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Pastuszka A, Rousseau GM, Somerville V, Levesque S, Fiset JP, Goulet A, Doyon Y, Moineau S. Dairy phages escape CRISPR defence of Streptococcus thermophilus via the anti-CRISPR AcrIIA3. Int J Food Microbiol 2023; 407:110414. [PMID: 37778080 DOI: 10.1016/j.ijfoodmicro.2023.110414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/22/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
Bacterial community collapse due to phage infection is a major risk in cheese making processes. As virulent phages are ubiquitous and diverse in milk fermentation factories, the use of phage-resistant lactic acid bacteria (LAB) is essential to obtain high-quality fermented dairy products. The LAB species Streptococcus thermophilus contains two type II-A CRISPR-Cas systems (CRISPR1 and CRISPR3) that can effectively protect against phage infection. However, virulent streptococcal phages carrying anti-CRISPR proteins (ACR) that block the activity of CRISPR-Cas systems have emerged in yogurt and cheese environments. For example, phages carrying AcrIIA5 can impede both CRISPR1 and CRISPR3 systems, while AcrIIA6 stops only CRISPR1. Here, we explore the activity and diversity of a third streptococcal phage anti-CRISPR protein, namely AcrIIA3. We were able to demonstrate that AcrIIA3 is efficiently active against the CRISPR3-Cas system of S. thermophilus. We used AlphaFold2 to infer the structure of AcrIIA3 and we predicted that this new family of functional ACR in virulent streptococcal phages has a new α-helical fold, with no previously identified structural homologs. Because ACR proteins are being explored as modulators in genome editing applications, we also tested AcrIIA3 against SpCas9. We found that AcrIIA3 could block SpCas9 in bacteria but not in human cells. Understanding the diversity and functioning of anti-defence mechanisms will be of importance in the design of long-term stable starter cultures.
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Affiliation(s)
- Adeline Pastuszka
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, Canada
| | - Vincent Somerville
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, Canada; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland; Agroscope, Bern, Switzerland
| | - Sébastien Levesque
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec, QC, Canada; Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Jean-Philippe Fiset
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec, QC, Canada; Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Adeline Goulet
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologies, CNRS UMR7255, Aix-Marseille Université, Marseille, France
| | - Yannick Doyon
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec, QC, Canada; Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, Canada; Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, QC, Canada.
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Mahony J, Goulet A, van Sinderen D, Cambillau C. Partial Atomic Model of the Tailed Lactococcal Phage TP901-1 as Predicted by AlphaFold2: Revelations and Limitations. Viruses 2023; 15:2440. [PMID: 38140681 PMCID: PMC10747895 DOI: 10.3390/v15122440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Bacteria are engaged in a constant battle against preying viruses, called bacteriophages (or phages). These remarkable nano-machines pack and store their genomes in a capsid and inject it into the cytoplasm of their bacterial prey following specific adhesion to the host cell surface. Tailed phages possessing dsDNA genomes are the most abundant phages in the bacterial virosphere, particularly those with long, non-contractile tails. All tailed phages possess a nano-device at their tail tip that specifically recognizes and adheres to a suitable host cell surface receptor, being proteinaceous and/or saccharidic. Adhesion devices of tailed phages infecting Gram-positive bacteria are highly diverse and, for the majority, remain poorly understood. Their long, flexible, multi-domain-encompassing tail limits experimental approaches to determine their complete structure. We have previously shown that the recently developed protein structure prediction program AlphaFold2 can overcome this limitation by predicting the structures of phage adhesion devices with confidence. Here, we extend this approach and employ AlphaFold2 to determine the structure of a complete phage, the lactococcal P335 phage TP901-1. Herein we report the structures of its capsid and neck, its extended tail, and the complete adhesion device, the baseplate, which was previously partially determined using X-ray crystallography.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
| | - Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université—CNRS, UMR 7255, 13009 Marseille, France;
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
| | - Christian Cambillau
- School of Microbiology & APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université—CNRS, UMR 7255, 13009 Marseille, France;
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3
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Abstract
Although more than 12,000 bacteriophages infecting mycobacteria (mycobacteriophages) have been isolated so far, there is a knowledge gap on their structure-function relationships. Here, we have explored the architecture of host-binding machineries from seven representative mycobacteriophages of the Siphoviridae family infecting Mycobacterium smegmatis, Mycobacterium abscessus, and Mycobacterium tuberculosis, using AlphaFold2 (AF2). AF2 enables confident structural analyses of large and flexible biological assemblies resistant to experimental methods, thereby opening new avenues to shed light on phage structure and function. Our results highlight the modularity and structural diversity of siphophage host-binding machineries that recognize host-specific receptors at the onset of viral infection. Interestingly, the studied mycobacteriophages' host-binding machineries present unique features compared with those of phages infecting other Gram-positive actinobacteria. Although they all assemble the classical Dit (distal tail), Tal (tail-associated lysin), and receptor-binding proteins, five of them contain two potential additional adhesion proteins. Moreover, we have identified brush-like domains formed of multiple polyglycine helices which expose hydrophobic residues as potential receptor-binding domains. These polyglycine-rich domains, which have been observed in only five native proteins, may be a hallmark of mycobacteriophages' host-binding machineries, and they may be more common in nature than expected. Altogether, the unique composition of mycobacteriophages' host-binding machineries indicate they might have evolved to bind to the peculiar mycobacterial cell envelope, which is rich in polysaccharides and mycolic acids. This work provides a rational framework to efficiently produce recombinant proteins or protein domains and test their host-binding function and, hence, to shed light on molecular mechanisms used by mycobacteriophages to infect their host. IMPORTANCE Mycobacteria include both saprophytes, such as the model system Mycobacterium smegmatis, and pathogens, such as Mycobacterium tuberculosis and Mycobacterium abscessus, that are poorly responsive to antibiotic treatments and pose a global public health problem. Mycobacteriophages have been collected at a very large scale over the last decade, and they have proven to be valuable tools for mycobacteria genetic manipulation, rapid diagnostics, and infection treatment. Yet, molecular mechanisms used by mycobacteriophages to infect their host remain poorly understood. Therefore, exploring the structural diversity of mycobacteriophages' host-binding machineries is important not only to better understand viral diversity and bacteriophage-host interactions, but also to rationally develop biotechnological tools. With the powerful protein structure prediction software AlphaFold2, which was publicly released a year ago, it is now possible to gain structural and functional insights on such challenging assemblies.
