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Labarde A, Jakutyte L, Billaudeau C, Fauler B, López-Sanz M, Ponien P, Jacquet E, Mielke T, Ayora S, Carballido-López R, Tavares P. Temporal compartmentalization of viral infection in bacterial cells. Proc Natl Acad Sci U S A 2021; 118:e2018297118. [PMID: 34244425 PMCID: PMC8285916 DOI: 10.1073/pnas.2018297118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Indexed: 11/18/2022] Open
Abstract
Virus infection causes major rearrangements in the subcellular architecture of eukaryotes, but its impact in prokaryotic cells was much less characterized. Here, we show that infection of the bacterium Bacillus subtilis by bacteriophage SPP1 leads to a hijacking of host replication proteins to assemble hybrid viral-bacterial replisomes for SPP1 genome replication. Their biosynthetic activity doubles the cell total DNA content within 15 min. Replisomes operate at several independent locations within a single viral DNA focus positioned asymmetrically in the cell. This large nucleoprotein complex is a self-contained compartment whose boundaries are delimited neither by a membrane nor by a protein cage. Later during infection, SPP1 procapsids localize at the periphery of the viral DNA compartment for genome packaging. The resulting DNA-filled capsids do not remain associated to the DNA transactions compartment. They bind to phage tails to build infectious particles that are stored in warehouse compartments spatially independent from the viral DNA. Free SPP1 structural proteins are recruited to the dynamic phage-induced compartments following an order that recapitulates the viral particle assembly pathway. These findings show that bacteriophages restructure the crowded host cytoplasm to confine at different cellular locations the sequential processes that are essential for their multiplication.
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Affiliation(s)
- Audrey Labarde
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lina Jakutyte
- Laboratoire de Virologie Moléculaire et Structurale, CNRS Unité Propre de Recherche 3296 and Institut Fédératif de Recherche 115, 91198 Gif-sur-Yvette, France
| | - Cyrille Billaudeau
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Beatrix Fauler
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Maria López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Prishila Ponien
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Eric Jacquet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Thorsten Mielke
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Rut Carballido-López
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Paulo Tavares
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
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Jaïs PH, Decroly E, Jacquet E, Le Boulch M, Jaïs A, Jean-Jean O, Eaton H, Ponien P, Verdier F, Canard B, Goncalves S, Chiron S, Le Gall M, Mayeux P, Shmulevitz M. C3P3-G1: first generation of a eukaryotic artificial cytoplasmic expression system. Nucleic Acids Res 2019; 47:2681-2698. [PMID: 30726994 PMCID: PMC6412113 DOI: 10.1093/nar/gkz069] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/03/2018] [Accepted: 01/25/2019] [Indexed: 12/25/2022] Open
Abstract
Most eukaryotic expression systems make use of host-cell nuclear transcriptional and post-transcriptional machineries. Here, we present the first generation of the chimeric cytoplasmic capping-prone phage polymerase (C3P3-G1) expression system developed by biological engineering, which generates capped and polyadenylated transcripts in host-cell cytoplasm by means of two components. First, an artificial single-unit chimeric enzyme made by fusing an mRNA capping enzyme and a DNA-dependent RNA polymerase. Second, specific DNA templates designed to operate with the C3P3-G1 enzyme, which encode for the transcripts and their artificial polyadenylation. This system, which can potentially be adapted to any in cellulo or in vivo eukaryotic expression applications, was optimized for transient expression in mammalian cells. C3P3-G1 shows promising results for protein production in Chinese Hamster Ovary (CHO-K1) cells. This work also provides avenues for enhancing the performances for next generation C3P3 systems.
