1
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Lin J, Alfastsen L, Bhoobalan-Chitty Y, Peng X. Molecular basis for inhibition of type III-B CRISPR-Cas by an archaeal viral anti-CRISPR protein. Cell Host Microbe 2023; 31:1837-1849.e5. [PMID: 37909049 DOI: 10.1016/j.chom.2023.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/03/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023]
Abstract
Despite a wide presence of type III clustered regularly interspaced short palindromic repeats, CRISPR-associated (CRISPR-Cas) in archaea and bacteria, very few anti-CRISPR (Acr) proteins inhibiting type III immunity have been identified, and even less is known about their inhibition mechanism. Here, we present the discovery of a type III CRISPR-Cas inhibitor, AcrIIIB2, encoded by Sulfolobus virus S. islandicus rod-shaped virus 3 (SIRV3). AcrIIIB2 inhibits type III-B CRISPR-Cas immune response to protospacers encoded in middle/late-expressed viral genes. Investigation of the interactions between S. islandicus type III-B CRISPR-Cas Cmr-α-related proteins and AcrIIIB2 reveals that the Acr does not bind to Csx1 but rather interacts with the Cmr-α effector complex. Furthermore, in vitro assays demonstrate that AcrIIIB2 can block the dissociation of cleaved target RNA from the Cmr-α complex, thereby inhibiting the Cmr-α turnover, thus preventing host cellular dormancy and further viral genome degradation by the type III-B CRISPR-Cas immunity.
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Affiliation(s)
- Jinzhong Lin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Lauge Alfastsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | | | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
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2
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Makarova KS, Wolf YI, Koonin EV. In Silico Approaches for Prediction of Anti-CRISPR Proteins. J Mol Biol 2023; 435:168036. [PMID: 36868398 PMCID: PMC10073340 DOI: 10.1016/j.jmb.2023.168036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023]
Abstract
Numerous viruses infecting bacteria and archaea encode CRISPR-Cas system inhibitors, known as anti-CRISPR proteins (Acr). The Acrs typically are highly specific for particular CRISPR variants, resulting in remarkable sequence and structural diversity and complicating accurate prediction and identification of Acrs. In addition to their intrinsic interest for understanding the coevolution of defense and counter-defense systems in prokaryotes, Acrs could be natural, potent on-off switches for CRISPR-based biotechnological tools, so their discovery, characterization and application are of major importance. Here we discuss the computational approaches for Acr prediction. Due to the enormous diversity and likely multiple origins of the Acrs, sequence similarity searches are of limited use. However, multiple features of protein and gene organization have been successfully harnessed to this end including small protein size and distinct amino acid compositions of the Acrs, association of acr genes in virus genomes with genes encoding helix-turn-helix proteins that regulate Acr expression (Acr-associated proteins, Aca), and presence of self-targeting CRISPR spacers in bacterial and archaeal genomes containing Acr-encoding proviruses. Productive approaches for Acr prediction also involve genome comparison of closely related viruses, of which one is resistant and the other one is sensitive to a particular CRISPR variant, and "guilt by association" whereby genes adjacent to a homolog of a known Aca are identified as candidate Acrs. The distinctive features of Acrs are employed for Acr prediction both by developing dedicated search algorithms and through machine learning. New approaches will be needed to identify novel types of Acrs that are likely to exist.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
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3
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Xuyang L, Cristina LM, Laura MA, Xu P. A clade of RHH proteins ubiquitous in Sulfolobales and their viruses regulates cell cycle progression. Nucleic Acids Res 2023; 51:1724-1739. [PMID: 36727447 PMCID: PMC9976892 DOI: 10.1093/nar/gkad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/30/2022] [Accepted: 01/29/2023] [Indexed: 02/03/2023] Open
Abstract
Cell cycle regulation is crucial for all living organisms and is often targeted by viruses to facilitate their own propagation, yet cell cycle progression control is largely underexplored in archaea. In this work, we reveal a cell cycle regulator (aCcr1) carrying a ribbon-helix-helix (RHH) domain and ubiquitous in the Thermoproteota of the order Sulfolobales and their viruses. Overexpression of several aCcr1 members including gp21 of rudivirus SIRV2 and its host homolog SiL_0190 of Saccharolobus islandicus LAL14/1 results in impairment of cell division, evidenced by growth retardation, cell enlargement and an increase in cellular DNA content. Additionally, both gp21 and SiL_0190 can bind to the motif AGTATTA conserved in the promoter of several genes involved in cell division, DNA replication and cellular metabolism thereby repressing or inducing their transcription. Our results suggest that aCcr1 silences cell division and drives progression to the S-phase in Sulfolobales, a function exploited by viruses to facilitate viral propagation.
