1
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Shore SFH, Leinberger FH, Fozo EM, Berghoff BA. Type I toxin-antitoxin systems in bacteria: from regulation to biological functions. EcoSal Plus 2024:eesp00252022. [PMID: 38767346 DOI: 10.1128/ecosalplus.esp-0025-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/11/2024] [Indexed: 05/22/2024]
Abstract
Toxin-antitoxin systems are ubiquitous in the prokaryotic world and widely distributed among chromosomes and mobile genetic elements. Several different toxin-antitoxin system types exist, but what they all have in common is that toxin activity is prevented by the cognate antitoxin. In type I toxin-antitoxin systems, toxin production is controlled by an RNA antitoxin and by structural features inherent to the toxin messenger RNA. Most type I toxins are small membrane proteins that display a variety of cellular effects. While originally discovered as modules that stabilize plasmids, chromosomal type I toxin-antitoxin systems may also stabilize prophages, or serve important functions upon certain stress conditions and contribute to population-wide survival strategies. Here, we will describe the intricate RNA-based regulation of type I toxin-antitoxin systems and discuss their potential biological functions.
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Affiliation(s)
- Selene F H Shore
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Florian H Leinberger
- Institute for Microbiology and Molecular Biology, Justus-Liebig University, Giessen, Germany
| | - Elizabeth M Fozo
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus-Liebig University, Giessen, Germany
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2
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Bergum OET, Singleton AH, Røst LM, Bodein A, Scott-Boyer MP, Rye MB, Droit A, Bruheim P, Otterlei M. SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated. Front Microbiol 2024; 15:1373344. [PMID: 38596376 PMCID: PMC11002266 DOI: 10.3389/fmicb.2024.1373344] [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] [Received: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
The DNA damage inducible SOS response in bacteria serves to increase survival of the species at the cost of mutagenesis. The SOS response first initiates error-free repair followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions, and a low dose of the antibiotic ciprofloxacin was used to activate the SOS response while avoiding extensive cell death. Our results show that expression of genes involved in error-free and error-prone repair were both induced shortly after DNA damage, thus, challenging the established perception that the expression of error-prone repair genes is delayed. By combining transcriptomics and a sub-proteomics approach termed signalomics, we found that the temporal segregation of error-free and error-prone repair is primarily regulated after transcription, supporting the current literature. Furthermore, the heterology index (i.e., the binding affinity of LexA to the SOS box) was correlated to the maximum increase in gene expression and not to the time of induction of SOS genes. Finally, quantification of metabolites revealed increasing pyrimidine pools as a late feature of the SOS response. Our results elucidate how the SOS response is coordinated, showing a rapid transcriptional response and temporal regulation of mutagenesis on the protein and metabolite levels.
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Affiliation(s)
| | - Amanda Holstad Singleton
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Antoine Bodein
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Arnaud Droit
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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3
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Bonabal S, Darfeuille F. Preventing toxicity in toxin-antitoxin systems: An overview of regulatory mechanisms. Biochimie 2024; 217:95-105. [PMID: 37473832 DOI: 10.1016/j.biochi.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
Toxin-antitoxin systems (TAs) are generally two-component genetic modules present in almost every prokaryotic genome. The production of the free and active toxin is able to disrupt key cellular processes leading to the growth inhibition or death of its host organism in absence of its cognate antitoxin. The functions attributed to TAs rely on this lethal phenotype ranging from mobile genetic elements stabilization to phage defense. Their abundance in prokaryotic genomes as well as their lethal potential make them attractive targets for new antibacterial strategies. The hijacking of TAs requires a deep understanding of their regulation to be able to design such approach. In this review, we summarize the accumulated knowledge on how bacteria cope with these toxic genes in their genome. The characterized TAs can be grouped based on the way they prevent toxicity. Some systems rely on a tight control of the expression to prevent the production of the toxin while others control the activity of the toxin at the post-translational level.
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Affiliation(s)
- Simon Bonabal
- University of Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, F-33000, Bordeaux, France
| | - Fabien Darfeuille
- University of Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, F-33000, Bordeaux, France.
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4
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Schott S, Scheuer R, Ermoli F, Glatter T, Evguenieva-Hackenberg E, Diepold A. A ParDE toxin-antitoxin system is responsible for the maintenance of the Yersinia virulence plasmid but not for type III secretion-associated growth inhibition. Front Cell Infect Microbiol 2023; 13:1166077. [PMID: 37228670 PMCID: PMC10203498 DOI: 10.3389/fcimb.2023.1166077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023] Open
Abstract
Many Gram-negative pathogens utilize the type III secretion system (T3SS) to translocate virulence-promoting effector proteins into eukaryotic host cells. The activity of this system results in a severe reduction of bacterial growth and division, summarized as secretion-associated growth inhibition (SAGI). In Yersinia enterocolitica, the T3SS and related proteins are encoded on a virulence plasmid. We identified a ParDE-like toxin-antitoxin system on this virulence plasmid in genetic proximity to yopE, encoding a T3SS effector. Effectors are strongly upregulated upon activation of the T3SS, indicating a potential role of the ParDE system in the SAGI or maintenance of the virulence plasmid. Expression of the toxin ParE in trans resulted in reduced growth and elongated bacteria, highly reminiscent of the SAGI. Nevertheless, the activity of ParDE is not causal for the SAGI. T3SS activation did not influence ParDE activity; conversely, ParDE had no impact on T3SS assembly or activity itself. However, we found that ParDE ensures the presence of the T3SS across bacterial populations by reducing the loss of the virulence plasmid, especially under conditions relevant to infection. Despite this effect, a subset of bacteria lost the virulence plasmid and regained the ability to divide under secreting conditions, facilitating the possible emergence of T3SS-negative bacteria in late acute and persistent infections.
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Affiliation(s)
- Saskia Schott
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Robina Scheuer
- Department of Microbiology and Molecular Biology, Justus Liebig University Gießen, Gießen, Germany
| | - Francesca Ermoli
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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5
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Kelly A, Arrowsmith TJ, Went SC, Blower TR. Toxin-antitoxin systems as mediators of phage defence and the implications for abortive infection. Curr Opin Microbiol 2023; 73:102293. [PMID: 36958122 DOI: 10.1016/j.mib.2023.102293] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 03/25/2023]
Abstract
Bacteria have evolved a broad range of defence mechanisms to protect against infection by their viral parasites, bacteriophages (phages). Toxin-antitoxin (TA) systems are small loci found throughout bacteria and archaea that in some cases provide phage defence. The recent explosion in phage defence system discovery has identified multiple novel TA systems with antiphage activity. Due to inherent toxicity, TA systems are thought to mediate abortive infection (Abi), wherein the host cell dies in response to phage infection, removing the phage, and protecting clonal siblings. Recent studies, however, have uncovered molecular mechanisms by which TA systems are activated by phages, how they mediate toxicity, and how phages escape the defences. These new models reveal dazzling complexity in phage-host interactions and provide further evidence that TA systems do not in all cases inherently perform classic Abi, suggesting an evolved conceptual definition is required.
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Affiliation(s)
- Abigail Kelly
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Tom J Arrowsmith
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Sam C Went
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK.
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6
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Sonika S, Singh S, Mishra S, Verma S. Toxin-antitoxin systems in bacterial pathogenesis. Heliyon 2023; 9:e14220. [PMID: 37101643 PMCID: PMC10123168 DOI: 10.1016/j.heliyon.2023.e14220] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Toxin-Antitoxin (TA) systems are abundant in prokaryotes and play an important role in various biological processes such as plasmid maintenance, phage inhibition, stress response, biofilm formation, and dormant persister cell generation. TA loci are abundant in pathogenic intracellular micro-organisms and help in their adaptation to the harsh host environment such as nutrient deprivation, oxidation, immune response, and antimicrobials. Several studies have reported the involvement of TA loci in establishing successful infection, intracellular survival, better colonization, adaptation to host stresses, and chronic infection. Overall, the TA loci play a crucial role in bacterial virulence and pathogenesis. Nonetheless, there are some controversies about the role of TA system in stress response, biofilm and persister formation. In this review, we describe the role of the TA systems in bacterial virulence. We discuss the important features of each type of TA system and the recent discoveries identifying key contributions of TA loci in bacterial pathogenesis.
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7
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Kurasz JE, Crawford MC, Porwollik S, Gregory O, Tadlock KR, Balding EC, Weinert EE, McClelland M, Karls AC. Strain-Specific Gifsy-1 Prophage Genes Are Determinants for Expression of the RNA Repair Operon during the SOS Response in Salmonella enterica Serovar Typhimurium. J Bacteriol 2023; 205:e0026222. [PMID: 36622230 PMCID: PMC9879122 DOI: 10.1128/jb.00262-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023] Open
Abstract
The adaptation of Salmonella enterica serovar Typhimurium to stress conditions involves expression of genes within the regulon of the alternative sigma factor RpoN (σ54). RpoN-dependent transcription requires an activated bacterial enhancer binding protein (bEBP) that hydrolyzes ATP to remodel the RpoN-holoenzyme-promoter complex for transcription initiation. The bEBP RtcR in S. Typhimurium strain 14028s is activated by genotoxic stress to direct RpoN-dependent expression of the RNA repair operon rsr-yrlBA-rtcBA. The molecular signal for RtcR activation is an oligoribonucleotide with a 3'-terminal 2',3'-cyclic phosphate. We show in S. Typhimurium 14028s that the molecular signal is not a direct product of nucleic acid damage, but signal generation is dependent on a RecA-controlled SOS-response pathway, specifically, induction of prophage Gifsy-1. A genome-wide mutant screen and utilization of Gifsy prophage-cured strains indicated that the nucleoid-associated protein Fis and the Gifsy-1 prophage significantly impact RtcR activation. Directed-deletion analysis and genetic mapping by transduction demonstrated that a three-gene region (STM14_3218-3220) in Gifsy-1, which is variable between S. Typhimurium strains, is required for RtcR activation in strain 14028s and that the absence of STM14_3218-3220 in the Gifsy-1 prophages of S. Typhimurium strains LT2 and 4/74, which renders these strains unable to activate RtcR during genotoxic stress, can be rescued by complementation in cis by the region encompassing STM14_3218-3220. Thus, even though RtcR and the RNA repair operon are highly conserved in Salmonella enterica serovars, RtcR-dependent expression of the RNA repair operon in S. Typhimurium is controlled by a variable region of a prophage present in only some strains. IMPORTANCE The transcriptional activator RtcR and the RNA repair proteins whose expression it regulates, RtcA and RtcB, are widely conserved in Proteobacteria. In Salmonella Typhimurium 14028s, genotoxic stress activates RtcR to direct RpoN-dependent expression of the rsr-yrlBA-rtcBA operon. This work identifies key elements of a RecA-dependent pathway that generates the signal for RtcR activation in strain 14028s. This signaling pathway requires the presence of a specific region within the prophage Gifsy-1, yet this region is absent in most other wild-type Salmonella strains. Thus, we show that the activity of a widely conserved regulatory protein can be controlled by prophages with narrow phylogenetic distributions. This work highlights an underappreciated phenomenon where bacterial physiological functions are altered due to genetic rearrangement of prophages.
