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Marks TJ, Rowland IR. The Diversity of Bacteriophages in Hot Springs. Methods Mol Biol 2024; 2738:73-88. [PMID: 37966592 DOI: 10.1007/978-1-0716-3549-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophages are ubiquitous in all environments that support microbial life. This includes hot springs, which can range in temperatures between 40 and 98 °C and pH levels between 1 and 9. Bacteriophages that survive in the higher temperatures of hot springs are known as thermophages. Thermophages have developed distinct adaptations allowing for thermostability in these extreme environments, including increased G + C DNA percentages, reliance upon the pentose phosphate metabolic pathway to avoid oxidative stress, and a codon preference for those with a GNA sequence leading to increased hydrophobic interactions and disulfide bonds. In this review, we discuss the diversity of characterized thermophages in hot spring environments that span five viral families: Myoviridae, Siphoviridae, Tectiviridae, Sphaerolipoviridae, and Inoviridae. Potential industrial and medicinal applications of thermophages will also be addressed.
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Affiliation(s)
- Timothy J Marks
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies Creek, NC, USA.
| | - Isabella R Rowland
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies Creek, NC, USA
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Moghimi SM, Haroon HB, Yaghmur A, Hunter AC, Papini E, Farhangrazi ZS, Simberg D, Trohopoulos PN. Perspectives on complement and phagocytic cell responses to nanoparticles: From fundamentals to adverse reactions. J Control Release 2023; 356:115-129. [PMID: 36841287 PMCID: PMC11000211 DOI: 10.1016/j.jconrel.2023.02.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 02/27/2023]
Abstract
The complement system, professional phagocytes and other cells such as Natural killer cells and mast cells are among the important components of the innate arm of the immune system. These constituents provide an orchestrated array of defences and responses against tissue injury and foreign particles, including nanopharmaceuticals. While interception of nanopharmaceuticals by the immune system is beneficial for immunomodulation and treatment of phagocytic cell disorders, it is imperative to understand the multifaceted mechanisms by which nanopharmaceuticals interacts with the immune system and evaluate the subsequent balance of beneficial versus adverse reactions. An example of the latter is adverse infusion reactions to regulatory-approved nanopharmaceuticals seen in human subjects. Here, we discuss collective opinions and findings from our laboratories in mapping nanoparticle-mediated complement and leucocyte/macrophage responses.
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Affiliation(s)
- S Moein Moghimi
- School of Pharmacy, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Translational and Clinical Research Institute, Faculty of Health and Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; Colorado Center for Nanomedicine and Nanosafety, University of Colorado Anschutz Medical Center, Aurora, CO, USA.
| | - Hajira B Haroon
- School of Pharmacy, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Translational and Clinical Research Institute, Faculty of Health and Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Anan Yaghmur
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - A Christy Hunter
- School of Pharmacy, College of Science, University of Lincoln, Lincoln LN6 7TS, UK
| | - Emanuele Papini
- Department of Biomedical Sciences, University of Padua, Padua 35121, Italy
| | - Z Shadi Farhangrazi
- S. M. Discovery Group Inc., Centennial, CO, USA; S. M. Discovery Group Ltd., Durham, UK
| | - Dmitri Simberg
- Colorado Center for Nanomedicine and Nanosafety, University of Colorado Anschutz Medical Center, Aurora, CO, USA; Translational Bio-Nanosciences Laboratory, Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado Anschutz Medical Center, Aurora, CO, USA
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3
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CRISPR-Cas adaptive immune systems in Sulfolobales: genetic studies and molecular mechanisms. SCIENCE CHINA-LIFE SCIENCES 2020; 64:678-696. [DOI: 10.1007/s11427-020-1745-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/25/2020] [Indexed: 12/26/2022]
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Das S, Kumari A, Sherpa MT, Najar IN, Thakur N. Metavirome and its functional diversity analysis through microbiome study of the Sikkim Himalayan hot spring solfataric mud sediments. CURRENT RESEARCH IN MICROBIAL SCIENCES 2020; 1:18-29. [PMID: 34841298 PMCID: PMC8610333 DOI: 10.1016/j.crmicr.2020.05.002] [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: 04/16/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 11/10/2022] Open
Abstract
This study is the first ever report on the virus diversity among the hot springs of Sikkim, India. The study revealed the dominance of Siphoviridae, Myoviridae and Phycodnaviridae in the two hot spring solfataric mud sediments. The metavirome ecology of the two hot springs have dsDNA viromes in abundance. Giant DNA viruses such as Pandoravirus and Pithovirus were found through metagenomic approach.
