1
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Putzeys L, Wicke L, Brandão A, Boon M, Pires DP, Azeredo J, Vogel J, Lavigne R, Gerovac M. Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches. Curr Opin Microbiol 2024; 77:102419. [PMID: 38271748 PMCID: PMC10884466 DOI: 10.1016/j.mib.2023.102419] [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: 08/14/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
In the last decade, powerful high-throughput sequencing approaches have emerged to analyse microbial transcriptomes at a global scale. However, to date, applications of these approaches to microbial viruses such as phages remain scarce. Tailoring these techniques to virus-infected bacteria promises to obtain a detailed picture of the underexplored RNA biology and molecular processes during infection. In addition, transcriptome study of stress and perturbations induced by phages in their infected bacterial hosts is likely to reveal new fundamental mechanisms of bacterial metabolism and gene regulation. Here, we provide references and blueprints to implement emerging transcriptomic approaches towards addressing transcriptome architecture, RNA-RNA and RNA-protein interactions, RNA modifications, structures and heterogeneity of transcription profiles in infected cells that will provide guides for future directions in phage-centric therapeutic applications and microbial synthetic biology.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium; Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Ana Brandão
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Diana P Pires
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - 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
| | - Rob Lavigne
- 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; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
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2
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Chaban A, Minakhin L, Goldobina E, Bae B, Hao Y, Borukhov S, Putzeys L, Boon M, Kabinger F, Lavigne R, Makarova KS, Koonin EV, Nair SK, Tagami S, Severinov K, Sokolova ML. Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail. Nat Commun 2024; 15:317. [PMID: 38182597 PMCID: PMC10770324 DOI: 10.1038/s41467-023-44630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of the P23-45 RNAPs with other RNAPs suggest that, despite the extensive functional differences, the two P23-45 RNAPs originate from an ancient gene duplication in an ancestral phage. Our findings demonstrate striking adaptability of RNAPs that can be attained within a single virus species.
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Affiliation(s)
- Anastasiia Chaban
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, 19107, USA
| | - Ekaterina Goldobina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Brain Bae
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yue Hao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ, 08084-1489, USA
| | - Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Florian Kabinger
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Institute of Molecular Genetics National Kurchatov Center, Moscow, 123182, Russia.
| | - Maria L Sokolova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany.
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3
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Gonzalez-Serrano R, Rosselli R, Roda-Garcia JJ, Martin-Cuadrado AB, Rodriguez-Valera F, Dunne M. Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps. Nat Commun 2023; 14:6517. [PMID: 37845226 PMCID: PMC10579305 DOI: 10.1038/s41467-023-42114-8] [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: 02/20/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023] Open
Abstract
The host recognition modules encoding the injection machinery and receptor binding proteins (RBPs) of bacteriophages are predisposed to mutation and recombination to maintain infectivity towards co-evolving bacterial hosts. In this study, we reveal how Alteromonas mediterranea schitovirus A5 shares its host recognition module, including tail fiber and cognate chaperone, with phages from distantly related families including Alteromonas myovirus V22. While the V22 chaperone is essential for producing active tail fibers, here we demonstrate production of functional A5 tail fibers regardless of chaperone co-expression. AlphaFold-generated models of tail fiber and chaperone pairs from phages A5, V22, and other Alteromonas phages reveal how amino acid insertions within both A5-like proteins results in a knob domain duplication in the tail fiber and a chaperone β-hairpin "tentacle" extension. These structural modifications are linked to differences in chaperone dependency between the A5 and V22 tail fibers. Structural similarity between the chaperones and intramolecular chaperone domains of other phage RBPs suggests an additional function of these chaperones as transient fiber "caps". Finally, our identification of homologous host recognition modules from morphologically distinct phages implies that horizontal gene transfer and recombination events between unrelated phages may be a more common process than previously thought among Caudoviricetes phages.
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Affiliation(s)
- Rafael Gonzalez-Serrano
- Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain
- Centro de Biología Molecular Severo Ochoa, CBMSO-CSIC, Madrid, Spain
| | - Riccardo Rosselli
- Research & Development Department, LABAQUA S.A. Las Atalayas, Alicante, Spain
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | | | | | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Switzerland.
