1
|
Eilers K, Hoong Yam JK, Liu X, Goh YF, To KN, Paracuellos P, Morton R, Brizuela J, Hui Yong AM, Givskov M, Freibert SA, Bange G, Rice SA, Steinchen W, Filloux A. The dual GGDEF/EAL domain enzyme PA0285 is a Pseudomonas species housekeeping phosphodiesterase regulating early attachment and biofilm architecture. J Biol Chem 2024; 300:105659. [PMID: 38237678 PMCID: PMC10874727 DOI: 10.1016/j.jbc.2024.105659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/23/2023] [Accepted: 01/04/2024] [Indexed: 02/15/2024] Open
Abstract
Bacterial lifestyles depend on conditions encountered during colonization. The transition between planktonic and biofilm growth is dependent on the intracellular second messenger c-di-GMP. High c-di-GMP levels driven by diguanylate cyclases (DGCs) activity favor biofilm formation, while low levels were maintained by phosphodiesterases (PDE) encourage planktonic lifestyle. The activity of these enzymes can be modulated by stimuli-sensing domains such as Per-ARNT-Sim (PAS). In Pseudomonas aeruginosa, more than 40 PDE/DGC are involved in c-di-GMP homeostasis, including 16 dual proteins possessing both canonical DGC and PDE motifs, that is, GGDEF and EAL, respectively. It was reported that deletion of the EAL/GGDEF dual enzyme PA0285, one of five c-di-GMP-related enzymes conserved across all Pseudomonas species, impacts biofilms. PA0285 is anchored in the membrane and carries two PAS domains. Here, we confirm that its role is conserved in various P. aeruginosa strains and in Pseudomonas putida. Deletion of PA0285 impacts the early stage of colonization, and RNA-seq analysis suggests that expression of cupA fimbrial genes is involved. We demonstrate that the C-terminal portion of PA0285 encompassing the GGDEF and EAL domains binds GTP and c-di-GMP, respectively, but only exhibits PDE activity in vitro. However, both GGDEF and EAL domains are important for PA0285 PDE activity in vivo. Complementation of the PA0285 mutant strain with a copy of the gene encoding the C-terminal GGDEF/EAL portion in trans was not as effective as complementation with the full-length gene. This suggests the N-terminal transmembrane and PAS domains influence the PDE activity in vivo, through modulating the protein conformation.
Collapse
Affiliation(s)
- Kira Eilers
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Yu Fen Goh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Ka-Ning To
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Patricia Paracuellos
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Richard Morton
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Jaime Brizuela
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Adeline Mei Hui Yong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Sven-Andreas Freibert
- Philipps University Marburg, Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Gert Bange
- Philipps University Marburg, Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Microbiomes for One Systems Health and Agriculture and Food, CSIRO, Westmead, New South Wales, Australia
| | - Wieland Steinchen
- Philipps University Marburg, Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
| | - Alain Filloux
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.
| |
Collapse
|
2
|
Filloux A. Bacterial type VI secretion system helps prevent cheating in microbial communities. ISME J 2024; 18:wrae003. [PMID: 38365258 PMCID: PMC10839747 DOI: 10.1093/ismejo/wrae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/26/2023] [Accepted: 01/04/2024] [Indexed: 02/18/2024]
Affiliation(s)
- Alain Filloux
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| |
Collapse
|
3
|
Abstract
The bacterial Tight adherence Secretion System (TadSS) assembles surface pili that drive cell adherence, biofilm formation and bacterial predation. The structure and mechanism of the TadSS is mostly unknown. This includes characterisation of the outer membrane secretin through which the pilus is channelled and recruitment of its pilotin. Here we investigate RcpA and TadD lipoprotein from Pseudomonas aeruginosa. Light microscopy reveals RcpA colocalising with TadD in P. aeruginosa and when heterologously expressed in Escherichia coli. We use cryogenic electron microscopy to determine how RcpA and TadD assemble a secretin channel with C13 and C14 symmetries. Despite low sequence homology, we show that TadD shares a similar fold to the type 4 pilus system pilotin PilF. We establish that the C-terminal four residues of RcpA bind TadD - an interaction essential for secretin formation. The binding mechanism between RcpA and TadD appears distinct from known secretin-pilotin pairings in other secretion systems.
Collapse
Affiliation(s)
- Matteo Tassinari
- Department of Infectious Disease, Imperial College, London, SW7 2AZ, UK
- Human Technopole, Milan, Italy
| | - Marta Rudzite
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Alain Filloux
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Harry H Low
- Department of Infectious Disease, Imperial College, London, SW7 2AZ, UK.
| |
Collapse
|
4
|
Teh WK, Ding Y, Gubellini F, Filloux A, Poyart C, Givskov M, Dramsi S. Characterization of TelE, a T7SS LXG Effector Exhibiting a Conserved C-Terminal Glycine Zipper Motif Required for Toxicity. Microbiol Spectr 2023; 11:e0148123. [PMID: 37432124 PMCID: PMC10434224 DOI: 10.1128/spectrum.01481-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 04/07/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023] Open
Abstract
Streptococcus gallolyticus subsp. gallolyticus (SGG) is an opportunistic bacterial pathogen strongly associated with colorectal cancer. Here, through comparative genomics analysis, we demonstrated that the genetic locus encoding the type VIIb secretion system (T7SSb) machinery is uniquely present in SGG in two different arrangements. SGG UCN34 carrying the most prevalent T7SSb genetic arrangement was chosen as the reference strain. To identify the effectors secreted by this secretion system, we inactivated the essC gene encoding the motor of this machinery. A comparison of the proteins secreted by UCN34 wild type and its isogenic ΔessC mutant revealed six T7SSb effector proteins, including the expected WXG effector EsxA and three LXG-containing proteins. In this work, we characterized an LXG-family toxin named herein TelE promoting the loss of membrane integrity. Seven homologs of TelE harboring a conserved glycine zipper motif at the C terminus were identified in different SGG isolates. Scanning mutagenesis of this motif showed that the glycine residue at position 470 was crucial for TelE membrane destabilization activity. TelE activity was antagonized by a small protein TipE belonging to the DUF5085 family. Overall, we report herein a unique SGG T7SSb effector exhibiting a toxic activity against nonimmune bacteria. IMPORTANCE In this study, 38 clinical isolates of Streptococcus gallolyticus subsp. gallolyticus (SGG) were sequenced and a genetic locus encoding the type VIIb secretion system (T7SSb) was found conserved and absent from 16 genomes of the closely related S. gallolyticus subsp. pasteurianus (SGP). The T7SSb is a bona fide pathogenicity island. Here, we report that the model organism SGG strain UCN34 secretes six T7SSb effectors. One of the six effectors named TelE displayed a strong toxicity when overexpressed in Escherichia coli. Our results indicate that TelE is probably a pore-forming toxin whose activity can be antagonized by a specific immunity protein named TipE. Overall, we report a unique toxin-immunity protein pair and our data expand the range of effectors secreted through T7SSb.
Collapse
Affiliation(s)
- Wooi Keong Teh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | | | - Alain Filloux
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Claire Poyart
- Université de Paris, Assistance Publique Hôpitaux de Paris, Service de Bactériologie, Centre National de Référence des Streptocoques, Groupe Hospitalier Paris Centre site Cochin, Paris, France
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Shaynoor Dramsi
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Biology of Gram-positive Pathogens Unit, Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2001, Paris, France
| |
Collapse
|
5
|
Kadeřábková N, Furniss RCD, Maslova E, Eisaiankhongi L, Bernal P, Filloux A, Landeta C, Gonzalez D, McCarthy RR, Mavridou DA. Antibiotic potentiation and inhibition of cross-resistance in pathogens associated with cystic fibrosis. bioRxiv 2023:2023.08.02.551661. [PMID: 37577508 PMCID: PMC10418187 DOI: 10.1101/2023.08.02.551661] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Critical Gram-negative pathogens, like Pseudomonas, Stenotrophomonas and Burkholderia, have become resistant to most antibiotics. Complex resistance profiles together with synergistic interactions between these organisms increase the likelihood of treatment failure in distinct infection settings, for example in the lungs of cystic fibrosis patients. Here, we discover that cell envelope protein homeostasis pathways underpin both antibiotic resistance and cross-protection in CF-associated bacteria. We find that inhibition of oxidative protein folding inactivates multiple species-specific resistance proteins. Using this strategy, we sensitize multi-drug resistant Pseudomonas aeruginosa to β-lactam antibiotics and demonstrate promise of new treatment avenues for the recalcitrant pathogen Stenotrophomonas maltophilia. The same approach also inhibits cross-protection between resistant S. maltophilia and susceptible P. aeruginosa, allowing eradication of both commonly co-occurring CF-associated organisms. Our results provide the basis for the development of next-generation strategies that target antibiotic resistance, while also impairing specific interbacterial interactions that enhance the severity of polymicrobial infections.
Collapse
Affiliation(s)
- Nikol Kadeřábková
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, Texas, USA
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - R. Christopher D. Furniss
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Evgenia Maslova
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Lara Eisaiankhongi
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Patricia Bernal
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Seville, 41012, Spain
| | - Alain Filloux
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Cristina Landeta
- Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA
| | - Diego Gonzalez
- Laboratoire de Microbiologie, Institut de Biologie, Université de Neuchâtel, Neuchâtel, 2000, Switzerland
| | - Ronan R. McCarthy
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Despoina A.I. Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, 78712, Texas, USA
- John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, 78712, Texas, USA
| |
Collapse
|
6
|
Rudzite M, Subramoni S, Endres RG, Filloux A. Effectiveness of Pseudomonas aeruginosa type VI secretion system relies on toxin potency and type IV pili-dependent interaction. PLoS Pathog 2023; 19:e1011428. [PMID: 37253075 DOI: 10.1371/journal.ppat.1011428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/17/2023] [Indexed: 06/01/2023] Open
Abstract
The type VI secretion system (T6SS) is an antibacterial weapon that is used by numerous Gram-negative bacteria to gain competitive advantage by injecting toxins into adjacent prey cells. Predicting the outcome of a T6SS-dependent competition is not only reliant on presence-absence of the system but instead involves a multiplicity of factors. Pseudomonas aeruginosa possesses 3 distinct T6SSs and a set of more than 20 toxic effectors with diverse functions including disruption of cell wall integrity, degradation of nucleic acids or metabolic impairment. We generated a comprehensive collection of mutants with various degrees of T6SS activity and/or sensitivity to each individual T6SS toxin. By imaging whole mixed bacterial macrocolonies, we then investigated how these P. aeruginosa strains gain a competitive edge in multiple attacker/prey combinations. We observed that the potency of single T6SS toxin varies significantly from one another as measured by monitoring the community structure, with some toxins acting better in synergy or requiring a higher payload. Remarkably the degree of intermixing between preys and attackers is also key to the competition outcome and is driven by the frequency of contact as well as the ability of the prey to move away from the attacker using type IV pili-dependent twitching motility. Finally, we implemented a computational model to better understand how changes in T6SS firing behaviours or cell-cell contacts lead to population level competitive advantages, thus providing conceptual insight applicable to all types of contact-based competition.