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Affiliation(s)
- Christian Cambillau
- School of Microbiology, University College Cork, Cork, Ireland
- AlphaGraphix, Formiguères, France
| | - Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologie, CNRS and Aix-Marseille Université, Marseille, France
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Balestri F, Goulet A, Tedeschi G. Editorial: The "proteine 2022" conference. Front Mol Biosci 2023; 10:1157442. [PMID: 36911527 PMCID: PMC9992957 DOI: 10.3389/fmolb.2023.1157442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Affiliation(s)
- Francesco Balestri
- Department of Biology, Biochemistry Unit-University of Pisa, Pisa, Italy
| | - Adeline Goulet
- Laboratoire d'Ingénierie des Systémes Macromoléculaires, LISM UMR7255 CNRS & Aix-Marseille Université, Marseille, France
| | - Gabriella Tedeschi
- Department of Veterinary Medicine and Animal Science-University of Milano, Lodi, Italy
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5
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Goulet A, Mahony J, Cambillau C, van Sinderen D. Exploring Structural Diversity among Adhesion Devices Encoded by Lactococcal P335 Phages with AlphaFold2. Microorganisms 2022; 10:2278. [PMID: 36422348 PMCID: PMC9692632 DOI: 10.3390/microorganisms10112278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 01/16/2024] Open
Abstract
Bacteriophages, or phages, are the most abundant biological entities on Earth. They possess molecular nanodevices to package and store their genome, as well as to introduce it into the cytoplasm of their bacterial prey. Successful phage infection commences with specific recognition of, and adhesion to, a suitable host cell surface. Adhesion devices of siphophages infecting Gram-positive bacteria are very diverse and remain, for the majority, poorly understood. These assemblies often comprise long, flexible, and multi-domain proteins, which limit their structural analyses by experimental approaches. The protein structure prediction program AlphaFold2 is exquisitely adapted to unveil structural and functional details of such molecular machineries. Here, we present structure predictions of adhesion devices from siphophages belonging to the P335 group infecting Lactococcus spp., one of the most extensively applied lactic acid bacteria in dairy fermentations. The predictions of representative adhesion devices from types I-IV P335 phages illustrate their very diverse topology. Adhesion devices from types III and IV phages share a common topology with that of Skunavirus p2, with a receptor binding protein anchored to the virion by a distal tail protein loop. This suggests that they exhibit an activation mechanism similar to that of phage p2 prior to host binding.
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Affiliation(s)
- Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université—CNRS, UMR 7255, 13288 Marseille, France
| | - Jennifer Mahony
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
| | - Christian Cambillau
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
- AlphaGraphix, 24 Carrer d’Amont, 66210 Formiguères, France
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6
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Goulet A, Joos R, Lavelle K, Van Sinderen D, Mahony J, Cambillau C. A structural discovery journey of streptococcal phages adhesion devices by AlphaFold2. Front Mol Biosci 2022; 9:960325. [PMID: 36060267 PMCID: PMC9437275 DOI: 10.3389/fmolb.2022.960325] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/30/2022] [Indexed: 12/04/2022] Open
Abstract
Successful bacteriophage infection starts with specific recognition and adhesion to the host cell surface. Adhesion devices of siphophages infecting Gram-positive bacteria are very diverse and remain, for the majority, poorly understood. These assemblies often comprise long, flexible, and multi-domain proteins, which limits their structural analyses by experimental approaches such as X-ray crystallography and electron microscopy. However, the protein structure prediction program AlphaFold2 is exquisitely adapted to unveil structural and functional details of such molecular machineries. Here, we present structure predictions of whole adhesion devices of five representative siphophages infecting Streptococcus thermophilus, one of the main lactic acid bacteria used in dairy fermentations. The predictions highlight the mosaic nature of these devices that share functional domains for which active sites and residues could be unambiguously identified. Such AlphaFold2 analyses of phage-encoded host adhesion devices should become a standard method to characterize phage-host interaction machineries and to reliably annotate phage genomes.
