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Delesalle VA, Tomko BE, Vill AC, Lichty KB, Krukonis GP. Forty Years without Family: Three Novel Bacteriophages with High Similarity to SPP1 Reveal Decades of Evolutionary Stasis since the Isolation of Their Famous Relative. Viruses 2022; 14:2106. [PMID: 36298661 PMCID: PMC9607348 DOI: 10.3390/v14102106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/12/2022] [Accepted: 09/17/2022] [Indexed: 11/26/2023] Open
Abstract
SPP1, an extensively studied bacteriophage of the Gram-positive Bacillus subtilis, is a model system for the study of phage-host interactions. Despite progress in the isolation and characterization of Bacillus phages, no previously fully sequenced phages have shared more than passing genetic similarity to SPP1. Here, we describe three virulent phages very similar to SPP1; SPP1 has greater than 80% nucleotide sequence identity and shares more that 85% of its protein coding genes with these phages. This is remarkable, given more than 40 years between the isolation of SPP1 and these phages. All three phages have somewhat larger genomes and more genes than SPP1. We identified a new putative gene in SPP1 based on a conserved sequence found in all phages. Gene conservation connotes purifying selection and is observed in structural genes and genes involved in DNA metabolism, but also in genes of unknown function, suggesting an important role in phage survival independent of the environment. Patterns of divergence point to genes or gene domains likely involved in adaptation to diverse hosts or different environments. Ultimately, comparative genomics of related phages provides insight into the long-term selective pressures that affect phage-bacteria interactions and alter phage genome content.
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Affiliation(s)
- Véronique A. Delesalle
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
| | - Brianne E. Tomko
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
| | - Albert C. Vill
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd., Ithaca, NY 14850, USA
| | - Katherine B. Lichty
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
- Department of Biological Sciences, University of Delaware, Wolf Hall, Newark, DE 19716, USA
| | - Greg P. Krukonis
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
- Department of Biology, Angelo State University, Cavness Science Building 101, ASU Station #10890, San Angelo, TX 76909, USA
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2
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A particle size threshold governs diffusion and segregation of PAR-3 during cell polarization. Cell Rep 2022; 39:110652. [PMID: 35417695 PMCID: PMC9093022 DOI: 10.1016/j.celrep.2022.110652] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/14/2021] [Accepted: 03/17/2022] [Indexed: 11/23/2022] Open
Abstract
The actomyosin cortex regulates the localization and function of proteins at the plasma membrane. Here, we study how membrane binding, cortical movements, and diffusion determine membrane protein distribution. In Caenorhabditis elegans zygotes, actomyosin flows transport PAR polarity proteins to establish the anterior-posterior axis. Oligomerization of a key scaffold protein, PAR-3, is required for polarization. PAR-3 oligomers are a heterogeneous population of many different sizes, and it remains unclear how oligomer size affects PAR-3 segregation. To address this question, we engineered PAR-3 to defined sizes. We report that PAR-3 trimers are necessary and sufficient for PAR-3 function during polarization and later embryo development. Quantitative analysis of PAR-3 diffusion shows that a threshold size of three subunits allows PAR-3 clusters to stably bind the membrane, where they are corralled and transported by the actomyosin cortex. Our study provides a quantitative model for size-dependent protein transportation of peripheral membrane proteins by cortical flow. The actomyosin cytoskeleton is a major regulator of cellular organization. Chang and Dickinson develop protein-engineering and particle-tracking tools to study how clustered membrane-bound proteins are transported by actomyosin contractions in vivo. Data-driven modeling reveals how membrane binding, diffusion, and collisions with F-actin contribute to protein movement.
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3
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Seul A, Brasilès S, Petitpas I, Lurz R, Campanacci V, Cambillau C, Weise F, Zairi M, Tavares P, Auzat I. Biogenesis of a Bacteriophage Long Non-Contractile Tail. J Mol Biol 2021; 433:167112. [PMID: 34153288 DOI: 10.1016/j.jmb.2021.167112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/22/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
Siphoviruses are main killers of bacteria. They use a long non-contractile tail to recognize the host cell and to deliver the genome from the viral capsid to the bacterial cytoplasm. Here, we define the molecular organization of the Bacillus subtilis bacteriophage SPP1 ~ 6.8 MDa tail and uncover its biogenesis mechanisms. A complex between gp21 and the tail distal protein (Dit) gp19.1 is assembled first to build the tail cap (gp19.1-gp21Nter) connected by a flexible hinge to the tail fiber (gp21Cter). The tip of the gp21Cter fiber is loosely associated to gp22. The cap provides a platform where tail tube proteins (TTPs) initiate polymerization around the tape measure protein gp18 (TMP), a reaction dependent on the non-structural tail assembly chaperones gp17.5 and gp17.5* (TACs). Gp17.5 is essential for stability of gp18 in the cell. Helical polymerization stops at a precise tube length followed by binding of proteins gp16.1 (TCP) and gp17 (THJP) to build the tail interface for attachment to the capsid portal system. This finding uncovers the function of the extensively conserved gp16.1-homologs in assembly of long tails. All SPP1 tail components, apart from gp22, share homology to conserved proteins whose coding genes' synteny is broadly maintained in siphoviruses. They conceivably represent the minimal essential protein set necessary to build functional long tails. Proteins homologous to SPP1 tail building blocks feature a variety of add-on modules that diversify extensively the tail core structure, expanding its capability to bind host cells and to deliver the viral genome to the bacterial cytoplasm.
