1
|
Muñoz-Gutierrez V, Cornejo FA, Schmidt K, Frese CK, Halte M, Erhardt M, Elsholz AKW, Turgay K, Charpentier E. Bacillus subtilis remains translationally active after CRISPRi-mediated replication initiation arrest. mSystems 2024; 9:e0022124. [PMID: 38546227 PMCID: PMC11019786 DOI: 10.1128/msystems.00221-24] [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: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 04/17/2024] Open
Abstract
Initiation of bacterial DNA replication takes place at the origin of replication (oriC), a region characterized by the presence of multiple DnaA boxes that serve as the binding sites for the master initiator protein DnaA. This process is tightly controlled by modulation of the availability or activity of DnaA and oriC during development or stress conditions. Here, we aimed to uncover the physiological and molecular consequences of stopping replication in the model bacterium Bacillus subtilis. We successfully arrested replication in B. subtilis by employing a clustered regularly interspaced short palindromic repeats interference (CRISPRi) approach to specifically target the key DnaA boxes 6 and 7, preventing DnaA binding to oriC. In this way, other functions of DnaA, such as a transcriptional regulator, were not significantly affected. When replication initiation was halted by this specific artificial and early blockage, we observed that non-replicating cells continued translation and cell growth, and the initial replication arrest did not induce global stress conditions such as the SOS response.IMPORTANCEAlthough bacteria constantly replicate under laboratory conditions, natural environments expose them to various stresses such as lack of nutrients, high salinity, and pH changes, which can trigger non-replicating states. These states can enable bacteria to (i) become tolerant to antibiotics (persisters), (ii) remain inactive in specific niches for an extended period (dormancy), and (iii) adjust to hostile environments. Non-replicating states have also been studied because of the possibility of repurposing energy for the production of additional metabolites or proteins. Using clustered regularly interspaced short palindromic repeats interference (CRISPRi) targeting bacterial replication initiation sequences, we were able to successfully control replication initiation in Bacillus subtilis. This precise approach makes it possible to study non-replicating phenotypes, contributing to a better understanding of bacterial adaptive strategies.
Collapse
Affiliation(s)
- Vanessa Muñoz-Gutierrez
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | | | - Katja Schmidt
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Manuel Halte
- Humboldt-Universität zu Berlin, Institute of Biology – Molecular Microbiology, Berlin, Germany
| | - Marc Erhardt
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology – Molecular Microbiology, Berlin, Germany
| | | | - Kürşad Turgay
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
2
|
Naseri G, Raasch H, Charpentier E, Erhardt M. A versatile regulatory toolkit of arabinose-inducible artificial transcription factors for Enterobacteriaceae. Commun Biol 2023; 6:1005. [PMID: 37789111 PMCID: PMC10547716 DOI: 10.1038/s42003-023-05363-3] [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: 05/31/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
The Gram-negative bacteria Salmonella enterica and Escherichia coli are important model organisms, powerful prokaryotic expression platforms for biotechnological applications, and pathogenic strains constitute major public health threats. To facilitate new approaches for research and biotechnological applications, we here develop a set of arabinose-inducible artificial transcription factors (ATFs) using CRISPR/dCas9 and Arabidopsis-derived DNA-binding proteins to control gene expression in E. coli and Salmonella over a wide inducer concentration range. The transcriptional output of the different ATFs, in particular when expressed in Salmonella rewired for arabinose catabolism, varies over a wide spectrum (up to 35-fold gene activation). As a proof-of-concept, we use the developed ATFs to engineer a Salmonella two-input biosensor strain, SALSOR 0.2 (SALmonella biosenSOR 0.2), which detects and quantifies alkaloid drugs through a measurable fluorescent output. Moreover, we use plant-derived ATFs to regulate β-carotene biosynthesis in E. coli, resulting in ~2.1-fold higher β-carotene production compared to expression of the biosynthesis pathway using a strong constitutive promoter.
Collapse
Affiliation(s)
- Gita Naseri
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany.
| | - Hannah Raasch
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany
| | - Marc Erhardt
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany.
| |
Collapse
|
3
|
Broglia L, Le Rhun A, Charpentier E. Methodologies for bacterial ribonuclease characterization using RNA-seq. FEMS Microbiol Rev 2023; 47:fuad049. [PMID: 37656885 PMCID: PMC10503654 DOI: 10.1093/femsre/fuad049] [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: 03/23/2023] [Revised: 08/06/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Bacteria adjust gene expression at the post-transcriptional level through an intricate network of small regulatory RNAs and RNA-binding proteins, including ribonucleases (RNases). RNases play an essential role in RNA metabolism, regulating RNA stability, decay, and activation. These enzymes exhibit species-specific effects on gene expression, bacterial physiology, and different strategies of target recognition. Recent advances in high-throughput RNA sequencing (RNA-seq) approaches have provided a better understanding of the roles and modes of action of bacterial RNases. Global studies aiming to identify direct targets of RNases have highlighted the diversity of RNase activity and RNA-based mechanisms of gene expression regulation. Here, we review recent RNA-seq approaches used to study bacterial RNases, with a focus on the methods for identifying direct RNase targets.
Collapse
Affiliation(s)
- Laura Broglia
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Center for Human Technologies, Istituto Italiano di Tecnologia, 16152 Genova, Italy
| | - Anaïs Le Rhun
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Institute for Biology, Humboldt University, D-10115 Berlin, Germany
| |
Collapse
|
4
|
Alagesan K, Charpentier E. Systems-Wide Site-Specific Analysis of Glycoproteins. Methods Mol Biol 2023; 2718:151-165. [PMID: 37665459 DOI: 10.1007/978-1-0716-3457-8_9] [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] [Indexed: 09/05/2023]
Abstract
Glycosylation is one of the most common and complex post-translation modifications that influence the structural and functional properties of proteins. Glycoproteins are highly heterogeneous and exhibit site- and protein-specific expression differences. Mass spectrometry in combination with liquid chromatography has emerged as the most powerful tool for the comprehensive characterization of glycosylation. The analysis of intact glycopeptides has emerged as a promising strategy to analyze glycoproteins for their glycan heterogeneity at both protein- and site-specific levels. Nevertheless, intact glycopeptide characterization is challenging as elucidation of the glycan and peptide moieties requires specific sample preparation workflows that, combined with the tandem mass spectrometry approach, enable the identification of single glycopeptide species. In this chapter, we provide a detailed description of the methods that include procedures for (i) proteolytic digestion using specific proteases, (ii) optional glycopeptide enrichment using hydrophilic interaction liquid chromatography, (iii) nano-LC-MS/MS analysis of glycopeptides, and (iv) data analysis for identification of glycopeptides. Together, our workflow provides a framework for the system-wide site-specific analysis of N- and O-glycopeptides derived from complex biological or clinical samples.
Collapse
Affiliation(s)
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute for Biology, Humboldt University, Berlin, Germany
| |
Collapse
|
5
|
Gallo A, Carreau V, Mondelli A, Zarai M, Charpentier E, Kachenoura N, Redheuil A, Bruckert E. Non-calcific atherosclerotic burden in HeFH: The FH-CALC study. Atherosclerosis 2022. [DOI: 10.1016/j.atherosclerosis.2022.06.082] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
6
|
Charpentier E, Musso A, Chamorey E, Delotte J, Maccagnan S, Bourgeois M, Roma J. Connaissances des moyens de contraception et implication : existe-t-il une corrélation ? Étude quantitative auprès de jeunes hommes de 15 à 25 ans résidant dans la région PACA. Rev Epidemiol Sante Publique 2022. [DOI: 10.1016/j.respe.2022.03.032] [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: 10/18/2022] Open
|
7
|
Pagonendji M, Ionéla G, Charpentier E, Sausy A, Lefaou A, Duval R, Hübschen J. Rubella epidemiology in the Central African Republic, 2015-2016 and molecular characterization of virus strains from 2008-2016. Int J Infect Dis 2022. [DOI: 10.1016/j.ijid.2021.12.274] [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: 11/28/2022] Open
|
8
|
Desbois A, Charpentier E, Chapelon C, Bergeret S, Badenco N, Redheuil A, Cacoub P, Saadoun D. Sarcoïdose cardiaque : stratégies diagnostiques et thérapeutiques actuelles. Rev Med Interne 2022; 43:212-224. [DOI: 10.1016/j.revmed.2021.08.018] [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] [Received: 06/11/2021] [Revised: 07/22/2021] [Accepted: 08/01/2021] [Indexed: 11/26/2022]
|
9
|
Abstract
![]()
Protein phosphorylation
in prokaryotes has gained more
attention in recent years as several
studies linked it to regulatory and signaling functions, indicating
importance similar to protein phosphorylation in eukaryotes. Studies
on bacterial phosphorylation have so far been conducted using manual
or HPLC-supported phosphopeptide enrichment, whereas automation of
phosphopeptide enrichment has been established in eukaryotes, allowing
for high-throughput sampling. To facilitate the prospect of studying
bacterial phosphorylation on a systems level, we here established
an automated Ser/Thr/Tyr phosphopeptide enrichment workflow on the
Agilent AssayMap platform. We present optimized buffer conditions
for TiO2 and Fe(III)-NTA-IMAC cartridge-based enrichment
and the most advantageous, species-specific loading amounts for Streptococcus pyogenes, Listeria monocytogenes, and Bacillus subtilis. For higher
sample amounts (≥250 μg), we observed superior performance
of the Fe(III)-NTA cartridges, whereas for lower sample amounts (≤100
μg), TiO2-based enrichment is equally efficient.