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Affiliation(s)
- Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix-Marseille Université, UMR7255, Marseille, France
- *Correspondence: Adeline Goulet, ; Jennifer Mahony, ; Christian Cambillau,
| | - Raphaela Joos
- School of Microbiology, University College Cork, Cork, Ireland
| | - Katherine Lavelle
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe Van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- *Correspondence: Adeline Goulet, ; Jennifer Mahony, ; Christian Cambillau,
| | - Christian Cambillau
- School of Microbiology, University College Cork, Cork, Ireland
- AlphaGraphix, Formiguères, France
- *Correspondence: Adeline Goulet, ; Jennifer Mahony, ; Christian Cambillau,
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7
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Goulet A, Cambillau C, Roussel A, Imbert I. Structure Prediction and Analysis of Hepatitis E Virus Non-Structural Proteins from the Replication and Transcription Machinery by AlphaFold2. Viruses 2022; 14:1537. [PMID: 35891516 PMCID: PMC9316534 DOI: 10.3390/v14071537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in humans globally. Considered for a long while a public health issue only in developing countries, the HEV infection is now a global public health concern. Most human infections are caused by the HEV genotypes 1, 2, 3 and 4 (HEV-1 to HEV-4). Although HEV-3 and HEV-4 can evolve to chronicity in immunocompromised patients, HEV-1 and HEV-2 lead to self-limited infections. HEV has a positive-sense single-stranded RNA genome of ~7.2 kb that is translated into a large pORF1 replicative polyprotein, essential for the viral RNA genome replication and transcription. Unfortunately, the composition and structure of these replicases are still unknown. The recent release of the powerful machine-learning protein structure prediction software AlphaFold2 (AF2) allows us to accurately predict the structure of proteins and their complexes. Here, we used AF2 with the replicase encoded by the polyprotein pORF1 of the human-infecting HEV-3. The boundaries and structures reveal five domains or nonstructural proteins (nsPs): the methyltransferase, Zn-binding domain, macro, helicase, and RNA-dependent RNA polymerase, reliably predicted. Their substrate-binding sites are similar to those observed experimentally for other related viral proteins. Precisely knowing enzyme boundaries and structures is highly valuable to recombinantly produce stable and active proteins and perform structural, functional and inhibition studies.
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Affiliation(s)
- Adeline Goulet
- Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7255, LISM, 31 Chemin Joseph Aiguier, 13009 Marseille, France; (A.G.); (A.R.)
| | - Christian Cambillau
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland;
- AlphaGraphix, 24 Carrer d’Amont, 66210 Formiguères, France
| | - Alain Roussel
- Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7255, LISM, 31 Chemin Joseph Aiguier, 13009 Marseille, France; (A.G.); (A.R.)
| | - Isabelle Imbert
- Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7255, LISM, 31 Chemin Joseph Aiguier, 13009 Marseille, France; (A.G.); (A.R.)
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8
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Philippe C, Morency C, Plante PL, Zufferey E, Achigar R, Tremblay DM, Rousseau GM, Goulet A, Moineau S. Author Correction: A truncated anti-CRISPR protein prevents spacer acquisition but not interference. Nat Commun 2022; 13:3873. [PMID: 35790758 PMCID: PMC9256600 DOI: 10.1038/s41467-022-31631-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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9
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Goulet A, Cambillau C. Present Impact of AlphaFold2 Revolution on Structural Biology, and an Illustration With the Structure Prediction of the Bacteriophage J-1 Host Adhesion Device. Front Mol Biosci 2022; 9:907452. [PMID: 35615740 PMCID: PMC9124777 DOI: 10.3389/fmolb.2022.907452] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/21/2022] [Indexed: 12/26/2022] Open
Abstract
In 2021, the release of AlphaFold2 - the DeepMind's machine-learning protein structure prediction program - revolutionized structural biology. Results of the CASP14 contest were an immense surprise as AlphaFold2 successfully predicted 3D structures of nearly all submitted protein sequences. The AlphaFold2 craze has rapidly spread the life science community since structural biologists as well as untrained biologists have now the possibility to obtain high-confidence protein structures. This revolution is opening new avenues to address challenging biological questions. Moreover, AlphaFold2 is imposing itself as an essential step of any structural biology project, and requires us to revisit our structural biology workflows. On one hand, AlphaFold2 synergizes with experimental methods including X-ray crystallography and cryo-electron microscopy. On the other hand, it is, to date, the only method enabling structural analyses of large and flexible assemblies resistant to experimental approaches. We illustrate this valuable application of AlphaFold2 with the structure prediction of the whole host adhesion device from the Lactobacillus casei bacteriophage J-1. With the ongoing improvement of AlphaFold2 algorithms and notebooks, there is no doubt that AlphaFold2-driven biological stories will increasingly be reported, which questions the future directions of experimental structural biology.
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Affiliation(s)
- Adeline Goulet
- Laboratoire D’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Aix-Marseille Université—CNRS, Marseille, France
| | - Christian Cambillau
- Laboratoire D’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Aix-Marseille Université—CNRS, Marseille, France
- School of Microbiology, University College Cork, Cork, Ireland
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10
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Grellet E, L'Hôte I, Goulet A, Imbert I. Replication of the coronavirus genome: A paradox among positive-strand RNA viruses. J Biol Chem 2022; 298:101923. [PMID: 35413290 PMCID: PMC8994683 DOI: 10.1016/j.jbc.2022.101923] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 01/18/2023] Open
Abstract
Coronavirus (CoV) genomes consist of positive-sense single-stranded RNA and are among the largest viral RNAs known to date (∼30 kb). As a result, CoVs deploy sophisticated mechanisms to replicate these extraordinarily large genomes as well as to transcribe subgenomic messenger RNAs. Since 2003, with the emergence of three highly pathogenic CoVs (SARS-CoV, MERS-CoV, and SARS-CoV-2), significant progress has been made in the molecular characterization of the viral proteins and key mechanisms involved in CoV RNA genome replication. For example, to allow for the maintenance and integrity of their large RNA genomes, CoVs have acquired RNA proofreading 3'-5' exoribonuclease activity (in nonstructural protein nsp14). In order to replicate the large genome, the viral-RNA-dependent RNA polymerase (RdRp; in nsp12) is supplemented by a processivity factor (made of the viral complex nsp7/nsp8), making it the fastest known RdRp. Lastly, a viral structural protein, the nucleocapsid (N) protein, which is primarily involved in genome encapsidation, is required for efficient viral replication and transcription. Therefore, CoVs are a paradox among positive-strand RNA viruses in the sense that they use both a processivity factor and have proofreading activity reminiscent of DNA organisms in addition to structural proteins that mediate efficient RNA synthesis, commonly used by negative-strand RNA viruses. In this review, we present a historical perspective of these unsuspected discoveries and detail the current knowledge on the core replicative machinery deployed by CoVs.
