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Yang Y, Shao Q, Guo M, Han L, Zhao X, Wang A, Li X, Wang B, Pan JA, Chen Z, Fokine A, Sun L, Fang Q. Capsid structure of bacteriophage ΦKZ provides insights into assembly and stabilization of jumbo phages. Nat Commun 2024; 15:6551. [PMID: 39095371 PMCID: PMC11297242 DOI: 10.1038/s41467-024-50811-1] [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: 01/12/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic pathogen leading to acute or chronic infection in immunocompromised individuals. It holds potential to be used as an antimicrobial agent and as a model for uncovering basic phage biology. Although previous low-resolution structural studies have indicated that jumbo phages may have more complicated capsid structures than smaller phages such as HK97, the detailed structures and the assembly mechanism of their capsids remain largely unknown. Here, we report a 3.5-Å-resolution cryo-EM structure of the ΦKZ capsid. The structure unveiled ten minor capsid proteins, with some decorating the outer surface of the capsid and the others forming a complex network attached to the capsid's inner surface. This network seems to play roles in driving capsid assembly and capsid stabilization. Similar mechanisms of capsid assembly and stabilization are probably employed by many other jumbo viruses.
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Affiliation(s)
- Yashan Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Qianqian Shao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Mingcheng Guo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Lin Han
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xinyue Zhao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Aohan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Xiangyun Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Bo Wang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zhenguo Chen
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Lei Sun
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Qianglin Fang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China.
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China.
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2
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de Martín Garrido N, Chen CS, Ramlaul K, Aylett CHS, Yakunina M. Structure of the Bacteriophage PhiKZ Non-virion RNA Polymerase Transcribing from its Promoter p119L. J Mol Biol 2024; 436:168713. [PMID: 39029888 DOI: 10.1016/j.jmb.2024.168713] [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: 04/08/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/21/2024]
Abstract
Bacteriophage ΦKZ (PhiKZ) is the founding member of a family of giant bacterial viruses. It has potential as a therapeutic as its host, Pseudomonas aeruginosa, kills tens of thousands of people worldwide each year. ΦKZ infection is independent of the host transcriptional apparatus; the virus forms a "nucleus", producing a proteinaceous barrier around the ΦKZ genome that excludes the host immune systems. It expresses its own non-canonical multi-subunit non-virion RNA polymerase (nvRNAP), which is imported into its "nucleus" to transcribe viral genes. The ΦKZ nvRNAP is formed by four polypeptides representing homologues of the eubacterial β/β' subunits, and a fifth that is likely to have evolved from an ancestral homologue to σ-factor. We have resolved the structure of the ΦKZ nvRNAP initiating transcription from its cognate promoter, p119L, including previously disordered regions. Our results shed light on the similarities and differences between ΦKZ nvRNAP mechanisms of transcription and those of canonical eubacterial RNAPs and the related non-canonical nvRNAP of bacteriophage AR9.
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Affiliation(s)
- Natàlia de Martín Garrido
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Chao-Sheng Chen
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Kailash Ramlaul
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Christopher H S Aylett
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom.
| | - Maria Yakunina
- Shenzhen MSU-BIT University, 1 International University Park Road, Dayun New Town, Longgang District, Shenzhen, Guangdong Province 518172, People's Republic of China.
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3
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Mozumdar D, Fossati A, Stevenson E, Guan J, Nieweglowska E, Rao S, Agard D, Swaney DL, Bondy-Denomy J. Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection. Cell Host Microbe 2024; 32:1050-1058.e7. [PMID: 38870941 PMCID: PMC11239273 DOI: 10.1016/j.chom.2024.05.016] [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: 03/24/2024] [Revised: 05/03/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Viral genomes are most vulnerable to cellular defenses at the start of the infection. A family of jumbo phages related to phage ΦKZ, which infects Pseudomonas aeruginosa, assembles a protein-based phage nucleus to protect replicating phage DNA, but how it is protected prior to phage nucleus assembly is unclear. We find that host proteins related to membrane and lipid biology interact with injected phage protein, clustering in an early phage infection (EPI) vesicle. The injected virion RNA polymerase (vRNAP) executes early gene expression until phage genome separation from the vRNAP and the EPI vesicle, moving into the nascent proteinaceous phage nucleus. Enzymes involved in DNA replication and CRISPR/restriction immune nucleases are excluded by the EPI vesicle. We propose that the EPI vesicle is rapidly constructed with injected phage proteins, phage DNA, host lipids, and host membrane proteins to enable genome protection, early transcription, localized translation, and to ensure faithful genome transfer to the proteinaceous nucleus.
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Affiliation(s)
- Deepto Mozumdar
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrea Fossati
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erica Stevenson
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jingwen Guan
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eliza Nieweglowska
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sanjana Rao
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Imaging Institute, Redwood City, CA 94065, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph Bondy-Denomy
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
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4
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Putzeys L, Wicke L, Boon M, van Noort V, Vogel J, Lavigne R. Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa. MICROLIFE 2024; 5:uqae002. [PMID: 38444699 PMCID: PMC10914365 DOI: 10.1093/femsml/uqae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/24/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
The introduction of high-throughput sequencing has resulted in a surge of available bacteriophage genomes, unveiling their tremendous genomic diversity. However, our current understanding of the complex transcriptional mechanisms that dictate their gene expression during infection is limited to a handful of model phages. Here, we applied ONT-cappable-seq to reveal the transcriptional architecture of six different clades of virulent phages infecting Pseudomonas aeruginosa. This long-read microbial transcriptomics approach is tailored to globally map transcription start and termination sites, transcription units, and putative RNA-based regulators on dense phage genomes. Specifically, the full-length transcriptomes of LUZ19, LUZ24, 14-1, YuA, PAK_P3, and giant phage phiKZ during early, middle, and late infection were collectively charted. Beyond pinpointing traditional promoter and terminator elements and transcription units, these transcriptional profiles provide insights in transcriptional attenuation and splicing events and allow straightforward validation of Group I intron activity. In addition, ONT-cappable-seq data can guide genome-wide discovery of novel regulatory element candidates, including noncoding RNAs and riboswitches. This work substantially expands the number of annotated phage-encoded transcriptional elements identified to date, shedding light on the intricate and diverse gene expression regulation mechanisms in Pseudomonas phages, which can ultimately be sourced as tools for biotechnological applications in phage and bacterial engineering.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
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Tsunemoto H, Sugie J, Enustun E, Pogliano K, Pogliano J. Bacterial cytological profiling reveals interactions between jumbo phage φKZ infection and cell wall active antibiotics in Pseudomonas aeruginosa. PLoS One 2023; 18:e0280070. [PMID: 37418366 PMCID: PMC10328376 DOI: 10.1371/journal.pone.0280070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/20/2022] [Indexed: 07/09/2023] Open
Abstract
The emergence of antibiotic resistance in bacteria has led to the investigation of alternative treatments, such as phage therapy. In this study, we examined the interactions between the nucleus-forming jumbo phage ФKZ and antibiotic treatment against Pseudomonas aeruginosa. Using the fluorescence microscopy technique of bacterial cytological profiling, we identified mechanism-of-action-specific interactions between antibiotics that target different biosynthetic pathways and ФKZ infection. We found that certain classes of antibiotics strongly inhibited phage replication, while others had no effect or only mildly affected progression through the lytic cycle. Antibiotics that caused an increase in host cell length, such as the cell wall active antibiotic ceftazidime, prevented proper centering of the ФKZ nucleus via the PhuZ spindle at midcell, leading us to hypothesize that the kinetic parameters of the PhuZ spindle evolved to match the average length of the host cell. To test this, we developed a computational model explaining how the dynamic properties of the PhuZ spindle contribute to phage nucleus centering and why some antibiotics affect nucleus positioning while others do not. These findings provide an understanding of the molecular mechanisms underlying the interactions between antibiotics and jumbo phage replication.
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Affiliation(s)
- Hannah Tsunemoto
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Eray Enustun
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
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Jo D, Kim H, Lee Y, Kim J, Ryu S. Characterization and genomic study of EJP2, a novel jumbo phage targeting antimicrobial resistant Escherichia coli. Front Microbiol 2023; 14:1194435. [PMID: 37250060 PMCID: PMC10213699 DOI: 10.3389/fmicb.2023.1194435] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
The emergence of antimicrobial resistance (AMR) Escherichia coli has noticeably increased in recent years worldwide and causes serious public health concerns. As alternatives to antibiotics, bacteriophages are regarded as promising antimicrobial agents. In this study, we isolated and characterized a novel jumbo phage EJP2 that specifically targets AMR E. coli strains. EJP2 belonged to the Myoviridae family with an icosahedral head (120.9 ± 2.9 nm) and a non-contractile tail (111.1 ± 0.6 nm), and contained 349,185 bp double-stranded DNA genome with 540 putative ORFs, suggesting that EJP2 could be classified as jumbo phage. The functions of genes identified in EJP2 genome were mainly related to nucleotide metabolism, DNA replication, and recombination. Comparative genomic analysis revealed that EJP2 was categorized in the group of Rak2-related virus and presented low sequence similarity at the nucleotide and amino acid level compared to other E. coli jumbo phages. EJP2 had a broad host spectrum against AMR E. coli as well as pathogenic E. coli and recognized LPS as a receptor for infection. Moreover, EJP2 treatment could remove over 80% of AMR E. coli biofilms on 96-well polystyrene, and exhibit synergistic antimicrobial activity with cefotaxime against AMR E. coli. These results suggest that jumbo phage EJP2 could be used as a potential biocontrol agent to combat the AMR issue in food processing and clinical environments.