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4
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Antonova D, Belousova VV, Zhivkoplias E, Sobinina M, Artamonova T, Vishnyakov IE, Kurdyumova I, Arseniev A, Morozova N, Severinov K, Khodorkovskii M, Yakunina MV. The Dynamics of Synthesis and Localization of Jumbo Phage RNA Polymerases inside Infected Cells. Viruses 2023; 15:2096. [PMID: 37896872 PMCID: PMC10612078 DOI: 10.3390/v15102096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
A nucleus-like structure composed of phage-encoded proteins and containing replicating viral DNA is formed in Pseudomonas aeruginosa cells infected by jumbo bacteriophage phiKZ. The PhiKZ genes are transcribed independently from host RNA polymerase (RNAP) by two RNAPs encoded by the phage. The virion RNAP (vRNAP) transcribes early viral genes and must be injected into the cell with phage DNA. The non-virion RNAP (nvRNAP) is composed of early gene products and transcribes late viral genes. In this work, the dynamics of phage RNAPs localization during phage phiKZ infection were studied. We provide direct evidence of PhiKZ vRNAP injection in infected cells and show that it is excluded from the phage nucleus. The nvRNAP is synthesized shortly after the onset of infection and localizes in the nucleus. We propose that spatial separation of two phage RNAPs allows coordinated expression of phage genes belonging to different temporal classes.
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Affiliation(s)
- Daria Antonova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Viktoriia V. Belousova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Erik Zhivkoplias
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Mariia Sobinina
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Tatyana Artamonova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Innokentii E. Vishnyakov
- Group of Molecular Cytology of Prokaryotes and Bacterial Invasion, Institute of Cytology of the Russian Academy of Science, St. Petersburg 194064, Russia;
| | - Inna Kurdyumova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Anatoly Arseniev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Natalia Morozova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Konstantin Severinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
- Institute of Molecular Genetics National Kurchatov Center, Moscow 123182, Russia
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Mikhail Khodorkovskii
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Maria V. Yakunina
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
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5
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Tsai YC, Lee YP, Lin NT, Yang HH, Teh SH, Lin LC. Therapeutic effect and anti-biofilm ability assessment of a novel phage, phiPA1-3, against carbapenem-resistant Pseudomonas aeruginosa. Virus Res 2023; 335:199178. [PMID: 37490958 PMCID: PMC10430585 DOI: 10.1016/j.virusres.2023.199178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023]
Abstract
Multiple drug-resistant (MDR) Pseudomonas aeruginosa commonly causes severe hospital-acquired infections. The gradual emergence of carbapenem-resistant P. aeruginosa has recently gained attention. A wide array of P. aeruginosa-mediated pathogenic mechanisms, including its biofilm-forming ability, limits the use of effective antimicrobial treatments against it. In the present study, we isolated and characterized the phenotypic, biological, and genomic characteristics of a bacteriophage, vB_PaP_phiPA1-3 (phiPA1-3). Biofilm eradication and phage rescue from bacterial infections were assessed to demonstrate the efficacy of the application potential. Host range spectrum analysis revealed that phiPA1-3 is a moderate host range phage that infects 20% of the clinically isolated strains of P. aeruginosa tested, including carbapenem-resistant P. aeruginosa (CRPA). The phage exhibited stability at pH 7.0 and 9.0, with significantly reduced viability below pH 5.0 and beyond pH 9.0. phiPA1-3 is a lytic phage with a burst size of 619 plaque-forming units/infected cell at 37 °C and can effectively lyse bacteria in a multiplicity of infection-dependent manner. The genome size of phiPA1-3 was found to be 73,402 bp, with a G+C content of 54.7%, containing 93 open reading frames, of which 62 were annotated as hypothetical proteins and the remaining 31 had known functions. The phage possesses several proteins similar to those found in N4-like phages, including three types of RNA polymerases. This study concluded that phiPA1-3 belongs to the N4-like Schitoviridae family, can potentially eradicate P. aeruginosa biofilms, and thus, serve as a valuable tool for controlling CRPA infections.
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Affiliation(s)
- Yu-Chuan Tsai
- Institute of Medical Sciences, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC
| | - Yi-Pang Lee
- Department of Dentistry, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC
| | - Nien-Tsung Lin
- Master Program in Biomedical Science, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC
| | - Hsueh-Hui Yang
- Department of Medical Research, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC
| | - Soon-Hian Teh
- Division of Infectious Diseases, Department of Internal Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 707, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC.
| | - Ling-Chun Lin
- Institute of Medical Sciences, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC; Master Program in Biomedical Science, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien 97004, Taiwan, ROC.
