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Bhoobalan-Chitty Y, Xu S, Martinez-Alvarez L, Karamycheva S, Makarova KS, Koonin EV, Peng X. Regulatory sequence-based discovery of anti-defense genes in archaeal viruses. Nat Commun 2024; 15:3699. [PMID: 38698035 PMCID: PMC11065993 DOI: 10.1038/s41467-024-48074-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 04/19/2024] [Indexed: 05/05/2024] Open
Abstract
In silico identification of viral anti-CRISPR proteins (Acrs) has relied largely on the guilt-by-association method using known Acrs or anti-CRISPR associated proteins (Acas) as the bait. However, the low number and limited spread of the characterized archaeal Acrs and Aca hinders our ability to identify Acrs using guilt-by-association. Here, based on the observation that the few characterized archaeal Acrs and Aca are transcribed immediately post viral infection, we hypothesize that these genes, and many other unidentified anti-defense genes (ADG), are under the control of conserved regulatory sequences including a strong promoter, which can be used to predict anti-defense genes in archaeal viruses. Using this consensus sequence based method, we identify 354 potential ADGs in 57 archaeal viruses and 6 metagenome-assembled genomes. Experimental validation identified a CRISPR subtype I-A inhibitor and the first virally encoded inhibitor of an archaeal toxin-antitoxin based immune system. We also identify regulatory proteins potentially akin to Acas that can facilitate further identification of ADGs combined with the guilt-by-association approach. These results demonstrate the potential of regulatory sequence analysis for extensive identification of ADGs in viruses of archaea and bacteria.
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Affiliation(s)
| | - Shuanshuan Xu
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | | | - Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Xu Peng
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
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2
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Sensevdi ER, Sourrouille ZA, Quax TE. Host range and cell recognition of archaeal viruses. Curr Opin Microbiol 2024; 77:102423. [PMID: 38232492 DOI: 10.1016/j.mib.2023.102423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
Archaea are members of a separate domain of life that have unique properties, such as the composition of their cell walls and the structure of their lipid bilayers. Consequently, archaeal viruses face different challenges to infect host cells in comparison with viruses of bacteria and eukaryotes. Despite their significant impact on shaping microbial communities, our understanding of infection processes of archaeal viruses remains limited. Several receptors used by archaeal viruses to infect cells have recently been identified. The interactions between viruses and receptors are one of the determinants of the host range of viruses. Here, we review the current literature on host ranges of archaeal viruses and factors that might impact the width of these host ranges.
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Affiliation(s)
- Emine Rabia Sensevdi
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands
| | - Zaloa Aguirre Sourrouille
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands
| | - Tessa Ef Quax
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands.
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3
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Kuiper BP, Schöntag AMC, Oksanen HM, Daum B, Quax TEF. Archaeal virus entry and egress. MICROLIFE 2024; 5:uqad048. [PMID: 38234448 PMCID: PMC10791045 DOI: 10.1093/femsml/uqad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these viruses enter and exit their host cells. Research on archaeal viruses has lately made significant progress due to advances in genetic tools and imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, a steady output of newly identified archaeal viral receptors and egress mechanisms has offered the first insight into how archaeal viruses interact with the archaeal cell envelope. As more details about archaeal viral entry and egress are unravelled, patterns are starting to emerge. This helps to better understand the interactions between viruses and the archaeal cell envelope and how these compare to infection strategies of viruses in other domains of life. Here, we provide an overview of recent developments in the field of archaeal viral entry and egress, shedding light onto the most elusive part of the virosphere.
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Affiliation(s)
- Bastiaan P Kuiper
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anna M C Schöntag
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Bertram Daum
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Tessa E F Quax
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
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4
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Overton MS, Manuel RD, Lawrence CM, Snyder JC. Viruses of the Turriviridae: an emerging model system for studying archaeal virus-host interactions. Front Microbiol 2023; 14:1258997. [PMID: 37808280 PMCID: PMC10551542 DOI: 10.3389/fmicb.2023.1258997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Viruses have played a central role in the evolution and ecology of cellular life since it first arose. Investigations into viral molecular biology and ecological dynamics have propelled abundant progress in our understanding of living systems, including genetic inheritance, cellular signaling and trafficking, and organismal development. As well, the discovery of viral lineages that infect members of all three domains suggest that these lineages originated at the earliest stages of biological evolution. Research into these viruses is helping to elucidate the conditions under which life arose, and the dynamics that directed its early development. Archaeal viruses have only recently become a subject of intense study, but investigations have already produced intriguing and exciting results. STIV was originally discovered in Yellowstone National Park and has been the focus of concentrated research. Through this research, a viral genetic system was created, a novel lysis mechanism was discovered, and the interaction of the virus with cellular ESCRT machinery was revealed. This review will summarize the discoveries within this group of viruses and will also discuss future work.
