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Birk MS, Ahmed-Begrich R, Tran S, Elsholz AKW, Frese CK, Charpentier E. Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation. mSystems 2021; 6:e0021521. [PMID: 34342529 PMCID: PMC8407217 DOI: 10.1128/msystems.00215-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/14/2021] [Indexed: 12/13/2022] Open
Abstract
The cellular proteome comprises all proteins expressed at a given time and defines an organism's phenotype under specific growth conditions. The proteome is shaped and remodeled by both protein synthesis and protein degradation. Here, we developed a new method which combines metabolic and chemical isobaric peptide labeling to simultaneously determine the time-resolved protein decay and de novo synthesis in an intracellular human pathogen. We showcase this method by investigating the Listeria monocytogenes proteome in the presence and absence of the AAA+ chaperone protein ClpC. ClpC associates with the peptidase ClpP to form an ATP-dependent protease complex and has been shown to play a role in virulence development in L. monocytogenes. However, the mechanism by which ClpC is involved in the survival and proliferation of intracellular L. monocytogenes remains elusive. Employing this new method, we observed extensive proteome remodeling in L. monocytogenes upon interaction with the host, supporting the hypothesis that ClpC-dependent protein degradation is required to initiate bacterial adaptation mechanisms. We identified more than 100 putative ClpC target proteins through their stabilization in a clpC deletion strain. Beyond the identification of direct targets, we also observed indirect effects of the clpC deletion on the protein abundance in diverse cellular and metabolic pathways, such as iron acquisition and flagellar assembly. Overall, our data highlight the crucial role of ClpC for L. monocytogenes adaptation to the host environment through proteome remodeling. IMPORTANCE Survival and proliferation of pathogenic bacteria inside the host depend on their ability to adapt to the changing environment. Profiling the underlying changes on the bacterial proteome level during the infection process is important to gain a better understanding of the pathogenesis and the host-dependent adaptation processes. The cellular protein abundance is governed by the interplay between protein synthesis and decay. The direct readout of these events during infection can be accomplished using pulsed stable-isotope labeling by amino acids in cell culture (SILAC). Combining this approach with tandem-mass-tag (TMT) labeling enabled multiplexed and time-resolved bacterial proteome quantification during infection. Here, we applied this integrated approach to investigate protein turnover during the temporal progression of adaptation of the human pathogen L. monocytogenes to its host on a system-wide scale. Our experimental approach can easily be transferred to probe the proteome remodeling in other bacteria under a variety of perturbations.
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Affiliation(s)
- Marlène S. Birk
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Stefan Tran
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
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Kulén M, Lindgren M, Hansen S, Cairns AG, Grundström C, Begum A, van der Lingen I, Brännström K, Hall M, Sauer UH, Johansson J, Sauer-Eriksson AE, Almqvist F. Structure-Based Design of Inhibitors Targeting PrfA, the Master Virulence Regulator of Listeria monocytogenes. J Med Chem 2018; 61:4165-4175. [PMID: 29667825 DOI: 10.1021/acs.jmedchem.8b00289] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Listeria monocytogenes is a bacterial pathogen that controls much of its virulence through the transcriptional regulator PrfA. In this study, we describe structure-guided design and synthesis of a set of PrfA inhibitors based on ring-fused 2-pyridone heterocycles. Our most effective compound decreased virulence factor expression, reduced bacterial uptake into eukaryotic cells, and improved survival of chicken embryos infected with L. monocytogenes compared to previously identified compounds. Crystal structures identified an intraprotein "tunnel" as the main inhibitor binding site (AI), where the compounds participate in an extensive hydrophobic network that restricts the protein's ability to form functional DNA-binding helix-turn-helix (HTH) motifs. Our studies also revealed a hitherto unsuspected structural plasticity of the HTH motif. In conclusion, we have designed 2-pyridone analogues that function as site-AI selective PrfA inhibitors with potent antivirulence properties.