Both cartridges largely enriched the same set of phosphopeptides,
suggesting no improvement of peptide yield by the complementary use
of the two cartridges. Our data represent, to the best of our knowledge,
the largest phosphoproteome identified in a single study for each
of these bacteria.
Collapse
Affiliation(s)
- Marlène S Birk
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | | |
Collapse
|
10
|
Birk MS, Ahmed-Begrich R, Tran S, Elsholz AKW, Frese CK, Charpentier E. Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation. mSystems 2021; 6:e0021521. [PMID: 34342529 PMCID: PMC8407217 DOI: 10.1128/msystems.00215-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/14/2021] [Indexed: 12/13/2022] Open
Abstract
The cellular proteome comprises all proteins expressed at a given time and defines an organism's phenotype under specific growth conditions. The proteome is shaped and remodeled by both protein synthesis and protein degradation. Here, we developed a new method which combines metabolic and chemical isobaric peptide labeling to simultaneously determine the time-resolved protein decay and de novo synthesis in an intracellular human pathogen. We showcase this method by investigating the Listeria monocytogenes proteome in the presence and absence of the AAA+ chaperone protein ClpC. ClpC associates with the peptidase ClpP to form an ATP-dependent protease complex and has been shown to play a role in virulence development in L. monocytogenes. However, the mechanism by which ClpC is involved in the survival and proliferation of intracellular L. monocytogenes remains elusive. Employing this new method, we observed extensive proteome remodeling in L. monocytogenes upon interaction with the host, supporting the hypothesis that ClpC-dependent protein degradation is required to initiate bacterial adaptation mechanisms. We identified more than 100 putative ClpC target proteins through their stabilization in a clpC deletion strain. Beyond the identification of direct targets, we also observed indirect effects of the clpC deletion on the protein abundance in diverse cellular and metabolic pathways, such as iron acquisition and flagellar assembly. Overall, our data highlight the crucial role of ClpC for L. monocytogenes adaptation to the host environment through proteome remodeling. IMPORTANCE Survival and proliferation of pathogenic bacteria inside the host depend on their ability to adapt to the changing environment. Profiling the underlying changes on the bacterial proteome level during the infection process is important to gain a better understanding of the pathogenesis and the host-dependent adaptation processes. The cellular protein abundance is governed by the interplay between protein synthesis and decay. The direct readout of these events during infection can be accomplished using pulsed stable-isotope labeling by amino acids in cell culture (SILAC). Combining this approach with tandem-mass-tag (TMT) labeling enabled multiplexed and time-resolved bacterial proteome quantification during infection. Here, we applied this integrated approach to investigate protein turnover during the temporal progression of adaptation of the human pathogen L. monocytogenes to its host on a system-wide scale. Our experimental approach can easily be transferred to probe the proteome remodeling in other bacteria under a variety of perturbations.
Collapse
Affiliation(s)
- Marlène S. Birk
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Stefan Tran
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | | | | |
Collapse
|
11
|
Hüsing S, Halte M, van Look U, Guse A, Gálvez EJC, Charpentier E, Blair DF, Erhardt M, Renault TT. Control of membrane barrier during bacterial type-III protein secretion. Nat Commun 2021; 12:3999. [PMID: 34183670 PMCID: PMC8239009 DOI: 10.1038/s41467-021-24226-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 11/17/2020] [Accepted: 06/02/2021] [Indexed: 11/09/2022] Open
Abstract
Type-III secretion systems (T3SSs) of the bacterial flagellum and the evolutionarily related injectisome are capable of translocating proteins with a remarkable speed of several thousand amino acids per second. Here, we investigate how T3SSs are able to transport proteins at such a high rate while preventing the leakage of small molecules. Our mutational and evolutionary analyses demonstrate that an ensemble of conserved methionine residues at the cytoplasmic side of the T3SS channel create a deformable gasket (M-gasket) around fast-moving substrates undergoing export. The unique physicochemical features of the M-gasket are crucial to preserve the membrane barrier, to accommodate local conformational changes during active secretion, and to maintain stability of the secretion pore in cooperation with a plug domain (R-plug) and a network of salt-bridges. The conservation of the M-gasket, R-plug, and salt-bridge network suggests a universal mechanism by which the membrane integrity is maintained during high-speed protein translocation in all T3SSs. Type-III secretion systems (T3SSs) are capable of translocating proteins with high speed while maintaining the membrane barrier for small molecules. Here, a structure-function analysis of the T3SS pore complex elucidates the precise mechanisms enabling the gating and the conformational changes required for protein substrate secretion.
Collapse
Affiliation(s)
- Svenja Hüsing
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany.,Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Manuel Halte
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulf van Look
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany.,Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Alina Guse
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Eric J C Gálvez
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - David F Blair
- School of Biology, University of Utah, Salt Lake City, UT, USA
| | - Marc Erhardt
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany. .,Max Planck Unit for the Science of Pathogens, Berlin, Germany.
| | - Thibaud T Renault
- Institute for Biology-Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany. .,Max Planck Unit for the Science of Pathogens, Berlin, Germany. .,CNRS, UMR 5234, Université de Bordeaux, Bordeaux, France. .,Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France.
| |
Collapse
|
12
|
Gálvez EJC, Iljazovic A, Amend L, Lesker TR, Renault T, Thiemann S, Hao L, Roy U, Gronow A, Charpentier E, Strowig T. Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp. Cell Host Microbe 2020; 28:838-852.e6. [PMID: 33113351 DOI: 10.1016/j.chom.2020.09.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/07/2020] [Accepted: 09/16/2020] [Indexed: 12/14/2022]
Abstract
Prevotella spp. are a dominant bacterial genus within the human gut. Multiple Prevotella spp. co-exist in some individuals, particularly those consuming plant-based diets. Additionally, Prevotella spp. exhibit variability in the utilization of diverse complex carbohydrates. To investigate the relationship between Prevotella competition and diet, we isolated Prevotella species from the mouse gut, analyzed their genomes and transcriptomes in vivo, and performed competition experiments between species in mice. Diverse dominant Prevotella species compete for similar metabolic niches in vivo, which is linked to the upregulation of specific polysaccharide utilization loci (PULs). Complex plant-derived polysaccharides are required for Prevotella spp. expansion, with arabinoxylans having a prominent impact on species abundance. The most dominant Prevotella species encodes a specific tandem-repeat trsusC/D PUL that enables arabinoxylan utilization and is conserved in human Prevotella copri strains, particularly among those consuming a vegan diet. These findings suggest that efficient (arabino)xylan-utilization is a factor contributing to Prevotella dominance.
Collapse
Affiliation(s)
- Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Aida Iljazovic
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Till Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Thibaud Renault
- Max Planck Unit for the Science of Pathogens, Berlin, Germany; CNRS/University of Bordeaux, UMR 5234, Microbiologie Fondamentale et Pathogénicité, France; Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac, France
| | - Sophie Thiemann
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lianxu Hao
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Urmi Roy
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Achim Gronow
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany; Institute for Biology, Humboldt University, Berlin, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Centre for Individualized Infection Medicine, Hannover, Germany.
| |
Collapse
|
13
|
Broglia L, Lécrivain AL, Renault TT, Hahnke K, Ahmed-Begrich R, Le Rhun A, Charpentier E. An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3'-to-5' exoRNases and RNase Y. Nat Commun 2020; 11:1587. [PMID: 32221293 PMCID: PMC7101322 DOI: 10.1038/s41467-020-15387-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 08/13/2019] [Accepted: 02/29/2020] [Indexed: 11/29/2022] Open
Abstract
RNA degradation is an essential process that allows bacteria to control gene expression and adapt to various environmental conditions. It is usually initiated by endoribonucleases (endoRNases), which produce intermediate fragments that are subsequently degraded by exoribonucleases (exoRNases). However, global studies of the coordinated action of these enzymes are lacking. Here, we compare the targetome of endoRNase Y with the targetomes of 3′-to-5′ exoRNases from Streptococcus pyogenes, namely, PNPase, YhaM, and RNase R. We observe that RNase Y preferentially cleaves after guanosine, generating substrate RNAs for the 3′-to-5′ exoRNases. We demonstrate that RNase Y processing is followed by trimming of the newly generated 3′ ends by PNPase and YhaM. Conversely, the RNA 5′ ends produced by RNase Y are rarely further trimmed. Our strategy enables the identification of processing events that are otherwise undetectable. Importantly, this approach allows investigation of the intricate interplay between endo- and exoRNases on a genome-wide scale. Bacterial RNA degradation is typically initiated by endoribonucleases and followed by exoribonucleases. Here the authors report the targetome of endoRNase Y in Streptococcus pyogenes, revealing the interplay between RNase Y and 3′-to-5′ exoribonuclease PNPase and YhaM.