Collapse
Affiliation(s)
- Marta Rudzite
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Sujatha Subramoni
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Robert G Endres
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| |
Collapse
|
7
|
Böhning J, Dobbelstein AW, Sulkowski N, Eilers K, von Kügelgen A, Tarafder AK, Peak-Chew SY, Skehel M, Alva V, Filloux A, Bharat TAM. Architecture of the biofilm-associated archaic Chaperone-Usher pilus CupE from Pseudomonas aeruginosa. PLoS Pathog 2023; 19:e1011177. [PMID: 37058467 PMCID: PMC10104325 DOI: 10.1371/journal.ppat.1011177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/03/2023] [Indexed: 04/15/2023] Open
Abstract
Chaperone-Usher Pathway (CUP) pili are major adhesins in Gram-negative bacteria, mediating bacterial adherence to biotic and abiotic surfaces. While classical CUP pili have been extensively characterized, little is known about so-called archaic CUP pili, which are phylogenetically widespread and promote biofilm formation by several human pathogens. In this study, we present the electron cryomicroscopy structure of the archaic CupE pilus from the opportunistic human pathogen Pseudomonas aeruginosa. We show that CupE1 subunits within the pilus are arranged in a zigzag architecture, containing an N-terminal donor β-strand extending from each subunit into the next, where it is anchored by hydrophobic interactions, with comparatively weaker interactions at the rest of the inter-subunit interface. Imaging CupE pili on the surface of P. aeruginosa cells using electron cryotomography shows that CupE pili adopt variable curvatures in response to their environment, which might facilitate their role in promoting cellular attachment. Finally, bioinformatic analysis shows the widespread abundance of cupE genes in isolates of P. aeruginosa and the co-occurrence of cupE with other cup clusters, suggesting interdependence of cup pili in regulating bacterial adherence within biofilms. Taken together, our study provides insights into the architecture of archaic CUP pili, providing a structural basis for understanding their role in promoting cellular adhesion and biofilm formation in P. aeruginosa.
Collapse
Affiliation(s)
- Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Adrian W. Dobbelstein
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Nina Sulkowski
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Kira Eilers
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Abul K. Tarafder
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Sew-Yeu Peak-Chew
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Tanmay A. M. Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| |
Collapse
|
8
|
Evans L, Kotar A, Valentini M, Filloux A, Jamshidi S, Plavec J, Rahman KM, Vilar R. Identification and characterisation of G-quadruplex DNA-forming sequences in the Pseudomonas aeruginosa genome. RSC Chem Biol 2023; 4:94-100. [PMID: 36685252 PMCID: PMC9811510 DOI: 10.1039/d2cb00205a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/13/2022] [Indexed: 11/16/2022] Open
Abstract
A number of Gram-negative bacteria such as Pseudomonas aeruginosa are becoming resistant to front-line antibiotics. Consequently, there is a pressing need to find alternative bio-molecular targets for the development of new drugs. Since non-canonical DNA structures such as guanine-quadruplexes (G4s) have been implicated in regulating transcription, we were interested in determining whether there are putative quadruplex-forming sequences (PQS) in the genome of Pseudomonas aeruginosa. Using bioinformatic tools, we screened 36 genes potentially relevant to drug resistance for the presence of PQS and 10 of these were selected for biophysical characterisation (i.e. circular dichroism and thermal difference UV/Vis spectroscopy). These studies showed that three of these G-rich sequences (linked to murE, ftsB and mexC genes) form stable guanine-quadruplexes which were studied by NMR spectroscopy; detailed analysis of one of the sequences (mexC) confirmed that it adopts a two-quartet antiparallel quadruplex structure in the presence of K+ ions. We also show by FRET melting assays that small molecules can stabilise these three new G4 DNA structures under physiological conditions. These initial results could be of future interest in the development of new antibiotics with alternative bio-molecular targets which in turn would help tackle antimicrobial resistance.
Collapse
Affiliation(s)
- Lindsay Evans
- Department of Chemistry, Imperial College London, White City CampusLondon W12 OBZUK
| | - Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 191000 LjubljanaSlovenia
| | - Martina Valentini
- Department of Life Sciences, MRC Centre for Molecular Microbiology and Infection, Imperial College London, South Kensington CampusLondon SW7 2AZUK
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Microbiology and Infection, Imperial College London, South Kensington CampusLondon SW7 2AZUK
| | - Shirin Jamshidi
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building150 Stamford StreetLondon SE1 9NHUK
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 191000 LjubljanaSlovenia
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building150 Stamford StreetLondon SE1 9NHUK
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, White City CampusLondon W12 OBZUK
| |
Collapse
|
9
|
Bernal P, Civantos C, Pacheco-Sánchez D, Quesada JM, Filloux A, Llamas MA. Transcriptional organization and regulation of the Pseudomonas putida K1 type VI secretion system gene cluster. Microbiology (Reading) 2023; 169:001295. [PMID: 36748579 PMCID: PMC9993120 DOI: 10.1099/mic.0.001295] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The type VI secretion system (T6SS) is an antimicrobial molecular weapon that is widespread in Proteobacteria and offers competitive advantages to T6SS-positive micro-organisms. Three T6SSs have recently been described in Pseudomonas putida KT2440 and it has been shown that one, K1-T6SS, is used to outcompete a wide range of phytopathogens, protecting plants from pathogen infections. Given the relevance of this system as a powerful and innovative mechanism of biological control, it is critical to understand the processes that govern its expression. Here, we experimentally defined two transcriptional units in the K1-T6SS cluster. One encodes the structural components of the system and is transcribed from two adjacent promoters. The other encodes two hypothetical proteins, the tip of the system and the associated adapters, and effectors and cognate immunity proteins, and it is also transcribed from two adjacent promoters. The four identified promoters contain the typical features of σ70-dependent promoters. We have studied the expression of the system under different conditions and in a number of mutants lacking global regulators. P. putida K1-T6SS expression is induced in the stationary phase, but its transcription does not depend on the stationary σ factor RpoS. In fact, the expression of the system is indirectly repressed by RpoS. Furthermore, it is also repressed by RpoN and the transcriptional regulator FleQ, an enhancer-binding protein typically acting in conjunction with RpoN. Importantly, expression of the K1-T6SS gene cluster is positively regulated by the GacS-GacA two-component regulatory system (TCS) and repressed by the RetS sensor kinase, which inhibits this TCS. Our findings identified a complex regulatory network that governs T6SS expression in general and P. putida K1-T6SS in particular, with implications for controlling and manipulating a bacterial agent that is highly relevant in biological control.
Collapse
Affiliation(s)
- Patricia Bernal
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK.,Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Cristina Civantos
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Daniel Pacheco-Sánchez
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - José M Quesada
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK.,Singapore Centre for Environmental Life Sciences Engineering. Nanyang Technological University, Singapore
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| |
Collapse
|
10
|
Falà AK, Álvarez-Ordóñez A, Filloux A, Gahan CGM, Cotter PD. Quorum sensing in human gut and food microbiomes: Significance and potential for therapeutic targeting. Front Microbiol 2022; 13:1002185. [PMID: 36504831 PMCID: PMC9733432 DOI: 10.3389/fmicb.2022.1002185] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/17/2022] [Indexed: 11/27/2022] Open
Abstract
Human gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.
Collapse
Affiliation(s)
- A. Kate Falà
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Cormac G. M. Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,School of Pharmacy, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland,*Correspondence: Paul D. Cotter,
| |
Collapse
|
11
|
Camara M, Filloux A. Supporting the strategic pillars of translational research in biofilms. NPJ Biofilms Microbiomes 2022; 8:90. [PMID: 36372799 PMCID: PMC9659558 DOI: 10.1038/s41522-022-00354-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/14/2022] Open
|
12
|
Eilers K, Kuok Hoong Yam J, Morton R, Mei Hui Yong A, Brizuela J, Hadjicharalambous C, Liu X, Givskov M, Rice SA, Filloux A. Phenotypic and integrated analysis of a comprehensive Pseudomonas aeruginosa PAO1 library of mutants lacking cyclic-di-GMP-related genes. Front Microbiol 2022; 13:949597. [PMID: 35935233 PMCID: PMC9355167 DOI: 10.3389/fmicb.2022.949597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that is able to survive and adapt in a multitude of niches as well as thrive within many different hosts. This versatility lies within its large genome of ca. 6 Mbp and a tight control in the expression of thousands of genes. Among the regulatory mechanisms widespread in bacteria, cyclic-di-GMP signaling is one which influences all levels of control. c-di-GMP is made by diguanylate cyclases and degraded by phosphodiesterases, while the intracellular level of this molecule drives phenotypic responses. Signaling involves the modification of enzymes’ or proteins’ function upon c-di-GMP binding, including modifying the activity of regulators which in turn will impact the transcriptome. In P. aeruginosa, there are ca. 40 genes encoding putative DGCs or PDEs. The combined activity of those enzymes should reflect the overall c-di-GMP concentration, while specific phenotypic outputs could be correlated to a given set of dgc/pde. This notion of specificity has been addressed in several studies and different strains of P. aeruginosa. Here, we engineered a mutant library for the 41 individual dgc/pde genes in P. aeruginosa PAO1. In most cases, we observed a significant to slight variation in the global c-di-GMP pool of cells grown planktonically, while several mutants display a phenotypic impact on biofilm including initial attachment and maturation. If this observation of minor changes in c-di-GMP level correlating with significant phenotypic impact appears to be true, it further supports the idea of a local vs global c-di-GMP pool. In contrast, there was little to no effect on motility, which differs from previous studies. Our RNA-seq analysis indicated that all PAO1 dgc/pde genes were expressed in both planktonic and biofilm growth conditions and our work suggests that c-di-GMP networks need to be reconstructed for each strain separately and cannot be extrapolated from one to another.
Collapse
Affiliation(s)
- Kira Eilers
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Richard Morton
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Adeline Mei Hui Yong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jaime Brizuela
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Medical Microbiology, Amsterdam UMC, Universitair Medische Centra, University of Amsterdam, Amsterdam, Netherlands
| | - Corina Hadjicharalambous
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Melbourne, VIC, Australia
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- *Correspondence: Alain Filloux,
| |
Collapse
|
13
|
Abstract
Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.