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Affiliation(s)
- Michael S. Overton
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Robert D. Manuel
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
| | - C. Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Jamie C. Snyder
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
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5
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Zhang W, Bhoobalan-Chitty Y, Zhai X, Hui Y, Hansen LH, Deng L, Peng X. Replication Protein Rep Provides Selective Advantage to Viruses in the Presence of CRISPR-Cas Immunity. CRISPR J 2023; 6:32-42. [PMID: 36576859 DOI: 10.1089/crispr.2022.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Anti-Clustered regularly interspaced small palindromic repeat (CRISPR) (Acr) phages cooperate to establish a successful infection in CRISPR-containing host. We report here the selective advantage provided by a replication initiator, Rep, toward cooperative host immunosuppression by viruses encoding Acrs. A rep knockout mutant (Δgp16) of Sulfolobus islandicus rod-shaped virus 2 produced around fourfold less virus in a CRISPR-null host, suggesting that Rep is the major replication initiator. In addition to Rep-dependent replication initiation from the viral genomic termini, we detected Rep-independent replication initiation from nonterminal sites. Intriguingly, despite the presence of Acrs, lack of Rep showed a profound effect on virus propagation in a host carrying CRISPR-Cas immunity. Accordingly, the co-infecting parental virus (rep-containing) outcompeted the Δgp16 mutant much more quickly in the CRISPR-containing host than in CRISPR-null host. Despite the nonessentiality, rep is carried by all known members of Rudiviridae, which is likely an evolutionary outcome driven by the ubiquitous presence of CRISPR-Cas in Sulfolobales.
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Affiliation(s)
- Weijia Zhang
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | | | - Xichuan Zhai
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Yan Hui
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Xu Peng
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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6
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Jørgensen J, Sundell K, Castillo D, Dramshøj LS, Jørgensen NB, Madsen SB, Landor L, Wiklund T, Donati VL, Madsen L, Dalsgaard I, Middelboe M. Reversible mutations in gliding motility and virulence genes: A flexible and efficient phage defence mechanism in Flavobacterium psychrophilum. Environ Microbiol 2022; 24:4915-4930. [PMID: 35837851 DOI: 10.1111/1462-2920.16126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/27/2022] [Accepted: 07/04/2022] [Indexed: 01/07/2023]
Abstract
Flavobacteria are among the most important pathogens in freshwater salmonid aquaculture worldwide. Due to concerns regarding development of antibiotic resistance, phage therapy has been proposed as a solution to decrease pathogen load. However, application of phages is challenged by the development of phage resistance, and knowledge of the mechanisms and implications of phage resistance is therefore required. To study this, 27 phage-resistant isolates of F. psychrophilum were genome sequenced and characterized to identify genetic modifications and evaluate changes in phenotypic traits, including virulence against rainbow trout. Phage-resistant isolates showed reduction or loss of gliding motility, proteolytic activity, and adhesion to surfaces, and most isolates were completely non-virulent against rainbow trout fry. Genomic analysis revealed that most phage-resistant isolates had mutations in genes associated with gliding motility and virulence. Reversal of these mutations in a sub-set of isolates led to regained motility, proteolytic activity, virulence and phage susceptibility. Although costly, the fast generation of phage resistance driven by single, reversible mutations likely represents a flexible and efficient phage defence mechanism in F. psychrophilum. The results further suggest that phage administration in aquaculture systems to prevent F. psychrophilum outbreaks selects for non-virulent phage-resistant phenotypes.
