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Saha R, Bhattacharje G, De S, Das AK. Deciphering the conformational stability of MazE7 antitoxin in Mycobacterium tuberculosis from molecular dynamics simulation study. J Biomol Struct Dyn 2023:1-17. [PMID: 37965715 DOI: 10.1080/07391102.2023.2280675] [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: 07/24/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
MazEF Toxin-antitoxin (TA) systems are associated with the persistent phenotype of the pathogen, Mycobacterium tuberculosis (Mtb), aiding their survival. Though extensively studied, the mode of action between the antitoxin-toxin and DNA of this family remains largely unclear. Here, the important interactions between MazF7 toxin and MazE7 antitoxin, and how MazE7 binds its promoter/operator region have been studied. To elucidate this, molecular dynamics (MD) simulation has been performed on MazE7, MazF7, MazEF7, MazEF7-DNA, and MazE7-DNA complexes to investigate how MazF7 and DNA affect the conformational change and dynamics of MazE7 antitoxin. This study demonstrated that the MazE7 dimer is disordered and one monomer (Chain C) attains stability after binding to the MazF7 toxin. Both the monomers (Chain C and Chain D) however are stabilized when MazE7 binds to DNA. MazE7 is also observed to sterically inhibit tRNA from binding to MazF7, thus suppressing its toxic activity. Comparative structural analysis performed on all the available antitoxins/antitoxin-toxin-DNA structures revealed MazEF7-DNA mechanism was similar to another TA system, AtaRT_E.coli. Simulation performed on the crystal structures of AtaR, AtaT, AtaRT, AtaRT-DNA, and AtaR-DNA showed that the disordered AtaR antitoxin attains stability by AtaT and DNA binding similar to MazE7. Based on these analyses it can thus be hypothesized that the disordered antitoxins enable tighter toxin and DNA binding thus preventing accidental toxin activation. Overall, this study provides crucial structural and dynamic insights into the MazEF7 toxin-antitoxin system and should provide a basis for targeting this TA system in combating Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rituparna Saha
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Gourab Bhattacharje
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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2
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Theis TJ, Daubert TA, Kluthe KE, Brodd KL, Nuxoll AS. Staphylococcus aureus persisters are associated with reduced clearance in a catheter-associated biofilm infection. Front Cell Infect Microbiol 2023; 13:1178526. [PMID: 37228667 PMCID: PMC10203555 DOI: 10.3389/fcimb.2023.1178526] [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: 03/02/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Background Staphylococcus aureus causes a wide variety of infections, many of which are chronic or relapsing in nature. Antibiotic therapy is often ineffective against S. aureus biofilm-mediated infections. Biofilms are difficult to treat partly due to their tolerance to antibiotics, however the underlying mechanism responsible for this remains unknown. One possible explanation is the presence of persister cells-dormant-like cells that exhibit tolerance to antibiotics. Recent studies have shown a connection between a fumC (fumarase C, a gene in the tricarboxylic acid cycle) knockout strain and increased survival to antibiotics, antimicrobial peptides, and in a Drosophila melanogaster model. Objective It remained unclear whether a S. aureus high persister strain would have a survival advantage in the presence of innate and adaptive immunity. To further investigate this, a fumC knockout and wild type strains were examined in a murine catheter-associated biofilm model. Results Interestingly, mice struggled to clear both S. aureus wild type and the fumC knockout strains. We reasoned both biofilm-mediated infections predominantly consisted of persister cells. To determine the persister cell population within biofilms, expression of a persister cell marker (Pcap5A::dsRED) in a biofilm was examined. Cell sorting of biofilms challenged with antibiotics revealed cells with intermediate and high expression of cap5A had 5.9-and 4.5-fold higher percent survival compared to cells with low cap5A expression. Based on previous findings that persisters are associated with reduced membrane potential, flow cytometry analysis was used to examine the metabolic state of cells within a biofilm. We confirmed cells within biofilms had reduced membrane potential compared to both stationary phase cultures (2.5-fold) and exponential phase cultures (22.4-fold). Supporting these findings, cells within a biofilm still exhibited tolerance to antibiotic challenge following dispersal of the matrix through proteinase K. Conclusion Collectively, these data show that biofilms are largely comprised of persister cells, and this may explain why biofilm infections are often chronic and/or relapsing in clinical settings.