Collapse
Affiliation(s)
- Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| |
Collapse
|
14
|
Demmer JK, Phillips BP, Uhrig OL, Filloux A, Allsopp LP, Bublitz M, Meier T. Structure of ATP synthase from ESKAPE pathogen Acinetobacter baumannii. Sci Adv 2022; 8:eabl5966. [PMID: 35171679 PMCID: PMC8849298 DOI: 10.1126/sciadv.abl5966] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
The global spread of multidrug-resistant Acinetobacter baumannii infections urgently calls for the identification of novel drug targets. We solved the electron cryo-microscopy structure of the F1Fo-adenosine 5'-triphosphate (ATP) synthase from A. baumannii in three distinct conformational states. The nucleotide-converting F1 subcomplex reveals a specific self-inhibition mechanism, which supports a unidirectional ratchet mechanism to avoid wasteful ATP consumption. In the membrane-embedded Fo complex, the structure shows unique structural adaptations along both the entry and exit pathways of the proton-conducting a-subunit. These features, absent in mitochondrial ATP synthases, represent attractive targets for the development of next-generation therapeutics that can act directly at the culmination of bioenergetics in this clinically relevant pathogen.
Collapse
Affiliation(s)
- Julius K. Demmer
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Ben P. Phillips
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - O. Lisa Uhrig
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Luke P. Allsopp
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
- National Heart and Lung Institute, Imperial College, London, UK
| | - Maike Bublitz
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas Meier
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK
- Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| |
Collapse
|
15
|
Allsopp LP, Collins ACZ, Hawkins E, Wood TE, Filloux A. RpoN/Sfa2-dependent activation of the Pseudomonas aeruginosa H2-T6SS and its cognate arsenal of antibacterial toxins. Nucleic Acids Res 2021; 50:227-243. [PMID: 34928327 PMCID: PMC8855297 DOI: 10.1093/nar/gkab1254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/27/2021] [Revised: 11/26/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa uses three type six secretion systems
(H1-, H2- and H3-T6SS) to manipulate its environment, subvert host cells and for
microbial competition. These T6SS machines are loaded with a variety of
effectors/toxins, many being associated with a specific VgrG. How P.
aeruginosa transcriptionally coordinates the main T6SS clusters and
the multiple vgrG islands spread through the genome is unknown.
Here we show an unprecedented level of control with RsmA repressing most known
T6SS-related genes. Moreover, each of the H2- and H3-T6SS clusters encodes a
sigma factor activator (SFA) protein
called, Sfa2 and Sfa3, respectively. SFA proteins are enhancer binding proteins
necessary for the sigma factor RpoN. Using a combination of RNA-seq, ChIP-seq
and molecular biology approaches, we demonstrate that RpoN coordinates the T6SSs
of P. aeruginosa by activating the H2-T6SS but repressing the
H1- and H3-T6SS. Furthermore, RpoN and Sfa2 control the expression of the
H2-T6SS-linked VgrGs and their effector arsenal to enable very effective
interbacterial killing. Sfa2 is specific as Sfa3 from the H3-T6SS cannot
complement loss of Sfa2. Our study further delineates the regulatory mechanisms
that modulate the deployment of an arsenal of T6SS effectors likely enabling
P. aeruginosa to adapt to a range of environmental
conditions.
Collapse
Affiliation(s)
- Luke P Allsopp
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Alice C Z Collins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Eleanor Hawkins
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Thomas E Wood
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| |
Collapse
|
16
|
Brinkman FSL, Winsor GL, Done RE, Filloux A, Francis VI, Goldberg JB, Greenberg EP, Han K, Hancock REW, Haney CH, Häußler S, Klockgether J, Lamont IL, Levesque RC, Lory S, Nikel PI, Porter SL, Scurlock MW, Schweizer HP, Tümmler B, Wang M, Welch M. The Pseudomonas aeruginosa whole genome sequence: A 20th anniversary celebration. Adv Microb Physiol 2021; 79:25-88. [PMID: 34836612 DOI: 10.1016/bs.ampbs.2021.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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] [Indexed: 12/16/2022]
Abstract
Toward the end of August 2000, the 6.3 Mbp whole genome sequence of Pseudomonas aeruginosa strain PAO1 was published. With 5570 open reading frames (ORFs), PAO1 had the largest microbial genome sequenced up to that point in time-including a large proportion of metabolic, transport and antimicrobial resistance genes supporting its ability to colonize diverse environments. A remarkable 9% of its ORFs were predicted to encode proteins with regulatory functions, providing new insight into bacterial network complexity as a function of network size. In this celebratory article, we fast forward 20 years, and examine how access to this resource has transformed our understanding of P. aeruginosa. What follows is more than a simple review or commentary; we have specifically asked some of the leaders in the field to provide personal reflections on how the PAO1 genome sequence, along with the Pseudomonas Community Annotation Project (PseudoCAP) and Pseudomonas Genome Database (pseudomonas.com), have contributed to the many exciting discoveries in this field. In addition to bringing us all up to date with the latest developments, we also ask our contributors to speculate on how the next 20 years of Pseudomonas research might pan out.
Collapse
Affiliation(s)
- Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Rachel E Done
- Department of Pediatrics, Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Emory Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, United States
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Vanessa I Francis
- Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Emory Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, United States
| | - E Peter Greenberg
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Kook Han
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | | | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Susanne Häußler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jens Klockgether
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Pavillon Charles-Eugène Marchand, Faculté of Médicine, Université Laval, Québec City, QC, Canada
| | - Stephen Lory
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Steven L Porter
- Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | | | - Herbert P Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Burkhard Tümmler
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Meng Wang
- Department of Biochemistry (Hopkins Building), University of Cambridge, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry (Hopkins Building), University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
17
|
Nolan LM, Cain AK, Clamens T, Furniss RCD, Manoli E, Sainz-Polo MA, Dougan G, Albesa-Jové D, Parkhill J, Mavridou DA, Filloux A. Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells. Nat Microbiol 2021; 6:1199-1210. [PMID: 34413503 PMCID: PMC7611593 DOI: 10.1038/s41564-021-00950-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
The Type VI secretion system (T6SS) is a bacterial nanomachine that delivers toxic effectors to kill competitors or subvert some of their key functions. Here, we use transposon directed insertion-site sequencing to identify T6SS toxins associated with the H1-T6SS, one of the three T6SS machines found in Pseudomonas aeruginosa. This approach identified several putative toxin-immunity pairs, including Tse8-Tsi8. Full characterization of this protein pair demonstrated that Tse8 is delivered by the VgrG1a spike complex into prey cells where it targets the transamidosome, a multiprotein complex involved in protein synthesis in bacteria that lack either one, or both, of the asparagine and glutamine transfer RNA synthases. Biochemical characterization of the interactions between Tse8 and the transamidosome components GatA, GatB and GatC suggests that the presence of Tse8 alters the fine-tuned stoichiometry of the transamidosome complex, and in vivo assays demonstrate that Tse8 limits the ability of prey cells to synthesize proteins. These data expand the range of cellular components targeted by the T6SS by identifying a T6SS toxin affecting protein synthesis and validate the use of a transposon directed insertion site sequencing-based global genomics approach to expand the repertoire of T6SS toxins in T6SS-encoding bacteria.
Collapse
Affiliation(s)
- Laura M. Nolan
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Amy K. Cain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas Clamens
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - R. Christopher D. Furniss
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Eleni Manoli
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Maria A. Sainz-Polo
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - David Albesa-Jové
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Despoina A.I. Mavridou
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom,Department of Molecular Biosciences, University of Texas at Austin, Austin, 78712, Texas, USA,Correspondence to Alain Filloux: ; Despoina Mavridou:
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom,Correspondence to Alain Filloux: ; Despoina Mavridou:
| |
Collapse
|
18
|
Jeannot K, Hagart K, Dortet L, Kostrzewa M, Filloux A, Plesiat P, Larrouy-Maumus G. Detection of Colistin Resistance in Pseudomonas aeruginosa Using the MALDIxin Test on the Routine MALDI Biotyper Sirius Mass Spectrometer. Front Microbiol 2021; 12:725383. [PMID: 34531843 PMCID: PMC8438524 DOI: 10.3389/fmicb.2021.725383] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022] Open
Abstract
Colistin is frequently a last resort treatment for Pseudomonas aeruginosa infections caused by multidrug-resistant (MDR) and extensively drug resistant (XDR) strains, and detection of colistin resistance is essential for the management of infected patients. Therefore, we evaluated the recently developed MALDIxin test for the detection of colistin resistance in P. aeruginosa clinical strains using the routine matrix-assisted laser desorption ionization (MALDI) Biotyper Sirius system. The test is based on the detection by mass spectrometry of modified lipid A by the addition of 4-amino-l-arabinose (l-ara4N) molecules on one or two phosphate groups, in strains resistant to colistin. Overproduction of l-Ara4N molecules is mainly due to the constitutive activation of the histidine kinase (PmrB) or the response regulator (PmrA) following an amino-acid substitution in clinical strains. The performance of the test was determined on a panel of 14 colistin-susceptible and 14 colistin-resistant P. aeruginosa clinical strains, the reference strain PAO1 and positive control mutants PmrB (V28G), PmrB (D172), PhoQ (D240-247), and ParR (M59I). In comparison with the broth microdilution (BMD) method, all the susceptible strains (n=14) and 8/14 colistin-resistant strains were detected in less than 1h, directly on whole bacteria. The remaining resistant strains (n=6) were all detected after a short pre-exposure (4h) to colistin before sample preparation. Validation of the method on a larger panel of strains will be the next step before its use in diagnostics laboratories. Our data showed that the MALDIxin test offers rapid and efficient detection of colistin resistant P. aeruginosa and is thus a valuable diagnostics tool to control the spread of these emerging resistant strains.