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Affiliation(s)
| | | | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California–Irvine School of Medicine, Irvine, California, USA
| | - Oliver Gregory
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | | | - Eve C. Balding
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Emily E. Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California–Irvine School of Medicine, Irvine, California, USA
| | - Anna C. Karls
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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8
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Bogati B, Shore SFH, Nipper TD, Stoiculescu O, Fozo EM. Charged Amino Acids Contribute to ZorO Toxicity. Toxins (Basel) 2022; 15:32. [PMID: 36668852 PMCID: PMC9860968 DOI: 10.3390/toxins15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Chromosomally encoded toxin-antitoxin systems have been increasingly identified and characterized across bacterial species over the past two decades. Overproduction of the toxin gene results in cell growth stasis or death for the producing cell, but co-expression of its antitoxin can repress the toxic effects. For the subcategory of type I toxin-antitoxin systems, many of the described toxin genes encode a small, hydrophobic protein with several charged residues distributed across the sequence of the toxic protein. Though these charged residues are hypothesized to be critical for the toxic effects of the protein, they have not been studied broadly across different type I toxins. Herein, we mutated codons encoding charged residues in the type I toxin zorO, from the zor-orz toxin-antitoxin system, to determine their impacts on growth inhibition, membrane depolarization, ATP depletion, and the localization of this small protein. The non-toxic variants of ZorO accumulated both in the membrane and cytoplasm, indicating that membrane localization alone is not sufficient for its toxicity. While mutation of a charged residue could result in altered toxicity, this was dependent not only on the position of the amino acid within the protein but also on the residue to which it was converted, suggesting a complex role of charged residues in ZorO-mediated toxicity. A previous study indicated that additional copies of the zor-orz system improved growth in aminoglycosides: within, we note that this improved growth is independent of ZorO toxicity. By increasing the copy number of the zorO gene fused with a FLAG-tag, we were able to detect the protein expressed from its native promoter elements: an important step for future studies of toxin expression and function.
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Affiliation(s)
| | | | | | | | - Elizabeth M. Fozo
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN 37996, USA
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9
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Toxin-Antitoxin Systems Alter Adaptation of Mycobacterium smegmatis to Environmental Stress. Microbiol Spectr 2022; 10:e0281522. [PMID: 36318013 PMCID: PMC9769933 DOI: 10.1128/spectrum.02815-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitous genetic elements in prokaryotes, but their biological importance is poorly understood. Mycobacterium smegmatis contains eight putative TA systems. Previously, seven TAs have been studied, with five of them being verified as functional. Here, we show that Ms0251-0252 is a novel TA system in that expression of the toxin Ms0251 leads to growth inhibition that can be rescued by the antitoxin Ms0252. To investigate the functional roles of TA systems in M. smegmatis, we deleted the eight putative TA loci and assayed the mutants for resistance to various stresses. Deletion of all eight TA loci resulted in decreased survival under starvation conditions and altered fitness when exposed to environmental stresses. Furthermore, we showed that deletion of the eight TA loci decreased resistance to phage infection in Sauton medium compared with the results using 7H10 medium, suggesting that TA systems might have different contributions depending on the nutrient environment. Furthermore, we found that MazEF specifically played a dominant role in resistance to phage infection. Finally, transcriptome analysis revealed that MazEF overexpression led to differential expression of multiple genes, including those related to iron acquisition. Altogether, we demonstrate that TA systems coordinately function to allow M. smegmatis to adapt to changing environmental conditions. IMPORTANCE Toxin-antitoxin (TA) systems are mechanisms for rapid adaptation of bacteria to environmental changes. Mycobacterium smegmatis, a model bacterium for studying Mycobacterium tuberculosis, encodes eight putative TA systems. Here, we constructed an M. smegmatis mutant with deletions of all eight TA-encoding genes and evaluated the resistance of these mutants to environmental stresses. Our results showed that different TA systems have overlapping and, in some cases, opposing functions in adaptation to various stresses. We suggest that complementary TA modules may function together to regulate the bacterial stress response, enabling adaptation to changing environments. Together, this study provides key insights into the roles of TA systems in resistance to various environmental stresses, drug tolerance, and defense against phage infection.
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10
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The RNA-Binding Protein ProQ Promotes Antibiotic Persistence in Salmonella. mBio 2022; 13:e0289122. [PMID: 36409088 PMCID: PMC9765298 DOI: 10.1128/mbio.02891-22] [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
Bacterial populations can survive exposure to antibiotics through transient phenotypic and gene expression changes. These changes can be attributed to a small subpopulation of bacteria, giving rise to antibiotic persistence. Although this phenomenon has been known for decades, much remains to be learned about the mechanisms that drive persister formation. The RNA-binding protein ProQ has recently emerged as a global regulator of gene expression. Here, we show that ProQ impacts persister formation in Salmonella. In vitro, ProQ contributes to growth arrest in a subset of cells that are able to survive treatment at high concentrations of different antibiotics. The underlying mechanism for ProQ-dependent persister formation involves the activation of metabolically costly processes, including the flagellar pathway and the type III protein secretion system encoded on Salmonella pathogenicity island 2. Importantly, we show that the ProQ-dependent phenotype is relevant during macrophage infection and allows Salmonella to survive the combined action of host immune defenses and antibiotics. Together, our data highlight the importance of ProQ in Salmonella persistence and pathogenesis. IMPORTANCE Bacteria can avoid eradication by antibiotics through a phenomenon known as persistence. Persister cells arise through phenotypic heterogeneity and constitute a small fraction of dormant cells within a population of actively growing bacteria, which is susceptible to antibiotic killing. In this study, we show that ProQ, an RNA-binding protein and global regulator of gene expression, promotes persisters in the human pathogen Salmonella enterica serovar Typhimurium. Bacteria lacking the proQ gene outcompete wild-type bacteria under laboratory conditions, are less prone to enter growth dormancy, and form fewer persister cells. The basis for these phenotypes lies in ProQ's ability to activate energy-consuming cellular processes, including flagellar motility and protein secretion. Importantly, we show that ProQ contributes to the persister phenotype during Salmonella infection of macrophages, indicating an important role of this global regulator in Salmonella pathogenesis.
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11
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Köbel T, Melo Palhares R, Fromm C, Szymanski W, Angelidou G, Glatter T, Georg J, Berghoff BA, Schindler D. An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria. ACS Synth Biol 2022; 11:2989-3003. [PMID: 36044590 PMCID: PMC9486967 DOI: 10.1021/acssynbio.2c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic biology approaches life from the perspective of an engineer. Standardized and de novo design of genetic parts to subsequently build reproducible and controllable modules, for example, for circuit design, is a key element. To achieve this, natural systems and elements often serve as a blueprint for researchers. Regulation of protein abundance is controlled at DNA, mRNA, and protein levels. Many tools for the activation or repression of transcription or the destabilization of proteins are available, but easy-to-handle minimal regulatory elements on the mRNA level are preferable when translation needs to be modulated. Regulatory RNAs contribute considerably to regulatory networks in all domains of life. In particular, bacteria use small regulatory RNAs (sRNAs) to regulate mRNA translation. Slowly, sRNAs are attracting the interest of using them for broad applications in synthetic biology. Here, we promote a "plug and play" plasmid toolset to quickly and efficiently create synthetic sRNAs to study sRNA biology or their application in bacteria. We propose a simple benchmarking assay by targeting the acrA gene of Escherichia coli and rendering cells sensitive toward the β-lactam antibiotic oxacillin. We further highlight that it may be necessary to test multiple seed regions and sRNA scaffolds to achieve the desired regulatory effect. The described plasmid toolset allows quick construction and testing of various synthetic sRNAs based on the user's needs.
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Affiliation(s)
- Tania
S. Köbel
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,MaxGENESYS
Biofoundry, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany
| | - Rafael Melo Palhares
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christin Fromm
- Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Witold Szymanski
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Georgia Angelidou
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Timo Glatter
- Mass
Spectrometry and Proteomics Core Facility, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, 35043 Marburg, Germany
| | - Jens Georg
- Institut
für Biologie III, Albert-Ludwigs-Universität
Freiburg, Schänzlestraße
1, 79104 Freiburg, Germany
| | - Bork A. Berghoff
- Institute
for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany,
| | - Daniel Schindler
- RG
Schindler, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,MaxGENESYS
Biofoundry, Max-Planck-Institute for Terrestrial
Microbiology, Karl-von-Frisch-Street
10, 35043 Marburg, Germany,
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12
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Qiu J, Zhai Y, Wei M, Zheng C, Jiao X. Toxin–antitoxin systems: Classification, biological roles, and applications. Microbiol Res 2022; 264:127159. [DOI: 10.1016/j.micres.2022.127159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022]
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13
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TisB Protein Protects Escherichia coli Cells Suffering Massive DNA Damage from Environmental Toxic Compounds. mBio 2022; 13:e0038522. [PMID: 35377167 PMCID: PMC9040746 DOI: 10.1128/mbio.00385-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Toxin-antitoxin systems are genetic elements that are widespread in prokaryotes. Although molecular mode of action of many of these toxins has been identified, their biological functions are mostly unknown. We investigated the functional integration of the TisB/IstR toxin-antitoxin system in the Escherichia coli SOS genotoxic stress response network. We showed that the tisB gene is induced in cells exposed to high doses of the genotoxic antibiotic trimethoprim. However, we also found that TisB contributes to trimethoprim-induced lethality. This is a consequence of the TisB-induced drop in the proton motive force (PMF), which results in blocking the thymine import and therefore the functioning of the pyrimidine salvage pathway. Conversely, a TisB-induced PMF drop protects cells by preventing the import of some other toxic compounds, like the aminoglycoside antibiotic gentamicin and colicin M, in the SOS-induced cells. Colicins are cytotoxic molecules produced by Enterobacterales when they are exposed to strong genotoxic stresses in order to compete with other microbiota members. We indeed found that TisB contributes to E. coli’s fitness during mouse gut colonization. Based on the results obtained here, we propose that the primary biological role of the TisB toxin is to increase the probability of survival and maintenance in the mammalian gut of their bacterial hosts when they have to simultaneously deal with massive DNA damages and a fierce chemical warfare with other microbiota members.