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Mass Spectral Analyses of Salmonella Myovirus SPN3US Reveal Conserved and Divergent Themes in Proteolytic Maturation of Large Icosahedral Capsids. Viruses 2023; 15:v15030723. [PMID: 36992431 PMCID: PMC10052503 DOI: 10.3390/v15030723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
Salmonella myovirus SPN3US has a T = 27 capsid composed of >50 different gene products, including many that are packaged along with the 240 kb genome and ejected into the host cell. Recently, we showed that an essential phage-encoded prohead protease gp245 is responsible for cleavage of proteins during SPN3US head assembly. This proteolytic maturation step induces major changes in precursor head particles, enabling them to expand and undergo genome packaging. To comprehensively define the composition of the mature SPN3US head and elucidate how it is modified by proteolysis during assembly, we conducted tandem mass spectrometry analysis of purified virions and tailless heads. Fourteen protease cleavage sites were identified in nine proteins, including eight sites not previously identified in head proteins in vivo. Among these was the maturation cleavage site of gp245 which was identical to the autocleavage site we had previously identified in purified recombinant gp245. Our findings underscore the value of employing multiple mass spectrometry-based experimental strategies as a way to enhance the detection of head protein cleavage sites in tailed phages. In addition, our results have identified a conserved set of head proteins in related giant phages that are similarly cleaved by their respective prohead proteases, suggesting that these proteins have important roles in governing the formation and function of large icosahedral capsids.
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Huiting E, Cao X, Ren J, Athukoralage JS, Luo Z, Silas S, An N, Carion H, Zhou Y, Fraser JS, Feng Y, Bondy-Denomy J. Bacteriophages inhibit and evade cGAS-like immune function in bacteria. Cell 2023; 186:864-876.e21. [PMID: 36750095 PMCID: PMC9975087 DOI: 10.1016/j.cell.2022.12.041] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 10/29/2022] [Accepted: 12/21/2022] [Indexed: 02/09/2023]
Abstract
A fundamental strategy of eukaryotic antiviral immunity involves the cGAS enzyme, which synthesizes 2',3'-cGAMP and activates the effector STING. Diverse bacteria contain cGAS-like enzymes that produce cyclic oligonucleotides and induce anti-phage activity, known as CBASS. However, this activity has only been demonstrated through heterologous expression. Whether bacteria harboring CBASS antagonize and co-evolve with phages is unknown. Here, we identified an endogenous cGAS-like enzyme in Pseudomonas aeruginosa that generates 3',3'-cGAMP during phage infection, signals to a phospholipase effector, and limits phage replication. In response, phages express an anti-CBASS protein ("Acb2") that forms a hexamer with three 3',3'-cGAMP molecules and reduces phospholipase activity. Acb2 also binds to molecules produced by other bacterial cGAS-like enzymes (3',3'-cUU/UA/UG/AA) and mammalian cGAS (2',3'-cGAMP), suggesting broad inhibition of cGAS-based immunity. Upon Acb2 deletion, CBASS blocks lytic phage replication and lysogenic induction, but rare phages evade CBASS through major capsid gene mutations. Altogether, we demonstrate endogenous CBASS anti-phage function and strategies of CBASS inhibition and evasion.
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Affiliation(s)
- Erin Huiting
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Xueli Cao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jie Ren
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Januka S Athukoralage
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zhaorong Luo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Sukrit Silas
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Na An
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Héloïse Carion
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yu Zhou
- National Institute of Biological Sciences, Beijing 102206, China
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA.
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9
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Evseev P, Gutnik D, Shneider M, Miroshnikov K. Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of Duplodnaviria Viruses. Biomolecules 2023; 13:biom13010110. [PMID: 36671495 PMCID: PMC9855967 DOI: 10.3390/biom13010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/31/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
The evaluation of the evolutionary relationships is exceptionally important for the taxonomy of viruses, which is a rapidly expanding area of research. The classification of viral groups belonging to the realm Duplodnaviria, which include tailed bacteriophages, head-tailed archaeal viruses and herpesviruses, has undergone many changes in recent years and continues to improve. One of the challenging tasks of Duplodnaviria taxonomy is the classification of high-ranked taxa, including families and orders. At the moment, only 17 of 50 families have been assigned to orders. The evaluation of the evolutionary relationships between viruses is complicated by the high level of divergence of viral proteins. However, the development of structure prediction algorithms, including the award-winning AlphaFold, encourages the use of the results of structural predictions to clarify the evolutionary history of viral proteins. In this study, the evolutionary relationships of two conserved viral proteins, the major capsid protein and terminase, representing different viruses, including all classified Duplodnaviria families, have been analysed using AlphaFold modelling. This analysis has been undertaken using structural comparisons and different phylogenetic methods. The results of the analyses mainly indicated the high quality of AlphaFold modelling and the possibility of using the AlphaFold predictions, together with other methods, for the reconstruction of the evolutionary relationships between distant viral groups. Based on the results of this integrated approach, assumptions have been made about refining the taxonomic classification of bacterial and archaeal Duplodnaviria groups, and problems relating to the taxonomic classification of Duplodnaviria have been discussed.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
| | - Daria Gutnik
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Mikhail Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
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10
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Rai P, Shetty SS, Prabell S, Kuntar A, Pinto D, Kumar BK, Divyashree M, Raj JRM, Premanath R, Deekshit VK, Karunasagar I, Karunasagar I. Characterisation of broad-spectrum phiKZ like jumbo phage and its utilisation in controlling multidrug-resistant Pseudomonas aeruginosa isolates. Microb Pathog 2022; 172:105767. [PMID: 36096457 DOI: 10.1016/j.micpath.2022.105767] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/25/2022] [Accepted: 09/05/2022] [Indexed: 12/01/2022]
Abstract
The emergence of highly virulent multidrug-resistant P. aeruginosa has become increasingly evident among hospital-acquired infections and has raised the need for alternative therapies. Phage therapy can be one such alternative to antibiotic therapy to combat multidrug-resistant pathogenic bacteria, but this requires the availability of phages with a broad host range. In this study, isolation and molecular characterisation of P. aeruginosa specific phages were carried out. A total of 17 phages isolated showed different spectra of activity and efficiency of lysis against 82 isolates of P. aeruginosa obtained from clinical samples (n = 13), hospital effluent (n = 46) and fish processing plant effluent (n = 23). Antibiotic susceptibility test results revealed multi-drug resistance in 61 of the total 82 isolates. Three new jumbo lytic P. aeruginosa specific broad host range phages were isolated and characterised in this present study belonged to the family Myoviridae (order Caudovirales). The genetic analysis of ɸU5 revealed that phage has a genome size of 282.6 kbp with 373 putative open reading frames (ORFs), and its genetic architecture is similar to phiKZ like jumbo phages infecting P. aeruginosa. The bacteriophages isolated in this study had lytic ability against biofilm-forming and multidrug-resistant P. aeruginosa and could be candidates for further studies towards phage therapy.
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Affiliation(s)
- Praveen Rai
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India.
| | - Shruthi Seetharam Shetty
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Sujana Prabell
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Akshatha Kuntar
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Deepak Pinto
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Ballamoole Krishna Kumar
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Mithoor Divyashree
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Juliet Roshini Mohan Raj
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Ramya Premanath
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Vijaya Kumar Deekshit
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Indrani Karunasagar
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Iddya Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangaluru, 575018, India
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11
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A cytoskeletal vortex drives phage nucleus rotation during jumbo phage replication in E. coli. Cell Rep 2022; 40:111179. [PMID: 35977483 PMCID: PMC9891218 DOI: 10.1016/j.celrep.2022.111179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/29/2022] [Accepted: 07/19/2022] [Indexed: 02/03/2023] Open
Abstract
Nucleus-forming jumbo phages establish an intricate subcellular organization, enclosing phage genomes within a proteinaceous shell called the phage nucleus. During infection in Pseudomonas, some jumbo phages assemble a bipolar spindle of tubulin-like PhuZ filaments that positions the phage nucleus at midcell and drives its intracellular rotation. This facilitates the distribution of capsids on its surface for genome packaging. Here we show that the Escherichia coli jumbo phage Goslar assembles a phage nucleus surrounded by an array of PhuZ filaments resembling a vortex instead of a bipolar spindle. Expression of a mutant PhuZ protein strongly reduces Goslar phage nucleus rotation, demonstrating that the PhuZ cytoskeletal vortex is necessary for rotating the phage nucleus. While vortex-like cytoskeletal arrays are important in eukaryotes for cytoplasmic streaming and nucleus alignment, this work identifies a coherent assembly of filaments into a vortex-like structure driving intracellular rotation within the prokaryotic cytoplasm.
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12
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Versoza CJ, Howell AA, Aftab T, Blanco M, Brar A, Chaffee E, Howell N, Leach W, Lobatos J, Luca M, Maddineni M, Mirji R, Mitra C, Strasser M, Munig S, Patel Z, So M, Sy M, Weiss S, Pfeifer SP. Comparative Genomics of Closely-Related Gordonia Cluster DR Bacteriophages. Viruses 2022; 14:v14081647. [PMID: 36016269 PMCID: PMC9413003 DOI: 10.3390/v14081647] [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: 05/16/2022] [Revised: 07/16/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Bacteriophages infecting bacteria of the genus Gordonia have increasingly gained interest in the scientific community for their diverse applications in agriculture, biotechnology, and medicine, ranging from biocontrol agents in wastewater management to the treatment of opportunistic pathogens in pulmonary disease patients. However, due to the time and costs associated with experimental isolation and cultivation, host ranges for many bacteriophages remain poorly characterized, hindering a more efficient usage of bacteriophages in these areas. Here, we perform a series of computational genomic inferences to predict the putative host ranges of all Gordonia cluster DR bacteriophages known to date. Our analyses suggest that BiggityBass (as well as several of its close relatives) is likely able to infect host bacteria from a wide range of genera—from Gordonia to Nocardia to Rhodococcus, making it a suitable candidate for future phage therapy and wastewater treatment strategies.
