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Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Martins Dosumu OJ, Paul K, Sanchez Castaño CE, Petherbridge R, Paull JS, Baym M. Diverse and abundant phages exploit conjugative plasmids. Nat Commun 2024; 15:3197. [PMID: 38609370 PMCID: PMC11015023 DOI: 10.1038/s41467-024-47416-z] [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: 01/04/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.
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Affiliation(s)
- Natalia Quinones-Olvera
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Siân V Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Lucy M McCully
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Maximillian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eleanor A Rand
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Alice C Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Boston University, Boston, MA, 02215, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Oluremi J Martins Dosumu
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Kay Paul
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Cleotilde E Sanchez Castaño
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Rachel Petherbridge
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jillian S Paull
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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2
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Bárdy P, MacDonald CI, Pantůček R, Antson AA, Fogg PC. Jorvik: A membrane-containing phage that will likely found a new family within Vinavirales. iScience 2023; 26:108104. [PMID: 37867962 PMCID: PMC10589892 DOI: 10.1016/j.isci.2023.108104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/23/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
Although membrane-containing dsDNA bacterial viruses are some of the most prevalent predators in aquatic environments, we know little about how they function due to their intractability in the laboratory. Here, we have identified and thoroughly characterized a new type of membrane-containing bacteriophage, Jorvik, that infects the freshwater mixotrophic model bacterium Rhodobacter capsulatus. Jorvik is extremely virulent, can persist in the host integrated into the RuBisCo operon and encodes two experimentally verified cell wall hydrolases. Jorvik-like prophages are abundant in the genomes of Alphaproteobacteria, are distantly related to known viruses of the class Tectiliviricetes, and we propose they should be classified as a new family. Crucially, we demonstrate how widely used phage manipulation methods should be adjusted to prevent loss of virus infectivity. Our thorough characterization of environmental phage Jorvik provides important experimental insights about phage diversity and interactions in microbial communities that are often unexplored in common metagenomic analyses.
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Affiliation(s)
- Pavol Bárdy
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Conor I.W. MacDonald
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5NG, UK
| | - Paul C.M. Fogg
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5NG, UK
- Biology Department, University of York, Wentworth Way, York YO10 5DD, UK
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3
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Hicks E, Rogers NMK, Hendren CO, Kuehn MJ, Wiesner MR. Extracellular Vesicles and Bacteriophages: New Directions in Environmental Biocolloid Research. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16728-16742. [PMID: 37898880 DOI: 10.1021/acs.est.3c05041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
There is a long-standing appreciation among environmental engineers and scientists regarding the importance of biologically derived colloidal particles and their environmental fate. This interest has been recently renewed in considering bacteriophages and extracellular vesicles, which are each poised to offer engineers unique insights into fundamental aspects of environmental microbiology and novel approaches for engineering applications, including advances in wastewater treatment and sustainable agricultural practices. Challenges persist due to our limited understanding of interactions between these nanoscale particles with unique surface properties and their local environments. This review considers these biological particles through the lens of colloid science with attention given to their environmental impact and surface properties. We discuss methods developed for the study of inert (nonbiological) particle-particle interactions and the potential to use these to advance our understanding of the environmental fate and transport of extracellular vesicles and bacteriophages.
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Affiliation(s)
- Ethan Hicks
- Department of Civil & Environmental Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for the Environmental Implications of Nanotechnology, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas M K Rogers
- Department of Mechanical Engineering, Porter School of Earth and Environmental Studies, Tel Aviv University, Tel Aviv 69978, Israel
| | - Christine Ogilvie Hendren
- Center for the Environmental Implications of Nanotechnology, Duke University, Durham, North Carolina 27708, United States
- Research Institute for Environment, Energy and Economics, Appalachian State University, Boone, North Carolina 28608, United States
| | - Meta J Kuehn
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Mark R Wiesner
- Department of Civil & Environmental Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for the Environmental Implications of Nanotechnology, Duke University, Durham, North Carolina 27708, United States
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4
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Brookes Z, Teoh L, Cieplik F, Kumar P. Mouthwash Effects on the Oral Microbiome: Are They Good, Bad, or Balanced? Int Dent J 2023; 73 Suppl 2:S74-S81. [PMID: 37867065 PMCID: PMC10690560 DOI: 10.1016/j.identj.2023.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 10/24/2023] Open
Abstract
This narrative review describes the oral microbiome, and its role in oral health and disease, before considering the impact of commonly used over-the-counter (OTC) mouthwashes on oral bacteria, viruses, bacteriophages, and fungi that make up these microbial communities in different niches of the mouth. Whilst certain mouthwashes have proven antimicrobial actions and clinical effectiveness supported by robust evidence, this review reports more recent metagenomics evidence, suggesting that mouthwashes such as chlorhexidine may cause "dysbiosis," whereby certain species of bacteria are killed, leaving others, sometimes unwanted, to predominate. There is little known about the effects of mouthwashes on fungi and viruses in the context of the oral microbiome (virome) in vivo, despite evidence that they "kill" certain viral pathogens ex vivo. Evidence for mouthwashes, much like antibiotics, is also emerging with regards to antimicrobial resistance, and this should further be considered in the context of their widespread use by clinicians and patients. Therefore, considering the potential of currently available OTC mouthwashes to alter the oral microbiome, this article finally proposes that the ideal mouthwash, whilst combatting oral disease, should "balance" antimicrobial communities, especially those associated with health. Which antimicrobial mouthwash best fits this ideal remains uncertain.
