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Ribeiro ALJL, Pérez-Arnaiz P, Sánchez-Costa M, Pérez L, Almendros M, van Vliet L, Gielen F, Lim J, Charnock S, Hollfelder F, González-Pastor JE, Berenguer J, Hidalgo A. Thermostable in vitro transcription-translation compatible with microfluidic droplets. Microb Cell Fact 2024; 23:169. [PMID: 38858677 PMCID: PMC11165818 DOI: 10.1186/s12934-024-02440-y] [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: 11/27/2023] [Accepted: 05/25/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND In vitro expression involves the utilization of the cellular transcription and translation machinery in an acellular context to produce one or more proteins of interest and has found widespread application in synthetic biology and in pharmaceutical biomanufacturing. Most in vitro expression systems available are active at moderate temperatures, but to screen large libraries of natural or artificial genetic diversity for highly thermostable enzymes or enzyme variants, it is instrumental to enable protein synthesis at high temperatures. OBJECTIVES Develop an in vitro expression system operating at high temperatures compatible with enzymatic assays and with technologies that enable ultrahigh-throughput protein expression in reduced volumes, such as microfluidic water-in-oil (w/o) droplets. RESULTS We produced cell-free extracts from Thermus thermophilus for in vitro translation including thermostable enzymatic cascades for energy regeneration and a moderately thermostable RNA polymerase for transcription, which ultimately limited the temperature of protein synthesis. The yield was comparable or superior to other thermostable in vitro expression systems, while the preparation procedure is much simpler and can be suited to different Thermus thermophilus strains. Furthermore, these extracts have enabled in vitro expression in microfluidic droplets at high temperatures for the first time. CONCLUSIONS Cell-free extracts from Thermus thermophilus represent a simpler alternative to heavily optimized or pure component thermostable in vitro expression systems. Moreover, due to their compatibility with droplet microfluidics and enzyme assays at high temperatures, the reported system represents a convenient gateway for enzyme screening at higher temperatures with ultrahigh-throughput.
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Grants
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- 324439, 635595, 685474, 695669 and 10100560 European Commission
- BIO-2013-44963-R, RED2022-134755-T, CEX2021-001154-S Ministerio de Ciencia e Innovación
- BIO-2013-44963-R, RED2022-134755-T, CEX2021-001154-S Ministerio de Ciencia e Innovación
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Affiliation(s)
- Ana L J L Ribeiro
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Instituto de Biología Molecular, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Patricia Pérez-Arnaiz
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Instituto de Biología Molecular, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Mercedes Sánchez-Costa
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Lara Pérez
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Marcos Almendros
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Liisa van Vliet
- Departament of Biochemistry, Cambridge University, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- DropTech Ltd, 91 Canterbury Court, Cambridge, CB4 3QU, UK
| | - Fabrice Gielen
- DropTech Ltd, 91 Canterbury Court, Cambridge, CB4 3QU, UK
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
| | - Jesmine Lim
- Prozomix Ltd, Building 4, West End Ind. Estate, Haltwhistle, Northumberland, NE49 9HA, UK
| | - Simon Charnock
- Prozomix Ltd, Building 4, West End Ind. Estate, Haltwhistle, Northumberland, NE49 9HA, UK
| | - Florian Hollfelder
- Departament of Biochemistry, Cambridge University, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - J Eduardo González-Pastor
- Centro de Astrobiología (CAB), CSIC-INTA, Ctra de Torrejón a Ajalvir, Km 4, 28850, Torrejón de Ardoz, Spain
| | - José Berenguer
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain
- Instituto de Biología Molecular, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Aurelio Hidalgo
- Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC), Nicolás Cabrera 1, 28049, Madrid, Spain.
- Instituto de Biología Molecular, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain.
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain.
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2
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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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3
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Tamakoshi M, Hijikata A, Yura K, Oshima K, Toh H, Mitsuoka K, Oshima T, Bessho Y. Isolation and genomic analysis of a type IV pili-independent Thermus thermophilus phage, φMN1 from a Japanese hot spring. J GEN APPL MICROBIOL 2023; 69:117-124. [PMID: 37423744 DOI: 10.2323/jgam.2023.06.008] [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: 07/11/2023]
Abstract
A Thermus thermophilus lytic phage was isolated from a Japanese hot spring using a type IV pili-deficient strain as an indicator host, and designated as φMN1. Electron microscopic (EM) examination revealed that φMN1 had an icosahedral head and a contractile tail, suggesting that φMN1 belonged to Myoviridae. An EM analysis focused on φMN1 adsorption to the Thermus host cell showed that the receptor molecules for the phage were uniformly distributed on the outer surface of the cells. The circular double-stranded DNA of φMN1 was 76,659 base pairs in length, and the guanine and cytosine content was 61.8%. It was predicted to contain 99 open reading frames, and its putative distal tail fiber protein, which is essential for non-piliated host cell surface receptor recognition, was dissimilar in terms of sequence and length with its counterpart in the type IV pili-dependent φYS40. A phage proteomic tree revealed that φMN1 and φYS40 are in the same cluster, but many genes had low sequence similarities and some seemed to be derived from both mesophilic and thermophilic organisms. The gene organization suggested that φMN1 evolved from a non-Thermus phage through large-scale recombination events of the genes determining the host specificity, followed by gradual evolution by recombination of both the thermophilic and mesophilic DNAs assimilated by the host Thermus cells. This newly isolated phage will provide evolutionary insights into thermophilic phages.
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Affiliation(s)
- Masatada Tamakoshi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Atsushi Hijikata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- Graduate School of Advanced Science and Engineering, Waseda University
| | | | - Hidehiro Toh
- Advanced Genomics Center, National Institute of Genetics
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University
| | - Tairo Oshima
- Institute of Environmental Microbiology, Kyowa Kako Co., Ltd
| | - Yoshitaka Bessho
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- RIKEN SPring-8 Center, Harima Institute
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4
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Liu H, Kheirvari M, Tumban E. Potential Applications of Thermophilic Bacteriophages in One Health. Int J Mol Sci 2023; 24:8222. [PMID: 37175929 PMCID: PMC10179064 DOI: 10.3390/ijms24098222] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/26/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Bacteriophages have a wide range of applications such as combating antibiotic resistance, preventing food contamination for food safety, and as biomarkers to indirectly assess the quality of water. Additionally, bacteriophage components (endolysins and coat proteins) have a lot of applications in food processing, vaccine design, and the delivery of cargo to the body. Therefore, bacteriophages/components have a multitude of applications in human, plant/veterinary, and environmental health (One Health). Despite their versatility, bacteriophage/component use is mostly limited to temperatures within 4-40 °C. This limits their applications (e.g., in food processing conditions, pasteurization, and vaccine design). Advances in thermophilic bacteriophage research have uncovered novel thermophilic endolysins (e.g., ΦGVE2 amidase and MMPphg) that can be used in food processing and in veterinary medicine. The endolysins are thermostable at temperatures > 65 °C and have broad antimicrobial activities. In addition to thermophilic endolysins, enzymes (DNA polymerase and ligases) derived from thermophages have different applications in molecular biology/biotechnology: to generate DNA libraries and develop diagnostics for human and animal pathogens. Furthermore, coat proteins from thermophages are being explored to develop virus-like particle platforms with versatile applications in human and animal health. Overall, bacteriophages, especially those that are thermophilic, have a plethora of applications in One Health.
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Affiliation(s)
| | | | - Ebenezer Tumban
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
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5
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Agnello E, Pajak J, Liu X, Kelch BA. Conformational dynamics control assembly of an extremely long bacteriophage tail tube. J Biol Chem 2023; 299:103021. [PMID: 36791911 PMCID: PMC10034513 DOI: 10.1016/j.jbc.2023.103021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Tail tube assembly is an essential step in the lifecycle of long-tailed bacteriophages. Limited structural and biophysical information has impeded an understanding of assembly and stability of their long, flexible tail tubes. The hyperthermophilic phage P74-26 is particularly intriguing as it has the longest tail of any known virus (nearly 1 μm) and is the most thermostable known phage. Here, we use structures of the P74-26 tail tube along with an in vitro system for studying tube assembly kinetics to propose the first molecular model for the tail tube assembly of long-tailed phages. Our high-resolution cryo-EM structure provides insight into how the P74-26 phage assembles through flexible loops that fit into neighboring rings through tight "ball-and-socket"-like interactions. Guided by this structure, and in combination with mutational, light scattering, and molecular dynamics simulations data, we propose a model for the assembly of conserved tube-like structures across phage and other entities possessing tail tube-like proteins. We propose that formation of a full ring promotes the adoption of a tube elongation-competent conformation among the flexible loops and their corresponding sockets, which is further stabilized by an adjacent ring. Tail assembly is controlled by the cooperative interaction of dynamic intraring and interring contacts. Given the structural conservation among tail tube proteins and tail-like structures, our model can explain the mechanism of high-fidelity assembly of long, stable tubes.
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Affiliation(s)
- Emily Agnello
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester Massachusetts, USA
| | - Joshua Pajak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester Massachusetts, USA
| | - Xingchen Liu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester Massachusetts, USA
| | - Brian A Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester Massachusetts, USA.