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Affiliation(s)
- Cyril J. Versoza
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Abigail A. Howell
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Tanya Aftab
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Madison Blanco
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Akarshi Brar
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Elaine Chaffee
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Nicholas Howell
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Willow Leach
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Jackelyn Lobatos
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Michael Luca
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Meghna Maddineni
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Ruchira Mirji
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Corinne Mitra
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Maria Strasser
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Saige Munig
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Zeel Patel
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Minerva So
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Makena Sy
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Sarah Weiss
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Susanne P. Pfeifer
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
- Correspondence:
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13
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Fraser A, Sokolova ML, Drobysheva AV, Gordeeva JV, Borukhov S, Jumper J, Severinov KV, Leiman PG. Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase. Nat Commun 2022; 13:3526. [PMID: 35725571 PMCID: PMC9209446 DOI: 10.1038/s41467-022-31214-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.
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Affiliation(s)
- Alec Fraser
- grid.176731.50000 0001 1547 9964Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0647 USA
| | - Maria L. Sokolova
- grid.176731.50000 0001 1547 9964Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0647 USA ,grid.454320.40000 0004 0555 3608Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - Arina V. Drobysheva
- grid.454320.40000 0004 0555 3608Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - Julia V. Gordeeva
- grid.454320.40000 0004 0555 3608Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - Sergei Borukhov
- grid.262671.60000 0000 8828 4546Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ 08084-1489 USA
| | - John Jumper
- grid.498210.60000 0004 5999 1726DeepMind Technologies Limited, London, UK
| | - Konstantin V. Severinov
- grid.454320.40000 0004 0555 3608Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia ,grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia ,grid.430387.b0000 0004 1936 8796Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Petr G. Leiman
- grid.176731.50000 0001 1547 9964Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0647 USA
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14
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The Beauty of Bacteriophage T4 Research: Lindsay W. Black and the T4 Head Assembly. Viruses 2022; 14:v14040700. [PMID: 35458430 PMCID: PMC9026906 DOI: 10.3390/v14040700] [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: 02/24/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023] Open
Abstract
Viruses are biochemically complex structures and mainly consist of folded proteins that contain nucleic acids. Bacteriophage T4 is one of most prominent examples, having a tail structure that contracts during the infection process. Intracellular phage multiplication leads to separate self-directed assembly reactions of proheads, tails and tail fibers. The proheads are packaged with concatemeric DNA produced by tandem replication reactions of the parental DNA molecule. Once DNA packaging is completed, the head is joined with the tail and six long fibers are attached. The mature particles are then released from the cell via lysis, another tightly regulated process. These processes have been studied in molecular detail leading to a fascinating view of the protein-folding dynamics that direct the structural interplay of assembled complexes. Lindsay W. Black dedicated his career to identifying and defining the molecular events required to form the T4 virion. He leaves us with rich insights into the astonishingly precise molecular clockwork that co-ordinates all of the players in T4 assembly, both viral and cellular. Here, we summarize Lindsay’s key research contributions that are certain to stimulate our future science for many years to come.
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15
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Trifonova TS, Moiseenko AV, Bourkaltseva MV, Shaburova OV, Shaytan AK, Krylov VN, Sokolova OS. [DNA mapping in the capsid of giant bacteriophage phiEL (Caudovirales: Myoviridae: Elvirus) by analytical electron microscopy]. Vopr Virusol 2022; 66:434-441. [PMID: 35019250 DOI: 10.36233/0507-4088-80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Giant phiKZ-like bacteriophages have a unique protein formation inside the capsid, an inner body (IB) with supercoiled DNA molecule wrapped around it. Standard cryo-electron microscopy (cryo-EM) approaches do not allow to distinguish this structure from the surrounding nucleic acid of the phage. We previously developed an analytical approach to visualize protein-DNA complexes on Escherichia coli bacterial cell slices using the chemical element phosphorus as a marker. In the study presented, we adapted this technique for much smaller objects, namely the capsids of phiKZ-like bacteriophages. MATERIAL AND METHODS Following electron microscopy techniques were used in the study: analytical (AEM) (electron energy loss spectroscopy, EELS), and cryo-EM (images of samples subjected to low and high dose of electron irradiation were compared). RESULTS We studied DNA packaging inside the capsids of giant bacteriophages phiEL from the Myoviridae family that infect Pseudomonas aeruginosa. Phosphorus distribution maps were obtained, showing an asymmetrical arrangement of DNA inside the capsid. DISCUSSION We developed and applied an IB imaging technique using a high angle dark-field detector (HAADF) and the STEM-EELS analytical approach. Phosphorus mapping by EELS and cryo-electron microscopy revealed a protein formation as IB within the phage phiEL capsid. The size of IB was estimated using theoretical calculations. CONCLUSION The developed technique can be applied to study the distribution of phosphorus in other DNA- or RNA-containing viruses at relatively low concentrations of the element sought.
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Affiliation(s)
- T S Trifonova
- FSAEI HE «People's Friendship University of Russia», Physical, Mathematical, and Natural Sciences Department; FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
| | - A V Moiseenko
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty; FSBIS «N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences»
| | | | - O V Shaburova
- FSBRI «I.I. Mechnikov Research Institute of Vaccines and Sera»
| | - A K Shaytan
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
| | - V N Krylov
- FSBRI «I.I. Mechnikov Research Institute of Vaccines and Sera»
| | - O S Sokolova
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
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16
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Nazir A, Ali A, Qing H, Tong Y. Emerging Aspects of Jumbo Bacteriophages. Infect Drug Resist 2021; 14:5041-5055. [PMID: 34876823 PMCID: PMC8643167 DOI: 10.2147/idr.s330560] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/30/2021] [Indexed: 01/21/2023] Open
Abstract
The bacteriophages have been explored at a huge scale as a model system for their applications in many biological-related fields. Jumbo phages with a large genome size from 200 to 500 kbp were not previously assigned a great value, and characterized by complex structures coupled with large virions with a wide variety of hosts. The origin of most of the jumbo phages was not well understood; however, many other prominent features have been discovered recently. In the current review, we strive to unearth the most advanced characteristics of jumbo phages, particularly their significance and structural organization that holds immense value to the viral life cycle. The unique characteristics of jumbo phages are the basis of variations in different types of phages concerning their organization at the genomic level, virion structure, evolution, and progeny propagation. The presence of tRNA and additional translation-related genes along with chaperonin genes mark the ability of these phages for being independent of host molecular machinery enabling them to have wide host options. A large number of jumbo phages have been isolated from various sources through advanced standard screening methods. The current review has summarized the available data on jumbo phages and discussed the genome orientation of jumbo phages, translational machinery, diversity and evolution of jumbo phages. In the studies conducted, jumbo phages possessed special additional genes that helps to reduce the dependence of jumbo phages on their hosts. Furthermore, their genomes might have evolved from smaller genome phages.
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Affiliation(s)
- Amina Nazir
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People’s Republic of China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Azam Ali
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People’s Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
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17
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Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness. ISME JOURNAL 2021; 16:533-542. [PMID: 34465897 PMCID: PMC8776877 DOI: 10.1038/s41396-021-01096-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 01/21/2023]
Abstract
When considering the interactions between bacteriophages and their host, the issue of phage-resistance emergence is a key element in understanding the ecological impact of phages on the bacterial population. It is also an essential parameter for the implementation of phage therapy to combat antibiotic-resistant pathogens. This study investigates the phenotypic and genetic responses of five Pseudomonas aeruginosa strains (PAO1, A5803, AA43, CHA, and PAK) to the infection by seven phages with distinct evolutionary backgrounds and recognised receptors (LPS/T4P). Emerging phage-insensitivity was generally accompanied by self and cross-resistance mechanisms. Significant differences were observed between the reference PAO1 responses compared to other clinical representatives. LPS-dependent phage infections in clinical strains selected for mutations in the "global regulatory" and "other" genes, rather than in the LPS-synthesis clusters detected in PAO1 clones. Reduced fitness, as proxied by the growth rate, was correlated with large deletion (20-500 kbp) and phage carrier state. Multi-phage resistance was significantly correlated with a reduced growth rate but only in the PAO1 population. In addition, we observed that the presence of prophages decreased the lytic phage maintenance seemingly protecting the host against carrier state and occasional lytic phage propagation, thus preventing a significant reduction in bacterial growth rate.
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18
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Moura de Sousa JA, Pfeifer E, Touchon M, Rocha EPC. Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa. Mol Biol Evol 2021; 38:2497-2512. [PMID: 33570565 PMCID: PMC8136500 DOI: 10.1093/molbev/msab044] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bacteriophages (phages) evolve rapidly by acquiring genes from other phages. This results in mosaic genomes. Here, we identify numerous genetic transfers between distantly related phages and aim at understanding their frequency, consequences, and the conditions favoring them. Gene flow tends to occur between phages that are enriched for recombinases, transposases, and nonhomologous end joining, suggesting that both homologous and illegitimate recombination contribute to gene flow. Phage family and host phyla are strong barriers to gene exchange, but phage lifestyle is not. Even if we observe four times more recent transfers between temperate phages than between other pairs, there is extensive gene flow between temperate and virulent phages, and between the latter. These predominantly involve virulent phages with large genomes previously classed as low gene flux, and lead to the preferential transfer of genes encoding functions involved in cell energetics, nucleotide metabolism, DNA packaging and injection, and virion assembly. Such exchanges may contribute to the observed twice larger genomes of virulent phages. We used genetic transfers, which occur upon coinfection of a host, to compare phage host range. We found that virulent phages have broader host ranges and can mediate genetic exchanges between narrow host range temperate phages infecting distant bacterial hosts, thus contributing to gene flow between virulent phages, as well as between temperate phages. This gene flow drastically expands the gene repertoires available for phage and bacterial evolution, including the transfer of functional innovations across taxa.