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Affiliation(s)
- Anait Seul
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France
| | - Sandrine Brasilès
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Isabelle Petitpas
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France
| | - Rudi Lurz
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Valérie Campanacci
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités d'Aix-Marseille I & II, Campus de Luminy, Marseille, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités d'Aix-Marseille I & II, Campus de Luminy, Marseille, France
| | - Frank Weise
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Mohamed Zairi
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France
| | - Paulo Tavares
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France.
| | - Isabelle Auzat
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France.
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A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection. Viruses 2020; 12:v12080797. [PMID: 32722163 PMCID: PMC7472136 DOI: 10.3390/v12080797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
The lactococcal virulent phage p2 is a model for studying the Skunavirus genus, the most prevalent group of phages causing milk fermentation failures in cheese factories worldwide. This siphophage infects Lactococcus lactis MG1363, a model strain used to study Gram-positive lactic acid bacteria. The structural proteins of phage p2 have been thoroughly described, while most of its non-structural proteins remain uncharacterized. Here, we developed an integrative approach, making use of structural biology, genomics, physiology, and proteomics to provide insights into the function of ORF47, the most conserved non-structural protein of unknown function among the Skunavirus genus. This small phage protein, which is composed of three α-helices, was found to have a major impact on the bacterial proteome during phage infection and to significantly reduce the emergence of bacteriophage-insensitive mutants.
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Goulet A, Spinelli S, Mahony J, Cambillau C. Conserved and Diverse Traits of Adhesion Devices from Siphoviridae Recognizing Proteinaceous or Saccharidic Receptors. Viruses 2020; 12:E512. [PMID: 32384698 PMCID: PMC7291167 DOI: 10.3390/v12050512] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 01/30/2023] Open
Abstract
Bacteriophages can play beneficial roles in phage therapy and destruction of food pathogens. Conversely, they play negative roles as they infect bacteria involved in fermentation, resulting in serious industrial losses. Siphoviridae phages possess a long non-contractile tail and use a mechanism of infection whose first step is host recognition and binding. They have evolved adhesion devices at their tails' distal end, tuned to recognize specific proteinaceous or saccharidic receptors on the host's surface that span a large spectrum of shapes. In this review, we aimed to identify common patterns beyond this apparent diversity. To this end, we analyzed siphophage tail tips or baseplates, evaluating their known structures, where available, and uncovering patterns with bioinformatics tools when they were not. It was thereby identified that a triad formed by three proteins in complex, i.e., the tape measure protein (TMP), the distal tail protein (Dit), and the tail-associated lysozyme (Tal), is conserved in all phages. This common scaffold may harbor various functional extensions internally while it also serves as a platform for plug-in ancillary or receptor-binding proteins (RBPs). Finally, a group of siphophage baseplates involved in saccharidic receptor recognition exhibits an activation mechanism reminiscent of that observed in Myoviridae.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France
| | - Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland;
- APC Microbiome Ireland, University College Cork, Cork T12 YN60, Ireland
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France
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The Revisited Genome of Bacillus subtilis Bacteriophage SPP1. Viruses 2018; 10:v10120705. [PMID: 30544981 PMCID: PMC6316719 DOI: 10.3390/v10120705] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 02/05/2023] Open
Abstract
Bacillus subtilis bacteriophage SPP1 is a lytic siphovirus first described 50 years ago [1]. Its complete DNA sequence was reported in 1997 [2]. Here we present an updated annotation of the 44,016 bp SPP1 genome and its correlation to different steps of the viral multiplication process. Five early polycistronic transcriptional units encode phage DNA replication proteins and lysis functions together with less characterized, mostly non-essential, functions. Late transcription drives synthesis of proteins necessary for SPP1 viral particles assembly and for cell lysis, together with a short set of proteins of unknown function. The extensive genetic, biochemical and structural biology studies on the molecular mechanisms of SPP1 DNA replication and phage particle assembly rendered it a model system for tailed phages research. We propose SPP1 as the reference species for a new SPP1-like viruses genus of the Siphoviridae family.