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6
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Maina AN, Mwaura FB, Wagacha JM, Jumba M, Aziz RK, Nour El-Din HT. Phenotypic characterization of phage vB_vcM_Kuja. J Basic Microbiol 2023; 63:481-488. [PMID: 36670071 DOI: 10.1002/jobm.202200635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/07/2022] [Accepted: 01/08/2023] [Indexed: 01/22/2023]
Abstract
Bacteriophage therapy targeting the increasingly resistant Vibrio cholerae is highly needed. Hence, studying the phenotypic behavior of potential phages under different conditions is a prerequisite to delivering the phage in an active infective form. The objective of this study was to characterize phage VP4 (vB_vcM_Kuja), an environmental vibriophage isolated from River Kuja in Migori County, Kenya in 2015. The phenotypic characteristics of the phage were determined using a one-step growth curve, restriction digestion profile, pH, and temperature stability tests. The results revealed that the phage is stable through a wide range of temperatures (20-50°C) and maintains its plaque-forming ability at pH ranging from 6 to 12. The one-step growth curve showed a latent period falling between 40 and 60 min, while burst size ranged from 23 to 30 plaque-forming units/10 µl at the same host strain. The restriction digestion pattern using EcoRI, SalI, HindIII, and XhoI enzymes showed that HindIII could cut the phage genome. The phage DNA could not be restricted by the other three enzymes. The findings of this study can be used in future studies to determine phage-host interactions.
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Affiliation(s)
- Alice N Maina
- Department of Biology, University of Nairobi, Nairobi, Kenya
| | | | - John M Wagacha
- Department of Biology, University of Nairobi, Nairobi, Kenya
| | - Miriam Jumba
- Department of Biology, University of Nairobi, Nairobi, Kenya
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.,Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Hanzada T Nour El-Din
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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7
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Droubogiannis S, Pavlidi L, Tsertou MI, Kokkari C, Skliros D, Flemetakis E, Katharios P. Vibrio Phage Artemius, a Novel Phage Infecting Vibrio alginolyticus. Pathogens 2022; 11:pathogens11080848. [PMID: 36014969 PMCID: PMC9416449 DOI: 10.3390/pathogens11080848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 02/04/2023] Open
Abstract
Vibrio alginolyticus is an important pathogen of marine animals and has been the target of phage therapy applications in marine aquaculture for many years. Here, we report the isolation and partial characterization of a novel species of the Siphoviridae family, the Vibrio phage Artemius. The novel phage was species-specific and could only infect strains of V. alginolyticus. It could efficiently reduce the growth of the host bacterium at various multiplicities of infection as assessed by an in vitro lysis assay. It had a genome length of 43,349 base pairs. The complete genome has double-stranded DNA with a G + C content of 43.61%. In total, 57 ORFs were identified, of which 19 were assigned a predicted function. A genomic analysis indicated that Vibrio phage Artemius is lytic and does not harbor genes encoding toxins and antibiotic resistance determinants.
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Affiliation(s)
- Stavros Droubogiannis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology & Aquaculture, 71500 Heraklion, Greece; (S.D.); (L.P.); (M.I.T.); (C.K.)
- Department of Biology, School of Sciences and Engineering, University of Crete, 71500 Heraklion, Greece
| | - Lydia Pavlidi
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology & Aquaculture, 71500 Heraklion, Greece; (S.D.); (L.P.); (M.I.T.); (C.K.)
| | - Maria Ioanna Tsertou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology & Aquaculture, 71500 Heraklion, Greece; (S.D.); (L.P.); (M.I.T.); (C.K.)
| | - Constantina Kokkari
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology & Aquaculture, 71500 Heraklion, Greece; (S.D.); (L.P.); (M.I.T.); (C.K.)
| | - Dimitrios Skliros
- Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece; (D.S.); (E.F.)
| | - Emmanouil Flemetakis
- Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece; (D.S.); (E.F.)
| | - Pantelis Katharios
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology & Aquaculture, 71500 Heraklion, Greece; (S.D.); (L.P.); (M.I.T.); (C.K.)
- Correspondence:
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8
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Fackler JR, Dworjan M, Gazi KS, Grogan DW. Diversity of SIRV-like Viruses from a North American Population. Viruses 2022; 14:v14071439. [PMID: 35891419 PMCID: PMC9319562 DOI: 10.3390/v14071439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
A small subset of acidic hot springs sampled in Yellowstone National Park yielded rod-shaped viruses which lysed liquid host cultures and formed clear plaques on lawns of host cells. Three isolates chosen for detailed analysis were found to be genetically related to previously described isolates of the Sulfolobus islandicus rod-shaped virus (SIRV), but distinct from them and from each other. Functional stability of the new isolates was assessed in a series of inactivation experiments. UV-C radiation inactivated one of the isolates somewhat faster than bacteriophage λ, suggesting that encapsidation in the SIRV-like virion did not confer unusual protection of the DNA from UV damage. With respect to high temperature, the new isolates were extremely, but not equally, stable. Several chemical treatments were found to inactivate the virions and, in some cases, to reveal apparent differences in virion stability among the isolates. Screening a larger set of isolates identified greater variation of these stability properties but found few correlations among the resulting profiles. The majority of host cells infected by the new isolates were killed, but survivors exhibited heritable resistance, which could not be attributed to CRISPR spacer acquisition or the loss of the pilus-related genes identified by earlier studies. Virus-resistant host variants arose at high frequency and most were resistant to multiple viral strains; conversely, resistant host clones generated virus-sensitive variants, also at high frequency. Virus-resistant cells lacked the ability of virus-sensitive cells to bind virions in liquid suspensions. Rapid interconversion of sensitive and resistant forms of a host strain suggests the operation of a yet-unidentified mechanism that acts to allow both the lytic virus and its host to propagate in highly localized natural populations, whereas variation of virion-stability phenotypes among the new viral isolates suggests that multiple molecular features contribute to the biological durability of these viruses.
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Affiliation(s)
- Joseph R. Fackler
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Adaptive Phage Therapeutics, Gaithersburg, MD 20878, USA
| | - Michael Dworjan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
| | - Khaled S. Gazi
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Department of Biology, Faculty of Science and Arts in Almandaq, Al-Baha University, Almandaq 65756, Saudi Arabia
| | - Dennis W. Grogan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Correspondence:
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Ahlqvist J, Linares-Pastén JA, Håkansson M, Jasilionis A, Kwiatkowska-Semrau K, Friðjónsson ÓH, Kaczorowska AK, Dabrowski S, Ævarsson A, Hreggviðsson GÓ, Al-Karadaghi S, Kaczorowski T, Nordberg Karlsson E. Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6. Acta Crystallogr D Struct Biol 2022; 78:212-227. [PMID: 35102887 PMCID: PMC8805305 DOI: 10.1107/s2059798321012298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
This study describes the production, characterization and structure determination of a novel Holliday junction-resolving enzyme. The enzyme, termed Hjc_15-6, is encoded in the genome of phage Tth15-6, which infects Thermus thermophilus. Hjc_15-6 was heterologously produced in Escherichia coli and high yields of soluble and biologically active recombinant enzyme were obtained in both complex and defined media. Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA–Holliday junctions (Hjs). The crystal structure of Hjc_15-6 was determined to 2.5 Å resolution using the selenomethionine single-wavelength anomalous dispersion method. To our knowledge, this is the first crystal structure of an Hj-resolving enzyme originating from a bacteriophage that can be classified as an archaeal type of Hj-resolving enzyme. As such, it represents a new fold for Hj-resolving enzymes from phages. Characterization of the structure of Hjc_15-6 suggests that it may form a dimer, or even a homodimer of dimers, and activity studies show endonuclease activity towards Hjs. Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E–SD–EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages.
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10
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Sui B, Han L, Ren H, Liu W, Zhang C. A Novel Polyvalent Bacteriophage vB_EcoM_swi3 Infects Pathogenic Escherichia coli and Salmonella enteritidis. Front Microbiol 2021; 12:649673. [PMID: 34335489 PMCID: PMC8317433 DOI: 10.3389/fmicb.2021.649673] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/17/2021] [Indexed: 12/21/2022] Open
Abstract
A novel virulent bacteriophage vB_EcoM_swi3 (swi3), isolated from swine feces, lyzed 9% (6/65) of Escherichia coli and isolates 54% (39/72) of Salmonella enteritidis isolates, which were all clinically pathogenic multidrug-resistant strains. Morphological observation showed that phage swi3 belonged to the Myoviridae family with an icosahedral head (80 nm in diameter) and a contractile sheathed tail (120 nm in length). At the optimal multiplicity of infection of 1, the one-step growth analysis of swi3 showed a 25-min latent period with a burst size of 25-plaque-forming units (PFU)/infected cell. Phage swi3 remained stable both at pH 6.0–8.0 and at less than 50°C for at least 1 h. Genomic sequencing and bioinformatics analysis based on genomic sequences and the terminase large subunit showed that phage swi3 was a novel member that was most closely related to Salmonella phages and belonged to the Rosemountvirus genus. Phage swi3 harbored a 52-kb double-stranded DNA genome with 46.02% GC content. Seventy-two potential open reading frames were identified and annotated, only 15 of which had been assigned to functional genes. No gene associated with pathogenicity and virulence was identified. The effects of phage swi3 in treating pathologic E. coli infections in vivo were evaluated using a mouse model. The administration of a single intraperitoneal injection of swi3 (106 PFU) at 2 h after challenge with the E. coli strain (serotype K88) (108 colony-forming units) sufficiently protected all mice without toxic side effects. This finding highlighted that phage swi3 might be used as an effective antibacterial agent to prevent E. coli and S. enteritidis infection.