Collapse
Affiliation(s)
- Laura Broglia
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany.,Institute for Biology, Humboldt University, D-10115, Berlin, Germany
| | - Anne-Laure Lécrivain
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187, Umeå, Sweden
| | - Thibaud T Renault
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany.,Institute for Biology, Humboldt University, D-10115, Berlin, Germany
| | - Karin Hahnke
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany
| | - Rina Ahmed-Begrich
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany
| | - Anaïs Le Rhun
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany. .,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany.
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, D-10117, Berlin, Germany. .,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117, Berlin, Germany. .,Institute for Biology, Humboldt University, D-10115, Berlin, Germany. .,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187, Umeå, Sweden.
| |
Collapse
|
14
|
Bratovič M, Fonfara I, Chylinski K, Gálvez EJC, Sullivan TJ, Boerno S, Timmermann B, Boettcher M, Charpentier E. Bridge helix arginines play a critical role in Cas9 sensitivity to mismatches. Nat Chem Biol 2020; 16:587-595. [PMID: 32123387 DOI: 10.1038/s41589-020-0490-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/30/2020] [Indexed: 12/31/2022]
Abstract
The RNA-programmable DNA-endonuclease Cas9 is widely used for genome engineering, where a high degree of specificity is required. To investigate which features of Cas9 determine the sensitivity to mismatches along the target DNA, we performed in vitro biochemical assays and bacterial survival assays in Escherichia coli. We demonstrate that arginines in the Cas9 bridge helix influence guide RNA, and target DNA binding and cleavage. They cluster in two groups that either increase or decrease the Cas9 sensitivity to mismatches. We show that the bridge helix is essential for R-loop formation and that R63 and R66 reduce Cas9 specificity by stabilizing the R-loop in the presence of mismatches. Additionally, we identify Q768 that reduces sensitivity of Cas9 to protospacer adjacent motif-distal mismatches. The Cas9_R63A/Q768A variant showed increased specificity in human cells. Our results provide a firm basis for function- and structure-guided mutagenesis to increase Cas9 specificity for genome engineering.
Collapse
Affiliation(s)
- Majda Bratovič
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Institute for Biology, Humboldt University, Berlin, Germany.,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ines Fonfara
- Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,The Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Krzysztof Chylinski
- The Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden.,Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.,Protein Technologies Facility, The Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Eric J C Gálvez
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Stefan Boerno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michael Boettcher
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Medical Faculty, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany. .,Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin, Germany. .,Institute for Biology, Humboldt University, Berlin, Germany. .,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany. .,The Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden.
| |
Collapse
|
15
|
Righetti F, Materne SL, Boss J, Eichner H, Charpentier E, Loh E. Characterization of a transcriptional TPP riboswitch in the human pathogen Neisseria meningitidis. RNA Biol 2020; 17:718-730. [PMID: 32079473 PMCID: PMC7237195 DOI: 10.1080/15476286.2020.1727188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Increasing evidence has demonstrated that regulatory RNA elements such as riboswitches (RS) play a pivotal role in the fine-tuning of bacterial gene expression. In this study, we investigated and characterized a novel transcriptional thiamine pyrophosphate (TPP) RS in the obligate human pathogen N. meningitidis MC58 (serogroup B). This RS is located in the 5´ untranslated region upstream of thiC gene, encoding a protein involved in TPP biosynthesis, an essential cofactor for all living beings. Primer extension revealed the transcriptional start site of thiC. Northern blot analysis of thiC mRNA and reporter gene studies confirmed the presence of an active TPP-sensing RS. Expression patterns of the wild-type RS and site-specific mutants showed that it is an OFF switch that controls transcription elongation of thiC mRNA. Interestingly, the regulatory mechanism of the meningococcal thiC RS resembles the Gram-positive Bacillus subtilis thiC RS rather than the Gram-negative Escherichia coli thiC RS. Therefore, the meningococcal thiC RS represents a rare example of transcriptional RS in a Gram-negative bacterium. We further observed that the RS is actively involved in modulating gene expression in response to different growth media and to supplemented bacterial and eukaryotic cell lysates as possible sources of nutrients in the nasopharynx. Our results suggest that RS-mediated gene regulation could influence meningococcal fitness, through the fine-tuning of biosynthesis and scavenging of nutrients and cofactors, such as thiamine.
Collapse
Affiliation(s)
- Francesco Righetti
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Solange Lise Materne
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - John Boss
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Hannes Eichner
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Institute for Biology, Humboldt University, Berlin, Germany.,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Edmund Loh
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden.,SCELSE, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
16
|
Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 2019; 18:67-83. [DOI: 10.1038/s41579-019-0299-x] [Citation(s) in RCA: 797] [Impact Index Per Article: 159.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 12/16/2022]
|
17
|
Colin M, Charpentier E, Klingelschmitt F, Bontemps C, De Champs C, Reffuveille F, Gangloff SC. Specific antibacterial activity of copper alloy touch surfaces in five long-term care facilities for older adults. J Hosp Infect 2019; 104:283-292. [PMID: 31809775 DOI: 10.1016/j.jhin.2019.11.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Pathogens involved in healthcare-associated infections can quickly spread in the environment, particularly to frequently touched surfaces, which can be reservoirs for pathogens. AIM The purpose of this study was to investigate naturally occurring bacterial contamination on touch surfaces in five French long-term care facilities and to compare bacterial populations recovered from copper and control surfaces. METHODS More than 1300 surfaces were sampled. The collected bacteria were identified to obtain a global view of the cultivable bacterial populations colonizing touch surfaces. Haemolytic colonies and putative pathogens were also screened using specific agar plates and then identified with matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. In total, more than 3400 colonies were analysed. FINDINGS Staphylococcus and Micrococcus were the two predominant genera present on touch surfaces, respectively occurring on 51.8% and 48.0% of control surfaces. In these facilities with relatively low bioburden, copper surfaces efficiently reduced the occurrence frequencies of three genera: Staphylococcus, Streptococcus and Roseomonas. Pathogenic species such as Staphylococcus aureus, Enterococcus faecalis and E. faecium were observed in very few samples. In addition, meticillin-resistant S. aureus was observed on five control surfaces and one copper surface. CONCLUSION Contamination of healthcare facilities touch surfaces can be the source for the spread of bacteria through the institution. This in situ study shows that the frequency of the contamination as well as the specific bacterial population bioburden is reduced on copper alloy surfaces.
Collapse
Affiliation(s)
- M Colin
- Université de Reims Champagne-Ardenne, EA 4691 Biomatériaux et Inflammation en site Osseux (BIOS), SFR CAP-Santé, France
| | - E Charpentier
- Université de Reims Champagne-Ardenne, EA 4691 Biomatériaux et Inflammation en site Osseux (BIOS), SFR CAP-Santé, France; Université de Reims Champagne-Ardenne, UFR de Pharmacie, Service de Microbiologie, France
| | - F Klingelschmitt
- Université de Reims Champagne-Ardenne, EA 4691 Biomatériaux et Inflammation en site Osseux (BIOS), SFR CAP-Santé, France
| | - C Bontemps
- Dynamique des génomes et adaptation microbienne, UMR1128, Université de Lorraine, INRA Vandœuvre-lès-Nancy, France
| | - C De Champs
- Université de Reims Champagne-Ardenne, Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Laboratoire de Bactériologie - Virologie - Hygiène hospitalière, CHU Reims, 51100 Reims, France
| | - F Reffuveille
- Université de Reims Champagne-Ardenne, EA 4691 Biomatériaux et Inflammation en site Osseux (BIOS), SFR CAP-Santé, France; Université de Reims Champagne-Ardenne, UFR de Pharmacie, Service de Microbiologie, France
| | - S C Gangloff
- Université de Reims Champagne-Ardenne, EA 4691 Biomatériaux et Inflammation en site Osseux (BIOS), SFR CAP-Santé, France; Université de Reims Champagne-Ardenne, UFR de Pharmacie, Service de Microbiologie, France.