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Affiliation(s)
- Li Xuyang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Lozano-Madueño Cristina
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Martínez-Alvarez Laura
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peng Xu
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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4
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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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5
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Sulfolobus islandicus Employs Orc1-2-Mediated DNA Damage Response in Defense against Infection by SSV2. J Virol 2022; 96:e0143822. [PMID: 36448807 PMCID: PMC9769372 DOI: 10.1128/jvi.01438-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
All living organisms have evolved DNA damage response (DDR) strategies in coping with threats to the integrity of their genome. In response to DNA damage, Sulfolobus islandicus activates its DDR network in which Orc1-2, an ortholog of the archaeal Orc1/Cdc6 superfamily proteins, plays a central regulatory role. Here, we show that pretreatment with UV irradiation reduced virus genome replication in S. islandicus infected with the fusellovirus SSV2. Like treatment with UV or the DNA-damaging agent 4-nitroquinoline-1-oxide (NQO), infection with SSV2 facilitated the expression of orc1-2 and significantly raised the cellular level of Orc1-2. The inhibitory effect of UV irradiation on the virus DNA level was no longer apparent in the infected culture of an S. islandicus orc1-2 deletion mutant strain. On the other hand, the overexpression of orc1-2 decreased virus genomic DNA by ~102-fold compared to that in the parent strain. Furthermore, as part of the Orc1-2-mediated DDR response genes for homologous recombination repair (HRR), cell aggregation and intercellular DNA transfer were upregulated, whereas genes for cell division were downregulated. However, the HRR pathway remained functional in host inhibition of SSV2 genome replication in the absence of UpsA, a subunit of pili essential for intercellular DNA transfer. In agreement with this finding, lack of the general transcriptional activator TFB3, which controls the expression of the ups genes, only moderately affected SSV2 genome replication. Our results demonstrate that infection of S. islandicus by SSV2 triggers the host DDR pathway that, in return, suppresses virus genome replication. IMPORTANCE Extremophiles thrive in harsh habitats and thus often face a daunting challenge to the integrity of their genome. How these organisms respond to virus infection when their genome is damaged remains unclear. We found that the thermophilic archaeon Sulfolobus islandicus became more inhibitory to genome replication of the virus SSV2 after preinfection UV irradiation than without the pretreatment. On the other hand, like treatment with UV or other DNA-damaging agents, infection of S. islandicus by SSV2 triggers the activation of Orc1-2-mediated DNA damage response, including the activation of homologous recombination repair, cell aggregation and DNA import, and the repression of cell division. The inhibitory effect of pretreatment with UV irradiation on SSV2 genome replication was no longer observed in an S. islandicus mutant lacking Orc1-2. Our results suggest that DNA damage response is employed by S. islandicus as a strategy to defend against virus infection.
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Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus. Proc Natl Acad Sci U S A 2022; 119:e2205037119. [PMID: 35994644 PMCID: PMC9436352 DOI: 10.1073/pnas.2205037119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses are important ecological, biogeochemical, and evolutionary drivers in every environment. Upon infection, they often cause the lysis of the host cell. However, some viruses exhibit alternative life cycles, such as chronic infections without cell lysis. The nature and the impact of chronic infections in prokaryotic host organisms remains largely unknown. Here, we characterize a novel haloarchaeal virus, Haloferax volcanii pleomorphic virus 1 (HFPV-1), which is currently the only virus infecting the model haloarchaeon Haloferax volcanii DS2, and demonstrate that HFPV-1 and H. volcanii are a great model system to study virus-host interactions in archaea. HFPV-1 is a pleomorphic virus that causes a chronic infection with continuous release of virus particles, but host and virus coexist without cell lysis or the appearance of resistant cells. Despite an only minor impact of the infection on host growth, we uncovered an extensive remodeling of the transcriptional program of the host (up to 1,049 differentially expressed genes). These changes are highlighted by a down-regulation of two endogenous provirus regions in the host genome, and we show that HFPV-1 infection is strongly influenced by a cross-talk between HFPV-1 and one of the proviruses mediated by a superinfection-like exclusion mechanism. Furthermore, HFPV-1 has a surprisingly wide host range among haloarchaea, and purified virus DNA can cause an infection after transformation into the host, making HFPV-1 a candidate for being developed into a genetic tool for a range of so far inaccessible haloarchaea.
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7
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Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales. Viruses 2021; 13:v13101934. [PMID: 34696364 PMCID: PMC8540584 DOI: 10.3390/v13101934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 01/05/2023] Open
Abstract
Today, the number of known viruses infecting methanogenic archaea is limited. Here, we report on a novel lytic virus, designated Blf4, and its host strain Methanoculleus bourgensis E02.3, a methanogenic archaeon belonging to the Methanomicrobiales, both isolated from a commercial biogas plant in Germany. The virus consists of an icosahedral head 60 nm in diameter and a long non-contractile tail of 125 nm in length, which is consistent with the new isolate belonging to the Siphoviridae family. Electron microscopy revealed that Blf4 attaches to the vegetative cells of M. bourgensis E02.3 as well as to cellular appendages. Apart from M. bourgensis E02.3, none of the tested Methanoculleus strains were lysed by Blf4, indicating a narrow host range. The complete 37 kb dsDNA genome of Blf4 contains 63 open reading frames (ORFs), all organized in the same transcriptional direction. For most of the ORFs, potential functions were predicted. In addition, the genome of the host M. bourgensis E02.3 was sequenced and assembled, resulting in a 2.6 Mbp draft genome consisting of nine contigs. All genes required for a hydrogenotrophic lifestyle were predicted. A CRISPR/Cas system (type I-U) was identified with six spacers directed against Blf4, indicating that this defense system might not be very efficient in fending off invading Blf4 virus.
