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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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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3
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Cheng T, Boneca IG. The shapeshifting Helicobacter pylori: From a corkscrew to a ball. Mol Microbiol 2024; 121:260-274. [PMID: 38173305 DOI: 10.1111/mmi.15218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/08/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024]
Abstract
There is growing evidence that bacterial morphology is closely related to their lifestyle. The helical Helicobacter pylori relies on its unique shape for survival and efficient colonization of the human stomach. Yet, they have been observed to transform into another distinctive morphology, the spherical coccoid. Despite being hypothesized to be involved in the persistence and transmission of this species, years of effort in deciphering the roles of the coccoid form remain fruitless since contrasting observations regarding its lifestyle were reported. Here, we discuss the two forms of H. pylori with a focus on the coccoid form, the molecular mechanism behind its morphological transformation, and experimental approaches to further develop our understanding of this phenomenon. We also propose a putative mechanism of the coccoid formation in H. pylori through induction of a type-I toxin-antitoxin (TA) system recently shown to influence the morphology of this species.
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Affiliation(s)
- Thimoro Cheng
- Institut Pasteur, Université Paris Cité, Unité Biologie et génétique de la paroi bactérienne, Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, Unité Biologie et génétique de la paroi bactérienne, Paris, France
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4
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Singh A, Lankapalli AK, Mendem SK, Semmler T, Ahmed N. Unraveling the evolutionary dynamics of toxin-antitoxin systems in diverse genetic lineages of Escherichia coli including the high-risk clonal complexes. mBio 2024; 15:e0302323. [PMID: 38117088 PMCID: PMC10790755 DOI: 10.1128/mbio.03023-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Large-scale genomic studies of E. coli provide an invaluable opportunity to understand how genomic fine-tuning contributes to the transition of bacterial lifestyle from being commensals to mutualists or pathogens. Within this context, through machine learning-based studies, it appears that TA systems play an important role in the classification of high-risk clonal lineages and could be attributed to their epidemiological success. Due to these profound indications and assumptions, we attempted to provide unique insights into the ordered world of TA systems at the population level by investigating the diversity and evolutionary patterns of TA genes across 19 different STs of E. coli. Further in-depth analysis of ST-specific TA structures and associated genetic coordinates holds the potential to elucidate the functional implications of TA systems in bacterial cell survival and persistence, by and large.
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Affiliation(s)
- Anuradha Singh
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
| | - Aditya Kumar Lankapalli
- Department of Biology and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Suresh Kumar Mendem
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
| | | | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
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5
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Kang SM. Focused Overview of Mycobacterium tuberculosis VapBC Toxin-Antitoxin Systems Regarding Their Structural and Functional Aspects: Including Insights on Biomimetic Peptides. Biomimetics (Basel) 2023; 8:412. [PMID: 37754163 PMCID: PMC10526153 DOI: 10.3390/biomimetics8050412] [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: 08/23/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, is a lethal infectious disease of significant public health concern. The rise of multidrug-resistant and drug-tolerant strains has necessitated novel approaches to combat the disease. Toxin-antitoxin (TA) systems, key players in bacterial adaptive responses, are prevalent in prokaryotic genomes and have been linked to tuberculosis. The genome of M. tuberculosis strains harbors an unusually high number of TA systems, prompting questions about their biological roles. The VapBC family, a representative type II TA system, is characterized by the VapC toxin, featuring a PilT N-terminal domain with nuclease activity. Its counterpart, VapB, functions as an antitoxin, inhibiting VapC's activity. Additionally, we explore peptide mimics designed to replicate protein helical structures in this review. Investigating these synthetic peptides offers fresh insights into molecular interactions, potentially leading to therapeutic applications. These synthetic peptides show promise as versatile tools for modulating cellular processes and protein-protein interactions. We examine the rational design strategies employed to mimic helical motifs, their biophysical properties, and potential applications in drug development and bioengineering. This review aims to provide an in-depth understanding of TA systems by introducing known complex structures, with a focus on both structural aspects and functional and molecular details associated with each system.
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Affiliation(s)
- Sung-Min Kang
- College of Pharmacy, Duksung Women's University, Seoul 01369, Republic of Korea
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6
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Ernits K, Saha CK, Brodiazhenko T, Chouhan B, Shenoy A, Buttress JA, Duque-Pedraza JJ, Bojar V, Nakamoto JA, Kurata T, Egorov AA, Shyrokova L, Johansson MJO, Mets T, Rustamova A, Džigurski J, Tenson T, Garcia-Pino A, Strahl H, Elofsson A, Hauryliuk V, Atkinson GC. The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems. Proc Natl Acad Sci U S A 2023; 120:e2305393120. [PMID: 37556498 PMCID: PMC10440598 DOI: 10.1073/pnas.2305393120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile genetic elements. Type II TAs are encoded as bicistronic (two-gene) operons that encode two proteins: a toxin and a neutralizing antitoxin. Using our tool NetFlax (standing for Network-FlaGs for toxins and antitoxins), we have performed a large-scale bioinformatic analysis of proteinaceous TAs, revealing interconnected clusters constituting a core network of TA-like gene pairs. To understand the structural basis of toxin neutralization by antitoxins, we have predicted the structures of 3,419 complexes with AlphaFold2. Together with mutagenesis and functional assays, our structural predictions provide insights into the neutralizing mechanism of the hyperpromiscuous Panacea antitoxin domain. In antitoxins composed of standalone Panacea, the domain mediates direct toxin neutralization, while in multidomain antitoxins the neutralization is mediated by other domains, such as PAD1, Phd-C, and ZFD. We hypothesize that Panacea acts as a sensor that regulates TA activation. We have experimentally validated 16 NetFlax TA systems and used domain annotations and metabolic labeling assays to predict their potential mechanisms of toxicity (such as membrane disruption, and inhibition of cell division or protein synthesis) as well as biological functions (such as antiphage defense). We have validated the antiphage activity of a RosmerTA system encoded by Gordonia phage Kita, and used fluorescence microscopy to confirm its predicted membrane-depolarizing activity. The interactive version of the NetFlax TA network that includes structural predictions can be accessed at http://netflax.webflags.se/.