Collapse
Affiliation(s)
- Katy Jeannot
- UMR 6249 Chrono-Environnement, UFR Sciences Médicales et Pharmaceutiques, University of Bourgogne-Franche Comté, Besançon, France
- French National Reference Centre for Antibiotic Resistance, Besançon, France
- Department of Bacteriology, University Hospital of Besançon, Besançon, France
| | - Katheryn Hagart
- Department of Life Sciences, Faculty of Natural Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Laurent Dortet
- French National Reference Centre for Antibiotic Resistance, Besançon, France
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique – Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- EA7361 “Structure, Dynamic, Function and Expression of Broad Spectrum β-lactamases,” LabEx Lermit, Faculty of Medecine, Paris-Sud University, Le Kremlin-Bicêtre, France
| | | | - Alain Filloux
- Department of Life Sciences, Faculty of Natural Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Patrick Plesiat
- UMR 6249 Chrono-Environnement, UFR Sciences Médicales et Pharmaceutiques, University of Bourgogne-Franche Comté, Besançon, France
- French National Reference Centre for Antibiotic Resistance, Besançon, France
- Department of Bacteriology, University Hospital of Besançon, Besançon, France
| | - Gerald Larrouy-Maumus
- Department of Life Sciences, Faculty of Natural Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| |
Collapse
|
19
|
Dortet L, Broda A, Bernabeu S, Glupczynski Y, Bogaerts P, Bonnin R, Naas T, Filloux A, Larrouy-Maumus G. Optimization of the MALDIxin test for the rapid identification of colistin resistance in Klebsiella pneumoniae using MALDI-TOF MS. J Antimicrob Chemother 2021; 75:110-116. [PMID: 31580426 PMCID: PMC6910190 DOI: 10.1093/jac/dkz405] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 06/25/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 12/24/2022] Open
Abstract
Background With the dissemination of carbapenemase producers, a revival of colistin was observed for the treatment of infections caused by MDR Gram-negatives. Unfortunately, the increasing usage of colistin led to the emergence of resistance. In Klebsiella pneumoniae, colistin resistance arises through addition of 4-amino-l-arabinose (l-Ara4N) or phosphoethanolamine (pEtN) to the native lipid A. The underlying mechanisms involve numerous chromosome-encoded genes or the plasmid-encoded pEtN transferase MCR. Currently, detection of colistin resistance is time-consuming since it still relies on MIC determination by broth microdilution. Recently, a rapid diagnostic test based on MALDI-TOF MS detection of modified lipid A was developed (the MALDIxin test) and tested on Escherichia coli and Acinetobacter baumannii. Objectives Optimize the MALDIxin test for the rapid detection of colistin resistance in K. pneumoniae. Methods This optimization consists of an additional mild-acid hydrolysis of 15 min in 1% acetic acid. The optimized method was tested on a collection of 81 clinical K. pneumoniae isolates, including 49 colistin-resistant isolates (45 with chromosome-encoded resistance, 3 with MCR-related resistance and 1 with both mechanisms). Results The optimized method allowed the rapid (<30 min) identification of l-Ara4N- and pEtN-modified lipid A of K. pneumoniae, which are known to be the real triggers of polymyxin resistance. At the same time, it discriminates between chromosome-encoded and MCR-related polymyxin resistance. Conclusions The MALDIxin test has the potential to become an accurate tool for the rapid determination of colistin resistance in clinically relevant Gram-negative bacteria.
Collapse
Affiliation(s)
- Laurent Dortet
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK.,Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Agnieszka Broda
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Sandrine Bernabeu
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Youri Glupczynski
- Laboratory of Clinical Microbiology, Belgian National Reference Centre for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Pierre Bogaerts
- Laboratory of Clinical Microbiology, Belgian National Reference Centre for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Rémy Bonnin
- EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| |
Collapse
|
20
|
Steinchen W, Ahmad S, Valentini M, Eilers K, Majkini M, Altegoer F, Lechner M, Filloux A, Whitney JC, Bange G. Dual role of a (p)ppGpp- and (p)ppApp-degrading enzyme in biofilm formation and interbacterial antagonism. Mol Microbiol 2021; 115:1339-1356. [PMID: 33448498 DOI: 10.1111/mmi.14684] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022]
Abstract
The guanosine nucleotide-based second messengers ppGpp and pppGpp (collectively: (p)ppGpp) enable adaptation of microorganisms to environmental changes and stress conditions. In contrast, the closely related adenosine nucleotides (p)ppApp are involved in type VI secretion system (T6SS)-mediated killing during bacterial competition. Long RelA-SpoT Homolog (RSH) enzymes regulate synthesis and degradation of (p)ppGpp (and potentially also (p)ppApp) through their synthetase and hydrolase domains, respectively. Small alarmone hydrolases (SAH) that consist of only a hydrolase domain are found in a variety of bacterial species, including the opportunistic human pathogen Pseudomonas aeruginosa. Here, we present the structure and mechanism of P. aeruginosa SAH showing that the enzyme promiscuously hydrolyses (p)ppGpp and (p)ppApp in a strictly manganese-dependent manner. While being dispensable for P. aeruginosa growth or swimming, swarming, and twitching motilities, its enzymatic activity is required for biofilm formation. Moreover, (p)ppApp-degradation by SAH provides protection against the T6SS (p)ppApp synthetase effector Tas1, suggesting that SAH enzymes can also serve as defense proteins during interbacterial competition.
Collapse
Affiliation(s)
- Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Shehryar Ahmad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Martina Valentini
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Kira Eilers
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Mohamad Majkini
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| |
Collapse
|
21
|
Lin HH, Filloux A, Lai EM. Role of Recipient Susceptibility Factors During Contact-Dependent Interbacterial Competition. Front Microbiol 2020; 11:603652. [PMID: 33281802 PMCID: PMC7690452 DOI: 10.3389/fmicb.2020.603652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
Bacteria evolved multiple strategies to survive and develop optimal fitness in their ecological niche. They deployed protein secretion systems for robust and efficient delivery of antibacterial toxins into their target cells, therefore inhibiting their growth or killing them. To maximize antagonism, recipient factors on target cells can be recognized or hijacked to enhance the entry or toxicity of these toxins. To date, knowledge regarding recipient susceptibility (RS) factors and their mode of action is mostly originating from studies on the type Vb secretion system that is also known as the contact-dependent inhibition (CDI) system. Yet, recent studies on the type VI secretion system (T6SS), and the CDI by glycine-zipper protein (Cdz) system, also reported the emerging roles of RS factors in interbacterial competition. Here, we review these RS factors and their mechanistic impact in increasing susceptibility of recipient cells in response to CDI, T6SS, and Cdz. Past and future strategies for identifying novel RS factors are also discussed, which will help in understanding the interplay between attacker and prey upon secretion system-dependent competition. Understanding these mechanisms would also provide insights for developing novel antibacterial strategies to antagonize aggressive bacteria-killing pathogens.
Collapse
Affiliation(s)
- Hsiao-Han Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
22
|
Wood TE, Howard SA, Förster A, Nolan LM, Manoli E, Bullen NP, Yau HCL, Hachani A, Hayward RD, Whitney JC, Vollmer W, Freemont PS, Filloux A. The Pseudomonas aeruginosa T6SS Delivers a Periplasmic Toxin that Disrupts Bacterial Cell Morphology. Cell Rep 2020; 29:187-201.e7. [PMID: 31577948 PMCID: PMC6899460 DOI: 10.1016/j.celrep.2019.08.094] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 07/02/2019] [Accepted: 08/27/2019] [Indexed: 01/10/2023] Open
Abstract
The type VI secretion system (T6SS) is crucial in interbacterial competition and is a virulence determinant of many Gram-negative bacteria. Several T6SS effectors are covalently fused to secreted T6SS structural components such as the VgrG spike for delivery into target cells. In Pseudomonas aeruginosa, the VgrG2b effector was previously proposed to mediate bacterial internalization into eukaryotic cells. In this work, we find that the VgrG2b C-terminal domain (VgrG2bC-ter) elicits toxicity in the bacterial periplasm, counteracted by a cognate immunity protein. We resolve the structure of VgrG2bC-ter and confirm it is a member of the zinc-metallopeptidase family of enzymes. We show that this effector causes membrane blebbing at midcell, which suggests a distinct type of T6SS-mediated growth inhibition through interference with cell division, mimicking the impact of β-lactam antibiotics. Our study introduces a further effector family to the T6SS arsenal and demonstrates that VgrG2b can target both prokaryotic and eukaryotic cells. The structure of the VgrG2b C-terminal domain presents a metallopeptidase fold VgrG2b exerts antibacterial activity in the periplasmic space Toxicity of VgrG2b is counteracted by a cognate periplasmic immunity protein VgrG2bC-ter-intoxicated prey cells bleb at the midcell and lyse
Collapse
Affiliation(s)
- Thomas E Wood
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sophie A Howard
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Andreas Förster
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Laura M Nolan
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Eleni Manoli
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Nathan P Bullen
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Hamish C L Yau
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Abderrahman Hachani
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Richard D Hayward
- Division of Microbiology and Parasitology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Paul S Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| |
Collapse
|
23
|
Howard S, Furniss C, Bonini D, Amin H, Paracuellos-Torrecilla P, Costa T, Mavridou D, Filloux A. The Type VI Secretion System of Pseudomonas aeruginosa: a gun loaded with antimicrobial bullets. Access Microbiol 2020. [DOI: 10.1099/acmi.ac2020.po0620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can cause severe respiratory infections in people who are immunocompromised. P. aeruginosa possesses the Type VI Secretion System (T6SS), a bacterial weapon that injects effectors into neighbouring prokaryotes and eukaryotes. The T6SS is crucial for bacterial warfare, allowing P. aeruginosa to kill its competitors, which promotes its dominance in mixed microbial environments. P. aeruginosa has three T6SSs, H1/2/3-T6SS, these are structural homologs but deliver unique effectors. Effectors are delivered via the secreted component, a Hcp tube topped with a VgrG and PAAR spike. Only the first three identified effectors are delivered by Hcp1. Since then, there has been a bias in identification of VgrG or PAAR delivered effectors, mostly as these are encoded next to the spike proteins. Some P. aeruginosa effectors not only kill bacteria but have a dual role in pathogenesis. Our aim was to identify a comprehensive set of Hcp-delivered effectors for all three systems. Using Hcp1/2/3, systematic pull-down screens were performed to identify novel interaction partners. After confirming interaction, antibacterial toxicity was evaluated, identifying new Hcp delivered T6SS effectors for Hcp2 and Hcp3, which are toxic in the bacterial cytoplasm. These new anti-bacterial effectors may kill bacteria in novel ways, which could lead to novel antibiotics. Additionally, a toxin fusion proved too large for secretion and blocked the T6SS, revealing a Hcp-delivered effector size limit. Future work will focus on fully characterising these new toxins, as well as to look into the potential eukaryotic role of other interaction partners.