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Affiliation(s)
- Emeline Grellet
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - India L'Hôte
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - Adeline Goulet
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - Isabelle Imbert
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France.
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11
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Goulet A, Cambillau C. Structure and Topology Prediction of Phage Adhesion Devices Using AlphaFold2: The Case of Two Oenococcus oeni Phages. Microorganisms 2021; 9:2151. [PMID: 34683471 PMCID: PMC8540738 DOI: 10.3390/microorganisms9102151] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/05/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
Lactic acid bacteria (LAB) are important microorganisms in food fermentation. In the food industry, bacteriophages (phages or bacterial viruses) may cause the disruption of LAB-dependent processes with product inconsistencies and economic losses. LAB phages use diverse adhesion devices to infect their host, yet the overall picture of host-binding mechanisms remains incomplete. Here, we aimed to determine the structure and topology of the adhesion devices of two lytic siphophages, OE33PA and Vinitor162, infecting the wine bacteria Oenococcus oeni. These phages possess adhesion devices with a distinct composition and morphology and likely use different infection mechanisms. We primarily used AlphaFold2, an algorithm that can predict protein structure with unprecedented accuracy, to obtain a 3D model of the adhesion devices' components. Using our prior knowledge of the architecture of the LAB phage host-binding machineries, we also reconstituted the topology of OE33PA and Vinitor162 adhesion devices. While OE33PA exhibits original structures in the assembly of its bulky adhesion device, Vinitor162 harbors several carbohydrate-binding modules throughout its long and extended adhesion device. Overall, these results highlight the ability of AlphaFold2 to predict protein structures and illustrate its great potential in the study of phage structures and host-binding mechanisms.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, CEDEX 09, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, CEDEX 09, 13288 Marseille, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, CEDEX 09, 13288 Marseille, France;
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, CEDEX 09, 13288 Marseille, France
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12
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Philippe C, Chaïb A, Jaomanjaka F, Cluzet S, Lagarde A, Ballestra P, Decendit A, Petrel M, Claisse O, Goulet A, Cambillau C, Le Marrec C. Wine Phenolic Compounds Differently Affect the Host-Killing Activity of Two Lytic Bacteriophages Infecting the Lactic Acid Bacterium Oenococcus oeni. Viruses 2020; 12:E1316. [PMID: 33213034 PMCID: PMC7698478 DOI: 10.3390/v12111316] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/15/2022] Open
Abstract
To provide insights into phage-host interactions during winemaking, we assessed whether phenolic compounds modulate the phage predation of Oenococcus oeni. Centrifugal partition chromatography was used to fractionate the phenolic compounds of a model red wine. The ability of lytic oenophage OE33PA to kill its host was reduced in the presence of two collected fractions in which we identified five compounds. Three, namely, quercetin, myricetin and p-coumaric acid, significantly reduced the phage predation of O. oeni when provided as individual pure molecules, as also did other structurally related compounds such as cinnamic acid. Their presence was correlated with a reduced adsorption rate of phage OE33PA on its host. Strikingly, none of the identified compounds affected the killing activity of the distantly related lytic phage Vinitor162. OE33PA and Vinitor162 were shown to exhibit different entry mechanisms to penetrate into bacterial cells. We propose that ligand-receptor interactions that mediate phage adsorption to the cell surface are diverse in O. oeni and are subject to differential interference by phenolic compounds. Their presence did not induce any modifications in the cell surface as visualized by TEM. Interestingly, docking analyses suggest that quercetin and cinnamic acid may interact with the tail of OE33PA and compete with host recognition.
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Affiliation(s)
- Cécile Philippe
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Amel Chaïb
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Fety Jaomanjaka
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Stéphanie Cluzet
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Aurélie Lagarde
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Patricia Ballestra
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Alain Decendit
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Mélina Petrel
- Bordeaux Imaging Center, UMS3420 CNRS-INSERM, University Bordeaux, F-33000 Bordeaux, France;
| | - Olivier Claisse
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
- INRAE, ISVV, USC 1366 Oenologie, F-33140 Villenave d’Ornon, France
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, F-13020 Marseille, France; (A.G.); (C.C.)
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, F-13020 Marseille, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, F-13020 Marseille, France; (A.G.); (C.C.)
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, F-13020 Marseille, France
| | - Claire Le Marrec
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
- Bordeaux INP, ISVV, EA4577 OEnologie, F-33140 Villenave d’Ornon, France
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13
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Lavelle K, Goulet A, McDonnell B, Spinelli S, van Sinderen D, Mahony J, Cambillau C. Revisiting the host adhesion determinants of Streptococcus thermophilus siphophages. Microb Biotechnol 2020; 13:1765-1779. [PMID: 32525270 PMCID: PMC7533335 DOI: 10.1111/1751-7915.13593] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 11/29/2022] Open
Abstract
Available 3D structures of bacteriophage modules combined with predictive bioinformatic algorithms enabled the identification of adhesion modules in 57 siphophages infecting Streptococcus thermophilus (St). We identified several carbohydrate-binding modules (CBMs) in so-called evolved distal tail (Dit) and tail-associated lysozyme (Tal) proteins of St phage baseplates. We examined the open reading frame (ORF) downstream of the Tal-encoding ORF and uncovered the presence of a putative p2-like receptor-binding protein (RBP). A 21 Å resolution electron microscopy structure of the baseplate of cos-phage STP1 revealed the presence of six elongated electron densities, surrounding the core of the baseplate, that harbour the p2-like RBPs at their tip. To verify the functionality of these modules, we expressed GFP- or mCherry-coupled Tal and putative RBP CBMs and observed by fluorescence microscopy that both modules bind to their corresponding St host, the putative RBP CBM with higher affinity than the Tal-associated one. The large number of CBM functional domains in St phages suggests that they play a contributory role in the infection process, a feature that we previously described in lactococcal phages and beyond, possibly representing a universal feature of the siphophage host-recognition apparatus.