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Affiliation(s)
- Zoë Brookes
- Peninsula Dental School, Plymouth University, Plymouth, UK.
| | - Leanne Teoh
- Melbourne Dental School, The University of Melbourne, Carlton, Victoria, Australia
| | - Fabian Cieplik
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Purnima Kumar
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, USA
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5
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Overton MS, Manuel RD, Lawrence CM, Snyder JC. Viruses of the Turriviridae: an emerging model system for studying archaeal virus-host interactions. Front Microbiol 2023; 14:1258997. [PMID: 37808280 PMCID: PMC10551542 DOI: 10.3389/fmicb.2023.1258997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Viruses have played a central role in the evolution and ecology of cellular life since it first arose. Investigations into viral molecular biology and ecological dynamics have propelled abundant progress in our understanding of living systems, including genetic inheritance, cellular signaling and trafficking, and organismal development. As well, the discovery of viral lineages that infect members of all three domains suggest that these lineages originated at the earliest stages of biological evolution. Research into these viruses is helping to elucidate the conditions under which life arose, and the dynamics that directed its early development. Archaeal viruses have only recently become a subject of intense study, but investigations have already produced intriguing and exciting results. STIV was originally discovered in Yellowstone National Park and has been the focus of concentrated research. Through this research, a viral genetic system was created, a novel lysis mechanism was discovered, and the interaction of the virus with cellular ESCRT machinery was revealed. This review will summarize the discoveries within this group of viruses and will also discuss future work.
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Affiliation(s)
- Michael S. Overton
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Robert D. Manuel
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
| | - C. Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Jamie C. Snyder
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
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6
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Cai L, Tian Y, Li Z, Yang Y, Ai C, Zhang R. A broad-host-range lytic phage vB_VhaS-R18L as a candidate against vibriosis. Front Microbiol 2023; 14:1191157. [PMID: 37333633 PMCID: PMC10272388 DOI: 10.3389/fmicb.2023.1191157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023] Open
Abstract
Vibriosis is one of the most common bacterial diseases that cause high rates of mortality and considerable economic losses in aquaculture. Phage therapy has been considered as a promising alternative method to antibiotics in the biocontrol of infectious diseases. Genome sequencing and characterization of the phage candidates are prerequisites before field applications to ensure environmental safety. In this study, a lytic phage, named vB_VhaS-R18L (R18L), was isolated from the coastal seawater of Dongshan Island, China. The phage was characterized in terms of morphology, genetic content, infection kinetics, lytic profile, and virion stability. Transmission electronic microscopy indicated that R18L is siphovirus-like, comprising an icosahedral head (diameter 88.6 ± 2.2 nm) and a long noncontractile tail (225 × 11 nm). Genome analysis indicated R18L to be a double-stranded DNA virus with a genome size of 80,965 bp and a G + C content of 44.96%. No genes that encode known toxins or genes implicated in lysogeny control were found in R18L. A one-step growth experiment showed that R18L had a latent period of approximately 40 min and a burst size of 54 phage particles per infected cell. R18L showed lytic activity against a wide range of at least five Vibrio species (V. alginolyticus, V. cholerae, V. harveyi, V. parahemolyticus, and V. proteolyticus). R18L was relatively stable at pH 6-11 and at temperatures ranging from 4°C to 50°C. The broad lytic activity across Vibrio species and the stability in the environment make R18L a potential candidate for phage therapy in controlling vibriosis in aquaculture systems.
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Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yuan Tian
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ziqiang Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Chunxiang Ai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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7
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Roberts SM, Aldis M, Wright ET, Gonzales CB, Lai Z, Weintraub ST, Hardies SC, Serwer P. Siphophage 0105phi7-2 of Bacillus thuringiensis: Novel Propagation, DNA, and Genome-Implied Assembly. Int J Mol Sci 2023; 24:ijms24108941. [PMID: 37240285 DOI: 10.3390/ijms24108941] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Diversity of phage propagation, physical properties, and assembly promotes the use of phages in ecological studies and biomedicine. However, observed phage diversity is incomplete. Bacillus thuringiensis siphophage, 0105phi-7-2, first described here, significantly expands known phage diversity, as seen via in-plaque propagation, electron microscopy, whole genome sequencing/annotation, protein mass spectrometry, and native gel electrophoresis (AGE). Average plaque diameter vs. plaque-supporting agarose gel concentration plots reveal unusually steep conversion to large plaques as agarose concentration decreases below 0.2%. These large plaques sometimes have small satellites and are made larger by orthovanadate, an ATPase inhibitor. Phage head-host-cell binding is observed by electron microscopy. We hypothesize that this binding causes plaque size-increase via biofilm evolved, ATP stimulated ride-hitching on motile host cells by temporarily inactive phages. Phage 0105phi7-2 does not propagate in liquid culture. Genomic sequencing/annotation reveals history as temperate phage and distant similarity, in a virion-assembly gene cluster, to prototypical siphophage SPP1 of Bacillus subtilis. Phage 0105phi7-2 is distinct in (1) absence of head-assembly scaffolding via either separate protein or classically sized, head protein-embedded peptide, (2) producing partially condensed, head-expelled DNA, and (3) having a surface relatively poor in AGE-detected net negative charges, which is possibly correlated with observed low murine blood persistence.