| |
Collapse
|
18
|
Salsé M, Gangneux JP, Cassaing S, Delhaes L, Fekkar A, Dupont D, Botterel F, Costa D, Bourgeois N, Bouteille B, Houzé S, Dannaoui E, Guegan H, Charpentier E, Persat F, Favennec L, Lachaud L, Sasso M. Multicentre study to determine the Etest epidemiological cut-off values of antifungal drugs in Candida spp. and Aspergillus fumigatus species complex. Clin Microbiol Infect 2019; 25:1546-1552. [DOI: 10.1016/j.cmi.2019.04.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/17/2019] [Accepted: 04/22/2019] [Indexed: 02/04/2023]
|
19
|
Augy JL, Aissaoui N, Richard C, Maury E, Fartoukh M, Mekontso-Dessap A, Paulet R, Anguel N, Blayau C, Cohen Y, Chiche JD, Gaudry S, Voicu S, Demoule A, Combes A, Megarbane B, Charpentier E, Haghighat S, Panczer M, Diehl JL. A 2-year multicenter, observational, prospective, cohort study on extracorporeal CO 2 removal in a large metropolis area. J Intensive Care 2019; 7:45. [PMID: 31452899 PMCID: PMC6701003 DOI: 10.1186/s40560-019-0399-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/12/2019] [Indexed: 11/17/2022] Open
Abstract
Background Extracorporeal carbon dioxide removal (ECCO2R) is a promising technique for the management of acute respiratory failure, but with a limited level of evidence to support its use outside clinical trials and/or data collection initiatives. We report a collaborative initiative in a large metropolis. Methods To assess on a structural basis the rate of utilization as well as efficacy and safety parameters of 2 ECCO2R devices in 10 intensive care units (ICU) during a 2-year period. Results Seventy patients were recruited in 10 voluntary and specifically trained centers. The median utilization rate was 0.19 patient/month/center (min 0.04; max 1.20). ECCO2R was started under invasive mechanical ventilation (IMV) in 59 patients and non-invasive ventilation in 11 patients. The Hemolung Respiratory Assist System (Alung) was used in 53 patients and the iLA Activve iLA kit (Xenios Novalung) in 17 patients. Main indications were ultraprotective ventilation for ARDS patients (n = 24), shortening the duration of IMV in COPD patients (n = 21), preventing intubation in COPD patients (n = 9), and controlling hypercapnia and dynamic hyperinflation in mechanically ventilated patients with severe acute asthma (n = 6). A reduction in median VT was observed in ARDS patients from 5.9 to 4.1 ml/kg (p <0.001). A reduction in PaCO2 values was observed in AE-COPD patients from 67.5 to 51 mmHg (p< 0.001). Median duration of ECCO2R was 5 days (IQR 3–8). Reasons for ECCO2R discontinuation were improvement (n = 33), ECCO2R-related complications (n = 18), limitation of life-sustaining therapies or measures decision (n = 10), and death (n = 9). Main adverse events were hemolysis (n = 21), bleeding (n = 17), and lung membrane clotting (n = 11), with different profiles between the devices. Thirty-five deaths occurred during the ICU stay, 3 of which being ECCO2R-related. Conclusions Based on a registry, we report a low rate of ECCO2R device utilization, mainly in severe COPD and ARDS patients. Physiological efficacy was confirmed in these two populations. We confirmed safety concerns such as hemolysis, bleeding, and thrombosis, with different profiles between the devices. Such results could help to design future studies aiming to enhance safety, to demonstrate a still-lacking strong clinical benefit of ECCO2R, and to guide the choice between different devices. Trial registration ClinicalTrials.gov: Identifier: NCT02965079 retrospectively registered https://clinicaltrials.gov/ct2/show/NCT02965079
Collapse
Affiliation(s)
- J L Augy
- 1Service de Médecine Intensive Réanimation, AP-HP, Hôpital Européen Georges Pompidou, Paris, France
| | - N Aissaoui
- 1Service de Médecine Intensive Réanimation, AP-HP, Hôpital Européen Georges Pompidou, Paris, France
| | - C Richard
- 2Service de Médecine Intensive Réanimation, AP-HP, Hôpital de Bicètre, Le Kremlin Bicètre, France
| | - E Maury
- 3Service de Médecine Intensive Réanimation, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - M Fartoukh
- Service de Réanimation Polyvalente, AP-HP, Hôpital Tenon, Paris, France
| | - A Mekontso-Dessap
- 5Service de Médecine Intensive Réanimation, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - R Paulet
- Service de Réanimation Polyvalente, Centre Hospitalier de Longjumeau, Longjumeau, France
| | - N Anguel
- 2Service de Médecine Intensive Réanimation, AP-HP, Hôpital de Bicètre, Le Kremlin Bicètre, France
| | - C Blayau
- Service de Réanimation Polyvalente, AP-HP, Hôpital Tenon, Paris, France
| | - Y Cohen
- 7Service de Réanimation Polyvalente, AP-HP, Hôpital Avicenne, Bobigny, France
| | - J D Chiche
- 8Service de Médecine Intensive Réanimation, AP-HP, Hôpital Cochin, Paris, France
| | - S Gaudry
- 9Service de Réanimation Polyvalente, AP-HP, Hôpital Louis Mourier, Colombes, France
| | - S Voicu
- 10Service de Médecine Intensive Réanimation, AP-HP, Hôpital Lariboisière, Paris, France
| | - A Demoule
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière Charles Foix, Service de Pneumologie, Médecine Intensive et Réanimation, Département R3S, Sorbonne Université, INSERM, UMRS1158 Neurophysiologie Respiratoire Expérimentale et Clinique, Paris, France
| | - A Combes
- 12Service de Médecine Intensive Réanimation, AP-HP, Hôpital Pitié-Salpétrière, Institut de Cardiologie, Paris, France
| | - B Megarbane
- 10Service de Médecine Intensive Réanimation, AP-HP, Hôpital Lariboisière, Paris, France
| | - E Charpentier
- 13AP-HP, Office du Transfert de Technologie et des Partenariats Industriels, Paris, France
| | - S Haghighat
- 14AP-HP, Agence Générale des Equipements et des Produits de Santé, Paris, France
| | - M Panczer
- 14AP-HP, Agence Générale des Equipements et des Produits de Santé, Paris, France
| | - J L Diehl
- 1Service de Médecine Intensive Réanimation, AP-HP, Hôpital Européen Georges Pompidou, Paris, France.,15Faculty of Pharmacy, INSERM UMR-S1140, Paris Descartes University, Paris, France
| |
Collapse
|
20
|
Ratner HK, Escalera-Maurer A, Le Rhun A, Jaggavarapu S, Wozniak JE, Crispell EK, Charpentier E, Weiss DS. Catalytically Active Cas9 Mediates Transcriptional Interference to Facilitate Bacterial Virulence. Mol Cell 2019; 75:498-510.e5. [PMID: 31256988 DOI: 10.1016/j.molcel.2019.05.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/14/2019] [Accepted: 05/21/2019] [Indexed: 12/26/2022]
Abstract
In addition to defense against foreign DNA, the CRISPR-Cas9 system of Francisella novicida represses expression of an endogenous immunostimulatory lipoprotein. We investigated the specificity and molecular mechanism of this regulation, demonstrating that Cas9 controls a highly specific regulon of four genes that must be repressed for bacterial virulence. Regulation occurs through a protospacer adjacent motif (PAM)-dependent interaction of Cas9 with its endogenous DNA targets, dependent on a non-canonical small RNA (scaRNA) and tracrRNA. The limited complementarity between scaRNA and the endogenous DNA targets precludes cleavage, highlighting the evolution of scaRNA to repress transcription without lethally targeting the chromosome. We show that scaRNA can be reprogrammed to repress other genes, and with engineered, extended complementarity to an exogenous target, the repurposed scaRNA:tracrRNA-FnoCas9 machinery can also direct DNA cleavage. Natural Cas9 transcriptional interference likely represents a broad paradigm of regulatory functionality, which is potentially critical to the physiology of numerous Cas9-encoding pathogenic and commensal organisms.
Collapse
Affiliation(s)
- Hannah K Ratner
- Microbiology and Molecular Genetics Program, Emory University, Atlanta, GA 30329, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30329, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Andrés Escalera-Maurer
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany; Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, 38124 Braunschweig, Germany; Institute for Biology, Humboldt University, 10115 Berlin, Germany
| | - Anaïs Le Rhun
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany; Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, 38124 Braunschweig, Germany
| | - Siddharth Jaggavarapu
- Emory Vaccine Center, Emory University, Atlanta, GA 30329, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Jessie E Wozniak
- Microbiology and Molecular Genetics Program, Emory University, Atlanta, GA 30329, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30329, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Emily K Crispell
- Microbiology and Molecular Genetics Program, Emory University, Atlanta, GA 30329, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30329, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany; Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, 38124 Braunschweig, Germany; Institute for Biology, Humboldt University, 10115 Berlin, Germany
| | - David S Weiss
- Microbiology and Molecular Genetics Program, Emory University, Atlanta, GA 30329, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30329, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA.
| |
Collapse
|
21
|
Affiliation(s)
| | - Alexander Elsholz
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, Berlin, Germany
| | | |
Collapse
|
22
|
Abstract
The discovery and characterization of the prokaryotic CRISPR-Cas immune system has led to a revolution in genome editing and engineering technologies. Despite the fact that most applications emerged after the discovery of the type II-A CRISPR-Cas9 system of Streptococcus pyogenes, its biological importance in this organism has received little attention. Here, we provide a comprehensive overview of the current knowledge about CRISPR-Cas systems from S. pyogenes. We discuss how the interplay between CRISPR-mediated immunity and horizontal gene transfer might have modeled the evolution of this pathogen. We review the current literature about the CRISPR-Cas systems present in S. pyogenes (types I-C and II-A), and describe their distinctive biochemical and functional features. Finally, we summarize the main biotechnological applications that have arisen from the discovery of the CRISPR-Cas9 system in S. pyogenes.