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8
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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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9
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Lee STM, Ding JY, Chiang PW, Dyall-Smith M, Tang SL. Insights into gene regulation of the halovirus His2 infecting Haloarcula hispanica. Microbiologyopen 2020; 9:e1016. [PMID: 32212320 PMCID: PMC7221443 DOI: 10.1002/mbo3.1016] [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: 09/03/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/16/2023] Open
Abstract
Gene expression in Haloarcula hispanica cells infected with the gammapleolipovirus His2 was studied using a custom DNA microarray. Total RNA from cells sampled at 0, 1, 2, 3, and 4.5 hr postinfection was reverse‐transcribed into labeled cDNA and hybridized to microarrays, revealing temporal and differential expression in both host and viral genes. His2 gene expression occurred in three main phases (early, middle, and late), and by 4.5 hr p.i. the majority of genes were actively transcribed, including those encoding the major structural proteins. Eighty host genes were differentially regulated ≥twofold postinfection, with most of them predicted to be involved in transport, translation, and metabolism. Differentially expressed host genes could also be grouped into early‐, middle‐, and late‐expressed genes based on the timing of their up‐ and downregulation postinfection. The altered host transcriptional pattern suggests regulation by His2 infection, which may reprogram host metabolism to facilitate its own DNA replication and propagation. This study enhances the characterization of many hypothetical viral genes and provides insights into the interaction between His2 and its host.
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Affiliation(s)
- Sonny T M Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, United States
| | - Jiun-Yan Ding
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mike Dyall-Smith
- Computational Biology Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany.,Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic., Australia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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10
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Bhoobalan-Chitty Y, Johansen TB, Di Cianni N, Peng X. Inhibition of Type III CRISPR-Cas Immunity by an Archaeal Virus-Encoded Anti-CRISPR Protein. Cell 2019; 179:448-458.e11. [PMID: 31564454 DOI: 10.1016/j.cell.2019.09.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/23/2019] [Accepted: 09/03/2019] [Indexed: 12/26/2022]
Abstract
Bacteria and archaea possess a striking diversity of CRISPR-Cas systems divided into six types, posing a significant barrier to viral infection. As part of the virus-host arms race, viruses encode protein inhibitors of type I, II, and V CRISPR-Cas systems, but whether there are natural inhibitors of the other, mechanistically distinct CRISPR-Cas types is unknown. Here, we present the discovery of a type III CRISPR-Cas inhibitor, AcrIIIB1, encoded by the Sulfolobus virus SIRV2. AcrIIIB1 exclusively inhibits CRISPR-Cas subtype III-B immunity mediated by the RNase activity of the accessory protein Csx1. AcrIIIB1 does not appear to bind Csx1 but, rather, interacts with two distinct subtype III-B effector complexes-Cmr-α and Cmr-γ-which, in response to protospacer transcript binding, are known to synthesize cyclic oligoadenylates (cOAs) that activate the Csx1 "collateral" RNase. Taken together, we infer that AcrIIIB1 inhibits type III-B CRISPR-Cas immunity by interfering with a Csx1 RNase-related process.
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Affiliation(s)
- Yuvaraj Bhoobalan-Chitty
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark; Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Thomas Baek Johansen
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Nadia Di Cianni
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark; Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
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11
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Mayo-Muñoz D, He F, Jørgensen JB, Madsen PK, Bhoobalan-Chitty Y, Peng X. Anti-CRISPR-Based and CRISPR-Based Genome Editing of Sulfolobus islandicus Rod-Shaped Virus 2. Viruses 2018; 10:E695. [PMID: 30544778 PMCID: PMC6315595 DOI: 10.3390/v10120695] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 12/14/2022] Open
Abstract
Genetic engineering of viruses has generally been challenging. This is also true for archaeal rod-shaped viruses, which carry linear double-stranded DNA genomes with hairpin ends. In this paper, we describe two different genome editing approaches to mutate the Sulfolobus islandicus rod-shaped virus 2 (SIRV2) using the archaeon Sulfolobus islandicus LAL14/1 and its derivatives as hosts. The anti-CRISPR (Acr) gene acrID1, which inhibits CRISPR-Cas subtype I-D immunity, was first used as a selection marker to knock out genes from SIRV2M, an acrID1-null mutant of SIRV2. Moreover, we harnessed the endogenous CRISPR-Cas systems of the host to knock out the accessory genes consecutively, which resulted in a genome comprised solely of core genes of the 11 SIRV members. Furthermore, infection of this series of knockout mutants in the CRISPR-null host of LAL14/1 (Δarrays) confirmed the non-essentiality of the deleted genes and all except the last deletion mutant propagated as efficiently as the WT SIRV2. This suggested that the last gene deleted, SIRV2 gp37, is important for the efficient viral propagation. The generated viral mutants will be useful for future functional studies including searching for new Acrs and the approaches described in this case are applicable to other viruses.