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Affiliation(s)
- Samantha M Roberts
- Department of Microbiology, Immunology and Molecular Genetics, UT Health, San Antonio, TX 78229, USA
| | - Miranda Aldis
- Department of Microbiology, Immunology and Molecular Genetics, UT Health, San Antonio, TX 78229, USA
| | - Elena T Wright
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
| | - Cara B Gonzales
- Department of Comprehensive Dentistry, UT Health, San Antonio, TX 78229, USA
| | - Zhao Lai
- Department of Molecular Medicine, UT Health, San Antonio, TX 78229, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
| | - Stephen C Hardies
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
| | - Philip Serwer
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
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8
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Conners R, León-Quezada RI, McLaren M, Bennett NJ, Daum B, Rakonjac J, Gold VAM. Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly. Nat Commun 2023; 14:2724. [PMID: 37169795 PMCID: PMC10175506 DOI: 10.1038/s41467-023-37915-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/04/2023] [Indexed: 05/13/2023] Open
Abstract
Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.
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Affiliation(s)
- Rebecca Conners
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Rayén Ignacia León-Quezada
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Nanophage Technologies, Palmerston North, New Zealand
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Nicholas J Bennett
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Jasna Rakonjac
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Nanophage Technologies, Palmerston North, New Zealand.
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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9
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Chen Y, Li W, Shi K, Fang Z, Yang Y, Zhang R. Isolation and characterization of a novel phage belonging to a new genus against Vibrio parahaemolyticus. Virol J 2023; 20:81. [PMID: 37127579 PMCID: PMC10152775 DOI: 10.1186/s12985-023-02036-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is a major foodborne pathogen that contaminates aquatic products and causes great economic losses to aquaculture. Because of the emergence of multidrug-resistant V. parahaemolyticus strains, bacteriophages are considered promising agents for their biocontrol as an alternative or supplement to antibiotics. In this study, a lytic vibriophage, vB_VpaM_R16F (R16F), infecting V. parahaemolyticus 1.1997T was isolated, characterized and evaluated for its biocontrol potential. METHODS A vibriophage R16F was isolated from sewage from a seafood market with the double-layer agar method. R16F was studied by transmission electron microscopy, host range, sensitivity of phage particles to chloroform, one-step growth curve and lytic activity. The phage genome was sequenced and in-depth characterized, including phylogenetic and taxonomic analysis. RESULTS R16F belongs to the myovirus morphotype and infects V. parahaemolyticus, but not nine other Vibrio spp. As characterized by determining its host range, one-step growth curve, and lytic activity, phage R16F was found to highly effective in lysing host cells with a short latent period (< 10 min) and a small burst size (13 plaque-forming units). R16F has a linear double-stranded DNA with genome size 139,011 bp and a G + C content of 35.21%. Phylogenetic and intergenomic nucleotide sequence similarity analysis revealed that R16F is distinct from currently known vibriophages and belongs to a novel genus. Several genes (e.g., encoding ultraviolet damage endonuclease and endolysin) that may enhance environmental competitiveness were found in the genome of R16F, while no antibiotic resistance- or virulence factor-related gene was detected. CONCLUSIONS In consideration of its biological and genetic properties, this newly discovered phage R16F belongs to a novel genus and may be a potential alternate biocontrol agent.
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Affiliation(s)
- Yubing Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900, Selangor, Malaysia
| | - Wenqing Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China
| | - Keming Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China
| | - Zheng Fang
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900, Selangor, Malaysia
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China.
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China.
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10
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Indelicato G, Cermelli P, Twarock R. Local rules for the self-assembly of a non-quasi-equivalent viral capsid. Phys Rev E 2022; 105:064403. [PMID: 35854534 DOI: 10.1103/physreve.105.064403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
The structures of many large bacteriophages, such as the P23-77 capsids, do not adhere strictly to the quasi-equivalence principle of viral architecture. Although the general architecture of the P23-77 capsids is classed as T=28d, it self-assembles from multiple copies of two types of coat protein subunits, and the resulting hexameric capsomers do not conform to the Caspar-Klug paradigm. There are two types of hexamers with distinct internal organization, that are located at specific positions in the capsid. It is an open problem which assembly mechanism can lead to such a complex capsid organization. Here we propose a simple set of local rules that can explain how such non-quasi-equivalent capsid structures can arise as a result of self-assembly.
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Affiliation(s)
| | - Paolo Cermelli
- Dipartimento di Matematica, Università di Torino, 10123 Torino TO, Italy
| | - Reidun Twarock
- Department of Mathematics and Department of Biology, University of York, York, YO10 5DD, United Kingdom
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11
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Amankwah S, Adisu M, Gorems K, Abdella K, Kassa T. Assessment of Phage-Mediated Inhibition and Removal of Multidrug-Resistant Pseudomonas aeruginosa Biofilm on Medical Implants. Infect Drug Resist 2022; 15:2797-2811. [PMID: 35668859 PMCID: PMC9166914 DOI: 10.2147/idr.s367460] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/27/2022] [Indexed: 11/27/2022] Open
Abstract
Purpose Despite the growing interest in bacteriophage (phage) usage for the prevention, control, and removal of bacterial biofilms, few scientific data exist on phage applications on medical implant surfaces, while none exists on multiple implants. In this study, we aimed to isolate, biophysically characterize and assess phages as potential antibiofilm agents to inhibit and remove multidrug-resistant (MDR) Pseudomonas aeruginosa biofilm on catheter and endotracheal tube surfaces. Methods The well-identified stored clinical isolates (n = 7) of MDR P. aeruginosa were obtained from Jimma Medical Center. Specific phages were isolated and characterized based on standard protocols. The phages were tested for their antibiofilm effects in preventing colonization and removing preformed biofilms of MDR P. aeruginosa, following phage coating and treatment of catheter and endotracheal tube segments. Results Two P. aeruginosa-specific phages (ΦJHS-PA1139 and ΦSMK-PA1139) were isolated from JMC compound sewage sources. The phages were biophysically characterized as being thermally stable up to 40°C and viable between pH 4.0 and 11.0. The two phages tested against clinical MDR strains of P. aeruginosa showed broad host ranges but not on other tested bacterial species. Both phages reduced MDR bacterial biofilms during the screening step. The phage-coated segments showed 1.2 log10 up to 3.2 log10 inhibition relative to non-coated segments following 6 h coating of segments prior to microbial load exposure. In both phages, 6 h treatment of the segments with 106 PFU/mL yielded 1.0 log10 up to 1.6 log10 reductions for ΦJHS and 1.6 log10 up to 2.4 log10 reductions for ΦSMK. Conclusion Our results suggest that phages have great potential to serve the dual purpose as surface coating agents for preventing MDR bacterial colonization in medical implants and as biofilm removal agents in implant-associated infections.
