1
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Price CTD, Hanford HE, Al-Quadan T, Santic M, Shin CJ, Da'as MSJ, Abu Kwaik Y. Amoebae as training grounds for microbial pathogens. mBio 2024:e0082724. [PMID: 38975782 DOI: 10.1128/mbio.00827-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.
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Affiliation(s)
- Christopher T D Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Hannah E Hanford
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Tasneem Al-Quadan
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | | | - Cheon J Shin
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Manal S J Da'as
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, Kentucky, USA
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2
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Barbachowska M, Arimondo PB. To target or not to target? The role of DNA and histone methylation in bacterial infections. Epigenetics 2023; 18:2242689. [PMID: 37731322 PMCID: PMC10515666 DOI: 10.1080/15592294.2023.2242689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/25/2023] [Indexed: 09/22/2023] Open
Abstract
Epigenetics describes chemical modifications of the genome that do not alter DNA sequence but participate in the regulation of gene expression and cellular processes such as proliferation, division, and differentiation of eukaryotic cell. Disruption of the epigenome pattern in a human cell is associated with different diseases, including infectious diseases. During infection pathogens induce epigenetic modifications in the host cell. This can occur by controlling expression of genes involved in immune response. That enables bacterial survival and replication within the host and evasion of the immune response. Methylation is an example of epigenetic modification that occurs on DNA and histones. Reasoning that DNA and histone methylation of human host cells plays a crucial role during pathogenesis, these modifications are promising targets for the development of alternative treatment strategies in infectious diseases. Here, we discuss the role of DNA and histone methyltransferases in human host cell upon bacterial infections. We further hypothesize that compounds targeting methyltransferases are tools to study epigenetics in the context of host-pathogen interactions and can open new avenues for the treatment of bacterial infections.
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Affiliation(s)
- Magdalena Barbachowska
- Institut Pasteur, Université Paris Cité, CNRS UMR n°3523 Chem4Life, Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Paris, France
- Universite Paris Cité, Ecole Doctorale MTCI, Paris, France
- Institut Pasteur, Pasteur- Paris University (PPU)- Oxford International Doctoral Program, Paris, France
| | - Paola B. Arimondo
- Institut Pasteur, Université Paris Cité, CNRS UMR n°3523 Chem4Life, Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Paris, France
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3
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Scheithauer L, Karagöz MS, Mayer BE, Steinert M. Protein sociology of ProA, Mip and other secreted virulence factors at the Legionella pneumophila surface. Front Cell Infect Microbiol 2023; 13:1140688. [PMID: 36936764 PMCID: PMC10017501 DOI: 10.3389/fcimb.2023.1140688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
The pathogenicity of L. pneumophila, the causative agent of Legionnaires' disease, depends on an arsenal of interacting proteins. Here we describe how surface-associated and secreted virulence factors of this pathogen interact with each other or target extra- and intracellular host proteins resulting in host cell manipulation and tissue colonization. Since progress of computational methods like AlphaFold, molecular dynamics simulation, and docking allows to predict, analyze and evaluate experimental proteomic and interactomic data, we describe how the combination of these approaches generated new insights into the multifaceted "protein sociology" of the zinc metalloprotease ProA and the peptidyl-prolyl cis/trans isomerase Mip (macrophage infectivity potentiator). Both virulence factors of L. pneumophila interact with numerous proteins including bacterial flagellin (FlaA) and host collagen, and play important roles in virulence regulation, host tissue degradation and immune evasion. The recent progress in protein-ligand analyses of virulence factors suggests that machine learning will also have a beneficial impact in early stages of drug discovery.