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Affiliation(s)
| | - Eugen Pfeifer
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
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19
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de Martín Garrido N, Orekhova M, Lai Wan Loong Y, Litvinova A, Ramlaul K, Artamonova T, Melnikov A, Serdobintsev P, Aylett CHS, Yakunina M. Structure of the bacteriophage PhiKZ non-virion RNA polymerase. Nucleic Acids Res 2021; 49:7732-7739. [PMID: 34181731 PMCID: PMC8287921 DOI: 10.1093/nar/gkab539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/04/2021] [Accepted: 06/24/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteriophage ΦKZ (PhiKZ) is the archetype of a family of massive bacterial viruses. It is considered to have therapeutic potential as its host, Pseudomonas aeruginosa, is an opportunistic, intrinsically antibiotic resistant, pathogen that kills tens of thousands worldwide each year. ΦKZ is an incredibly interesting virus, expressing many systems that the host already possesses. On infection, it forms a ‘nucleus’, erecting a barrier around its genome to exclude host endonucleases and CRISPR-Cas systems. ΦKZ infection is independent of the host transcriptional apparatus. It expresses two different multi-subunit RNA polymerases (RNAPs): the virion RNAP (vRNAP) is injected with the viral DNA during infection to transcribe early genes, including those encoding the non-virion RNAP (nvRNAP), which transcribes all further genes. ΦKZ nvRNAP is formed by four polypeptides thought to represent homologues of the eubacterial β/β′ subunits, and a fifth with unclear homology, but essential for transcription. We have resolved the structure of ΦKZ nvRNAP to better than 3.0 Å, shedding light on its assembly, homology, and the biological role of the fifth subunit: it is an embedded, integral member of the complex, the position, structural homology and biochemical role of which imply that it has evolved from an ancestral homologue to σ-factor.
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Affiliation(s)
| | | | | | - Anna Litvinova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Kailash Ramlaul
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Alexei S Melnikov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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20
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Xie Y, Thompson T, O'Leary C, Crosby S, Nguyen QX, Liu M, Gill JJ. Differential Bacteriophage Efficacy in Controlling Salmonella in Cattle Hide and Soil Models. Front Microbiol 2021; 12:657524. [PMID: 34262535 PMCID: PMC8273493 DOI: 10.3389/fmicb.2021.657524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 06/04/2021] [Indexed: 01/18/2023] Open
Abstract
Asymptomatic Salmonella carriage in beef cattle is a food safety concern and the beef feedlot environment and cattle hides are reservoirs of this pathogen. Bacteriophages present an attractive non-antibiotic strategy for control of Salmonella in beef. In this study, four diverse and genetically unrelated Salmonella phages, Sergei, Season12, Sw2, and Munch, were characterized and tested alone and in combination for their ability to control Salmonella in cattle hide and soil systems, which are relevant models for Salmonella control in beef production. Phage Sergei is a member of the genus Sashavirus, phage Season12 was identified as a member of the Chivirus genus, Sw2 was identified as a member of the T5-like Epseptimavirus genus, and Munch was found to be a novel “jumbo” myovirus. Observed pathogen reductions in the model systems ranged from 0.50 to 1.75 log10 CFU/cm2 in hides and from 0.53 to 1.38 log10 CFU/g in soil, with phages Sergei and Sw2 producing greater reductions (∼1 log10 CFU/cm2 or CFU/g) than Season12 and Munch. These findings are in accordance with previous observations of phage virulence, suggesting the simple ability of a phage to form plaques on a bacterial strain is not a strong indicator of antimicrobial activity, but performance in liquid culture assays provides a better predictor. The antimicrobial efficacies of phage treatments were found to be phage-specific across model systems, implying that a phage capable of achieving bacterial reduction in one model is more likely to perform well in another. Phage combinations did not produce significantly greater efficacy than single phages even after 24 h in the soil model, and phage-insensitive colonies were not isolated from treated samples, suggesting that the emergence of phage resistance was not a major factor limiting efficacy in this system.
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Affiliation(s)
- Yicheng Xie
- Department of Animal Science, Texas A&M University, College Station, TX, United States.,Center for Phage Technology, Texas A&M University, College Station, TX, United States
| | - Tyler Thompson
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Chandler O'Leary
- Center for Phage Technology, Texas A&M University, College Station, TX, United States.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Stephen Crosby
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Quang X Nguyen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Mei Liu
- Center for Phage Technology, Texas A&M University, College Station, TX, United States
| | - Jason J Gill
- Department of Animal Science, Texas A&M University, College Station, TX, United States.,Center for Phage Technology, Texas A&M University, College Station, TX, United States
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21
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Serwer P, Wright ET, De La Chapa J, Gonzales CB. Basics for Improved Use of Phages for Therapy. Antibiotics (Basel) 2021; 10:antibiotics10060723. [PMID: 34208477 PMCID: PMC8234457 DOI: 10.3390/antibiotics10060723] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/17/2022] Open
Abstract
Blood-borne therapeutic phages and phage capsids increasingly reach therapeutic targets as they acquire more persistence, i.e., become more resistant to non-targeted removal from blood. Pathogenic bacteria are targets during classical phage therapy. Metastatic tumors are potential future targets, during use of drug delivery vehicles (DDVs) that are phage derived. Phage therapy has, to date, only sometimes been successful. One cause of failure is low phage persistence. A three-step strategy for increasing persistence is to increase (1) the speed of lytic phage isolation, (2) the diversity of phages isolated, and (3) the effectiveness and speed of screening phages for high persistence. The importance of high persistence-screening is illustrated by our finding here of persistence dramatically higher for coliphage T3 than for its relative, coliphage T7, in murine blood. Coliphage T4 is more persistent, long-term than T3. Pseudomonas chlororaphis phage 201phi2-1 has relatively low persistence. These data are obtained with phages co-inoculated and separately assayed. In addition, highly persistent phage T3 undergoes dispersal to several murine organs and displays tumor tropism in epithelial tissue (xenografted human oral squamous cell carcinoma). Dispersal is an asset for phage therapy, but a liability for phage-based DDVs. We propose increased focus on phage persistence—and dispersal—screening.
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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;
- Correspondence: ; Tel.: +1-210-567-3765
| | - Elena T. Wright
- Department of Biochemistry and Structural Biology, The University of Texas Health Center, San Antonio, TX 78229-3900, USA;
| | - Jorge De La Chapa
- Department of Comprehensive Dentistry, The University of Texas Health Center, San Antonio, TX 78229-3900, USA; (J.D.L.C.); (C.B.G.)
| | - Cara B. Gonzales
- Department of Comprehensive Dentistry, The University of Texas Health Center, San Antonio, TX 78229-3900, USA; (J.D.L.C.); (C.B.G.)
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22
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Nguyen KT, Sugie J, Khanna K, Egan ME, Birkholz EA, Lee J, Beierschmitt C, Villa E, Pogliano J. Selective transport of fluorescent proteins into the phage nucleus. PLoS One 2021; 16:e0251429. [PMID: 34111132 PMCID: PMC8191949 DOI: 10.1371/journal.pone.0251429] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Upon infection of Pseudomonas cells, jumbo phages 201Φ2-1, ΦPA3, and ΦKZ assemble a phage nucleus. Viral DNA is enclosed within the phage-encoded proteinaceous shell along with proteins associated with DNA replication, recombination and transcription. Ribosomes and proteins involved in metabolic processes are excluded from the nucleus. RNA synthesis occurs inside the phage nucleus and messenger RNA is presumably transported into the cytoplasm to be translated. Newly synthesized proteins either remain in the cytoplasm or specifically translocate into the nucleus. The molecular mechanisms governing selective protein sorting and nuclear import in these phage infection systems are currently unclear. To gain insight into this process, we studied the localization of five reporter fluorescent proteins (GFP+, sfGFP, GFPmut1, mCherry, CFP). During infection with ΦPA3 or 201Φ2-1, all five fluorescent proteins were excluded from the nucleus as expected; however, we have discovered an anomaly with the ΦKZ nuclear transport system. The fluorescent protein GFPmut1, expressed by itself, was transported into the ΦKZ phage nucleus. We identified the amino acid residues on the surface of GFPmut1 required for nuclear targeting. Fusing GFPmut1 to any protein, including proteins that normally reside in the cytoplasm, resulted in transport of the fusion into the nucleus. Although the mechanism of transport is still unknown, we demonstrate that GFPmut1 is a useful tool that can be used for fluorescent labelling and targeting of proteins into the ΦKZ phage nucleus.
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Affiliation(s)
- Katrina T. Nguyen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Joseph Sugie
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Kanika Khanna
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - MacKennon E. Egan
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Erica A. Birkholz
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Jina Lee
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Christopher Beierschmitt
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Elizabeth Villa
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
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23
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Hill N, De Peña AC, Miller A, Lapizco-Encinas BH. On the potential of microscale electrokinetic cascade devices. Electrophoresis 2021; 42:2474-2482. [PMID: 33970503 DOI: 10.1002/elps.202100069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/20/2021] [Accepted: 04/24/2021] [Indexed: 12/22/2022]
Abstract
Phages used for phage therapy of multidrug resistant bacteria must be highly purified prior to use. There are limited purification approaches that are broadly applicable to many phage types. Electrokinetics has shown great potential to manipulate phages, but obstructions from the cell debris produced during phage propagation can severely diminish the capacity of an electrokinetic device to concentrate and purify phage samples. A multipart insulator-based electrokinetic device is proposed here to remove the larger, undesirable components of mixtures from phage preparations while transferring the freshly purified and concentrated sample to a second stage for downstream analysis. By combining the large debris prescreen and analysis stages in a streamlined system, this approach simultaneously reduces the impact of clogging and minimizes the sample loss observed during manual transferring of purified samples. Polystyrene particles were used to demonstrate a diminished sample loss of approximately one order of magnitude when using the cascade device as opposed to a manual transfer scheme. The purification and concentration of three different phage samples were demonstrated using the first stage of the cascade device as a prescreen. This design provides a simple method of purifying and concentrating valuable samples from a complex mixture that might impede separation capacity in a single channel.