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Affiliation(s)
| | - Krister Sundell
- Laboratory of Aquatic Pathobiology, Åbo Akademi University, Turku, Finland
| | - Daniel Castillo
- Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Liv S Dramshøj
- Department of Biology, University of Copenhagen, Helsingør, Denmark
| | | | - Susie B Madsen
- Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lotta Landor
- Laboratory of Aquatic Pathobiology, Åbo Akademi University, Turku, Finland.,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Tom Wiklund
- Laboratory of Aquatic Pathobiology, Åbo Akademi University, Turku, Finland
| | - Valentina L Donati
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lone Madsen
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Inger Dalsgaard
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
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7
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Fackler JR, Dworjan M, Gazi KS, Grogan DW. Diversity of SIRV-like Viruses from a North American Population. Viruses 2022; 14:v14071439. [PMID: 35891419 PMCID: PMC9319562 DOI: 10.3390/v14071439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
A small subset of acidic hot springs sampled in Yellowstone National Park yielded rod-shaped viruses which lysed liquid host cultures and formed clear plaques on lawns of host cells. Three isolates chosen for detailed analysis were found to be genetically related to previously described isolates of the Sulfolobus islandicus rod-shaped virus (SIRV), but distinct from them and from each other. Functional stability of the new isolates was assessed in a series of inactivation experiments. UV-C radiation inactivated one of the isolates somewhat faster than bacteriophage λ, suggesting that encapsidation in the SIRV-like virion did not confer unusual protection of the DNA from UV damage. With respect to high temperature, the new isolates were extremely, but not equally, stable. Several chemical treatments were found to inactivate the virions and, in some cases, to reveal apparent differences in virion stability among the isolates. Screening a larger set of isolates identified greater variation of these stability properties but found few correlations among the resulting profiles. The majority of host cells infected by the new isolates were killed, but survivors exhibited heritable resistance, which could not be attributed to CRISPR spacer acquisition or the loss of the pilus-related genes identified by earlier studies. Virus-resistant host variants arose at high frequency and most were resistant to multiple viral strains; conversely, resistant host clones generated virus-sensitive variants, also at high frequency. Virus-resistant cells lacked the ability of virus-sensitive cells to bind virions in liquid suspensions. Rapid interconversion of sensitive and resistant forms of a host strain suggests the operation of a yet-unidentified mechanism that acts to allow both the lytic virus and its host to propagate in highly localized natural populations, whereas variation of virion-stability phenotypes among the new viral isolates suggests that multiple molecular features contribute to the biological durability of these viruses.
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Affiliation(s)
- Joseph R. Fackler
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Adaptive Phage Therapeutics, Gaithersburg, MD 20878, USA
| | - Michael Dworjan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
| | - Khaled S. Gazi
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Department of Biology, Faculty of Science and Arts in Almandaq, Al-Baha University, Almandaq 65756, Saudi Arabia
| | - Dennis W. Grogan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Correspondence:
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8
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Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
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Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
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9
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Isaev AB, Musharova OS, Severinov KV. Microbial Arsenal of Antiviral Defenses - Part I. BIOCHEMISTRY (MOSCOW) 2021; 86:319-337. [PMID: 33838632 DOI: 10.1134/s0006297921030081] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). Constant threat of phage infection is a major force that shapes evolution of the microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering have been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection, with a focus on novel systems discovered in recent years. First chapter covers defense associated with cell surface, role of small molecules, and innate immunity systems relying on DNA modification.
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Affiliation(s)
- Artem B Isaev
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.
| | - Olga S Musharova
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia. .,Institute of Molecular Genetics, Moscow, 119334, Russia
| | - Konstantin V Severinov
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia. .,Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
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10
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Tittes C, Schwarzer S, Quax TEF. Viral Hijack of Filamentous Surface Structures in Archaea and Bacteria. Viruses 2021; 13:v13020164. [PMID: 33499367 PMCID: PMC7911016 DOI: 10.3390/v13020164] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
The bacterial and archaeal cell surface is decorated with filamentous surface structures that are used for different functions, such as motility, DNA exchange and biofilm formation. Viruses hijack these structures and use them to ride to the cell surface for successful entry. In this review, we describe currently known mechanisms for viral attachment, translocation, and entry via filamentous surface structures. We describe the different mechanisms used to exploit various surface structures bacterial and archaeal viruses. This overview highlights the importance of filamentous structures at the cell surface for entry of prokaryotic viruses.