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6
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Kumar A, Yadav A. Synthetic phage and its application in phage therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:61-89. [PMID: 37739560 DOI: 10.1016/bs.pmbts.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Synthetic phage analysis has been implemented in progressive various areas of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been altered for developing gene circuits to program biological systems. Due to their extremely potent potency, phages also provide greater medical availability against bacterial agents and bacterial diagnostic agents. Its host specificity and our growing ability to manipulate, them further expand its possibility. New Phages also genetically redesign programmable biomaterials with highly tunable properties. Moreover, new phages are central to powerful directed evolution platforms. It is used to enhance existing biological, functions to create new phages. In other sites, the mining of antibiotics, and the emergence and dissemination of more than one type of drug-resistant microbe, a human health concerns. The major point in controlling and treating microbial infections. At present, genetic modifications and biochemical treatments are used to modify phages. Among these, genetic engineering involves the identification of defective proteins, modification of host bodies, recognized receptors, and disruption of bacterial phage resistance signaling gateways.
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Affiliation(s)
- Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India.
| | - Anuj Yadav
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India
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7
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Pectobacterium versatile Bacteriophage Possum: A Complex Polysaccharide-Deacetylating Tail Fiber as a Tool for Host Recognition in Pectobacterial Schitoviridae. Int J Mol Sci 2022; 23:ijms231911043. [PMID: 36232343 PMCID: PMC9569702 DOI: 10.3390/ijms231911043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Novel, closely related phages Possum and Horatius infect Pectobacterium versatile, a phytopathogen causing soft rot in potatoes and other essential plants. Their properties and genomic composition define them as N4-like bacteriophages of the genus Cbunavirus, a part of a recently formed family Schitoviridae. It is proposed that the adsorption apparatus of these phages consists of tail fibers connected to the virion through an adapter protein. Tail fibers possess an enzymatic domain. Phage Possum uses it to deacetylate O-polysaccharide on the surface of the host strain to provide viral attachment. Such an infection mechanism is supposed to be common for all Cbunavirus phages and this feature should be considered when designing cocktails for phage control of soft rot.
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8
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Putzeys L, Boon M, Lammens EM, Kuznedelov K, Severinov K, Lavigne R. Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages. Comput Struct Biotechnol J 2022; 20:2624-2638. [PMID: 35685363 PMCID: PMC9163698 DOI: 10.1016/j.csbj.2022.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
- Corresponding author.
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9
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Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nat Commun 2020; 11:5294. [PMID: 33082347 PMCID: PMC7576135 DOI: 10.1038/s41467-020-19124-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022] Open
Abstract
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host. Non-model bacteria offer unique and versatile metabolisms for synthetic biology. In this Perspective, the authors explore the limited availability of well-characterised biological parts in these species and argue that bacteriophages represent a diverse trove of orthogonal parts.
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10
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Zhang W, Wu Q. Applications of phage-derived RNA-based technologies in synthetic biology. Synth Syst Biotechnol 2020; 5:343-360. [PMID: 33083579 PMCID: PMC7564126 DOI: 10.1016/j.synbio.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering tools. At the same time, phages are crucial for establishing and improving basic theories of molecular biology. Studies on phages provide rich sources of essential elements for synthetic circuit design as well as powerful support for the improvement of directed evolution platforms. Therefore, phages play a vital role in the development of new technologies and central scientific concepts. After the RNA world hypothesis was proposed and developed, novel biological functions of RNA continue to be discovered. RNA and its related elements are widely used in many fields such as metabolic engineering and medical diagnosis, and their versatility led to a major role of RNA in synthetic biology. Further development of RNA-based technologies will advance synthetic biological tools as well as provide verification of the RNA world hypothesis. Most synthetic biology efforts are based on reconstructing existing biological systems, understanding fundamental biological processes, and developing new technologies. RNA-based technologies derived from phages will offer abundant sources for synthetic biological components. Moreover, phages as well as RNA have high impact on biological evolution, which is pivotal for understanding the origin of life, building artificial life-forms, and precisely reprogramming biological systems. This review discusses phage-derived RNA-based technologies terms of phage components, the phage lifecycle, and interactions between phages and bacteria. The significance of RNA-based technology derived from phages for synthetic biology and for understanding the earliest stages of biological evolution will be highlighted.
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Affiliation(s)
- Wenhui Zhang
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- Corresponding author. MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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11
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Bebel A, Walsh MA, Mir-Sanchis I, Rice PA. A novel DNA primase-helicase pair encoded by SCC mec elements. eLife 2020; 9:55478. [PMID: 32945259 PMCID: PMC7581432 DOI: 10.7554/elife.55478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 09/17/2020] [Indexed: 01/18/2023] Open
Abstract
Mobile genetic elements (MGEs) are a rich source of new enzymes, and conversely, understanding the activities of MGE-encoded proteins can elucidate MGE function. Here, we biochemically characterize three proteins encoded by a conserved operon carried by the Staphylococcal Cassette Chromosome (SCCmec), an MGE that confers methicillin resistance to Staphylococcus aureus, creating MRSA strains. The first of these proteins, CCPol, is an active A-family DNA polymerase. The middle protein, MP, binds tightly to CCPol and confers upon it the ability to synthesize DNA primers de novo. The CCPol-MP complex is therefore a unique primase-polymerase enzyme unrelated to either known primase family. The third protein, Cch2, is a 3’-to-5’ helicase. Cch2 additionally binds specifically to a dsDNA sequence downstream of its gene that is also a preferred initiation site for priming by CCPol-MP. Taken together, our results suggest that this is a functional replication module for SCCmec.