Collapse
Affiliation(s)
| | | | - Dora Bonini
- University of Bristol,Bristol,United Kingdom
| | - Himani Amin
- Imperial College London,London,United Kingdom
| | | | - Tiago Costa
- Imperial College London,London,United Kingdom
| | | | | |
Collapse
|
24
|
Wettstadt S, Lai EM, Filloux A. Solving the Puzzle: Connecting a Heterologous Agrobacterium tumefaciens T6SS Effector to a Pseudomonas aeruginosa Spike Complex. Front Cell Infect Microbiol 2020; 10:291. [PMID: 32656098 PMCID: PMC7324665 DOI: 10.3389/fcimb.2020.00291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/18/2020] [Indexed: 12/27/2022] Open
Abstract
The type VI secretion system (T6SS) is a contractile injection apparatus that translocates a spike loaded with various effectors directly into eukaryotic and prokaryotic target cells. Such T6SS spike consists of a needle-shaped trimer of VgrG proteins topped by a conical and sharp PAAR protein that facilitates puncturing of the target membrane. T6SS-delivered effector proteins can be either fused to one of the two spike proteins or interact with either in a highly specific manner. In Agrobacterium tumefaciens the T6SS effector Tde1 is targeted to its cognate VgrG1 protein. Here, we attempted to use a VgrG shuttle to deliver a heterologous T6SS effector by directing Tde1 onto a T6SS spike in Pseudomonas aeruginosa. For this, we designed chimeras between VgrG1 from A. tumefaciens and VgrG1a from P. aeruginosa and showed that modification of the spike protein hampered T6SS functionality in the presence of the Tde1 effector complex. We provide evidence suggesting that Tde1 specifically binds to the VgrG spike in the heterologous environment and propose that there are additional requirements to allow proper effector delivery and translocation. Our work sheds light on complex aspects of the molecular mechanisms of T6SS delivery and highlights some limitations on how effectors can be translocated using this nanomachine.
Collapse
Affiliation(s)
- Sarah Wettstadt
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| |
Collapse
|
25
|
Abstract
The intracellular signaling molecule cyclic di-GMP (c-di-GMP) regulates the lifestyle of bacteria and controls many key functions and mechanisms. In the case of bacterial pathogens, a wide variety of virulence lifestyle factors have been shown to be regulated by c-di-GMP. Evidence of the importance of this molecule for bacterial pathogenesis has become so great that new antimicrobial agents are tested for their capacity of targeting c-di-GMP signaling. This review summarizes the current knowledge on this topic and reveals its application for the development of new antivirulence intervention strategies.
Collapse
Affiliation(s)
- Martina Valentini
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva 4, Switzerland;
| | - Alain Filloux
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom;
| |
Collapse
|
26
|
Abstract
The type VI secretion system (T6SS) is a contractile injection apparatus that translocates a spike loaded with various effectors directly into eukaryotic or prokaryotic target cells. Pseudomonas aeruginosa can load either one of its three T6SSs with a variety of toxic bullets using different but specific modes. The T6SS spike, which punctures the bacterial cell envelope allowing effector transport, consists of a torch-like VgrG trimer on which sits a PAAR protein sharpening the VgrG tip. VgrG itself sits on the Hcp tube and all elements, packed into a T6SS sheath, are propelled out of the cell and into target cells. On occasion, effectors are covalent extensions of VgrG, PAAR or Hcp proteins, which are then coined "evolved" components as opposed to canonical. Here, we show how various passenger domains could be fused to the C terminus of a canonical VgrG, VgrG1a from P. aeruginosa, and be sent into the bacterial culture supernatant. There is no restriction on the passenger type, although the efficacy may vary greatly, since we used either an unrelated T6SS protein, β-lactamase, a covalent extension of an "evolved" VgrG, VgrG2b, or a Hcp-dependent T6SS toxin, Tse2. Our data further highlights an exceptional modularity/flexibility for loading the T6SS nano-weapon. Refining the parameters to optimize delivery of passenger proteins of interest would have attractive medical and industrial applications. This may for example involve engineering the T6SS as a delivery system to shuttle toxins into either bacterial pathogens or tumour cells which would be an original approach in the fight against antimicrobial resistant bacteria or cancer.
Collapse
Affiliation(s)
- Sarah Wettstadt
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| |
Collapse
|
27
|
Abstract
Bacteria exist in polymicrobial environments and compete to prevail in a niche. The type VI secretion system (T6SS) is a nanomachine employed by Gram-negative bacteria to deliver effector proteins into target cells. Consequently, T6SS-positive bacteria produce a wealth of antibacterial effector proteins to promote their survival among a prokaryotic community. These toxins are loaded onto the VgrG–PAAR spike and Hcp tube of the T6SS apparatus and recent work has started to document the specificity of effectors for certain spike components. Pseudomonas aeruginosa encodes several PAAR proteins, whose roles have been poorly investigated. Here we describe a phospholipase family antibacterial effector immunity pair from Pseudomonas aeruginosa and demonstrate that a specific PAAR protein is necessary for the delivery of the effector and its cognate VgrG. Furthermore, the PAAR protein appears to restrict the delivery of other phospholipase effectors that utilise distinct VgrG proteins. We provide further evidence for competition for PAAR protein recruitment to the T6SS apparatus, which determines the identities of the delivered effectors.
Collapse
Affiliation(s)
- Thomas E Wood
- Present address: Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Present address: Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Cambridge, MA, USA.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, London, SW7 2AZ, UK
| | - Sophie A Howard
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, London, SW7 2AZ, UK
| | - Sarah Wettstadt
- Present address: Department of Environmental Protection, Estación Experimental de Zaidín - Consejo Superior de Investigaciones Científicas, Granada, Spain.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, London, SW7 2AZ, UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, London, SW7 2AZ, UK
| |
Collapse
|
28
|
Allsopp LP, Bernal P, Nolan LM, Filloux A. Causalities of war: The connection between type VI secretion system and microbiota. Cell Microbiol 2020; 22:e13153. [PMID: 31872954 PMCID: PMC7540082 DOI: 10.1111/cmi.13153] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 09/01/2019] [Revised: 11/23/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022]
Abstract
Microbiota niches have space and/or nutrient restrictions, which has led to the coevolution of cooperation, specialisation, and competition within the population. Different animal and environmental niches contain defined resident microbiota that tend to be stable over time and offer protection against undesired intruders. Yet fluxes can occur, which alter the composition of a bacterial population. In humans, the microbiota are now considered a key contributor to maintenance of health and homeostasis, and its alteration leads to dysbiosis. The bacterial type VI secretion system (T6SS) transports proteins into the environment, directly into host cells or can function as an antibacterial weapon by killing surrounding competitors. Upon contact with neighbouring cells, the T6SS fires, delivering a payload of effector proteins. In the absence of an immunity protein, this results in growth inhibition or death of prey leading to a competitive advantage for the attacker. It is becoming apparent that the T6SS has a role in modulating and shaping the microbiota at multiple levels, which is the focus of this review. Discussed here is the T6SS, its role in competition, key examples of its effect upon the microbiota, and future avenues of research.
Collapse
Affiliation(s)
- Luke P Allsopp
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Patricia Bernal
- Department of Biology, Faculty of Sciences, Universidad Autónoma de Madrid, Madrid, Spain
| | - Laura M Nolan
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| |
Collapse
|
29
|
Dortet L, Bonnin RA, Le Hello S, Fabre L, Bonnet R, Kostrzewa M, Filloux A, Larrouy-Maumus G. Detection of Colistin Resistance in Salmonella enterica Using MALDIxin Test on the Routine MALDI Biotyper Sirius Mass Spectrometer. Front Microbiol 2020; 11:1141. [PMID: 32582090 PMCID: PMC7283459 DOI: 10.3389/fmicb.2020.01141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Resistance to polymyxins in most Gram-negative bacteria arises from chemical modifications to the lipid A portion of their lipopolysaccharide (LPS) mediated by chromosomally encoded mutations or the recently discovered plasmid-encoded mcr genes that have further complicated the landscape of colistin resistance. Currently, minimal inhibitory concentration (MIC) determination by broth microdilution, the gold standard for the detection of polymyxin resistance, is time consuming (24 h) and challenging to perform in clinical and veterinary laboratories. Here we present the use of the MALDIxin to detect colistin resistant Salmonella enterica using the MALDxin test on the routine matrix-assisted laser desorption ionization (MALDI) Biotyper Sirius system.
Collapse
Affiliation(s)
- Laurent Dortet
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom.,Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 "Structure, Dynamic, Function and Expression of Broad Spectrum ß-Lactamases", Paris-Sud University, LabEx Lermit, Faculty of Medecine, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 "Structure, Dynamic, Function and Expression of Broad Spectrum ß-Lactamases", Paris-Sud University, LabEx Lermit, Faculty of Medecine, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Simon Le Hello
- Institut Pasteur, French National Reference Centre for E. coli, Shigella and Salmonella, Paris, France
| | - Laetitia Fabre
- Institut Pasteur, French National Reference Centre for E. coli, Shigella and Salmonella, Paris, France
| | - Richard Bonnet
- French National Reference Centre for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Department of Bacteriology, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| |
Collapse
|
30
|
Cain AK, Nolan LM, Sullivan GJ, Whitchurch CB, Filloux A, Parkhill J. Complete Genome Sequence of Pseudomonas aeruginosa Reference Strain PAK. Microbiol Resour Announc 2019; 8:e00865-19. [PMID: 31601664 PMCID: PMC6787321 DOI: 10.1128/mra.00865-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/09/2019] [Indexed: 11/29/2022] Open
Abstract
We report the complete genome of Pseudomonas aeruginosa strain PAK, a strain which has been instrumental in the study of a range of P. aeruginosa virulence and pathogenesis factors and has been used for over 50 years as a laboratory reference strain.
Collapse
Affiliation(s)
- Amy K Cain
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Molecular Sciences, Macquarie University, North Ryde, Australia
| | - Laura M Nolan
- Imperial College London, MRC Centre for Molecular Bacteriology and Infection, South Kensington, London, United Kingdom
| | | | - Cynthia B Whitchurch
- The ithree institute, Faculty of Science, University of Technology Sydney, Ultimo, Australia
| | - Alain Filloux
- Imperial College London, MRC Centre for Molecular Bacteriology and Infection, South Kensington, London, United Kingdom
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
31
|
Abstract
The proteins injected by bacteria into eukaryotic organisms can lead to fates as diverse as death and metamorphosis.
Collapse
Affiliation(s)
- Sophie A Howard
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonUnited Kingdom
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonUnited Kingdom
| |
Collapse
|
32
|
McCarthy RR, Yu M, Eilers K, Wang Y, Lai E, Filloux A. Cyclic di-GMP inactivates T6SS and T4SS activity in Agrobacterium tumefaciens. Mol Microbiol 2019; 112:632-648. [PMID: 31102484 PMCID: PMC6771610 DOI: 10.1111/mmi.14279] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 01/17/2023]
Abstract
The Type VI secretion system (T6SS) is a bacterial nanomachine that delivers effector proteins into prokaryotic and eukaryotic preys. This secretion system has emerged as a key player in regulating the microbial diversity in a population. In the plant pathogen Agrobacterium tumefaciens, the signalling cascades regulating the activity of this secretion system are poorly understood. Here, we outline how the universal eubacterial second messenger cyclic di-GMP impacts the production of T6SS toxins and T6SS structural components. We demonstrate that this has a significant impact on the ability of the phytopathogen to compete with other bacterial species in vitro and in planta. Our results suggest that, as opposed to other bacteria, c-di-GMP turns down the T6SS in A. tumefaciens thus impacting its ability to compete with other bacterial species within the rhizosphere. We also demonstrate that elevated levels of c-di-GMP within the cell decrease the activity of the Type IV secretion system (T4SS) and subsequently the capacity of A. tumefaciens to transform plant cells. We propose that such peculiar control reflects on c-di-GMP being a key second messenger that silences energy-costing systems during early colonization phase and biofilm formation, while low c-di-GMP levels unleash T6SS and T4SS to advance plant colonization.