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14
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Edelmann D, Berghoff BA. A Shift in Perspective: A Role for the Type I Toxin TisB as Persistence-Stabilizing Factor. Front Microbiol 2022; 13:871699. [PMID: 35369430 PMCID: PMC8969498 DOI: 10.3389/fmicb.2022.871699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial persistence is a phenomenon that is founded by the existence of a subpopulation of multidrug-tolerant cells. These so-called persister cells endure otherwise lethal stress situations and enable restoration of bacterial populations upon return to favorable conditions. Persisters are especially notorious for their ability to survive antibiotic treatments without conventional resistance genes and to cause infection relapse. The persister state is typically correlated with reduction or inhibition of cellular activity. Early on, chromosomal toxin-antitoxin (TA) systems were suspected to induce the persister state in response to environmental stress. However, this idea has been challenged during the last years. Especially the involvement of toxins from type II TA systems in persister formation is put into question. For toxins from type I TA systems the debate has just started. Here, we would like to summarize recent knowledge gained for the type I TA system tisB/istR-1 from Escherichia coli. TisB is a small, membrane-targeting toxin, which disrupts the proton motive force (PMF), leading to membrane depolarization. Based on experimental data, we hypothesize that TisB primarily stabilizes the persister state through depolarization and further, secondary effects. We will present a simple model that will provide a framework for future directions.
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15
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Yadavalli SS, Yuan J. Bacterial Small Membrane Proteins: the Swiss Army Knife of Regulators at the Lipid Bilayer. J Bacteriol 2022; 204:e0034421. [PMID: 34516282 PMCID: PMC8765417 DOI: 10.1128/jb.00344-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small membrane proteins represent a subset of recently discovered small proteins (≤100 amino acids), which are a ubiquitous class of emerging regulators underlying bacterial adaptation to environmental stressors. Until relatively recently, small open reading frames encoding these proteins were not designated genes in genome annotations. Therefore, our understanding of small protein biology was primarily limited to a few candidates associated with previously characterized larger partner proteins. Following the first systematic analyses of small proteins in Escherichia coli over a decade ago, numerous small proteins across different bacteria have been uncovered. An estimated one-third of these newly discovered proteins in E. coli are localized to the cell membrane, where they may interact with distinct groups of membrane proteins, such as signal receptors, transporters, and enzymes, and affect their activities. Recently, there has been considerable progress in functionally characterizing small membrane protein regulators aided by innovative tools adapted specifically to study small proteins. Our review covers prototypical proteins that modulate a broad range of cellular processes, such as transport, signal transduction, stress response, respiration, cell division, sporulation, and membrane stability. Thus, small membrane proteins represent a versatile group of physiology regulators at the membrane and the whole cell. Additionally, small membrane proteins have the potential for clinical applications, where some of the proteins may act as antibacterial agents themselves while others serve as alternative drug targets for the development of novel antimicrobials.
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Affiliation(s)
- Srujana S. Yadavalli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Jing Yuan
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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16
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Abstract
Toxin-antitoxin systems are widespread in bacterial genomes. They are usually composed of two elements: a toxin that inhibits an essential cellular process and an antitoxin that counteracts its cognate toxin. In the past decade, a number of new toxin-antitoxin systems have been described, bringing new growth inhibition mechanisms to light as well as novel modes of antitoxicity. However, recent advances in the field profoundly questioned the role of these systems in bacterial physiology, stress response and antimicrobial persistence. This shifted the paradigm of the functions of toxin-antitoxin systems to roles related to interactions between hosts and their mobile genetic elements, such as viral defence or plasmid stability. In this Review, we summarize the recent progress in understanding the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin-antitoxin systems.
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Singh G, Yadav M, Ghosh C, Rathore JS. Bacterial toxin-antitoxin modules: classification, functions, and association with persistence. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100047. [PMID: 34841338 PMCID: PMC8610362 DOI: 10.1016/j.crmicr.2021.100047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 11/24/2022] Open
Abstract
Ubiquitously present bacterial Toxin-Antitoxin (TA) modules consist of stable toxin associated with labile antitoxin. Classification of TAs modules based on inhibition of toxin through antitoxin in 8 different classes. Variety of specific toxin targets and the abundance of TA modules in various deadly pathogens. Specific role of TAs modules in conservation of the resistant genes, emergence of persistence & biofilm formation. Proposed antibacterial strategies involving TA modules for elimination of multi-drug resistance.
Toxin-antitoxin (TA) modules are ubiquitous gene loci among bacteria and are comprised of a toxin part and its cognate antitoxin part. Under normal physiological conditions, antitoxin counteracts the toxicity of the toxin whereas, during stress conditions, TA modules play a crucial role in bacterial physiology through involvement in the post-segregational killing, abortive infection, biofilms, and persister cell formation. Most of the toxins are proteinaceous that affect translation or DNA replication, although some other intracellular molecular targets have also been described. While antitoxins may be a protein or RNA, that generally neutralizes its cognate toxin by direct interaction or with the help of other signaling elements and thus helps in the TA module regulation. In this review, we have discussed the current state of the multifaceted TA (type I–VIII) modules by highlighting their classification and specific targets. We have also discussed the presence of TA modules in the various pathogens and their role in antibiotic persistence development as well as biofilm formation, by influencing the different cellular processes. In the end, assembling knowledge about ubiquitous TA systems from pathogenic bacteria facilitated us to propose multiple novel antibacterial strategies involving artificial activation of TA modules.
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Affiliation(s)
- Garima Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Uttar Pradesh, India
| | - Mohit Yadav
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Uttar Pradesh, India
| | - Chaitali Ghosh
- Department of Zoology Gargi College, University of Delhi, New Delhi, India
| | - Jitendra Singh Rathore
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Uttar Pradesh, India
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18
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Toxin Induction or Inhibition of Transcription or Translation Posttreatment Increases Persistence to Fluoroquinolones. mBio 2021; 12:e0198321. [PMID: 34399616 PMCID: PMC8406316 DOI: 10.1128/mbio.01983-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Toxin-antitoxin modules are widespread in prokaryotes, and the capacity of toxin accumulation to increase the tolerances of bacteria to antibiotics has been well documented. The conventional model for this functionality implies that an overabundance of toxin arrests bacterial growth, which inhibits processes targeted by antibiotics and thereby limits their corruption and the lethal damage that would ensue. Implicit in this model is that toxins exert their influence on antibiotic lethality before and/or during treatment, even though they are also present and functional after treatment concludes. Given recent evidence establishing that the period following antibiotic treatment (recovery) is important for the survival of nongrowing bacterial populations treated with fluoroquinolones (FQs), we assayed to what extent toxins influence bacterial survival during the recovery period. With both LdrD and MazF, toxins of type I and II systems, respectively, controlling accumulation to occur only after FQ treatment of nongrowing cultures resulted in significant increases in persisters. Further genetic investigation revealed important roles for homologous recombination and nucleotide excision repair machinery. Focusing on the wild type, we did not observe any SOS-induced toxin functioning in this manner; however, an analogous phenomenon was observed for wild-type Escherichia coli as well as uropathogenic E. coli (UPEC) when transcription or translation was inhibited during the post-FQ recovery period. Collectively, these data reveal the capacity of toxins to thwart FQ killing even after the treatment has concluded and show that FQ treatment of nongrowing bacteria can be rendered largely ineffective if bacteria cannot readily resume translation and growth at the conclusion of treatment.
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Wang R, Lu D, Wang H, Zou H, Bai T, Feng C, Lin Q. "Kill-release" antibacterial polysaccharides multilayer coating based therapeutic contact lens for effective bacterial keratitis treatment. RSC Adv 2021; 11:26160-26167. [PMID: 35479473 PMCID: PMC9037525 DOI: 10.1039/d1ra02472h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/24/2021] [Indexed: 01/06/2023] Open
Abstract
Contact lenses (CLs) are an important medical device for ophthalmic disease treatment. They can be used not only to correct refractive errors, such as myopia, but also can serve as a drug carrier for ocular surface disease treatment. In this study, a therapeutic CL was designed for bacterial keratitis treatment by constructing an antibacterial surface coating via a layer-by-layer (LbL) electrostatic self-assembly method. Vancomycin-incorporated chitosan nanoparticles were firstly prepared by ionic condensation of sodium tripolyphosphate (abbreviated as CTVNP). The positively charged CTVNP were then used for LbL deposition with negatively charged heparin (HEP), obtaining a (HEP/CTVNP)n polyelectrolyte multilayer on the CL surface. It is shown that such antibiotic incorporated surface coating doesn't influence the light transmittance of the CL, so it should not affect the patients' visual acuity when wearing them. The in vitro bacteriostatic effect evaluation was performed via live and dead bacteria staining and scanning electron microscope (SEM), which demonstrated the effective antibacterial property of such a surface. The fabricated therapeutic CL was then used to treat bacterial keratitis on a rabbit model. The results showed that such CL could effectively control the development of the bacteria-infected cornea and had a significant therapeutic effect. Therapeutic contact lenses fabricated by polysaccharides multilayer surface modification, shows “kill-release” antibacterial performance, can serve as an effective treatment for bacterial keratitis.![]()
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Affiliation(s)
- Rui Wang
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University 270 Xueyuan Road Wenzhou 325027 China
| | - Duoduo Lu
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University 270 Xueyuan Road Wenzhou 325027 China
| | - Hui Wang
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University 270 Xueyuan Road Wenzhou 325027 China
| | - Haoyu Zou
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University 270 Xueyuan Road Wenzhou 325027 China
| | - Ting Bai
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University 270 Xueyuan Road Wenzhou 325027 China
| | - Chulei Feng
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University 270 Xueyuan Road Wenzhou 325027 China
| | - Quankui Lin
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University 270 Xueyuan Road Wenzhou 325027 China
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20
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Nonin-Lecomte S, Fermon L, Felden B, Pinel-Marie ML. Bacterial Type I Toxins: Folding and Membrane Interactions. Toxins (Basel) 2021; 13:toxins13070490. [PMID: 34357962 PMCID: PMC8309996 DOI: 10.3390/toxins13070490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
Bacterial type I toxin-antitoxin systems are two-component genetic modules that encode a stable toxic protein whose ectopic overexpression can lead to growth arrest or cell death, and an unstable RNA antitoxin that inhibits toxin translation during growth. These systems are widely spread among bacterial species. Type I antitoxins are cis- or trans-encoded antisense small RNAs that interact with toxin-encoding mRNAs by pairing, thereby inhibiting toxin mRNA translation and/or inducing its degradation. Under environmental stress conditions, the up-regulation of the toxin and/or the antitoxin degradation by specific RNases promote toxin translation. Most type I toxins are small hydrophobic peptides with a predicted α-helical transmembrane domain that induces membrane depolarization and/or permeabilization followed by a decrease of intracellular ATP, leading to plasmid maintenance, growth adaptation to environmental stresses, or persister cell formation. In this review, we describe the current state of the art on the folding and the membrane interactions of these membrane-associated type I toxins from either Gram-negative or Gram-positive bacteria and establish a chronology of their toxic effects on the bacterial cell. This review also includes novel structural results obtained by NMR concerning the sprG1-encoded membrane peptides that belong to the sprG1/SprF1 type I TA system expressed in Staphylococcus aureus and discusses the putative membrane interactions allowing the lysis of competing bacteria and host cells.
