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Molecular Characterization of New Archaeal Viruses from High Salinity Environments TATIANA DEMINA

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Molecular Characterization of New Archaeal Viruses from High Salinity Environments TATIANA DEMINA YEB Recent Publications in this Series TATIANA DEMINA Molecular Characterization of New Archaeal Viruses from High Salinity Environments 9/2016 Satu Olkkola Antimicrobial Resistance and Its Mechanisms among Campylobacter coli and Campylobacter upsaliensis with a Special Focus on Streptomycin 10/2016 Windi Indra Muziasari Impact of Fish Farming on Antibiotic Resistome and Mobile Elements in Baltic Sea Sediment 11/2016 Kari Kylä-Nikkilä DISSERTATIONES SCHOLA DOCTORALIS SCIENTIAE CIRCUMIECTALIS, Genetic Engineering of Lactic Acid Bacteria to Produce Optically Pure Lactic Acid and to Develop ALIMENTARIAE, BIOLOGICAE. UNIVERSITATIS HELSINKIENSIS 26/2016 a Novel Cell Immobilization Method Suitable for Industrial Fermentations 12/2016 Jane Etegeneng Besong epse Ndika Molecular Insights into a Putative Potyvirus RNA Encapsidation Pathway and Potyvirus Particles as Enzyme Nano-Carriers 13/2016 Lijuan Yan Bacterial Community Dynamics and Perennial Crop Growth in Motor Oil-Contaminated Soil in a TATIANA DEMINA Boreal Climate 14/2016 Pia Rasinkangas New Insights into the Biogenesis of Lactobacillus rhamnosus GG Pili and the in vivo Effects of Molecular Characterization of New Archaeal Pili 15/2016 Johanna Rytioja Viruses from High Salinity Environments Enzymatic Plant Cell Wall Degradation by the White Rot Fungus Dichomitus squalens 16/2016 Elli Koskela Genetic and Environmental Control of Flowering in Wild and Cultivated Strawberries 17/2016 Riikka Kylväjä Staphylococcus aureus and Lactobacillus crispatus: Adhesive Characteristics of Two Gram- Positive Bacterial Species 18/2016 Hanna Aarnos Photochemical Transformation of Dissolved Organic Matter in Aquatic Environment – From a Boreal Lake and Baltic Sea to Global Coastal Ocean 19/2016 Riikka Puntila Trophic Interactions and Impacts of Non-Indigenous Species in the Baltic Sea Coastal Ecosystems 20/2016 Jaana Kuuskeri Genomics and Systematics of the White-Rot Fungus Phlebia radiata: Special Emphasis on Wood-Promoted Transcriptome and Proteome 21/2016 Qiao Shi Synthesis and Structural Characterization of Glucooligosaccharides and Dextran from Weissella confusa Dextransucrases 22/2016 Tapani Jokiniemi Energy Efficiency in Grain Preservation 23/2016 Outi Nyholm Virulence Variety and Hybrid Strains of Diarrheagenic Escherichia coli in Finland and Burkina Faso 24/2016 Anu Riikonen INSTITUTE OF BIOTECHNOLOGY AND Some Ecosystem Service Aspects of Young Street Tree Plantings DIVISION OF GENERAL MICROBIOLOGY 25/2016 Jing Cheng DEPARTMENT OF BIOSCIENCES The Development of Intestinal Microbiota in Childhood and Host-Microbe Interactions in Pediatric Celiac Diseases FACULTY OF BIOLOGICAL AND ENVIRONMENTAL SCIENCES DOCTORAL PROGRAMME IN MICROBIOLOGY AND BIOTECHNOLOGY UNIVERSITY OF HELSINKI 26/2016 Helsinki 2016 ISSN 2342-5423 ISBN 978-951-51-2706-8 Molecular characterization of new archaeal viruses from high salinity environments Tatiana A. Demina Institute of Biotechnology and Division of General Microbiology Department of Biosciences Faculty of Biological and Environmental Sciences and Viikki Doctoral Programme in Molecular Biosciences and Doctoral Programme in Microbiology and Biotechnology University of Helsinki ACADEMIC DISSERTATION To be presented, with the permission of the Faculty of Biological and Environmental Sciences of the University of Helsinki, for public examination in lecture room 511 of Info Center Korona, Viikinkaari 11, Helsinki, on 16th of December 2016, at 12 noon. Helsinki 2016 Supervisors Reviewers Docent Hanna M. Oksanen Professor Kenneth Stedman Institute of Biotechnology and Department of Biology Department of Biosciences Portland State University University of Helsinki U.S.A. Finland Associate Professor Josefa Antón Docent Maija K. Pietilä Department of Physiology, Genetics, and Department of Food and Environmental Microbiology Sciences University of Alicante University of Helsinki Spain Finland Opponent PhD Nina S. Atanasova Institute of Biotechnology and Professor Jarkko Hantula Department of Biosciences Natural Resources Institute (LUKE) University of Helsinki Finland Finland Custos Thesis advisory committee Academy Professor Academy Professor Dennis H. Bamford Dennis H. Bamford Institute of Biotechnology and Institute of Biotechnology and Department of Biosciences Department of Biosciences University of Helsinki University of Helsinki Finland Finland Docent Sari Timonen Department of Food and Environmental Sciences University of Helsinki Finland ©Tatiana Demina Cover image: Tatiana Demina ISBN 978-951-51-2706-8 (paperback) ISBN 978-951-51-2707-5 (PDF) ISSN 2342-5423 (print) ISSN 2342-5431 (online) Hansaprint Helsinki 2016 “Science is the poetry of reality” Richard Dawkins List of original publications This thesis is based on the following publications referred to by their Roman numerals: I. Atanasova, N.S., Demina, T.A., Buivydas, A., Bamford, D.H., Oksanen, H.M., 2015. Archaeal viruses multiply: temporal screening in a solar saltern. Viruses 7, 4, 1902-1926. II. Demina, T.A., Pietilä, M.K., Svirskaite, J., Ravantti, J.J., Atanasova, N.S., Bamford, D.H., Oksanen, H.M., 2016. Archaeal Haloarcula californiae icosahedral virus 1 highlights conserved elements in icosahedral membrane- containing DNA viruses from extreme environments. mBio 7, 4. III. Demina, T.A.