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Affiliation(s)
- Bingrui Sui
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Lili Han
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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11
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Viruses in Extreme Environments, Current Overview, and Biotechnological Potential. Viruses 2021; 13:v13010081. [PMID: 33430116 PMCID: PMC7826561 DOI: 10.3390/v13010081] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 12/27/2022] Open
Abstract
Virus research has advanced significantly since the discovery of the tobacco mosaic virus (TMV), the characterization of its infection mechanisms and the factors that determine their pathogenicity. However, most viral research has focused on pathogenic viruses to humans, animals and plants, which represent only a small fraction in the virosphere. As a result, the role of most viral genes, and the mechanisms of coevolution between mutualistic viruses, their host and their environment, beyond pathogenicity, remain poorly understood. This review focuses on general aspects of viruses that interact with extremophile organisms, characteristics and examples of mechanisms of adaptation. Finally, this review provides an overview on how knowledge of extremophile viruses sheds light on the application of new tools of relevant use in modern molecular biology, discussing their value in a biotechnological context.
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12
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Lopatina A, Medvedeva S, Artamonova D, Kolesnik M, Sitnik V, Ispolatov Y, Severinov K. Natural diversity of CRISPR spacers of Thermus: evidence of local spacer acquisition and global spacer exchange. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180092. [PMID: 30905291 PMCID: PMC6452258 DOI: 10.1098/rstb.2018.0092] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We investigated the diversity of CRISPR spacers of Thermus communities from two locations in Italy, two in Chile and one location in Russia. Among the five sampling sites, a total of more than 7200 unique spacers belonging to different CRISPR-Cas systems types and subtypes were identified. Most of these spacers are not found in CRISPR arrays of sequenced Thermus strains. Comparison of spacer sets revealed that samples within the same area (separated by few to hundreds of metres) have similar spacer sets, which appear to be largely stable at least over the course of several years. While at further distances (hundreds of kilometres and more) the similarity of spacer sets is decreased, there are still multiple common spacers in Thermus communities from different continents. The common spacers can be reconstructed in identical or similar CRISPR arrays, excluding their independent appearance and suggesting an extensive migration of thermophilic bacteria over long distances. Several new Thermus phages were isolated in the sampling sites. Mapping of spacers to bacteriophage sequences revealed examples of local acquisition of spacers from some phages and distinct patterns of targeting of phage genomes by different CRISPR-Cas systems. This article is part of a discussion meeting issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
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Affiliation(s)
- Anna Lopatina
- 1 Institute of Molecular Genetics, Russian Academy of Sciences , Moscow , Russia.,2 Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia.,7 Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Sofia Medvedeva
- 3 Skolkovo Institute of Science and Technology , Skolkovo , Russia.,4 Pasteur Institute , Paris , France
| | - Daria Artamonova
- 3 Skolkovo Institute of Science and Technology , Skolkovo , Russia
| | - Matvey Kolesnik
- 3 Skolkovo Institute of Science and Technology , Skolkovo , Russia
| | - Vasily Sitnik
- 3 Skolkovo Institute of Science and Technology , Skolkovo , Russia
| | - Yaroslav Ispolatov
- 5 Department of Physics, University of Santiago de Chile , Santiago , Chile
| | - Konstantin Severinov
- 1 Institute of Molecular Genetics, Russian Academy of Sciences , Moscow , Russia.,3 Skolkovo Institute of Science and Technology , Skolkovo , Russia.,6 Waksman Institute, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey , Piscataway, NJ , USA.,7 Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 76100 , Israel
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13
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A Novel Genus of Actinobacterial Tectiviridae. Viruses 2019; 11:v11121134. [PMID: 31817897 PMCID: PMC6950372 DOI: 10.3390/v11121134] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/31/2023] Open
Abstract
Streptomyces phages WheeHeim and Forthebois are two novel members of the Tectiviridae family. These phages were isolated on cultures of the plant pathogen Streptomyces scabiei, known for its worldwide economic impact on potato crops. Transmission electron microscopy showed viral particles with double-layered icosahedral capsids, and frequent instances of protruding nanotubes harboring a collar-like structure. Mass-spectrometry confirmed the presence of lipids in the virion, and serial purification of colonies from turbid plaques and immunity testing revealed that both phages are temperate. Streptomycesphages WheeHeim and Forthebois have linear dsDNA chromosomes (18,266 bp and 18,251 bp long, respectively) with the characteristic two-segment architecture of the Tectiviridae. Both genomes encode homologs of the canonical tectiviral proteins (major capsid protein, packaging ATPase and DNA polymerase), as well as PRD1-type virion-associated transglycosylase and membrane DNA delivery proteins. Comparative genomics and phylogenetic analyses firmly establish that these two phages, together with Rhodococcusphage Toil, form a new genus within the Tectiviridae, which we have tentatively named Deltatectivirus. The identification of a cohesive clade of Actinobacteria-infecting tectiviruses with conserved genome structure but with scant sequence similarity to members of other tectiviral genera confirms that the Tectiviridae are an ancient lineage infecting a broad range of bacterial hosts.
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14
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Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure. Nat Commun 2019; 10:4471. [PMID: 31578335 PMCID: PMC6775164 DOI: 10.1038/s41467-019-12341-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 08/31/2019] [Indexed: 12/21/2022] Open
Abstract
The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we use cryoelectron microscopy to determine the capsid structure of thermostable phage P74-26 to 2.8-Å resolution. We find P74-26 capsids exhibit an overall architecture very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T = 7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased with a larger, flatter major capsid protein. Given these results, we predict decreased icosahedral complexity (i.e. T ≤ 7) leads to a more stable capsid assembly. Viral capsids need to protect the genome against harsh environmental conditions and cope with high internal pressure from the packaged genome. Here, the authors determine the structure of the thermostable phage P74-26 capsid at 2.8-Å resolution and identify features underlying enhanced capsid capacity and structural stability.
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15
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A novel thermophilic Aeribacillus bacteriophage AP45 isolated from the Valley of Geysers, Kamchatka: genome analysis suggests the existence of a new genus within the Siphoviridae family. Extremophiles 2019; 23:599-612. [PMID: 31376001 DOI: 10.1007/s00792-019-01119-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/21/2019] [Indexed: 12/12/2022]
Abstract
A novel thermophilic bacteriophage AP45 and its host strain Aeribacillus sp. CEMTC656 were isolated from the Valley of Geysers, Kamchatka Peninsula, Russia. Bacteriophage AP45 was identified as a member of the Siphoviridae family by electron microscopy. It showed high thermostability and had a slow cycle of reproduction. The AP45 genome had 51,606 base pairs (bp) and contained 71 open reading frames (ORFs), 40 of them encoding proteins of predicted function. Genes encoding DNA and RNA polymerases were not identified, indicating that AP45 used host polymerases. Based on the ORF65 encoding putative endolysin, the recombinant protein rAP45Lys was developed and its peptidoglycan-hydrolyzing activity was demonstrated. The AP45 genome exhibited limited identity to other phage sequences; the highest identity, 36%, was with the genome of the thermophilic Geobacillus myovirus D6E. The majority of putative proteins encoded by the AP45 genome had higher similarity to proteins from bacteria belonging to the Bacillaceae family, than to bacteriophages. In addition, more than half of the putative ORFs in the AP45 genome were highly similar to prophage sequences of A. pallidus strain 8m3, which was isolated in north-east China. The AP45 phage and revealed prophages might be members of a new genus belonging to the Siphoviridae family.
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16
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Loderer C, Holmfeldt K, Lundin D. Non-host class II ribonucleotide reductase in Thermus viruses: sequence adaptation and host interaction. PeerJ 2019; 7:e6700. [PMID: 30993041 PMCID: PMC6459318 DOI: 10.7717/peerj.6700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/01/2019] [Indexed: 01/14/2023] Open
Abstract
Ribonucleotide reductases (RNR) are essential enzymes for all known life forms. Their current taxonomic distribution suggests extensive horizontal gene transfer e.g., by processes involving viruses. To improve our understanding of the underlying processes, we characterized a monomeric class II RNR (NrdJm) enzyme from a Thermus virus, a subclass not present in any sequenced Thermus spp. genome. Phylogenetic analysis revealed a distant origin of the nrdJm gene with the most closely related sequences found in mesophiles or moderate thermophiles from the Firmicutes phylum. GC-content, codon usage and the ratio of coding to non-coding substitutions (dN/dS) suggest extensive adaptation of the gene in the virus in terms of nucleotide composition and amino acid sequence. The NrdJm enzyme is a monomeric B12-dependent RNR with nucleoside triphosphate specificity. It exhibits a temperature optimum at 60–70 °C, which is in the range of the growth optimum of Thermus spp. Experiments in combination with the Thermus thermophilus thioredoxin system show that the enzyme is able to retrieve electrons from the host NADPH pool via host thioredoxin and thioredoxin reductases. This is different from other characterized viral RNRs such as T4 phage RNR, where a viral thioredoxin is present. We hence show that the monomeric class II RNR, present in Thermus viruses, was likely transferred from an organism phylogenetically distant from the one they were isolated from, and adapted to the new host in genetic signature and amino acids sequence.
