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Rakonjac J, Gold VAM, León-Quezada RI, Davenport CH. Structure, Biology, and Applications of Filamentous Bacteriophages. Cold Spring Harb Protoc 2024; 2024:pdb.over107754. [PMID: 37460152 DOI: 10.1101/pdb.over107754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
The closely related Escherichia coli Ff filamentous phages (f1, fd, and M13) have taken a fantastic journey over the past 60 years, from the urban sewerage from which they were first isolated, to their use in high-end technologies in multiple fields. Their relatively small genome size, high titers, and the virions that tolerate fusion proteins make the Ffs an ideal system for phage display. Folding of the fusions in the oxidizing environment of the E. coli periplasm makes the Ff phages a platform that allows display of eukaryotic surface and secreted proteins, including antibodies. Resistance of the Ffs to a broad range of pH and detergents facilitates affinity screening in phage display, whereas the stability of the virions at ambient temperature makes them suitable for applications in material science and nanotechnology. Among filamentous phages, only the Ffs have been used in phage display technology, because of the most advanced state of knowledge about their biology and the various tools developed for E. coli as a cloning host for them. Filamentous phages have been thought to be a rather small group, infecting mostly Gram-negative bacteria. A recent discovery of more than 10 thousand diverse filamentous phages in bacteria and archaea, however, opens a fascinating prospect for novel applications. The main aim of this review is to give detailed biological and structural information to researchers embarking on phage display projects. The secondary aim is to discuss the yet-unresolved puzzles, as well as recent developments in filamentous phage biology, from a viewpoint of their impact on current and future applications.
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Affiliation(s)
- Jasna Rakonjac
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
| | - Vicki A M Gold
- Living Systems Institute University of Exeter, Exeter, EX4 4QD, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, United Kingdom
| | - Rayén I León-Quezada
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
| | - Catherine H Davenport
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
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2
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Ahmed H, Lopez H, Boselli F, Tarricone G, Vercellino S, Costantini PE, Castagnola V, Veronesi M, Benfenati F, Danielli A, Boselli L, Pompa PP. Biomimetic Plasmonic Nanophages by Head/Tail Self-Assembling: Gold Nanoparticle/Virus Interactions. ACS NANO 2024. [PMID: 39083652 DOI: 10.1021/acsnano.4c05198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Gold nanoparticles (AuNPs), because of their dual plasmonic and catalytic functionalities, are among the most promising nanomaterials for the development of therapeutic and diagnostic tools for severe diseases such as cancer and neurodegeneration. Bacteriophages, massively present in human biofluids, are emerging as revolutionary biotechnological tools as they can be engineered to display multiple specific binding moieties, providing effective targeting ability, high stability, low cost, and sustainable production. Coupling AuNPs with phages can lead to an advanced generation of nanotools with great potential for biomedical applications. In the present study, we analyzed the interactions between differently sized AuNPs and filamentous M13 phages, establishing an advanced characterization platform that combines analytical techniques and computational models for an in-depth understanding of these hybrid self-assembling systems. A precise and structurally specific interaction of the AuNP-M13 hybrid complexes was observed, leading to a peculiar head/tail "tadpole-like" configuration. In silico simulations allowed explaining the mechanisms underlying the preferential assembly route and providing information about AuNPs' size-dependent interplay with specific M13 capsid proteins. The AuNP-M13 structures were proven to be biomimetic, eluding the formation of biomolecular corona. By keeping the biological identity of the virion, hybrid nanostructures maintained their natural recognition/targeting ability even in the presence of biomolecular crowding. In addition, we were able to tune the hybrid nanostructures' tropism toward E. coli based on the AuNP size. Overall, our results set the fundamental basis and a standard workflow for the development of phage-based targeting nanotools, valuable for a wide spectrum of nanotechnology applications.