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Affiliation(s)
- Aleksandra Bebel
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Melissa A Walsh
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Ignacio Mir-Sanchis
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
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12
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Clokie MR, Blasdel BG, Demars BO, Sicheritz-Pontén T. Rethinking Phage Ecology by Rooting it Within an Established Plant Framework. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:121-136. [PMID: 36147824 PMCID: PMC9041459 DOI: 10.1089/phage.2020.0015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Despite the abundance and significance of bacteriophages to microbial ecosystems, no broad ecological frameworks exist within which to determine "bacteriophage types" that reflect their ecological strategies and ways in which they interact with bacterial cells. To address this, we repurposed the well-established Grime's triangular CSR framework, which classifies plants according to three axes: competitiveness (C), ability to tolerate stress (S), and capacity to cope with disturbance (R). This framework is distinguished from other accepted schemes, as it seeks to identify individual characteristics of plants to understand their biological strategies and roles within an ecosystem. Our repurposing of the CSR triangle is based on phage transcription and the observation that typically phages have three major distinguishable transcription phases: early, middle, and late. We hypothesize that the proportion of genes expressed in these phases reflects key information about the phage "ecological strategy," namely the C, S, and R strategies, allowing us to examine phages in a similar way to how plants are projected onto the triangle. In the "phage version" of this scheme, we suggest: (1) that some phages prioritize the early phase of transcription that shuts off host defense mechanisms, which reflects competitiveness; (2) other phages prioritize tuning resource management mechanisms in the cell such as nucleotide metabolism during their "mid" expression profile to tolerate stress; and (3) a further subset of phages (termed Ruderals) survive disturbance by investing significant resources into regeneration so they express a higher proportion of their genes during late infection. We examined 42 published phage transcriptomes and show that they fall into discrete CSR categories according to their expression profiles. We discuss these positions in the context of their biology, which is largely consistent with our predictions of specific phage characteristics. In this opinion article, we suggest a starting point to ascribe phages into different functional types and thus understand them in an ecological framework. We suggest that this may have far-reaching implications for the application of phages in therapy and their exploitation to manipulate bacterial communities. We invite further use of this framework via our online tool; www.PhageCSR.ml.
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Affiliation(s)
- Martha R.J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Address correspondence to: Martha R.J. Clokie, PhD, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | | | - Thomas Sicheritz-Pontén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Address correspondence to: Thomas Sicheritz Pontén, PhD, Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Bygning 7, Copenhagen 1353, Denmark
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13
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Cheng M, Luo M, Xi H, Zhao Y, Le S, Chen LK, Tan D, Guan Y, Wang T, Han W, Wu N, Zhu T, Gu J. The characteristics and genome analysis of vB_ApiP_XC38, a novel phage infecting Acinetobacter pittii. Virus Genes 2020; 56:498-507. [PMID: 32449140 DOI: 10.1007/s11262-020-01766-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/11/2020] [Indexed: 12/27/2022]
Abstract
Acinetobacter pittii is an important pathogen causing nosocomial infection worldwide. In this study, a multidrug-resistant A. pittii ABC38 was used as host bacterium to isolate the lytic phage vB_ApiP_XC38. The biological characteristics of vB_ApiP_XC38 were studied and the genome was sequenced and analyzed. vB_ApiP_XC38 belonged to Podoviridae family. The phage had double-stranded genome, which comprised 79,328 bp with 39.58% G+C content displaying very low similarity (< 1% identity) with published genomes of other phages and bacteria. A total of 97 open reading frames (ORFs) were predicted and contained nucleotide metabolism and replication module, structural components module, and lysis module. The ANI, AAI, and phylogenetic analysis indicated that all phages were found distant from vB_ApiP_XC38. Altogether, morphological, genomics, and phylogenetic analysis suggest that vB_ApiP_XC38 is more likely a novel phage of A. pittii.