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Affiliation(s)
- Stephen Amankwah
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
- Accra Medical Centre, Accra, Ghana
| | - Mekonen Adisu
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
- Department of Medical Laboratory Sciences, Wollega University, Nekemte, Ethiopia
| | - Kasahun Gorems
- Microbiology Laboratory of Jimma Medical Center, Jimma, Ethiopia
- St Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Kedir Abdella
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
| | - Tesfaye Kassa
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
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12
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Abstract
Lactococcus lactis strains residing in the microbial community of a complex dairy starter culture named “Ur” are hosts to prophages belonging to the family Siphoviridae. L. lactis strains (TIFN1 to TIFN7) showed detectable spontaneous phage production and release (109 to 1010 phage particles/ml) and up to 10-fold increases upon prophage induction, while in both cases we observed no obvious cell lysis typically described for the lytic life cycle of Siphoviridae phages. Intrigued by this phenomenon, we investigated the host-phage interaction using strain TIFN1 (harboring prophage proPhi1) as a representative. We confirmed that during the massive phage release, all bacterial cells remain viable. Further, by monitoring phage replication in vivo, using a green fluorescence protein reporter combined with flow cytometry, we demonstrated that the majority of the bacterial population (over 80%) is actively producing phage particles when induced with mitomycin C. The released tailless phage particles were found to be engulfed in lipid membranes, as evidenced by electron microscopy and lipid staining combined with chemical lipid analysis. Based on the collective observations, we propose a model of phage-host interaction in L. lactis TIFN1 where the phage particles are engulfed in membranes upon release, thereby leaving the producing host intact. Moreover, we discuss possible mechanisms of chronic, or nonlytic, release of LAB Siphoviridae phages and its impact on the bacterial host. IMPORTANCE In complex microbial consortia such as fermentation starters, bacteriophages can alter the dynamics and diversity of microbial communities. Bacteriophages infecting Lactococcus lactis are mostly studied for their detrimental impact on industrial dairy fermentation processes. In this study, we describe a novel form of phage-bacterium interaction in an L. lactis strain isolated from a complex dairy starter culture: when the prophages harbored in the L. lactis genome are activated, the phage particles are engulfed in lipid membranes upon release, leaving the producing host intact. Findings from this study provide additional insights into the diverse manners of phage-bacterium interactions and coevolution, which are essential for understanding the population dynamics in complex microbial communities like fermentation starters.
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13
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Fernandez de la Mora J, Angel DM, Peccia J. How Narrow Is the Gas Phase Mobility Distribution of Enveloped Viruses? The Case of the Φ6 Bacteriophage. Anal Chem 2021; 93:12938-12943. [PMID: 34520175 DOI: 10.1021/acs.analchem.1c02402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We use the Φ6 bacteriophage previously exploited as a BSL-1 surrogate of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome (MERS) coronavirus to obtain the first high-resolution gas phase mobility spectra of an enveloped virus. The relative full width at half-maximum found for the viral mobility distribution (FWHMZ < 3.7%) is substantially narrower than that reported by prior mobility or microscopy studies with other enveloped viruses. It is nevertheless not as narrow as that recently found for several non-enveloped viruses (FWHMZ ≈ 2%), presumably due to particle to particle variability of enveloped viruses. This 3.7% is an upper bound to the actual width. Nevertheless, the well-defined mobility peaks obtained indicate that gas phase mobility analysis is a more discriminating methodology than that previously demonstrated for physically based non-genetic viral diagnostic of enveloped viruses. These results are obtained by analysis of the original cell culture medium containing the virus, purified only by passage through a 0.22 μm filter and by dialysis into a 10 mM aqueous ammonium acetate buffer. We confirmed that this buffer exchange preserves infectivity. Therefore, the 63.7 nm mobility diameter found, although smaller than the 75 nm previously inferred by microscopy, corresponds to the full particle including the envelope.