Collapse
Affiliation(s)
- Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany
| | - Andrés Escalera-Maurer
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Majda Bratovič
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| |
Collapse
|
23
|
Davies K, Charpentier E. Finding Her Niche: An Interview with Emmanuelle Charpentier. CRISPR J 2019; 2:17-22. [DOI: 10.1089/crispr.2019.29042.kda] [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: 11/13/2022] Open
|
24
|
Abstract
Endoribonuclease Y (RNase Y) is a crucial regulator of virulence in Gram-positive bacteria. In the human pathogen Streptococcus pyogenes, RNase Y is required for the expression of the major secreted virulence factor streptococcal pyrogenic exotoxin B (SpeB), but the mechanism involved in this regulation remains elusive. Here, we demonstrate that the 5′ untranslated region of speB mRNA is processed by several RNases including RNase Y. In particular, we identify two RNase Y cleavage sites located downstream of a guanosine (G) residue. To assess whether this nucleotide is required for RNase Y activity in vivo, we mutated it and demonstrate that the presence of this G residue is essential for the processing of the speB mRNA 5′ UTR by RNase Y. Although RNase Y directly targets and processes speB, we show that RNase Y-mediated regulation of speB expression occurs primarily at the transcriptional level and independently of the processing in the speB mRNA 5′ UTR. To conclude, we demonstrate for the first time that RNase Y processing of an mRNA target requires the presence of a G. We also provide new insights on the speB 5′ UTR and on the role of RNase Y in speB regulation.
Collapse
Affiliation(s)
- Laura Broglia
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,c Institute for Biology , Humboldt University , Berlin , Germany.,d Department of Regulation in Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany
| | - Solange Materne
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany
| | - Anne-Laure Lécrivain
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,e The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology , Umeå University , Umeå , Sweden
| | - Karin Hahnke
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany
| | - Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,d Department of Regulation in Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany.,e The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology , Umeå University , Umeå , Sweden
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,c Institute for Biology , Humboldt University , Berlin , Germany.,d Department of Regulation in Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany.,e The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology , Umeå University , Umeå , Sweden
| |
Collapse
|
25
|
Tsatsaronis JA, Franch-Arroyo S, Resch U, Charpentier E. Extracellular Vesicle RNA: A Universal Mediator of Microbial Communication? Trends Microbiol 2018; 26:401-410. [PMID: 29548832 DOI: 10.1016/j.tim.2018.02.009] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/08/2018] [Accepted: 02/14/2018] [Indexed: 01/18/2023]
Abstract
Both extracellular RNAs and extracellular vesicles (EVs) have recently garnered attention as novel mediators of intercellular communication in eukaryotes and prokaryotes alike. EVs not only permit export of RNA, but also facilitate delivery and trans-kingdom exchange of these and other biomolecules, for instance between microbes and their hosts. In this Opinion article, we propose that EV-mediated export of RNA represents a universal mechanism for interkingdom and intrakingdom communication that is conserved among bacterial, archaeal, and eukaryotic microbes. We speculate how microbes might use EV RNA to influence target cell gene expression or manipulate host immune responses.
Collapse
Affiliation(s)
- James A Tsatsaronis
- Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany; Current address: School of Biological Sciences, University of Wollongong, 2522 Wollongong, Australia; Both authors contributed equally to this work
| | - Sandra Franch-Arroyo
- Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany; Both authors contributed equally to this work
| | - Ulrike Resch
- Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany; The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden; Institute for Biology, Humboldt University, 10115 Berlin, Germany.
| |
Collapse
|
26
|
|
27
|
Charpentier E. Spotlight on… Emmanuelle Charpentier. FEMS Microbiol Lett 2018; 365:4830095. [PMID: 29390135 DOI: 10.1093/femsle/fnx271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden.,Institute for Biology, Humboldt University, 10115 Berlin, Germany
| |
Collapse
|
28
|
Abstract
The RNA-programmable CRISPR-Cas9 technology allows precise and efficient engineering or correction of mutations, modulation of gene expression and marking of DNA in a wide variety of cell types and organisms in the three domains of life. Because of its versatility and ease of design, this powerful technology has been rapidly and universally adopted for genome editing applications in life science research. It is also recognized for its promising and potentially transformative applications in biotechnology, medicine and agriculture.
Collapse
|
29
|
Abstract
Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes—termed spacers—into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent. This article is part of the themed issue ‘The new bacteriology’.
Collapse
Affiliation(s)
- Frank Hille
- Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin 10117, Germany The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
| |
Collapse
|
30
|
Hurwitz JL, Jones BG, Charpentier E, Woodland DL. Hypothesis: RNA and DNA Viral Sequence Integration into the Mammalian Host Genome Supports Long-Term B Cell and T Cell Adaptive Immunity. Viral Immunol 2017; 30:628-632. [PMID: 29028182 DOI: 10.1089/vim.2017.0099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Viral sequence integration into the mammalian genome has long been perceived as a health risk. In some cases, integration translates to chronic viral infection, and in other instances, oncogenic gene mutations occur. However, research also shows that animal cells can benefit from integrated viral sequences (e.g., to support host cell development or to silence foreign invaders). Here we propose that, comparable with the clustered regularly interspaced short palindromic repeats that provide bacteria with adaptive immunity against invasive bacteriophages, animal cells may co-opt integrated viral sequences to support immune memory. We hypothesize that host cells express viral peptides from open reading frames in integrated sequences to boost adaptive B cell and T cell responses long after replicating viruses are cleared. In support of this hypothesis, we examine previous literature describing (1) viruses that infect acutely (e.g., vaccinia viruses and orthomyxoviruses) followed by unexplained, long-term persistence of viral nucleotide sequences, viral peptides, and virus-specific adaptive immunity, (2) the high frequency of endogenous viral genetic elements found in animal genomes, and (3) mechanisms with which animal host machinery supports foreign sequence integration.
Collapse
Affiliation(s)
- Julia L Hurwitz
- 1 Department of Infectious Diseases, St. Jude Children's Research Hospital , Memphis, Tennessee.,2 Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center , Memphis, Tennessee
| | - Bart G Jones
- 1 Department of Infectious Diseases, St. Jude Children's Research Hospital , Memphis, Tennessee
| | - Emmanuelle Charpentier
- 3 Max Planck Institute for Infection Biology , Berlin, Germany .,4 Humboldt University , Berlin, Germany .,5 The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University , Umeå, Sweden
| | | |
Collapse
|
31
|
Fabiani FD, Renault TT, Peters B, Dietsche T, Gálvez EJC, Guse A, Freier K, Charpentier E, Strowig T, Franz-Wachtel M, Macek B, Wagner S, Hensel M, Erhardt M. A flagellum-specific chaperone facilitates assembly of the core type III export apparatus of the bacterial flagellum. PLoS Biol 2017; 15:e2002267. [PMID: 28771474 PMCID: PMC5542435 DOI: 10.1371/journal.pbio.2002267] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [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: 02/22/2017] [Accepted: 06/30/2017] [Indexed: 11/21/2022] Open
Abstract
Many bacteria move using a complex, self-assembling nanomachine, the bacterial flagellum. Biosynthesis of the flagellum depends on a flagellar-specific type III secretion system (T3SS), a protein export machine homologous to the export machinery of the virulence-associated injectisome. Six cytoplasmic (FliH/I/J/G/M/N) and seven integral-membrane proteins (FlhA/B FliF/O/P/Q/R) form the flagellar basal body and are involved in the transport of flagellar building blocks across the inner membrane in a proton motive force-dependent manner. However, how the large, multi-component transmembrane export gate complex assembles in a coordinated manner remains enigmatic. Specific for most flagellar T3SSs is the presence of FliO, a small bitopic membrane protein with a large cytoplasmic domain. The function of FliO is unknown, but homologs of FliO are found in >80% of all flagellated bacteria. Here, we demonstrate that FliO protects FliP from proteolytic degradation and promotes the formation of a stable FliP–FliR complex required for the assembly of a functional core export apparatus. We further reveal the subcellular localization of FliO by super-resolution microscopy and show that FliO is not part of the assembled flagellar basal body. In summary, our results suggest that FliO functions as a novel, flagellar T3SS-specific chaperone, which facilitates quality control and productive assembly of the core T3SS export machinery. Many bacteria use the bacterial flagellum for directed movement in various environments. The assembly and function of the bacterial flagellum and the related virulence-associated injectisome relies on protein export via a conserved type III secretion system (T3SS). The multicomponent transmembrane core export apparatus of the flagellar T3SS consists of FlhA/B and FliP/Q/R and must assemble in a highly coordinated manner. In the present study, we determined the role of the transmembrane protein FliO in the maturation of the flagellar core protein export apparatus. We show that FliO functions as a flagellum-specific chaperone during the initial step of export apparatus assembly. FliO facilitates the efficient formation of a stable FliP–FliR core complex and is thus required for quality management and productive assembly of the flagellar export apparatus. Our results suggest a coordinated assembly process of the flagellar core export apparatus that nucleates with the FliO-dependent formation of a FliP–FliR complex. Subsequent incorporation of FliQ, FlhB, and FlhA leads to the assembly of a secretion-competent flagellar T3SS.