*, Atanasova, N.S.*, Pietilä, M.K., Oksanen, H.M., Bamford, D.H. Vesicle-like virion of Haloarcula hispanica pleomorphic virus 3 preserves high infectivity in saturated salt. Virology 499, 40-51. *These authors contributed equally. Doctoral candidate’s contribution: In I, TD participated in performing experiments, data analysis and handling, and writing the manuscript. In II, TD contributed to the study design, acquisition of data, its analysis and interpretation, as well as drafring and editing the manuscript. In III, TD was involved in project design, performing experiments, processing of obtained data, and writing the manuscript. i Abbreviations ATP adenosine triphosphate ATPase adenosine triphosphatase 3-D three-dimensional acc. no. accession number BLAST Basic Local Alignment Search Tool bp base pair BREX bacteriophage exclusion cas clustered regularly interspaced short palindromic repeats-associated proteins CRISPR clustered regularly interspaced short palindromic repeats cryo-EM cryo-electron microscopy DNA deoxyribonucleic acid ds double-stranded ICTV International Committee on Taxonomy of Viruses ITR inverted terminal repeat MCP major capsid protein MEGA Molecular Evolutionary Genetics Analysis MUSCLE Multiple Sequence Comparison by Log-Expectation n.r. non-redundant nt nucleotide ORF open reading frame p.i. post infection PCR polymerase chain reaction PFU plaque forming unit RNA ribonucleic acid rRNA ribosomal RNA SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis ss single-stranded TEM transmission electron microscopy TLC thin layer chromatography tRNA transfer RNA VLP virus-like particle VP virion protein ii Abbreviated virus names BTV Bluetongue virus EHP-1 environmental halophage 1 EHP-12 environmental halophage 12 EHP-6 environmental halophage 6 HATV-1 Haloarcula head-tailed virus 1 HATV-2 Haloarcula head-tailed virus 2 HCIV-1 Haloarcula californiae icosahedral virus 1 HCTV-1 Haloarcula californiae head-tailed virus 1 HCTV-2 Haloarcula californiae head-tailed virus 2 HCTV-5 Haloarcula californiae head-tailed virus 5 HGPV-1 Halogeometricum pleomorphic virus 1 HGTV-1 Halogeometricum head-tailed virus 1 HHIV-2 Haloarcula hispanica icosahedral virus 2 HHPV-1 Haloarcula hispanica pleomorphic virus 1 HHPV-2 Haloarcula hispanica pleomorphic virus 2 HHPV3 Haloarcula hispanica pleomorphic virus 3 HHTV-1 Haloarcula hispanica head-tailed virus 1 HHTV-2 Haloarcula hispanica head-tailed virus 2 HJTV-1 Haloarcula japonica head-tailed virus 1 HJTV-2 Haloarcula japonica head-tailed virus 2 HRPV-1 Halorubrum pleomorphic virus 1 HRPV-2 Halorubrum pleomorphic virus 2 HRPV-3 Halorubrum pleomorphic virus 3 HRPV-6 Halorubrum pleomorphic virus 6 HRTV-1 Halorubrum head-tailed virus 1 HRTV-10 Halorubrum head-tailed virus 10 HRTV-11 Halorubrum head-tailed virus 11 HRTV-12 Halorubrum head-tailed virus 12 HRTV-2 Halorubrum head-tailed virus 2 HRTV-3 Halorubrum head-tailed virus 3 HRTV-4 Halorubrum head-tailed virus 4 HRTV-5 Halorubrum head-tailed virus 5 HRTV-6 Halorubrum head-tailed virus 6 HRTV-7 Halorubrum head-tailed virus 7 HRTV-8 Halorubrum head-tailed virus 8 HRTV-9 Halorubrum head-tailed virus 9 HSTV-1 Haloarcula sinaiiensis head-tailed virus 1 HSTV-2 Halorubrum sodomense head-tailed virus 2 HSTV-3 Halorubrum sodomense head-tailed virus 3 HVTV-1 Haloarcula vallismortis head-tailed virus 1 HVTV-2 Haloarcula vallismortis head-tailed virus 2 NHV-1 nanohaloarchaeal virus 1 OLPV Organic Lake phycodnavirus iii OLV Organic Lake virophage PBCV-1 Paramecium bursaria chlorella virus 1 SCTP-1 Salicola head-tailed phage 1 SCTP-2 Salicola head-tailed phage 2 SCTP-3 Salicola head-tailed phage 3 SIRV2 Sulfolobus islandicus rod-shaped virus 2 SSIP-1 Salisaeta icosahedral phage 1 STIV Sulfolobus turreted icosahedral virus iv Summary Viruses are important ecological and biological actors and one of the major evolutionary forces that cells encounter. In contrast to their overwhelming genetic diversity, all known virus isolates display a limited number of morphotypes. It has been suggested that due to structural constraints and limitations in protein fold space, virus morphological diversity is restricted to certain possible architectures. Thus, the huge and complex virosphere can be ordered by grouping viruses into
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