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Affiliation(s)
- Karin Ernits
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | - Chayan Kumar Saha
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | | | - Bhanu Chouhan
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
- Department of Molecular Biology, Umeå University, Umeå901 87, Sweden
| | - Aditi Shenoy
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna171 21, Sweden
| | - Jessica A. Buttress
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon TyneNE2 4AX, United Kingdom
| | | | - Veda Bojar
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | - Jose A. Nakamoto
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | - Tatsuaki Kurata
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | - Artyom A. Egorov
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | - Lena Shyrokova
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | | | - Toomas Mets
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
- Institute of Technology, University of Tartu, Tartu50411, Estonia
| | - Aytan Rustamova
- Institute of Technology, University of Tartu, Tartu50411, Estonia
| | | | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu50411, Estonia
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles, Brussels1050, Belgium
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon TyneNE2 4AX, United Kingdom
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna171 21, Sweden
| | - Vasili Hauryliuk
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
- Institute of Technology, University of Tartu, Tartu50411, Estonia
- Science for Life Laboratory, Lund221 84, Sweden
- Lund University Virus Centre, Lund221 84, Sweden
| | - Gemma C. Atkinson
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
- Lund University Virus Centre, Lund221 84, Sweden
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7
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Kang YS, Kirby JE. A Versatile Nanoluciferase Reporter Reveals Structural Properties Associated with a Highly Efficient, N-Terminal Legionella pneumophila Type IV Secretion Translocation Signal. Microbiol Spectr 2023; 11:e0233822. [PMID: 36815834 PMCID: PMC10100965 DOI: 10.1128/spectrum.02338-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
Many Gram-negative pathogens rely on type IV secretion systems (T4SS) for infection. One limitation has been the lack of ideal reporters to identify T4SS translocated effectors and study T4SS function. Most reporter systems make use of fusions to reporter proteins, in particular, β-lactamase (TEM) and calmodulin-dependent adenylate cyclase (CYA), that allow detection of translocated enzymatic activity inside host cells. However, both systems require costly reagents and use complex, multistep procedures for loading host cells with substrate (TEM) or for analysis (CYA). Therefore, we have developed and characterized a novel reporter system using nanoluciferase (NLuc) fusions to address these limitations. Serendipitously, we discovered that Nluc itself is efficiently translocated by Legionella pneumophila T4SS in an IcmSW chaperone-dependent manner via an N-terminal translocation signal. Extensive mutagenesis in the NLuc N terminus suggested the importance of an α-helical domain spanning D5 to V9, as mutations predicted to disrupt this structure, with one exception, were translocation defective. Notably, NLuc was capable of translocating several proteins examined when fused to the N or C terminus, while maintaining robust luciferase activity. In particular, it delivered the split GFP11 fragment into J774 macrophages transfected with GFPopt, thereby resulting in in vivo assembly of superfolder green fluorescent protein (GFP). This provided a bifunctional assay in which translocation could be assayed by fluorescence microplate, confocal microscopy, and/or luciferase assays. We further identified an optimal NLuc substrate which allowed a robust, inexpensive, one-step, high-throughput screening assay to identify T4SS translocation substrates and inhibitors. Taken together, these results indicate that NLuc provides both new insight into and also tools for studying T4SS biology. IMPORTANCE Type IV secretion systems (T4SS) are used by Gram-negative pathogens to coopt host cell function. However, the translocation signals recognized by T4SS are not fully explained by primary amino acid sequence, suggesting yet-to-be-defined contributions of secondary and tertiary structure. Here, we unexpectedly identified nanoluciferase (NLuc) as an efficient IcmSW-dependent translocated T4SS substrate, and we provide extensive mutagenesis data suggesting that the first N-terminal, alpha-helix domain is a critical translocation recognition motif. Notably, most existing reporter systems for studying translocated proteins make use of fusions to reporters to permit detection of translocated enzymatic activity inside the host cell. However, existing systems require extremely costly substrates, complex technical procedures to isolate eukaryotic cytoplasm for analysis, and/or are insensitive. Importantly, we found that NLuc provides a powerful, cost-effective new tool to address these limitations and facilitate high-throughput exploration of secretion system biology.
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Affiliation(s)
- Yoon-Suk Kang
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - James E. Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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8
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Gosain TP, Singh M, Singh C, Thakur KG, Singh R. Disruption of MenT2 toxin impairs the growth of Mycobacterium tuberculosis in guinea pigs. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36342835 DOI: 10.1099/mic.0.001246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Toxin-antitoxin (TA) systems are abundantly present in the genomes of various bacterial pathogens. TA systems have been implicated in either plasmid maintenance or protection against phage infection, stress adaptation or disease pathogenesis. The genome of Mycobacterium tuberculosis encodes for more than 90 TA systems and 4 of these belong to the type IV subfamily (MenAT family). The toxins and antitoxins belonging to type IV TA systems share sequence homology with the AbiEii family of nucleotidyl transferases and the AbiEi family of putative transcriptional regulators, respectively. Here, we have performed experiments to understand the role of MenT2, a toxin from the type IV TA system, in mycobacterial physiology and disease pathogenesis. The ectopic expression of MenT2 using inducible vectors does not inhibit bacterial growth in liquid cultures. Bioinformatic and molecular modelling analysis suggested that the M. tuberculosis genome has an alternative start site upstream of the annotated menT2 gene. The overexpression of the reannotated MenT2 resulted in moderate growth inhibition of Mycobacterium smegmatis. We show that both menT2 and menA2 transcript levels are increased when M. tuberculosis is exposed to nitrosative stress, in vitro. When compared to the survival of the wild-type and the complemented strain, the ΔmenT2 mutant strain of M. tuberculosis was more resistant to being killed by nitrosative stress. However, the survival of both the ΔmenT2 mutant and the wild-type strain was similar in macrophages and when exposed to other stress conditions. Here, we show that MenT2 is required for the establishment of disease in guinea pigs. Gross pathology and histopathology analysis of lung tissues from guinea pigs infected with the ∆menT2 strain revealed significantly reduced tissue damage and inflammation. In summary, these results provide new insights into the role of MenT2 in mycobacterial pathogenesis.