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Affiliation(s)
- Christoph Loderer
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Karin Holmfeldt
- Centre for Ecology and Evolution in Microbial model Systems-EEMiS, Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial model Systems-EEMiS, Linnaeus University, Kalmar, Sweden.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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17
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Guajardo-Leiva S, Pedrós-Alió C, Salgado O, Pinto F, Díez B. Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs. Front Microbiol 2018; 9:2039. [PMID: 30233525 PMCID: PMC6129581 DOI: 10.3389/fmicb.2018.02039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/13/2018] [Indexed: 01/16/2023] Open
Abstract
Cyanophages are viruses with a wide distribution in aquatic ecosystems, that specifically infect Cyanobacteria. These viruses can be readily isolated from marine and fresh waters environments; however, their presence in cosmopolitan thermophilic phototrophic mats remains largely unknown. This study investigates the morphological diversity (TEM), taxonomic composition (metagenomics), and active infectivity (metatranscriptomics) of viral communities over a thermal gradient in hot spring phototrophic mats from Northern Patagonia (Chile). The mats were dominated (up to 53%) by cosmopolitan thermophilic filamentous true-branching cyanobacteria from the genus Mastigocladus, the associated viral community was predominantly composed of Caudovirales (70%), with most of the active infections driven by cyanophages (up to 90% of Caudovirales transcripts). Metagenomic assembly lead to the first full genome description of a T7-like Thermophilic Cyanophage recovered from a hot spring (Porcelana Hot Spring, Chile), with a temperature of 58°C (TC-CHP58). This could potentially represent a world-wide thermophilic lineage of podoviruses that infect cyanobacteria. In the hot spring, TC-CHP58 was active over a temperature gradient from 48 to 66°C, showing a high population variability represented by 1979 single nucleotide variants (SNVs). TC-CHP58 was associated to the Mastigocladus spp. by CRISPR spacers. Marked differences in metagenomic CRISPR loci number and spacers diversity, as well as SNVs, in the TC-CHP58 proto-spacers at different temperatures, reinforce the theory of co-evolution between natural virus populations and cyanobacterial hosts. Considering the importance of cyanobacteria in hot spring biogeochemical cycles, the description of this new cyanopodovirus lineage may have global implications for the functioning of these extreme ecosystems.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Pedrós-Alió
- Programa de Biología de Sistemas, Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Oscar Salgado
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fabián Pinto
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center for Climate and Resilience Research, Santiago, Chile
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18
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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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19
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Stone NP, Hilbert BJ, Hidalgo D, Halloran KT, Lee J, Sontheimer EJ, Kelch BA. A Hyperthermophilic Phage Decoration Protein Suggests Common Evolutionary Origin with Herpesvirus Triplex Proteins and an Anti-CRISPR Protein. Structure 2018; 26:936-947.e3. [PMID: 29779790 PMCID: PMC6277972 DOI: 10.1016/j.str.2018.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/16/2018] [Accepted: 04/10/2018] [Indexed: 11/18/2022]
Abstract
Virus capsids are protein shells that protect the viral genome from environmental assaults, while maintaining the high internal pressure of the tightly packaged genome. To elucidate how capsids maintain stability under harsh conditions, we investigated the capsid components of the hyperthermophilic phage P74-26. We determined the structure of capsid protein gp87 and show that it has the same fold as decoration proteins in many other phages, despite lacking significant sequence homology. We also find that gp87 is significantly more stable than mesophilic homologs. Our analysis of the gp87 structure reveals that the core "β tulip" domain is conserved in trimeric capsid components across numerous double-stranded DNA viruses, including Herpesviruses. Moreover, this β barrel domain is found in anti-CRISPR protein AcrIIC1, suggesting a mechanism for the evolution of this Cas9 inhibitor. Our work illustrates the principles for increased stability of gp87, and extends the evolutionary reach of the β tulip domain.
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Affiliation(s)
- Nicholas P Stone
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Brendan J Hilbert
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Daniel Hidalgo
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Kevin T Halloran
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jooyoung Lee
- RNA Therapeutics Institute, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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20
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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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21
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Berliner AJ, Mochizuki T, Stedman KM. Astrovirology: Viruses at Large in the Universe. ASTROBIOLOGY 2018; 18:207-223. [PMID: 29319335 DOI: 10.1089/ast.2017.1649] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viruses are the most abundant biological entities on modern Earth. They are highly diverse both in structure and genomic sequence, play critical roles in evolution, strongly influence terran biogeochemistry, and are believed to have played important roles in the origin and evolution of life. However, there is yet very little focus on viruses in astrobiology. Viruses arguably have coexisted with cellular life-forms since the earliest stages of life, may have been directly involved therein, and have profoundly influenced cellular evolution. Viruses are the only entities on modern Earth to use either RNA or DNA in both single- and double-stranded forms for their genetic material and thus may provide a model for the putative RNA-protein world. With this review, we hope to inspire integration of virus research into astrobiology and also point out pressing unanswered questions in astrovirology, particularly regarding the detection of virus biosignatures and whether viruses could be spread extraterrestrially. We present basic virology principles, an inclusive definition of viruses, review current virology research pertinent to astrobiology, and propose ideas for future astrovirology research foci. Key Words: Astrobiology-Virology-Biosignatures-Origin of life-Roadmap. Astrobiology 18, 207-223.
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Affiliation(s)
| | | | - Kenneth M Stedman
- 3 Center for Life in Extreme Environments and Biology Department, Portland State University , Oregon, USA
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22
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Fibre diffraction studies of biological macromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 127:43-87. [DOI: 10.1016/j.pbiomolbio.2017.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/21/2017] [Accepted: 04/05/2017] [Indexed: 12/27/2022]
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23
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Tripathi C, Mishra H, Khurana H, Dwivedi V, Kamra K, Negi RK, Lal R. Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes. Front Microbiol 2017; 8:1410. [PMID: 28798737 PMCID: PMC5529391 DOI: 10.3389/fmicb.2017.01410] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/11/2017] [Indexed: 01/27/2023] Open
Abstract
Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) comprises a chromosome (1.87 Mbp) and a plasmid (143 Kbp), designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%). We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI), conserved marker genes (31 and 400), pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5) by recruiting raw metagenomic data (from the same niche) against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.
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Affiliation(s)
- Charu Tripathi
- Department of Zoology, University of DelhiNew Delhi, India
| | | | - Himani Khurana
- Department of Zoology, University of DelhiNew Delhi, India
| | | | - Komal Kamra
- Ciliate Biology Laboratory, Sri Guru Tegh Bahadar Khalsa College, University of DelhiNew Delhi, India
| | - Ram K Negi
- Department of Zoology, University of DelhiNew Delhi, India
| | - Rup Lal
- Department of Zoology, University of DelhiNew Delhi, India
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24
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Gao Y, Liu Q, Wang M, Zhao G, Jiang Y, Malin G, Gong Z, Meng X, Liu Z, Lin T, Li Y, Shao H. Characterization and Genome Sequence of Marine Alteromonas gracilis Phage PB15 Isolated from the Yellow Sea, China. Curr Microbiol 2017; 74:821-826. [PMID: 28424938 DOI: 10.1007/s00284-017-1251-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/11/2017] [Indexed: 10/19/2022]
Abstract
A novel marine Alteromonas gracilis siphovirus, phage PB15, was isolated from the surface water of the Yellow Sea in August 2015. It has a head diameter of 58 ± 5 nm head and a contractile tail approximately 105 ± 10 nm in length, and overall, the morphology suggests that PB15 belongs to the family Siphoviridae. PB15 phage is stable at over the temperature range 0-60 °C. The best MOI of these phage was 0.1, and infectivity decreased above 60 °C. The results suggest that phage is stable at pH value ranging between 3.0 and 11.0. Chloroform test shows that PB15 is not a lipid-containing phage. A one-step growth curve with a strain of A. gracilis gave a latent period of 16 min and rise period of 24 min and burst size of 60 PFU/cell. Genomic analysis of PB15 reveals a genome size of 37,333 bp with 45.52% G+C content, and 61 ORFs. ORF sequences accounted for 30.36% of the genome sequence. There is no obvious similarity between PB15 and other known phages by genomic comparison using the BLASTN tool in the NCBI database.
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Affiliation(s)
- Yu Gao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Qian Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China. .,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003, China.
| | - Guihua Zhao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China. .,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003, China.
| | - Gill Malin
- Centre for Ocean and Atmospheric Sciences, School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Zheng Gong
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xue Meng
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Zhaoyang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Tongtong Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yutong Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
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25
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Hilbert BJ, Hayes JA, Stone NP, Xu RG, Kelch BA. The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain. Nucleic Acids Res 2017; 45:3591-3605. [PMID: 28082398 PMCID: PMC5389665 DOI: 10.1093/nar/gkw1356] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/05/2017] [Indexed: 01/07/2023] Open
Abstract
Many viruses use a powerful terminase motor to pump their genome inside an empty procapsid shell during virus maturation. The large terminase (TerL) protein contains both enzymatic activities necessary for packaging in such viruses: the adenosine triphosphatase (ATPase) that powers DNA translocation and an endonuclease that cleaves the concatemeric genome at both initiation and completion of genome packaging. However, how TerL binds DNA during translocation and cleavage remains mysterious. Here we investigate DNA binding and cleavage using TerL from the thermophilic phage P74-26. We report the structure of the P74-26 TerL nuclease domain, which allows us to model DNA binding in the nuclease active site. We screened a large panel of TerL variants for defects in binding and DNA cleavage, revealing that the ATPase domain is the primary site for DNA binding, and is required for nuclease activity. The nuclease domain is dispensable for DNA binding but residues lining the active site guide DNA for cleavage. Kinetic analysis of DNA cleavage suggests flexible tethering of the nuclease domains during DNA cleavage. We propose that interactions with the procapsid during DNA translocation conformationally restrict the nuclease domain, inhibiting cleavage; TerL release from the capsid upon completion of packaging unlocks the nuclease domains to cleave DNA.