Collapse
Affiliation(s)
- Ronan R. McCarthy
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonSW7 2AZUK
- Division of Biosciences, Department of Life SciencesCollege of Health and Life Sciences, Brunel University LondonUxbridgeUB8 3PHUK
| | - Manda Yu
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Kira Eilers
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonSW7 2AZUK
| | - Yi‐Chieh Wang
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Erh‐Min Lai
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonSW7 2AZUK
| |
Collapse
|
33
|
Wettstadt S, Wood TE, Fecht S, Filloux A. Delivery of the Pseudomonas aeruginosa Phospholipase Effectors PldA and PldB in a VgrG- and H2-T6SS-Dependent Manner. Front Microbiol 2019; 10:1718. [PMID: 31417515 PMCID: PMC6684961 DOI: 10.3389/fmicb.2019.01718] [Citation(s) in RCA: 37] [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: 12/20/2018] [Accepted: 07/11/2019] [Indexed: 11/13/2022] Open
Abstract
The bacterial pathogen Pseudomonas aeruginosa uses three type VI secretion systems (T6SSs) to drive a multitude of effector proteins into eukaryotic or prokaryotic target cells. The T6SS is a supramolecular nanomachine, involving a set of 13 core proteins, which resembles the contractile tail of bacteriophages and whose tip is considered as a puncturing device helping to cross membranes. Effectors can attach directly to the T6SS spike which is composed of a VgrG (valine-glycine-rich proteins) trimer, of which P. aeruginosa produces several. We have previously shown that the master regulator RsmA controls the expression of all three T6SS gene clusters (H1-, H2- and H3-T6SS) and a range of remote vgrG and effector genes. We also demonstrated that specific interactions between VgrGs and various T6SS effectors are prerequisite for effector delivery in a process we called "à la carte delivery." Here, we provide an in-depth description on how the two H2-T6SS-dependent effectors PldA and PldB are delivered via their cognate VgrGs, VgrG4b and VgrG5, respectively. We show that specific recognition of the VgrG C terminus is required and effector specificity can be swapped by exchanging these C-terminal domains. Importantly, we established that effector recognition by a cognate VgrG is not always sufficient to achieve successful secretion, but it is crucial to provide effector stability. This study highlights the complexity of effector adaptation to the T6SS nanomachine and shows how the VgrG tip can possibly be manipulated to achieve effector delivery.
Collapse
Affiliation(s)
- Sarah Wettstadt
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Thomas E Wood
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Selina Fecht
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| |
Collapse
|
34
|
Affiliation(s)
- Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Microbiology and Infection, Imperial College, London, UK.
| | - Jane C Davies
- The Cystic Fibrosis and Chronic Infection Group, National Heart and Lung Institute, Imperial College, London, UK. .,The Royal Brompton and Harefield NHS Foundation Trust, London, UK.
| |
Collapse
|
35
|
Abstract
The 8th ASM Conference on Biofilms was held in Washington D.C. on October 7-11, 2018. This very highly subscribed meeting represented a wide breadth of current research in biofilms, and included over 500 attendees, 12 sessions with 64 oral presentations, and four poster sessions with about 400 posters.
Collapse
Affiliation(s)
- Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College, London, United Kingdom
| | - Jean-Marc Ghigo
- Institut Pasteur, Unité de Génétique des Biofilms, Département de Microbiologie, Paris, France
| | - Karen L. Visick
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| |
Collapse
|
36
|
Lorenz A, Preuße M, Bruchmann S, Pawar V, Grahl N, Pils MC, Nolan LM, Filloux A, Weiss S, Häussler S. Importance of flagella in acute and chronicPseudomonas aeruginosainfections. Environ Microbiol 2018; 21:883-897. [DOI: 10.1111/1462-2920.14468] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Anne Lorenz
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
| | - Matthias Preuße
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
| | - Sebastian Bruchmann
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
- Wellcome Sanger Institute Cambridge UK
| | - Vinay Pawar
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Immunology, Medical School Hannover Hannover Germany
| | - Nora Grahl
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
| | - Marina C. Pils
- Mouse PathologyAnimal Experimental Unit, Helmholtz Centre for Infection Research Braunschweig Germany
| | - Laura M. Nolan
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life SciencesImperial College London London UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life SciencesImperial College London London UK
| | - Siegfried Weiss
- Institute of Immunology, Medical School Hannover Hannover Germany
| | - Susanne Häussler
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
| |
Collapse
|
37
|
Dortet L, Bonnin RA, Pennisi I, Gauthier L, Jousset AB, Dabos L, Furniss RCD, Mavridou DAI, Bogaerts P, Glupczynski Y, Potron A, Plesiat P, Beyrouthy R, Robin F, Bonnet R, Naas T, Filloux A, Larrouy-Maumus G. Rapid detection and discrimination of chromosome- and MCR-plasmid-mediated resistance to polymyxins by MALDI-TOF MS in Escherichia coli: the MALDIxin test. J Antimicrob Chemother 2018; 73:3359-3367. [PMID: 30184212 DOI: 10.1093/jac/dky330] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
Background Polymyxins are currently considered a last-resort treatment for infections caused by MDR Gram-negative bacteria. Recently, the emergence of carbapenemase-producing Enterobacteriaceae has accelerated the use of polymyxins in the clinic, resulting in an increase in polymyxin-resistant bacteria. Polymyxin resistance arises through modification of lipid A, such as the addition of phosphoethanolamine (pETN). The underlying mechanisms involve numerous chromosome-encoded genes or, more worryingly, a plasmid-encoded pETN transferase named MCR. Currently, detection of polymyxin resistance is difficult and time consuming. Objectives To develop a rapid diagnostic test that can identify polymyxin resistance and at the same time differentiate between chromosome- and plasmid-encoded resistances. Methods We developed a MALDI-TOF MS-based method, named the MALDIxin test, which allows the detection of polymyxin resistance-related modifications to lipid A (i.e. pETN addition), on intact bacteria, in <15 min. Results Using a characterized collection of polymyxin-susceptible and -resistant Escherichia coli, we demonstrated that our method is able to identify polymyxin-resistant isolates in 15 min whilst simultaneously discriminating between chromosome- and plasmid-encoded resistance. We validated the MALDIxin test on different media, using fresh and aged colonies and show that it successfully detects all MCR-1 producers in a blindly analysed set of carbapenemase-producing E. coli strains. Conclusions The MALDIxin test is an accurate, rapid, cost-effective and scalable method that represents a major advance in the diagnosis of polymyxin resistance by directly assessing lipid A modifications in intact bacteria.
Collapse
Affiliation(s)
- Laurent Dortet
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.,Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Remy A Bonnin
- EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Ivana Pennisi
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Lauraine Gauthier
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Agnès B Jousset
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Laura Dabos
- EA7361 'Structure, dynamic, function and expression of broad spectrum ß-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - R Christopher D Furniss
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Despoina A I Mavridou
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Pierre Bogaerts
- Laboratory of Clinical Microbiology, Belgian National Reference Center for Monitoring Antimicrobial Resistance in Gram-negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Youri Glupczynski
- Laboratory of Clinical Microbiology, Belgian National Reference Center for Monitoring Antimicrobial Resistance in Gram-negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Anais Potron
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Bacteriology Unit, University Hospital of Besançon, Besançon, France
| | - Patrick Plesiat
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Bacteriology Unit, University Hospital of Besançon, Besançon, France
| | - Racha Beyrouthy
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Bacteriology Unit, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Frédéric Robin
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Bacteriology Unit, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Richard Bonnet
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,Bacteriology Unit, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Paris-Sud University, Paris Saclay University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France.,French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| |
Collapse
|
38
|
Dortet L, Potron A, Bonnin RA, Plesiat P, Naas T, Filloux A, Larrouy-Maumus G. Rapid detection of colistin resistance in Acinetobacter baumannii using MALDI-TOF-based lipidomics on intact bacteria. Sci Rep 2018; 8:16910. [PMID: 30442963 PMCID: PMC6237936 DOI: 10.1038/s41598-018-35041-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/30/2018] [Indexed: 12/13/2022] Open
Abstract
With the dissemination of extremely drug resistant bacteria, colistin is now considered as the last-resort therapy for the treatment of infection caused by Gram-negative bacilli (including carbapenemase producers). Unfortunately, the increase use of colistin has resulted in the emergence of resistance as well. In A. baumannii, colistin resistance is mostly caused by the addition of phosphoethanolamine to the lipid A through the action of a phosphoethanolamine transferase chromosomally-encoded by the pmrC gene, which is regulated by the two-component system PmrA/PmrB. In A. baumannii clinical isolate the main resistance mechanism to colistin involves mutations in pmrA, pmrB or pmrC genes leading to the overexpression of pmrC. Although, rapid detection of resistance is one of the key issues to improve the treatment of infected patient, detection of colistin resistance in A. baumannii still relies on MIC determination through microdilution, which is time-consuming (16-24 h). Here, we evaluated the performance of a recently described MALDI-TOF-based assay, the MALDIxin test, which allows the rapid detection of colistin resistance-related modifications to lipid A (i.e phosphoethanolamine addition). This test accurately detected all colistin-resistant A. baumannii isolates in less than 15 minutes, directly on intact bacteria with a very limited sample preparation prior MALDI-TOF analysis.
Collapse
Affiliation(s)
- Laurent Dortet
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK.
- Department of Bacteriology- Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.
- EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Paris-Sud University, LabEx Lermit, Faculty of Medecine, Le Kremlin-Bicêtre, France.