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Affiliation(s)
- Hazem Ahmed
- Nanobiointeractions & Nanodiagnostics Lab, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Hender Lopez
- School of Physics, Clinical and Optometric Sciences, Technological University Dublin, Grangegorman D07 ADY7, Ireland
| | - Francesco Boselli
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, U.K
- Department of Engineering, Durham University, South Road, Durham DH1 3LE, U.K
| | - Giulia Tarricone
- Nanobiointeractions & Nanodiagnostics Lab, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Silvia Vercellino
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Paolo Emidio Costantini
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum Università di Bologna, Via Francesco Selmi 3, Bologna 40126, Italy
| | - Valentina Castagnola
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, Genova 16132, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Marina Veronesi
- Structural Biophysics Lab, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, Genova 16132, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Alberto Danielli
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum Università di Bologna, Via Francesco Selmi 3, Bologna 40126, Italy
| | - Luca Boselli
- Nanobiointeractions & Nanodiagnostics Lab, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Pier Paolo Pompa
- Nanobiointeractions & Nanodiagnostics Lab, Istituto Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
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3
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Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
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Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
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4
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Hampton JT, Liu WR. Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification. Chem Rev 2024; 124:6051-6077. [PMID: 38686960 PMCID: PMC11082904 DOI: 10.1021/acs.chemrev.4c00004] [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: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide libraries for the identification of therapeutic compounds, with phage display being one of the most accessible techniques. Although traditional phage display can generate billions of peptides simultaneously, it is limited to expression of canonical amino acids. Recently, several groups have successfully undergone efforts to apply genetic code expansion to introduce noncanonical amino acids (ncAAs) with novel reactivities and chemistries into phage-displayed peptide libraries. In addition to biological methods, several different chemical approaches have also been used to install noncanonical motifs into phage libraries. This review focuses on these recent advances that have taken advantage of both biological and chemical means for diversification of phage libraries with ncAAs.
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Affiliation(s)
- J. Trae Hampton
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843, United States
- Department
of Cell Biology and Genetics, College of Medicine, Texas A&M University, College
Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas 77843, United States
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5
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Ouyang R, Ongenae V, Muok A, Claessen D, Briegel A. Phage fibers and spikes: a nanoscale Swiss army knife for host infection. Curr Opin Microbiol 2024; 77:102429. [PMID: 38277900 DOI: 10.1016/j.mib.2024.102429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/19/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024]
Abstract
Bacteriophages are being rediscovered as potent agents for medical and industrial applications. However, finding a suitable phage relies on numerous factors, including host specificity, burst size, and infection cycle. The host range of a phage is, besides phage defense systems, initially determined by the recognition and attachment of receptor-binding proteins (RBPs) to the target receptors of susceptible bacteria. RBPs include tail (or occasionally head) fibers and tailspikes. Owing to the potential flexibility and heterogeneity of these structures, they are often overlooked during structural studies. Recent advances in cryo-electron microscopy studies and computational approaches have begun to unravel their structural and fundamental mechanisms during phage infection. In this review, we discuss the current state of research on different phage tail and head fibers, spike models, and molecular mechanisms. These details may facilitate the manipulation of phage-host specificity, which in turn will have important implications for science and society.
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Affiliation(s)
- Ruochen Ouyang
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xianning West Road 28, Xi'an 710049, China
| | - Véronique Ongenae
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Alise Muok
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Dennis Claessen
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Ariane Briegel
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands.
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6
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Li Y, Yang KD, Kong DC, Li XM, Duan HY, Ye JF. Harnessing filamentous phages for enhanced stroke recovery. Front Immunol 2024; 14:1343788. [PMID: 38299142 PMCID: PMC10829096 DOI: 10.3389/fimmu.2023.1343788] [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: 11/24/2023] [Accepted: 12/27/2023] [Indexed: 02/02/2024] Open
Abstract
Stroke poses a critical global health challenge, leading to substantial morbidity and mortality. Existing treatments often miss vital timeframes and encounter limitations due to adverse effects, prompting the pursuit of innovative approaches to restore compromised brain function. This review explores the potential of filamentous phages in enhancing stroke recovery. Initially antimicrobial-centric, bacteriophage therapy has evolved into a regenerative solution. We explore the diverse role of filamentous phages in post-stroke neurological restoration, emphasizing their ability to integrate peptides into phage coat proteins, thereby facilitating recovery. Experimental evidence supports their efficacy in alleviating post-stroke complications, immune modulation, and tissue regeneration. However, rigorous clinical validation is essential to address challenges like dosing and administration routes. Additionally, genetic modification enhances their potential as injectable biomaterials for complex brain tissue issues. This review emphasizes innovative strategies and the capacity of filamentous phages to contribute to enhanced stroke recovery, as opposed to serving as standalone treatment, particularly in addressing stroke-induced brain tissue damage.