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Affiliation(s)
- Philippe H Jaïs
- Eukarÿs SAS, Génopole Campus 3, 4 rue Pierre Fontaine, 91058 Evry Cedex, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257 CNRS/AMU, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Marine Le Boulch
- Eukarÿs SAS, Génopole Campus 3, 4 rue Pierre Fontaine, 91058 Evry Cedex, France
| | - Aurélien Jaïs
- Eukarÿs SAS, Génopole Campus 3, 4 rue Pierre Fontaine, 91058 Evry Cedex, France
| | - Olivier Jean-Jean
- Sorbonne Université, CNRS-UMR8256, Biological Adaptation and Ageing, Institut de Biologie Paris Seine (B2A-IBPS), F-75252 Paris, France
| | - Heather Eaton
- Medical Microbiology and Immunology, University of Alberta, 6-142J Katz Group Centre for Pharmacy and Health Research, 114 Street NW, Edmonton, Alberta T6G 2E1, Canada
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Fréderique Verdier
- INSERM Unit 1016, Institut Cochin, Bâtiment Gustave Roussy, 27 rue du faubourg Saint-Jacques, 75014 Paris, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257 CNRS/AMU, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Sergio Goncalves
- Eukarÿs SAS, Génopole Campus 3, 4 rue Pierre Fontaine, 91058 Evry Cedex, France
| | - Stéphane Chiron
- Eukarÿs SAS, Génopole Campus 3, 4 rue Pierre Fontaine, 91058 Evry Cedex, France
| | - Maude Le Gall
- Gastrointestinal and Metabolic Dysfunctions in Nutritional Pathologies, INSERM UMRS1149, 16 rue Henri Huchard, 75890 Paris Cedex 18, France
| | - Patrick Mayeux
- INSERM Unit 1016, Institut Cochin, Bâtiment Gustave Roussy, 27 rue du faubourg Saint-Jacques, 75014 Paris, France
| | - Maya Shmulevitz
- Medical Microbiology and Immunology, University of Alberta, 6-142J Katz Group Centre for Pharmacy and Health Research, 114 Street NW, Edmonton, Alberta T6G 2E1, Canada
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Molina CE, Jacquet E, Ponien P, Muñoz-Guijosa C, Baczkó I, Maier LS, Donzeau-Gouge P, Dobrev D, Fischmeister R, Garnier A. Identification of optimal reference genes for transcriptomic analyses in normal and diseased human heart. Cardiovasc Res 2019; 114:247-258. [PMID: 29036603 DOI: 10.1093/cvr/cvx182] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Aims Quantitative real-time RT-PCR (RT-qPCR) has become the method of choice for mRNA quantification, but requires an accurate normalization based on the use of reference genes showing invariant expression across various pathological conditions. Only few data exist on appropriate reference genes for the human heart. The objective of this study was to determine a set of suitable reference genes in human atrial and ventricular tissues, from right and left cavities in control and in cardiac diseases. Methods and results We assessed the expression of 16 reference genes (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC, YWHAZ, 18S) in tissues from: right and left ventricles from healthy controls and heart failure (HF) patients; right-atrial tissue from patients in sinus rhythm with (SRd) or without (SRnd) atrial dilatation, patients with paroxysmal (pAF) or chronic (cAF) atrial fibrillation or with HF; and left-atrial tissue from patients in SR or cAF. Consensual analysis (by geNorm and Normfinder algorithms, BestKeeper software tool and comparative delta-Ct method) of the variability scores obtained for each reference gene expression shows that the most stably expressed genes are: GAPDH, GUSB, IPO8, POLR2A, and YWHAZ when comparing either right and left ventricle or ventricle from healthy controls and HF patients; GAPDH, IPO8, POLR2A, PPIA, and RPLP0 when comparing either right and left atrium or right atria from all pathological groups. ACTB, TBP, TFRC, and 18S genes were identified as the least stable. Conclusions The overall most stable reference genes across different heart cavities and disease conditions were GAPDH, IPO8, POLR2A and PPIA. YWHAZ or GUSB could be added to this set for some specific experiments. This study should provide useful guidelines for reference gene selection in RT-qPCR studies in human heart.
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Affiliation(s)
- Cristina E Molina
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France.,Institute of Pharmacology and Toxicology, Heart Research Center Göttingen, University Medical Center, Georg-August University Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Istvan Baczkó
- Department Pharmacology and Pharmacotherapy, University of Szeged, Hungary
| | - Lars S Maier
- Department Internal Medicine II, University Heart Center, University Hospital Regensburg, Regensburg, Germany
| | | | - Dobromir Dobrev
- West German Heart and Vascular Center, Institute of Pharmacology, University Duisburg-Essen, Essen, Germany
| | - Rodolphe Fischmeister
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Anne Garnier
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
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Rochat T, Bohn C, Morvan C, Le Lam T, Razvi F, Pain A, Toffano-Nioche C, Ponien P, Jacq A, Jacquet E, Fey PD, Gautheret D, Bouloc P. The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus. Nucleic Acids Res 2018; 46:8803-8816. [PMID: 29986060 PMCID: PMC6158497 DOI: 10.1093/nar/gky584] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 11/04/2017] [Revised: 05/28/2018] [Accepted: 06/29/2018] [Indexed: 01/31/2023] Open
Abstract
RsaE is a regulatory RNA highly conserved amongst Firmicutes that lowers the amount of mRNAs associated with the TCA cycle and folate metabolism. A search for new RsaE targets in Staphylococcus aureus revealed that in addition to previously described substrates, RsaE down-regulates several genes associated with arginine catabolism. In particular, RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. The faster growth rate of ΔrsaE compared to its parental strain in media containing amino acids as sole carbon source points to an underlying role for RsaE in amino acid catabolism. Collectively, the data support a model in which RsaE acts as a global regulator of functions associated with metabolic adaptation.