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Affiliation(s)
- Juan Fernandez de la Mora
- Department of Mechanical Engineering and Materials Science, Yale University, Mason Laboratory, 9 Hillhouse Avenue, New Haven, Connecticut 06520-8286, United States
| | - Darryl Marissa Angel
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
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14
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Gillis A, Hock L, Mahillon J. Comparative Genomics of Prophages Sato and Sole Expands the Genetic Diversity Found in the Genus Betatectivirus. Microorganisms 2021; 9:1335. [PMID: 34205474 PMCID: PMC8234876 DOI: 10.3390/microorganisms9061335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/16/2022] Open
Abstract
Tectiviruses infecting the Bacillus cereus group represent part of the bacterial "plasmid repertoire" as they behave as linear plasmids during their lysogenic cycle. Several novel tectiviruses have been recently found infecting diverse strains belonging the B. cereus lineage. Here, we report and analyze the complete genome sequences of phages Sato and Sole. The linear dsDNA genome of Sato spans 14,852 bp with 32 coding DNA sequences (CDSs), whereas the one of Sole has 14,444 bp comprising 30 CDSs. Both phage genomes contain inverted terminal repeats and no tRNAs. Genomic comparisons and phylogenetic analyses placed these two phages within the genus Betatectivirus in the family Tectiviridae. Additional comparative genomic analyses indicated that the "gene regulation-genome replication" module of phages Sato and Sole is more diverse than previously observed among other fully sequenced betatectiviruses, displaying very low sequence similarities and containing some ORFans. Interestingly, the ssDNA binding protein encoded in this genomic module in phages Sato and Sole has very little amino acid similarity with those of reference betatectiviruses. Phylogenetic analyses showed that both Sato and Sole represent novel tectivirus species, thus we propose to include them as two novel species in the genus Betatectivirus.
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Affiliation(s)
- Annika Gillis
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Croix du Sud 2, L7.05.12, B-1348 Louvain-la-Neuve, Belgium;
| | | | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Croix du Sud 2, L7.05.12, B-1348 Louvain-la-Neuve, Belgium;
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15
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Abolaban FA, Djouider FM. Gamma irradiation-mediated inactivation of enveloped viruses with conservation of genome integrity: Potential application for SARS-CoV-2 inactivated vaccine development. Open Life Sci 2021; 16:558-570. [PMID: 34131589 PMCID: PMC8174122 DOI: 10.1515/biol-2021-0051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 03/12/2021] [Accepted: 04/13/2021] [Indexed: 12/23/2022] Open
Abstract
Radiation inactivation of enveloped viruses occurs as the result of damages at the molecular level of their genome. The rapidly emerging and ongoing coronavirus disease 2019 (COVID-19) pneumonia pandemic prompted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is now a global health crisis and an economic devastation. The readiness of an active and safe vaccine against the COVID-19 has become a race against time in this unqualified global panic caused by this pandemic. In this review, which we hope will be helpful in the current situation of COVID-19, we analyze the potential use of γ-irradiation to inactivate this virus by damaging at the molecular level its genetic material. This inactivation is a vital step towards the design and development of an urgently needed, effective vaccine against this disease.
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Affiliation(s)
- Fouad A. Abolaban
- Nuclear Engineering Department, Faculty of Engineering, King Abdulaziz University, PO Box 80204, Jeddah, 21589, Saudi Arabia
| | - Fathi M. Djouider
- Nuclear Engineering Department, Faculty of Engineering, King Abdulaziz University, PO Box 80204, Jeddah, 21589, Saudi Arabia
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16
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Łobocka M, Dąbrowska K, Górski A. Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future. BioDrugs 2021; 35:255-280. [PMID: 33881767 PMCID: PMC8084836 DOI: 10.1007/s40259-021-00480-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/20/2022]
Abstract
The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.
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Affiliation(s)
- Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Krystyna Dąbrowska
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
| | - Andrzej Górski
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
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17
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Tittes C, Schwarzer S, Pfeiffer F, Dyall-Smith M, Rodriguez-Franco M, Oksanen HM, Quax TEF. Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1. Front Microbiol 2021; 12:625599. [PMID: 33664716 PMCID: PMC7921747 DOI: 10.3389/fmicb.2021.625599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/28/2021] [Indexed: 01/14/2023] Open
Abstract
Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus–host models. Recently, a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belonging to the genus Haloferax, but it is not infectious on the widely used model euryarcheon Haloferax volcanii. To gain more insight into the biology of HFTV1 host strain LR2-5, we studied characteristics that might play a role in its virus susceptibility: growth-dependent motility, surface layer, filamentous surface structures, and cell shape. Its genome sequence showed that LR2-5 is a new strain of Haloferax gibbonsii. LR2-5 lacks obvious viral defense systems, such as CRISPR-Cas, and the composition of its cell surface is different from Hfx. volcanii, which might explain the different viral host range. This work provides first deep insights into the relationship between the host of halovirus HFTV1 and other members of the genus Haloferax. Given the close relationship to the genetically accessible Hfx. volcanii, LR2-5 has high potential as a new model for virus–host studies in euryarchaea.
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Affiliation(s)
- Colin Tittes
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sabine Schwarzer
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mike Dyall-Smith
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
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18
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Vishnyakov AE, Karagodina NP, Lim-Fong G, Ivanov PA, Schwaha TF, Letarov AV, Ostrovsky AN. First evidence of virus-like particles in the bacterial symbionts of Bryozoa. Sci Rep 2021; 11:4. [PMID: 33420126 PMCID: PMC7794531 DOI: 10.1038/s41598-020-78616-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/12/2020] [Indexed: 01/29/2023] Open
Abstract
Bacteriophage communities associated with humans and vertebrate animals have been extensively studied, but the data on phages living in invertebrates remain scarce. In fact, they have never been reported for most animal phyla. Our ultrastructural study showed for the first time a variety of virus-like particles (VLPs) and supposed virus-related structures inside symbiotic bacteria in two marine species from the phylum Bryozoa, the cheilostomes Bugula neritina and Paralicornia sinuosa. We also documented the effect of VLPs on bacterial hosts: we explain different bacterial 'ultrastructural types' detected in bryozoan tissues as stages in the gradual destruction of prokaryotic cells caused by viral multiplication during the lytic cycle. We speculate that viruses destroying bacteria regulate symbiont numbers in the bryozoan hosts, a phenomenon known in some insects. We develop two hypotheses explaining exo- and endogenous circulation of the viruses during the life-cycle of B. neritina. Finally, we compare unusual 'sea-urchin'-like structures found in the collapsed bacteria in P. sinuosa with so-called metamorphosis associated contractile structures (MACs) formed in the cells of the marine bacterium Pseudoalteromonas luteoviolacea which are known to trigger larval metamorphosis in a polychaete worm.