Viruses are the most prodigious repertory of the genetic material on the earth. They are elusive, breakneck, evolutionary life particles that constitute a riveting concealed world. Environmental viruses have been obscurely explored, and hence, such an intriguing world of viruses was studied in the Himalayan Geothermal Belt of Indian peninsula at Sikkim corridor through hot springs. The hot springs located at the North Sikkim district were selected for the current study. The solfataric mud sediment samples were pooled from both the hot springs. The virus community showed significant diversity among the two hot springs of Yume Samdung. Reads for viruses among the mud sediments at Old Yume Samdung hot springs (OYS) was observed to be 11% and in the case of New Yume Samdung hot springs (NYS) it was 6%. Both the hot springs were abundant in dsDNA viromes. The metavirome reads in both the OYS and NYS hot spring mud sediments showed the predominance of Caudovirales; Herpesvirales; Ortervirales among which viral reads from Siphoviridae, Myoviridae, Phycodnaviridae and Podoviridae were abundantly present. Other viral communities belonged to families like Baculoviridae, Mimiviridae, Parvoviridae, Marseilleviridae etc. Interestingly, in the case of NYS, the unassigned group reads belonged to some unclassified giant DNA viruses like genera Pandoravirus and Pithovirus. Other interesting findings were – reads for Badnavirus having ds (RT-DNA) was exclusively found in NYS whereas Rubulavirus having ss(-)RNA was exclusively found in OYS sample. This is the first ever report on viruses from any hot springs of Sikkim till date.
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Affiliation(s)
- Sayak Das
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok 737102, Sikkim, India
| | - Ankita Kumari
- Bionivid Technology Private Limited, Bangalore 560043, India
| | - Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok 737102, Sikkim, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok 737102, Sikkim, India
| | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok 737102, Sikkim, India
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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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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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Ramos‐Barbero MD, Martínez JM, Almansa C, Rodríguez N, Villamor J, Gomariz M, Escudero C, Rubin SDC, Antón J, Martínez‐García M, Amils R. Prokaryotic and viral community structure in the singular chaotropic salt lake Salar de Uyuni. Environ Microbiol 2019; 21:2029-2042. [DOI: 10.1111/1462-2920.14549] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 01/19/2019] [Accepted: 01/29/2019] [Indexed: 02/01/2023]
Affiliation(s)
| | - José M. Martínez
- Department of Virology and Microbiology, Centro de Biología Molecular Severo OchoaUniversidad Autónoma de Madrid (CBMSO, CSIC‐UAM) Cantoblanco, 28049 Madrid Spain
| | - Cristina Almansa
- Department of Physiology, Genetics and MicrobiologyUniversidad de Alicante Alicante Spain
| | - Nuria Rodríguez
- Department of Planetology and HabitabilityCentro de Astrobiología (CAB, INTA‐CSIC) 28055 Torrejón de Ardoz Spain
| | - Judith Villamor
- Department of Physiology, Genetics and MicrobiologyUniversidad de Alicante Alicante Spain
| | - María Gomariz
- Department of Physiology, Genetics and MicrobiologyUniversidad de Alicante Alicante Spain
| | - Cristina Escudero
- Department of Virology and Microbiology, Centro de Biología Molecular Severo OchoaUniversidad Autónoma de Madrid (CBMSO, CSIC‐UAM) Cantoblanco, 28049 Madrid Spain
| | - Sergio dC Rubin
- Department of Virology and Microbiology, Centro de Biología Molecular Severo OchoaUniversidad Autónoma de Madrid (CBMSO, CSIC‐UAM) Cantoblanco, 28049 Madrid Spain
- Université catholique de LouvainEarth and Life Institute, Georges Lemaître Centre for Earth and Climate Research Belgium
| | - Josefa Antón
- Department of Physiology, Genetics and MicrobiologyUniversidad de Alicante Alicante Spain
| | - Manuel Martínez‐García
- Department of Physiology, Genetics and MicrobiologyUniversidad de Alicante Alicante Spain
| | - Ricardo Amils
- Department of Virology and Microbiology, Centro de Biología Molecular Severo OchoaUniversidad Autónoma de Madrid (CBMSO, CSIC‐UAM) Cantoblanco, 28049 Madrid Spain
- Department of Planetology and HabitabilityCentro de Astrobiología (CAB, INTA‐CSIC) 28055 Torrejón de Ardoz Spain
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Zablocki O, van Zyl L, Trindade M. Biogeography and taxonomic overview of terrestrial hot spring thermophilic phages. Extremophiles 2018; 22:827-837. [PMID: 30121708 DOI: 10.1007/s00792-018-1052-5] [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] [Received: 05/28/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
Abstract
Bacterial viruses ("phages") play important roles in the regulation and evolution of microbial communities in most ecosystems. Terrestrial hot springs typically contain thermophilic bacterial communities, but the diversity and impacts of its associated viruses ("thermophilic phages") are largely unexplored. Here, we provide a taxonomic overview of phages that have been isolated strictly from terrestrial hot springs around the world. In addition, we placed 17 thermophilic phage genomes in a global phylogenomic context to detect evolutionary patterns. Thermophilic phages have diverse morphologies (e.g., tailed, filamentous), unique virion structures (e.g., extremely long tailed siphoviruses), and span five taxonomic families encompassing strictly thermophilic phage genera. Within the phage proteomic tree, six thermophilic phage-related clades were identified, with evident genomic relatedness between thermophilic phages and archaeal viruses. Moreover, whole proteome analyses showed clustering between phages that infect distinct host phyla, such as Firmicutes and Deinococcus-Thermus. The potential for discovery of novel phage-host systems in terrestrial hot springs remain mostly untapped, thus additional emphasis on thermophilic phages in ecological prospecting is encouraged to gain insights into the microbial population dynamics of these environments.