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11
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Peng X, Mayo-Muñoz D, Bhoobalan-Chitty Y, Martínez-Álvarez L. Anti-CRISPR Proteins in Archaea. Trends Microbiol 2020; 28:913-921. [PMID: 32499102 DOI: 10.1016/j.tim.2020.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/26/2022]
Abstract
Anti-CRISPR (Acr) proteins are natural inhibitors of CRISPR-Cas immune systems. To date, Acrs inhibiting types I, II, III, V, and VI CRISPR-Cas systems have been characterized. While most known Acrs are derived from bacterial phages and prophages, very few have been characterized in the domain Archaea, despite the nearly ubiquitous presence of CRISPR-Cas in archaeal cells. Here we summarize the discovery and characterization of the archaeal Acrs with the representatives encoded by a model archaeal virus, Sulfolobus islandicus rod-shaped virus 2 (SIRV2). AcrID1 inhibits subtype I-D CRISPR-Cas immunity through direct interaction with the large subunit Cas10d of the effector complex, and AcrIIIB1 inhibits subtype III-B CRISPR-Cas immunity through a mechanism interfering with middle/late gene targeting. Future development of efficient screening methods will be key to uncovering the diversity of archaeal Acrs.
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Affiliation(s)
- Xu Peng
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
| | - David Mayo-Muñoz
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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12
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Rowland EF, Bautista MA, Zhang C, Whitaker RJ. Surface resistance to SSVs and SIRVs in pilin deletions of Sulfolobus islandicus. Mol Microbiol 2019; 113:718-727. [PMID: 31774609 PMCID: PMC7217056 DOI: 10.1111/mmi.14435] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/15/2019] [Indexed: 01/25/2023]
Abstract
Characterizing the molecular interactions of viruses in natural microbial populations offers insights into virus–host dynamics in complex ecosystems. We identify the resistance of Sulfolobus islandicus to Sulfolobus spindle‐shaped virus (SSV9) conferred by chromosomal deletions of pilin genes, pilA1 and pilA2 that are individually able to complement resistance. Mutants with deletions of both pilA1 and pilA2 or the prepilin peptidase, PibD, show the reduction in the number of pilins observed in TEM and reduced surface adherence but still adsorb SSV9. The proteinaceous outer S‐layer proteins, SlaA and SlaB, are not required for adsorption nor infection demonstrating that the S‐layer is not the primary receptor for SSV9 surface binding. Strains lacking both pilins are resistant to a broad panel of SSVs as well as a panel of unrelated S. islandicus rod‐shaped viruses (SIRVs). Unlike SSV9, we show that pilA1 or pilA2 is required for SIRV8 adsorption. In sequenced Sulfolobus strains from around the globe, one copy of each pilA1 and pilA2 is maintained and show codon‐level diversification, demonstrating their importance in nature. By characterizing the molecular interactions at the initiation of infection between S. islandicus and two different types of viruses we hope to increase the understanding of virus–host interactions in the archaeal domain.
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Affiliation(s)
- Elizabeth F Rowland
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Maria A Bautista
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Changyi Zhang
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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13
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Hartman R, Eilers BJ, Bollschweiler D, Munson-McGee JH, Engelhardt H, Young MJ, Lawrence CM. The Molecular Mechanism of Cellular Attachment for an Archaeal Virus. Structure 2019; 27:1634-1646.e3. [PMID: 31587916 DOI: 10.1016/j.str.2019.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/21/2019] [Accepted: 09/16/2019] [Indexed: 12/17/2022]
Abstract
Sulfolobus turreted icosahedral virus (STIV) is a model archaeal virus and member of the PRD1-adenovirus lineage. Although STIV employs pyramidal lysis structures to exit the host, knowledge of the viral entry process is lacking. We therefore initiated studies on STIV attachment and entry. Negative stain and cryoelectron micrographs showed virion attachment to pili-like structures emanating from the Sulfolobus host. Tomographic reconstruction and sub-tomogram averaging revealed pili recognition by the STIV C381 turret protein. Specifically, the triple jelly roll structure of C381 determined by X-ray crystallography shows that pilus recognition is mediated by conserved surface residues in the second and third domains. In addition, the STIV petal protein (C557), when present, occludes the pili binding site, suggesting that it functions as a maturation protein. Combined, these results demonstrate a role for the namesake STIV turrets in initial cellular attachment and provide the first molecular model for viral attachment in the archaeal domain of life.