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Affiliation(s)
- Yang Li
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
- School of Nursing, Jilin University, Changchun, China
| | - Kai-di Yang
- School of Nursing, Jilin University, Changchun, China
| | - De-cai Kong
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiao-meng Li
- School of Nursing, Jilin University, Changchun, China
| | - Hao-yu Duan
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jun-feng Ye
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
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7
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Zavala-Martínez AB, Grelet E. M13-Phage-Based Star-Shaped Particles with Internal Flexibility. ACS NANO 2024; 18:281-287. [PMID: 38113352 DOI: 10.1021/acsnano.3c06134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
We report on the construction and the dynamics of monodisperse star-shaped particles, mimicking, at the mesoscale, star polymers. Such multiarm star-like particles result from the self-assembly of gold nanoparticles, forming the core, with tip-linked filamentous viruses (M13 bacteriophages) acting as spines in a sea urchin-like structure. By combining fluorescence and dark-field microscopy with dynamic light scattering, we investigate the diffusion of these hybrid spiny particles. We reveal the internal dynamics of the star particles by probing their central metallic core, which exhibits a hindered motion that can be described as a Brownian particle trapped in a harmonic potential. We therefore show that the filamentous viruses and specifically their tip proteins behave as entropic springs, extending the relevance of the study of such hybrid mesoscopic analogues of star polymers to phage biotechnology.
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Affiliation(s)
- Arantza B Zavala-Martínez
- Univ. Bordeaux, CNRS, Centre de Recherche Paul-Pascal, UMR 5031,115Avenue du Dr. Schweitzer, F-33600 Pessac, France
| | - Eric Grelet
- Univ. Bordeaux, CNRS, Centre de Recherche Paul-Pascal, UMR 5031,115Avenue du Dr. Schweitzer, F-33600 Pessac, France
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Yang Y, Chen IA. Visualization of Engineered M13 Phages Bound to Bacterial Targets by Transmission Electron Microscopy. Methods Mol Biol 2024; 2793:175-183. [PMID: 38526731 PMCID: PMC11296667 DOI: 10.1007/978-1-0716-3798-2_12] [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] [Indexed: 03/27/2024]
Abstract
The filamentous phage M13 is one of the most well-studied and characterized phages, particularly since it was introduced as a scaffold for phage display, a technique to express and evolve fusion proteins on the M13 phage's coat to study protein or peptide binding interactions. Since phages can be engineered or evolved to specifically bind to a variety of targets, engineered M13 phages have been explored for applications such as drug delivery, biosensing, and cancer therapy, among others. Specifically, with the rising challenge of antimicrobial resistance among bacteria, chimeric M13 phages have been explored both as detection and therapeutic agents due to the flexibility in tuning target specificity. Transmission electron microscopy (TEM) is a powerful tool enabling researchers to directly visualize and characterize binding of phages to bacterial surfaces. However, the filamentous phage structure poses a challenge for this technique, as the phages have similar morphology to bacterial structures such as pili. In order to differentiate between bacterial structures and the filamentous phages, here we describe a protocol to prepare TEM samples of engineered M13 phages bound to bacterial cells, in which the phage virions have been specifically labeled by decoration of the major capsid proteins with gold nanoparticles. This protocol enables clear visualization and unambiguous identification of attached filamentous phages within the context of bacterial cells expressing numerous pili.
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Affiliation(s)
- Yanxi Yang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA.