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Halvorsen TM, Ricci DP, Park DM, Jiao Y, Yung MC. Comparison of Kill Switch Toxins in Plant-Beneficial Pseudomonas fluorescens Reveals Drivers of Lethality, Stability, and Escape. ACS Synth Biol 2022; 11:3785-3796. [PMID: 36346907 DOI: 10.1021/acssynbio.2c00386] [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: 11/09/2022]
Abstract
Kill switches provide a biocontainment strategy in which unwanted growth of an engineered microorganism is prevented by expression of a toxin gene. A major challenge in kill switch engineering is balancing evolutionary stability with robust cell killing activity in application relevant host strains. Understanding host-specific containment dynamics and modes of failure helps to develop potent yet stable kill switches. To guide the design of robust kill switches in the agriculturally relevant strain Pseudomonas fluorescens SBW25, we present a comparison of lethality, stability, and genetic escape of eight different toxic effectors in the presence of their cognate inactivators (i.e., toxin-antitoxin modules, polymorphic exotoxin-immunity systems, restriction endonuclease-methyltransferase pair). We find that cell killing capacity and evolutionary stability are inversely correlated and dependent on the level of protection provided by the inactivator gene. Decreasing the proteolytic stability of the inactivator protein can increase cell killing capacity, but at the cost of long-term circuit stability. By comparing toxins within the same genetic context, we determine that modes of genetic escape increase with circuit complexity and are driven by toxin activity, the protective capacity of the inactivator, and the presence of mutation-prone sequences within the circuit. Collectively, the results of our study reveal that circuit complexity, toxin choice, inactivator stability, and DNA sequence design are powerful drivers of kill switch stability and valuable targets for optimization of biocontainment systems.
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Affiliation(s)
- Tiffany M Halvorsen
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Dante P Ricci
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Dan M Park
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Yongqin Jiao
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Mimi C Yung
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
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4
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Mohiuddin SG, Ghosh S, Ngo HG, Sensenbach S, Karki P, Dewangan NK, Angardi V, Orman MA. Cellular Self-Digestion and Persistence in Bacteria. Microorganisms 2021; 9:2269. [PMID: 34835393 PMCID: PMC8626048 DOI: 10.3390/microorganisms9112269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/30/2022] Open
Abstract
Cellular self-digestion is an evolutionarily conserved process occurring in prokaryotic cells that enables survival under stressful conditions by recycling essential energy molecules. Self-digestion, which is triggered by extracellular stress conditions, such as nutrient depletion and overpopulation, induces degradation of intracellular components. This self-inflicted damage renders the bacterium less fit to produce building blocks and resume growth upon exposure to fresh nutrients. However, self-digestion may also provide temporary protection from antibiotics until the self-digestion-mediated damage is repaired. In fact, many persistence mechanisms identified to date may be directly or indirectly related to self-digestion, as these processes are also mediated by many degradative enzymes, including proteases and ribonucleases (RNases). In this review article, we will discuss the potential roles of self-digestion in bacterial persistence.
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Affiliation(s)
| | | | | | | | | | | | | | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77004, USA; (S.G.M.); (S.G.); (H.G.N.); (S.S.); (P.K.); (N.K.D.); (V.A.)
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5
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A minimal model for gene expression dynamics of bacterial type II toxin-antitoxin systems. Sci Rep 2021; 11:19516. [PMID: 34593858 PMCID: PMC8484670 DOI: 10.1038/s41598-021-98570-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
Toxin-antitoxin (TA) modules are part of most bacteria's regulatory machinery for stress responses and general aspects of their physiology. Due to the interplay of a long-lived toxin with a short-lived antitoxin, TA modules have also become systems of interest for mathematical modelling. Here we resort to previous modelling efforts and extract from these a minimal model of type II TA system dynamics on a timescale of hours, which can be used to describe time courses derived from gene expression data of TA pairs. We show that this model provides a good quantitative description of TA dynamics for the 11 TA pairs under investigation here, while simpler models do not. Our study brings together aspects of Biophysics with its focus on mathematical modelling and Computational Systems Biology with its focus on the quantitative interpretation of 'omics' data. This mechanistic model serves as a generic transformation of time course information into kinetic parameters. The resulting parameter vector can, in turn, be mechanistically interpreted. We expect that TA pairs with similar mechanisms are characterized by similar vectors of kinetic parameters, allowing us to hypothesize on the mode of action for TA pairs still under discussion.
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6
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Abstract
Toxin-antitoxin modules function in the genetic stability of mobile genetic elements, bacteriophage defense, and antibiotic tolerance. A gain-of-function mutation of the Escherichia coli K-12 hipBA module can induce antibiotic tolerance in a subpopulation of bacterial cells, a phenomenon known as persistence. HipA is a Ser/Thr kinase that phosphorylates and inactivates glutamyl tRNA synthetase, inhibiting cellular translation and inducing the stringent response. Additional characterized HipA homologues include HipT from pathogenic E. coli O127 and YjjJ of E. coli K-12, which are encoded by tricistronic hipBST and monocistronic operons, respectively. The apparent diversity of HipA homologues in bacterial genomes inspired us to investigate overall phylogeny. Here, we present a comprehensive phylogenetic analysis of the Hip kinases in bacteria and archaea that expands on this diversity by revealing seven novel kinase families. Kinases of one family, encoded by monocistronic operons, consist of an N-terminal core kinase domain, a HipS-like domain, and a HIRAN (HIP116 Rad5p N-terminal) domain. HIRAN domains bind single- or double-stranded DNA ends. Moreover, five types of bicistronic kinase operons encode putative antitoxins with HipS-HIRAN, HipS, γδ-resolvase, or Stl repressor-like domains. Finally, our analysis indicates that reversion of hipBA gene order happened independently several times during evolution.