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Affiliation(s)
- Ross Hartman
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Brian J Eilers
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Daniel Bollschweiler
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | - Jacob H Munson-McGee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Harald Engelhardt
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | - Mark J Young
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA; Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; The Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
| | - C Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA; The Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
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14
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Papathanasiou P, Erdmann S, Leon-Sobrino C, Sharma K, Urlaub H, Garrett RA, Peng X. Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1. RNA Biol 2018; 16:557-565. [PMID: 30146914 DOI: 10.1080/15476286.2018.1511674] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Carrier state viral infection constitutes an equilibrium state in which a limited fraction of a cellular population is infected while the remaining cells are transiently resistant to infection. This type of infection has been characterized for several bacteriophages but not, to date, for archaeal viruses. Here we demonstrate that the rudivirus SIRV3 can produce a host-dependent carrier state infection in the model crenarchaeon Sulfolobus. SIRV3 only infected a fraction of a Sulfolobus islandicus REY15A culture over several days during which host growth was unimpaired and no chromosomal DNA degradation was observed. CRISPR spacer acquisition from SIRV3 DNA was induced by coinfecting with the monocaudavirus SMV1 and it was coincident with increased transcript levels from subtype I-A adaptation and interference cas genes. However, this response did not significantly affect the carrier state infection of SIRV3 and both viruses were maintained in the culture over 12 days during which SIRV3 anti-CRISPR genes were shown to be expressed. Transcriptome and proteome analyses demonstrated that most SIRV3 genes were expressed at varying levels over time whereas SMV1 gene expression was generally low. The study yields insights into the basis for the stable infection of SIRV3 and the resistance to the different host CRISPR-Cas interference mechanisms. It also provides a rationale for the commonly observed coinfection of archaeal cells by different viruses in natural environments.
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Affiliation(s)
- Pavlos Papathanasiou
- a Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark
| | - Susanne Erdmann
- a Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark.,b ithree Institute, University of Technology Sydney , Sydney , Australia
| | - Carlos Leon-Sobrino
- a Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark.,c Centre for Microbial Ecology and Genomics, Department of Genetics , University of Pretoria , Hatfield , South Africa
| | - Kundan Sharma
- d Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, D37077 Göttingen , Germany.,e Ludwig Institute for Cancer Research, University of Oxford , Oxford , UK
| | - Henning Urlaub
- d Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, D37077 Göttingen , Germany.,f Bioanalytics Research Group, Institute of Clinical Chemistry, University Medical Center Göttingen , Göttingen , Germany
| | - Roger A Garrett
- a Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark
| | - Xu Peng
- a Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark
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15
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Anderson RE, Kouris A, Seward CH, Campbell KM, Whitaker RJ. Structured Populations of Sulfolobus acidocaldarius with Susceptibility to Mobile Genetic Elements. Genome Biol Evol 2018. [PMID: 28633403 PMCID: PMC5554439 DOI: 10.1093/gbe/evx104] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S. acidocaldarius apart from its sister Sulfolobus species. To test this hypothesis, we conducted a comparative analysis of 47 genomes of S. acidocaldarius from spatial and temporal sampling of two hot springs in Yellowstone National Park. While we confirm the low diversity in the core genome, we observe differentiation among S. acidocaldarius populations, likely resulting from low migration among hot spring “islands” in Yellowstone National Park. Patterns of genomic variation indicate that differing geological contexts result in the elimination or preservation of diversity among differentiated populations. We observe multiple deletions associated with a large genomic island rich in glycosyltransferases, differential integrations of the Sulfolobus turreted icosahedral virus, as well as two different plasmid elements. These data demonstrate that neither rapid dispersal nor lack of mobile genetic elements result in low diversity in the S. acidocaldarius genomes. We suggest instead that significant differences in the recent evolutionary history, or the intrinsic evolutionary rates, of sister Sulfolobus species result in the relatively low diversity of the S. acidocaldarius genome.