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.
| | - Anais Potron
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
- Bacteriology unit, University hospital of Besançon, Besançon, France
| | - Rémy A Bonnin
- Department of Bacteriology- Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Paris-Sud University, LabEx Lermit, Faculty of Medecine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Patrick Plesiat
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
- Bacteriology unit, University hospital of Besançon, Besançon, France
| | - Thierry Naas
- Department of Bacteriology- Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Paris-Sud University, LabEx Lermit, Faculty of Medecine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK.
| |
Collapse
|
39
|
Nolan LM, Whitchurch CB, Barquist L, Katrib M, Boinett CJ, Mayho M, Goulding D, Charles IG, Filloux A, Parkhill J, Cain AK. A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa. Microb Genom 2018; 4. [PMID: 30383525 PMCID: PMC6321873 DOI: 10.1099/mgen.0.000229] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is an extremely successful pathogen able to cause both acute and chronic infections in a range of hosts, utilizing a diverse arsenal of cell-associated and secreted virulence factors. A major cell-associated virulence factor, the Type IV pilus (T4P), is required for epithelial cell adherence and mediates a form of surface translocation termed twitching motility, which is necessary to establish a mature biofilm and actively expand these biofilms. P. aeruginosa twitching motility-mediated biofilm expansion is a coordinated, multicellular behaviour, allowing cells to rapidly colonize surfaces, including implanted medical devices. Although at least 44 proteins are known to be involved in the biogenesis, assembly and regulation of the T4P, with additional regulatory components and pathways implicated, it is unclear how these components and pathways interact to control these processes. In the current study, we used a global genomics-based random-mutagenesis technique, transposon directed insertion-site sequencing (TraDIS), coupled with a physical segregation approach, to identify all genes implicated in twitching motility-mediated biofilm expansion in P. aeruginosa. Our approach allowed identification of both known and novel genes, providing new insight into the complex molecular network that regulates this process in P. aeruginosa. Additionally, our data suggest that the flagellum-associated gene products have a differential effect on twitching motility, based on whether components are intra- or extracellular. Overall the success of our TraDIS approach supports the use of this global genomic technique for investigating virulence genes in bacterial pathogens.
Collapse
Affiliation(s)
- Laura M Nolan
- 1MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Cynthia B Whitchurch
- 2The ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Lars Barquist
- 3Institute for Molecular Infection Biology, University of Würzburg, Würzburg D-97080, Germany.,4Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Marilyn Katrib
- 2The ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Christine J Boinett
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,†Present address: Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Matthew Mayho
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - David Goulding
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian G Charles
- 6Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK
| | - Alain Filloux
- 1MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Julian Parkhill
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Amy K Cain
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,‡Present address: Chemical and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
40
|
Boulant T, Boudehen YM, Filloux A, Plesiat P, Naas T, Dortet L. Higher Prevalence of PldA, a Pseudomonas aeruginosa Trans-Kingdom H2-Type VI Secretion System Effector, in Clinical Isolates Responsible for Acute Infections and in Multidrug Resistant Strains. Front Microbiol 2018; 9:2578. [PMID: 30420847 PMCID: PMC6215852 DOI: 10.3389/fmicb.2018.02578] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 08/29/2018] [Accepted: 10/09/2018] [Indexed: 12/17/2022] Open
Abstract
Pseudomonas aeruginosa can manipulate eukaryotic host cells using secreted effectors delivered by the type III or the type VI Secretion Systems (T3SS and T6SS). The T3SS allows the injection of bacterial effectors (Exo toxins) into eukaryotic cell. P. aeruginosa, encodes three T6SSs, H1-, H2- and H3-T6SS. The H1-T6SS is mainly involved in delivering toxins to kill bacterial competitors. Recently, two T6SS-secreted phospholipases D, PldA (H2-T6SS) and PldB (H3-T6SS), were identified as trans-kingdom virulence effectors, triggering both killing of bacterial competitors and internalization into non-phagocytic cells. We deciphered the prevalence of T3SS and T6SS effectors encoding genes in 185 clinical isolates responsible for infections (septicaemia, pulmonary infections, urinary tract infections, and chronic infections in CF patients), 47 environmental strains, and on 33 carbapenemase-producers. We included 107 complete genomes of P. aeruginosa available in public databases. The prevalence of pldA is increased in clinical isolates responsible for severe acute infection and particularly in multi-drug resistant strains. In contrast, the pldB prevalence was high (96.8%) in all isolates. Regarding T3SS effectors, exoT and exoY are present in nearly all isolates while exoS and exoU were found to be exclusive with a higher prevalence of exoU+ strains in severe acute infections. The hypervirulent exoU+ isolates are more prone to be pldA+, suggesting a role of PldA in virulence. Finally, we observed that extremely drug resistant isolates producing an IMP-type carbapenemase were all pldA+. Our results suggest that PldA might have a role during pulmonary infections and have been co-selected in multidrug resistant strains particularly IMP-producers.
Collapse
Affiliation(s)
- Thibaud Boulant
- EA7361 Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases, LabEx Lermit, Faculty of Medicine, Université Paris Sud - Université Paris Saclay, Le Kremlin-Bicêtre, France
| | - Yves-Marie Boudehen
- EA7361 Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases, LabEx Lermit, Faculty of Medicine, Université Paris Sud - Université Paris Saclay, Le Kremlin-Bicêtre, France
| | - Alain Filloux
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Patrick Plesiat
- Bacteriology Unit, University Hospital of Besançon, Besançon, France
| | - Thierry Naas
- EA7361 Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases, LabEx Lermit, Faculty of Medicine, Université Paris Sud - Université Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- EA7361 Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases, LabEx Lermit, Faculty of Medicine, Université Paris Sud - Université Paris Saclay, Le Kremlin-Bicêtre, France.,MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| |
Collapse
|
41
|
Lin JS, Pissaridou P, Wu HH, Tsai MD, Filloux A, Lai EM. TagF-mediated repression of bacterial type VI secretion systems involves a direct interaction with the cytoplasmic protein Fha. J Biol Chem 2018; 293:8829-8842. [PMID: 29599293 PMCID: PMC5995506 DOI: 10.1074/jbc.ra117.001618] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 12/21/2017] [Revised: 03/09/2018] [Indexed: 01/09/2023] Open
Abstract
The bacterial type VI secretion system (T6SS) delivers effectors into eukaryotic host cells or toxins into bacterial competitor for survival and fitness. The T6SS is positively regulated by the threonine phosphorylation pathway (TPP) and negatively by the T6SS-accessory protein TagF. Here, we studied the mechanisms underlying TagF-mediated T6SS repression in two distinct bacterial pathogens, Agrobacterium tumefaciens and Pseudomonas aeruginosa. We found that in A. tumefaciens, T6SS toxin secretion and T6SS-dependent antibacterial activity are suppressed by a two-domain chimeric protein consisting of TagF and PppA, a putative phosphatase. Remarkably, this TagF domain is sufficient to post-translationally repress the T6SS, and this inhibition is independent of TPP. This repression requires interaction with a cytoplasmic protein, Fha, critical for activating T6SS assembly. In P. aeruginosa, PppA and TagF are two distinct proteins that repress T6SS in TPP-dependent and -independent pathways, respectively. P. aeruginosa TagF interacts with Fha1, suggesting that formation of this complex represents a conserved TagF-mediated regulatory mechanism. Using TagF variants with substitutions of conserved amino acid residues at predicted protein–protein interaction interfaces, we uncovered evidence that the TagF–Fha interaction is critical for TagF-mediated T6SS repression in both bacteria. TagF inhibits T6SS without affecting T6SS protein abundance in A. tumefaciens, but TagF overexpression reduces the protein levels of all analyzed T6SS components in P. aeruginosa. Our results indicate that TagF interacts with Fha, which in turn could impact different stages of T6SS assembly in different bacteria, possibly reflecting an evolutionary divergence in T6SS control.
Collapse
Affiliation(s)
- Jer-Sheng Lin
- From the Institute of Plant and Microbial Biology and
| | - Panayiota Pissaridou
- the Medical Research Council Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hsin-Hui Wu
- the Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan and
| | - Ming-Daw Tsai
- the Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan and
| | - Alain Filloux
- the Medical Research Council Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Erh-Min Lai
- From the Institute of Plant and Microbial Biology and
| |
Collapse
|
42
|
Abstract
Bacterial secretins are outer membrane proteins that provide a path for secreted proteins to access the cell exterior/surface. They are one of the core components of secretion machines and are found in type II and type III secretion systems (T2SS and T3SS, respectively). The secretins comprise giant ring-shaped homo-oligomers whose precise atomic organization was only recently deciphered thanks to spectacular developments in cryo-electron microscopy (cryo-EM) imaging techniques.
Collapse
Affiliation(s)
- Alain Filloux
- Imperial College London, Department of Life Sciences, MRC-CMBI, London, United Kingdom
| | - Romé Voulhoux
- Aix Marseille University, CNRS, IMM, LISM, Marseille, France
| |
Collapse
|
43
|
Dortet L, Lombardi C, Cretin F, Dessen A, Filloux A. Pore-forming activity of the Pseudomonas aeruginosa type III secretion system translocon alters the host epigenome. Nat Microbiol 2018; 3:378-386. [PMID: 29403015 DOI: 10.1038/s41564-018-0109-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022]
Abstract
Recent studies highlight that bacterial pathogens can reprogram target cells by influencing epigenetic factors. The type III secretion system (T3SS) is a bacterial nanomachine that resembles a syringe on the bacterial surface. The T3SS 'needle' delivers translocon proteins into eukaryotic cell membranes, subsequently allowing injection of bacterial effectors into the cytosol. Here we show that Pseudomonas aeruginosa induces early T3SS-dependent dephosphorylation and deacetylation of histone H3 in eukaryotic cells. This is not triggered by any of the P. aeruginosa T3SS effectors, but results from the insertion of the PopB-PopD translocon into the membrane. This suggests that the P. aeruginosa translocon is a genuine T3SS effector acting as a pore-forming toxin. We visualized the translocon plugged into the host cell membrane after the bacterium has left the site of contact, and demonstrate that subsequent ion exchange through this pore is responsible for histone H3 modifications and host cell subversion.