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Affiliation(s)
| | - Laurence Fermon
- BRM (Bacterial Regulatory RNAs and Medicine), Inserm, UMR_S 1230, Université de Rennes 1, 35000 Rennes, France; (L.F.); (B.F.)
| | - Brice Felden
- BRM (Bacterial Regulatory RNAs and Medicine), Inserm, UMR_S 1230, Université de Rennes 1, 35000 Rennes, France; (L.F.); (B.F.)
| | - Marie-Laure Pinel-Marie
- BRM (Bacterial Regulatory RNAs and Medicine), Inserm, UMR_S 1230, Université de Rennes 1, 35000 Rennes, France; (L.F.); (B.F.)
- Correspondence:
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21
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Sarpong DD, Murphy ER. RNA Regulated Toxin-Antitoxin Systems in Pathogenic Bacteria. Front Cell Infect Microbiol 2021; 11:661026. [PMID: 34084755 PMCID: PMC8167048 DOI: 10.3389/fcimb.2021.661026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/29/2021] [Indexed: 01/05/2023] Open
Abstract
The dynamic host environment presents a significant hurdle that pathogenic bacteria must overcome to survive and cause diseases. Consequently, these organisms have evolved molecular mechanisms to facilitate adaptation to environmental changes within the infected host. Small RNAs (sRNAs) have been implicated as critical regulators of numerous pathways and systems in pathogenic bacteria, including that of bacterial Toxin-Antitoxin (TA) systems. TA systems are typically composed of two factors, a stable toxin, and a labile antitoxin which functions to protect against the potentially deleterious activity of the associated toxin. Of the six classes of bacterial TA systems characterized to date, the toxin component is always a protein. Type I and Type III TA systems are unique in that the antitoxin in these systems is an RNA molecule, whereas the antitoxin in all other TA systems is a protein. Though hotly debated, the involvement of TA systems in bacterial physiology is recognized by several studies, with the Type II TA system being the most extensively studied to date. This review focuses on RNA-regulated TA systems, highlighting the role of Type I and Type III TA systems in several pathogenic bacteria.
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Affiliation(s)
- David D. Sarpong
- Department of Biological Sciences, Ohio University, Athens, OH, United States
- Infectious and Tropical Diseases Institute, Ohio University, Athens, OH, United States
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
| | - Erin R. Murphy
- Infectious and Tropical Diseases Institute, Ohio University, Athens, OH, United States
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Biomedical Sciences, Ohio University, Heritage College of Osteopathic Medicine, Athens, OH, United States
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22
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Edelmann D, Leinberger FH, Schmid NE, Oberpaul M, Schäberle TF, Berghoff BA. Elevated Expression of Toxin TisB Protects Persister Cells against Ciprofloxacin but Enhances Susceptibility to Mitomycin C. Microorganisms 2021; 9:943. [PMID: 33925723 PMCID: PMC8145889 DOI: 10.3390/microorganisms9050943] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/02/2022] Open
Abstract
Bacterial chromosomes harbor toxin-antitoxin (TA) systems, some of which are implicated in the formation of multidrug-tolerant persister cells. In Escherichia coli, toxin TisB from the tisB/istR-1 TA system depolarizes the inner membrane and causes ATP depletion, which presumably favors persister formation. Transcription of tisB is induced upon DNA damage due to activation of the SOS response by LexA degradation. Transcriptional activation of tisB is counteracted on the post-transcriptional level by structural features of tisB mRNA and RNA antitoxin IstR-1. Deletion of the regulatory RNA elements (mutant Δ1-41 ΔistR) uncouples TisB expression from LexA-dependent SOS induction and causes a 'high persistence' (hip) phenotype upon treatment with different antibiotics. Here, we demonstrate by the use of fluorescent reporters that TisB overexpression in mutant Δ1-41 ΔistR inhibits cellular processes, including the expression of SOS genes. The failure in SOS gene expression does not affect the hip phenotype upon treatment with the fluoroquinolone ciprofloxacin, likely because ATP depletion avoids strong DNA damage. By contrast, Δ1-41 ΔistR cells are highly susceptible to the DNA cross-linker mitomycin C, likely because the expression of SOS-dependent repair systems is impeded. Hence, the hip phenotype of the mutant is conditional and strongly depends on the DNA-damaging agent.
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Affiliation(s)
- Daniel Edelmann
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, 35392 Giessen, Germany; (D.E.); (F.H.L.); (N.E.S.)
| | - Florian H. Leinberger
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, 35392 Giessen, Germany; (D.E.); (F.H.L.); (N.E.S.)
| | - Nicole E. Schmid
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, 35392 Giessen, Germany; (D.E.); (F.H.L.); (N.E.S.)
| | - Markus Oberpaul
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 35392 Giessen, Germany; (M.O.); (T.F.S.)
| | - Till F. Schäberle
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 35392 Giessen, Germany; (M.O.); (T.F.S.)
- Institute for Insect Biotechnology, Justus Liebig University Giessen, 35392 Giessen, Germany
- Partner Site Giessen-Marburg-Langen, German Center for Infection Research (DZIF), 35392 Giessen, Germany
| | - Bork A. Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, 35392 Giessen, Germany; (D.E.); (F.H.L.); (N.E.S.)
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23
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Lauxen AI, Kobauri P, Wegener M, Hansen MJ, Galenkamp NS, Maglia G, Szymanski W, Feringa BL, Kuipers OP. Mechanism of Resistance Development in E. coli against TCAT, a Trimethoprim-Based Photoswitchable Antibiotic. Pharmaceuticals (Basel) 2021; 14:ph14050392. [PMID: 33919397 PMCID: PMC8143356 DOI: 10.3390/ph14050392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 11/16/2022] Open
Abstract
During the last decades, a continuous rise of multi-drug resistant pathogens has threatened antibiotic efficacy. To tackle this key challenge, novel antimicrobial therapies are needed with increased specificity for the site of infection. Photopharmacology could enable such specificity by allowing for the control of antibiotic activity with light, as exemplified by trans/cis-tetra-ortho-chloroazobenzene-trimethoprim (TCAT) conjugates. Resistance development against the on (irradiated, TCATa) and off (thermally adapted, TCATd) states of TCAT were compared to that of trimethoprim (TMP) in Escherichia coli mutant strain CS1562. Genomics and transcriptomics were used to explore the acquired resistance. Although TCAT shows TMP-like dihydrofolate reductase (DHFR) inhibition in vitro, transcriptome analyses show different responses in acquired resistance. Resistance against TCATa (on) relies on the production of exopolysaccharides and overexpression of TolC. While resistance against TCATd (off) follows a slightly different gene expression profile, both indicate hampering the entrance of the molecule into the cell. Conversely, resistance against TMP is based on alterations in cell metabolism towards a more persister-like phenotype, as well as alteration of expression levels of enzymes involved in the folate biosynthesis. This study provides a deeper understanding of the development of new therapeutic strategies and the consequences on resistance development against photopharmacological drugs.
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Affiliation(s)
- Anna I. Lauxen
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands;
| | - Piermichele Kobauri
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
| | - Michael Wegener
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
| | - Mickel J. Hansen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
| | - Nicole S. Galenkamp
- Groningen Biomolecular Science & Biotechnology Institute, University of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands; (N.S.G.); (G.M.)
| | - Giovanni Maglia
- Groningen Biomolecular Science & Biotechnology Institute, University of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands; (N.S.G.); (G.M.)
| | - Wiktor Szymanski
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
- Medical Imaging Center, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
- Correspondence: (W.S.); (B.L.F.); (O.P.K.)
| | - Ben L. Feringa
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
- Correspondence: (W.S.); (B.L.F.); (O.P.K.)
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands;
- Correspondence: (W.S.); (B.L.F.); (O.P.K.)