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Affiliation(s)
- A. E. Vishnyakov
- grid.15447.330000 0001 2289 6897Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaja nab. 7/9, Saint Petersburg, Russian Federation 199034
| | - N. P. Karagodina
- grid.15447.330000 0001 2289 6897Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaja nab. 7/9, Saint Petersburg, Russian Federation 199034
| | - G. Lim-Fong
- grid.262455.20000 0001 2205 6070Department of Biology, Randolph-Macon College, 304 Caroline Street, Ashland, VA 23005 USA
| | - P. A. Ivanov
- grid.4886.20000 0001 2192 9124Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7 bld. 2, Moscow, Russian Federation 117312
| | - T. F. Schwaha
- grid.10420.370000 0001 2286 1424Department of Evolutionary Biology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - A. V. Letarov
- grid.4886.20000 0001 2192 9124Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7 bld. 2, Moscow, Russian Federation 117312 ,grid.14476.300000 0001 2342 9668Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, Russian Federation 119234
| | - A. N. Ostrovsky
- grid.15447.330000 0001 2289 6897Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaja nab. 7/9, Saint Petersburg, Russian Federation 199034 ,grid.10420.370000 0001 2286 1424Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, Geozentrum, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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19
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Misol GN, Kokkari C, Katharios P. Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, vB_VhaM_pir03 with Broad Host Lytic Activity against Vibrio harveyi. Pathogens 2020; 9:E1051. [PMID: 33333990 PMCID: PMC7765460 DOI: 10.3390/pathogens9121051] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/25/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022] Open
Abstract
Vibrio harveyi is a Gram-negative marine bacterium that causes major disease outbreaks and economic losses in aquaculture. Phage therapy has been considered as a potential alternative to antibiotics however, candidate bacteriophages require comprehensive characterization for a safe and practical phage therapy. In this work, a lytic novel jumbo bacteriophage, vB_VhaM_pir03 belonging to the Myoviridae family was isolated and characterized against V. harveyi type strain DSM19623. It had broad host lytic activity against 31 antibiotic-resistant strains of V. harveyi, V. alginolyticus, V. campbellii and V. owensii. Adsorption time of vB_VhaM_pir03 was determined at 6 min while the latent-phase was at 40 min and burst-size at 75 pfu/mL. vB_VhaM_pir03 was able to lyse several host strains at multiplicity-of-infections (MOI) 0.1 to 10. The genome of vB_VhaM_pir03 consists of 286,284 base pairs with 334 predicted open reading frames (ORFs). No virulence, antibiotic resistance, integrase encoding genes and transducing potential were detected. Phylogenetic and phylogenomic analysis showed that vB_VhaM_pir03 is a novel bacteriophage displaying the highest similarity to another jumbo phage, vB_BONAISHI infecting Vibrio coralliilyticus. Experimental phage therapy trial using brine shrimp, Artemia salina infected with V. harveyi demonstrated that vB_VhaM_pir03 was able to significantly reduce mortality 24 h post infection when administered at MOI 0.1 which suggests that it can be an excellent candidate for phage therapy.
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Affiliation(s)
- Gerald N. Misol
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, 71500 Heraklion, Crete, Greece; (G.N.M.J.); (C.K.)
- Department of Biology, University of Crete, 71003 Heraklion, Crete, Greece
| | - Constantina Kokkari
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, 71500 Heraklion, Crete, Greece; (G.N.M.J.); (C.K.)
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, 71500 Heraklion, Crete, Greece; (G.N.M.J.); (C.K.)
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20
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Edwards KF, Steward GF, Schvarcz CR. Making sense of virus size and the tradeoffs shaping viral fitness. Ecol Lett 2020; 24:363-373. [PMID: 33146939 DOI: 10.1111/ele.13630] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/26/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022]
Abstract
Viruses span an impressive size range, with genome length varying a thousandfold and virion volume nearly a millionfold. For cellular organisms the scaling of traits with size is a pervasive influence on ecological processes, but whether size plays a central role in viral ecology is unknown. Here, we focus on viruses of aquatic unicellular organisms, which exhibit the greatest known range of virus size. We outline hypotheses within a quantitative framework, and analyse data where available, to consider how size affects the primary components of viral fitness. We argue that larger viruses have fewer offspring per infection and slower contact rates with host cells, but a larger genome tends to increase infection efficiency, broaden host range, and potentially increase attachment success and decrease decay rate. These countervailing selective pressures may explain why a breadth of sizes exist and even coexist when infecting the same host populations. Oligotrophic ecosystems may be enriched in "giant" viruses, because environments with resource-limited phagotrophs at low concentrations may select for broader host range, better control of host metabolism, lower decay rate and a physical size that mimics bacterial prey. Finally, we describe where further research is needed to understand the ecology and evolution of viral size diversity.
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Affiliation(s)
- Kyle F Edwards
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Grieg F Steward
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
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21
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Assalauova D, Kim YY, Bobkov S, Khubbutdinov R, Rose M, Alvarez R, Andreasson J, Balaur E, Contreras A, DeMirci H, Gelisio L, Hajdu J, Hunter MS, Kurta RP, Li H, McFadden M, Nazari R, Schwander P, Teslyuk A, Walter P, Xavier PL, Yoon CH, Zaare S, Ilyin VA, Kirian RA, Hogue BG, Aquila A, Vartanyants IA. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. IUCRJ 2020; 7:1102-1113. [PMID: 33209321 PMCID: PMC7642788 DOI: 10.1107/s2052252520012798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/21/2020] [Indexed: 05/06/2023]
Abstract
An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.