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Affiliation(s)
- Nicole Hill
- Microscale Bioseparations Laboratory and Biomedical Engineering Department, Rochester Institute of Technology, Rochester, NY, USA
| | - Adriana Coll De Peña
- Microscale Bioseparations Laboratory and Biomedical Engineering Department, Rochester Institute of Technology, Rochester, NY, USA.,Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Abbi Miller
- Microscale Bioseparations Laboratory and Biomedical Engineering Department, Rochester Institute of Technology, Rochester, NY, USA
| | - Blanca H Lapizco-Encinas
- Microscale Bioseparations Laboratory and Biomedical Engineering Department, Rochester Institute of Technology, Rochester, NY, USA
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24
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Lee Y, Son B, Cha Y, Ryu S. Characterization and Genomic Analysis of PALS2, a Novel Staphylococcus Jumbo Bacteriophage. Front Microbiol 2021; 12:622755. [PMID: 33763042 PMCID: PMC7982418 DOI: 10.3389/fmicb.2021.622755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/09/2021] [Indexed: 12/30/2022] Open
Abstract
Staphylococcus aureus is an important human pathogen that can be frequently encountered in clinical and food-processing surroundings. Among the various countermeasures, bacteriophages have been considered to be promising alternatives to antibiotics. In this study, the bacteriophage PALS2 was isolated from bird feces, and the genomic and biological characteristics of this phage were investigated. PALS2 was determined to belong to the Myoviridae family and exhibited extended host inhibition that persisted for up to 24 h with repeated bursts of 12 plaque-forming units/cell. The complete genome of PALS2 measured 268,746 base pairs (bp), indicating that PALS2 could be classified as a jumbo phage. The PALS2 genome contained 279 ORFs and 1 tRNA covering asparagine, and the majority of predicted PALS2 genes encoded hypothetical proteins. Additional genes involved in DNA replication and repair, nucleotide metabolism, and genes encoding multisubunit RNA polymerase were identified in the PALS2 genome, which is a common feature of typical jumbo phages. Comparative genomic analysis indicated that PALS2 is a phiKZ-related virus and is more similar to typical jumbo phages than to staphylococcal phages. Additionally, the effective antimicrobial activities of phage PALS2 suggest its possible use as a biocontrol agent in various clinical and food processing environments.
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Affiliation(s)
- Yoona Lee
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Bokyung Son
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yoyeon Cha
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
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25
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A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions. mBio 2021; 12:mBio.03454-20. [PMID: 33563827 PMCID: PMC8545117 DOI: 10.1128/mbio.03454-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Gram-negative rod-shaped bacterium Pseudomonas aeruginosa is not only a major cause of nosocomial infections but also serves as a model species of bacterial RNA biology. While its transcriptome architecture and posttranscriptional regulation through the RNA-binding proteins Hfq, RsmA, and RsmN have been studied in detail, global information about stable RNA-protein complexes in this human pathogen is currently lacking. Here, we implement gradient profiling by sequencing (Grad-seq) in exponentially growing P. aeruginosa cells to comprehensively predict RNA and protein complexes, based on glycerol gradient sedimentation profiles of >73% of all transcripts and ∼40% of all proteins. As to benchmarking, our global profiles readily reported complexes of stable RNAs of P. aeruginosa, including 6S RNA with RNA polymerase and associated product RNAs (pRNAs). We observe specific clusters of noncoding RNAs, which correlate with Hfq and RsmA/N, and provide a first hint that P. aeruginosa expresses a ProQ-like FinO domain-containing RNA-binding protein. To understand how biological stress may perturb cellular RNA/protein complexes, we performed Grad-seq after infection by the bacteriophage ΦKZ. This model phage, which has a well-defined transcription profile during host takeover, displayed efficient translational utilization of phage mRNAs and tRNAs, as evident from their increased cosedimentation with ribosomal subunits. Additionally, Grad-seq experimentally determines previously overlooked phage-encoded noncoding RNAs. Taken together, the Pseudomonas protein and RNA complex data provided here will pave the way to a better understanding of RNA-protein interactions during viral predation of the bacterial cell.
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26
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Krylov V, Bourkaltseva M, Pleteneva E, Shaburova O, Krylov S, Karaulov A, Zhavoronok S, Svitich O, Zverev V. Phage phiKZ-The First of Giants. Viruses 2021; 13:149. [PMID: 33498475 PMCID: PMC7909554 DOI: 10.3390/v13020149] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
The paper covers the history of the discovery and description of phiKZ, the first known giant bacteriophage active on Pseudomonas aeruginosa. It also describes its unique features, especially the characteristic manner of DNA packing in the head around a cylinder-shaped structure ("inner body"), which probably governs an ordered and tight packaging of the phage genome. Important properties of phiKZ-like phages include a wide range of lytic activity and the blue opalescence of their negative colonies, and provide a background for the search and discovery of new P. aeruginosa giant phages. The importance of the phiKZ species and of other giant phage species in practical phage therapy is noted given their broad use in commercial phage preparations.
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Affiliation(s)
- Victor Krylov
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Maria Bourkaltseva
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Elena Pleteneva
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Olga Shaburova
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Sergey Krylov
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Alexander Karaulov
- Department of Clinical Immunology and Allergy, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia;
| | - Sergey Zhavoronok
- Department of Infectious Diseases, Belarusian State Medical University, 220116 Minsk, Belarus;
| | - Oxana Svitich
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
- Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
| | - Vitaly Zverev
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
- Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
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27
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Abstract
Since their discovery more than 100 years ago, the viruses that infect bacteria (bacteriophages) have been widely studied as model systems. Largely overlooked, however, have been "jumbo phages," with genome sizes ranging from 200 to 500 kbp. Jumbo phages generally have large virions with complex structures and a broad host spectrum. While the majority of jumbo phage genes are poorly functionally characterized, recent work has discovered many unique biological features, including a conserved tubulin homolog that coordinates a proteinaceous nucleus-like compartment that houses and segregates phage DNA. The tubulin spindle displays dynamic instability and centers the phage nucleus within the bacterial host during phage infection for optimal reproduction. The shell provides robust physical protection for the enclosed phage genomes against attack from DNA-targeting bacterial immune systems, thereby endowing jumbo phages with broad resistance. In this review, we focus on the current knowledge of the cytoskeletal elements and the specialized nuclear compartment derived from jumbo phages, and we highlight their importance in facilitating spatial and temporal organization over the viral life cycle. Additionally, we discuss the evolutionary relationships between jumbo phages and eukaryotic viruses, as well as the therapeutic potential and drawbacks of jumbo phages as antimicrobial agents in phage therapy.
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28
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Landyshev NN, Voronko YG, Kulikov EE, Sykilinda NN, Miroshnikov KA. Preparative Purification of Pseudomonas aeruginosa Bacteriophages via the Combination of Gel-Permeation and Anion-Exchage Chromatography. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820060095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Wicke L, Ponath F, Coppens L, Gerovac M, Lavigne R, Vogel J. Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ. RNA Biol 2020; 18:1099-1110. [PMID: 33103565 PMCID: PMC8244752 DOI: 10.1080/15476286.2020.1827785] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of Pseudomonas aeruginosa jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (cdrAB) and iron storage (bfrB), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (atpCDGHF and cyoABCDE). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.
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Affiliation(s)
- Laura Wicke
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lucas Coppens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
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30
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Maturation of Pseudo-Nucleus Compartment in P. aeruginosa, Infected with Giant phiKZ Phage. Viruses 2020; 12:v12101197. [PMID: 33096802 PMCID: PMC7589130 DOI: 10.3390/v12101197] [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: 08/26/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 12/25/2022] Open
Abstract
The giant phiKZ phage infection induces the appearance of a pseudo-nucleus inside the bacterial cytoplasm. Here, we used RT-PCR, fluorescent in situ hybridization (FISH), electron tomography, and analytical electron microscopy to study the morphology of this unique nucleus-like shell and to demonstrate the distribution of phiKZ and bacterial DNA in infected Pseudomonas aeruginosa cells. The maturation of the pseudo-nucleus was traced in short intervals for 40 min after infection and revealed the continuous spatial separation of the phage and host DNA. Immediately after ejection, phage DNA was located inside the newly-identified round compartments; at a later infection stage, it was replicated inside the pseudo-nucleus; in the mature pseudo-nucleus, a saturated internal network of filaments was observed. This network consisted of DNA bundles in complex with DNA-binding proteins. On the other hand, the bacterial nucleoid underwent significant rearrangements during phage infection, yet the host DNA did not completely degrade until at least 40 min after phage application. Energy dispersive x-ray spectroscopy (EDX) analysis revealed that, during the infection, the sulfur content in the bacterial cytoplasm increased, which suggests an increase of methionine-rich DNA-binding protein synthesis, whose role is to protect the bacterial DNA from stress caused by infection.
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31
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Multisubunit RNA Polymerases of Jumbo Bacteriophages. Viruses 2020; 12:v12101064. [PMID: 32977622 PMCID: PMC7598289 DOI: 10.3390/v12101064] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
Prokaryotic viruses with DNA genome longer than 200 kb are collectively referred to as “jumbo phages”. Some representatives of this phylogenetically diverse group encode two DNA-dependent RNA polymerases (RNAPs)—a virion RNAP and a non-virion RNAP. In contrast to most other phage-encoded RNAPs, the jumbo phage RNAPs are multisubunit enzymes related to RNAPs of cellular organisms. Unlike all previously characterized multisubunit enzymes, jumbo phage RNAPs lack the universally conserved alpha subunits required for enzyme assembly. The mechanism of promoter recognition is also different from those used by cellular enzymes. For example, the AR9 phage non-virion RNAP requires uracils in its promoter and is able to initiate promoter-specific transcription from single-stranded DNA. Jumbo phages encoding multisubunit RNAPs likely have a common ancestor allowing making them a separate subgroup within the very diverse group of jumbo phages. In this review, we describe transcriptional strategies used by RNAP-encoding jumbo phages and describe the properties of characterized jumbo phage RNAPs.