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Good JAD, Andersson C, Hansen S, Wall J, Krishnan KS, Begum A, Grundström C, Niemiec MS, Vaitkevicius K, Chorell E, Wittung-Stafshede P, Sauer UH, Sauer-Eriksson AE, Almqvist F, Johansson J. Attenuating Listeria monocytogenes Virulence by Targeting the Regulatory Protein PrfA. Cell Chem Biol 2016; 23:404-14. [PMID: 26991105 PMCID: PMC4802734 DOI: 10.1016/j.chembiol.2016.02.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 01/27/2016] [Accepted: 02/19/2016] [Indexed: 01/28/2023]
Abstract
The transcriptional activator PrfA, a member of the Crp/Fnr family, controls the expression of some key virulence factors necessary for infection by the human bacterial pathogen Listeria monocytogenes. Phenotypic screening identified ring-fused 2-pyridone molecules that at low micromolar concentrations attenuate L. monocytogenes cellular uptake by reducing the expression of virulence genes. These inhibitors bind the transcriptional regulator PrfA and decrease its affinity for the consensus DNA-binding site. Structural characterization of this interaction revealed that one of the ring-fused 2-pyridones, compound 1, binds at two separate sites on the protein: one within a hydrophobic pocket or tunnel, located between the C- and N-terminal domains of PrfA, and the second in the vicinity of the DNA-binding helix-turn-helix motif. At both sites the compound interacts with residues important for PrfA activation and helix-turn-helix formation. Ring-fused 2-pyridones represent a new class of chemical probes for studying virulence in L. monocytogenes. Inhibitors of L. monocytogenes infectivity reduce virulence gene expression Binding of inhibitor to the PrfA regulator reduces affinity for its DNA motif First crystal structure of a Crp family regulator with an inhibitor Provides rationale for screening with Crp family transcriptional regulators
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Affiliation(s)
- James A D Good
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | - Christopher Andersson
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Sabine Hansen
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Jessica Wall
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - K Syam Krishnan
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | - Afshan Begum
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | - Christin Grundström
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | | | - Karolis Vaitkevicius
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | | | - Uwe H Sauer
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
| | - A Elisabeth Sauer-Eriksson
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden.
| | - Fredrik Almqvist
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden.
| | - Jörgen Johansson
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden.
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Quereda JJ, García-Del Portillo F, Pucciarelli MG. Listeria monocytogenes remodels the cell surface in the blood-stage. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:641-648. [PMID: 27085096 DOI: 10.1111/1758-2229.12416] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
After crossing the intestinal barrier, the bacterial pathogen Listeria monocytogenes disseminates via the blood to the liver, spleen, brain and placenta. Transcriptomic studies have shown that L. monocytogenes changes expression of many genes during this blood-stage. However, no comparable data at the protein level are known. As main interactors with the environment, we focused in surface proteins produced by L. monocytogenes in an ex vivo bovine blood model. Bacteria exposed to blood alter selectively the amount of several surface proteins compared with bacteria grown in laboratory media. Increased levels were detected for Lmo0514 and Internalin A, two surface proteins covalently bound to peptidoglycan, and the moonlighting protein alcohol-acetaldehyde dehydrogenase, also known as Lap for 'Listeria adhesion protein'. Lmo0514, induced by L. monocytogenes inside epithelial cells, is required for survival in plasma and for virulence in mice at early infection stages. Lmo0514 is also important to cope with low pH stress. By contrast, L. monocytogenes down-regulates other surface proteins following exposure to blood and plasma such as Internalin I. These data provide evidence for remodelling of the L. monocytogenes cell surface during the blood-stage, which it could facilitate pathogen dissemination to deep organs.