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Affiliation(s)
- Lina Scheithauer
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Mustafa Safa Karagöz
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Benjamin E. Mayer
- Computational Biology & Simulation, Technische Universität Darmstadt, Darmstadt, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
- *Correspondence: Michael Steinert,
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4
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Herbel SM, Moyon L, Christ M, Elsayed EM, Caffrey BE, Malmsheimer S, Grin I, Hoffmann K, Surmann K, Blankenburg S, Jung AL, Herkt CE, Borsò M, Bozdag B, Imhof A, Becker A, Wagner S, Bange G, Völker U, Bertrams W, Marsico A, Schmeck B. Screening for eukaryotic motifs in Legionella pneumophila reveals Smh1 as bacterial deacetylase of host histones. Virulence 2022; 13:2042-2058. [PMID: 36411449 PMCID: PMC9704406 DOI: 10.1080/21505594.2022.2149973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Legionella pneumophila (L.p.) is a bacterial pathogen which is a common causative agent of pneumonia. In humans, it infects alveolar macrophages and transfers hundreds of virulence factors that interfere with cellular signalling pathways and the transcriptomic landscape to sustain its own replication. By this interaction, it has acquired eukaryote-like protein motifs by gene transfer events that partake in the pathogenicity of Legionella. In a computational screening approach for eukaryotic motifs in the transcriptome of Legionella, we identified the L.p. strain Corby protein ABQ55614 as putative histone-deacetylase and named it "suppressing modifier of histones 1" (Smh1). During infection, Smh1 is translocated from the Legionella vacuole into the host cytosol. When expressed in human macrophage THP-1 cells, Smh1 was localized predominantly in the nucleus, leading to broad histone H3 and H4 deacetylation, blunted expression of a large number of genes (e.g. IL-1β and IL-8), and fostered intracellular bacterial replication. L.p. with a Smh1 knockdown grew normally in media but showed a slight growth defect inside the host cell. Furthermore, Smh1 showed a very potent histone deacetylation activity in vitro, e.g. at H3K14, that could be inhibited by targeted mutation of the putative catalytic center inferred by analogy with eukaryotic HDAC8, and with the deacetylase inhibitor trichostatin A. In summary, Smh1 displays functional homology with class I/II type HDACs. We identified Smh1 as a new Legionella virulence factor with a eukaryote-like histone-deacetylase activity that moderates host gene expression and might pave the way for further histone modifications.IMPORTANCELegionella pneumophila (L.p.) is a prominent bacterial pathogen, which is a common causative agent of pneumonia. In order to survive inside the host cell, the human macrophage, it profoundly interacts with host cell processes to advance its own replication. In this study, we identify a bacterial factor, Smh1, with yet unknown function as a host histone deacetylase. The activity of this factor in the host cell leads to attenuated gene expression and increased intracellular bacterial replication.
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Affiliation(s)
- Stefanie M. Herbel
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Lambert Moyon
- Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marvin Christ
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Eslam M. Elsayed
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany,Department of Biology, Philipps-Universität Marburg, Marburg, Germany,Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Brian E. Caffrey
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Silke Malmsheimer
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Iwan Grin
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Kerstin Hoffmann
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Kristin Surmann
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Sascha Blankenburg
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Anna Lena Jung
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Christina E. Herkt
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Marco Borsò
- Zentrallabor für Proteinanalytik, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Planegg-Martinsried
| | - Beyza Bozdag
- Zentrallabor für Proteinanalytik, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Planegg-Martinsried
| | - Axel Imhof
- Zentrallabor für Proteinanalytik, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Planegg-Martinsried
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany,Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Samuel Wagner
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany,German Center for Infection Research (DZIF), Partner-site Tübingen, Tübingen, Germany
| | - Gert Bange
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Wilhelm Bertrams
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany,Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, Philipps-University, Member of the German Center for Lung Research (DZL), Marburg, Germany,Institute for Lung Health (ILH), Justus-Liebig-University, Giessen, Germany,Member of the German Center for Infectious Disease Research (DZIF), Marburg, Germany,CONTACT Bernd Schmeck
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5
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Lockwood DC, Amin H, Costa TRD, Schroeder GN. The Legionella pneumophila Dot/Icm type IV secretion system and its effectors. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35639581 DOI: 10.1099/mic.0.001187] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To prevail in the interaction with eukaryotic hosts, many bacterial pathogens use protein secretion systems to release virulence factors at the host–pathogen interface and/or deliver them directly into host cells. An outstanding example of the complexity and sophistication of secretion systems and the diversity of their protein substrates, effectors, is the Defective in organelle trafficking/Intracellular multiplication (Dot/Icm) Type IVB secretion system (T4BSS) of
Legionella pneumophila
and related species.