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Affiliation(s)
- Olivier Zablocki
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Leonardo van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.
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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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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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Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea. SCIENCE CHINA-LIFE SCIENCES 2017; 60:370-385. [DOI: 10.1007/s11427-016-0355-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/18/2016] [Indexed: 12/26/2022]
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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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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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Contursi P, Farina B, Pirone L, Fusco S, Russo L, Bartolucci S, Fattorusso R, Pedone E. Structural and functional studies of Stf76 from the Sulfolobus islandicus plasmid-virus pSSVx: a novel peculiar member of the winged helix-turn-helix transcription factor family. Nucleic Acids Res 2014; 42:5993-6011. [PMID: 24682827 PMCID: PMC4027180 DOI: 10.1093/nar/gku215] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The hybrid plasmid–virus pSSVx from Sulfolobus islandicus presents an open reading frame encoding a 76 amino acid protein, namely Stf76, that does not show significant sequence homology with any protein with known 3D structure. The recombinant protein recognizes specifically two DNA-binding sites located in its own promoter, thus suggesting an auto-regulated role of its expression. Circular dichroism, spectrofluorimetric, light scattering and isothermal titration calorimetry experiments indicated a 2:1 molar ratio (protein:DNA) upon binding to the DNA target containing a single site. Furthermore, the solution structure of Stf76, determined by nuclear magnetic resonance (NMR) using chemical shift Rosetta software, has shown that the protein assumes a winged helix–turn–helix fold. NMR chemical shift perturbation analysis has been performed for the identification of the residues responsible for DNA interaction. In addition, a model of the Stf76–DNA complex has been built using as template a structurally related homolog.
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Affiliation(s)
- Patrizia Contursi
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Biancamaria Farina
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | | | - Salvatore Fusco
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta 81100, Italy
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta 81100, Italy
| | - Emilia Pedone
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy Istituto di Biostrutture e Bioimmagini, C.N.R., Napoli 80134, Italy
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16
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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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17
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Erdmann S, Chen B, Huang X, Deng L, Liu C, Shah SA, Le Moine Bauer S, Sobrino CL, Wang H, Wei Y, She Q, Garrett RA, Huang L, Lin L. A novel single-tailed fusiform Sulfolobus virus STSV2 infecting model Sulfolobus species. Extremophiles 2013; 18:51-60. [PMID: 24163004 DOI: 10.1007/s00792-013-0591-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
Abstract
A newly isolated single-tailed fusiform virus, Sulfolobus tengchongensis spindle-shaped virus STSV2, from Hamazui, China, is characterised. It contains a double-stranded modified DNA genome of 76,107 bp and is enveloped by a lipid membrane structure. Virions exhibit a single coat protein that forms oligomers when isolated. STSV2 is related to the single-tailed fusiform virus STSV1 and, more distantly, to the two-tailed bicaudavirus ATV. The virus can be stably cultured over long periods in laboratory strains of Sulfolobus and no evidence was found for cell lysis under different stress conditions. Therefore, it constitutes an excellent model virus for archaeal virus-host studies.