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Affiliation(s)
- Mengjun Cheng
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Man Luo
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Hengyu Xi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yunze Zhao
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Shuai Le
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,Department of Microbiology, Army Medical University, Chongqing, 400038, China
| | - Li-Kuang Chen
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Demeng Tan
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yuan Guan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Tianqi Wang
- College of Clinical Medicine, Jilin University, Changchun, 130021, China
| | - Wenyu Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, China
| | - Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
| | - Tongyu Zhu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
| | - Jingmin Gu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China. .,Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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14
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Shi X, Zhao F, Sun H, Yu X, Zhang C, Liu W, Pan Q, Ren H. Characterization and Complete Genome Analysis of Pseudomonas aeruginosa Bacteriophage vB_PaeP_LP14 Belonging to Genus Litunavirus. Curr Microbiol 2020; 77:2465-2474. [PMID: 32367280 DOI: 10.1007/s00284-020-02011-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/24/2020] [Indexed: 12/17/2022]
Abstract
A lytic Pseudomonas aeruginosa phage vB_PaeP_LP14 belonging to the family Podoviridae was isolated from infected mink. The microbiological characterization revealed that LP14 was stable at 40 to 50 °C and stable over a broad range of pH (5 to 12). The latent period was 5 min, and the burst size was 785 pfu/infected cell. The whole-genome sequencing showed that LP14 was a dsDNA virus and has a genome of 73,080 bp. The genome contained 93 predicted open reading frames (ORFs), 17 of which have known functions including DNA replication and modification, transcriptional regulation, structural and packaging proteins, and host cell lysis. No tRNA genes were identified. BLASTn analysis revealed that phage LP14 had a high-sequence identity (96%) with P. aeruginosa phage YH6. Both morphological characterization and genome annotation indicate that phage LP14 is a memberof the family Podoviridae genus Litunavirus. The study of phage LP14 will provide basic information for further research on treatment of P. aeruginosa infections.
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Affiliation(s)
- Xiaojie Shi
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Feiyang Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Huzhi Sun
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Xiaoyan Yu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China.
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15
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Boon M, De Zitter E, De Smet J, Wagemans J, Voet M, Pennemann FL, Schalck T, Kuznedelov K, Severinov K, Van Meervelt L, De Maeyer M, Lavigne R. 'Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses. Nucleic Acids Res 2020; 48:445-459. [PMID: 31724707 PMCID: PMC7145618 DOI: 10.1093/nar/gkz1048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial viruses encode a vast number of ORFan genes that lack similarity to any other known proteins. Here, we present a 2.20 Å crystal structure of N4-related Pseudomonas virus LUZ7 ORFan gp14, and elucidate its function. We demonstrate that gp14, termed here as Drc (ssDNA-binding RNA Polymerase Cofactor), preferentially binds single-stranded DNA, yet contains a structural fold distinct from other ssDNA-binding proteins (SSBs). By comparison with other SSB folds and creation of truncation and amino acid substitution mutants, we provide the first evidence for the binding mechanism of this unique fold. From a biological perspective, Drc interacts with the phage-encoded RNA Polymerase complex (RNAPII), implying a functional role as an SSB required for the transition from early to middle gene transcription during phage infection. Similar to the coliphage N4 gp2 protein, Drc likely binds locally unwound middle promoters and recruits the phage RNA polymerase. However, unlike gp2, Drc does not seem to need an additional cofactor for promoter melting. A comparison among N4-related phage genera highlights the evolutionary diversity of SSB proteins in an otherwise conserved transcription regulation mechanism.
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Affiliation(s)
- Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Elke De Zitter
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Jeroen De Smet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Jeroen Wagemans
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Marleen Voet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Friederike L Pennemann
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Thomas Schalck
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Luc Van Meervelt
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Marc De Maeyer
- Department of Chemistry, Laboratory of Biomolecular Modelling and Design, KU Leuven, Leuven 3001, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
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16
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Cubo MT, Alías-Villegas C, Balsanelli E, Mesa D, de Souza E, Espuny MR. Diversity of Sinorhizobium (Ensifer) meliloti Bacteriophages in the Rhizosphere of Medicago marina: Myoviruses, Filamentous and N4-Like Podovirus. Front Microbiol 2020; 11:22. [PMID: 32038600 PMCID: PMC6992544 DOI: 10.3389/fmicb.2020.00022] [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: 10/31/2019] [Accepted: 01/07/2020] [Indexed: 02/02/2023] Open
Abstract
Using different Sinorhizobium meliloti strains as hosts, we isolated eight new virulent phages from the rhizosphere of the coastal legume Medicago marina. Half of the isolated phages showed a very narrow host range while the other half exhibited a wider host range within the strains tested. Electron microscopy studies showed that phages M_ort18, M_sf1.2, and M_sf3.33 belonged to the Myoviridae family with feature long, contractile tails and icosaedral head. Phages I_sf3.21 and I_sf3.10T appeared to have filamentous shape and produced turbid plaques, which is a characteristic of phages from the Inoviridae family. Phage P_ort11 is a member of the Podoviridae, with an icosahedral head and a short tail and was selected for further characterization and genome sequencing. P_ort11 contained linear, double-stranded DNA with a length of 75239 bp and 103 putative open reading frames. BLASTP analysis revealed strong similarities to Escherichia phage N4 and other N4-like phages. This is the first report of filamentous and N4-like phages that infect S. meliloti.