Collapse
Affiliation(s)
- Florian D. Fabiani
- Junior Research Group Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Thibaud T. Renault
- Junior Research Group Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Britta Peters
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, University of Osnabrück, Osnabrück, Germany
| | - Tobias Dietsche
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, University of Tübingen, Tübingen, Germany
| | - Eric J. C. Gálvez
- Junior Research Group Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Alina Guse
- Junior Research Group Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Karen Freier
- Junior Research Group Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Till Strowig
- Junior Research Group Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Samuel Wagner
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner-site Tübingen, Tübingen, Germany
| | - Michael Hensel
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, University of Osnabrück, Osnabrück, Germany
| | - Marc Erhardt
- Junior Research Group Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Braunschweig, Germany
- * E-mail:
| |
Collapse
|
32
|
Le Rhun A, Lécrivain AL, Reimegård J, Proux-Wéra E, Broglia L, Della Beffa C, Charpentier E. Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes. Nucleic Acids Res 2017; 45:2329-2340. [PMID: 28082390 PMCID: PMC5389636 DOI: 10.1093/nar/gkw1316] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/02/2017] [Indexed: 01/18/2023] Open
Abstract
A better understanding of transcriptional and post-transcriptional regulation of gene expression in bacteria relies on studying their transcriptome. RNA sequencing methods are used not only to assess RNA abundance but also the exact boundaries of primary and processed transcripts. Here, we developed a method, called identification of specific cleavage position (ISCP), which enables the identification of direct endoribonuclease targets in vivo by comparing the 5΄ and 3΄ ends of processed transcripts between wild type and RNase deficient strains. To demonstrate the ISCP method, we used as a model the double-stranded specific RNase III in the human pathogen Streptococcus pyogenes. We mapped 92 specific cleavage positions (SCPs) among which, 48 were previously described and 44 are new, with the characteristic 2 nucleotides 3΄ overhang of RNase III. Most SCPs were located in untranslated regions of RNAs. We screened for RNase III targets using transcriptomic differential expression analysis (DEA) and compared those with the RNase III targets identified using the ISCP method. Our study shows that in S. pyogenes, under standard growth conditions, RNase III has a limited impact both on antisense transcripts and on global gene expression with the expression of most of the affected genes being downregulated in an RNase III deletion mutant.
Collapse
Affiliation(s)
- Anaïs Le Rhun
- The Laboratory for Molecular Infection Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117 Berlin, Germany.,Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, D-38124 Braunschweig, Germany
| | - Anne-Laure Lécrivain
- The Laboratory for Molecular Infection Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117 Berlin, Germany
| | - Johan Reimegård
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, S-75123 Uppsala, Sweden
| | - Estelle Proux-Wéra
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Laura Broglia
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117 Berlin, Germany.,Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, D-38124 Braunschweig, Germany
| | - Cristina Della Beffa
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, D-38124 Braunschweig, Germany
| | - Emmanuelle Charpentier
- The Laboratory for Molecular Infection Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden.,Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, D-10117 Berlin, Germany.,Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, D-38124 Braunschweig, Germany.,Humboldt University, D-10115 Berlin, Germany
| |
Collapse
|
33
|
Elsholz AKW, Birk MS, Charpentier E, Turgay K. Functional Diversity of AAA+ Protease Complexes in Bacillus subtilis. Front Mol Biosci 2017; 4:44. [PMID: 28748186 PMCID: PMC5506225 DOI: 10.3389/fmolb.2017.00044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/15/2017] [Indexed: 12/20/2022] Open
Abstract
Here, we review the diverse roles and functions of AAA+ protease complexes in protein homeostasis, control of stress response and cellular development pathways by regulatory and general proteolysis in the Gram-positive model organism Bacillus subtilis. We discuss in detail the intricate involvement of AAA+ protein complexes in controlling sporulation, the heat shock response and the role of adaptor proteins in these processes. The investigation of these protein complexes and their adaptor proteins has revealed their relevance for Gram-positive pathogens and their potential as targets for new antibiotics.
Collapse
Affiliation(s)
- Alexander K W Elsholz
- Department of Regulation in Infection Biology, Max Planck Institute for Infection BiologyBerlin, Germany
| | - Marlene S Birk
- Department of Regulation in Infection Biology, Max Planck Institute for Infection BiologyBerlin, Germany
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Max Planck Institute for Infection BiologyBerlin, Germany.,The Laboratory for Molecular Infection Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden.,Humboldt UniversityBerlin, Germany
| | - Kürşad Turgay
- Faculty of Natural Sciences, Institute of Microbiology, Leibniz UniversitätHannover, Germany
| |
Collapse
|
34
|
Renault TT, Abraham AO, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, Tu Y, Namba K, Keener JP, Minamino T, Erhardt M. Bacterial flagella grow through an injection-diffusion mechanism. eLife 2017; 6. [PMID: 28262091 PMCID: PMC5386592 DOI: 10.7554/elife.23136] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/04/2017] [Indexed: 11/30/2022] Open
Abstract
The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ∼1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell. DOI:http://dx.doi.org/10.7554/eLife.23136.001 Most bacteria are able to move in a directed manner towards nutrients or other locations of interest. Many move by rotating long tail-like filaments called flagella that stick out from the cell. The flagellum is a remarkably complex nanomachine. It is several times longer than the main body of the bacterial cell body and its external filament is made of thousands of building blocks of a single protein called flagellin. This protein is made inside the cell and a structure at the base of the flagellum known as a type III secretion system uses chemical energy to pump it out of the cell so that it can be incorporated into the growing flagellum. The exported building blocks travel through a narrow channel within the flagellum and self-assemble at the tip. It has been a mystery for several decades how bacteria manage to assemble the building blocks of flagella outside of the cell, where no discernible energy source is available. Renault et al. used mathematical modeling, biochemical and microscopy techniques to observe how the flagella of a bacterium called Salmonella enterica assemble in real time. The experiments demonstrate that simple biophysical principles regulate the assembly of the flagellum. The building blocks are pumped into the channel of the flagellum by the type III secretion system and then diffuse to the tip of the filament. Accordingly, the longer the flagellum gets, the slower it grows. This molecular mechanism also explains why the growth of bacterial flagella will eventually stop even without any other control mechanisms in place. Further work will be needed to understand how the type III secretion system harnesses chemical energy to drive the movement of flagellin out of the cell into the growing flagellum. A molecular understanding of these processes will aid the design of new antibiotics targeted against type III secretion systems. DOI:http://dx.doi.org/10.7554/eLife.23136.002
Collapse
Affiliation(s)
- Thibaud T Renault
- Junior Research Group, Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - Anthony O Abraham
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Tobias Bergmiller
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Guillaume Paradis
- Department of Physics, Engineering Physics and Optics, Laval University, Quebec City, Quebec, Canada
| | - Simon Rainville
- Department of Physics, Engineering Physics and Optics, Laval University, Quebec City, Quebec, Canada
| | | | - Călin C Guet
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Yuhai Tu
- IBM Thomas J Watson Research Center, New York, United States
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,RIKEN Quantitative Biology Center, Suita, Japan
| | - James P Keener
- Department of Mathematics, University of Utah, Salt Lake City, United States
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Marc Erhardt
- Junior Research Group, Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Braunschweig, Germany
| |
Collapse
|
35
|
Abstract
Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation.
Collapse
Affiliation(s)
- Anaïs Le Rhun
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany
| | - Yan Yan Beer
- b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany
| | - Johan Reimegård
- c Science for Life Laboratory , Department of Cell and Molecular Biology, Uppsala University, S-75003 , Uppsala , Sweden
| | - Krzysztof Chylinski
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,d Max F. Perutz Laboratories (MFPL), University of Vienna, A-1030 , Vienna , Austria
| | - Emmanuelle Charpentier
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany.,e Hannover Medical School (MHH), D-30625 , Hannover , Germany.,f Max Planck Institute for Infection Biology , Department of Regulation in Infection Biology, D-10117 , Berlin , Germany
| |
Collapse
|
36
|
Richter F, Fonfara I, Bouazza B, Schumacher CH, Bratovič M, Charpentier E, Möglich A. Engineering of temperature- and light-switchable Cas9 variants. Nucleic Acids Res 2016; 44:10003-10014. [PMID: 27744350 PMCID: PMC5175372 DOI: 10.1093/nar/gkw930] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [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: 07/25/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 01/18/2023] Open
Abstract
Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function. We hence explored whether the homodimeric Rhodobacter sphaeroides light-oxygen-voltage (LOV) domain (RsLOV) that dissociates upon blue-light exposure can confer light sensitivity onto effector proteins, via a mechanism of light-induced functional site release. We chose the RNA-guided programmable DNA endonuclease Cas9 as proof-of-principle effector, and constructed a comprehensive library of RsLOV inserted throughout the Cas9 protein. Screening with a high-throughput assay based on transcriptional repression in Escherichia coli yielded paRC9, a moderately light-activatable variant. As domain insertion can lead to protein destabilization, we also screened the library for temperature-sensitive variants and isolated tsRC9, a variant with robust activity at 29°C but negligible activity at 37°C. Biochemical assays confirmed temperature-dependent DNA cleavage and binding for tsRC9, but indicated that the light sensitivity of paRC9 is specific to the cellular setting. Using tsRC9, the first temperature-sensitive Cas9 variant, we demonstrate temperature-dependent transcriptional control over ectopic and endogenous genetic loci. Taken together, RsLOV can confer light sensitivity onto an unrelated effector; unexpectedly, the same LOV domain can also impart strong temperature sensitivity.