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Affiliation(s)
- Rika E Anderson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign.,Biology Department, Carleton College, Northfield, Minnesota
| | - Angela Kouris
- Energy, Bioengineering and Geomicrobiology Group, University of Calgary, Alberta, Canada
| | - Christopher H Seward
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign
| | - Kate M Campbell
- U.S. Geological Survey National Research Program, Boulder, Colorado
| | - Rachel J Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign.,Department of Microbiology, University of Illinois at Urbana-Champaign
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16
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He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X. Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity. Nat Microbiol 2018; 3:461-469. [DOI: 10.1038/s41564-018-0120-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/30/2018] [Indexed: 11/09/2022]
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17
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Chaudhury P, Quax TEF, Albers SV. Versatile cell surface structures of archaea. Mol Microbiol 2017; 107:298-311. [PMID: 29194812 DOI: 10.1111/mmi.13889] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
Abstract
Archaea are ubiquitously present in nature and colonize environments with broadly varying growth conditions. Several surface appendages support their colonization of new habitats. A hallmark of archaea seems to be the high abundance of type IV pili (T4P). However, some unique non T4 filaments are present in a number of archaeal species. Archaeal surface structures can mediate different processes such as cellular surface adhesion, DNA exchange, motility and biofilm formation and represent an initial attachment site for infecting viruses. In addition to the functionally characterized archaeal T4P, archaeal genomes encode a large number of T4P components that might form yet undiscovered surface structures with novel functions. In this review, we summarize recent advancement in structural and functional characterizations of known archaeal surface structures and highlight the diverse processes in which they play a role.
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Affiliation(s)
- Paushali Chaudhury
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Tessa E F Quax
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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18
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Abstract
One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats. In this Review, we summarize recent advances in our understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus-host interactions, including interactions with archaeal CRISPR-Cas systems. We also examine the potential origins and evolution of archaeal viruses and discuss their place in the global virosphere.
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19
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Huang Q, Zhong Q, Mayaka JBA, Ni J, Shen Y. Autophosphorylation and Cross-Phosphorylation of Protein Kinases from the Crenarchaeon Sulfolobus islandicus. Front Microbiol 2017; 8:2173. [PMID: 29163450 PMCID: PMC5682000 DOI: 10.3389/fmicb.2017.02173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/23/2017] [Indexed: 11/17/2022] Open
Abstract
Protein phosphorylation, one of the most important post-translational modifications, regulates almost every cellular process. Although signal transduction by protein phosphorylation is extensively studied in Eukaryotes and Bacteria, the knowledge of this process in archaea is greatly lagging behind, especially for Ser/Thr/Tyr phosphorylation by eukaryotic-like protein kinases (ePKs). So far, only a few studies on archaeal ePKs have been reported, most of which focused on the phosphorylation activities in vitro, but their physiological functions and interacting network are still largely unknown. In this study, we systematically investigated the autophosphorylation and cross-phosphorylation activities of ePKs from Sulfolobus islandicus REY15A using proteins expressed in Escherichia coli or S. islandicus. In vitro kinase assay showed that 7 out of the 11 putative ePKs have autophosphorylation activity. A protein Ser/Thr phosphatase, SiRe_1009, was able to dephosphorylate various autophosphorylated ePKs, confirming that these proteins are Ser/Thr kinases. Two ePKs, SiRe_2030 and SiRe_2056, homologs of typical eukaryotic PKs involved in peptide synthesis in response to various cellular stresses, exhibit highly efficient phosphorylation activities on both themselves and other ePKs. Overexpression of the protein kinases in vivo revealed that elevated level of either SiRe_1531 or SiRe_2056 inhibited the cell growth of S. islandicus cells. Finally, a phosphorylation network of the protein kinases was proposed and their putative physiological roles were discussed.
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Affiliation(s)
- Qihong Huang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Qing Zhong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Joseph B A Mayaka
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Jinfeng Ni
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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20
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He F, Vestergaard G, Peng W, She Q, Peng X. CRISPR-Cas type I-A Cascade complex couples viral infection surveillance to host transcriptional regulation in the dependence of Csa3b. Nucleic Acids Res 2017; 45:1902-1913. [PMID: 27980065 PMCID: PMC5389559 DOI: 10.1093/nar/gkw1265] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/07/2016] [Indexed: 12/25/2022] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats and the associated genes) constitute adaptive immune systems in bacteria and archaea and they provide sequence specific immunity against foreign nucleic acids. CRISPR-Cas systems are activated by viral infection. However, little is known about how CRISPR-Cas systems are activated in response to viral infection or how their expression is controlled in the absence of viral infection. Here, we demonstrate that both the transcriptional regulator Csa3b, and the type I-A interference complex Cascade, are required to transcriptionally repress the interference gene cassette in the archaeon Sulfolobus. Csa3b binds to two palindromic repeat sites in the promoter region of the cassette and facilitates binding of the Cascade to the promoter region. Upon viral infection, loading of Cascade complexes onto crRNA-matching protospacers leads to relief of the transcriptional repression. Our data demonstrate a mechanism coupling CRISPR-Cas surveillance of protospacers to transcriptional regulation of the interference gene cassette thereby allowing a fast response to viral infection.