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Affiliation(s)
- Tannu Priya Gosain
- Infection and Immunology Group, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurugram Expressway, Faridabad-121001, India
| | - Manisha Singh
- Infection and Immunology Group, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurugram Expressway, Faridabad-121001, India
| | - Charandeep Singh
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh-160036, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh-160036, India
| | - Ramandeep Singh
- Infection and Immunology Group, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurugram Expressway, Faridabad-121001, India
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9
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Abstract
Toxin-antitoxin (TA) systems are ubiquitous genetic elements in bacteria that consist of a growth-inhibiting toxin and its cognate antitoxin. These systems are prevalent in bacterial chromosomes, plasmids, and phage genomes, but individual systems are not highly conserved, even among closely related strains. The biological functions of TA systems have been controversial and enigmatic, although a handful of these systems have been shown to defend bacteria against their viral predators, bacteriophages. Additionally, their patterns of conservation-ubiquitous, but rapidly acquired and lost from genomes-as well as the co-occurrence of some TA systems with known phage defense elements are suggestive of a broader role in mediating phage defense. Here, we review the existing evidence for phage defense mediated by TA systems, highlighting how toxins are activated by phage infection and how toxins disrupt phage replication. We also discuss phage-encoded systems that counteract TA systems, underscoring the ongoing coevolutionary battle between bacteria and phage. We anticipate that TA systems will continue to emerge as central players in the innate immunity of bacteria against phage. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Michele LeRoux
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; .,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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10
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Awuni E. Modeling the MreB-CbtA Interaction to Facilitate the Prediction and Design of Candidate Antibacterial Peptides. Front Mol Biosci 2022; 8:814935. [PMID: 35155572 PMCID: PMC8828653 DOI: 10.3389/fmolb.2021.814935] [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: 11/14/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Protein-protein interactions (PPIs) have emerged as promising targets for PPI modulators as alternative drugs because they are essential for most biochemical processes in living organisms. In recent years, a spotlight has been put on the development of peptide-based PPI inhibitors as the next-generation therapeutics to combat antimicrobial resistance taking cognizance of protein-based PPI-modulators that interact with target proteins to inhibit function. Although protein-based PPI inhibitors are not effective therapeutic agents because of their high molecular weights, they could serve as sources for peptide-based pharmaceutics if the target-inhibitor complex is accessible and well characterized. The Escherichia coli (E. coli) toxin protein, CbtA, has been identified as a protein-based PPI modulator that binds to the bacterial actin homolog MreB leading to the perturbation of its polymerization dynamics; and consequently has been suggested to have antibacterial properties. Unfortunately, however, the three-dimensional structures of CbtA and the MreB-CbtA complex are currently not available to facilitate the optimization process of the pharmacological properties of CbtA. In this study, computer modeling strategies were used to predict key MreB-CbtA interactions to facilitate the design of antiMreB peptide candidates. A model of the E. coli CbtA was built using the trRosetta software and its stability was assessed through molecular dynamics (MD) simulations. The modeling and simulations data pointed to a model with reasonable quality and stability. Also, the HADDOCK software was used to predict a possible MreB-CbtA complex, which was characterized through MD simulations and compared with MreB-MreB dimmer. The results suggest that CbtA inhibits MreB through the competitive mechanism whereby CbtA competes with MreB monomers for the interprotofilament interface leading to interference with double protofilament formation. Additionally, by using the antiBP software to predict antibacterial peptides in CbtA, and the MreB-CbtA complex as the reference structure to determine important interactions and contacts, candidate antiMreB peptides were suggested. The peptide sequences could be useful in a rational antimicrobial peptide hybridization strategy to design novel antibiotics. All-inclusive, the data reveal the molecular basis of MreB inhibition by CbtA and can be incorporated in the design/development of the next-generation antibacterial peptides targeting MreB.
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11
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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: 21] [Impact Index Per Article: 7.0] [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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12
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Abstract
Methods for detecting and dissecting the interactions of virally encoded proteins are essential for probing basic viral biology and providing a foundation for therapeutic advances. The dearth of targeted therapeutics for the treatment of coronavirus disease 2019 (COVID-19), an ongoing global health crisis, underscores the importance of gaining a deeper understanding of the interactions of proteins encoded by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we describe the use of a convenient bacterial cell-based two-hybrid (B2H) system to analyze the SARS-CoV-2 proteome. We identified 16 distinct intraviral protein-protein interactions (PPIs), involving 16 proteins. We found that many of the identified proteins interact with more than one partner. Further, our system facilitates the genetic dissection of these interactions, enabling the identification of selectively disruptive mutations. We also describe a modified B2H system that permits the detection of disulfide bond-dependent PPIs in the normally reducing Escherichia coli cytoplasm, and we used this system to detect the interaction of the SARS-CoV-2 spike protein receptor-binding domain (RBD) with its cognate cell surface receptor ACE2. We then examined how the RBD-ACE2 interaction is perturbed by several RBD amino acid substitutions found in currently circulating SARS-CoV-2 variants. Our findings illustrate the utility of a genetically tractable bacterial system for probing the interactions of viral proteins and investigating the effects of emerging mutations. In principle, the system could also facilitate the identification of potential therapeutics that disrupt specific interactions of virally encoded proteins. More generally, our findings establish the feasibility of using a B2H system to detect and dissect disulfide bond-dependent interactions of eukaryotic proteins.