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Affiliation(s)
- David Mayo-Muñoz
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Fei He
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Jacob Bruun Jørgensen
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Poul Kári Madsen
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Yuvaraj Bhoobalan-Chitty
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
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12
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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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13
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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. [PMID: 29507349 PMCID: PMC11249088 DOI: 10.1038/s41564-018-0120-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/30/2018] [Indexed: 11/09/2022]
Abstract
Viruses employ a range of strategies to counteract the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas), including mutational escape and physical blocking of enzymatic function using anti-CRISPR proteins (Acrs). Acrs have been found in many bacteriophages but so far not in archaeal viruses, despite the near ubiquity of CRISPR-Cas systems in archaea. Here, we report the functional and structural characterization of two archaeal Acrs from the lytic rudiviruses, SIRV2 and SIRV3. We show that a 4 kb deletion in the SIRV2 genome dramatically reduces infectivity in Sulfolobus islandicus LAL14/1 that carries functional CRISPR-Cas subtypes I-A, I-D and III-B. Subsequent insertion of a single gene from SIRV3, gp02 (AcrID1), which is conserved in the deleted fragment, successfully restored infectivity. We demonstrate that AcrID1 protein inhibits the CRISPR-Cas subtype I-D system by interacting directly with Cas10d protein, which is required for the interference stage. Sequence and structural analysis of AcrID1 show that it belongs to a conserved family of compact, dimeric αβ-sandwich proteins characterized by extreme pH and temperature stability and a tendency to form protein fibres. We identify about 50 homologues of AcrID1 in four archaeal viral families demonstrating the broad distribution of this group of anti-CRISPR proteins.
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Affiliation(s)
- Fei He
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Lan B Van
- Centre for Bacterial Stress Response and Persistence, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Anders L Kjeldsen
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Matteo Dedola
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - 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
| | - Ditlev E Brodersen
- Centre for Bacterial Stress Response and Persistence, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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14
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Parikka KJ, Jacquet S, Colombet J, Guillaume D, Le Romancer M. Abundance and observations of thermophilic microbial and viral communities in submarine and terrestrial hot fluid systems of the French Southern and Antarctic Lands. Polar Biol 2018. [DOI: 10.1007/s00300-018-2288-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Krupovic M, Cvirkaite-Krupovic V, Iranzo J, Prangishvili D, Koonin EV. Viruses of archaea: Structural, functional, environmental and evolutionary genomics. Virus Res 2017; 244:181-193. [PMID: 29175107 DOI: 10.1016/j.virusres.2017.11.025] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022]
Abstract
Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr. Roux, Paris 75015, Paris, France.
| | | | - Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - David Prangishvili
- Department of Microbiology, Institut Pasteur, 25 rue du Dr. Roux, Paris 75015, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
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Methanosarcina Spherical Virus, a Novel Archaeal Lytic Virus Targeting Methanosarcina Strains. J Virol 2017; 91:JVI.00955-17. [PMID: 28878086 DOI: 10.1128/jvi.00955-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022] Open
Abstract
A novel archaeal lytic virus targeting species of the genus Methanosarcina was isolated using Methanosarcina mazei strain Gö1 as the host. Due to its spherical morphology, the virus was designated Methanosarcina spherical virus (MetSV). Molecular analysis demonstrated that MetSV contains double-stranded linear DNA with a genome size of 10,567 bp containing 22 open reading frames (ORFs), all oriented in the same direction. Functions were predicted for some of these ORFs, i.e., such as DNA polymerase, ATPase, and DNA-binding protein as well as envelope (structural) protein. MetSV-derived spacers in CRISPR loci were detected in several published Methanosarcina draft genomes using bioinformatic tools, revealing a potential protospacer-adjacent motif (PAM) motif (TTA/T). Transcription and expression of several predicted viral ORFs were validated by reverse transcription-PCR (RT-PCR), PAGE analysis, and liquid chromatography-mass spectrometry (LC-MS)-based proteomics. Analysis of core lipids by atmospheric pressure chemical ionization (APCI) mass spectrometry showed that MetSV and Methanosarcina mazei both contain archaeol and glycerol dialkyl glycerol tetraether without a cyclopentane moiety (GDGT-0). The MetSV host range is limited to Methanosarcina strains growing as single cells (M. mazei, Methanosarcina barkeri and Methanosarcina soligelidi). In contrast, strains growing as sarcina-like aggregates were apparently protected from infection. Heterogeneity related to morphology phases in M. mazei cultures allowed acquisition of resistance to MetSV after challenge by growing cultures as sarcina-like aggregates. CRISPR/Cas-mediated resistance was excluded since neither of the two CRISPR arrays showed MetSV-derived spacer acquisition. Based on these findings, we propose that changing the morphology from single cells to sarcina-like aggregates upon rearrangement of the envelope structure prevents infection and subsequent lysis by MetSV.IMPORTANCE Methanoarchaea are among the most abundant organisms on the planet since they are present in high numbers in major anaerobic environments. They convert various carbon sources, e.g., acetate, methylamines, or methanol, to methane and carbon dioxide; thus, they have a significant impact on the emission of major greenhouse gases. Today, very little is known about viruses specifically infecting methanoarchaea that most probably impact the abundance of methanoarchaea in microbial consortia. Here, we characterize the first identified Methanosarcina-infecting virus (MetSV) and show a mechanism for acquiring resistance against MetSV. Based on our results, we propose that growth as sarcina-like aggregates prevents infection and subsequent lysis. These findings allow new insights into the virus-host relationship in methanogenic community structures, their dynamics, and their phase heterogeneity. Moreover, the availability of a specific virus provides new possibilities to deepen our knowledge of the defense mechanisms of potential hosts and offers tools for genetic manipulation.