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Affiliation(s)
- María Teresa Cubo
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Cynthia Alías-Villegas
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Eduardo Balsanelli
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Dany Mesa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanuel de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - María Rosario Espuny
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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17
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Sun X, Huang S, Long L. Characterization, complete genome and proteome of a bacteriophage infecting a coral-derived Vibrio strain. Mar Genomics 2019. [DOI: 10.1016/j.margen.2019.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Dendooven T, Lavigne R. Dip-a-Dee-Doo-Dah: Bacteriophage-Mediated Rescoring of a Harmoniously Orchestrated RNA Metabolism. Annu Rev Virol 2019; 6:199-213. [DOI: 10.1146/annurev-virology-092818-015644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA turnover and processing in bacteria are governed by the structurally divergent but functionally convergent RNA degradosome, and the mechanisms have been researched extensively in Gram-positive and Gram-negative bacteria. An emerging research field focuses on how bacterial viruses hijack all aspects of the bacterial metabolism, including the host machinery of RNA metabolism. This review addresses research on phage-based influence on RNA turnover, which can act either indirectly or via dedicated effector molecules that target degradosome assemblies. The structural divergence of host RNA turnover mechanisms likely explains the limited number of phage proteins directly targeting these specialized, host-specific complexes. The unique and nonconserved structure of DIP, a phage-encoded inhibitor of the Pseudomonas degradosome, illustrates this hypothesis. However, the natural occurrence of phage-encoded mechanisms regulating RNA turnover indicates a clear evolutionary benefit for this mode of host manipulation. Further exploration of the viral dark matter of unknown phage proteins may reveal more structurally novel interference strategies that, in turn, could be exploited for biotechnological applications.
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Affiliation(s)
- T. Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - R. Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium
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19
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Ren H, Li Z, Xu L, Li X, Wang L, Xu Y. Genome sequence analysis of Vibrio parahaemolyticus lytic phage Vp_R1 with a C3 morphotype. Arch Virol 2019; 164:2865-2871. [PMID: 31401694 DOI: 10.1007/s00705-019-04364-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/09/2019] [Indexed: 02/05/2023]
Abstract
Phage Vp_R1 belongs to the family Podoviridae and has a C3 morphotype, with an elongated head with a diameter of 190 ± 1.1 nm and an ultrashort tail with a length of 9 ± 1.2 nm. The double-stranded DNA genome is 112.1 kb long, has a mol% G + C content of 40.3, contains 129 ORFs, and encodes four tRNAs. Phylogenetic analysis suggests that phage Vp_R1 is a novel member of the genus Kuravirus.
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Affiliation(s)
- Hongyu Ren
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, People's Republic of China
| | - Zhen Li
- School of Ocean and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, People's Republic of China
- Postdoctoral Work Center in Dalian SEM Biological Engineering Co. Ltd, Dalian, 116620, People's Republic of China
| | - Le Xu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, People's Republic of China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, People's Republic of China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, People's Republic of China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, People's Republic of China.
- Postdoctoral Work Center in Dalian SEM Biological Engineering Co. Ltd, Dalian, 116620, People's Republic of China.
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20
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Molodtsov V, Murakami KS. Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II. J Biol Chem 2018; 293:13616-13625. [PMID: 29991593 PMCID: PMC6120196 DOI: 10.1074/jbc.ra118.003447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/19/2018] [Indexed: 01/07/2023] Open
Abstract
Genomes of phages, mitochondria, and chloroplasts are transcribed by a diverse group of transcriptional machineries with structurally related single-subunit RNA polymerases (RNAPs). Our understanding of transcription mechanisms of these enzymes is predominantly based on biochemical and structural studies of three most-studied members, transcription factor-independent phage T7 RNAP, transcription factor-dependent phage N4 virion-encapsidated RNAP, and transcription factor-dependent mitochondrial RNAPs (mtRNAP). Although these RNAPs employ completely different mechanisms for promoter recognition and transcription termination, these enzymes are relatively large and formed by single polypeptides. Historically being a model enzyme for studying the mechanisms of transcription by T7-like RNAPs, however, T7 RNAP represents only a small group of RNAPs in this family. The vast majority of T7-like RNAPs are transcription factor-dependent, and several of them are heterodimeric enzymes. Here, we report X-ray crystal structures of transcription complexes of the smallest and heterodimeric form of T7-like RNAP, bacteriophage N4 RNAPII, providing insights into the structural organization of a minimum RNAP in this family. We analyze structural and functional aspects of heterodimeric architecture of N4 RNAPII concerning the mechanisms of transcription initiation and transition to processive RNA elongation. Interestingly, N4 RNAPII maintains the same conformation in promoter-bound and elongation transcription complexes, revealing a novel transcription mechanism for single-subunit RNAPs. This work establishes a structural basis for studying mechanistic aspects of transcription by factor-dependent minimum RNAP.