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13
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Synergistic Antibacterial and Antibiofilm Activity of the MreB Inhibitor A22 Hydrochloride in Combination with Conventional Antibiotics against Pseudomonas aeruginosa and Escherichia coli Clinical Isolates. Int J Microbiol 2021; 2021:3057754. [PMID: 34484344 PMCID: PMC8413048 DOI: 10.1155/2021/3057754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/19/2021] [Accepted: 08/12/2021] [Indexed: 01/12/2023] Open
Abstract
In the era of antibiotic resistance, the bacterial cytoskeletal protein MreB is presented as a potential target for the development of novel antimicrobials. Combined treatments of clinical antibiotics with anti-MreB compounds may be promising candidates in combating the resistance crisis, but also in preserving the potency of many conventional drugs. This study aimed to evaluate the synergistic antibacterial and antibiofilm activities of the MreB inhibitor A22 hydrochloride in combination with various antibiotics. The minimum inhibitory concentration (MIC) values of the individual compounds were determined by the broth microdilution method against 66 clinical isolates of Gram-negative bacteria. Synergy was assessed by the checkerboard assay. The fractional inhibitory concentration index was calculated for each of the A22-antibiotic combination. Bactericidal activity of the combinations was evaluated by time-kill curve assays. The antibiofilm activity of the most synergistic combinations was determined by crystal violet stain, methyl thiazol tetrazolium assay, and confocal laser scanning microscopy analysis. The combined cytotoxic and hemolytic activity was also evaluated toward human cells. According to our results, Pseudomonas aeruginosa and Escherichia coli isolates were resistant to conventional antibiotics to varying degrees. A22 inhibited the bacterial growth in a dose-dependent manner with MIC values ranging between 2 and 64 μg/mL. In combination studies, synergism occurred most frequently with A22-ceftazidime and A22-meropemen against Pseudomonas aeruginosa and A22-cefoxitin and A22-azithromycin against Escherichia coli. No antagonism was observed. In time-kill studies, synergism was observed with all expected combinations. Synergistic combinations even at the lowest tested concentrations were able to inhibit biofilm formation and eradicate mature biofilms in both strains. Cytotoxic and hemolytic effects of the same combinations toward human cells were not observed. The findings of the present study support previous research regarding the use of MreB as a novel antibiotic target. The obtained data expand the existing knowledge about the antimicrobial and antibiofilm activity of the A22 inhibitor, and they indicate that A22 can serve as a leading compound for studying potential synergism between MreB inhibitors and antibiotics in the future.
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Wang L, Niu TC, Valladares A, Lin GM, Zhang JY, Herrero A, Chen WL, Zhang CC. The developmental regulator PatD modulates assembly of the cell-division protein FtsZ in the cyanobacterium Anabaena sp. PCC 7120. Environ Microbiol 2021; 23:4823-4837. [PMID: 34296514 DOI: 10.1111/1462-2920.15682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/07/2021] [Accepted: 07/19/2021] [Indexed: 01/02/2023]
Abstract
FtsZ is a tubulin-like GTPase that polymerizes to initiate the process of cell division in bacteria. Heterocysts are terminally differentiated cells of filamentous cyanobacteria that have lost the capacity for cell division and in which the ftsZ gene is downregulated. However, mechanisms of FtsZ regulation during heterocyst differentiation have been scarcely investigated. The patD gene is NtcA dependent and involved in the optimization of heterocyst frequency in Anabaena sp. PCC 7120. Here, we report that the inactivation of patD caused the formation of multiple FtsZ-rings in vegetative cells, cell enlargement, and the retention of peptidoglycan synthesis activity in heterocysts, whereas its ectopic expression resulted in aberrant FtsZ polymerization and cell division. PatD interacted with FtsZ, increased FtsZ precipitation in sedimentation assays, and promoted the formation of thick straight FtsZ bundles that differ from the toroidal aggregates formed by FtsZ alone. These results suggest that in the differentiating heterocysts, PatD interferes with the assembly of FtsZ. We propose that in Anabaena FtsZ is a bifunctional protein involved in both vegetative cell division and regulation of heterocyst differentiation. In the differentiating cells PatD-FtsZ interactions appear to set an FtsZ activity that is insufficient for cell division but optimal to foster differentiation.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Tian-Cai Niu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Ana Valladares
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Gui-Ming Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Wen-Li Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,Institut AMU-WUT, Aix-Marseille University and Wuhan University of Technology, Wuhan, Hubei, 430070, China
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15
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Ansari S, Walsh JC, Bottomley AL, Duggin IG, Burke C, Harry EJ. A newly identified prophage-encoded gene, ymfM, causes SOS-inducible filamentation in Escherichia coli. J Bacteriol 2021; 203:JB.00646-20. [PMID: 33722843 PMCID: PMC8117526 DOI: 10.1128/jb.00646-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/26/2021] [Indexed: 12/29/2022] Open
Abstract
Rod-shaped bacteria such as Escherichia coli can regulate cell division in response to stress, leading to filamentation, a process where cell growth and DNA replication continues in the absence of division, resulting in elongated cells. The classic example of stress is DNA damage which results in the activation of the SOS response. While the inhibition of cell division during SOS has traditionally been attributed to SulA in E. coli, a previous report suggests that the e14 prophage may also encode an SOS-inducible cell division inhibitor, previously named SfiC. However, the exact gene responsible for this division inhibition has remained unknown for over 35 years. A recent high-throughput over-expression screen in E. coli identified the e14 prophage gene, ymfM, as a potential cell division inhibitor. In this study, we show that the inducible expression of ymfM from a plasmid causes filamentation. We show that this expression of ymfM results in the inhibition of Z ring formation and is independent of the well characterised inhibitors of FtsZ ring assembly in E. coli, SulA, SlmA and MinC. We confirm that ymfM is the gene responsible for the SfiC phenotype as it contributes to the filamentation observed during the SOS response. This function is independent of SulA, highlighting that multiple alternative division inhibition pathways exist during the SOS response. Our data also highlight that our current understanding of cell division regulation during the SOS response is incomplete and raises many questions regarding how many inhibitors there actually are and their purpose for the survival of the organism.Importance:Filamentation is an important biological mechanism which aids in the survival, pathogenesis and antibiotic resistance of bacteria within different environments, including pathogenic bacteria such as uropathogenic Escherichia coli Here we have identified a bacteriophage-encoded cell division inhibitor which contributes to the filamentation that occurs during the SOS response. Our work highlights that there are multiple pathways that inhibit cell division during stress. Identifying and characterising these pathways is a critical step in understanding survival tactics of bacteria which become important when combating the development of bacterial resistance to antibiotics and their pathogenicity.