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32
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A Cut above the Rest: Characterization of the Assembly of a Large Viral Icosahedral Capsid. Viruses 2020; 12:v12070725. [PMID: 32635654 PMCID: PMC7411985 DOI: 10.3390/v12070725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022] Open
Abstract
The head of Salmonella virus SPN3US is composed of ~50 different proteins and is unusual because within its packaged genome there is a mass (>40 MDa) of ejection or E proteins that enter the Salmonella cell. The assembly mechanisms of this complex structure are poorly understood. Previous studies showed that eight proteins in the mature SPN3US head had been cleaved by the prohead protease. In this study, we present the characterization of SPN3US prohead protease mutants using transmission electron microscopy and mass spectrometry. In the absence of the prohead protease, SPN3US head formation was severely impeded and proheads accumulated on the Salmonella inner membrane. This impediment is indicative of proteolysis being necessary for the release and subsequent DNA packaging of proheads in the wild-type phage. Proteomic analyses of gp245- proheads that the normal proteolytic processing of head proteins had not occurred. Assays of a recombinant, truncated form of the protease found it was active, leading us to hypothesize that the C-terminal propeptide has a role in targeting the protease into the prohead core. Our findings provide new evidence regarding the essential role of proteolysis for correct head assembly in this remarkable parasite.
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33
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Ong SP, Azam AH, Sasahara T, Miyanaga K, Tanji Y. Characterization of Pseudomonas lytic phages and their application as a cocktail with antibiotics in controlling Pseudomonas aeruginosa. J Biosci Bioeng 2020; 129:693-699. [DOI: 10.1016/j.jbiosc.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/30/2019] [Accepted: 02/01/2020] [Indexed: 12/27/2022]
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34
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Lood C, Danis‐Wlodarczyk K, Blasdel BG, Jang HB, Vandenheuvel D, Briers Y, Noben J, van Noort V, Drulis‐Kawa Z, Lavigne R. Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages. Environ Microbiol 2020; 22:2165-2181. [PMID: 32154616 PMCID: PMC7318152 DOI: 10.1111/1462-2920.14979] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 03/06/2020] [Indexed: 11/28/2022]
Abstract
Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage-bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA-Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non-coding RNAs (ncRNAs) and 93 virion-associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA-Seq revealed a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA-pncB1-nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene-sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage-encoded hijacking mechanisms.
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Affiliation(s)
- Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
- Department of Microbial and Molecular Systems, Laboratory of Computational Systems Biology, KU LeuvenLeuvenBelgium
| | - Katarzyna Danis‐Wlodarczyk
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
- Department of Pathogen Biology and ImmunologyInstitute of Genetics and Microbiology, University of WroclawWroclawPoland
| | - Bob G. Blasdel
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Ho Bin Jang
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Dieter Vandenheuvel
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Yves Briers
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Jean‐Paul Noben
- Biomedical Research Institute and Transnational University LimburgHasselt UniversityDiepenbeekBelgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems, Laboratory of Computational Systems Biology, KU LeuvenLeuvenBelgium
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | - Zuzanna Drulis‐Kawa
- Department of Pathogen Biology and ImmunologyInstitute of Genetics and Microbiology, University of WroclawWroclawPoland
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
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35
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Abstract
Huge bacteriophages display genome sizes that bridge the gap between viral and bacterial genomes. Large Pseudomonas phages elaborate a nucleus-like structure in the infected bacterial cell and a tubulin-like phage protein forms a kind of spindle apparatus. While this probably represents cases of convergent evolution, these observations revive the discussion on the origin of eukaryotic cells.
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Affiliation(s)
- Harald Brüssow
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven, Belgium
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36
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Lewis R, Clooney AG, Stockdale SR, Buttimer C, Draper LA, Ross RP, Hill C. Isolation of a Novel Jumbo Bacteriophage Effective Against Klebsiella aerogenes. Front Med (Lausanne) 2020; 7:67. [PMID: 32185177 PMCID: PMC7058600 DOI: 10.3389/fmed.2020.00067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/13/2020] [Indexed: 12/14/2022] Open
Abstract
Increasing levels of bacterial resistance to many common and last resort antibiotics has increased interest in finding new treatments. The low rate of approval of new antibiotics has led to the search for new and alternative antimicrobial compounds. Bacteriophages (phages) are bacterial viruses found in almost every environment. Phage therapy was historically investigated to control bacterial infections and is still in use in Georgia and as a treatment of last resort. Phage therapy is increasingly recognized as an alternative antimicrobial treatment for antibiotic resistant pathogens. A novel lytic Klebsiella aerogenes phage N1M2 was isolated from maize silage. Klebsiella aerogenes, a member of the ESKAPE bacterial pathogens, is an important target for new antimicrobial therapies. Klebsiella aerogenes can form biofilms on medical devices which aids its environmental persistence and for this reason we tested the effect of phage N1M2 against biofilms. Phage N1M2 successfully removed a pre-formed Klebsiella aerogenes biofilm. Biofilm assays were also carried out with Staphylococcus aureus and Phage K. Phage K successfully removed a preformed Staphylococcus aureus biofilm. Phage N1M2 and Phage K in combination were significantly better at removing a mixed community biofilm of Klebsiella aerogenes and Staphylococcus aureus than either phage alone.
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Affiliation(s)
- Rhea Lewis
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Adam G Clooney
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Stephen R Stockdale
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Buttimer
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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37
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A jumbo phage that forms a nucleus-like structure evades CRISPR-Cas DNA targeting but is vulnerable to type III RNA-based immunity. Nat Microbiol 2019; 5:48-55. [PMID: 31819217 DOI: 10.1038/s41564-019-0612-5] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages1. However, DNA modification2,3, the production of anti-CRISPR proteins4,5 and potentially other strategies enable phages to evade CRISPR-Cas. Here, we discovered a Serratia jumbo phage that evades type I CRISPR-Cas systems, but is sensitive to type III immunity. Jumbo phage infection resulted in a nucleus-like structure enclosed by a proteinaceous phage shell-a phenomenon only reported recently for distantly related Pseudomonas phages6,7. All three native CRISPR-Cas complexes in Serratia-type I-E, I-F and III-A-were spatially excluded from the phage nucleus and phage DNA was not targeted. However, the type III-A system still arrested jumbo phage infection by targeting phage RNA in the cytoplasm in a process requiring Cas7, Cas10 and an accessory nuclease. Type III, but not type I, systems frequently targeted nucleus-forming jumbo phages that were identified in global viral sequence datasets. The ability to recognize jumbo phage RNA and elicit immunity probably contributes to the presence of both RNA- and DNA-targeting CRISPR-Cas systems in many bacteria1,8. Together, our results support the model that jumbo phage nucleus-like compartments serve as a barrier to DNA-targeting, but not RNA-targeting, defences, and that this phenomenon is widespread among jumbo phages.
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38
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Imam M, Alrashid B, Patel F, Dowah ASA, Brown N, Millard A, Clokie MRJ, Galyov EE. vB_PaeM_MIJ3, a Novel Jumbo Phage Infecting Pseudomonas aeruginosa, Possesses Unusual Genomic Features. Front Microbiol 2019; 10:2772. [PMID: 31849908 PMCID: PMC6892783 DOI: 10.3389/fmicb.2019.02772] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/13/2019] [Indexed: 01/06/2023] Open
Abstract
Phages are the most abundant biological entity on Earth. There are many variants in phage virion sizes, morphology, and genome sizes. Large virion sized phages, with genome sizes greater than 200 kbp have been identified and termed as Jumbo phages. These phages exhibit certain characteristics that have not been reported in phages with smaller genomes. In this work, a jumbo phage named MIJ3 (vB_PaeM_MIJ3) that infects Pseudomonas aeruginosa PAO1 was isolated from an equine livery yard in Leicestershire, United Kingdom. The genome and biological characteristics of this phage have been investigated. MIJ3 is a Myovirus with multiple long tail fibers. Assessment of the host range of MIJ3 revealed that it has the ability to infect many clinical isolates of P. aeruginosa. Bioinformatics analysis of the phage genome indicated that MIJ3 is closely related to the Pseudomonas phage, PA5oct. MIJ3 possesses several unusual features that are either rarely present in other phages or have not yet been reported. In particular, MIJ3 encodes a FtsH-like protein, and a putative lysidine synthase, TilS. These two proteins have not been reported in phages. MIJ3 also possesses a split DNA polymerase B with a novel intein. Of particular interest, unlike other jumbo phages infecting Pseudomonas spp., MIJ3 lacks the genetic elements required for the formation of the phage nucleus, which was believed to be conserved across jumbo Pseudomonas phages.
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Affiliation(s)
- Mohammed Imam
- Department of Respiratory Sciences, College of Life Sciences, University of Leicester, Leicester, United Kingdom.,Laboratory Department, University Medical Center, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Bandar Alrashid
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom.,King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Faizal Patel
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Ahmed S A Dowah
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Nathan Brown
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
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39
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Leon-Velarde CG, Jun JW, Skurnik M. Yersinia Phages and Food Safety. Viruses 2019; 11:E1105. [PMID: 31795231 PMCID: PMC6950378 DOI: 10.3390/v11121105] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022] Open
Abstract
One of the human- and animal-pathogenic species in genus Yersinia is Yersinia enterocolitica, a food-borne zoonotic pathogen that causes enteric infections, mesenteric lymphadenitis, and sometimes sequelae such as reactive arthritis and erythema nodosum. Y. enterocolitica is able to proliferate at 4 C, making it dangerous if contaminated food products are stored under refrigeration. The most common source of Y. enterocolitica is raw pork meat. Microbiological detection of the bacteria from food products is hampered by its slow growth rate as other bacteria overgrow it. Bacteriophages can be exploited in several ways to increase food safety with regards to contamination by Y. enterocolitica. For example, Yersinia phages could be useful in keeping the contamination of food products under control, or, alternatively, the specificity of the phages could be exploited in developing rapid and sensitive diagnostic tools for the identification of the bacteria in food products. In this review, we will discuss the present state of the research on these topics.