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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: 32] [Impact Index Per Article: 4.6] [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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18
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Han W, Li Y, Deng L, Feng M, Peng W, Hallstrøm S, Zhang J, Peng N, Liang YX, White MF, She Q. A type III-B CRISPR-Cas effector complex mediating massive target DNA destruction. Nucleic Acids Res 2017; 45:1983-1993. [PMID: 27986854 PMCID: PMC5389615 DOI: 10.1093/nar/gkw1274] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/07/2016] [Indexed: 12/26/2022] Open
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) system protects archaea and bacteria by eliminating nucleic acid invaders in a crRNA-guided manner. The Sulfolobus islandicus type III-B Cmr–α system targets invading nucleic acid at both RNA and DNA levels and DNA targeting relies on the directional transcription of the protospacer in vivo. To gain further insight into the involved mechanism, we purified a native effector complex of III-B Cmr–α from S. islandicus and characterized it in vitro. Cmr–α cleaved RNAs complementary to crRNA present in the complex and its ssDNA destruction activity was activated by target RNA. The ssDNA cleavage required mismatches between the 5΄-tag of crRNA and the 3΄-flanking region of target RNA. An invader plasmid assay showed that mutation either in the histidine-aspartate acid (HD) domain (a quadruple mutation) or in the GGDD motif of the Cmr–2α protein resulted in attenuation of the DNA interference in vivo. However, double mutation of the HD motif only abolished the DNase activity in vitro. Furthermore, the activated Cmr–α binary complex functioned as a highly active DNase to destroy a large excess DNA substrate, which could provide a powerful means to rapidly degrade replicating viral DNA.
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Affiliation(s)
- Wenyuan Han
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, DK-2200 Copenhagen N, Denmark
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ling Deng
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, DK-2200 Copenhagen N, Denmark
| | - Mingxia Feng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Wenfang Peng
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, DK-2200 Copenhagen N, Denmark
| | - Søren Hallstrøm
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, DK-2200 Copenhagen N, Denmark
| | - Jing Zhang
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yun Xiang Liang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, DK-2200 Copenhagen N, Denmark.,State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
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19
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Wu L, Uldahl KB, Chen F, Benasutti H, Logvinski D, Vu V, Banda NK, Peng X, Simberg D, Moghimi SM. Interaction of extremophilic archaeal viruses with human and mouse complement system and viral biodistribution in mice. Mol Immunol 2017; 90:273-279. [PMID: 28846925 DOI: 10.1016/j.molimm.2017.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/06/2017] [Accepted: 08/14/2017] [Indexed: 12/19/2022]
Abstract
Archaeal viruses offer exceptional biophysical properties for modification and exploration of their potential in bionanotechnology, bioengineering and nanotherapeutic developments. However, the interaction of archaeal viruses with elements of the innate immune system has not been explored, which is a necessary prerequisite if their potential for biomedical applications to be realized. Here we show complement activation through lectin (via direct binding of MBL/MASPs) and alternative pathways by two extremophilic archaeal viruses (Sulfolobus monocaudavirus 1 and Sulfolobus spindle-shaped virus 2) in human serum. We further show some differences in initiation of complement activation pathways between these viruses. Since, Sulfolobus monocaudavirus 1 was capable of directly triggering the alternative pathway, we also demonstrate that the complement regulator factor H has no affinity for the viral surface, but factor H deposition is purely C3-dependent. This suggests that unlike some virulent pathogens Sulfolobus monocaudavirus 1 does not acquire factor H for protection. Complement activation with Sulfolobus monocaudavirus 1 also proceeds in murine sera through MBL-A/C as well as factor D-dependent manner, but C3 deficiency has no overall effect on viral clearance by organs of the reticuloendothelial system on intravenous injection. However, splenic deposition was significantly higher in C3 knockout animals compared with the corresponding wild type mice. We discuss the potential application of these viruses in biomedicine in relation to their complement activating properties.