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Affiliation(s)
- Tatiana Rochat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Chantal Bohn
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Claire Morvan
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Thao Nguyen Le Lam
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Fareha Razvi
- University of Nebraska Medical Center, Department of Pathology and Microbiology, Omaha, NE, USA
| | - Adrien Pain
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Claire Toffano-Nioche
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Annick Jacq
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Paul D Fey
- University of Nebraska Medical Center, Department of Pathology and Microbiology, Omaha, NE, USA
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
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Andreazza S, Bouleau S, Martin B, Lamouroux A, Ponien P, Papin C, Chélot E, Jacquet E, Rouyer F. Daytime CLOCK Dephosphorylation Is Controlled by STRIPAK Complexes in Drosophila. Cell Rep 2015; 11:1266-79. [PMID: 25981041 DOI: 10.1016/j.celrep.2015.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 02/23/2015] [Accepted: 04/16/2015] [Indexed: 11/29/2022] Open
Abstract
In the Drosophila circadian oscillator, the CLOCK/CYCLE complex activates transcription of period (per) and timeless (tim) in the evening. PER and TIM proteins then repress CLOCK (CLK) activity during the night. The pace of the oscillator depends upon post-translational regulation that affects both positive and negative components of the transcriptional loop. CLK protein is highly phosphorylated and inactive in the morning, whereas hypophosphorylated active forms are present in the evening. How this critical dephosphorylation step is mediated is unclear. We show here that two components of the STRIPAK complex, the CKA regulatory subunit of the PP2A phosphatase and its interacting protein STRIP, promote CLK dephosphorylation during the daytime. In contrast, the WDB regulatory PP2A subunit stabilizes CLK without affecting its phosphorylation state. Inhibition of the PP2A catalytic subunit and CKA downregulation affect daytime CLK similarly, suggesting that STRIPAK complexes are the main PP2A players in producing transcriptionally active hypophosphorylated CLK.
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Affiliation(s)
- Simonetta Andreazza
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Sylvina Bouleau
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Béatrice Martin
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Annie Lamouroux
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, 91190 Gif-sur-Yvette, France
| | - Christian Papin
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Elisabeth Chélot
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, 91190 Gif-sur-Yvette, France
| | - François Rouyer
- Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Institut des Neurosciences Paris-Saclay, 91190 Gif-sur-Yvette, France.
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Szabó Á, Papin C, Zorn D, Ponien P, Weber F, Raabe T, Rouyer F. The CK2 kinase stabilizes CLOCK and represses its activity in the Drosophila circadian oscillator. PLoS Biol 2013; 11:e1001645. [PMID: 24013921 PMCID: PMC3754892 DOI: 10.1371/journal.pbio.1001645] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [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: 06/11/2013] [Accepted: 07/19/2013] [Indexed: 12/21/2022] Open
Abstract
Phosphorylation is a pivotal regulatory mechanism for protein stability and activity in circadian clocks regardless of their evolutionary origin. It determines the speed and strength of molecular oscillations by acting on transcriptional activators and their repressors, which form negative feedback loops. In Drosophila, the CK2 kinase phosphorylates and destabilizes the PERIOD (PER) and TIMELESS (TIM) proteins, which inhibit CLOCK (CLK) transcriptional activity. Here we show that CK2 also targets the CLK activator directly. Downregulating the activity of the catalytic α subunit of CK2 induces CLK degradation, even in the absence of PER and TIM. Unexpectedly, the regulatory β subunit of the CK2 holoenzyme is not required for the regulation of CLK stability. In addition, downregulation of CK2α activity decreases CLK phosphorylation and increases per and tim transcription. These results indicate that CK2 inhibits CLK degradation while reducing its activity. Since the CK1 kinase promotes CLK degradation, we suggest that CLK stability and transcriptional activity result from counteracting effects of CK1 and CK2.
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Affiliation(s)
- Áron Szabó
- Institut de Neurobiologie Alfred Fessard, Centre National de la Recherche Scientifique Unité Propre de Recherche 3294, Gif-sur-Yvette, France
- Département de Biologie, Université Paris Sud, Orsay, France
| | - Christian Papin
- Institut de Neurobiologie Alfred Fessard, Centre National de la Recherche Scientifique Unité Propre de Recherche 3294, Gif-sur-Yvette, France
- Département de Biologie, Université Paris Sud, Orsay, France
| | - Daniela Zorn
- Heidelberg University, Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg, Germany
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Gif-sur-Yvette, France
- IMAGIF, Centre de Recherche de Gif, Gif-sur-Yvette, France
| | - Frank Weber
- Heidelberg University, Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg, Germany
| | - Thomas Raabe
- University of Wuerzburg, Institute of Medical Radiation and Cell Research, Wuerzburg, Germany
| | - François Rouyer
- Institut de Neurobiologie Alfred Fessard, Centre National de la Recherche Scientifique Unité Propre de Recherche 3294, Gif-sur-Yvette, France
- Département de Biologie, Université Paris Sud, Orsay, France
- * E-mail:
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