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9
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Hille F, Gieschler S, Brinks E, Franz CMAP. Characterisation of the Novel Filamentous Phage PMBT54 Infecting the Milk Spoilage Bacteria Pseudomonas carnis and Pseudomonas lactis. Viruses 2023; 15:1781. [PMID: 37766190 PMCID: PMC10534721 DOI: 10.3390/v15091781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/09/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
Filamentous bacteriophages are lysogenic and pseudo-lysogenic viruses that do not lyse their host but are often continuously secreted from the infected cell. They belong to the order Tubulavirales, which encompasses three families, with the Inoviridae being the largest. While the number of identified inoviral sequences has greatly increased in recent years due to metagenomic studies, morphological and physiological characterisation is still restricted to only a few members of the filamentous phages. Here, we describe the novel filamentous phage PMBT54, which infects the spoilage-relevant Pseudomonas species P. carnis and P. lactis. Its genome is 7320 bp in size, has a mol% GC content of 48.37, and codes for 13 open-reading frames, two of which are located on the (-) strand. The virion exhibits a typical filamentous morphology and is secreted from the host cell at various lengths. The phage was shown to promote biofilm formation in both host strains and, therefore, has potential implications for milk spoilage, as biofilms are a major concern in the dairy industry.
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Affiliation(s)
- Frank Hille
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany; (S.G.); (E.B.); (C.M.A.P.F.)
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10
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Pellegri C, Moreau A, Duché D, Houot L. Direct interaction between fd phage pilot protein pIII and the TolQ-TolR proton-dependent motor provides new insights into the import of filamentous phages. J Biol Chem 2023; 299:105048. [PMID: 37451481 PMCID: PMC10424213 DOI: 10.1016/j.jbc.2023.105048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
Filamentous phages are one of the simplest examples of viruses with a protein capsid that protects a circular single-stranded DNA genome. The infection is very specific, nonlytic, and can strongly affect the physiology or provide new pathogenic factors to its bacterial host. The infection process is proposed to rely on a pore-forming mechanism similar to that of certain nonenveloped eukaryotic viruses. The Ff coliphages (including M13, fd, and f1) have been intensively studied and were used to establish the sequence of events taking place for efficient crossing of the host envelope structure. However, the mechanism involved in the penetration of the cell inner membrane is not well understood. Here, we identify new host players involved in the phage translocation mechanism. Interaction studies by a combination of in vivo biochemical methods demonstrate that the adhesion protein pIII located at the tip of the phage binds to TolQ and TolR, two proteins that form a conserved proton-dependent molecular motor in the inner membrane of the host cell. Moreover, in vivo cysteine cross-linking studies reveal that the interactions between the pIII and TolQ or TolR occur between their transmembrane helix domains and may be responding to the proton motive force status of the cell. These results allow us to propose a model for the late stage of filamentous phage translocation mediated by multiple interactions with each individual component of the host TolQRA complex.
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Affiliation(s)
- Callypso Pellegri
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille Cedex, France
| | - Ambre Moreau
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille Cedex, France
| | - Denis Duché
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille Cedex, France
| | - Laetitia Houot
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille Cedex, France.
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11
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Billaud M, Petit MA, Lossouarn J. The Clostridium-infecting filamentous phage CAK1 genome analysis allows to define a new potential clade of Tubulavirales. FEMS Microbiol Lett 2023; 370:fnad099. [PMID: 37791400 DOI: 10.1093/femsle/fnad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/21/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023] Open
Abstract
What we know about Tubulavirales, i.e. filamentous phages, essentially comes from Gram-negative-infecting Inoviridae. However, metagenomics recently suggests filamentous phages are much more widespread and diverse. Here, we report the complete sequence and functional annotation of CAK1, a 6.6 kb filamentous phage that was shown to chronically infect Clostridium beijerinckii 30 years ago and only represents the second filamentous phage cultivated on a Gram-positive bacterium. CAK1 has a typical filamentous phage modular genome with no homologs in databases and we were interested to compare it with a pig gut filamentous phage metagenomics dataset that we previously assembled and for which many filamentous phages were predicted to infect Clostridium species by bioinformatics means. CAK1 is distantly related to nine of these sequences, two of which have been predicted as Clostridium-associated. In itself, this small cluster of CAK1-connected sequences sheds light on the diversity of filamentous phages that putatively infect Clostridium species, and probably many other Gram-positive genera.
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Affiliation(s)
- Maud Billaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
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