Collapse
Affiliation(s)
- Florian Richter
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Ines Fonfara
- Max-Planck-Institute for Infection Biology, 10117 Berlin, Germany.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
| | - Boris Bouazza
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | | | - Majda Bratovič
- Max-Planck-Institute for Infection Biology, 10117 Berlin, Germany
| | - Emmanuelle Charpentier
- Max-Planck-Institute for Infection Biology, 10117 Berlin, Germany.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
| | - Andreas Möglich
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany .,Lehrstuhl für Biochemie, Universität Bayreuth, 95447 Bayreuth, Germany
| |
Collapse
|
37
|
Taron-Brocard C, Looten V, Fahlgren B, Charpentier E, Guillevin L, Barna A. [Congestive heart failure: Treatment with ultrafiltration]. Ann Cardiol Angeiol (Paris) 2016; 65:240-244. [PMID: 27344095 DOI: 10.1016/j.ancard.2016.04.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 07/21/2015] [Accepted: 04/29/2016] [Indexed: 06/06/2023]
Abstract
INTRODUCTION The prevalence rate of congestive heart failure is approximately 2% in high-income countries. The aim of this study was to assess the overall benefit of ultrafiltration therapy in patients with acute or persistent congestive heart failure. METHODS We conducted a health technology assessment following the EUnetHTA guidelines, with systematic literature review from bibliographic medical databases, independent experts and manufacturer interviews. RESULTS Thirteen clinical trials and five meta-analyses were examined. In the most recent one, 608 patients were included, of which 304 received ultrafiltration therapy and 304 received intravenous loop diuretics. Ultrafiltration therapy seems to be more beneficial regarding the fluid removal and the body weight reduction, (mean difference respectively 1.44kg, IC95% [0.29; 2.59], P-value=0.01 and 1.28L [0.43; 2.12], P-value=0.003). No difference has been showed in overall mortality, renal function, hospital readmission or safety. Medico-economic studies are incomplete and contradictory. CONCLUSION Ultrafiltration therapy seems to be effective, most likely for patients ineligible or resistant to intravenous diuretics. But most topics remain uncertain, mainly impact on overall mortality, safety and cost-effectiveness. Given these knowledge-gaps, the generalization of ultrafiltration therapy should be examined cautiously, and conditional upon a large-scale systematic evaluation.
Collapse
Affiliation(s)
- C Taron-Brocard
- Comité d'évaluation et de diffusion des innovations technologiques (CEDIT), AP-HP, 3, avenue Victoria, 75004 Paris, France.
| | - V Looten
- Comité d'évaluation et de diffusion des innovations technologiques (CEDIT), AP-HP, 3, avenue Victoria, 75004 Paris, France
| | - B Fahlgren
- Comité d'évaluation et de diffusion des innovations technologiques (CEDIT), AP-HP, 3, avenue Victoria, 75004 Paris, France
| | - E Charpentier
- Comité d'évaluation et de diffusion des innovations technologiques (CEDIT), AP-HP, 3, avenue Victoria, 75004 Paris, France
| | - L Guillevin
- Comité d'évaluation et de diffusion des innovations technologiques (CEDIT), AP-HP, 3, avenue Victoria, 75004 Paris, France
| | - A Barna
- Comité d'évaluation et de diffusion des innovations technologiques (CEDIT), AP-HP, 3, avenue Victoria, 75004 Paris, France
| |
Collapse
|
38
|
Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 2016; 532:517-21. [PMID: 27096362 DOI: 10.1038/nature17945] [Citation(s) in RCA: 564] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/30/2016] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas systems that provide defence against mobile genetic elements in bacteria and archaea have evolved a variety of mechanisms to target and cleave RNA or DNA. The well-studied types I, II and III utilize a set of distinct CRISPR-associated (Cas) proteins for production of mature CRISPR RNAs (crRNAs) and interference with invading nucleic acids. In types I and III, Cas6 or Cas5d cleaves precursor crRNA (pre-crRNA) and the mature crRNAs then guide a complex of Cas proteins (Cascade-Cas3, type I; Csm or Cmr, type III) to target and cleave invading DNA or RNA. In type II systems, RNase III cleaves pre-crRNA base-paired with trans-activating crRNA (tracrRNA) in the presence of Cas9 (refs 13, 14). The mature tracrRNA-crRNA duplex then guides Cas9 to cleave target DNA. Here, we demonstrate a novel mechanism in CRISPR-Cas immunity. We show that type V-A Cpf1 from Francisella novicida is a dual-nuclease that is specific to crRNA biogenesis and target DNA interference. Cpf1 cleaves pre-crRNA upstream of a hairpin structure formed within the CRISPR repeats and thereby generates intermediate crRNAs that are processed further, leading to mature crRNAs. After recognition of a 5'-YTN-3' protospacer adjacent motif on the non-target DNA strand and subsequent probing for an eight-nucleotide seed sequence, Cpf1, guided by the single mature repeat-spacer crRNA, introduces double-stranded breaks in the target DNA to generate a 5' overhang. The RNase and DNase activities of Cpf1 require sequence- and structure-specific binding to the hairpin of crRNA repeats. Cpf1 uses distinct active domains for both nuclease reactions and cleaves nucleic acids in the presence of magnesium or calcium. This study uncovers a new family of enzymes with specific dual endoribonuclease and endonuclease activities, and demonstrates that type V-A constitutes the most minimalistic of the CRISPR-Cas systems so far described.
Collapse
MESH Headings
- Bacterial Proteins/metabolism
- Base Sequence
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Calcium/metabolism
- Calcium/pharmacology
- Catalytic Domain
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- DNA Cleavage/drug effects
- Francisella/enzymology
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/biosynthesis
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Substrate Specificity
Collapse
Affiliation(s)
- Ines Fonfara
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
| | - Hagen Richter
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
| | - Majda Bratovič
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
- Hannover Medical School, Hannover 30625, Germany
| | - Anaïs Le Rhun
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
| | - Emmanuelle Charpentier
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
- Hannover Medical School, Hannover 30625, Germany
| |
Collapse
|
39
|
Labenski V, Suerth JD, Barczak E, Heckl D, Levy C, Bernadin O, Charpentier E, Williams DA, Fehse B, Verhoeyen E, Schambach A. Alpharetroviral self-inactivating vectors produced by a superinfection-resistant stable packaging cell line allow genetic modification of primary human T lymphocytes. Biomaterials 2016; 97:97-109. [PMID: 27162078 DOI: 10.1016/j.biomaterials.2016.04.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 10/09/2015] [Revised: 04/09/2016] [Accepted: 04/20/2016] [Indexed: 01/06/2023]
Abstract
Primary human T lymphocytes represent an important cell population for adoptive immunotherapies, including chimeric-antigen and T-cell receptor applications, as they have the capability to eliminate non-self, virus-infected and tumor cells. Given the increasing numbers of clinical immunotherapy applications, the development of an optimal vector platform for genetic T lymphocyte engineering, which allows cost-effective high-quality vector productions, remains a critical goal. Alpharetroviral self-inactivating vectors (ARV) have several advantages compared to other vector platforms, including a more random genomic integration pattern and reduced likelihood for inducing aberrant splicing of integrated proviruses. We developed an ARV platform for the transduction of primary human T lymphocytes. We demonstrated functional transgene transfer using the clinically relevant herpes-simplex-virus thymidine kinase variant TK.007. Proof-of-concept of alpharetroviral-mediated T-lymphocyte engineering was shown in vitro and in a humanized transplantation model in vivo. Furthermore, we established a stable, human alpharetroviral packaging cell line in which we deleted the entry receptor (SLC1A5) for RD114/TR-pseudotyped ARVs to prevent superinfection and enhance genomic integrity of the packaging cell line and viral particles. We showed that superinfection can be entirely prevented, while maintaining high recombinant virus titers. Taken together, this resulted in an improved production platform representing an economic strategy for translating the promising features of ARVs for therapeutic T-lymphocyte engineering.