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Affiliation(s)
- Juan J Quereda
- Laboratory of Intracellular Bacterial Pathogens, Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Francisco García-Del Portillo
- Laboratory of Intracellular Bacterial Pathogens, Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - M Graciela Pucciarelli
- Laboratory of Intracellular Bacterial Pathogens, Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Centro de Biología Molecular 'Severo Ochoa' (CBMSO-CSIC), Departamento de Biología Molecular, Universidad Autónoma de Madrid, Spain
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Hernández SB, Cava F, Pucciarelli MG, García-Del Portillo F, de Pedro MA, Casadesús J. Bile-induced peptidoglycan remodelling in Salmonella enterica. Environ Microbiol 2014; 17:1081-9. [PMID: 24762004 DOI: 10.1111/1462-2920.12491] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/11/2014] [Accepted: 04/20/2014] [Indexed: 02/02/2023]
Abstract
Changes in the peptidoglycan (PG) structure of Salmonella enterica are detected in the presence of a sublethal concentration of sodium deoxycholate (DOC): (i) lower proportions of Braun lipoprotein (Lpp)-bound muropeptides; (ii) reduced levels of muropeptides cross-linked by L(meso)-diaminopimelyl-D(meso)-diaminopimelic acid (L-D) peptide bridges (3-3 cross-links). Similar structural changes are found in S. enterica cultures adapted to grow in the presence of a lethal concentration of DOC, suggesting that reduced anchoring of Braun protein to PG and low occurrence of 3-3 cross-links may increase S. enterica resistance to bile. This view is further supported by additional observations: (i) A triple mutant lacking L,D-transpeptidases YbiS, ErfK, and YcfS, which does not contain Lpp anchored to PG, is hyper-resistant to bile; (ii) enhanced 3-3 cross-linking upon overexpression of YnhG transpeptidase causes a decrease in bile resistance. These observations suggest that remodelling of the cell wall may be added to the list of adaptive responses that permit survival of S. enterica in the presence of bile.
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Affiliation(s)
- Sara B Hernández
- Facultad de Biología, Departamento de Genética, Universidad de Sevilla, Apartado 1095, 41080, Sevilla, Spain
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Carvalho F, Sousa S, Cabanes D. How Listeria monocytogenes organizes its surface for virulence. Front Cell Infect Microbiol 2014; 4:48. [PMID: 24809022 PMCID: PMC4010754 DOI: 10.3389/fcimb.2014.00048] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/02/2014] [Indexed: 02/04/2023] Open
Abstract
Listeria monocytogenes is a Gram-positive pathogen responsible for the manifestation of human listeriosis, an opportunistic foodborne disease with an associated high mortality rate. The key to the pathogenesis of listeriosis is the capacity of this bacterium to trigger its internalization by non-phagocytic cells and to survive and even replicate within phagocytes. The arsenal of virulence proteins deployed by L. monocytogenes to successfully promote the invasion and infection of host cells has been progressively unveiled over the past decades. A large majority of them is located at the cell envelope, which provides an interface for the establishment of close interactions between these bacterial factors and their host targets. Along the multistep pathways carrying these virulence proteins from the inner side of the cytoplasmic membrane to their cell envelope destination, a multiplicity of auxiliary proteins must act on the immature polypeptides to ensure that they not only maturate into fully functional effectors but also are placed or guided to their correct position in the bacterial surface. As the major scaffold for surface proteins, the cell wall and its metabolism are critical elements in listerial virulence. Conversely, the crucial physical support and protection provided by this structure make it an ideal target for the host immune system. Therefore, mechanisms involving fine modifications of cell envelope components are activated by L. monocytogenes to render it less recognizable by the innate immunity sensors or more resistant to the activity of antimicrobial effectors. This review provides a state-of-the-art compilation of the mechanisms used by L. monocytogenes to organize its surface for virulence, with special focus on those proteins that work “behind the frontline”, either supporting virulence effectors or ensuring the survival of the bacterium within its host.