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Affiliation(s)
- Brendan J. Hilbert
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Janelle A. Hayes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nicholas P. Stone
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Rui-Gang Xu
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Brian A. Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA,To whom correspondence should be addressed. Tel: +1 508 856 8322; Fax: +1 508 856 6464;
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Demina TA, Pietilä MK, Svirskaitė J, Ravantti JJ, Atanasova NS, Bamford DH, Oksanen HM. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae. Viruses 2017; 9:v9020032. [PMID: 28218714 PMCID: PMC5332951 DOI: 10.3390/v9020032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 01/10/2017] [Accepted: 02/13/2017] [Indexed: 11/16/2022] Open
Abstract
Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1), has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV) in 2016.
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Affiliation(s)
- Tatiana A Demina
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Maija K Pietilä
- Department of Food and Environmental Sciences, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Julija Svirskaitė
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Janne J Ravantti
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Nina S Atanasova
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
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Rapid screening of waterborne pathogens using phage-mediated separation coupled with real-time PCR detection. Anal Bioanal Chem 2016; 408:4169-78. [PMID: 27071764 DOI: 10.1007/s00216-016-9511-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/14/2016] [Accepted: 03/22/2016] [Indexed: 12/26/2022]
Abstract
Escherichia coli O157:H7 is a ubiquitous pathogen which can be linked to foodborne outbreaks worldwide. In addition to the significant illnesses, hospitalizations, and deaths resulting from the outbreaks, there can be severe economic consequences to farmers, food manufacturers, and municipalities. A rapid detection assay which can validate sanitation and water quality would prove beneficial to these situations. Here, we report a novel bacteriophage-mediated detection of E. coli O157:H7 which utilizes the specific recognition between phages and their host cell as well as the natural lysis component of the infection cycle for DNA release. Carboxylic acid-functionalized magnetic beads were conjugated with bacteriophage and used to separate and concentrate E. coli O157:H7. The effects of bead incubation time, salinity, pH, and temperature on the bio-magnetic separation were investigated and compared to an antibody-based counterpart. The conditions of 0.01 M PBS, pH 7.0, and 20 min of reaction at 37 °C were found to be optimal. The capture efficiency of the coupled assay was approximately 20 % higher than that of antibody-based separation under extreme conditions. The resulting bead-phage-bacteria complexes were quantitatively detected by real-time PCR (qPCR). Our results demonstrated that the use of phage-based magnetic separation coupled with qPCR improved the sensitivity of detection by 2 orders of magnitude compared that without phage-based pre-concentration. Specificity and selectivity of the assay system was evaluated, and no cross-reactivity occurred when Salmonella typhimurium, Staphylococcus aureus, and Pseudomonas aeruginosa were tested. The total assay time was less than 2 h.
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28
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Nagayoshi Y, Kumagae K, Mori K, Tashiro K, Nakamura A, Fujino Y, Hiromasa Y, Iwamoto T, Kuhara S, Ohshima T, Doi K. Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage φOH3 Which Infects Thermus thermophilus HB8. Front Microbiol 2016; 7:50. [PMID: 26941711 PMCID: PMC4763002 DOI: 10.3389/fmicb.2016.00050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/12/2016] [Indexed: 12/11/2022] Open
Abstract
A filamentous bacteriophage, φOH3, was isolated from hot spring sediment in Obama hot spring in Japan with the hyperthermophilic bacterium Thermus thermophilus HB8 as its host. Phage φOH3, which was classified into the Inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φOH3 was stable at temperatures ranging from 70 to 90°C and at pHs ranging from 6 to 9. A one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, followed by intracellular virus particle production during the subsequent 40 min. The released virion number of φOH3 was 109. During the latent period, both single stranded DNA (ssDNA) and the replicative form (RF) of phage DNA were multiplied from min 40 onward. During the release period, the copy numbers of both ssDNA and RF DNA increased sharply. The size of the φOH3 genome is 5688 bp, and eight putative open reading frames (ORFs) were annotated. These ORFs were encoded on the plus strand of RF DNA and showed no significant homology with any known phage genes, except ORF 5, which showed 60% identity with the gene VIII product of the Thermus filamentous phage PH75. All the ORFs were similar to predicted genes annotated in the Thermus aquaticus Y51MC23 and Meiothermus timidus DSM 17022 genomes at the amino acid sequence level. This is the first report of the whole genome structure and DNA multiplication of a filamentous T. thermophilus phage within its host cell.
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Affiliation(s)
- Yuko Nagayoshi
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
| | - Kenta Kumagae
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
| | - Kazuki Mori
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Kosuke Tashiro
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Ayano Nakamura
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
| | - Yasuhiro Fujino
- Faculty of Arts and Science, Kyushu University Fukuoka, Japan
| | - Yasuaki Hiromasa
- Faculty of Agriculture, Attached Promotive Center for International Education and Research of Agriculture, Kyushu University Fukuoka, Japan
| | - Takeo Iwamoto
- Core Research Facilities, Research Center for Medical Sciences, Jikei University School of Medicine Tokyo, Japan
| | - Satoru Kuhara
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology Osaka, Japan
| | - Katsumi Doi
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
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Krupovic M, Dutilh BE, Adriaenssens EM, Wittmann J, Vogensen FK, Sullivan MB, Rumnieks J, Prangishvili D, Lavigne R, Kropinski AM, Klumpp J, Gillis A, Enault F, Edwards RA, Duffy S, Clokie MRC, Barylski J, Ackermann HW, Kuhn JH. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Arch Virol 2016; 161:1095-9. [PMID: 26733293 DOI: 10.1007/s00705-015-2728-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 12/12/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Mart Krupovic
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University, Medical Centre, Nijmegen, The Netherlands
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Evelien M Adriaenssens
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Johannes Wittmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Finn K Vogensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Mathew B Sullivan
- Department of Microbiology, Ohio State University, 496 W 12th Ave, Columbus, OH, 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, 470 Hitchcock Hall, 2070 Neil Avenue, Columbus, OH, 43210, USA
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV, 1067, Latvia
| | - David Prangishvili
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21-box 2462, 3001, Leuven, Belgium
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biology, and Pathobiology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, Croix du Sud 2, L7.05.12, 1348, Louvain-la-Neuve, Belgium
| | - Francois Enault
- Clermont Université, Université Blaise Pascal, Laboratoire "Microorganismes: Génome et Environnement", Clermont-Ferrand, France
- CNRS UMR 6023, LMGE, Aubière, France
| | - Rob A Edwards
- Bioinformatics Lab, Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-7720, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Rd, New Brunswick, NJ, 08901, USA
| | - Martha R C Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester, LE1 9HN, UK
| | - Jakub Barylski
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
| | - Hans-Wolfgang Ackermann
- L'Institut de biologie intégrative et des systems, Université Laval, Pavillon Charles-Eugène-Marchand, 1030, avenue de la Médecine, Quebec, QC, G1V 0A6, Canada
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
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30
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Brumm PJ, Monsma S, Keough B, Jasinovica S, Ferguson E, Schoenfeld T, Lodes M, Mead DA. Complete Genome Sequence of Thermus aquaticus Y51MC23. PLoS One 2015; 10:e0138674. [PMID: 26465632 PMCID: PMC4605624 DOI: 10.1371/journal.pone.0138674] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/02/2015] [Indexed: 12/29/2022] Open
Abstract
Thermus aquaticus Y51MC23 was isolated from a boiling spring in the Lower Geyser Basin of Yellowstone National Park. Remarkably, this T. aquaticus strain is able to grow anaerobically and produces multiple morphological forms. Y51MC23 is a Gram-negative, rod-shaped organism that grows well between 50°C and 80°C with maximum growth rate at 65°C to 70°C. Growth studies suggest that Y51MC23 primarily scavenges protein from the environment, supported by the high number of secreted and intracellular proteases and peptidases as well as transporter systems for amino acids and peptides. The genome was assembled de novo using a 350 bp fragment library (paired end sequencing) and an 8 kb long span mate pair library. A closed and finished genome was obtained consisting of a single chromosome of 2.15 Mb and four plasmids of 11, 14, 70, and 79 kb. Unlike other Thermus species, functions usually found on megaplasmids were identified on the chromosome. The Y51MC23 genome contains two full and two partial prophage as well as numerous CRISPR loci. The high identity and synteny between Y51MC23 prophage 2 and that of Thermus sp. 2.9 is interesting, given the 8,800 km separation of the two hot springs from which they were isolated. The anaerobic lifestyle of Y51MC23 is complex, with multiple morphologies present in cultures. The use of fluorescence microscopy reveals new details about these unusual morphological features, including the presence of multiple types of large and small spheres, often forming a confluent layer of spheres. Many of the spheres appear to be formed not from cell envelope or outer membrane components as previously believed, but from a remodeled peptidoglycan cell wall. These complex morphological forms may serve multiple functions in the survival of the organism, including food and nucleic acid storage as well as colony attachment and organization.