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Affiliation(s)
- Vadim Molodtsov
- From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, To whom correspondence may be addressed. E-mail:
| | - Katsuhiko S. Murakami
- From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, To whom correspondence may be addressed. E-mail:
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21
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Abstract
Bacteriophage research has been instrumental to advancing many fields of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been adapted for building gene circuits to program biological systems. Phages also exhibit significant medical potential as antibacterial agents and bacterial diagnostics due to their extreme specificity for their host, and our growing ability to engineer them further enhances this potential. Phages have also been used as scaffolds for genetically programmable biomaterials that have highly tunable properties. Furthermore, phages are central to powerful directed evolution platforms, which are being leveraged to enhance existing biological functions and even produce new ones. In this review, we discuss recent examples of how phage research is influencing these next-generation biotechnologies.
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Affiliation(s)
- Sebastien Lemire
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Kevin M Yehl
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Timothy K Lu
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; .,Synthetic Biology Group, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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22
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Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves. PLoS One 2017; 12:e0190083. [PMID: 29284014 PMCID: PMC5746245 DOI: 10.1371/journal.pone.0190083] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/07/2017] [Indexed: 12/04/2022] Open
Abstract
A novel virulent bacteriophage, vB_VspP_pVa5, infecting a strain of Vibrio splendidus was isolated from a sea-cage aquaculture farm in Greece, and characterized using microbiological methods and genomic analysis. Bacteriophage vB_VspP_pVa5 is a N4-like podovirus with an icosahedral head measuring 85 nm in length and a short non-contractile tail. The phage had a narrow host range infecting only the bacterial host, a latent period of 30 min and a burst size of 24 virions per infected bacterium. Its genome size was 78,145 bp and genomic analysis identified 107 densely-packed genes, 40 of which could be annotated. In addition to the very large virion encapsulated DNA-dependent RNA polymerase which is the signature of the N4-like genus, an interesting feature of the novel phage is the presence of a self-splicing group I intron in the thymidylate synthase gene. A tRNAStop interrupted by a ~2.5kb open reading frame–containing area was also identified. The absence of genes related to lysogeny along with the high efficacy observed during in vitro cell lysis trials, indicate that the vB_VspP_pVa5 is a potential candidate component in a bacteriophage cocktail suitable for the biological control of V. splendidus in aquaculture.
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23
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Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. J Bacteriol 2017; 199:JB.00245-17. [PMID: 28559295 PMCID: PMC5512222 DOI: 10.1128/jb.00245-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/17/2017] [Indexed: 12/29/2022] Open
Abstract
Intense biological conflicts between prokaryotic genomes and their genomic parasites have resulted in an arms race in terms of the molecular “weaponry” deployed on both sides. Using a recursive computational approach, we uncovered a remarkable class of multidomain proteins with 2 to 15 domains in the same polypeptide deployed by viruses and plasmids in such conflicts. Domain architectures and genomic contexts indicate that they are part of a widespread conflict strategy involving proteins injected into the host cell along with parasite DNA during the earliest phase of infection. Their unique feature is the combination of domains with highly disparate biochemical activities in the same polypeptide; accordingly, we term them polyvalent proteins. Of the 131 domains in polyvalent proteins, a large fraction are enzymatic domains predicted to modify proteins, target nucleic acids, alter nucleotide signaling/metabolism, and attack peptidoglycan or cytoskeletal components. They further contain nucleic acid-binding domains, virion structural domains, and 40 novel uncharacterized domains. Analysis of their architectural network reveals both pervasive common themes and specialized strategies for conjugative elements and plasmids or (pro)phages. The themes include likely processing of multidomain polypeptides by zincin-like metallopeptidases and mechanisms to counter restriction or CRISPR/Cas systems and jump-start transcription or replication. DNA-binding domains acquired by eukaryotes from such systems have been reused in XPC/RAD4-dependent DNA repair and mitochondrial genome replication in kinetoplastids. Characterization of the novel domains discovered here, such as RNases and peptidases, are likely to aid in the development of new reagents and elucidation of the spread of antibiotic resistance. IMPORTANCE This is the first report of the widespread presence of large proteins, termed polyvalent proteins, predicted to be transmitted by genomic parasites such as conjugative elements, plasmids, and phages during the initial phase of infection along with their DNA. They are typified by the presence of multiple domains with disparate activities combined in the same protein. While some of these domains are predicted to assist the invasive element in replication, transcription, or protection of their DNA, several are likely to target various host defense systems or modify the host to favor the parasite's life cycle. Notably, DNA-binding domains from these systems have been transferred to eukaryotes, where they have been incorporated into DNA repair and mitochondrial genome replication systems.