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Affiliation(s)
- Fei He
- Archaea Centre, Department of Biology, Copenhagen University, DK2200 Copenhagen N, Denmark
| | - Gisle Vestergaard
- Helmholtz Zentrum München, Research Unit Environmental Genomics, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Germany
| | - Wenfang Peng
- Archaea Centre, Department of Biology, Copenhagen University, DK2200 Copenhagen N, Denmark
| | - Qunxin She
- Archaea Centre, Department of Biology, Copenhagen University, DK2200 Copenhagen N, Denmark
| | - Xu Peng
- Archaea Centre, Department of Biology, Copenhagen University, DK2200 Copenhagen N, Denmark
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21
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Formation of a Viral Replication Focus in Sulfolobus Cells Infected by the Rudivirus Sulfolobus islandicus Rod-Shaped Virus 2. J Virol 2017; 91:JVI.00486-17. [PMID: 28424282 DOI: 10.1128/jvi.00486-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 04/11/2017] [Indexed: 01/05/2023] Open
Abstract
Viral factories are compartmentalized centers for viral replication and assembly in infected eukaryotic cells. Here, we report the formation of a replication focus by prototypical archaeal Sulfolobus islandicus rod-shaped virus 2 (SIRV2) in the model archaeon Sulfolobus This rod-shaped virus belongs to the viral family Rudiviridae, carrying linear double-stranded DNA (dsDNA) genomes, which are very common in geothermal environments. We demonstrate that SIRV2 DNA synthesis is confined to a focus near the periphery of infected cells. Moreover, viral and cellular replication proteins are recruited to, and concentrated in, the viral replication focus. Furthermore, we show that of the four host DNA polymerases (DNA polymerase I [Dpo1] to Dpo4), only Dpo1 participates in viral DNA synthesis. This constitutes the first report of the formation of a viral replication focus in archaeal cells, suggesting that organization of viral replication in foci is a widespread strategy employed by viruses of the three domains of life.IMPORTANCE The organization of viral replication in foci or viral factories has been mostly described for different eukaryotic viruses and for several bacteriophages. This work constitutes the first report of the formation of a viral replication center by a virus infecting members of the Archaea domain.
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22
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A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea. J Virol 2017; 91:JVI.00589-17. [PMID: 28424284 DOI: 10.1128/jvi.00589-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 04/11/2017] [Indexed: 11/20/2022] Open
Abstract
Encapsidation of genetic material into polyhedral particles is one of the most common structural solutions employed by viruses infecting hosts in all three domains of life. Here, we describe a new virus of hyperthermophilic archaea, Sulfolobus polyhedral virus 1 (SPV1), which condenses its circular double-stranded DNA genome in a manner not previously observed for other known viruses. The genome complexed with virion proteins is wound up sinusoidally into a spherical coil which is surrounded by an envelope and further encased by an outer polyhedral capsid apparently composed of the 20-kDa virion protein. Lipids selectively acquired from the pool of host lipids are integral constituents of the virion. None of the major virion proteins of SPV1 show similarity to structural proteins of known viruses. However, minor structural proteins, which are predicted to mediate host recognition, are shared with other hyperthermophilic archaeal viruses infecting members of the order Sulfolobales The SPV1 genome consists of 20,222 bp and contains 45 open reading frames, only one-fifth of which could be functionally annotated.IMPORTANCE Viruses infecting hyperthermophilic archaea display a remarkable morphological diversity, often presenting architectural solutions not employed by known viruses of bacteria and eukaryotes. Here we present the isolation and characterization of Sulfolobus polyhedral virus 1, which condenses its genome into a unique spherical coil. Due to the original genomic and architectural features of SPV1, the virus should be considered a representative of a new viral family, "Portogloboviridae."