Collapse
Affiliation(s)
- Laurent Dortet
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, UK.,EA7361 'Structure, dynamic, function and expression of broad spectrum β-lactamases', Faculty of Medicine, Paris-Sud University, LabEx Lermit, Le Kremlin-Bicêtre, France
| | - Charlotte Lombardi
- Institut de Biologie Structurale (IBS), University Grenoble-Alpes, CEA, CNRS, Bacterial Pathogenesis Group, Grenoble, France
| | - François Cretin
- University Grenoble-Alpes, Bacterial Pathogenesis and Cellular Responses, CNRS-ERL5261, U1036_S, INSERM, Biosciences and Biotechnology Institute of Grenoble, CEA-Grenoble, Grenoble, France
| | - Andréa Dessen
- Institut de Biologie Structurale (IBS), University Grenoble-Alpes, CEA, CNRS, Bacterial Pathogenesis Group, Grenoble, France.,Brazilian Biosciences National Laboratory (LNBio), CNPEM, São Paulo, Brazil
| | - Alain Filloux
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, London, UK.
| |
Collapse
|
44
|
Salih O, He S, Planamente S, Stach L, MacDonald JT, Manoli E, Scheres SHW, Filloux A, Freemont PS. Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa. Structure 2018; 26:329-336.e3. [PMID: 29307484 PMCID: PMC5807055 DOI: 10.1016/j.str.2017.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/28/2017] [Accepted: 12/06/2017] [Indexed: 01/01/2023]
Abstract
Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form tubules that conserve structural/functional homology with tail sheaths of contractile bacteriophages and pyocins. Here, we used cryoelectron microscopy to solve the structure of the H1-T6SS P. aeruginosa TssB1C1 sheath at 3.3 Å resolution. Our structure allowed us to resolve some features of the T6SS sheath that were not resolved in the Vibrio cholerae VipAB and Francisella tularensis IglAB structures. Comparison with sheath structures from other contractile machines, including T4 phage and R-type pyocins, provides a better understanding of how these systems have conserved similar functions/mechanisms despite evolution. We used the P. aeruginosa R2 pyocin as a structural template to build an atomic model of the TssB1C1 sheath in its extended conformation, allowing us to propose a coiled-spring-like mechanism for T6SS sheath contraction. We solved a T6SS sheath structure from Pseudomonas aeruginosa (group 3 T6SSi) Comparisons between T6SS groups suggest a conserved sheath contraction mechanism Extended-state model led to proposal of a spring-like sheath contraction mechanism
Collapse
Affiliation(s)
- Osman Salih
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Shaoda He
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Sara Planamente
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Lasse Stach
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - James T MacDonald
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Eleni Manoli
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | | | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Paul S Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.
| |
Collapse
|
45
|
Valentini M, Gonzalez D, Mavridou DA, Filloux A. Lifestyle transitions and adaptive pathogenesis of Pseudomonas aeruginosa. Curr Opin Microbiol 2017; 41:15-20. [PMID: 29166621 DOI: 10.1016/j.mib.2017.11.006] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/31/2017] [Accepted: 11/04/2017] [Indexed: 02/06/2023]
Abstract
Pseudomonas aeruginosa acute and chronic infections are of great concern to human health, especially in hospital settings. It is currently assumed that P. aeruginosa has two antagonistic pathogenic strategies that parallel two different lifestyles; free-living cells are predominantly cytotoxic and induce an acute inflammatory reaction, while biofilm-forming communities cause refractory chronic infections. Recent findings suggest that the planktonic-to-sessile transition is a complex, reversible and overall dynamic differentiation process. Here, we examine how the Gac/Rsm regulatory cascade, a key player in this lifestyle switch, endows P. aeruginosa with both a permissive lifecycle in nature and flexible virulence strategy during infection.
Collapse
Affiliation(s)
- Martina Valentini
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom.
| | - Diego Gonzalez
- Département de Microbiologie Fondamentale, Université de Lausanne, CH-1015 Lausanne, Switzerland
| | - Despoina Ai Mavridou
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Alain Filloux
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom.
| |
Collapse
|
46
|
Wen KY, Cameron L, Chappell J, Jensen K, Bell DJ, Kelwick R, Kopniczky M, Davies JC, Filloux A, Freemont PS. A Cell-Free Biosensor for Detecting Quorum Sensing Molecules in P. aeruginosa-Infected Respiratory Samples. ACS Synth Biol 2017; 6:2293-2301. [PMID: 28981256 DOI: 10.1021/acssynbio.7b00219] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Synthetic biology designed cell-free biosensors are a promising new tool for the detection of clinically relevant biomarkers in infectious diseases. Here, we report that a modular DNA-encoded biosensor in cell-free protein expression systems can be used to measure a bacterial biomarker of Pseudomonas aeruginosa infection from human sputum samples. By optimizing the cell-free system and sample extraction, we demonstrate that the quorum sensing molecule 3-oxo-C12-HSL in sputum samples from cystic fibrosis lungs can be quantitatively measured at nanomolar levels using our cell-free biosensor system, and is comparable to LC-MS measurements of the same samples. This study further illustrates the potential of modular cell-free biosensors as rapid, low-cost detection assays that can inform clinical practice.
Collapse
Affiliation(s)
- Ke Yan Wen
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K
| | - Loren Cameron
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London , London SW7 2AZ, U.K
| | - James Chappell
- Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K
| | - Kirsten Jensen
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K.,SynbiCITE, Imperial College London , London SW7 2AZ, U.K
| | - David J Bell
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,SynbiCITE, Imperial College London , London SW7 2AZ, U.K
| | - Richard Kelwick
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K
| | - Margarita Kopniczky
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K
| | - Jane C Davies
- Chronic Suppurative Lung Disease, National Heart and Lung Institute, Imperial College London , London SW7 2AZ, U.K.,Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust , London SW3 6NP, U.K
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London , London SW7 2AZ, U.K
| | - Paul S Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London , London SW7 2AZ, U.K.,Centre for Synthetic Biology and Innovation, Imperial College London , London SW7 2AZ, U.K.,SynbiCITE, Imperial College London , London SW7 2AZ, U.K
| |
Collapse
|
47
|
Bernal P, Llamas MA, Filloux A. Type VI secretion systems in plant-associated bacteria. Environ Microbiol 2017; 20:1-15. [PMID: 29027348 PMCID: PMC5813230 DOI: 10.1111/1462-2920.13956] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [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: 08/26/2017] [Revised: 10/02/2017] [Accepted: 10/05/2017] [Indexed: 11/28/2022]
Abstract
The type VI secretion system (T6SS) is a bacterial nanomachine used to inject effectors into prokaryotic or eukaryotic cells and is thus involved in both host manipulation and interbacterial competition. The T6SS is widespread among Gram‐negative bacteria, mostly within the Proteobacterium Phylum. This secretion system is commonly found in commensal and pathogenic plant‐associated bacteria. Phylogenetic analysis of phytobacterial T6SS clusters shows that they are distributed in the five main clades previously described (group 1–5). The even distribution of the system among commensal and pathogenic phytobacteria suggests that the T6SS provides fitness and colonization advantages in planta and that the role of the T6SS is not restricted to virulence. This manuscript reviews the phylogeny and biological roles of the T6SS in plant‐associated bacteria, highlighting a remarkable diversity both in terms of mechanism and function.
Collapse
Affiliation(s)
- Patricia Bernal
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Flowers Building, 1st floor South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Flowers Building, 1st floor South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| |
Collapse
|
48
|
Karampatzakis A, Song CZ, Allsopp LP, Filloux A, Rice SA, Cohen Y, Wohland T, Török P. Probing the internal micromechanical properties of Pseudomonas aeruginosa biofilms by Brillouin imaging. NPJ Biofilms Microbiomes 2017; 3:20. [PMID: 28900539 PMCID: PMC5591272 DOI: 10.1038/s41522-017-0028-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 04/12/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 12/17/2022] Open
Abstract
Biofilms are organised aggregates of bacteria that adhere to each other or surfaces. The matrix of extracellular polymeric substances that holds the cells together provides the mechanical stability of the biofilm. In this study, we have applied Brillouin microscopy, a technique that is capable of measuring mechanical properties of specimens on a micrometre scale based on the shift in frequency of light incident upon a sample due to thermal fluctuations, to investigate the micromechanical properties of an active, live Pseudomonas aeruginosa biofilm. Using this non-contact and label-free technique, we have extracted information about the internal stiffness of biofilms under continuous flow. No correlation with colony size was found when comparing the averages of Brillouin shifts of two-dimensional cross-sections of randomly selected colonies. However, when focusing on single colonies, we observed two distinct spatial patterns: in smaller colonies, stiffness increased towards their interior, indicating a more compact structure of the centre of the colony, whereas, larger (over 45 μm) colonies were found to have less stiff interiors. A specialized microscopy technique can monitor biofilm stiffness in a non-destructive manner, yielding insights into biofilm structure and development. The technique, called Brillouin imaging, uses changes in the frequency of light interacting with a substance to reveal fine detail about the material’s mechanical properties. Peter Török and colleagues at Imperial College London, with co-workers in Singapore, used Brillouin imaging to study biofilms of Pseudomonas aeruginosa bacteria at different stages in their life cycle. In young colonies, stiffness increased towards the interior of the biofilm, while mature colonies had less stiff interiors. The older biofilms may therefore have hollow interiors or may have been moving towards a phase of bacterial dispersal from the biofilm state. This non-disruptive method to study mechanical variations within and between living biofilms may help efforts to combat biofilms in clinical, environmental and industrial situations.
Collapse
Affiliation(s)
- A Karampatzakis
- Centre for BioImaging Sciences, National University of Singapore, Singapore, 117557 Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 117557 Singapore.,Blackett Laboratory, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2BZ United Kingdom
| | - C Z Song
- Blackett Laboratory, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2BZ United Kingdom
| | - L P Allsopp
- Imperial College London, Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, South Kensington Campus, Flowers Building, SW7 2AZ London, United Kingdom
| | - A Filloux
- Imperial College London, Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, South Kensington Campus, Flowers Building, SW7 2AZ London, United Kingdom
| | - S A Rice
- Singapore Centre for Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University Singapore, Singapore, 637551 Singapore
| | - Y Cohen
- Singapore Centre for Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University Singapore, Singapore, 637551 Singapore
| | - T Wohland
- Centre for BioImaging Sciences, National University of Singapore, Singapore, 117557 Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 117557 Singapore.,Department of Biological Sciences and Department of Chemistry, National University of Singapore, Singapore, 117346 Singapore
| | - P Török
- Blackett Laboratory, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2BZ United Kingdom
| |
Collapse
|
49
|
Heeb S, Càmara M, Filloux A, Williams P. Professor Dieter Haas (1945-2017). FEMS Microbiol Rev 2017; 41:597-598. [PMID: 28961757 DOI: 10.1093/femsre/fux040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/19/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Stephan Heeb
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Miguel Càmara
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection and Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Paul Williams
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| |
Collapse
|
50
|
Smith WD, Bardin E, Cameron L, Edmondson CL, Farrant KV, Martin I, Murphy RA, Soren O, Turnbull AR, Wierre-Gore N, Alton EW, Bundy JG, Bush A, Connett GJ, Faust SN, Filloux A, Freemont PS, Jones AL, Takats Z, Webb JS, Williams HD, Davies JC. Current and future therapies for Pseudomonas aeruginosa infection in patients with cystic fibrosis. FEMS Microbiol Lett 2017; 364:3868374. [DOI: 10.1093/femsle/fnx121] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/12/2017] [Indexed: 12/12/2022] Open
|