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24
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Chevallereau A, Blasdel BG, De Smet J, Monot M, Zimmermann M, Kogadeeva M, Sauer U, Jorth P, Whiteley M, Debarbieux L, Lavigne R. Next-Generation "-omics" Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa. PLoS Genet 2016; 12:e1006134. [PMID: 27380413 PMCID: PMC4933390 DOI: 10.1371/journal.pgen.1006134] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/31/2016] [Indexed: 01/08/2023] Open
Abstract
As interest in the therapeutic and biotechnological potentials of bacteriophages has grown, so has value in understanding their basic biology. However, detailed knowledge of infection cycles has been limited to a small number of model bacteriophages, mostly infecting Escherichia coli. We present here the first analysis coupling data obtained from global next-generation approaches, RNA-Sequencing and metabolomics, to characterize interactions between the virulent bacteriophage PAK_P3 and its host Pseudomonas aeruginosa. We detected a dramatic global depletion of bacterial transcripts coupled with their replacement by viral RNAs over the course of infection, eventually leading to drastic changes in pyrimidine metabolism. This process relies on host machinery hijacking as suggested by the strong up-regulation of one bacterial operon involved in RNA processing. Moreover, we found that RNA-based regulation plays a central role in PAK_P3 lifecycle as antisense transcripts are produced mainly during the early stage of infection and viral small non coding RNAs are massively expressed at the end of infection. This work highlights the prominent role of RNA metabolism in the infection strategy of a bacteriophage belonging to a new characterized sub-family of viruses with promising therapeutic potential.
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Affiliation(s)
- Anne Chevallereau
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Bob G. Blasdel
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jeroen De Smet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Marc Monot
- Institut Pasteur, Laboratoire Pathogenèse des bactéries anaérobies, Département de Microbiologie, Paris, France
| | - Michael Zimmermann
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Maria Kogadeeva
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Peter Jorth
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Infectious Disease, University of Texas, Austin, Texas, United States of America
| | - Marvin Whiteley
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Infectious Disease, University of Texas, Austin, Texas, United States of America
| | - Laurent Debarbieux
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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25
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Yakunina M, Artamonova T, Borukhov S, Makarova KS, Severinov K, Minakhin L. A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage. Nucleic Acids Res 2015; 43:10411-20. [PMID: 26490960 PMCID: PMC4666361 DOI: 10.1093/nar/gkv1095] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/10/2015] [Indexed: 11/21/2022] Open
Abstract
The infection of Pseudomonas aeruginosa by the giant bacteriophage phiKZ is resistant to host RNA polymerase (RNAP) inhibitor rifampicin. phiKZ encodes two sets of polypeptides that are distantly related to fragments of the two largest subunits of cellular multisubunit RNAPs. Polypeptides of one set are encoded by middle phage genes and are found in the phiKZ virions. Polypeptides of the second set are encoded by early phage genes and are absent from virions. Here, we report isolation of a five-subunit RNAP from phiKZ-infected cells. Four subunits of this enzyme are cellular RNAP subunits homologs of the non-virion set; the fifth subunit is a protein of unknown function. In vitro, this complex initiates transcription from late phiKZ promoters in rifampicin-resistant manner. Thus, this enzyme is a non-virion phiKZ RNAP responsible for transcription of late phage genes. The phiKZ RNAP lacks identifiable assembly and promoter specificity subunits/factors characteristic for eukaryal, archaeal and bacterial RNAPs and thus provides a unique model for comparative analysis of the mechanism, regulation and evolution of this important class of enzymes.
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Affiliation(s)
- Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Sergei Borukhov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1501, USA
| | - Kira S Makarova
- National Center for Biotechnology Information NLM, National Institutes of Health Bethesda, MD 20894, USA
| | - Konstantin Severinov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA Skolkovo Institute of Science and Technology, Skolkovo, 143026, Russia
| | - Leonid Minakhin
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8020, USA
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