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24
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Edelmann D, Oberpaul M, Schäberle TF, Berghoff BA. Post-transcriptional deregulation of the tisB/istR-1 toxin-antitoxin system promotes SOS-independent persister formation in Escherichia coli. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:159-168. [PMID: 33350069 DOI: 10.1111/1758-2229.12919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Bacterial dormancy is a valuable strategy to endure unfavourable conditions. The term 'persister' has been coined for cells that tolerate antibiotic treatments due to reduced cellular activity. The type I toxin-antitoxin system tisB/istR-1 is linked to persistence in Escherichia coli, because toxin TisB depolarizes the inner membrane and causes ATP depletion. Transcription of tisB is induced upon activation of the SOS response by DNA-damaging drugs. However, translation is repressed both by a 5' structure within the tisB mRNA and by RNA antitoxin IstR-1. This tight regulation limits TisB production to SOS conditions. Deletion of both regulatory RNA elements produced a 'high persistence' mutant, which was previously assumed to depend on stochastic SOS induction and concomitant TisB production. Here, we demonstrate that the mutant generates a subpopulation of growth-retarded cells during late stationary phase, likely due to SOS-independent TisB accumulation. Cell sorting experiments revealed that the stationary phase-derived subpopulation contains most of the persister cells. Collectively our data show that deletion of the regulatory RNA elements uncouples the persister formation process from the intended stress situation and enables the formation of TisB-dependent persisters in an SOS-independent manner.
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Affiliation(s)
- Daniel Edelmann
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, 35392, Germany
| | - Markus Oberpaul
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, 35392, Germany
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, 35392, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, 35392, Germany
- German Centre for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, 35392, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, 35392, Germany
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25
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Srivastava A, Pati S, Kaushik H, Singh S, Garg LC. Toxin-antitoxin systems and their medical applications: current status and future perspective. Appl Microbiol Biotechnol 2021; 105:1803-1821. [PMID: 33582835 DOI: 10.1007/s00253-021-11134-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Almost all bacteria synthesize two types of toxins-one for its survival by regulating different cellular processes and another as a strategy to interact with host cells for pathogenesis. Usually, "bacterial toxins" are contemplated as virulence factors that harm the host organism. However, toxins produced by bacteria, as a survival strategy against the host, also hamper its cellular processes. To overcome this, the bacteria have evolved with the production of a molecule, referred to as antitoxin, to negate the deleterious effect of the toxin against itself. The toxin and antitoxins are encoded by a two-component toxin-antitoxin (TA) system. The antitoxin, a protein or RNA, sequesters the toxins of the TA system for neutralization within the bacterial cell. In this review, we have described different TA systems of bacteria and their potential medical and biotechnological applications. It is of interest to note that while bacterial toxin-antitoxin systems have been well studied, the TA system in unicellular eukaryotes, though predicted by the investigators, have never been paid the desired attention. In the present review, we have also touched upon the TA system of eukaryotes identified to date. KEY POINTS: Bacterial toxins harm the host and also affect the bacterial cellular processes. The antitoxin produced by bacteria protect it from the toxin's harmful effects. The toxin-antitoxin systems can be targeted for various medical applications.
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Affiliation(s)
- Akriti Srivastava
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh, 201314, India
| | - Soumya Pati
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh, 201314, India
| | - Himani Kaushik
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Lalit C Garg
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India.
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26
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Activation of metabolic and stress responses during subtoxic expression of the type I toxin hok in Erwinia amylovora. BMC Genomics 2021; 22:74. [PMID: 33482720 PMCID: PMC7821729 DOI: 10.1186/s12864-021-07376-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/08/2021] [Indexed: 11/15/2022] Open
Abstract
Background Toxin-antitoxin (TA) systems, abundant in prokaryotes, are composed of a toxin gene and its cognate antitoxin. Several toxins are implied to affect the physiological state and stress tolerance of bacteria in a population. We previously identified a chromosomally encoded hok-sok type I TA system in Erwinia amylovora, the causative agent of fire blight disease on pome fruit trees. A high-level induction of the hok gene was lethal to E. amylovora cells through unknown mechanisms. The molecular targets or regulatory roles of Hok were unknown. Results Here, we examined the physiological and transcriptomic changes of Erwinia amylovora cells expressing hok at subtoxic levels that were confirmed to confer no cell death, and at toxic levels that resulted in killing of cells. In both conditions, hok caused membrane rupture and collapse of the proton motive force in a subpopulation of E. amylovora cells. We demonstrated that induction of hok resulted in upregulation of ATP biosynthesis genes, and caused leakage of ATP from cells only at toxic levels. We showed that overexpression of the phage shock protein gene pspA largely reversed the cell death phenotype caused by high levels of hok induction. We also showed that induction of hok at a subtoxic level rendered a greater proportion of stationary phase E. amylovora cells tolerant to the antibiotic streptomycin. Conclusions We characterized the molecular mechanism of toxicity by high-level of hok induction and demonstrated that low-level expression of hok primes the stress responses of E. amylovora against further membrane and antibiotic stressors. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07376-w.
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Eisenreich W, Rudel T, Heesemann J, Goebel W. Persistence of Intracellular Bacterial Pathogens-With a Focus on the Metabolic Perspective. Front Cell Infect Microbiol 2021; 10:615450. [PMID: 33520740 PMCID: PMC7841308 DOI: 10.3389/fcimb.2020.615450] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
Persistence has evolved as a potent survival strategy to overcome adverse environmental conditions. This capability is common to almost all bacteria, including all human bacterial pathogens and likely connected to chronic infections caused by some of these pathogens. Although the majority of a bacterial cell population will be killed by the particular stressors, like antibiotics, oxygen and nitrogen radicals, nutrient starvation and others, a varying subpopulation (termed persisters) will withstand the stress situation and will be able to revive once the stress is removed. Several factors and pathways have been identified in the past that apparently favor the formation of persistence, such as various toxin/antitoxin modules or stringent response together with the alarmone (p)ppGpp. However, persistence can occur stochastically in few cells even of stress-free bacterial populations. Growth of these cells could then be induced by the stress conditions. In this review, we focus on the persister formation of human intracellular bacterial pathogens, some of which belong to the most successful persister producers but lack some or even all of the assumed persistence-triggering factors and pathways. We propose a mechanism for the persister formation of these bacterial pathogens which is based on their specific intracellular bipartite metabolism. We postulate that this mode of metabolism ultimately leads, under certain starvation conditions, to the stalling of DNA replication initiation which may be causative for the persister state.
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Affiliation(s)
- Wolfgang Eisenreich
- Department of Chemistry, Chair of Biochemistry, Technische Universität München, Garching, Germany
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
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Berghoff BA. Analyzing Persister Proteomes with SILAC and Label-Free Methods. Methods Mol Biol 2021; 2357:149-159. [PMID: 34590257 DOI: 10.1007/978-1-0716-1621-5_10] [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] [Indexed: 06/13/2023]
Abstract
State-of-the-art mass spectrometry enables in-depth analysis of proteomes in virtually all organisms. This chapter describes methods for the analysis of persister proteomes by mass spectrometry. Stable isotope labeling by amino acids in cell culture (SILAC) is applied to assess protein biosynthesis in persister cells, which are isolated by treatment with beta-lactam antibiotics. Furthermore, persister proteomes during the postantibiotic recovery phase are analyzed by label-free quantification. The presented methods are valuable tools to shed light on persister physiology.
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Affiliation(s)
- Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany.
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29
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Bogati B, Wadsworth N, Barrera F, Fozo EM. Improved growth of Escherichia coli in aminoglycoside antibiotics by the zor-orz toxin-antitoxin system. J Bacteriol 2021; 204:JB0040721. [PMID: 34570627 PMCID: PMC8765423 DOI: 10.1128/jb.00407-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/21/2021] [Indexed: 11/20/2022] Open
Abstract
Type I toxin-antitoxin systems consist of a small protein (under 60 amino acids) whose overproduction can result in cell growth stasis or death, and a small RNA that represses translation of the toxin mRNA. Despite their potential toxicity, type I toxin proteins are increasingly linked to improved survival of bacteria in stressful environments and antibiotic persistence. While the interaction of toxin mRNAs with their cognate antitoxin sRNAs in some systems are well characterized, additional translational control of many toxins and their biological roles are not well understood. Using an ectopic overexpression system, we show that the efficient translation of a chromosomally encoded type I toxin, ZorO, requires mRNA processing of its long 5' untranslated region (UTR; Δ28 UTR). The severity of ZorO induced toxicity on growth inhibition, membrane depolarization, and ATP depletion were significantly increased if expressed from the Δ28 UTR versus the full-length UTR. ZorO did not form large pores as evident via a liposomal leakage assay, in vivo morphological analyses, and measurement of ATP loss. Further, increasing the copy number of the entire zor-orz locus significantly improved growth of bacterial cells in the presence of kanamycin and increased the minimum inhibitory concentration against kanamycin and gentamycin; however, no such benefit was observed against other antibiotics. This supports a role for the zor-orz locus as a protective measure against specific stress agents and is likely not part of a general stress response mechanism. Combined, these data shed more insights into the possible native functions for type I toxin proteins. IMPORTANCE Bacterial species can harbor gene pairs known as type I toxin-antitoxin systems where one gene encodes a small protein that is toxic to the bacteria producing it and a second gene that encodes a small RNA antitoxin to prevent toxicity. While artificial overproduction of type I toxin proteins can lead to cell growth inhibition and cell lysis, the endogenous translation of type I toxins appears to be tightly regulated. Here, we show translational regulation controls production of the ZorO type I toxin and prevents subsequent negative effects on the cell. Further, we demonstrate a role for zorO and its cognate antitoxin in improved growth of E. coli in the presence of aminoglycoside antibiotics.
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Affiliation(s)
- Bikash Bogati
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Nicholas Wadsworth
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Francisco Barrera
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Elizabeth M. Fozo
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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Huemer M, Mairpady Shambat S, Brugger SD, Zinkernagel AS. Antibiotic resistance and persistence-Implications for human health and treatment perspectives. EMBO Rep 2020; 21:e51034. [PMID: 33400359 PMCID: PMC7726816 DOI: 10.15252/embr.202051034] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/13/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance (AMR) and persistence are associated with an elevated risk of treatment failure and relapsing infections. They are thus important drivers of increased morbidity and mortality rates resulting in growing healthcare costs. Antibiotic resistance is readily identifiable with standard microbiological assays, and the threat imposed by antibiotic resistance has been well recognized. Measures aiming to reduce resistance development and spreading of resistant bacteria are being enforced. However, the phenomenon of bacteria surviving antibiotic exposure despite being fully susceptible, so-called antibiotic persistence, is still largely underestimated. In contrast to antibiotic resistance, antibiotic persistence is difficult to measure and therefore often missed, potentially leading to treatment failures. In this review, we focus on bacterial mechanisms allowing evasion of antibiotic killing and discuss their implications on human health. We describe the relationship between antibiotic persistence and bacterial heterogeneity and discuss recent studies that link bacterial persistence and tolerance with the evolution of antibiotic resistance. Finally, we review persister detection methods, novel strategies aiming at eradicating bacterial persisters and the latest advances in the development of new antibiotics.
