my experiences with Max Perutz in the study of hemoglobin to the recognition of the conserved nucleotide-binding fold and to the recognition of the jelly roll fold in the capsid protein of a large variety of viruses.
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Affiliation(s)
- Michael G Rossmann
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, West Lafayette, Indiana 47907, USA.
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49
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Wulfmeyer T, Polzer C, Hiepler G, Hamacher K, Shoeman R, Dunigan DD, Van Etten JL, Lolicato M, Moroni A, Thiel G, Meckel T. Structural organization of DNA in chlorella viruses. PLoS One 2012; 7:e30133. [PMID: 22359540 PMCID: PMC3281028 DOI: 10.1371/journal.pone.0030133] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 12/09/2011] [Indexed: 11/19/2022] Open
Abstract
Chlorella viruses have icosahedral capsids with an internal membrane enclosing their large dsDNA genomes and associated proteins. Their genomes are packaged in the particles with a predicted DNA density of ca. 0.2 bp nm−3. Occasionally infection of an algal cell by an individual particle fails and the viral DNA is dynamically ejected from the capsid. This shows that the release of the DNA generates a force, which can aid in the transfer of the genome into the host in a successful infection. Imaging of ejected viral DNA indicates that it is intimately associated with proteins in a periodic fashion. The bulk of the protein particles detected by atomic force microscopy have a size of ∼60 kDa and two proteins (A278L and A282L) of about this size are among 6 basic putative DNA binding proteins found in a proteomic analysis of DNA binding proteins packaged in the virion. A combination of fluorescence images of ejected DNA and a bioinformatics analysis of the DNA reveal periodic patterns in the viral DNA. The periodic distribution of GC rich regions in the genome provides potential binding sites for basic proteins. This DNA/protein aggregation could be responsible for the periodic concentration of fluorescently labeled DNA observed in ejected viral DNA. Collectively the data indicate that the large chlorella viruses have a DNA packaging strategy that differs from bacteriophages; it involves proteins and share similarities to that of chromatin structure in eukaryotes.
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Affiliation(s)
- Timo Wulfmeyer
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Christian Polzer
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gregor Hiepler
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kay Hamacher
- Computational Biology Group, Technische Universität Darmstadt, Darmstadt, Germany
| | - Robert Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - David D. Dunigan
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - James L. Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Marco Lolicato
- Department of Biology and CNR IBF-Mi, Università degli Studi di Milano, Milano, Italy
| | - Anna Moroni
- Department of Biology and CNR IBF-Mi, Università degli Studi di Milano, Milano, Italy
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
- * E-mail:
| | - Tobias Meckel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
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50
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Van Etten JL, Dunigan DD. Chloroviruses: not your everyday plant virus. TRENDS IN PLANT SCIENCE 2012; 17:1-8. [PMID: 22100667 PMCID: PMC3259250 DOI: 10.1016/j.tplants.2011.10.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 10/20/2011] [Accepted: 10/25/2011] [Indexed: 05/29/2023]
Abstract
Viruses infecting higher plants are among the smallest viruses known and typically have four to ten protein-encoding genes. By contrast, many viruses that infect algae (classified in the virus family Phycodnaviridae) are among the largest viruses found to date and have up to 600 protein-encoding genes. This brief review focuses on one group of plaque-forming phycodnaviruses that infect unicellular chlorella-like green algae. The prototype chlorovirus PBCV-1 has more than 400 protein-encoding genes and 11 tRNA genes. About 40% of the PBCV-1 encoded proteins resemble proteins of known function including many that are completely unexpected for a virus. In many respects, chlorovirus infection resembles bacterial infection by tailed bacteriophages.
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Affiliation(s)
- James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, USA.
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