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Affiliation(s)
- Filipe Carvalho
- Group of Molecular Microbiology, Unit of Infection and Immunity, Instituto de Biologia Molecular e Celular, University of Porto Porto, Portugal
| | - Sandra Sousa
- Group of Molecular Microbiology, Unit of Infection and Immunity, Instituto de Biologia Molecular e Celular, University of Porto Porto, Portugal
| | - Didier Cabanes
- Group of Molecular Microbiology, Unit of Infection and Immunity, Instituto de Biologia Molecular e Celular, University of Porto Porto, Portugal
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Mariscotti JF, Quereda JJ, García-Del Portillo F, Pucciarelli MG. The Listeria monocytogenes LPXTG surface protein Lmo1413 is an invasin with capacity to bind mucin. Int J Med Microbiol 2014; 304:393-404. [PMID: 24572033 DOI: 10.1016/j.ijmm.2014.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/14/2014] [Accepted: 01/19/2014] [Indexed: 01/14/2023] Open
Abstract
Many Gram-positive bacterial pathogens use surface proteins covalently anchored to the peptidoglycan to cause disease. Bacteria of the genus Listeria have the largest number of surface proteins of this family. Every Listeria genome sequenced to date contains more than forty genes encoding surface proteins bearing anchoring-domains with an LPXTG motif that is recognized for covalent linkage to the peptidoglycan. About one-third of these proteins are present exclusively in pathogenic Listeria species, with some of them acting as adhesins or invasins that promote bacterial entry into eukaryotic cells. Here, we investigated two LPXTG surface proteins of the pathogen L. monocytogenes, Lmo1413 and Lmo2085, of unknown function and absent in non-pathogenic Listeria species. Lack of these two proteins does not affect bacterial adhesion or invasion of host cells using in vitro infection models. However, expression of Lmo1413 promotes entry of the non-invasive species L. innocua into non-phagocytic host cells, an effect not observed with Lmo2085. Moreover, overproduction of Lmo1413, but not Lmo2085, increases the invasion rate in non-phagocytic eukaryotic cells of an L. monocytogenes mutant deficient in the acting-binding protein ActA. Unexpectedly, production of full-length Lmo1413 and InlA exhibited opposite trends in a high percentage of L. monocytogenes isolates obtained from different sources. The idea of Lmo1413 playing a role as a new auxiliary invasin was also sustained by assays revealing that purified Lmo1413 binds to mucin via its MucBP domains. Taken together, these data indicate that Lmo1413, which we rename LmiA, for Listeria-mucin-binding invasin-A, may promote interaction of bacteria with adhesive host protective components and, in this manner, facilitate bacterial entry.
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Affiliation(s)
- Javier F Mariscotti
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Juan J Quereda
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Francisco García-Del Portillo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - M Graciela Pucciarelli
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049 Madrid, Spain; Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Biología Molecular 'Severo Ochoa'-Consejo Superior de Investigaciones Científicas (CBMSO-CSIC), 28049 Madrid, Spain.
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Ammendolia MG, Iosi F, De Berardis B, Guccione G, Superti F, Conte MP, Longhi C. Listeria monocytogenes behaviour in presence of non-UV-irradiated titanium dioxide nanoparticles. PLoS One 2014; 9:e84986. [PMID: 24416327 PMCID: PMC3887020 DOI: 10.1371/journal.pone.0084986] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/27/2013] [Indexed: 01/04/2023] Open
Abstract
Listeria monocytogenes is the agent of listeriosis, a food-borne disease. It represents a serious problem for the food industry because of its environmental persistence mainly due to its ability to form biofilm on a variety of surfaces. Microrganisms attached on the surfaces are a potential source of contamination for environment and animals and humans. Titanium dioxide nanoparticles (TiO2 NPs) are used in food industry in a variety of products and it was reported that daily exposure to these nanomaterials is very high. Anti-listerial activity of TiO2 NPs was investigated only with UV-irradiated nanomaterials, based on generation of reactive oxigen species (ROS) with antibacterial effect after UV exposure. Since both Listeria monocytogenes and TiO2 NPs are veicolated with foods, this study explores the interaction between Listeria monocytogenes and non UV-irradiated TiO2 NPs, with special focus on biofilm formation and intestinal cell interaction. Scanning electron microscopy and quantitative measurements of biofilm mass indicate that NPs influence both production and structural architecture of listerial biofilm. Moreover, TiO2 NPs show to interfere with bacterial interaction to intestinal cells. Increased biofilm production due to TiO2 NPs exposure may favour bacterial survival in environment and its transmission to animal and human hosts.
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Affiliation(s)
| | - Francesca Iosi
- Department of Technology and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Barbara De Berardis
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Giuliana Guccione
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, Rome, Italy
| | - Fabiana Superti
- Department of Technology and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Pia Conte
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, Rome, Italy
| | - Catia Longhi
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, Rome, Italy
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