Legionella
species are facultative intracellular pathogens of environmental protozoa and opportunistic human respiratory pathogens. The Dot/Icm T4BSS translocates an exceptionally large number of effectors, more than 300 per
L. pneumophila
strain, and is essential for evasion of phagolysosomal degradation and exploitation of protozoa and human macrophages as replicative niches. Recent technological advancements in the imaging of large protein complexes have provided new insight into the architecture of the T4BSS and allowed us to propose models for the transport mechanism. At the same time, significant progress has been made in assigning functions to about a third of
L. pneumophila
effectors, discovering unprecedented new enzymatic activities and concepts of host subversion. In this review, we describe the current knowledge of the workings of the Dot/Icm T4BSS machinery and provide an overview of the activities and functions of the to-date characterized effectors in the interaction of
L. pneumophila
with host cells.
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Affiliation(s)
- Daniel C Lockwood
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland, UK
| | - Himani Amin
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Tiago R D Costa
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Gunnar N Schroeder
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland, UK
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6
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Sui J, Qiao W, Xiang X, Luo Y. Epigenetic Changes in Mycobacterium tuberculosis and its Host Provide Potential Targets or Biomarkers for Drug Discovery and Clinical Diagnosis. Pharmacol Res 2022; 179:106195. [DOI: 10.1016/j.phrs.2022.106195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/14/2022] [Accepted: 03/25/2022] [Indexed: 11/26/2022]
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7
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Weirich S, Jeltsch A. Specificity Analysis of Protein Methyltransferases and Discovery of Novel Substrates Using SPOT Peptide Arrays. Methods Mol Biol 2022; 2529:313-325. [PMID: 35733022 DOI: 10.1007/978-1-0716-2481-4_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Posttranslational methylation of amino acid side chains in proteins mainly occurs on lysine, arginine, glutamine, and histidine residues. It is introduced by different protein methyltransferases (PMTs) and regulates many aspects of protein function including stability, activity, localization, and protein/protein interactions. Although the biological effects of PMTs are mediated by their methylation substrates, the full substrate spectrum of most PMTs is not known. For many PMTs, their activity on a particular potential substrate depends, among other factors, on the peptide sequence containing the target residue for methylation. In this protocol, we describe the application of SPOT peptide arrays to investigate the substrate specificity of PMTs and identify novel substrates. Methylation of SPOT peptide arrays makes it possible to study the methylation of many different peptides in one experiment at reasonable costs and thereby provides detailed information about the specificity of the PMT under investigation. In these experiments, a known substrate sequence is used as template to design a SPOT peptide array containing peptides with single amino acid exchanges at all positions of the sequence. Methylation of the array with the PMT provides detailed preferences for each amino acid at each position in the substrate sequence, yielding a substrate sequence specificity profile. This information can then be used to identify novel potential PMT substrates by in silico data base searches. Methylation of novel substrate candidates can be validated in SPOT arrays at peptide level, followed by validation at protein level in vitro and in cells.
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Affiliation(s)
- Sara Weirich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.
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8
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Abstract
Through coevolution with host cells, microorganisms have acquired mechanisms to avoid the detection by the host surveillance system and to use the cell's supplies to establish themselves. Indeed, certain pathogens have evolved proteins that imitate specific eukaryotic cell proteins, allowing them to manipulate host pathways, a phenomenon termed molecular mimicry. Bacterial "eukaryotic-like proteins" are a remarkable example of molecular mimicry. They are defined as proteins that strongly resemble eukaryotic proteins or that carry domains that are predominantly present in eukaryotes and that are generally absent from prokaryotes. The widest diversity of eukaryotic-like proteins known to date can be found in members of the bacterial genus Legionella, some of which cause a severe pneumonia in humans. The characterization of a number of these proteins shed light on their importance during infection. The subsequent identification of eukaryotic-like genes in the genomes of other amoeba-associated bacteria and bacterial symbionts suggested that eukaryotic-like proteins are a common means of bacterial evasion and communication, shaped by the continuous interactions between bacteria and their protozoan hosts. In this review, we discuss the concept of molecular mimicry using Legionella as an example and show that eukaryotic-like proteins effectively manipulate host cell pathways. The study of the function and evolution of such proteins is an exciting field of research that is leading us toward a better understanding of the complex world of bacterium-host interactions. Ultimately, this knowledge will teach us how host pathways are manipulated and how infections may possibly be tackled.