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Affiliation(s)
- Linping Wu
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
| | - Kristine Buch Uldahl
- Danish Archaea Center, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, Copenhagen 2200, Denmark
| | - Fangfang Chen
- Department of Gastrointestinal Surgery, China-Japan Union Hospital, Jilin University, 126 Xiantai Street, Changchun, Jilin 130033, People's Republic of China; Tranlational Bio-Nanosciences Laboratory and Colorado Center for Nanomedicine and Nanosafety, The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus, 1250 East Mountview Blvd., Aurora, CO 80045, USA
| | - Halli Benasutti
- Tranlational Bio-Nanosciences Laboratory and Colorado Center for Nanomedicine and Nanosafety, The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus, 1250 East Mountview Blvd., Aurora, CO 80045, USA
| | - Deborah Logvinski
- Tranlational Bio-Nanosciences Laboratory and Colorado Center for Nanomedicine and Nanosafety, The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus, 1250 East Mountview Blvd., Aurora, CO 80045, USA
| | - Vivian Vu
- Tranlational Bio-Nanosciences Laboratory and Colorado Center for Nanomedicine and Nanosafety, The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus, 1250 East Mountview Blvd., Aurora, CO 80045, USA
| | - Nirmal K Banda
- Division of Rheumatology, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, 1775 Aurora Court, Aurora, CO 80045, USA
| | - Xu Peng
- Danish Archaea Center, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, Copenhagen 2200, Denmark
| | - Dmitri Simberg
- Tranlational Bio-Nanosciences Laboratory and Colorado Center for Nanomedicine and Nanosafety, The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus, 1250 East Mountview Blvd., Aurora, CO 80045, USA
| | - Seyed Moein Moghimi
- Tranlational Bio-Nanosciences Laboratory and Colorado Center for Nanomedicine and Nanosafety, The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, University of Colorado Denver, Anschutz Medical Campus, 1250 East Mountview Blvd., Aurora, CO 80045, USA; School of Medicine, Pharmacy and Health, Durham University, Queen's Campus, Stockton-on-Tees TS17 6BH, United Kingdom.
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20
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Peeters E, Boon M, Rollie C, Willaert RG, Voet M, White MF, Prangishvili D, Lavigne R, Quax TEF. DNA-Interacting Characteristics of the Archaeal Rudiviral Protein SIRV2_Gp1. Viruses 2017; 9:v9070190. [PMID: 28718834 PMCID: PMC5537682 DOI: 10.3390/v9070190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 12/02/2022] Open
Abstract
Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rod-shaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally characterize gp1, which is a SIRV2 gene with unknown function. The SIRV2_Gp1 protein is highly expressed during early stages of infection and it is the only protein that is encoded twice on the viral genome. It harbours a helix-turn-helix motif and was therefore hypothesized to bind DNA. The DNA-binding behavior of SIRV2_Gp1 was characterized with electrophoretic mobility shift assays and atomic force microscopy. We provide evidence that the protein interacts with DNA and that it forms large aggregates, thereby causing extreme condensation of the DNA. Furthermore, the N-terminal domain of the protein mediates toxicity to the viral host Sulfolobus. Our findings may lead to biotechnological applications, such as the development of a toxic peptide for the containment of pathogenic bacteria, and add to our understanding of the Rudiviral infection cycle.
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Affiliation(s)
- Eveline Peeters
- Research Group of Microbiology, Department of Bio-Engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
| | - Clare Rollie
- Biomedical Sciences Research Complex, University of St Andrews, Fife, North Haugh, St. Andrews KY16 9AJ, UK.
| | - Ronnie G Willaert
- Alliance Research Group VUB-UGhent NanoMicrobiology, IJRG VUB-EPFL, BioNanotechnology & NanoMedicine, Research Group Structural Biology Brussels, Department of Bio-Engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, Fife, North Haugh, St. Andrews KY16 9AJ, UK.
| | | | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
| | - Tessa E F Quax
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
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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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Samson RY, Dobro MJ, Jensen GJ, Bell SD. The Structure, Function and Roles of the Archaeal ESCRT Apparatus. Subcell Biochem 2017; 84:357-377. [PMID: 28500532 DOI: 10.1007/978-3-319-53047-5_12] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although morphologically resembling bacteria, archaea constitute a distinct domain of life with a closer affiliation to eukaryotes than to bacteria. This similarity is seen in the machineries for a number of essential cellular processes, including DNA replication and gene transcription. Perhaps surprisingly, given their prokaryotic morphology, some archaea also possess a core cell division apparatus that is related to that involved in the final stages of membrane abscission in vertebrate cells, the ESCRT machinery.
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Affiliation(s)
- Rachel Y Samson
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA
| | - Megan J Dobro
- School of Natural Science, Hampshire College, Amherst, MA, 01002, USA
| | - Grant J Jensen
- Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Stephen D Bell
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA.