Collapse
Affiliation(s)
- Verena Labenski
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Julia D Suerth
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Elke Barczak
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Dirk Heckl
- Department of Pediatric Hematology & Oncology, Hannover Medical School, Hannover, Germany; Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Camille Levy
- CIRI, EVIR Team, Inserm, U1111, CNRS, UMR5308, Université de Lyon-1, ENS de Lyon, Lyon, France
| | - Ornellie Bernadin
- CIRI, EVIR Team, Inserm, U1111, CNRS, UMR5308, Université de Lyon-1, ENS de Lyon, Lyon, France
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - David A Williams
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Dept. of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Els Verhoeyen
- CIRI, EVIR Team, Inserm, U1111, CNRS, UMR5308, Université de Lyon-1, ENS de Lyon, Lyon, France; Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), équipe "contrôle métabolique des morts cellulaires", Nice, France
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
40
|
|
41
|
Bosley KS, Botchan M, Bredenoord AL, Carroll D, Charo RA, Charpentier E, Cohen R, Corn J, Doudna J, Feng G, Greely HT, Isasi R, Ji W, Kim JS, Knoppers B, Lanphier E, Li J, Lovell-Badge R, Martin GS, Moreno J, Naldini L, Pera M, Perry ACF, Venter JC, Zhang F, Zhou Q. CRISPR germline engineering--the community speaks. Nat Biotechnol 2016; 33:478-86. [PMID: 25965754 DOI: 10.1038/nbt.3227] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Michael Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Annelien L Bredenoord
- Department of Medical Humanities, University Medical Center, Utrecht, the Netherlands
| | - Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - R Alta Charo
- School of Law, and Department of Medical History and Bioethics, University of Wisconsin School of Medicine &Public Health, Madison, Wisconsin, USA
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ron Cohen
- Acorda Therapeutics, Ardsley, New York, USA
| | - Jacob Corn
- Innovative Genomics Initiative, Berkeley, California, USA
| | - Jennifer Doudna
- Department of Molecular &Cell Biology and Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Guoping Feng
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
| | | | - Rosario Isasi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Weihzi Ji
- Kunming Biomed International and National Engineering Research Center of Biomedicine and Animal Science, Kunming, China
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science and Department of Chemistry, Seoul National University, Seoul, Korea
| | - Bartha Knoppers
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Jinsong Li
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - G Steven Martin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | | | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, Milan, Italy
| | - Martin Pera
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia
| | - Anthony C F Perry
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | | | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
42
|
Affiliation(s)
- Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden Hannover Medical School, Hannover, Germany
| |
Collapse
|
43
|
|
44
|
Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJM, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 2015; 13:722-36. [PMID: 26411297 DOI: 10.1038/nrmicro3569] [Citation(s) in RCA: 1530] [Impact Index Per Article: 170.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
Collapse
Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Omer S Alkhnbashi
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany
| | - Fabrizio Costa
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany
| | - Shiraz A Shah
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Sita J Saunders
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27606, USA
| | - Stan J J Brouns
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703HB Wageningen, Netherlands
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
| | - Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Philippe Horvath
- DuPont Nutrition and Health, BP10, Dangé-Saint-Romain 86220, France
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Francisco J M Mojica
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante. 03080-Alicante, Spain
| | - Rebecca M Terns
- Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia, Davison Life Sciences Complex, Green Street, Athens, Georgia 30602, USA
| | - Michael P Terns
- Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia, Davison Life Sciences Complex, Green Street, Athens, Georgia 30602, USA
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, M5S 3E5, Canada
| | - Roger A Garrett
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703HB Wageningen, Netherlands
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany.,BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, University of Freiburg, Germany
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| |
Collapse
|
45
|
Hübschen J, Charpentier E, Weicherding P, Muller C. Seroprevalence of IgG antibodies against vaccine-preventable diseases in newcomers to Luxembourg. J Clin Virol 2015. [DOI: 10.1016/j.jcv.2015.07.080] [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: 10/23/2022]
|
46
|
Abstract
Targeted regulation of gene expression holds huge promise for biomedical research. In a series of recent publications (Gilbert et al., 2014; Konermann et al., 2015; Zalatan et al., 2015), sophisticated, multiplex-compatible transcriptional activator systems based on the CRISPR-Cas9 technology and genome-scale libraries advance the field toward whole-transcriptome control.
Collapse
Affiliation(s)
- Dirk Heckl
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover 30625, Germany.
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany; The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå 90187, Sweden; Department of Regulation in Infection Biology, Hannover Medical School, Hannover 30625, Germany.
| |
Collapse
|
47
|
Charpentier E, Richter H, van der Oost J, White MF. Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiol Rev 2015; 39:428-41. [PMID: 25994611 PMCID: PMC5965381 DOI: 10.1093/femsre/fuv023] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2015] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas is an RNA-mediated adaptive immune system that defends bacteria and archaea against mobile genetic elements. Short mature CRISPR RNAs (crRNAs) are key elements in the interference step of the immune pathway. A CRISPR array composed of a series of repeats interspaced by spacer sequences acquired from invading mobile genomes is transcribed as a precursor crRNA (pre-crRNA) molecule. This pre-crRNA undergoes one or two maturation steps to generate the mature crRNAs that guide CRISPR-associated (Cas) protein(s) to cognate invading genomes for their destruction. Different types of CRISPR-Cas systems have evolved distinct crRNA biogenesis pathways that implicate highly sophisticated processing mechanisms. In Types I and III CRISPR-Cas systems, a specific endoribonuclease of the Cas6 family, either standalone or in a complex with other Cas proteins, cleaves the pre-crRNA within the repeat regions. In Type II systems, the trans-acting small RNA (tracrRNA) base pairs with each repeat of the pre-crRNA to form a dual-RNA that is cleaved by the housekeeping RNase III in the presence of the protein Cas9. In this review, we present a detailed comparative analysis of pre-crRNA recognition and cleavage mechanisms involved in the biogenesis of guide crRNAs in the three CRISPR-Cas types. This review presents a detailed comparative analysis of pre-crRNA recognition and cleavage mechanisms involved in the biogenesis of guide crRNAs in the different bacterial and archaeal CRISPR-Cas immune systems.
Collapse
Affiliation(s)
- Emmanuelle Charpentier
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden Hannover Medical School, Hannover 30625, Germany
| | - Hagen Richter
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen 6703 HB, the Netherlands
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| |
Collapse
|
48
|
Bosley KS, Botchan M, Bredenoord AL, Carroll D, Charo RA, Charpentier E, Cohen R, Corn J, Doudna J, Feng G, Greely HT, Isasi R, Ji W, Kim JS, Knoppers B, Lanphier E, Li J, Lovell-Badge R, Martin GS, Moreno J, Naldini L, Pera M, Perry ACF, Venter JC, Zhang F, Zhou Q. CRISPR germline engineering--the community speaks. Nat Biotechnol 2015. [PMID: 25965754 DOI: 10.1038/nbt.3227.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Michael Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Annelien L Bredenoord
- Department of Medical Humanities, University Medical Center, Utrecht, the Netherlands
| | - Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - R Alta Charo
- School of Law, and Department of Medical History and Bioethics, University of Wisconsin School of Medicine &Public Health, Madison, Wisconsin, USA
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ron Cohen
- Acorda Therapeutics, Ardsley, New York, USA
| | - Jacob Corn
- Innovative Genomics Initiative, Berkeley, California, USA
| | - Jennifer Doudna
- Department of Molecular &Cell Biology and Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Guoping Feng
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
| | | | - Rosario Isasi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Weihzi Ji
- Kunming Biomed International and National Engineering Research Center of Biomedicine and Animal Science, Kunming, China
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science and Department of Chemistry, Seoul National University, Seoul, Korea
| | - Bartha Knoppers
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Jinsong Li
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - G Steven Martin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | | | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, Milan, Italy
| | - Martin Pera
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia
| | - Anthony C F Perry
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | | | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
49
|
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) adaptive immune systems use small guide RNAs, the CRISPR RNAs (crRNAs), to mark foreign genetic material, e.g. viral nucleic acids, for degradation. Archaea and bacteria encode a large variety of Cas proteins that bind crRNA molecules and build active ribonucleoprotein surveillance complexes. The evolution of CRISPR-Cas systems has resulted in a diversification of cas genes and a classification of the systems into three types and additional subtypes characterized by distinct surveillance and interfering complexes. Recent crystallographic and biochemical advances have revealed detailed insights into the assembly and DNA/RNA targeting mechanisms of the various complexes. Here, we review our knowledge on the molecular mechanism involved in the DNA and RNA interference stages of type I (Cascade: CRISPR-associated complex for antiviral defense), type II (Cas9) and type III (Csm, Cmr) CRISPR-Cas systems. We further highlight recently reported structural and mechanistic themes shared among these systems. This review details and compares the assembly and the DNA/RNA targeting mechanisms of the various surveillance complexes of prokaryotic CRISPR-Cas immune systems.
Collapse
Affiliation(s)
- André Plagens
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
| | - Hagen Richter
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
| | - Emmanuelle Charpentier
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden Hannover Medical School, Hannover 30625, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
| |
Collapse
|
50
|
Abstract
The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics.
Collapse
Affiliation(s)
- Jennifer A Doudna
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. Department of Chemistry, University of California, Berkeley, CA 94720, USA. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany. Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden. Hannover Medical School, D-30625 Hannover, Germany.
| |
Collapse
|