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Mahony J, van Sinderen D. Structural aspects of the interaction of dairy phages with their host bacteria. Viruses 2012; 4:1410-24. [PMID: 23170165 PMCID: PMC3499812 DOI: 10.3390/v4091410] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 12/25/2022] Open
Abstract
Knowledge of phage-host interactions at a fundamental level is central to the design of rational strategies for the development of phage-resistant strains that may be applied in industrial settings. Phages infecting lactic acid bacteria, in particular Lactococcus lactis and Streptococcus thermophilus, negatively impact on dairy fermentation processes with serious economic implications. In recent years a wealth of information on structural protein assembly and topology has become available relating to phages infecting Escherichia coli, Bacillus subtilis and Lactococcus lactis, which act as models for structural analyses of dairy phages. In this review, we explore the role of model tailed phages, such as T4 and SPP1, in advancing our knowledge regarding interactions between dairy phages and their hosts. Furthermore, the potential of currently investigated dairy phages to in turn serve as model systems for this particular group of phages is discussed.
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Affiliation(s)
- Jennifer Mahony
- Department of Microbiology, University College Cork, Western Road, Cork, Ireland;
| | - Douwe van Sinderen
- Department of Microbiology, University College Cork, Western Road, Cork, Ireland;
- Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Western Road, Cork, Ireland
- Author to whom correspondence should be addressed: ; Tel.: +353-21-4901365; Fax: +353-21-4903101
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Vinga I, Baptista C, Auzat I, Petipas I, Lurz R, Tavares P, Santos MA, São-José C. Role of bacteriophage SPP1 tail spike protein gp21 on host cell receptor binding and trigger of phage DNA ejection. Mol Microbiol 2011; 83:289-303. [DOI: 10.1111/j.1365-2958.2011.07931.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Shepherd DA, Veesler D, Lichière J, Ashcroft AE, Cambillau C. Unraveling lactococcal phage baseplate assembly by mass spectrometry. Mol Cell Proteomics 2011; 10:M111.009787. [PMID: 21646642 PMCID: PMC3186816 DOI: 10.1074/mcp.m111.009787] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bacteriophages belonging to the Caudovirales order possess a tail acting as a molecular machine used during infection to recognize the host and ensure high-efficiency genome delivery to the cell cytoplasm. They bear a large and sophisticated multiprotein organelle at their distal tail end, either a baseplate or a tail-tip, which is the control center for infectivity. We report here insights into the baseplate assembly pathways of two lactoccocal phages (p2 and TP901-1) using electrospray ionization-mass spectrometry. Based on our "block cloning" strategy we have expressed large complexes of their baseplates as well as several significant structural subcomplexes. Previous biophysical characterization using size-exclusion chromatography coupled with on-line light scattering and refractometry demonstrated that the overproduced recombinant proteins interact with each other to form large (up to 1.9 MDa) and stable assemblies. The structures of several of these complexes have been determined by x-ray diffraction or by electron microscopy. In this contribution, we demonstrate that electrospray ionization-mass spectrometry yields accurate mass measurements for the different baseplate complexes studied from which their stoichiometries can be discerned, and that the subspecies observed in the spectra provide valuable information on the assembly mechanisms of these large organelles.
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Affiliation(s)
- Dale A Shepherd
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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Goulet A, Lai-Kee-Him J, Veesler D, Auzat I, Robin G, Shepherd DA, Ashcroft AE, Richard E, Lichière J, Tavares P, Cambillau C, Bron P. The opening of the SPP1 bacteriophage tail, a prevalent mechanism in Gram-positive-infecting siphophages. J Biol Chem 2011; 286:25397-405. [PMID: 21622577 DOI: 10.1074/jbc.m111.243360] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The SPP1 siphophage uses its long non-contractile tail and tail tip to recognize and infect the Gram-positive bacterium Bacillus subtilis. The tail-end cap and its attached tip are the critical components for host recognition and opening of the tail tube for genome exit. In the present work, we determined the cryo-electron microscopic (cryo-EM) structure of a complex formed by the cap protein gp19.1 (Dit) and the N terminus of the downstream protein of gp19.1 in the SPP1 genome, gp21(1-552) (Tal). This complex assembles two back-to-back stacked gp19.1 ring hexamers, interacting loosely, and two gp21(1-552) trimers interacting with gp19.1 at both ends of the stack. Remarkably, one gp21(1-552) trimer displays a "closed" conformation, whereas the second is "open" delineating a central channel. The two conformational states dock nicely into the EM map of the SPP1 cap domain, respectively, before and after DNA release. Moreover, the open/closed conformations of gp19.1-gp21(1-552) are consistent with the structures of the corresponding proteins in the siphophage p2 baseplate, where the Tal protein (ORF16) attached to the ring of Dit (ORF15) was also found to adopt these two conformations. Therefore, the present contribution allowed us to revisit the SPP1 tail distal-end architectural organization. Considering the sequence conservation among Dit and the N-terminal region of Tal-like proteins in Gram-positive-infecting Siphoviridae, it also reveals the Tal opening mechanism as a hallmark of siphophages probably involved in the generation of the firing signal initiating the cascade of events that lead to phage DNA release in vivo.
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Affiliation(s)
- Adeline Goulet
- Centre de Biochimie Structurale, INSERM UMR 1054/CNRS UMR 5048 and Universités Montpellier I & II, 29 rue de Navacelles, Montpellier 34090, France
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