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Affiliation(s)
- Dameli Assalauova
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Young Yong Kim
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Sergey Bobkov
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
| | - Ruslan Khubbutdinov
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation
| | - Max Rose
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Roberto Alvarez
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- School of Mathematics and Statistical Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
| | - Eugeniu Balaur
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria 3086, Australia
| | - Alice Contreras
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
| | - Luca Gelisio
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Janos Hajdu
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-75124, Sweden
| | - Mark S. Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Haoyuan Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Physics Department, Stanford University, 450 Jane Stanford Way, Stanford, CA 94305-2004, USA
| | - Matthew McFadden
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Reza Nazari
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | | | - Anton Teslyuk
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation
| | - Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - P. Lourdu Xavier
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, D-22761, Germany
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sahba Zaare
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Viacheslav A. Ilyin
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation
| | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation
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22
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Zhong Q, Yang L, Li L, Shen W, Li Y, Xu H, Zhong Z, Chen M, Le S. Transcriptomic Analysis Reveals the Dependency of Pseudomonas aeruginosa Genes for Double-Stranded RNA Bacteriophage phiYY Infection Cycle. iScience 2020; 23:101437. [PMID: 32827855 PMCID: PMC7452160 DOI: 10.1016/j.isci.2020.101437] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/16/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
Bacteriophage phiYY is currently the only double-stranded RNA (dsRNA) phage that infects Pseudomonas aeruginosa and is a potential candidate for phage therapy. Here we applied RNA-seq to investigate the lytic cycle of phiYY infecting P. aeruginosa strain PAO1r. About 12.45% (651/5,229) of the host genes were determined to be differentially expressed genes. Moreover, oxidative stress response genes katB and ahpB are upregulated 64- to 128-fold after phage infection, and the single deletion of each gene blocked phiYY infection, indicating that phiYY is extremely sensitive to oxidative stress. On the contrary, another upregulated gene PA0800 might constrain phage infection, because the deletion of PA0800 resulted in a 3.5-fold increase of the efficiency of plating. Our study highlights a complicated dsRNA phage-phage global interaction and raises new questions toward the host defense mechanisms against dsRNA phage and dsRNA phage-encoded hijacking mechanisms.
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Affiliation(s)
- Qiu Zhong
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing 400038, China
- Department of Clinical Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing 400038, China
| | - Lan Yang
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Linlin Li
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Wei Shen
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Yang Li
- Medical Center of Trauma and War Injury, Daping Hospital, Army Medical University, Chongqing 400038, China
- State Key Laboratory of Trauma, Burns and Combined Injuries, Army Medical University, Chongqing 400038, China
| | - Huan Xu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Zhuojun Zhong
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing 400038, China
- State Key Laboratory of Trauma, Burns and Combined Injuries, Army Medical University, Chongqing 400038, China
| | - Shuai Le
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
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23
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López-Laguna H, Sánchez-García L, Serna N, Voltà-Durán E, Sánchez JM, Sánchez-Chardi A, Unzueta U, Łoś M, Villaverde A, Vázquez E. Engineering Protein Nanoparticles Out from Components of the Human Microbiome. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001885. [PMID: 32578402 DOI: 10.1002/smll.202001885] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/13/2020] [Indexed: 05/14/2023]
Abstract
Nanoscale protein materials are highly convenient as vehicles for targeted drug delivery because of their structural and functional versatility. Selective binding to specific cell surface receptors and penetration into target cells require the use of targeting peptides. Such homing stretches should be incorporated to larger proteins that do not interact with body components, to prevent undesired drug release into nontarget organs. Because of their low interactivity with human body components and their tolerated immunogenicity, proteins derived from the human microbiome are appealing and fully biocompatible building blocks for the biofabrication of nonreactive, inert protein materials within the nanoscale. Several phage and phage-like bacterial proteins with natural structural roles are produced in Escherichia coli as polyhistidine-tagged recombinant proteins, looking for their organization as discrete, nanoscale particulate materials. While all of them self-assemble in a variety of sizes, the stability of the resulting constructs at 37 °C is found to be severely compromised. However, the fine adjustment of temperature and Zn2+ concentration allows the formation of robust nanomaterials, fully stable in complex media and under physiological conditions. Then, microbiome-derived proteins show promise for the regulatable construction of scaffold protein nanomaterials, which can be tailored and strengthened by simple physicochemical approaches.