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9
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Schuhmacher MK, Beldar S, Khella MS, Bröhm A, Ludwig J, Tempel W, Weirich S, Min J, Jeltsch A. Sequence specificity analysis of the SETD2 protein lysine methyltransferase and discovery of a SETD2 super-substrate. Commun Biol 2020; 3:511. [PMID: 32939018 PMCID: PMC7495481 DOI: 10.1038/s42003-020-01223-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
SETD2 catalyzes methylation at lysine 36 of histone H3 and it has many disease connections. We investigated the substrate sequence specificity of SETD2 and identified nine additional peptide and one protein (FBN1) substrates. Our data showed that SETD2 strongly prefers amino acids different from those in the H3K36 sequence at several positions of its specificity profile. Based on this, we designed an optimized super-substrate containing four amino acid exchanges and show by quantitative methylation assays with SETD2 that the super-substrate peptide is methylated about 290-fold more efficiently than the H3K36 peptide. Protein methylation studies confirmed very strong SETD2 methylation of the super-substrate in vitro and in cells. We solved the structure of SETD2 with bound super-substrate peptide containing a target lysine to methionine mutation, which revealed better interactions involving three of the substituted residues. Our data illustrate that substrate sequence design can strongly increase the activity of protein lysine methyltransferases. Schuhmacher, Beldar et al. design a super-substrate peptide based on the substrate sequence specificity of the SETD2 protein lysine methyltransferase. SETD2 methylates this super-substrate 290-fold more efficiently than the original H3K36 peptide. This study illustrates that substrate sequence design can improve the activity of protein lysine methyltransferases.
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Affiliation(s)
- Maren Kirstin Schuhmacher
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Serap Beldar
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Mina S Khella
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.,Biochemistry Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo, 11566, Egypt
| | - Alexander Bröhm
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jan Ludwig
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Sara Weirich
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada.
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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10
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Bacterial Factors Targeting the Nucleus: The Growing Family of Nucleomodulins. Toxins (Basel) 2020; 12:toxins12040220. [PMID: 32244550 PMCID: PMC7232420 DOI: 10.3390/toxins12040220] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/23/2020] [Accepted: 03/29/2020] [Indexed: 12/18/2022] Open
Abstract
Pathogenic bacteria secrete a variety of proteins that manipulate host cell function by targeting components of the plasma membrane, cytosol, or organelles. In the last decade, several studies identified bacterial factors acting within the nucleus on gene expression or other nuclear processes, which has led to the emergence of a new family of effectors called “nucleomodulins”. In human and animal pathogens, Listeria monocytogenes for Gram-positive bacteria and Anaplasma phagocytophilum, Ehrlichia chaffeensis, Chlamydia trachomatis, Legionella pneumophila, Shigella flexneri, and Escherichia coli for Gram-negative bacteria, have led to pioneering discoveries. In this review, we present these paradigms and detail various mechanisms and core elements (e.g., DNA, histones, epigenetic regulators, transcription or splicing factors, signaling proteins) targeted by nucleomodulins. We particularly focus on nucleomodulins interacting with epifactors, such as LntA of Listeria and ankyrin repeat- or tandem repeat-containing effectors of Rickettsiales, and nucleomodulins from various bacterial species acting as post-translational modification enzymes. The study of bacterial nucleomodulins not only generates important knowledge about the control of host responses by microbes but also creates new tools to decipher the dynamic regulations that occur in the nucleus. This research also has potential applications in the field of biotechnology. Finally, this raises questions about the epigenetic effects of infectious diseases.