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Affiliation(s)
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
| | | | - Silvia Spinelli
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
| | - Douwe van Sinderen
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Jennifer Mahony
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Christian Cambillau
- School of MicrobiologyUniversity College CorkCorkIreland
- Architecture et Fonction des Macromolécules BiologiquesAix‐Marseille UniversitéCampus de LuminyMarseilleFrance
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Campus de LuminyMarseilleFrance
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14
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Spinelli S, Tremblay D, Moineau S, Cambillau C, Goulet A. Structural Insights into Lactococcal Siphophage p2 Baseplate Activation Mechanism. Viruses 2020; 12:v12080878. [PMID: 32796652 PMCID: PMC7472080 DOI: 10.3390/v12080878] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/18/2022] Open
Abstract
Virulent phages infecting L. lactis, an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated lactococcal phages in the cheese environments and phage p2 is the model siphophage for this viral genus. The baseplate of phage p2, which is used to recognize its host, was previously shown to display two conformations by X-ray crystallography, a rested state and an activated state ready to bind to the host. The baseplate became only activated and opened in the presence of Ca2+. However, such an activated state was not previously observed in the virion. Here, using nanobodies binding to the baseplate, we report on the negative staining electron microscopy structure of the activated form of the baseplate directly observed in the p2 virion, that is compatible with the activated baseplate crystal structure. Analyses of this new structure also established the presence of a second distal tail (Dit) hexamer as a component of the baseplate, the topology of which differs largely from the first one. We also observed an uncoupling between the baseplate activation and the tail tip protein (Tal) opening, suggesting an infection mechanism more complex than previously expected.
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Affiliation(s)
- Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille CEDEX 09, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille CEDEX 09, France
| | - Denise Tremblay
- Département de Biochimie, de Microbiologie, et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V 0A6, Canada; (D.T.); (S.M.)
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V 0A6, Canada; (D.T.); (S.M.)
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille CEDEX 09, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille CEDEX 09, France
- Correspondence: (C.C.); (A.G.)
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille CEDEX 09, France;
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille CEDEX 09, France
- Correspondence: (C.C.); (A.G.)
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Agudelo D, Carter S, Velimirovic M, Duringer A, Rivest JF, Levesque S, Loehr J, Mouchiroud M, Cyr D, Waters PJ, Laplante M, Moineau S, Goulet A, Doyon Y. Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9. Genome Res 2020; 30:107-117. [PMID: 31900288 PMCID: PMC6961573 DOI: 10.1101/gr.255414.119] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/17/2019] [Indexed: 12/18/2022]
Abstract
Targeting definite genomic locations using CRISPR-Cas systems requires a set of enzymes with unique protospacer adjacent motif (PAM) compatibilities. To expand this repertoire, we engineered nucleases, cytosine base editors, and adenine base editors from the archetypal Streptococcus thermophilus CRISPR1-Cas9 (St1Cas9) system. We found that St1Cas9 strain variants enable targeting to five distinct A-rich PAMs and provide a structural basis for their specificities. The small size of this ortholog enables expression of the holoenzyme from a single adeno-associated viral vector for in vivo editing applications. Delivery of St1Cas9 to the neonatal liver efficiently rewired metabolic pathways, leading to phenotypic rescue in a mouse model of hereditary tyrosinemia. These robust enzymes expand and complement current editing platforms available for tailoring mammalian genomes.
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Affiliation(s)
- Daniel Agudelo
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Sophie Carter
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Minja Velimirovic
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Alexis Duringer
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Jean-François Rivest
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Sébastien Levesque
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Jeremy Loehr
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Mathilde Mouchiroud
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ)-Université Laval, Québec, Québec G1V 4G5, Canada
| | - Denis Cyr
- Service de Génétique médicale, Département de Pédiatrie, Centre Hospitalier Universitaire de Sherbrooke (CHUS), et CRCHUS, Sherbrooke, Québec J1H 5N4, Canada
| | - Paula J Waters
- Service de Génétique médicale, Département de Pédiatrie, Centre Hospitalier Universitaire de Sherbrooke (CHUS), et CRCHUS, Sherbrooke, Québec J1H 5N4, Canada
| | - Mathieu Laplante
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ)-Université Laval, Québec, Québec G1V 4G5, Canada.,Université Laval Cancer Research Centre, Québec, Québec G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille Cedex 09, France.,Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille Cedex 09, France
| | - Yannick Doyon
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada.,Université Laval Cancer Research Centre, Québec, Québec G1V 0A6, Canada
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17
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Hynes AP, Rousseau GM, Agudelo D, Goulet A, Amigues B, Loehr J, Romero DA, Fremaux C, Horvath P, Doyon Y, Cambillau C, Moineau S. Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins. Nat Commun 2018; 9:2919. [PMID: 30046034 PMCID: PMC6060171 DOI: 10.1038/s41467-018-05092-w] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/13/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are bacterial anti-viral systems, and bacterial viruses (bacteriophages, phages) can carry anti-CRISPR (Acr) proteins to evade that immunity. Acrs can also fine-tune the activity of CRISPR-based genome-editing tools. While Acrs are prevalent in phages capable of lying dormant in a CRISPR-carrying host, their orthologs have been observed only infrequently in virulent phages. Here we identify AcrIIA6, an Acr encoded in 33% of virulent Streptococcus thermophilus phage genomes. The X-ray structure of AcrIIA6 displays some features unique to this Acr family. We compare the activity of AcrIIA6 to those of other Acrs, including AcrIIA5 (also from S. thermophilus phages), and characterize their effectiveness against a range of CRISPR-Cas systems. Finally, we demonstrate that both Acr families from S. thermophilus phages inhibit Cas9-mediated genome editing of human cells.