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23
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Differentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations. Viruses 2017; 9:v9050120. [PMID: 28534836 PMCID: PMC5454432 DOI: 10.3390/v9050120] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/04/2017] [Accepted: 05/10/2017] [Indexed: 11/17/2022] Open
Abstract
In the past decade, molecular surveys of viral diversity have revealed that viruses are the most diverse and abundant biological entities on Earth. In culture, however, most viral isolates that infect microbes are represented by a few variants isolated on type strains, limiting our ability to study how natural variation affects virus-host interactions in the laboratory. We screened a set of 137 hot spring samples for viruses that infect a geographically diverse panel of the hyperthemophilic crenarchaeon Sulfolobus islandicus. We isolated and characterized eight SIRVs (Sulfolobus islandicus rod-shaped viruses) from two different regions within Yellowstone National Park (USA). Comparative genomics revealed that all SIRV sequenced isolates share 30 core genes that represent 50–60% of the genome. The core genome phylogeny, as well as the distribution of variable genes (shared by some but not all SIRVs) and the signatures of host-virus interactions recorded on the CRISPR (clustered regularly interspaced short palindromic repeats) repeat-spacer arrays of S. islandicus hosts, identify different SIRV lineages, each associated with a different geographic location. Moreover, our studies reveal that SIRV core genes do not appear to be under diversifying selection and thus we predict that the abundant and diverse variable genes govern the coevolutionary arms race between SIRVs and their hosts.
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24
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Quemin ERJ, Quax TEF. Archaeal viruses at the cell envelope: entry and egress. Front Microbiol 2015; 6:552. [PMID: 26097469 PMCID: PMC4456609 DOI: 10.3389/fmicb.2015.00552] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/19/2015] [Indexed: 11/13/2022] Open
Abstract
The cell envelope represents the main line of host defense that viruses encounter on their way from one cell to another. The cytoplasmic membrane in general is a physical barrier that needs to be crossed both upon viral entry and exit. Therefore, viruses from the three domains of life employ a wide range of strategies for perforation of the cell membrane, each adapted to the cell surface environment of their host. Here, we review recent insights on entry and egress mechanisms of viruses infecting archaea. Due to the unique nature of the archaeal cell envelope, these particular viruses exhibit novel and unexpected mechanisms to traverse the cellular membrane.
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Affiliation(s)
| | - Tessa E F Quax
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, University of Freiburg , Freiburg, Germany
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25
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Guo Y, Kragelund BB, White MF, Peng X. Functional Characterization of a Conserved Archaeal Viral Operon Revealing Single-Stranded DNA Binding, Annealing and Nuclease Activities. J Mol Biol 2015; 427:2179-91. [DOI: 10.1016/j.jmb.2015.03.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 11/15/2022]
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26
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Snyder JC, Bolduc B, Young MJ. 40 Years of archaeal virology: Expanding viral diversity. Virology 2015; 479-480:369-78. [PMID: 25866378 DOI: 10.1016/j.virol.2015.03.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/07/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
The first archaeal virus was isolated over 40 years ago prior to the recognition of the three domain structure of life. In the ensuing years, our knowledge of Archaea and their viruses has increased, but they still remain the most mysterious of life's three domains. Currently, over 100 archaeal viruses have been discovered, but few have been described in biochemical or structural detail. However, those that have been characterized have revealed a new world of structural, biochemical and genetic diversity. Several model systems for studying archaeal virus-host interactions have been developed, revealing evolutionary linkages between viruses infecting the three domains of life, new viral lysis systems, and unusual features of host-virus interactions. It is likely that the study of archaeal viruses will continue to provide fertile ground for fundamental discoveries in virus diversity, structure and function.
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Affiliation(s)
- Jamie C Snyder
- Department of Biological Sciences, California State Polytechnic University - Pomona, Pomona, CA, USA
| | - Benjamin Bolduc
- Departments of Plant Sciences and Microbiology, Montana State University, Bozeman, MT, USA
| | - Mark J Young
- Departments of Plant Sciences and Microbiology, Montana State University, Bozeman, MT, USA.
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27
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He F, Chen L, Peng X. First Experimental Evidence for the Presence of a CRISPR Toxin in Sulfolobus. J Mol Biol 2014; 426:3683-3688. [DOI: 10.1016/j.jmb.2014.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/16/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
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