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Affiliation(s)
- Shirin Ansari
- The ithree institute, Faculty of Science, University of Technology Sydney, Sydney, Australia
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - James C Walsh
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Amy L Bottomley
- The ithree institute, Faculty of Science, University of Technology Sydney, Sydney, Australia
| | - Iain G Duggin
- The ithree institute, Faculty of Science, University of Technology Sydney, Sydney, Australia
| | - Catherine Burke
- The ithree institute, Faculty of Science, University of Technology Sydney, Sydney, Australia
| | - Elizabeth J Harry
- The ithree institute, Faculty of Science, University of Technology Sydney, Sydney, Australia
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16
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Wang CD, Mansky R, LeBlanc H, Gravel CM, Berry KE. Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA-DNA adapter protein. RNA (NEW YORK, N.Y.) 2021; 27:513-526. [PMID: 33500316 PMCID: PMC7962490 DOI: 10.1261/rna.077404.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/19/2021] [Indexed: 05/25/2023]
Abstract
Noncoding RNAs regulate gene expression in every domain of life. In bacteria, small RNAs (sRNAs) regulate gene expression in response to stress and are often assisted by RNA-chaperone proteins, such as Hfq. We have recently developed a bacterial three-hybrid (B3H) assay that detects the strong binding interactions of certain E. coli sRNAs with proteins Hfq and ProQ. Despite the promise of this system, the signal-to-noise has made it challenging to detect weaker interactions. In this work, we use Hfq-sRNA interactions as a model system to optimize the B3H assay, so that weaker RNA-protein interactions can be more reliably detected. We find that the concentration of the RNA-DNA adapter is an important parameter in determining the signal in the system and have modified the plasmid expressing this component to tune its concentration to optimal levels. In addition, we have systematically perturbed the binding affinity of Hfq-RNA interactions to define, for the first time, the relationship between B3H signal and in vitro binding energetics. The new pAdapter construct presented here substantially expands the range of detectable interactions in the B3H assay, broadening its utility. This improved assay will increase the likelihood of identifying novel protein-RNA interactions with the B3H system and will facilitate exploration of the binding mechanisms of these interactions.
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Affiliation(s)
- Clara D Wang
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Rachel Mansky
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Hannah LeBlanc
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Chandra M Gravel
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Katherine E Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
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17
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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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18
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Sharma K, Sultana T, Dahms TES, Dillon JAR. CcpN: a moonlighting protein regulating catabolite repression of gluconeogenic genes in Bacillus subtilis also affects cell length and interacts with DivIVA. Can J Microbiol 2020; 66:723-732. [PMID: 32762636 DOI: 10.1139/cjm-2020-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
CcpN is a transcriptional repressor in Bacillus subtilis that binds to the promoter region of gapB and pckA, downregulating their expression in the presence of glucose. CcpN also represses sr1, which encodes a small noncoding regulatory RNA that suppresses the arginine biosynthesis gene cluster. CcpN has homologues in other Gram-positive bacteria, including Enterococcus faecalis. We report the interaction of CcpN with DivIVA of B. subtilis as determined using bacterial two-hybrid and glutathione S-transferase pull-down assays. Insertional inactivation of CcpN leads to cell elongation and formation of straight chains of cells. These findings suggest that CcpN is a moonlighting protein involved in both gluconeogenesis and cell elongation.
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Affiliation(s)
- Kusum Sharma
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.,Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK S7N 5E3, Canada
| | - Taranum Sultana
- Department of Chemistry and Biochemistry, 3737 Wascana Parkway, University of Regina, Regina, SK S4S 0A2, Canada
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, 3737 Wascana Parkway, University of Regina, Regina, SK S4S 0A2, Canada
| | - Jo-Anne R Dillon
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.,Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK S7N 5E3, Canada
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19
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AimB Is a Small Protein Regulator of Cell Size and MreB Assembly. Biophys J 2020; 119:593-604. [PMID: 32416080 DOI: 10.1016/j.bpj.2020.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/17/2020] [Accepted: 04/27/2020] [Indexed: 12/27/2022] Open
Abstract
The MreB actin-like cytoskeleton assembles into dynamic polymers that coordinate cell shape in many bacteria. In contrast to most other cytoskeleton systems, few MreB-interacting proteins have been well characterized. Here, we identify a small protein from Caulobacter crescentus, an assembly inhibitor of MreB (AimB). AimB overexpression mimics inhibition of MreB polymerization, leading to increased cell width and MreB delocalization. Furthermore, aimB appears to be essential, and its depletion results in decreased cell width and increased resistance to A22, a small-molecule inhibitor of MreB assembly. Molecular dynamics simulations suggest that AimB binds MreB at its monomer-monomer protofilament interaction cleft and that this interaction is favored for C. crescentus MreB over Escherichia coli MreB because of a closer match in the degree of opening with AimB size, suggesting coevolution of AimB with MreB conformational dynamics in C. crescentus. We support this model through functional analysis of point mutants in both AimB and MreB, photo-cross-linking studies with site-specific unnatural amino acids, and species-specific activity of AimB. Together, our findings are consistent with AimB promoting MreB dynamics by inhibiting monomer-monomer assembly interactions, representing a new mechanism for regulating actin-like polymers and the first identification of a non-toxin MreB assembly inhibitor. Because AimB has only 104 amino acids and small proteins are often poorly characterized, our work suggests the possibility of more bacterial cytoskeletal regulators to be found in this class. Thus, like FtsZ and eukaryotic actin, MreB may have a rich repertoire of regulators to tune its precise assembly and dynamics.