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Affiliation(s)
- Alexander P Hynes
- Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University. Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Daniel Agudelo
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
| | - Beatrice Amigues
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
| | - Jeremy Loehr
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Dennis A Romero
- DuPont Nutrition and Health, 3329 Agriculture Dr, Madison, WI, 53716, USA
| | | | - Philippe Horvath
- DuPont Nutrition and Health, BP 10, 86220, Dangé-Saint-Romain, France
| | - Yannick Doyon
- Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.
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18
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Baklouti A, Goulet A, Lichière J, Canard B, Charrel RN, Ferron F, Coutard B, Papageorgiou N. Toscana virus nucleoprotein oligomer organization observed in solution. Acta Crystallogr D Struct Biol 2017; 73:650-659. [PMID: 28777080 DOI: 10.1107/s2059798317008774] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/12/2017] [Indexed: 11/10/2022]
Abstract
Toscana virus (TOSV) is an arthropod-borne virus belonging to the Phlebovirus genus within the Bunyaviridae family. As in other bunyaviruses, the genome of TOSV is made up of three RNA segments. They are encapsidated by the nucleoprotein (N), which also plays an essential role in virus replication. To date, crystallographic structures of phlebovirus N have systematically revealed closed-ring organizations which do not fully match the filamentous organization of the ribonucleoprotein (RNP) complex observed by electron microscopy. In order to further bridge the gap between crystallographic data on N and observations of the RNP by electron microscopy, the structural organization of recombinant TOSV N was investigated by an integrative approach combining X-ray diffraction crystallography, transmission electron microscopy, small-angle X-ray scattering, size-exclusion chromatography and multi-angle laser light scattering. It was found that in solution TOSV N forms open oligomers consistent with the encapsidation mechanism of phlebovirus RNA.
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Affiliation(s)
- Amal Baklouti
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
| | - Julie Lichière
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
| | - Rémi N Charrel
- Emergence des Pathologies Virales (EPV), Aix-Marseille Université, UMR_D 190 IRD French Institute of Research for Development, U1207 INSERM, EHESP French School of Public Health, Marseille, France; IHU Méditerranée Infection, APHM Public Hospital Samsos of Marseille, Marseille, France
| | - François Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
| | - Bruno Coutard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
| | - Nicolas Papageorgiou
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
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Muretta JM, Behnke-Parks WM, Major J, Petersen KJ, Goulet A, Moores CA, Thomas DD, Rosenfeld SS. Loop L5 assumes three distinct orientations during the ATPase cycle of the mitotic kinesin Eg5: a transient and time-resolved fluorescence study. J Biol Chem 2013; 288:34839-49. [PMID: 24145034 DOI: 10.1074/jbc.m113.518845] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the kinesin superfamily of molecular motors differ in several key structural domains, which probably allows these molecular motors to serve the different physiologies required of them. One of the most variable of these is a stem-loop motif referred to as L5. This loop is longest in the mitotic kinesin Eg5, and previous structural studies have shown that it can assume different conformations in different nucleotide states. However, enzymatic domains often consist of a mixture of conformations whose distribution shifts in response to substrate binding or product release, and this information is not available from the "static" images that structural studies provide. We have addressed this issue in the case of Eg5 by attaching a fluorescent probe to L5 and examining its fluorescence, using both steady state and time-resolved methods. This reveals that L5 assumes an equilibrium mixture of three orientations that differ in their local environment and segmental mobility. Combining these studies with transient state kinetics demonstrates that there is a major shift in this distribution during transitions that interconvert weak and strong microtubule binding states. Finally, in conjunction with previous cryo-EM reconstructions of Eg5·microtubule complexes, these fluorescence studies suggest a model in which L5 regulates both nucleotide and microtubule binding through a set of reversible interactions with helix α3. We propose that these features facilitate the production of sustained opposing force by Eg5, which underlies its role in supporting formation of a bipolar spindle in mitosis.
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Affiliation(s)
- Joseph M Muretta
- From the Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
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20
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Goulet A, Behnke-Parks WM, Sindelar CV, Major J, Rosenfeld SS, Moores CA. The Structural Basis of Force Generation by the Mitotic Motor Kinesin-5. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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21
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Abstract
Kinesin-5 motors are members of a superfamily of microtubule-dependent ATPases and are widely conserved among eukaryotes. Kinesin-5s typically form homotetramers with pairs of motor domains located at either end of a dumbbell-shaped molecule. This quaternary structure enables cross-linking and ATP-driven sliding of pairs of microtubules, although the exact molecular mechanism of this activity is still unclear. Kinesin-5 function has been characterized in greatest detail in cell division, although a number of interphase roles have also been defined. The kinesin-5 ATPase is tuned for slow microtubule sliding rather than cellular transport and-in vertebrates-can be inhibited specifically by allosteric small molecules currently in cancer clinical trials. The biophysical and structural basis of kinesin-5 mechanochemistry is being elucidated and has provided further insight into kinesin-5 activities. However, it is likely that the precise mechanism of these important motors has evolved according to functional context and regulation in individual organisms.