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Affiliation(s)
- Susanne Erdmann
- Biotechnology Research Center, Faculty of Biological and Engineering, Cenggong Campus, Kunming University of Science and Technology (KUST), Kunming, 650500, Yunnan, China
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18
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Contursi P, Fusco S, Limauro D, Fiorentino G. Host and viral transcriptional regulators in Sulfolobus: an overview. Extremophiles 2013; 17:881-95. [PMID: 24085522 DOI: 10.1007/s00792-013-0586-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022]
Abstract
The genus Sulfolobus includes microorganisms belonging to the domain Archaea, sub-kingdom Crenarchaeota, living in geographically distant acidic hot springs. Their adaptation to such particular habitats requires finely regulated mechanisms of gene expression, among which, those modulated by sequence-specific transcription factors (TFs) play a key role. In this review, we summarize the current knowledge on the repertoires of TFs found in Sulfolobus spp. and their viruses, focusing on the description of their DNA-binding domains and their structure-function relationship.
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Affiliation(s)
- Patrizia Contursi
- Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia, Edificio 7, 80126, Napoli, Italy
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19
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Living side by side with a virus: characterization of two novel plasmids from Thermococcus prieurii, a host for the spindle-shaped virus TPV1. Appl Environ Microbiol 2013; 79:3822-8. [PMID: 23584787 DOI: 10.1128/aem.00525-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial cells often serve as an evolutionary battlefield for different types of mobile genetic elements, such as viruses and plasmids. Here, we describe the isolation and characterization of two new archaeal plasmids which share the host with the spindle-shaped Thermococcus prieurii virus 1 (TPV1). The two plasmids, pTP1 and pTP2, were isolated from the hyperthermophilic archaeon Thermococcus prieurii (phylum Euryarchaeota), a resident of a deep-sea hydrothermal vent located at the East Pacific Rise at 2,700-m depth (7°25'24 S, 107°47'66 W). pTP1 (3.1 kb) and pTP2 (2.0 kb) are among the smallest known plasmids of hyperthermophilic archaea, and both are predicted to replicate via the rolling-circle mechanism. The two plasmids and the virus TPV1 do not have a single gene in common and stably propagate in infected cells without any apparent antagonistic effect on each other. The compatibility of the three genetic elements and the high copy number of pTP1 and pTP2 plasmids (50 copies/cell) might be useful for developing new genetic tools for studying hyperthermophilic euryarchaea and their viruses.
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20
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Ren Y, She Q, Huang L. Transcriptomic analysis of the SSV2 infection of Sulfolobus solfataricus with and without the integrative plasmid pSSVi. Virology 2013; 441:126-34. [PMID: 23579037 DOI: 10.1016/j.virol.2013.03.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 01/25/2013] [Accepted: 03/15/2013] [Indexed: 12/31/2022]
Abstract
The fusellovirus SSV2 and the integrative plasmid pSSVi, which constitute a unique helper-satellite virus system, replicate in Sulfolobus solfataricus P2. In this study, we investigated the interplay among SSV2, pSSVi and their host by transcriptomic analysis. Following infection of S. solfataricus P2, SSV2 activated its promoters in a temporal and distributive fashion, starting from the transcription of ORF305. Expression of several host genes encoding DNA replication and transcription proteins was up-regulated, suggesting that SSV2 depended heavily on the host replication machinery for its replication. SSV2 gene expression appeared to follow a similar pattern in S. solfataricus P2 harboring pSSVi to that in S. solfataricus P2 lacking the plasmid. Several early genes of the virus were transcribed earlier and more efficiently in the presence of pSSVi than in its absence. These results provide valuable clues to the understanding of the three-way interactions among SSV2, pSSVi and the host.
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Affiliation(s)
- Yi Ren
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, PR China
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21
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Norais C, Moisan A, Gaspin C, Clouet-d'Orval B. Diversity of CRISPR systems in the euryarchaeal Pyrococcales. RNA Biol 2013; 10:659-70. [PMID: 23422322 DOI: 10.4161/rna.23927] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Pyrococcales are members of the order Thermococcales, a group of hyperthermophilic euryarchaea that are frequently found in deep sea hydrothermal vents. Infectious genetic elements, such as plasmids and viruses, remain a threat even in this remote environment and these microorganisms have developed several ways to fight their genetic invaders. Among these are the recently discovered CRISPR systems. In this review, we have combined and condensed available information on genetic elements infecting the Thermococcales and on the multiple CRISPR systems found in the Pyrococcales to fight them. Their organization and mode of action will be presented with emphasis on the Type III-B system that is the only CRISPR system known to target RNA molecules in a process reminiscent of RNA interference. The intriguing case of Pyrococcus abyssi, which is among the rare strains to present a CRISPR system devoid of the universal cas1 and cas2 genes, is also discussed.
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Affiliation(s)
- Cédric Norais
- Laboratoire de Biochimie, UMR CNRS 7654, Département de Biologie, Ecole Polytechnique, Palaiseau, France
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