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Affiliation(s)
- Carlos G. Leon-Velarde
- Agriculture and Food Laboratory, Laboratory Services Division, University of Guelph, Guelph, ON N1H 8J7, Canada;
| | - Jin Woo Jun
- Department of Aquaculture, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 HY Helsinki, Finland
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, 00029 HUS Helsinki, Finland
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40
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Olszak T, Danis-Wlodarczyk K, Arabski M, Gula G, Maciejewska B, Wasik S, Lood C, Higgins G, Harvey BJ, Lavigne R, Drulis-Kawa Z. Pseudomonas aeruginosa PA5oct Jumbo Phage Impacts Planktonic and Biofilm Population and Reduces Its Host Virulence. Viruses 2019; 11:E1089. [PMID: 31771160 PMCID: PMC6950013 DOI: 10.3390/v11121089] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
The emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. Here, we analyze the impact of PA5oct jumbo phage treatment on planktonic/cell line associated and sessile P. aeruginosa population. Besides its broad-spectrum activity and efficient bacteria reduction in both airway surface liquid (ASL) model, and biofilm matrix degradation, PA5oct appears to persist in most of phage-resistant clones. Indeed, a high percentage of resistance (20/30 clones) to PA5oct is accompanied by the presence of phage DNA within bacterial culture. Moreover, the maintenance of this phage in the bacterial population correlates with reduced P. aeruginosa virulence, coupled with a sensitization to innate immune mechanisms, and a significantly reduced growth rate. We observed rather unusual consequences of PA5oct infection causing an increased inflammatory response of monocytes to P. aeruginosa. This phenomenon, combined with the loss or modification of the phage receptor, makes most of the phage-resistant clones significantly less pathogenic in in vivo model. These findings provide new insights into the general knowledge of giant phages biology and the impact of their application in phage therapy.
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Affiliation(s)
- Tomasz Olszak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Katarzyna Danis-Wlodarczyk
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Michal Arabski
- Department of Biochemistry and Genetics, Institute of Biology, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Grzegorz Gula
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Slawomir Wasik
- Department of Molecular Physics, Institute of Physics, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Cédric Lood
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
- Laboratory of Computational Systems Biology, KU Leuven, 3000 Leuven, Belgium
| | - Gerard Higgins
- National Children Research Centre, Our Lady’s Children’s Hospital, Crumlin, 12 Dublin, Ireland;
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Brian J. Harvey
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
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41
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Sharma R, Pielstick BA, Bell KA, Nieman TB, Stubbs OA, Yeates EL, Baltrus DA, Grose JH. A Novel, Highly Related Jumbo Family of Bacteriophages That Were Isolated Against Erwinia. Front Microbiol 2019; 10:1533. [PMID: 31428059 PMCID: PMC6690015 DOI: 10.3389/fmicb.2019.01533] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 01/17/2023] Open
Abstract
Erwinia amylovora is a plant pathogen from the Erwiniaceae family and a causative agent of the devastating agricultural disease fire blight. Here we characterize eight lytic bacteriophages of E. amylovora that we isolated from the Wasatch front (Utah, United States) that are highly similar to vB_EamM_Ea35-70 which was isolated in Ontario, Canada. With the genome size ranging from 271 to 275 kb, this is a novel jumbo family of bacteriophages. These jumbo bacteriophages were further characterized through genomic and proteomic comparison, mass spectrometry, host range and burst size. Their proteomes are highly unstudied, with over 200 putative proteins with no known homologs. The production of 27 of these putative proteins was confirmed by mass spectrometry analysis. These bacteriophages appear to be most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity, however, we were only able to detect infection of Erwinia and the closely related strains of Pantoea.
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Affiliation(s)
- Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Brittany A. Pielstick
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Kimberly A. Bell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Tanner B. Nieman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Olivia A. Stubbs
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Edward L. Yeates
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - David A. Baltrus
- School of Plant Sciences, The University of Arizona, Tucson, AZ, United States
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
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42
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Analysis of Bacteriophages with Insulator-Based Dielectrophoresis. MICROMACHINES 2019; 10:mi10070450. [PMID: 31277396 PMCID: PMC6680707 DOI: 10.3390/mi10070450] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 02/07/2023]
Abstract
Bacterial viruses or phages have great potential in the medical and agricultural fields as alternatives to antibiotics to control nuisance populations of pathogenic bacteria. However, current analysis and purification protocols for phages tend to be resource intensive and have numbers of limitations, such as impacting phage viability. The present study explores the potential of employing the electrokinetic technique of insulator-based dielectrophoresis (iDEP) for virus assessment, separation and enrichment. In particular, the application of the parameter "trapping value" (Tv) is explored as a standardized iDEP signature for each phage species. The present study includes mathematical modeling with COMSOL Multiphysics and extensive experimentation. Three related, but genetically and structurally distinct, phages were studied: Salmonella enterica phage SPN3US, Pseudomonas aeruginosa phage ϕKZ and P. chlororaphis phage 201ϕ2-1. This is the first iDEP study on bacteriophages with large and complex virions and the results illustrate their virions can be successfully enriched with iDEP systems and still retain infectivity. In addition, our results indicate that characterization of the negative dielectrophoretic response of a phage in terms of Tv could be used for predicting individual virus behavior in iDEP systems. The findings reported here can contribute to the establishment of protocols to analyze, purify and/or enrich samples of known and unknown phages.
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43
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Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches. ISME JOURNAL 2019; 13:2500-2522. [PMID: 31201356 PMCID: PMC6776037 DOI: 10.1038/s41396-019-0450-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/07/2019] [Accepted: 05/26/2019] [Indexed: 12/19/2022]
Abstract
Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human body. Genome mining with comparative genomics, screening of clinical isolates, and profiling of metagenomes allowed characterization of 346 phages grouped in 52 clusters and 18 superclusters. Less than 10% of the identified phage clusters were represented by previously characterized phages. Prophage diversity patterns varied significantly for different phage types, host clades, and environmental niches. A more diverse phage community lysogenizes Haemophilus influenzae and Haemophilus parainfluenzae strains than Aggregatibacter actinomycetemcomitans and “Haemophilus ducreyi”. Co-infections occurred more often in “H. ducreyi”. Phages from Aggregatibacter actinomycetemcomitans preferably lysogenized strains of specific serotype. Prophage patterns shared by subspecies clades of different bacterial species suggest similar ecoevolutionary drivers. Changes in frequencies of DNA uptake signal sequences and guanine–cytosine content reflect phage-host long-term coevolution. Aggregatibacter and Haemophilus phages were prevalent at multiple oral sites. Together, these findings should help exploring the ecoevolutionary forces shaping virus-host interactions in the human microbiome. Putative lytic phages, especially phiKZ-like, may provide new therapeutic options.
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44
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Korf IHE, Meier-Kolthoff JP, Adriaenssens EM, Kropinski AM, Nimtz M, Rohde M, van Raaij MJ, Wittmann J. Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy. Viruses 2019; 11:E454. [PMID: 31109012 PMCID: PMC6563267 DOI: 10.3390/v11050454] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/29/2019] [Accepted: 05/15/2019] [Indexed: 12/18/2022] Open
Abstract
The aim of this study was to gain further insight into the diversity of Escherichia coli phagesfollowed by enhanced work on taxonomic issues in that field. Therefore, we present the genomiccharacterization and taxonomic classification of 50 bacteriophages against E. coli isolated fromvarious sources, such as manure or sewage. All phages were examined for their host range on a setof different E. coli strains, originating, e.g., from human diagnostic laboratories or poultry farms.Transmission electron microscopy revealed a diversity of morphotypes (70% Myo-, 22% Sipho-, and8% Podoviruses), and genome sequencing resulted in genomes sizes from ~44 to ~370 kb.Annotation and comparison with databases showed similarities in particular to T4- and T5-likephages, but also to less-known groups. Though various phages against E. coli are already describedin literature and databases, we still isolated phages that showed no or only few similarities to otherphages, namely phages Goslar, PTXU04, and KWBSE43-6. Genome-based phylogeny andclassification of the newly isolated phages using VICTOR resulted in the proposal of new generaand led to an enhanced taxonomic classification of E. coli phages.
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Affiliation(s)
- Imke H E Korf
- Leibniz Institute DSMZ⁻German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig,Germany.
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ⁻German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig,Germany.
| | | | - Andrew M Kropinski
- Departments of Food Science and Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Manfred Nimtz
- Protein Analytics Platform, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig,Germany.
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig,Germany.
| | - Mark J van Raaij
- Department of Macromolecular Structure, Centro Nacional de Biotecnologia CNB-CSIC, 28049 Madrid,Spain.
| | - Johannes Wittmann
- Leibniz Institute DSMZ⁻German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig,Germany.
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45
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Burrowes BH, Molineux IJ, Fralick JA. Directed in Vitro Evolution of Therapeutic Bacteriophages: The Appelmans Protocol. Viruses 2019; 11:v11030241. [PMID: 30862096 PMCID: PMC6466182 DOI: 10.3390/v11030241] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/27/2019] [Accepted: 03/08/2019] [Indexed: 01/07/2023] Open
Abstract
The ‘Appelmans protocol’ is used by Eastern European researchers to generate therapeutic phages with novel lytic host ranges. Phage cocktails are iteratively grown on a suite of mostly refractory bacterial isolates until the evolved cocktail can lyse the phage-resistant strains. To study this process, we developed a modified protocol using a cocktail of three Pseudomonas phages and a suite of eight phage-resistant (including a common laboratory strain) and two phage-sensitive Pseudomona aeruginosa strains. After 30 rounds of selection, phages were isolated from the evolved cocktail with greatly increased host range. Control experiments with individual phages showed little host-range expansion, and genomic analysis of one of the broad-host-range output phages showed its recombinatorial origin, suggesting that the protocol works predominantly via recombination between phages. The Appelmans protocol may be useful for evolving therapeutic phage cocktails as required from well-defined precursor phages.
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Affiliation(s)
- Ben H Burrowes
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA.