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Affiliation(s)
- Adeline Goulet
- Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom
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22
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Goulet A, Behnke-Parks WM, Sindelar CV, Major J, Rosenfeld SS, Moores CA. The structural basis of force generation by the mitotic motor kinesin-5. J Biol Chem 2012; 287:44654-66. [PMID: 23135273 DOI: 10.1074/jbc.m112.404228] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinesin-5 is required for forming the bipolar spindle during mitosis. Its motor domain, which contains nucleotide and microtubule binding sites and mechanical elements to generate force, has evolved distinct properties for its spindle-based functions. In this study, we report subnanometer resolution cryoelectron microscopy reconstructions of microtubule-bound human kinesin-5 before and after nucleotide binding and combine this information with studies of the kinetics of nucleotide-induced neck linker and cover strand movement. These studies reveal coupled, nucleotide-dependent conformational changes that explain many of this motor's properties. We find that ATP binding induces a ratchet-like docking of the neck linker and simultaneous, parallel docking of the N-terminal cover strand. Loop L5, the binding site for allosteric inhibitors of kinesin-5, also undergoes a dramatic reorientation when ATP binds, suggesting that it is directly involved in controlling nucleotide binding. Our structures indicate that allosteric inhibitors of human kinesin-5, which are being developed as anti-cancer therapeutics, bind to a motor conformation that occurs in the course of normal function. However, due to evolutionarily defined sequence variations in L5, this conformation is not adopted by invertebrate kinesin-5s, explaining their resistance to drug inhibition. Together, our data reveal the precision with which the molecular mechanism of kinesin-5 motors has evolved for force generation.
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Affiliation(s)
- Adeline Goulet
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Goulet A, Vestergaard G, Felisberto-Rodrigues C, Campanacci V, Garrett RA, Cambillau C, Ortiz-Lombardía M. Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATV. Acta Crystallogr D Biol Crystallogr 2010; 66:304-8. [PMID: 20179342 DOI: 10.1107/s0907444909051798] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 12/01/2009] [Indexed: 11/10/2022]
Abstract
The structure of a 14 kDa structural protein from Acidianus two-tailed virus (ATV) was solved by single-wavelength anomalous diffraction (SAD) phasing using X-ray data collected at 2.0 A wavelength. Although the anomalous signal from methionine sulfurs was expected to suffice to solve the structure, one chloride ion turned out to be essential to achieve phasing. The minimal data requirements and the relative contributions of the Cl and S atoms to phasing are discussed. This work supports the feasibility of a systematic approach for the solution of protein crystal structures by SAD based on intrinsic protein light atoms along with associated chloride ions from the solvent. In such cases, data collection at long wavelengths may be a time-efficient alternative to selenomethionine substitution and heavy-atom derivatization.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques UMR 6098, CNRS, Universités d'Aix-Marseille I et II, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
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25
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Goulet A, Blangy S, Redder P, Prangishvili D, Felisberto-Rodrigues C, Forterre P, Campanacci V, Cambillau C. Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage. Proc Natl Acad Sci U S A 2009; 106:21155-60. [PMID: 19934032 PMCID: PMC2795548 DOI: 10.1073/pnas.0909893106] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Indexed: 11/18/2022] Open
Abstract
Acidianus filamentous virus 1 (AFV1), a member of the Lipothrixviridae family, infects the hyperthermophilic, acidophilic crenarchaeaon Acidianus hospitalis. The virion, covered with a lipidic outer shell, is 9,100-A long and contains a 20.8-kb linear dsDNA genome. We have identified the two major coat proteins of the virion (MCPs; 132 and 140 amino acids). They bind DNA and form filaments when incubated with linear dsDNA. A C-terminal domain is identified in their crystal structure with a four-helix-bundle fold. In the topological model of the virion filament core, the genomic dsDNA superhelix wraps around the AFV1-132 basic protein, and the AFV1-140 basic N terminus binds genomic DNA, while its lipophilic C-terminal domain is imbedded in the lipidic outer shell. The four-helix bundle fold of the MCPs from AFV1 is identical to that of the coat protein (CP) of Sulfolobus islandicus rod-shaped virus (SIRV), a member of the Rudiviridae family. Despite low sequence identity between these proteins, their high degree of structural similarity suggests that they could have derived from a common ancestor and could thus define an yet undescribed viral lineage.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Stéphanie Blangy
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Peter Redder
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France; and
| | - David Prangishvili
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France; and
| | - Catarina Felisberto-Rodrigues
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Patrick Forterre
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France; and
- Institut de Génétique et Microbiologie, Université Paris-Sud and Centre national de la recherche scientifique, Unité Mixte de Recherche 8621, 91405 Orsay Cedex, France
| | - Valérie Campanacci
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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26
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Goulet A, Spinelli S, Blangy S, van Tilbeurgh H, Leulliot N, Basta T, Prangishvili D, Cambillau C, Campanacci V. The thermo- and acido-stable ORF-99 from the archaeal virus AFV1. Protein Sci 2009; 18:1316-20. [PMID: 19472363 DOI: 10.1002/pro.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Acidianus Filamentous Virus 1 (AFV1), isolated from acidic hot springs, is an enveloped lipid-containing archaeal filamentous virus with a linear double-stranded DNA genome. It infects Acidianus, which is a hyperthermostable archaea growing at 85 degrees C and acidic pHs, below pH 3. AFV1-99, a protein of 99 amino acids of unknown function, has homologues in the archaeal virus families Lipothrixviridae and Rudiviridae. We determined the crystal structure of AFV1-99 at 2.05 A resolution. AFV1-99 has a new fold, is hyperthermostable (up to 95 degrees C) and resists to extreme pH (between pH 0 and 11) and to the combination of high temperature (95 degrees C) and low pH (pH 0). It possesses characteristics of hyperthermostable proteins, such as a high content of charged residues.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I & II, 163 avenue de Luminy, Marseille cedex 9, France