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Affiliation(s)
- Markus Huemer
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
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31
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Romilly C, Lippegaus A, Wagner E. An RNA pseudoknot is essential for standby-mediated translation of the tisB toxin mRNA in Escherichia coli. Nucleic Acids Res 2020; 48:12336-12347. [PMID: 33231643 PMCID: PMC7708055 DOI: 10.1093/nar/gkaa1139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/03/2020] [Accepted: 11/07/2020] [Indexed: 01/20/2023] Open
Abstract
In response to DNA damage, Escherichia coli cells activate the expression of the toxin gene tisB of the toxin-antitoxin system tisB-istR1. Of three isoforms, only the processed, highly structured +42 tisB mRNA is active. Translation requires a standby site, composed of two essential elements: a single-stranded region located 100 nucleotides upstream of the sequestered RBS, and a structure near the 5'-end of the active mRNA. Here, we propose that this 5'-structure is an RNA pseudoknot which is required for 30S and protein S1-alone binding to the mRNA. Point mutations that prevent formation of this pseudoknot inhibit formation of translation initiation complexes, impair S1 and 30S binding to the mRNA, and render the tisB mRNA non-toxic in vivo. A set of mutations created in either the left or right arm of stem 2 of the pseudoknot entailed loss of toxicity upon overexpression of the corresponding mRNA variants. Combining the matching right-left arm mutations entirely restored toxicity levels to that of the wild-type, active mRNA. Finally, since many pseudoknots have high affinity for S1, we predicted similar pseudoknots in non-homologous type I toxin-antitoxin systems that exhibit features similar to that of tisB-IstR1, suggesting a shared requirement for standby acting at great distances.
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MESH Headings
- Bacterial Toxins/genetics
- Bacterial Toxins/metabolism
- Base Pairing
- Base Sequence
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Gene Expression Regulation, Bacterial
- Nucleic Acid Conformation
- Point Mutation
- Protein Binding
- Protein Biosynthesis
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Small, Bacterial/genetics
- Ribosome Subunits, Small, Bacterial/metabolism
- Toxin-Antitoxin Systems/genetics
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Affiliation(s)
- Cédric Romilly
- Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden
| | - Anne Lippegaus
- Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden
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32
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Liu S, Brul S, Zaat SAJ. Bacterial Persister-Cells and Spores in the Food Chain: Their Potential Inactivation by Antimicrobial Peptides (AMPs). Int J Mol Sci 2020; 21:E8967. [PMID: 33260797 PMCID: PMC7731242 DOI: 10.3390/ijms21238967] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022] Open
Abstract
The occurrence of bacterial pathogens in the food chain has caused a severe impact on public health and welfare in both developing and developed countries. Moreover, the existence of antimicrobial-tolerant persisting morphotypes of these pathogens including both persister-cells as well as bacterial spores contributes to difficulty in elimination and in recurrent infection. Therefore, comprehensive understanding of the behavior of these persisting bacterial forms in their environmental niche and upon infection of humans is necessary. Since traditional antimicrobials fail to kill persisters and spores due to their (extremely) low metabolic activities, antimicrobial peptides (AMPs) have been intensively investigated as one of the most promising strategies against these persisting bacterial forms, showing high efficacy of inactivation. In addition, AMP-based foodborne pathogen detection and prevention of infection has made significant progress. This review focuses on recent research on common bacterial pathogens in the food chain, their persisting morphotypes, and on AMP-based solutions. Challenges in research and application of AMPs are described.
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Affiliation(s)
- Shiqi Liu
- Swammerdam Institute for Life Sciences, Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Stanley Brul
- Swammerdam Institute for Life Sciences, Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Sebastian A. J. Zaat
- Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
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33
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A peptide of a type I toxin-antitoxin system induces Helicobacter pylori morphological transformation from spiral shape to coccoids. Proc Natl Acad Sci U S A 2020; 117:31398-31409. [PMID: 33229580 DOI: 10.1073/pnas.2016195117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Toxin-antitoxin systems are found in many bacterial chromosomes and plasmids with roles ranging from plasmid stabilization to biofilm formation and persistence. In these systems, the expression/activity of the toxin is counteracted by an antitoxin, which, in type I systems, is an antisense RNA. While the regulatory mechanisms of these systems are mostly well defined, the toxins' biological activity and expression conditions are less understood. Here, these questions were investigated for a type I toxin-antitoxin system (AapA1-IsoA1) expressed from the chromosome of the human pathogen Helicobacter pylori We show that expression of the AapA1 toxin in H. pylori causes growth arrest associated with rapid morphological transformation from spiral-shaped bacteria to round coccoid cells. Coccoids are observed in patients and during in vitro growth as a response to different stress conditions. The AapA1 toxin, first molecular effector of coccoids to be identified, targets H. pylori inner membrane without disrupting it, as visualized by cryoelectron microscopy. The peptidoglycan composition of coccoids is modified with respect to spiral bacteria. No major changes in membrane potential or adenosine 5'-triphosphate (ATP) concentration result from AapA1 expression, suggesting coccoid viability. Single-cell live microscopy tracking the shape conversion suggests a possible association of this process with cell elongation/division interference. Oxidative stress induces coccoid formation and is associated with repression of the antitoxin promoter and enhanced processing of its transcript, leading to an imbalance in favor of AapA1 toxin expression. Our data support the hypothesis of viable coccoids with characteristics of dormant bacteria that might be important in H. pylori infections refractory to treatment.
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34
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Antibiotic-induced DNA damage results in a controlled loss of pH homeostasis and genome instability. Sci Rep 2020; 10:19422. [PMID: 33173044 PMCID: PMC7655802 DOI: 10.1038/s41598-020-76426-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/27/2020] [Indexed: 11/08/2022] Open
Abstract
Extracellular pH has been assumed to play little if any role in how bacteria respond to antibiotics and antibiotic resistance development. Here, we show that the intracellular pH of Escherichia coli equilibrates to the environmental pH following treatment with the DNA damaging antibiotic nalidixic acid. We demonstrate that this allows the environmental pH to influence the transcription of various DNA damage response genes and physiological processes such as filamentation. Using purified RecA and a known pH-sensitive mutant variant RecA K250R we show how pH can affect the biochemical activity of a protein central to control of the bacterial DNA damage response system. Finally, two different mutagenesis assays indicate that environmental pH affects antibiotic resistance development. Specifically, at environmental pH's greater than six we find that mutagenesis plays a significant role in producing antibiotic resistant mutants. At pH's less than or equal to 6 the genome appears more stable but extensive filamentation is observed, a phenomenon that has previously been linked to increased survival in the presence of macrophages.
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35
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Huang X, Chen R, Sun M, Peng Y, Pu Q, Yuan Y, Chen G, Dong J, Du F, Cui X, Tang Z. Frame-shifted proteins of a given gene retain the same function. Nucleic Acids Res 2020; 48:4396-4404. [PMID: 32187359 PMCID: PMC7192591 DOI: 10.1093/nar/gkaa169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 01/21/2023] Open
Abstract
Frameshift mutations are generally considered to be lethal because it could result in radical changes of the protein sequence behind. However, the protein of frameshift mutants of a type I toxin (ibsc) was found to be still toxic to bacteria, retaining the similar function as wild-type protein to arrest the cellular growth by impairing the membrane's integrity. Additionally, we have verified that this observation is not an individual event as the same phenomenon had been found in other toxins subsequently. After analyzing the coding sequence of these genes, we proposed a hypothesis to search this kind of hidden gene, through which a dihydrofolate reductase-encoding gene (dfrB3) was found out. Like the wild-type reductase, both +1 and -1 frame-shifted proteins of dfrB3 gene were also proved to catalyze the reduction of dihydrofolate to tetrahydrofolate by using NADPH.
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Affiliation(s)
- Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Rong Chen
- Ethnomedicine College, Chengdu University of Traditional Chinese Medicine, Chengdu 610041, P. R. China
| | - Meiling Sun
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Yan Peng
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
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Garai P, Blanc‐Potard A. Uncovering small membrane proteins in pathogenic bacteria: Regulatory functions and therapeutic potential. Mol Microbiol 2020; 114:710-720. [DOI: 10.1111/mmi.14564] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Preeti Garai
- Laboratory of Pathogen‐Host Interactions Université de MontpellierCNRS‐UMR5235 Montpellier France
| | - Anne Blanc‐Potard
- Laboratory of Pathogen‐Host Interactions Université de MontpellierCNRS‐UMR5235 Montpellier France
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37
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Kang SM, Koo JS, Kim CM, Kim DH, Lee BJ. mRNA Interferase Bacillus cereus BC0266 Shows MazF-Like Characteristics Through Structural and Functional Study. Toxins (Basel) 2020; 12:toxins12060380. [PMID: 32521689 PMCID: PMC7354611 DOI: 10.3390/toxins12060380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 11/16/2022] Open
Abstract
Toxin–antitoxin (TA) systems are prevalent in bacteria and are known to regulate cellular growth in response to stress. As various functions related to TA systems have been revealed, the importance of TA systems are rapidly emerging. Here, we present the crystal structure of putative mRNA interferase BC0266 and report it as a type II toxin MazF. The MazF toxin is a ribonuclease activated upon and during stressful conditions, in which it cleaves mRNA in a sequence-specific, ribosome-independent manner. Its prolonged activity causes toxic consequences to the bacteria which, in turn, may lead to bacterial death. In this study, we conducted structural and functional investigations of Bacillus cereus MazF and present the first toxin structure in the TA system of B. cereus. Specifically, B. cereus MazF adopts a PemK-like fold and also has an RNA substrate-recognizing loop, which is clearly observed in the high-resolution structure. Key residues of B. cereus MazF involved in the catalytic activity are also proposed, and in vitro assay together with mutational studies affirm the ribonucleic activity and the active sites essential for its cellular toxicity.