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Affiliation(s)
- Hèctor López-Laguna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid, 28029, Spain
| | - Laura Sánchez-García
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid, 28029, Spain
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid, 28029, Spain
| | - Eric Voltà-Durán
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid, 28029, Spain
| | - Julieta M Sánchez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid, 28029, Spain
- Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT) (CONICET-Universidad Nacional de Córdoba), ICTA & Cátedra de Química Biológica, Departamento de Química, FCEFyN, UNC. Av. Velez Sarsfield 1611, Córdoba, X 5016GCA, Argentina
| | - Alejandro Sánchez-Chardi
- Servei de Microscòpia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - Ugutz Unzueta
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid, 28029, Spain
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, Barcelona, 08041, Spain
| | - Marcin Łoś
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza Street 59, Gdansk, 80-308, Poland
- Phage Consultants, Partyzantow Street 10/18, Gdansk, 80-254, Poland
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid, 28029, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid, 28029, Spain
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24
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Serwer P. Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist. Antibiotics (Basel) 2020; 9:antibiotics9050255. [PMID: 32429032 PMCID: PMC7277631 DOI: 10.3390/antibiotics9050255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
Recently, the research community has had a real-world look at reasons for improving vaccine responses to emerging RNA viruses. Here, a vaccine non-specialist suggests how this might be done. I propose two alternative options and compare the primary alternative option with current practice. The basis of comparison is feasibility in achieving what we need: a safe, mass-produced, emerging virus-targeted vaccine on 2–4 week notice. The primary option is the following. (1) Start with a platform based on live viruses that infect bacteria, but not humans (bacteriophages, or phages). (2) Isolate phages (to be called pathogen homologs) that resemble and provide antigenic context for membrane-covered, pathogenic RNA viruses; coronavirus-phage homologs will probably be found if the search is correctly done. (3) Upon isolating a viral pathogen, evolve its phage homolog to bind antibodies neutralizing for the viral pathogen. Vaccinate with the evolved phage homolog by generating a local, non-hazardous infection with the phage host and then curing the infection by propagating the phage in the artificially infecting bacterial host. I discuss how this alternative option has the potential to provide what is needed after appropriate platforms are built.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Center, San Antonio, TX 78229-3900, USA
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25
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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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26
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Hartman R, Eilers BJ, Bollschweiler D, Munson-McGee JH, Engelhardt H, Young MJ, Lawrence CM. The Molecular Mechanism of Cellular Attachment for an Archaeal Virus. Structure 2019; 27:1634-1646.e3. [PMID: 31587916 DOI: 10.1016/j.str.2019.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/21/2019] [Accepted: 09/16/2019] [Indexed: 12/17/2022]
Abstract
Sulfolobus turreted icosahedral virus (STIV) is a model archaeal virus and member of the PRD1-adenovirus lineage. Although STIV employs pyramidal lysis structures to exit the host, knowledge of the viral entry process is lacking. We therefore initiated studies on STIV attachment and entry. Negative stain and cryoelectron micrographs showed virion attachment to pili-like structures emanating from the Sulfolobus host. Tomographic reconstruction and sub-tomogram averaging revealed pili recognition by the STIV C381 turret protein. Specifically, the triple jelly roll structure of C381 determined by X-ray crystallography shows that pilus recognition is mediated by conserved surface residues in the second and third domains. In addition, the STIV petal protein (C557), when present, occludes the pili binding site, suggesting that it functions as a maturation protein. Combined, these results demonstrate a role for the namesake STIV turrets in initial cellular attachment and provide the first molecular model for viral attachment in the archaeal domain of life.
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Affiliation(s)
- Ross Hartman
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Brian J Eilers
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Daniel Bollschweiler
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | - Jacob H Munson-McGee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Harald Engelhardt
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | - Mark J Young
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA; Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; The Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
| | - C Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA; The Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
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27
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Reddy HK, Carroni M, Hajdu J, Svenda M. Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture. eLife 2019; 8:48496. [PMID: 31513011 PMCID: PMC6750898 DOI: 10.7554/elife.48496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022] Open
Abstract
Bacteriophage PR772, a member of the Tectiviridae family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.
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Affiliation(s)
- Hemanth Kn Reddy
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Janos Hajdu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden.,Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Martin Svenda
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden.,Department of Applied Physics, Biomedical and X-Ray Physics, KTH Royal Institute of Technology, Stockholm, Sweden
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28
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Guo P, Driver D, Zhao Z, Zheng Z, Chan C, Cheng X. Controlling the Revolving and Rotating Motion Direction of Asymmetric Hexameric Nanomotor by Arginine Finger and Channel Chirality. ACS NANO 2019; 13:6207-6223. [PMID: 31067030 PMCID: PMC6595433 DOI: 10.1021/acsnano.8b08849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nanomotors in nanotechnology are as important as engines in daily life. Many ATPases are nanoscale biomotors classified into three categories based on the motion mechanisms in transporting substrates: linear, rotating, and the recently discovered revolving motion. Most biomotors adopt a multisubunit ring-shaped structure that hydrolyzes ATP to generate force. How these biomotors control the motion direction and regulate the sequential action of their multiple subunits is intriguing. Many ATPases are hexameric with each monomer containing a conserved arginine finger. This review focuses on recent findings on how the arginine finger controls motion direction and coordinates adjacent subunit interactions in both revolving and rotating biomotors. Mechanisms of intersubunit interactions and sequential movements of individual subunits are evidenced by the asymmetrical appearance of one dimer and four monomers in high-resolution structural complexes. The arginine finger is situated at the interface of two subunits and extends into the ATP binding pocket of the downstream subunit. An arginine finger mutation results in deficiency in ATP binding/hydrolysis, substrate binding, and transport, highlighting the importance of the arginine finger in regulating energy transduction and motor function. Additionally, the roles of channel chirality and channel size are discussed as related to controlling one-way trafficking and differentiating the revolving and rotating mechanisms. Finally, the review concludes by discussing the conformational changes and entropy conversion triggered by ATP binding/hydrolysis, offering a view different from the traditional concept of ATP-mediated mechanochemical energy coupling. The elucidation of the motion mechanism and direction control in ATPases could facilitate nanomotor fabrication in nanotechnology.
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Affiliation(s)
- Peixuan Guo
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
- E-mail:
| | - Dana Driver
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhengyi Zhao
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhen Zheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Chun Chan
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Xiaolin Cheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
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