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Affiliation(s)
- Phillip J. Brumm
- C5-6 Technologies LLC, Fitchburg, Wisconsin, United States of America
- * E-mail:
| | - Scott Monsma
- Lucigen Corporation, Middleton, Wisconsin, United States of America
| | - Brendan Keough
- Lucigen Corporation, Middleton, Wisconsin, United States of America
| | | | - Erin Ferguson
- Lucigen Corporation, Middleton, Wisconsin, United States of America
| | | | - Michael Lodes
- Lucigen Corporation, Middleton, Wisconsin, United States of America
| | - David A. Mead
- Lucigen Corporation, Middleton, Wisconsin, United States of America
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31
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Structure and mechanism of the ATPase that powers viral genome packaging. Proc Natl Acad Sci U S A 2015; 112:E3792-9. [PMID: 26150523 DOI: 10.1073/pnas.1506951112] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many viruses package their genomes into procapsids using an ATPase machine that is among the most powerful known biological motors. However, how this motor couples ATP hydrolysis to DNA translocation is still unknown. Here, we introduce a model system with unique properties for studying motor structure and mechanism. We describe crystal structures of the packaging motor ATPase domain that exhibit nucleotide-dependent conformational changes involving a large rotation of an entire subdomain. We also identify the arginine finger residue that catalyzes ATP hydrolysis in a neighboring motor subunit, illustrating that previous models for motor structure need revision. Our findings allow us to derive a structural model for the motor ring, which we validate using small-angle X-ray scattering and comparisons with previously published data. We illustrate the model's predictive power by identifying the motor's DNA-binding and assembly motifs. Finally, we integrate our results to propose a mechanistic model for DNA translocation by this molecular machine.
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32
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The Minor Capsid Protein VP11 of Thermophilic Bacteriophage P23-77 Facilitates Virus Assembly by Using Lipid-Protein Interactions. J Virol 2015; 89:7593-603. [PMID: 25972558 DOI: 10.1128/jvi.00262-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/05/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Thermus thermophilus bacteriophage P23-77 is the type member of a new virus family of icosahedral, tailless, inner-membrane-containing double-stranded DNA (dsDNA) viruses infecting thermophilic bacteria and halophilic archaea. The viruses have a unique capsid architecture consisting of two major capsid proteins assembled in various building blocks. We analyzed the function of the minor capsid protein VP11, which is the third known capsid component in bacteriophage P23-77. Our findings show that VP11 is a dynamically elongated dimer with a predominantly α-helical secondary structure and high thermal stability. The high proportion of basic amino acids in the protein enables electrostatic interaction with negatively charged molecules, including nucleic acid and large unilamellar lipid vesicles (LUVs). The plausible biological function of VP11 is elucidated by demonstrating the interactions of VP11 with Thermus-derived LUVs and with the major capsid proteins by means of the dynamic-light-scattering technique. In particular, the major capsid protein VP17 was able to link VP11-complexed LUVs into larger particles, whereas the other P23-77 major capsid protein, VP16, was unable to link VP11-comlexed LUVs. Our results rule out a previously suggested penton function for VP11. Instead, the electrostatic membrane association of VP11 triggers the binding of the major capsid protein VP17, thus facilitating a controlled incorporation of the two different major protein species into the assembling capsid. IMPORTANCE The study of thermophilic viruses with inner membranes provides valuable insights into the mechanisms used for stabilization and assembly of protein-lipid systems at high temperatures. Our results reveal a novel way by which an internal membrane and outer capsid shell are linked in a virus that uses two different major protein species for capsid assembly. We show that a positive protein charge is important in order to form electrostatic interactions with the lipid surface, thereby facilitating the incorporation of other capsid proteins on the membrane surface. This implies an alternative function for basic proteins present in the virions of other lipid-containing thermophilic viruses, whose proposed role in genome packaging is based on their capability to bind DNA. The unique minor capsid protein of bacteriophage P23-77 resembles in its characteristics the scaffolding proteins of tailed phages, though it constitutes a substantial part of the mature virion.
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33
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Atanasova NS, Senčilo A, Pietilä MK, Roine E, Oksanen HM, Bamford DH. Comparison of lipid-containing bacterial and archaeal viruses. Adv Virus Res 2015; 92:1-61. [PMID: 25701885 DOI: 10.1016/bs.aivir.2014.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Lipid-containing bacteriophages were discovered late and considered to be rare. After further phage isolations and the establishment of the domain Archaea, several new prokaryotic viruses with lipids were observed. Consequently, the presence of lipids in prokaryotic viruses is reasonably common. The wealth of information about how prokaryotic viruses use their lipids comes from a few well-studied model viruses (PM2, PRD1, and ϕ6). These bacteriophages derive their lipid membranes selectively from the host during the virion assembly process which, in the case of PM2 and PRD1, culminates in the formation of protein capsid with an inner membrane, and for ϕ6 an outer envelope. Several inner membrane-containing viruses have been described for archaea, and their lipid acquisition models are reminiscent to those of PM2 and PRD1. Unselective acquisition of lipids has been observed for bacterial mycoplasmaviruses and archaeal pleolipoviruses, which resemble each other by size, morphology, and life style. In addition to these shared morphotypes of bacterial and archaeal viruses, archaea are infected by viruses with unique morphotypes, such as lemon-shaped, helical, and globular ones. It appears that structurally related viruses may or may not have a lipid component in the virion, suggesting that the significance of viral lipids might be to provide viruses extended means to interact with the host cell.
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Affiliation(s)
- Nina S Atanasova
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ana Senčilo
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maija K Pietilä
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Elina Roine
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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34
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Gillis A, Mahillon J. Phages preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: past, present and future. Viruses 2014; 6:2623-72. [PMID: 25010767 PMCID: PMC4113786 DOI: 10.3390/v6072623] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/19/2014] [Accepted: 06/18/2014] [Indexed: 01/18/2023] Open
Abstract
Many bacteriophages (phages) have been widely studied due to their major role in virulence evolution of bacterial pathogens. However, less attention has been paid to phages preying on bacteria from the Bacillus cereus group and their contribution to the bacterial genetic pool has been disregarded. Therefore, this review brings together the main information for the B. cereus group phages, from their discovery to their modern biotechnological applications. A special focus is given to phages infecting Bacillus anthracis, B. cereus and Bacillus thuringiensis. These phages belong to the Myoviridae, Siphoviridae, Podoviridae and Tectiviridae families. For the sake of clarity, several phage categories have been made according to significant characteristics such as lifestyles and lysogenic states. The main categories comprise the transducing phages, phages with a chromosomal or plasmidial prophage state, γ-like phages and jumbo-phages. The current genomic characterization of some of these phages is also addressed throughout this work and some promising applications are discussed here.
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Affiliation(s)
- Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, Croix du Sud 2, L7.05.12, B-1348 Louvain-la-Neuve, Belgium.
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, Croix du Sud 2, L7.05.12, B-1348 Louvain-la-Neuve, Belgium.
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35
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Severinov K, Minakhin L, Sekine SI, Lopatina A, Yokoyama S. Molecular basis of RNA polymerase promoter specificity switch revealed through studies of Thermus bacteriophage transcription regulator. BACTERIOPHAGE 2014; 4:e29399. [PMID: 25105059 PMCID: PMC4124052 DOI: 10.4161/bact.29399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/29/2014] [Accepted: 05/29/2014] [Indexed: 12/12/2022]
Abstract
Transcription initiation is the central point of gene expression regulation. Understanding of molecular mechanism of transcription regulation requires, ultimately, the structural understanding of consequences of transcription factors binding to DNA-dependent RNA polymerase (RNAP), the enzyme of transcription. We recently determined a structure of a complex between transcription factor gp39 encoded by a Thermus bacteriophage and Thermus RNAP holoenzyme. In this addendum to the original publication, we highlight structural insights that explain the ability of gp39 to act as an RNAP specificity switch which inhibits transcription initiation from a major class of bacterial promoters, while allowing transcription from a minor promoter class to continue.
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Affiliation(s)
- Konstantin Severinov
- Waksman Institute; Rutgers; The State University of New Jersey; Piscataway, NJ USA ; St. Petersburg Polytechnical State University; St. Petersburg, Russia ; Skolkovo Institute of Science and Technology; Skolkovo, Russia
| | - Leonid Minakhin
- Waksman Institute; Rutgers; The State University of New Jersey; Piscataway, NJ USA
| | - Shun-Ichi Sekine
- RIKEN Systems and Structural Biology Center; Tsurumi-ku, Yokohama Japan ; Division of Structural and Synthetic Biology; RIKEN Center for Life Science Technologies; Tsurumi-ku, Yokohama Japan
| | - Anna Lopatina
- St. Petersburg Polytechnical State University; St. Petersburg, Russia ; Institutes of Gene Biology and Molecular Genetics; Russian Academy of Sciences; Moscow, Russia
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center; Tsurumi-ku, Yokohama Japan ; RIKEN Structural Biology Laboratory; Tsurumi-ku, Yokohama Japan
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36
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Marvin DA, Symmons MF, Straus SK. Structure and assembly of filamentous bacteriophages. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:80-122. [PMID: 24582831 DOI: 10.1016/j.pbiomolbio.2014.02.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/09/2014] [Indexed: 12/24/2022]
Abstract
Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of "minor" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.