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Affiliation(s)
- Sung-Min Kang
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
| | - Ji Sung Koo
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
| | - Chang-Min Kim
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
| | - Do-Hee Kim
- College of Pharmacy, Jeju National University, Jeju 63243, Korea;
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
- Correspondence: ; Tel.: +82-2-880-7869
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38
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Rosendahl S, Tamman H, Brauer A, Remm M, Hõrak R. Chromosomal toxin-antitoxin systems in Pseudomonas putida are rather selfish than beneficial. Sci Rep 2020; 10:9230. [PMID: 32513960 PMCID: PMC7280312 DOI: 10.1038/s41598-020-65504-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
Chromosomal toxin-antitoxin (TA) systems are widespread genetic elements among bacteria, yet, despite extensive studies in the last decade, their biological importance remains ambivalent. The ability of TA-encoded toxins to affect stress tolerance when overexpressed supports the hypothesis of TA systems being associated with stress adaptation. However, the deletion of TA genes has usually no effects on stress tolerance, supporting the selfish elements hypothesis. Here, we aimed to evaluate the cost and benefits of chromosomal TA systems to Pseudomonas putida. We show that multiple TA systems do not confer fitness benefits to this bacterium as deletion of 13 TA loci does not influence stress tolerance, persistence or biofilm formation. Our results instead show that TA loci are costly and decrease the competitive fitness of P. putida. Still, the cost of multiple TA systems is low and detectable in certain conditions only. Construction of antitoxin deletion strains showed that only five TA systems code for toxic proteins, while other TA loci have evolved towards reduced toxicity and encode non-toxic or moderately potent proteins. Analysis of P. putida TA systems’ homologs among fully sequenced Pseudomonads suggests that the TA loci have been subjected to purifying selection and that TA systems spread among bacteria by horizontal gene transfer.
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Affiliation(s)
- Sirli Rosendahl
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Hedvig Tamman
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Age Brauer
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Rita Hõrak
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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39
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Kubatova N, Pyper DJ, Jonker HRA, Saxena K, Remmel L, Richter C, Brantl S, Evguenieva‐Hackenberg E, Hess WR, Klug G, Marchfelder A, Soppa J, Streit W, Mayzel M, Orekhov VY, Fuxreiter M, Schmitz RA, Schwalbe H. Rapid Biophysical Characterization and NMR Spectroscopy Structural Analysis of Small Proteins from Bacteria and Archaea. Chembiochem 2020; 21:1178-1187. [PMID: 31705614 PMCID: PMC7217052 DOI: 10.1002/cbic.201900677] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Indexed: 01/08/2023]
Abstract
Proteins encoded by small open reading frames (sORFs) have a widespread occurrence in diverse microorganisms and can be of high functional importance. However, due to annotation biases and their technically challenging direct detection, these small proteins have been overlooked for a long time and were only recently rediscovered. The currently rapidly growing number of such proteins requires efficient methods to investigate their structure-function relationship. Herein, a method is presented for fast determination of the conformational properties of small proteins. Their small size makes them perfectly amenable for solution-state NMR spectroscopy. NMR spectroscopy can provide detailed information about their conformational states (folded, partially folded, and unstructured). In the context of the priority program on small proteins funded by the German research foundation (SPP2002), 27 small proteins from 9 different bacterial and archaeal organisms have been investigated. It is found that most of these small proteins are unstructured or partially folded. Bioinformatics tools predict that some of these unstructured proteins can potentially fold upon complex formation. A protocol for fast NMR spectroscopy structure elucidation is described for the small proteins that adopt a persistently folded structure by implementation of new NMR technologies, including automated resonance assignment and nonuniform sampling in combination with targeted acquisition.
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Affiliation(s)
- Nina Kubatova
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Laura Remmel
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Sabine Brantl
- AG BakteriengenetikMatthias-Schleiden-InstitutPhilosophenweg 1207743JenaGermany
| | - Elena Evguenieva‐Hackenberg
- Institute for Microbiology and Molecular BiologyJustus Liebig University GiessenHeinrich-Buff-Ring 2635392GiessenGermany
| | - Wolfgang R. Hess
- Faculty of Biology, Genetics and Experimental BioinformaticsAlbert Ludwigs University FreiburgSchänzlestrasse 179104FreiburgGermany
| | - Gabriele Klug
- Institute for Microbiology and Molecular BiologyJustus Liebig University GiessenHeinrich-Buff-Ring 2635392GiessenGermany
| | | | - Jörg Soppa
- Institute for Molecular BiosciencesJohann Wolfgang Goethe UniversityMax-von-Laue-Strasse 960438Frankfurt am MainGermany
| | - Wolfgang Streit
- Department of Microbiology and BiotechnologyUniversity of HamburgOhnhorststrasse 1822609HamburgGermany
| | - Maxim Mayzel
- Swedish NMR CentreUniversity of GothenburgP. O. Box 46540530GothenburgSweden
| | - Vladislav Y. Orekhov
- Swedish NMR CentreUniversity of GothenburgP. O. Box 46540530GothenburgSweden
- Department of Chemistry and Molecular BiologyUniversity of GothenburgKemigården 441296GothenburgSweden
| | - Monika Fuxreiter
- MTA-DE Laboratory of Protein DynamicsDepartment of Biochemistry and Molecular BiologyUniversity of DebrecenNagyerdei krt 984032DebrecenHungary
| | - Ruth A. Schmitz
- Institute for General MicrobiologyChristian Albrechts University KielAm Botanischen Garten 1–924118KielGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
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Liu X, Wang C, Yan B, Lyu L, Takiff HE, Gao Q. The potassium transporter KdpA affects persister formation by regulating ATP levels in Mycobacterium marinum. Emerg Microbes Infect 2020; 9:129-139. [PMID: 31913766 PMCID: PMC6968386 DOI: 10.1080/22221751.2019.1710090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mycobacterial persistence mechanisms remain to be fully characterized. Screening a transposon insertion library of Mycobacterium marinum identified kdpA, whose inactivation reduced the fraction of persisters after exposure to rifampicin. kdpA encodes a transmembrane protein that is part of the Kdp-ATPase, an ATP-dependent high-affinity potassium (K+) transport system. We found that kdpA is induced under low K+ conditions and is required for pH homeostasis and growth in media with low concentrations of K+. The inactivation of the Kdp system in a kdpA insertion mutant caused hyperpolarization of the cross-membrane potential, increased proton motive force (PMF) and elevated levels of intracellular ATP. The KdpA mutant phenotype could be complemented with a functional kdpA gene or supplementation with high K+ concentrations. Taken together, our results suggest that the Kdp system is required for ATP homeostasis and persister formation. The results also confirm that ATP-mediated regulation of persister formation is a general mechanism in bacteria, and suggest that K+ transporters could play a role in the regulation of ATP levels and persistence. These findings could have implications for the development of new drugs that could either target persisters or reduce their presence.
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Affiliation(s)
- Xiaofan Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Bo Yan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Liangdong Lyu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Howard E Takiff
- Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, Paris, France
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
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Zamakhaev MV, Goncharenko AV, Shumkov MS. Toxin-Antitoxin Systems and Bacterial Persistence (Review). APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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42
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Edelmann D, Berghoff BA. Type I toxin-dependent generation of superoxide affects the persister life cycle of Escherichia coli. Sci Rep 2019; 9:14256. [PMID: 31582786 PMCID: PMC6776643 DOI: 10.1038/s41598-019-50668-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/17/2019] [Indexed: 12/15/2022] Open
Abstract
Induction of growth stasis by bacterial toxins from chromosomal toxin-antitoxin systems is suspected to favor formation of multidrug-tolerant cells, named persisters. Recurrent infections are often attributed to resuscitation and regrowth of persisters upon termination of antibiotic therapy. Several lines of evidence point to oxidative stress as a crucial factor during the persister life cycle. Here, we demonstrate that the membrane-depolarizing type I toxins TisB, DinQ, and HokB have the potential to provoke reactive oxygen species formation in Escherichia coli. More detailed work with TisB revealed that mainly superoxide is formed, leading to activation of the SoxRS regulon. Deletion of the genes encoding the cytoplasmic superoxide dismutases SodA and SodB caused both a decline in TisB-dependent persisters and a delay in persister recovery upon termination of antibiotic treatment. We hypothesize that expression of depolarizing toxins during the persister formation process inflicts an oxidative challenge. The ability to counteract oxidative stress might determine whether cells will survive and how much time they need to recover from dormancy.
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Affiliation(s)
- Daniel Edelmann
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, 35392, Giessen, Germany.
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Structural insights into the AapA1 toxin of Helicobacter pylori. Biochim Biophys Acta Gen Subj 2019; 1864:129423. [PMID: 31476357 DOI: 10.1016/j.bbagen.2019.129423] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/12/2019] [Accepted: 08/28/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND We previously reported the identification of the aapA1/IsoA1 locus as part of a new family of toxin-antitoxin (TA) systems in the human pathogen Helicobacter pylori. AapA1 belongs to type I TA bacterial toxins, and both its mechanism of action towards the membrane and toxicity features are still unclear. METHODS The biochemical characterization of the AapA1 toxic peptide was carried out using plasmid-borne expression and mutational approaches to follow its toxicity and localization. Biophysical properties of the AapA1 interaction with lipid membranes were studied by solution and solid-state NMR spectroscopy, plasmon waveguide resonance (PWR) and molecular modeling. RESULTS We show that despite a low hydrophobic index, this toxin has a nanomolar affinity to the prokaryotic membrane. NMR spectroscopy reveals that the AapA1 toxin is structurally organized into three distinct domains: a positively charged disordered N-terminal domain (D), a single α-helix (H), and a basic C-terminal domain (R). The R domain interacts and destabilizes the membrane, while the H domain adopts a transmembrane conformation. These results were confirmed by alanine scanning of the minimal sequence required for toxicity. CONCLUSION Our results have shown that specific amino acid residues along the H domain, as well as the R domain, are essential for the toxicity of the AapA1 toxin. GENERAL SIGNIFICANCE Untangling and understanding the mechanism of action of small membrane-targeting toxins are difficult, but nevertheless contributes to a promising search and development of new antimicrobial drugs.