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20
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Horesh G, Fino C, Harms A, Dorman MJ, Parts L, Gerdes K, Heinz E, Thomson NR. Type II and type IV toxin-antitoxin systems show different evolutionary patterns in the global Klebsiella pneumoniae population. Nucleic Acids Res 2020; 48:4357-4370. [PMID: 32232417 PMCID: PMC7192599 DOI: 10.1093/nar/gkaa198] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 02/21/2020] [Accepted: 03/16/2020] [Indexed: 12/15/2022] Open
Abstract
The Klebsiella pneumoniae species complex includes important opportunistic pathogens which have become public health priorities linked to major hospital outbreaks and the recent emergence of multidrug-resistant hypervirulent strains. Bacterial virulence and the spread of multidrug resistance have previously been linked to toxin-antitoxin (TA) systems. TA systems encode a toxin that disrupts essential cellular processes, and a cognate antitoxin which counteracts this activity. Whilst associated with the maintenance of plasmids, they also act in bacterial immunity and antibiotic tolerance. However, the evolutionary dynamics and distribution of TA systems in clinical pathogens are not well understood. Here, we present a comprehensive survey and description of the diversity of TA systems in 259 clinically relevant genomes of K. pneumoniae. We show that TA systems are highly prevalent with a median of 20 loci per strain. Importantly, these toxins differ substantially in their distribution patterns and in their range of cognate antitoxins. Classification along these properties suggests different roles of TA systems and highlights the association and co-evolution of toxins and antitoxins.
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Affiliation(s)
- Gal Horesh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
| | - Cinzia Fino
- Centre of Excellence for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Alexander Harms
- Centre of Excellence for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Matthew J Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
| | - Leopold Parts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
- Department of Computer Science, University of Tartu, Tartu, 50090, Estonia
| | - Kenn Gerdes
- Centre of Excellence for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Eva Heinz
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
- Department of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
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21
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Regulation of filamentation by bacteria and its impact on the productivity of compounds in biotechnological processes. Appl Microbiol Biotechnol 2020; 104:4631-4642. [DOI: 10.1007/s00253-020-10590-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/29/2022]
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22
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Liu L, Li F, Xu L, Wang J, Li M, Yuan J, Wang H, Yang R, Li B. Cyclic AMP-CRP Modulates the Cell Morphology of Klebsiella pneumoniae in High-Glucose Environment. Front Microbiol 2020; 10:2984. [PMID: 32038513 PMCID: PMC6985210 DOI: 10.3389/fmicb.2019.02984] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/10/2019] [Indexed: 11/21/2022] Open
Abstract
Bacteria can modify their morphology in response to environmental stimuli for survival or host defense evasion. The rich glucose in vivo or in the Luria–Bertani (LB) medium shortened the cell length of Klebsiella pneumoniae. The environmental glucose decreased the levels of cyclic AMP (cAMP) and the transcription of crp, which declined the cAMP–cAMP receptor protein (cAMP-CRP) activity. The cell length of crp deletion mutant was significantly shorter than that of the wild type (0.981 ± 0.057 μm vs. 2.415 ± 0.075 μm, P < 0.001). These results indicated that the high environmental glucose alters the bacterial morphology to a round form through regulating the activity of cAMP-CRP complex. Comparative proteomics analysis showed increased expression of 10 proteins involved in cell division or cell wall biosynthesis in the crp deletion strain. Five of them (ompA, tolB, ybgC, ftsI, and rcsF) were selected to verify their expression in the high-glucose environment, and overexpression of tolB or rcsF shortened the bacterial length similar to that of the crp deletion strain. Electrophoretic mobility shift assay indicated that CRP directly negatively regulates the transcription of tolB and rcsF by binding to the promoter regions. This study first proved the role and partial regulation mechanism of CRP in altering cell morphology during infection and provided a theoretical basis for elucidating the mechanism in diabetes mellitus susceptible to K. pneumoniae.
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Affiliation(s)
- Long Liu
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China.,Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Feiyu Li
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Li Xu
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
| | - Jingjie Wang
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Moran Li
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Jie Yuan
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Hui Wang
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Ruiping Yang
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
| | - Bei Li
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China.,Biomedical Research Institute, Hubei University of Medicine, Shiyan, China
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23
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Awuni E. Status of Targeting MreB for the Development of Antibiotics. Front Chem 2020; 7:884. [PMID: 31998684 PMCID: PMC6965359 DOI: 10.3389/fchem.2019.00884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
Although many prospective antibiotic targets are known, bacterial infections and resistance to antibiotics remain a threat to public health partly because the druggable potentials of most of these targets have yet to be fully tapped for the development of a new generation of therapeutics. The prokaryotic actin homolog MreB is one of the important antibiotic targets that are yet to be significantly exploited. MreB is a bacterial cytoskeleton protein that has been widely studied and is associated with the determination of rod shape as well as important subcellular processes including cell division, chromosome segregation, cell wall morphogenesis, and cell polarity. Notwithstanding that MreB is vital and conserved in most rod-shaped bacteria, no approved antibiotics targeting it are presently available. Here, the status of targeting MreB for the development of antibiotics is concisely summarized. Expressly, the known therapeutic targets and inhibitors of MreB are presented, and the way forward in the search for a new generation of potent inhibitors of MreB briefly discussed.