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Affiliation(s)
- D A Marvin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - M F Symmons
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - S K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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Pawlowski A, Rissanen I, Bamford JKH, Krupovic M, Jalasvuori M. Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae. Arch Virol 2014; 159:1541-54. [PMID: 24395078 DOI: 10.1007/s00705-013-1970-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/20/2013] [Indexed: 11/30/2022]
Abstract
A new family of viruses named Sphaerolipoviridae has been proposed recently. It comprises icosahedral, tailless haloarchaeal viruses with an internal lipid membrane located between the protein capsid and the dsDNA genome. The proposed family Sphaerolipoviridae was divided into two genera: Alphasphaerolipovirus, including Haloarcula hispanica viruses SH1, PH1 and HHIV-2, and Betasphaerolipovirus, including Natrinema virus SNJ1. Here, we propose to expand the family Sphaerolipoviridae to include a group of bacteriophages infecting extreme thermophilic Thermus thermophilus and sharing a number of structural and genomic properties with archaeal sphaerolipoviruses. This new group comprises two members, lytic phage P23-77 and temperate phage IN93, as well as putative members P23-72 and P23-65H. In addition, several related proviruses have been discovered as integrated elements in bacterial genomes of the families Thermus and Meiothermus. Morphology of the virus particles and the overall capsid architecture of these bacteriophages resembles that of archaeal members of the Sphaerolipoviridae, including an unusual capsid arrangement in a T = 28 dextro lattice. Alpha- and betasphaerolipoviruses share with P23-77-like bacteriophages a conserved block of core genes that encode a putative genome-packaging ATPase and the two major capsid proteins (MCPs). The recently determined X-ray structure of the small and large MCPs of P23-77 revealed a single beta-barrel (jelly-roll) fold that is superimposable with the cryo-EM density maps of the SH1 capsomers. Given the common features of these viruses, we propose to include the so far unclassified P23-77-like bacteriophages into a new genus, "Gammasphaerolipovirus", within the family Sphaerolipoviridae.
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Affiliation(s)
- Alice Pawlowski
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, 40014, Jyväskylä, Finland
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Hjorleifsdottir S, Aevarsson A, Hreggvidsson GO, Fridjonsson OH, Kristjansson JK. Isolation, growth and genome of the Rhodothermus RM378 thermophilic bacteriophage. Extremophiles 2013; 18:261-70. [PMID: 24318108 DOI: 10.1007/s00792-013-0613-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 11/21/2013] [Indexed: 01/04/2023]
Abstract
Several bacteriophages that infect different strains of the thermophilic bacterium Rhodothermus marinus were isolated and their infection pattern was studied. One phage, named RM378 was cultivated and characterized. The RM378 genome was also sequenced and analyzed. The phage was grouped as a member of the Myoviridae family with A2 morphology. It had a moderately elongated head, with dimensions of 85 and 95 nm between opposite apices and a 150 nm long tail, attached with a connector to the head. RM378 showed a virulent behavior that followed a lytic cycle of infection. It routinely gave lysates with 10(11) pfu/ml, and sometimes reached titers as high as 10(13) pfu/ml. The titer remained stable up to 65 °C but the phage lost viability when incubated at higher temperatures. Heating for 30 min at 96 °C lowered the titer by 10(4). The RM378 genome consisted of ds DNA of 129.908 bp with a GC ratio of 42.0% and contained about 120 ORFs. A few structural proteins, such as the major head protein corresponding to the gp23 in T4, could be identified. Only 29 gene products as probable homologs to other proteins of known function could be predicted, with most showing only low similarity to known proteins in other bacteriophages. These and other studies based on sequence analysis of a large number of phage genomes showed RM378 to be distantly related to all other known T4-like phages.
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Peng X, Xu H, Jones B, Chen S, Zhou H. Silicified virus-like nanoparticles in an extreme thermal environment: implications for the preservation of viruses in the geological record. GEOBIOLOGY 2013; 11:511-526. [PMID: 24102946 DOI: 10.1111/gbi.12052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/20/2013] [Indexed: 06/02/2023]
Abstract
Biofilms that grow around Gumingquan hot spring (T = 71 °C, pH = 9.2) in the Rehai geothermal area, Tengchong, China, are formed of various cyanobacteria, Firmicutes, Aquificae, Thermodesulfobacteria, Desulfurococcales, and Thermoproteales. Silicified virus-like nanoparticles, 40-200 nm in diameter, are common inside the microbial cells and the extracellular polymeric substances around the cells. These nanoparticles, which are formed of a core encased by a silica cortex, are morphologically akin to known viruses and directly comparable to silicified virus-like particles that were produced in biofilms cultured in the laboratory. The information obtained from examination of the natural and laboratory-produced samples suggests that viruses can be preserved by silicification, especially while they are still encased in their host cells. These results expand our views of virus-host mineral interaction in extreme thermal environments and imply that viruses can be potentially preserved and identified in the geological record.
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Affiliation(s)
- X Peng
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China; Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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Yu YP, Gong T, Jost G, Liu WH, Ye DZ, Luo ZH. Isolation and characterization of five lytic bacteriophages infecting aVibriostrain closely related toVibrio owensii. FEMS Microbiol Lett 2013; 348:112-9. [DOI: 10.1111/1574-6968.12277] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 01/26/2023] Open
Affiliation(s)
- Yan-Ping Yu
- Key Laboratory of Marine Biogenetic Resources; Third Institute of Oceanography; State Oceanic Administration; Xiamen China
- Marine Biology Institute; Shantou University; Shantou China
| | - Ting Gong
- Key Laboratory of Marine Biogenetic Resources; Third Institute of Oceanography; State Oceanic Administration; Xiamen China
| | - Günter Jost
- Leibniz Institute for Baltic Sea Research Warnemünde; Rostock Germany
| | - Wen-Hua Liu
- Marine Biology Institute; Shantou University; Shantou China
| | - De-Zan Ye
- Key Laboratory of Marine Biogenetic Resources; Third Institute of Oceanography; State Oceanic Administration; Xiamen China
| | - Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources; Third Institute of Oceanography; State Oceanic Administration; Xiamen China
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van Wolferen M, Ajon M, Driessen AJM, Albers SV. How hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions. Extremophiles 2013; 17:545-63. [PMID: 23712907 DOI: 10.1007/s00792-013-0552-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/12/2013] [Indexed: 01/24/2023]
Abstract
Transfer of DNA has been shown to be involved in genome evolution. In particular with respect to the adaptation of bacterial species to high temperatures, DNA transfer between the domains of bacteria and archaea seems to have played a major role. In addition, DNA exchange between similar species likely plays a role in repair of DNA via homologous recombination, a process that is crucial under DNA damaging conditions such as high temperatures. Several mechanisms for the transfer of DNA have been described in prokaryotes, emphasizing its general importance. However, until recently, not much was known about this process in prokaryotes growing in highly thermophilic environments. This review describes the different mechanisms of DNA transfer in hyperthermophiles, and how this may contribute to the survival and adaptation of hyperthermophilic archaea and bacteria to extreme environments.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
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Rissanen I, Grimes J, Pawlowski A, Mäntynen S, Harlos K, Bamford J, Stuart D. Bacteriophage P23-77 capsid protein structures reveal the archetype of an ancient branch from a major virus lineage. Structure 2013; 21:718-26. [PMID: 23623731 PMCID: PMC3919167 DOI: 10.1016/j.str.2013.02.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/18/2013] [Accepted: 02/20/2013] [Indexed: 12/24/2022]
Abstract
It has proved difficult to classify viruses unless they are closely related since their rapid evolution hinders detection of remote evolutionary relationships in their genetic sequences. However, structure varies more slowly than sequence, allowing deeper evolutionary relationships to be detected. Bacteriophage P23-77 is an example of a newly identified viral lineage, with members inhabiting extreme environments. We have solved multiple crystal structures of the major capsid proteins VP16 and VP17 of bacteriophage P23-77. They fit the 14 Å resolution cryo-electron microscopy reconstruction of the entire virus exquisitely well, allowing us to propose a model for both the capsid architecture and viral assembly, quite different from previously published models. The structures of the capsid proteins and their mode of association to form the viral capsid suggest that the P23-77-like and adeno-PRD1 lineages of viruses share an extremely ancient common ancestor. High-resolution structures of the two major capsid proteins of bacteriophage P23-77 P23-77 capsid proteins exhibit a conserved single β-barrel core fold P23-77 is an ancient relative of the double β-barrel lineage of viruses Capsid model illustrates that P23-77 uses a novel method of organization
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Affiliation(s)
- Ilona Rissanen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
- Diamond Light Source, Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
| | - Alice Pawlowski
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Sari Mäntynen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Jaana K.H. Bamford
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä 40014, Finland
- Corresponding author
| | - David I. Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
- Diamond Light Source, Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
- Corresponding author
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43
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Schoenfeld TW, Murugapiran SK, Dodsworth JA, Floyd S, Lodes M, Mead DA, Hedlund BP. Lateral gene transfer of family A DNA polymerases between thermophilic viruses, aquificae, and apicomplexa. Mol Biol Evol 2013; 30:1653-64. [PMID: 23608703 DOI: 10.1093/molbev/mst078] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bioinformatics and functional screens identified a group of Family A-type DNA Polymerase (polA) genes encoded by viruses inhabiting circumneutral and alkaline hot springs in Yellowstone National Park and the US Great Basin. The proteins encoded by these viral polA genes (PolAs) shared no significant sequence similarity with any known viral proteins but were remarkably similar to PolAs encoded by two of three families of the bacterial phylum Aquificae and by several apicoplast-targeted PolA-like proteins found in the eukaryotic phylum Apicomplexa, which includes the obligate parasites Plasmodium, Babesia, and Toxoplasma. The viral gene products share signature elements previously associated only with Aquificae and Apicomplexa PolA-like proteins and were similar to proteins encoded by prophage elements of a variety of otherwise unrelated Bacteria, each of which additionally encoded a prototypical bacterial PolA. Unique among known viral DNA polymerases, the viral PolA proteins of this study share with the Apicomplexa proteins large amino-terminal domains with putative helicase/primase elements but low primary sequence similarity. The genomic context and distribution, phylogeny, and biochemistry of these PolA proteins suggest that thermophilic viruses transferred polA genes to the Apicomplexa, likely through secondary endosymbiosis of a virus-infected proto-apicoplast, and to the common ancestor of two of three Aquificae families, where they displaced the orthologous cellular polA gene. On the basis of biochemical activity, gene structure, and sequence similarity, we speculate that the xenologous viral-type polA genes may have functions associated with diversity-generating recombination in both Bacteria and Apicomplexa.