- Roche Molecular Systems, 983 University Avenue B200, Los Gatos, CA 95032, USA.
| | - Ian J Molineux
- Center for Infectious Disease, Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX 78712, USA.
| | - Joe A Fralick
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA.
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Weintraub ST, Mohd Redzuan NH, Barton MK, Md Amin NA, Desmond MI, Adams LE, Ali B, Pardo S, Molleur D, Wu W, Newcomb WW, Osier MV, Black LW, Steven AC, Thomas JA. Global Proteomic Profiling of Salmonella Infection by a Giant Phage. J Virol 2019; 93:e01833-18. [PMID: 30541839 PMCID: PMC6384053 DOI: 10.1128/jvi.01833-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/19/2018] [Indexed: 11/20/2022] Open
Abstract
The 240-kb Salmonella phage SPN3US genome encodes 264 gene products, many of which are functionally uncharacterized. We have previously used mass spectrometry to define the proteomes of wild-type and mutant forms of the SPN3US virion. In this study, we sought to determine whether this technique was suitable for the characterization of the SPN3US proteome during liquid infection. Mass spectrometry of SPN3US-infected cells identified 232 SPN3US and 1,994 Salmonella proteins. SPN3US proteins with related functions, such as proteins with roles in DNA replication, transcription, and virion formation, were coordinately expressed in a temporal manner. Mass spectral counts showed the four most abundant SPN3US proteins to be the major capsid protein, two head ejection proteins, and the functionally unassigned protein gp22. This high abundance of gp22 in infected bacteria contrasted with its absence from mature virions, suggesting that it might be the scaffold protein, an essential head morphogenesis protein yet to be identified in giant phages. We identified homologs to SPN3US gp22 in 45 related giant phages, including ϕKZ, whose counterpart is also abundant in infected bacteria but absent in the virion. We determined the ϕKZ counterpart to be cleaved in vitro by its prohead protease, an event that has been observed to promote head maturation of some other phages. Our findings are consistent with a scaffold protein assignment for SPN3US gp22, although direct evidence is required for its confirmation. These studies demonstrate the power of mass spectral analyses for facilitating the acquisition of new knowledge into the molecular events of viral infection.IMPORTANCE "Giant" phages with genomes >200 kb are being isolated in increasing numbers from a range of environments. With hosts such as Salmonella enterica, Pseudomonas aeruginosa, and Erwinia amylovora, these phages are of interest for phage therapy of multidrug-resistant pathogens. However, our understanding of how these complex phages interact with their hosts is impeded by the proportion (∼80%) of their gene products that are functionally uncharacterized. To develop the repertoire of techniques for analysis of phages, we analyzed a liquid infection of Salmonella phage SPN3US (240-kb genome) using third-generation mass spectrometry. We observed the temporal production of phage proteins whose genes collectively represent 96% of the SPN3US genome. These findings demonstrate the sensitivity of mass spectrometry for global proteomic profiling of virus-infected cells, and the identification of a candidate for a major head morphogenesis protein will facilitate further studies into giant phage head assembly.
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Affiliation(s)
- Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, Texas, USA
| | | | - Melissa K Barton
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Nur Amira Md Amin
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Maxim I Desmond
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Lily E Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Bazla Ali
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Sammy Pardo
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, Texas, USA
| | - Dana Molleur
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, Texas, USA
| | - Weimin Wu
- Laboratory of Structural Biology Research, National Institute for Arthritis, Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - William W Newcomb
- Laboratory of Structural Biology Research, National Institute for Arthritis, Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael V Osier
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Lindsay W Black
- Department of Biochemistry and Molecular Biology, The University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute for Arthritis, Musculoskeletal and Skin Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Julie A Thomas
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
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Genome Sequences of Nine Erwinia amylovora Bacteriophages. Microbiol Resour Announc 2018; 7:MRA00944-18. [PMID: 30533701 PMCID: PMC6256631 DOI: 10.1128/mra.00944-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 09/12/2018] [Indexed: 02/07/2023] Open
Abstract
Erwinia amylovora is a plant pathogen belonging to the Enterobacteriaceae family, a family containing many plant and animal pathogens. Herein, we announce nine genome sequences of E. amylovora bacteriophages isolated from infected apple trees along the Wasatch Front in Utah.
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48
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Duerkop BA, Kleiner M, Paez-Espino D, Zhu W, Bushnell B, Hassell B, Winter SE, Kyrpides NC, Hooper LV. Murine colitis reveals a disease-associated bacteriophage community. Nat Microbiol 2018; 3:1023-1031. [PMID: 30038310 PMCID: PMC6112176 DOI: 10.1038/s41564-018-0210-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/27/2018] [Indexed: 02/08/2023]
Abstract
The dysregulation of intestinal microbial communities is associated with inflammatory bowel diseases (IBD). Studies aimed at understanding the contribution of the microbiota to inflammatory diseases have primarily focused on bacteria, yet the intestine harbors a viral component dominated by prokaryotic viruses known as bacteriophages (phages). Phage numbers are elevated at the intestinal mucosal surface and phages increase in abundance during IBD, suggesting that phages play an unidentified role in IBD. We used a sequence independent approach for the selection of viral contigs and then applied quantitative metagenomics to study intestinal phages in a mouse model of colitis. We discovered that during colitis the intestinal phage population is altered and transitions from an ordered state to a stochastic dysbiosis. We identified phages specific to pathobiotic hosts associated with intestinal disease, whose abundances are significantly altered during colitis. Additionally, phage populations in healthy and diseased mice overlapped with phages from healthy humans and humans with IBD. Our findings indicate that intestinal phage communities are altered during inflammatory disease establishing a platform for investigating phage involvement in IBD.
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Affiliation(s)
- Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA.
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
| | | | - Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Brian Bushnell
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Brian Hassell
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Lora V Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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49
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McCutcheon JG, Peters DL, Dennis JJ. Identification and Characterization of Type IV Pili as the Cellular Receptor of Broad Host Range Stenotrophomonas maltophilia Bacteriophages DLP1 and DLP2. Viruses 2018; 10:E338. [PMID: 29925793 PMCID: PMC6024842 DOI: 10.3390/v10060338] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/10/2018] [Accepted: 06/15/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteriophages DLP1 and DLP2 are capable of infecting both Stenotrophomonas maltophilia and Pseudomonas aeruginosa strains, two highly antibiotic resistant bacterial pathogens, which is unusual for phages that typically exhibit extremely limited host range. To explain their unusual cross-order infectivity and differences in host range, we have identified the type IV pilus as the primary receptor for attachment. Screening of a P. aeruginosa PA01 mutant library, a host that is susceptible to DLP1 but not DLP2, identified DLP1-resistant mutants with disruptions in pilus structural and regulatory components. Subsequent complementation of the disrupted pilin subunit genes in PA01 restored DLP1 infection. Clean deletion of the major pilin subunit, pilA, in S. maltophilia strains D1585 and 280 prevented phage binding and lysis by both DLP1 and DLP2, and complementation restored infection by both. Transmission electron microscopy shows a clear interaction between DLP1 and pili of both D1585 and PA01. These results support the identity of the type IV pilus as the receptor for DLP1 and DLP2 infection across their broad host ranges. This research further characterizes DLP1 and DLP2 as potential “anti-virulence” phage therapy candidates for the treatment of multidrug resistant bacteria from multiple genera.
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MESH Headings
- Bacterial Proteins/genetics
- Bacteriophages/metabolism
- Bacteriophages/ultrastructure
- Drug Resistance, Multiple, Bacterial
- Fimbriae Proteins/deficiency
- Fimbriae Proteins/genetics
- Fimbriae, Bacterial/chemistry
- Fimbriae, Bacterial/genetics
- Fimbriae, Bacterial/metabolism
- Fimbriae, Bacterial/ultrastructure
- Genetic Complementation Test
- Host Specificity
- Humans
- Microscopy, Electron, Transmission
- Mutation
- Phage Therapy
- Pseudomonas Phages/metabolism
- Pseudomonas aeruginosa/genetics
- Pseudomonas aeruginosa/virology
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Stenotrophomonas maltophilia/chemistry
- Stenotrophomonas maltophilia/genetics
- Stenotrophomonas maltophilia/virology
- Virulence
- Virus Attachment
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Affiliation(s)
- Jaclyn G McCutcheon
- CW405 Biological Sciences Building, 11455 Saskatchewan Dr. NW, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Danielle L Peters
- CW405 Biological Sciences Building, 11455 Saskatchewan Dr. NW, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jonathan J Dennis
- CW405 Biological Sciences Building, 11455 Saskatchewan Dr. NW, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
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50
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Chaikeeratisak V, Nguyen K, Egan ME, Erb ML, Vavilina A, Pogliano J. The Phage Nucleus and Tubulin Spindle Are Conserved among Large Pseudomonas Phages. Cell Rep 2018; 20:1563-1571. [PMID: 28813669 DOI: 10.1016/j.celrep.2017.07.064] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/13/2017] [Accepted: 07/24/2017] [Indexed: 01/27/2023] Open
Abstract
We recently demonstrated that the large Pseudomonas chlororaphis bacteriophage 201φ2-1 assembles a nucleus-like structure that encloses phage DNA and segregates proteins according to function, with DNA processing proteins inside and metabolic enzymes and ribosomes outside the nucleus. Here, we investigate the replication pathway of the Pseudomonas aeruginosa bacteriophages φKZ and φPA3. Bacteriophages φKZ and φPA3 encode a proteinaceous shell that assembles a nucleus-like structure that compartmentalizes proteins and DNA during viral infection. We show that the tubulin-like protein PhuZ encoded by each phage assembles a bipolar spindle that displays dynamic instability and positions the nucleus at midcell. Our results suggest that the phage spindle and nucleus play the same functional role in all three phages, 201φ2-1, φKZ, and φPA3, demonstrating that these key structures are conserved among large Pseudomonas phages.
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Affiliation(s)
- Vorrapon Chaikeeratisak
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katrina Nguyen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - MacKennon E Egan
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marcella L Erb
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anastasia Vavilina
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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