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6. Numerous cultivated and uncultivated viruses encode ribosomal proteins.

Author

Mizuno, Carolina M, Guyomar, Charlotte, Roux, Simon, Lavigne, Régis, Rodriguez-Valera, Francisco, Sullivan, Matthew B, Gillet, Reynald, Forterre, Patrick, and Krupovic, Mart

Subjects
Vaccine Related, Prevention, Biodefense, Genetics, Infectious Diseases, 2.2 Factors relating to physical environment, Infection, MD Multidisciplinary
Abstract

Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses. Viruses tend to encode dynamic RPs, easily exchangeable between ribosomes, suggesting these proteins can replace cellular versions in host ribosomes. Functional assays confirm that the two most common virus-encoded RPs, bS21 and bL12, are incorporated into 70S ribosomes when expressed in Escherichia coli. Ecological distribution of virus-encoded RPs suggests some level of ecosystem adaptations as aquatic viruses and viruses of animal-associated bacteria are enriched for different subsets of RPs. Finally, RP genes are under purifying selection and thus likely retained an important function after being horizontally transferred into virus genomes.

Published
2019

11. Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging

Author

Ptchelkine, Denis, Gillum, Ashley, Mochizuki, Tomohiro, Lucas-Staat, Soizick, Liu, Ying, Krupovic, Mart, Phillips, Simon E. V., Prangishvili, David, Huiskonen, Juha T., University of Oxford [Oxford], STFC Rutherford Appleton Laboratory (RAL), Science and Technology Facilities Council (STFC), The Wellcome Trust Centre for Human Genetics [Oxford], Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Tokyo Institute of Technology [Tokyo] (TITECH), University of Helsinki, The OPIC electron microscopy facility was founded by a Wellcome Trust JIF award (060208/Z/00/Z) and is supported by a WT equipment grant (093305/Z/10/Z). Work in D.P.’s laboratory is supported by l'Agence Nationale de la Recherche (France) and by the European Union's Horizon 2020 research and innovation program under grant agreement 685778, project VIRUS-X. Work in J.T.H.’s laboratory is supported by European Research Council (649053) under the European Union’s Horizon 2020 research and innovation program. The Wellcome Trust Centre for Human Genetics is supported by a Wellcome Trust Core Award (203141/Z/16/Z)., European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016), European Project: 649053,H2020,ERC-2014-CoG,BIZEB(2015), University of Oxford, Institut Pasteur [Paris] (IP), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Helsinki Institute of Life Science HiLIFE

Subjects
Archaeal Viruses, Models, Molecular, MESH: Virus Assembly, Glycosylation, PROTEINS, Science, [SDV]Life Sciences [q-bio], viruses, DIVERSITY, MESH: Viral Structural Proteins, MESH: Imaging, Three-Dimensional, Genome, Viral, Article, Imaging, Three-Dimensional, MESH: Aeropyrum, MESH: Archaeal Viruses, SPACE, lcsh:Science, 1183 Plant biology, microbiology, virology, REAL, TOOLS, Viral Structural Proteins, HELICAL RECONSTRUCTION, DNA, Superhelical, ELECTRON CRYOMICROSCOPY, Virus Assembly, MESH: Hydrophobic and Hydrophilic Interactions, Cryoelectron Microscopy, 1184 Genetics, developmental biology, physiology, Aeropyrum, MESH: Protein Subunits, MESH: Glycosylation, MESH: DNA, Viral, Protein Subunits, RESOLUTION, MESH: DNA, Superhelical, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, DNA, Viral, lcsh:Q, MESH: Cryoelectron Microscopy, MESH: Genome, Viral, Hydrophobic and Hydrophilic Interactions, MESH: Models, Molecular
Abstract

Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. However, there is a paucity of information on archaeal virion structures, genome packaging, and determinants of temperature resistance. The rod-shaped virus APBV1 (Aeropyrum pernix bacilliform virus 1) is among the most thermostable viruses known; it infects a hyperthermophile Aeropyrum pernix, which grows optimally at 90 °C. Here we report the structure of APBV1, determined by cryo-electron microscopy at near-atomic resolution. Tight packing of the major virion glycoprotein (VP1) is ensured by extended hydrophobic interfaces, and likely contributes to the extreme thermostability of the helical capsid. The double-stranded DNA is tightly packed in the capsid as a left-handed superhelix and held in place by the interactions with positively charged residues of VP1. The assembly is closed by specific capping structures at either end, which we propose to play a role in DNA packing and delivery., The rod-shaped virus APBV1 is among the most thermostable viruses known. Here, Ptchelkine et al. determine its structure at near-atomic resolution, show that the DNA is packed as left-handed superhelix and identify extended hydrophobic interfaces that likely contribute to the extreme thermostability of the capsid.

Published
2017

12. Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile.