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11
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Revealing eukaryotic histone-modifying mechanisms through bacterial infection. Semin Immunopathol 2020; 42:201-213. [DOI: 10.1007/s00281-019-00778-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/27/2019] [Indexed: 12/12/2022]
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12
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Weirich S, Schuhmacher MK, Kudithipudi S, Lungu C, Ferguson AD, Jeltsch A. Analysis of the Substrate Specificity of the SMYD2 Protein Lysine Methyltransferase and Discovery of Novel Non-Histone Substrates. Chembiochem 2019; 21:256-264. [PMID: 31612581 PMCID: PMC7003753 DOI: 10.1002/cbic.201900582] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Indexed: 12/13/2022]
Abstract
The SMYD2 protein lysine methyltransferase methylates various histone and non‐histone proteins and is overexpressed in several cancers. Using peptide arrays, we investigated the substrate specificity of the enzyme, revealing a recognition of leucine (or weaker phenylalanine) at the −1 peptide site and disfavor of acidic residues at the +1 to +3 sites. Using this motif, novel SMYD2 peptide substrates were identified, leading to the discovery of 32 novel peptide substrates with a validated target site. Among them, 19 were previously reported to be methylated at the target lysine in human cells, strongly suggesting that SMYD2 is the protein lysine methyltransferase responsible for this activity. Methylation of some of the novel peptide substrates was tested at the protein level, leading to the identification of 14 novel protein substrates of SMYD2, six of which were more strongly methylated than p53, the best SMYD2 substrate described so far. The novel SMYD2 substrate proteins are involved in diverse biological processes such as chromatin regulation, transcription, and intracellular signaling. The results of our study provide a fundament for future investigations into the role of this important enzyme in normal development and cancer.
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Affiliation(s)
- Sara Weirich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Maren Kirstin Schuhmacher
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Srikanth Kudithipudi
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Cristiana Lungu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | | | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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13
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Best AM, Abu Kwaik Y. Evasion of phagotrophic predation by protist hosts and innate immunity of metazoan hosts by Legionella pneumophila. Cell Microbiol 2018; 21:e12971. [PMID: 30370624 DOI: 10.1111/cmi.12971] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/08/2018] [Accepted: 10/24/2018] [Indexed: 12/18/2022]
Abstract
Legionella pneumophila is a ubiquitous environmental bacterium that has evolved to infect and proliferate within amoebae and other protists. It is thought that accidental inhalation of contaminated water particles by humans is what has enabled this pathogen to proliferate within alveolar macrophages and cause pneumonia. However, the highly evolved macrophages are equipped with more sophisticated innate defence mechanisms than are protists, such as the evolution of phagotrophic feeding into phagocytosis with more evolved innate defence processes. Not surprisingly, the majority of proteins involved in phagosome biogenesis (~80%) have origins in the phagotrophy stage of evolution. There are a plethora of highly evolved cellular and innate metazoan processes, not represented in protist biology, that are modulated by L. pneumophila, including TLR2 signalling, NF-κB, apoptotic and inflammatory processes, histone modification, caspases, and the NLRC-Naip5 inflammasomes. Importantly, L. pneumophila infects haemocytes of the invertebrate Galleria mellonella, kill G. mellonella larvae, and proliferate in and kill Drosophila adult flies and Caenorhabditis elegans. Although coevolution with protist hosts has provided a substantial blueprint for L. pneumophila to infect macrophages, we discuss the further evolutionary aspects of coevolution of L. pneumophila and its adaptation to modulate various highly evolved innate metazoan processes prior to becoming a human pathogen.
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Affiliation(s)
- Ashley M Best
- Department of Microbiology and Immunology, College of Medicine, University of Louisville, Louisville, Kentucky
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, College of Medicine, University of Louisville, Louisville, Kentucky.,Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, Kentucky
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