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Affiliation(s)
- Elvis Awuni
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
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24
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At the Heart of Bacterial Cytokinesis: The Z Ring. Trends Microbiol 2019; 27:781-791. [PMID: 31171437 DOI: 10.1016/j.tim.2019.04.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/22/2019] [Accepted: 04/29/2019] [Indexed: 11/20/2022]
Abstract
Bacterial cell division is mediated by the divisome which is organized by the Z ring, a cytoskeletal element formed by the polymerization of the tubulin homologue FtsZ. Despite billions of years of bacterial evolution, the Z ring is nearly universal among bacteria that have a cell wall and divide by binary fission. Recent studies have revealed the mechanism of cooperative assembly of FtsZ and that the Z ring consists of patches of FtsZ filaments tethered to the membrane that treadmill to distribute the septal biosynthetic machinery. Here, we summarize these advances and discuss questions raised by these new findings.
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25
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Long Y, Fu W, Li S, Ren H, Li M, Liu C, Zhang B, Xia Y, Fan Z, Xu C, Liu J, Jin Y, Bai F, Cheng Z, Liu X, Jin S, Wu W. Identification of novel genes that promote persister formation by repressing transcription and cell division in Pseudomonas aeruginosa. J Antimicrob Chemother 2019; 74:2575-2587. [DOI: 10.1093/jac/dkz214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/14/2019] [Accepted: 04/18/2019] [Indexed: 12/24/2022] Open
Abstract
AbstractObjectivesBacterial persisters are a small subpopulation of cells that are highly tolerant of antibiotics and contribute to chronic and recalcitrant infections. Global gene expression in Pseudomonas aeruginosa persister cells and genes contributing to persister formation remain largely unknown. The objective of this study was to examine the gene expression profiles of the persister cells and those that regained growth in fresh medium, as well as to identify novel genes related to persister formation.MethodsP. aeruginosa persister cells and those that regrew in fresh medium were collected and subjected to RNA sequencing analysis. Genes up-regulated in the persister cells were overexpressed to evaluate their roles in persister formation. The functions of the persister-contributing genes were assessed with pulse–chase assay, affinity chromatography, fluorescence and electron microscopy, as well as a light-scattering assay.ResultsAn operon containing PA2282–PA2287 was up-regulated in the persister cells and down-regulated in the regrowing cells. PA2285 and PA2287 play key roles in persister formation. PA2285 and PA2287 were found to bind to RpoC and FtsZ, which are involved in transcription and cell division, respectively. Pulse–chase assays demonstrated inhibitory effects of PA2285 and PA2287 on the overall transcription. Meanwhile, light-scattering and microscopy assays demonstrated that PA2285 and PA2287 interfere with cell division by inhibiting FtsZ aggregation. PA2285 and PA2287 are conserved in pseudomonads and their homologous genes in Pseudomonas putida contribute to persister formation.ConclusionsPA2285 and PA2287 are novel bifunctional proteins that contribute to persister formation in P. aeruginosa.
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Affiliation(s)
- Yuqing Long
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Weixin Fu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Shouyi Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Huan Ren
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Mei Li
- Meishan Product Quality Supervision and Inspection Institute and National Pickle Quality Inspection Center, Meishan, P.R. China
| | - Chang Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Buyu Zhang
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P.R. China
| | - Yushan Xia
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Zheng Fan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Chang Xu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, P.R. China
| | - Jianfeng Liu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, P.R. China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P.R. China
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Shouguang Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
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26
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Shidore T, Zeng Q, Triplett LR. Survey of Toxin⁻Antitoxin Systems in Erwinia amylovora Reveals Insights into Diversity and Functional Specificity. Toxins (Basel) 2019; 11:toxins11040206. [PMID: 30959879 PMCID: PMC6521040 DOI: 10.3390/toxins11040206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 11/16/2022] Open
Abstract
Toxin–antitoxin (TA) systems are diverse genetic modules with demonstrated roles in plasmid stability, stress management, biofilm formation and antibiotic persistence. However, relatively little is known about their functional significance in plant pathogens. In this study we characterize type II and IV TA systems in the economically important plant pathogen Erwinia amylovora. Hidden Markov Model (HMM) and BLAST-based programs were used to predict the identity and distribution of putative TA systems among sequenced genomes of E. amylovora and other plant-associated Erwinia spp. Of six conserved TA systems tested for function from E. amylovora, three (CbtA/CbeA, ParE/RHH and Doc/PhD) were validated as functional. CbtA was toxic to E. amylovora, but not to Escherichia coli. While the E. coli homolog of CbtA elicits the formation of lemon-shaped cells upon overexpression and targets cytoskeletal proteins FtsZ and MreB, E. amylovora CbtA led to cell elongation and did not interact with these cytoskeletal proteins. Phylogenetic analysis revealed that E. amylovora CbtA belongs to a distinct clade from the CbtA of pathogenic E. coli. This study expands the repertoire of experimentally validated TA systems in plant pathogenic bacteria, and suggests that the E. amylovora homolog of CbtA is functionally distinct from that of E. coli.
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Affiliation(s)
- Teja Shidore
- Department of Plant Pathology and Ecology, the Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA.
| | - Quan Zeng
- Department of Plant Pathology and Ecology, the Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA.
| | - Lindsay R Triplett
- Department of Plant Pathology and Ecology, the Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA.