- Department of Biology, Indiana University, Simon Hall MSB, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA.
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23
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Uldahl KB, Wu L, Hall A, Papathanasiou P, Peng X, Moghimi SM. Recognition of extremophilic archaeal viruses by eukaryotic cells: a promising nanoplatform from the third domain of life. Sci Rep 2016; 6:37966. [PMID: 27892499 PMCID: PMC5125014 DOI: 10.1038/srep37966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/19/2016] [Indexed: 01/08/2023] Open
Abstract
Viruses from the third domain of life, Archaea, exhibit unusual features including extreme stability that allow their survival in harsh environments. In addition, these species have never been reported to integrate into human or any other eukaryotic genomes, and could thus serve for exploration of novel medical nanoplatforms. Here, we selected two archaeal viruses Sulfolobus monocaudavirus 1 (SMV1) and Sulfolobus spindle shaped virus 2 (SSV2) owing to their unique spindle shape, hyperthermostable and acid-resistant nature and studied their interaction with mammalian cells. Accordingly, we followed viral uptake, intracellular trafficking and cell viability in human endothelial cells of brain (hCMEC/D3 cells) and umbilical vein (HUVEC) origin. Whereas SMV1 is efficiently internalized into both types of human cells, SSV2 differentiates between HUVECs and hCMEC/D3 cells, thus opening a path for selective cell targeting. On internalization, both viruses localize to the lysosomal compartments. Neither SMV1, nor SSV2 induced any detrimental effect on cell morphology, plasma membrane and mitochondrial functionality. This is the first study demonstrating recognition of archaeal viruses by eukaryotic cells which provides good basis for future exploration of archaeal viruses in bioengineering and development of multifunctional vectors.
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Affiliation(s)
- Kristine Buch Uldahl
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, Copenhagen, 2200, Denmark
| | - Linping Wu
- Nanomedicine Research Group, Centre for Pharmaceutical Nanotechnology and Nanotoxicology, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Arnaldur Hall
- Nanomedicine Research Group, Centre for Pharmaceutical Nanotechnology and Nanotoxicology, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Pavlos Papathanasiou
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, Copenhagen, 2200, Denmark
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, Copenhagen, 2200, Denmark
| | - Seyed Moein Moghimi
- Nanomedicine Research Group, Centre for Pharmaceutical Nanotechnology and Nanotoxicology, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.,School of Medicine, Pharmacy and Health, Durham University, Wolfson building, Queens campus, Stockton on Tees, TS17 6BS, UK
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24
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Martínez-Alvarez L, Bell SD, Peng X. Multiple consecutive initiation of replication producing novel brush-like intermediates at the termini of linear viral dsDNA genomes with hairpin ends. Nucleic Acids Res 2016; 44:8799-8809. [PMID: 27407114 PMCID: PMC5062984 DOI: 10.1093/nar/gkw636] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 11/14/2022] Open
Abstract
Linear dsDNA replicons with hairpin ends are found in the three domains of life, mainly associated with plasmids and viruses including the poxviruses, some phages and archaeal rudiviruses. However, their replication mechanism is not clearly understood. In this study, we find that the rudivirus SIRV2 undergoes multiple consecutive replication reinitiation events at the genomic termini. Using a strand-displacement replication strategy, the multiple reinitiation events from one parental template yield highly branched intermediates corresponding to about 30 genome units which generate exceptional 'brush-like' structures. Moreover, our data support the occurrence of an additional strand-coupled bidirectional replication from a circular dimeric intermediate. The multiple reinitiation process ensures rapid copying of the parental viral genome and will enable protein factors involved in viral genome replication to be specifically localised intracellularly, thereby helping the virus to avoid host defence mechanisms.
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Affiliation(s)
- Laura Martínez-Alvarez
- Archaea Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Stephen D Bell
- Department of Molecular and Cellular Biochemistry, Department of Biology, Indiana University, Simon Hall MSB, IN 47405, USA
| | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
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25
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Life Cycle Characterization of Sulfolobus Monocaudavirus 1, an Extremophilic Spindle-Shaped Virus with Extracellular Tail Development. J Virol 2016; 90:5693-5699. [PMID: 27053548 DOI: 10.1128/jvi.00075-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/15/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED We provide here, for the first time, insights into the initial infection stages of a large spindle-shaped archaeal virus and explore the following life cycle events. Our observations suggest that Sulfolobus monocaudavirus 1 (SMV1) exhibits a high adsorption rate and that virions adsorb to the host cells via three distinct attachment modes: nosecone association, body association, and body/tail association. In the body/tail association mode, the entire virion, including the tail(s), aligns to the host cell surface and the main body is greatly flattened, suggesting a possible fusion entry mechanism. Upon infection, the intracellular replication cycle lasts about 8 h, at which point the virions are released as spindle-shaped tailless particles. Replication of the virus retarded host growth but did not cause lysis of the host cells. Once released from the host and at temperatures resembling that of its natural habitat, SMV1 starts developing one or two tails. This exceptional property of undergoing a major morphological development outside, and independently of, the host cell has been reported only once before for the related Acidianus two-tailed virus. Here, we show that SMV1 can develop tails of more than 900 nm in length, more than quadrupling the total virion length. IMPORTANCE Very little is known about the initial life cycle stages of viruses infecting hosts of the third domain of life, Archaea This work describes the first example of an archaeal virus employing three distinct association modes. The virus under study, Sulfolobus monocaudavirus 1, is a representative of the large spindle-shaped viruses that are frequently found in acidic hot springs. The results described here will add valuable knowledge about Archaea, the least studied domain in the virology field.