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The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5' structure element. Proc Natl Acad Sci U S A 2019; 116:15901-15906. [PMID: 31320593 PMCID: PMC6690012 DOI: 10.1073/pnas.1904309116] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ribosome standby is a mechanism that allows translation initiation at ribosome-binding sites that display stable, inhibitory structures. It involves initiator-tRNA-independent 30S subunit binding to single-stranded RNA regions, and the subsequent relocation to the sequestered ribosome-binding sites (RBS). Direct evidence for 30S preloading had previously been elusive. We report here on a detailed characterization of the standby site in tisB mRNA. 30S subunits bind to a single-stranded region and a 5′-stem-loop structure, as shown by fluorescence anisotropy experiments and footprint mapping by cross-linking–immunoprecipitation experiments. Ribosomal protein S1, on its own and in the context of the 30S ribosome, binds to the standby site. This is required for standby-dependent translation, likely reflecting S1-dependent directional unfolding over more than ≈100 nt to reach the sequestered RBS. In bacteria, stable RNA structures that sequester ribosome-binding sites (RBS) impair translation initiation, and thus protein output. In some cases, ribosome standby can overcome inhibition by structure: 30S subunits bind sequence-nonspecifically to a single-stranded region and, on breathing of the inhibitory structure, relocate to the RBS for initiation. Standby can occur over long distances, as in the active, +42 tisB mRNA, encoding a toxin. This mRNA is translationally silenced by an antitoxin sRNA, IstR-1, that base pairs to the standby site. In tisB and other cases, a direct interaction between 30S subunits and a standby site has remained elusive. Based on fluorescence anisotropy experiments, ribosome toeprinting results, in vitro translation assays, and cross-linking–immunoprecipitation (CLIP) in vitro, carried out on standby-proficient and standby-deficient tisB mRNAs, we provide a thorough characterization of the tisB standby site. 30S subunits and ribosomal protein S1 alone display high-affinity binding to standby-competent fluorescein-labeled +42 mRNA, but not to mRNAs that lack functional standby sites. Ribosomal protein S1 is essential for standby, as 30∆S1 subunits do not support standby-dependent toeprints and TisB translation in vitro. S1 alone- and 30S-CLIP followed by RNA-seq mapping shows that the functional tisB standby site consists of the expected single-stranded region, but surprisingly, also a 5′-end stem-loop structure. Removal of the latter by 5′-truncations, or disruption of the stem, abolishes 30S binding and standby activity. Based on the CLIP-read mapping, the long-distance standby effect in +42 tisB mRNA (∼100 nt) is tentatively explained by S1-dependent directional unfolding toward the downstream RBS.
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45
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Goormaghtigh F, Van Melderen L. Single-cell imaging and characterization of Escherichia coli persister cells to ofloxacin in exponential cultures. SCIENCE ADVANCES 2019; 5:eaav9462. [PMID: 31223653 PMCID: PMC6584399 DOI: 10.1126/sciadv.aav9462] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/10/2019] [Indexed: 06/02/2023]
Abstract
Bacterial persistence refers to the capacity of small subpopulations within clonal populations to tolerate antibiotics. Persisters are thought to originate from dormant cells in which antibiotic targets are less active and cannot be corrupted. Here, we report that in exponentially growing cultures, ofloxacin persisters originate from metabolically active cells: These cells are dividing before the addition of ofloxacin and do endure DNA damages during the treatment, similar to their nonpersister siblings. We observed that growth rate, DNA content, and SOS induction vary among persisters, as in the bulk of the population and therefore do not constitute predictive markers for persistence. Persister cells typically form long polynucleoid filaments and reach maximum SOS induction after removal of ofloxacin. Eventually, cell division resumes, giving rise to a new population. Our findings highlight the heterogeneity of persister cells and therefore the need to analyze these low-frequency phenotypic variants on a case-by-case basis at the single-cell level.
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Affiliation(s)
- Frédéric Goormaghtigh
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
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46
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Brantl S, Müller P. Toxin⁻Antitoxin Systems in Bacillus subtilis. Toxins (Basel) 2019; 11:toxins11050262. [PMID: 31075979 PMCID: PMC6562991 DOI: 10.3390/toxins11050262] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/30/2019] [Accepted: 05/07/2019] [Indexed: 12/31/2022] Open
Abstract
Toxin-antitoxin (TA) systems were originally discovered as plasmid maintenance systems in a multitude of free-living bacteria, but were afterwards found to also be widespread in bacterial chromosomes. TA loci comprise two genes, one coding for a stable toxin whose overexpression kills the cell or causes growth stasis, and the other coding for an unstable antitoxin that counteracts toxin action. Of the currently known six types of TA systems, in Bacillus subtilis, so far only type I and type II TA systems were found, all encoded on the chromosome. Here, we review our present knowledge of these systems, the mechanisms of antitoxin and toxin action, and the regulation of their expression, and we discuss their evolution and possible physiological role.
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Affiliation(s)
- Sabine Brantl
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany.
| | - Peter Müller
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany.
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47
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Spanka DT, Konzer A, Edelmann D, Berghoff BA. High-Throughput Proteomics Identifies Proteins With Importance to Postantibiotic Recovery in Depolarized Persister Cells. Front Microbiol 2019; 10:378. [PMID: 30894840 PMCID: PMC6414554 DOI: 10.3389/fmicb.2019.00378] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial populations produce phenotypic variants called persisters to survive harmful conditions. Persisters are highly tolerant to antibiotics and repopulate environments after the stress has vanished. In order to resume growth, persisters have to recover from the persistent state, but the processes behind recovery remain mostly elusive. Deciphering these processes is an essential step toward understanding the persister phenomenon in its entirety. High-throughput proteomics by mass spectrometry is a valuable tool to assess persister physiology during any stage of the persister life cycle, and is expected to considerably contribute to our understanding of the recovery process. In the present study, an Escherichia coli strain, that overproduces the membrane-depolarizing toxin TisB, was established as a model for persistence by the use of high-throughput proteomics. Labeling of TisB persisters with stable isotope-containing amino acids (pulsed-SILAC) revealed an active translational response to ampicillin, including several RpoS-dependent proteins. Subsequent investigation of the persister proteome during postantibiotic recovery by label-free quantitative proteomics identified proteins with importance to the recovery process. Among them, AhpF, a component of alkyl hydroperoxide reductase, and the outer membrane porin OmpF were found to affect the persistence time of TisB persisters. Assessing the role of AhpF and OmpF in TisB-independent persisters demonstrated that the importance of a particular protein for the recovery process strongly depends on the physiological condition of a persister cell. Our study provides important insights into persister physiology and the processes behind recovery of depolarized cells.
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Affiliation(s)
- Daniel-Timon Spanka
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Daniel Edelmann
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
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48
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Schneider V, Wadhwani P, Reichert J, Bürck J, Elstner M, Ulrich AS, Kubař T. Tetrameric Charge-Zipper Assembly of the TisB Peptide in Membranes—Computer Simulation and Experiment. J Phys Chem B 2019; 123:1770-1779. [DOI: 10.1021/acs.jpcb.8b12087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021 Karlsruhe, Germany
| | - Johannes Reichert
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P. O. Box 3640, 76021 Karlsruhe, Germany
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Type I Toxin-Antitoxin Systems: Regulating Toxin Expression via Shine-Dalgarno Sequence Sequestration and Small RNA Binding. Microbiol Spectr 2019; 6. [PMID: 30051800 DOI: 10.1128/microbiolspec.rwr-0030-2018] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Toxin-antitoxin (TA) systems are small genetic loci composed of two adjacent genes: a toxin and an antitoxin that prevents toxin action. Despite their wide distribution in bacterial genomes, the reasons for TA systems being on chromosomes remain enigmatic. In this review, we focus on type I TA systems, composed of a small antisense RNA that plays the role of an antitoxin to control the expression of its toxin counterpart. It does so by direct base-pairing to the toxin-encoding mRNA, thereby inhibiting its translation and/or promoting its degradation. However, in many cases, antitoxin binding is not sufficient to avoid toxicity. Several cis-encoded mRNA elements are also required for repression, acting to uncouple transcription and translation via the sequestration of the ribosome binding site. Therefore, both antisense RNA binding and compact mRNA folding are necessary to tightly control toxin synthesis and allow the presence of these toxin-encoding systems on bacterial chromosomes.
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50
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Chen X, Li G, Liao X, Fang J, Li B, Yu S, Sun M, Wu J, Zhang L, Hu Y, Jiao J, Liu T, Xu L, Chen X, Liu M, Li H, Hu F, Sun K. A switch in the poly(dC)/RmlB complex regulates bacterial persister formation. Nat Commun 2019; 10:27. [PMID: 30604752 PMCID: PMC6318315 DOI: 10.1038/s41467-018-07861-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 11/27/2018] [Indexed: 01/16/2023] Open
Abstract
Bacterial persisters are phenotypic variants that tolerate exposure to lethal antibiotics. These dormant cells are responsible for chronic and recurrent infections. Multiple mechanisms have been linked to persister formation. Here, we report that a complex, consisting of an extracellular poly(dC) and its membrane-associated binding protein RmlB, appears to be associated with persistence of the opportunistic pathogen Pseudomonas aeruginosa. Environmental stimuli triggers a switch in the complex physiological state (from poly(dC)/RmlB to P-poly(dC)/RmlB or RmlB). In response to the switch, bacteria decrease proton motive force and intracellular ATP levels, forming dormant cells. This alteration in complex status is linked to a (p)ppGpp-controlled signaling pathway that includes inorganic polyphosphate, Lon protease, exonuclease VII (XseA/XseB), and the type III secretion system. The persistence might be also an adaptive response to the lethal action of the dTDP-l-rhamnose pathway shutdown, which occurs due to switching of poly(dC)/RmlB. The mechanisms underlying bacterial persisters formation remain poorly understood. Here, Chen et al. identify a complex formed by extracellular poly(dC) and the binding protein RmlB that controls Pseudomonas aeruginosa persister formation in response to environmental stimuli.
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Affiliation(s)
- Xu Chen
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Gen Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xuewei Liao
- Center for Analysis and Testing, Nanjing Normal University, Nanjing, China
| | - Jie Fang
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Bo Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shanshan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jun Wu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Lihao Zhang
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yi Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiaguo Jiao
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ting Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Li Xu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyun Chen
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Manqiang Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China.,Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, China
| | - Huixin Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Kouhong Sun
- Zoonbio Biotechnology Co., Ltd, Nanjing, China
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