Author

Ying Liu, Osinsk, Tomasz, Wang, Fengbin, Krupovic, Mart, Schouten, Stefan, Kasson, Peter, Prangishvili, David, and Egelma, Edward H.

Abstract

Different forms of viruses that infect archaea inhabiting extreme environments continue to be discovered at a surprising rate, suggesting that the current sampling of these viruses is sparse. We describe here Sulfolobus filamentous virus 1 (SFV1), a membrane-enveloped virus infecting Sulfolobus shibatae. The virus encodes two major coat proteins which display no apparent sequence similarity with each other or with any other proteins in databases. We have used cryo-electron microscopy at 3.7 Å resolution to show that these two proteins form a nearly symmetrical heterodimer, which wraps around A-form DNA, similar to what has been shown for SIRV2 and AFV1, two other archaeal filamentous viruses. The thin (~ 20 Å) membrane of SFV1 is mainly archaeol, a lipid species that accounts for only 1% of the host lipids. Our results show how relatively conserved structural features can be maintained across evolution by both proteins and lipids that have diverged considerably. [ABSTRACT FROM AUTHOR]

Published
2018
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14. Numerous cultivated and uncultivated viruses encode ribosomal proteins

Author

Mart Krupovic, Matthew B. Sullivan, Charlotte Guyomar, Carolina Megumi Mizuno, Francisco Rodriguez-Valera, Reynald Gillet, Régis Lavigne, Patrick Forterre, Simon Roux, Krupovic, Mart, Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées - - ENVIRA2017 - ANR-17-CE15-0005 - AAPG2017 - VALID, Virus-X: Viral Metagenomics for Innovation Value - Virus-X - - H20202016-04-01 - 2020-03-31 - 685778 - VALID, Supporting transnational mobility within the European life sciences by cofunding of the EMBO Fellowship Programme - LTFCOFUND2013 - - EC:FP7:PEOPLE2014-11-10 - 2018-08-09 - 609409 - VALID, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Universidad Miguel Hernández [Elche] (UMH), Ohio State University [Columbus] (OSU), This work was supported by grant ERC UE 340440 to PF, Agence Nationale pour la Recherche grants to M.K. (#ANR-17-CE15–0005–01) and R.G. (Direction Générale de l’Armement, ANR-14-ASTR-0001), the Virus-X project (EU Horizon 2020, No. 685778) to M.K.. C.M.M. was supported by the European Molecular Biology Organization (ALTF 1562-2015) and Marie Curie Actions program from the European Commission (LTFCOFUND2013, GA-2013-609409), C.G. was supported by Direction Générale de l’Armement and Ministère de l’Enseignement supérieur et de la Recherche, M.B.S. was supported by Gordon and Betty Moore Foundation (#3305, 3790) and National Science Foundation (OCE#1536989) awards. F.R.-V. was supported by grant VIREVO CGL2016-76273-P [AEI/FEDER, EU] (cofounded with FEDER funds). The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231., We thank Fanny Demay for the technical assistance and Sophie Chat for help with electron microscopy., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016), European Project: 609409,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,LTFCOFUND2013(2014), Institut Pasteur [Paris], Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université d'Angers (UA)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )

Subjects
0301 basic medicine, [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], viruses, General Physics and Astronomy, 02 engineering and technology, medicine.disease_cause, Genome, Ribosome, 2.2 Factors relating to physical environment, Negative selection, 2.2 Factors relating to the physical environment, Aetiology, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Genetics, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0303 health sciences, Multidisciplinary, biology, food and beverages, Translation (biology), 021001 nanoscience & nanotechnology, 3. Good health, [SDV] Life Sciences [q-bio], Infectious Diseases, [SDE]Environmental Sciences, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0210 nano-technology, Infection, Science, Article, General Biochemistry, Genetics and Molecular Biology, Virus, Vaccine Related, 03 medical and health sciences, Ribosomal protein, Biodefense, MD Multidisciplinary, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, Escherichia coli, 030304 developmental biology, 030306 microbiology, Prevention, fungi, General Chemistry, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Metagenomics, lcsh:Q, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Function (biology), Bacteria
Abstract

Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses. Viruses tend to encode dynamic RPs, easily exchangeable between ribosomes, suggesting these proteins can replace cellular versions in host ribosomes. Functional assays confirm that the two most common virus-encoded RPs, bS21 and bL12, are incorporated into 70S ribosomes when expressed in Escherichia coli. Ecological distribution of virus-encoded RPs suggests some level of ecosystem adaptations as aquatic viruses and viruses of animal-associated bacteria are enriched for different subsets of RPs. Finally, RP genes are under purifying selection and thus likely retained an important function after being horizontally transferred into virus genomes., Viruses can encode genes that regulate the host's translational machinery to their advantage. Here, the authors show that viruses encode ribosomal proteins that can be incorporated into the host’s ribosome and may affect translation.

Published
2019

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