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León-Sobrino C, Kot WP, Garrett RA. Transcriptome changes in STSV2-infected Sulfolobus islandicus REY15A undergoing continuous CRISPR spacer acquisition. Mol Microbiol 2015; 99:719-28. [PMID: 26514343 DOI: 10.1111/mmi.13263] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2015] [Indexed: 12/21/2022]
Abstract
A transcriptome study was performed on Sulfolobus islandicus REY15A actively undergoing CRISPR spacer acquisition from the crenarchaeal monocaudavirus STSV2 in rich and basal media over a 6 day period. Spacer acquisition preceded strong host growth retardation, altered transcriptional activity of four different CRISPR-Cas modules and changes in viral copy numbers, and with significant differences in the two media. Transcript levels of proteins involved in the cell cycle were reduced, whereas those of DNA replication, DNA repair, transcriptional regulation and some antitoxin-toxin pairs and transposases were unchanged or enhanced. Antisense RNAs were implicated in the transcriptional regulation of adaptation and interference modules of the type I-A CRISPR-Cas system, and evidence was found for the occurrence of functional co-ordination between the single CRISPR-Cas adaptation module and the functionally diverse interference modules.
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Affiliation(s)
- Carlos León-Sobrino
- Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Witold P Kot
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Roger A Garrett
- Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
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Fusco S, Liguori R, Limauro D, Bartolucci S, She Q, Contursi P. Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system. Biochimie 2015; 118:322-32. [DOI: 10.1016/j.biochi.2015.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/08/2015] [Indexed: 11/26/2022]
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Abstract
SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade.
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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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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: 32] [Impact Index Per Article: 3.6] [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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Garrett RA, Shah SA, Erdmann S, Liu G, Mousaei M, León-Sobrino C, Peng W, Gudbergsdottir S, Deng L, Vestergaard G, Peng X, She Q. CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity. Life (Basel) 2015; 5:783-817. [PMID: 25764276 PMCID: PMC4390879 DOI: 10.3390/life5010783] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/24/2015] [Accepted: 02/27/2015] [Indexed: 12/26/2022] Open
Abstract
The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.
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Affiliation(s)
- Roger A Garrett
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Shiraz A Shah
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Susanne Erdmann
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052 Sydney NSW, Australia.
| | - Guannan Liu
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Marzieh Mousaei
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Carlos León-Sobrino
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Wenfang Peng
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Soley Gudbergsdottir
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Ling Deng
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Gisle Vestergaard
- Helmholtz Zentrum München, Research Unit Environmental Genomics, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Germany.
| | - Xu Peng
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Qunxin She
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
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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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Unveiling cell surface and type IV secretion proteins responsible for archaeal rudivirus entry. J Virol 2014; 88:10264-8. [PMID: 24965447 DOI: 10.1128/jvi.01495-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Sulfolobus mutants resistant to archaeal lytic virus Sulfolobus islandicus rod-shaped virus 2 (SIRV2) were isolated, and mutations were identified in two gene clusters, cluster sso3138 to sso3141 and cluster sso2386 and sso2387, encoding cell surface and type IV secretion proteins, respectively. The involvement of the mutations in the resistance was confirmed by genetic complementation. Blocking of virus entry into the mutants was demonstrated by the lack of early gene transcription, strongly supporting the idea of a role of the proteins in SIRV2 entry.
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Protein-protein interactions leading to recruitment of the host DNA sliding clamp by the hyperthermophilic Sulfolobus islandicus rod-shaped virus 2. J Virol 2014; 88:7105-8. [PMID: 24696494 DOI: 10.1128/jvi.00636-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses infecting hyperthermophilic archaea typically do not encode DNA polymerases, raising questions regarding their genome replication. Here, using a yeast two-hybrid approach, we have assessed interactions between proteins of Sulfolobus islandicus rod-shaped virus 2 (SIRV2) and the host-encoded proliferating cell nuclear antigen (PCNA), a key DNA replication protein in archaea. Five SIRV2 proteins were found to interact with PCNA, providing insights into the recruitment of host replisome for viral DNA replication.
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Molecular biology of fuselloviruses and their satellites. Extremophiles 2014; 18:473-89. [DOI: 10.1007/s00792-014-0634-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
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36
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