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27
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Goulet A, Spinelli S, Blangy S, van Tilbeurgh H, Leulliot N, Basta T, Prangishvili D, Cambillau C, Campanacci V. The crystal structure of ORF14 from Sulfolobus islandicus
filamentous virus. Proteins 2009; 76:1020-2. [DOI: 10.1002/prot.22448] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Goulet A, Kostyuchenko V, Leulliot N, van Tilbeurgh H, Prangishvili D, Cambillau C, Rossmann M, Campanacci V. A new virus structure: the nucleosome-like organization of the filamentous archaeal virus AFV1. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308097808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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29
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Goulet A, Spinelli S, Campanacci V, Porciero S, Blangy S, Garrett RA, van Tilbeurgh H, Leulliot N, Basta T, Prangishvili D, Cambillau C. Crystallization and preliminary X-ray diffraction analysis of protein 14 from Sulfolobus islandicus filamentous virus (SIFV). Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:884-6. [PMID: 16946470 PMCID: PMC2242861 DOI: 10.1107/s1744309106029150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 07/27/2006] [Indexed: 11/10/2022]
Abstract
A large-scale programme has been embarked upon aiming towards the structural determination of conserved proteins from viruses infecting hyperthermophilic archaea. Here, the crystallization of protein 14 from the archaeal virus SIFV is reported. This protein, which contains 111 residues (MW 13 465 Da), was cloned and expressed in Escherichia coli with an N-terminal His(6) tag and purified to homogeneity. The tag was subsequently cleaved and the protein was crystallized using PEG 1000 or PEG 4000 as a precipitant. Large crystals were obtained of the native and the selenomethionine-labelled protein using sitting drops of 100-300 nl. Crystals belong to space group P6(2)22 or P6(4)22, with unit-cell parameters a = b = 68.1, c = 132.4 A. Diffraction data were collected to a maximum acceptable resolution of 2.95 and 3.20 A for the SeMet-labelled and native protein, respectively.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Valérie Campanacci
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Sophie Porciero
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Stéphanie Blangy
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
| | - Roger A. Garrett
- Danish Archaea Centre, Institute of Molecular Biology, Copenhagen University, Soelvgade 83H, DK1307 Copenhagen K, Denmark
| | - Herman van Tilbeurgh
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris 11, Bâtiment 430, 91405 Orsay, France
| | - Nicolas Leulliot
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris 11, Bâtiment 430, 91405 Orsay, France
| | - Tamara Basta
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 25 Rue du Dr Roux, 75724 Paris CEDEX 15, France
| | - David Prangishvili
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 25 Rue du Dr Roux, 75724 Paris CEDEX 15, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d’Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France
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Ouellette GB, Chamberland H, Goulet A, Lachapelle M, Lafontaine JG. Fine structure of the extracellular sheath and cell walls inOphiostoma novo-ulmigrowing on various substrates. Can J Microbiol 1999. [DOI: 10.1139/w99-045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The presence of microfilamentous-like structures of tubular appearance (MFS) in cell walls and extracellular sheath material (ES) in a number of isolates of Ophiostoma novo-ulmi Brasier grown on various substrates and following various treatments is reported. Standard fixation or high-pressure freezing methods were used, and cytochemical tests were carried out to detect fungal and host wall components and, in some cases, fungal DNA. In some cases, serial 0.2-μm-thick sections were examined at 120 kV and tilted to obtain stereoscopic images. Whether the fungal cell walls were thick and composed of an outer opaque and inner more electron-lucent layers, or thin and barely perceptible, MFS were observed to extend from the cell cytoplasm as parallel structures across the walls into the surrounding medium, including host cell components in infected elm tissues. MFS were associated (in samples from inoculated trees) with cleavage and desquamation of fungal walls. ES and MFS did not label for cellulose or chitin, but generally labelled slightly for β-(1-3)-glucan and mannose, and strongly for galactose. Only the lucent, inner fungal wall layer labelled for chitin and cellulose. DNA labelling was confined to nuclei and mitochondria in fungal cells from cultures on agar medium; in cells from cultures on millipore membranes, it was pronounced over imprecisely delimited cell regions. The possible ontogeny of MFS components and their importance are discussed. Key words: chitin, Dutch elm disease, fungal fimbriae, fungal walls, gold-complexed probes, microfilamentous structures (MFS).
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Ouellette G, Chamberland H, Goulet A, Lachapelle M, Lafontaine JG. Fine structure of the extracellular sheath and cell walls in Ophiostoma novo-ulmi growing on various substrates. Can J Microbiol 1999. [DOI: 10.1139/cjm-45-7-582] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Kirk A, Goulet A, Thienpont H, McArdle N, Brenner KH, Kuijk M, Heremans P, Veretennicoff I. Compact optical imaging system for arrays of optical thyristors. Appl Opt 1997; 36:3070-3078. [PMID: 18253312 DOI: 10.1364/ao.36.003070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A compact and modular optical system that employs gradient-refractive-index rod lenses to image arrays of Lambertian sources is characterized both experimentally and by ray-tracing simulations. A hybrid optical system that incorporates additional microlens arrays to reduce transmittance losses and aberrations is also modeled, and the two systems are compared.
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Léger L, Lambert J, Goulet A, Rowan C, Dinelle Y. [Aerobic capacity of 6 to 17-year-old Quebecois--20 meter shuttle run test with 1 minute stages]. Can J Appl Sport Sci 1984; 9:64-9. [PMID: 6733834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Norms for the 20-m shuttle run test (with 1 min stages) for the functional and maximal aerobic power (FMAP) are given by age or academic year for boys and girls from 6 to 17 years old for the province of Quebec in May 1981. The sample, 3669 boys and 3355 girls, was selected by stratum according to the scholar population of each region in Quebec. Weight and height for both sexes are similar to those obtained in a recent Canadian study (CAHPER, 1980). The FMAP or the 20-m test results (as a function of age and sex) varies like other published FMAP indices. This supports the validity of the norms of the 20-m test, a test that various advantages in school testing (group testing, progressive protocol and valid test).
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