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27
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Regrowth-delay body as a bacterial subcellular structure marking multidrug-tolerant persisters. Cell Discov 2019; 5:8. [PMID: 30675381 PMCID: PMC6341109 DOI: 10.1038/s41421-019-0080-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/28/2018] [Accepted: 01/01/2019] [Indexed: 02/08/2023] Open
Abstract
Bacteria have long been recognized to be capable of entering a phenotypically non-growing persister state, in which the cells exhibit an extended regrowth lag and a multidrug tolerance, thus posing a great challenge in treating infectious diseases. Owing to their non-inheritability, low abundance of existence, lack of metabolic activities, and high heterogeneity, properties of persisters remain poorly understood. Here, we report our accidental discovery of a subcellular structure that we term the regrowth-delay body, which is formed only in non-growing bacterial cells and sequesters multiple key proteins. This structure, that dissolves when the cell resumes growth, is able to be viewed as a marker of persisters. Our studies also indicate that persisters exhibit different depth of persistence, as determined by the status of their regrowth-delay bodies. Our findings imply that suppressing the formation and/or promoting the dissolution of regrowth-delay bodies could be viable strategies for eradicating persisters.
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28
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Ting SY, Bosch DE, Mangiameli SM, Radey MC, Huang S, Park YJ, Kelly KA, Filip SK, Goo YA, Eng JK, Allaire M, Veesler D, Wiggins PA, Peterson SB, Mougous JD. Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins. Cell 2018; 175:1380-1392.e14. [PMID: 30343895 PMCID: PMC6239978 DOI: 10.1016/j.cell.2018.09.037] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/13/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022]
Abstract
ADP-ribosylation of proteins can profoundly impact their function and serves as an effective mechanism by which bacterial toxins impair eukaryotic cell processes. Here, we report the discovery that bacteria also employ ADP-ribosylating toxins against each other during interspecies competition. We demonstrate that one such toxin from Serratia proteamaculans interrupts the division of competing cells by modifying the essential bacterial tubulin-like protein, FtsZ, adjacent to its protomer interface, blocking its capacity to polymerize. The structure of the toxin in complex with its immunity determinant revealed two distinct modes of inhibition: active site occlusion and enzymatic removal of ADP-ribose modifications. We show that each is sufficient to support toxin immunity; however, the latter additionally provides unprecedented broad protection against non-cognate ADP-ribosylating effectors. Our findings reveal how an interbacterial arms race has produced a unique solution for safeguarding the integrity of bacterial cell division machinery against inactivating post-translational modifications.
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Affiliation(s)
- See-Yeun Ting
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Dustin E Bosch
- Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Matthew C Radey
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Shuo Huang
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine A Kelly
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Young Ah Goo
- Proteomics Center of Excellence, Northwestern University, Chicago, IL 60611, USA
| | - Jimmy K Eng
- Proteomics Resource, University of Washington, Seattle, WA 98195, USA
| | - Marc Allaire
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Veesler
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Paul A Wiggins
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Physics, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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29
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Mediati DG, Burke CM, Ansari S, Harry EJ, Duggin IG. High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division. BMC Genomics 2018; 19:781. [PMID: 30373517 PMCID: PMC6206680 DOI: 10.1186/s12864-018-5187-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 10/19/2018] [Indexed: 11/24/2022] Open
Abstract
Background Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich filamentous clones from an inducible expression library, and then identified the cloned DNA with high-throughput DNA sequencing. We applied the method to an expression library made from fragmented genomic DNA of uropathogenic E. coli UTI89, which undergoes extensive reversible filamentation in urinary tract infections and might encode additional regulators of division. Results We identified 55 genomic regions that reproducibly caused filamentation when expressed from the plasmid vector, and then further localized the cause of filamentation in several of these to specific genes or sub-fragments. Many of the identified genomic fragments encode genes that are known to participate in cell division or its regulation, and others may play previously-unknown roles. Some of the prophage genes identified were previously implicated in cell division arrest. A number of the other fragments encoded potential short transcripts or peptides. Conclusions The results provided evidence of potential new links between cell division and distinct cellular processes including central carbon metabolism and gene regulation. Candidate regulators of the UTI-associated filamentation response or others were identified amongst the results. In addition, some genomic fragments that caused filamentation may not have evolved to control cell division, but may have applications as artificial inhibitors. Our approach offers the opportunity to carry out in depth surveys of diverse DNA libraries to identify new genes or sequences encoding the capacity to inhibit division and cause filamentation. Electronic supplementary material The online version of this article (10.1186/s12864-018-5187-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel G Mediati
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Catherine M Burke
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Shirin Ansari
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Elizabeth J Harry
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Iain G Duggin
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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30
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Harms A, Brodersen DE, Mitarai N, Gerdes K. Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology. Mol Cell 2018; 70:768-784. [PMID: 29398446 DOI: 10.1016/j.molcel.2018.01.003] [Citation(s) in RCA: 398] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/06/2017] [Accepted: 01/02/2018] [Indexed: 12/01/2022]
Abstract
Bacterial toxin-antitoxin (TA) modules are abundant genetic elements that encode a toxin protein capable of inhibiting cell growth and an antitoxin that counteracts the toxin. The majority of toxins are enzymes that interfere with translation or DNA replication, but a wide variety of molecular activities and cellular targets have been described. Antitoxins are proteins or RNAs that often control their cognate toxins through direct interactions and, in conjunction with other signaling elements, through transcriptional and translational regulation of TA module expression. Three major biological functions of TA modules have been discovered, post-segregational killing ("plasmid addiction"), abortive infection (bacteriophage immunity through altruistic suicide), and persister formation (antibiotic tolerance through dormancy). In this review, we summarize the current state of the field and highlight how multiple levels of regulation shape the conditions of toxin activation to achieve the different biological functions of TA modules.
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Affiliation(s)
- Alexander Harms
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Ditlev Egeskov Brodersen
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Namiko Mitarai
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; Niels Bohr Institute, Department of Physics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Kenn Gerdes
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
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