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44
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Rissanen I, Pawlowski A, Harlos K, Grimes JM, Stuart DI, Bamford JKH. Crystallization and preliminary crystallographic analysis of the major capsid proteins VP16 and VP17 of bacteriophage P23-77. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:580-3. [PMID: 22691792 PMCID: PMC3374517 DOI: 10.1107/s1744309112010330] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 03/08/2012] [Indexed: 02/08/2023]
Abstract
The major capsid proteins VP16 and VP17 of bacteriophage P23-77 have been crystallized using both recombinant and purified virus and preliminary diffraction analyses have been performed. Members of the diverse double-β-barrel lineage of viruses are identified by the conserved structure of their major coat protein. New members of this lineage have been discovered based on structural analysis and we are interested in identifying relatives that utilize unusual versions of the double-β-barrel fold. One candidate for such studies is P23-77, an icosahedral dsDNA bacteriophage that infects the extremophile Thermus thermophilus. P23-77 has two major coat proteins, namely VP16 and VP17, of a size consistent with a single-β-barrel core fold. These previously unstudied proteins have now been successfully expressed as recombinant proteins, purified and crystallized using hanging-drop and sitting-drop vapour-diffusion methods. Crystals of coat proteins VP16 and VP17 have been obtained as well as of a putative complex. In addition, virus-derived material has been crystallized. Diffraction data have been collected to beyond 3 Å resolution for five crystal types and structure determinations are in progress.
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Affiliation(s)
- Ilona Rissanen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, PO Box 35, 40014 University of Jyväskylä, Finland
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Krupovic M, Prangishvili D, Hendrix RW, Bamford DH. Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 2011; 75:610-35. [PMID: 22126996 PMCID: PMC3232739 DOI: 10.1128/mmbr.00011-11] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, 25 rue du Dr. Roux, 75015 Paris, France.
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Tamakoshi M, Murakami A, Sugisawa M, Tsuneizumi K, Takeda S, Saheki T, Izumi T, Akiba T, Mitsuoka K, Toh H, Yamashita A, Arisaka F, Hattori M, Oshima T, Yamagishi A. Genomic and proteomic characterization of the large Myoviridae bacteriophage ϕTMA of the extreme thermophile Thermus thermophilus. BACTERIOPHAGE 2011; 1:152-164. [PMID: 22164349 DOI: 10.4161/bact.1.3.16712] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 11/19/2022]
Abstract
A lytic phage, designated as ϕTMA, was isolated from a Japanese hot spring using Thermus thermophilus HB27 as an indicator strain. Electron microscopic examination showed that ϕTMA had an icosahedral head and a contractile tail. The circular double-stranded DNA sequence of ϕTMA was 151,483 bp in length, and its organization was essentially same as that of ϕYS40 except that the ϕTMA genome contained genes for a pair of transposase and resolvase, and a gene for a serine to asparagine substituted ortholog of the protein involved in the initiation of the ϕYS40 genomic DNA synthesis. The different host specificities of ϕTMA and ϕYS40 could be explained by the sequence differences in the C-terminal regions of their distal tail fiber proteins. The ΔpilA knockout strains of T. thermophilus showed simultaneous loss of sensitivity to their cognate phages, pilus structure, twitching motility and competence for natural transformation, thus suggesting that the phage infection required the intact host pili. Pulsed-field gel electrophoresis analysis of the ϕTMA and ϕYS40 genomes revealed that the length of their DNA exceeded 200 kb, indicating that the terminal redundancy is more than 30% of the closed circular form. Proteomic analysis of the ϕTMA virion using a combination of N-terminal sequencing and mass spectrometric analysis of peptide fragments suggested that the maturation of several proteins involved in the phage assembly process was mediated by a trypsin-like protease. The gene order of the phage structural proteins was also discussed.
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Affiliation(s)
- Masatada Tamakoshi
- Department of Molecular Biology; Tokyo University of Pharmacy and Life Sciences; Hachioji, Tokyo
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Isolation and characterization of a new bacteriophage MMP17 from Meiothermus. Extremophiles 2011; 15:253-8. [PMID: 21225300 DOI: 10.1007/s00792-010-0354-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 12/22/2010] [Indexed: 10/18/2022]
Abstract
Thermophiles and their viruses are extraordinarily important because of their roles in processes of evolution, biogeochemistry and ecology. Species of the genus Meiothermus share close relationship with genus Thermus, but no Meiothermus bacteriophage has been reported yet. In this work, a new thermophilic bacteriophage named MMP17 (Meiothermus Myoviridae phage 17) was isolated from a Meiothermus strain and was further characterized. MMP17 was a typical myovirus with an icosahedral head (42 nm in diameter) and a tail (120 nm in length and 17 nm in width). Its DNA was about 33.5-39.5 kb in size. MMP17 was very stable at 55-60°C and pH 6-7. According to the one-step growth curve, the latent period and the burst period were 60 and 30 min, respectively. An average of 15 phage particles was released from each infected cell. Four major bands were detected in purified virion preparation by SDS-PAGE. As MMP17 was a thermophilic bacteriophage with lower production temperature, its characterization and the relationship between MMP17 and Thermus bacteriophages deserved for further study.
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Lin L, Hong W, Ji X, Han J, Huang L, Wei Y. Isolation and characterization of an extremely long tail Thermus bacteriophage from Tengchong hot springs in China. J Basic Microbiol 2010; 50:452-6. [PMID: 20806260 DOI: 10.1002/jobm.201000116] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Thermus strains are regarded as models to investigate the mechanism of thermostability of thermophiles, and phages from Thermus are particularly interesting because of their way to regulate gene expression. In this research, a Thermus bacteriophage named TSP4 (Thermus Siphoviridae phage) was isolated from Tengchong hot springs in China, and characteristics of morphology, temperature for phage production, pH and organic solvent sensitivity, DNA restriction endonuclease digestion and protein composition of TSP4 were further studied. TSP4 belonged to the Siphoviridae family and had a hexagonal head of 73 nm in diameter, an extremely long and flexible tail of 785 nm in length and 10 nm in width. TSP4 was very stable at 65 °C and pH 7.6. The capsid was apparently devoid of lipid. By SDS-PAGE, six protein bands were found in purified virions. Despite their exceptional habitats separated by thousands of kilometers, the characteristics of this thermophilic phage showed high similarity to Thermus siphoviruses P23-45 and P74-26 isolated from Kamchatka peninsula hot springs in the Far East, Russia.
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Affiliation(s)
- Lianbing Lin
- Biotechnology Research Center, Kunming University of Science and Technology Kunming, China.
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Abstract
In deep-sea hydrothermal vent communities, viruses play very important roles. However vent thermophilic bacteriophages remain largely unexplored. In this investigation, a novel vent Geobacillus bacteriophage, D6E, was characterized. Based on comparative genomics and proteomics analyses, the results showed an extensive mosaicism of D6E genome with other mesophilic or thermophilic phages.
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50
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Mazaheri Nezhad Fard R, Barton MD, Heuzenroeder MW. Novel Bacteriophages in Enterococcus spp. Curr Microbiol 2009; 60:400-6. [PMID: 19967374 DOI: 10.1007/s00284-009-9555-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2009] [Accepted: 11/13/2009] [Indexed: 02/06/2023]
Abstract
Most of the bacteriophages (phages) currently reported in Enterococcus spp. belong to tailed families of bacteriophages Podoviridae, Siphoviridae, and Myoviridae. There is a little information on non-tailed bacteriophages isolated from enterococci. Samples of sewage and piggery effluents were tested on pig and chicken isolates of Enterococcus faecalis, E. faecium and E. gallinarum for lytic phages. In addition, isolates were exposed to mitomycin C to induce lysogenic phages. Bacteriophages that were detected were visualized by electron microscopy. Ten bacteriophages were of isometric shape with long flexible or non-flexible tails, while one had a long head with a long flexible tail; all contained double-stranded DNA molecules. Seven Polyhedral, filamentous, and pleomorphic-shaped phages containing DNA or RNA were also observed. The pleomorphic phages were droplet- or lemon-shaped in morphology. This study is the first report on polyhedral phages in Enterococcus spp. of animal origin and also the first report of filamentous and pleomorphic phages in enterococci.
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