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7
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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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8
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Zou J, Kou SH, Xie R, VanNieuwenhze MS, Qu J, Peng B, Zheng J. Non-walled spherical Acinetobacter baumannii is an important type of persister upon β-lactam antibiotic treatment. Emerg Microbes Infect 2021; 9:1149-1159. [PMID: 32419626 PMCID: PMC7448848 DOI: 10.1080/22221751.2020.1770630] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bacterial persistence is one of the major causes of antibiotic treatment failure and the step stone for antibiotic resistance. However, the mechanism by which persisters arise has not been well understood. Maintaining a dormant state to prevent antibiotics from taking effect is believed to be the fundamental mechanistic basis, and persisters normally maintain an intact cellular structure. Here we examined the morphologies of persisters in Acinetobacter baumannii survived from the treatment by three major classes of antibiotics (i.e. β-lactam, aminoglycoside, and fluoroquinolone) with microcopy and found that a fraction of enlarged spherical bacteria constitutes a major sub-population of bacterial survivors from β-lactam antibiotic treatment, whereas survivors from the treatment of aminoglycoside and fluoroquinolone were less changed morphologically. Further studies showed that these spherical bacteria had completely lost their cell wall structures but could survive without any osmoprotective reagent. The spherical bacteria were not the viable-but-non-culturable cells and they could revive upon the removal of β-lactam antibiotics. Importantly, these non-walled spherical bacteria also persisted during antibiotic therapy in vivo using Galleria mellonella as the infection model. Additionally, the combinational treatment on A. baumannii by β-lactam and membrane-targeting antibiotic significantly enhanced the killing efficacy. Our results indicate that in addition to the dormant, structure intact persisters, the non-wall spherical bacterium is another important type of persister in A. baumannii. The finding suggests that targeting the bacterial cell membrane during β-lactam chemotherapy could enhance therapeutic efficacy on A. baumannii infection, which might also help to reduce the resistance development of A. baumannii.
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Affiliation(s)
- Jin Zou
- Faculty of Health Sciences, University of Macau, Macau SAR, People's Republic of China
| | - Si-Hoi Kou
- Faculty of Health Sciences, University of Macau, Macau SAR, People's Republic of China
| | - Ruiqiang Xie
- Faculty of Health Sciences, University of Macau, Macau SAR, People's Republic of China
| | | | - Jiuxin Qu
- Department of Clinical Laboratory, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Shenzhen, People's Republic of China
| | - Bo Peng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| | - Jun Zheng
- Faculty of Health Sciences, University of Macau, Macau SAR, People's Republic of China.,Institute of Translational Medicine, University of Macau, Macau SAR, People's Republic of China
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9
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Wadie B, Abdel-Fattah MA, Yousef A, Mouftah SF, Elhadidy M, Salem TZ. In Silico Characterization of Toxin-Antitoxin Systems in Campylobacter Isolates Recovered from Food Sources and Sporadic Human Illness. Genes (Basel) 2021; 12:genes12010072. [PMID: 33430508 PMCID: PMC7826846 DOI: 10.3390/genes12010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/16/2022] Open
Abstract
Campylobacter spp. represents the most common cause of gastroenteritis worldwide with the potential to cause serious sequelae. The ability of Campylobacter to survive stressful environmental conditions has been directly linked with food-borne illness. Toxin-antitoxin (TA) modules play an important role as defense systems against antimicrobial agents and are considered an invaluable strategy harnessed by bacterial pathogens to survive in stressful environments. Although TA modules have been extensively studied in model organisms such as Escherichia coli K12, the TA landscape in Campylobacter remains largely unexplored. Therefore, in this study, a comprehensive in silico screen of 111 Campylobacter (90 C.
jejuni and 21 C.
coli) isolates recovered from different food and clinical sources was performed. We identified 10 type II TA systems belonging to four TA families predicted in Campylobacter genomes. Furthermore, there was a significant association between the clonal population structure and distribution of TA modules; more specifically, most (12/13) of the Campylobacter isolates belonging to ST-21 isolates possess HicB-HicA TA modules. Finally, we observed a high degree of shared synteny among isolates bearing certain TA systems or even coexisting pairs of TA systems. Collectively, these findings provide useful insights about the distribution of TA modules in a heterogeneous pool of Campylobacter isolates from different sources, thus developing a better understanding regarding the mechanisms by which these pathogens survive stressful environmental conditions, which will further aid in the future designing of more targeted antimicrobials.
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Affiliation(s)
- Bishoy Wadie
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt; (B.W.); (A.Y.); (S.F.M.)
| | - Mohamed A. Abdel-Fattah
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt;
| | - Alshymaa Yousef
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt; (B.W.); (A.Y.); (S.F.M.)
| | - Shaimaa F. Mouftah
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt; (B.W.); (A.Y.); (S.F.M.)
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt; (B.W.); (A.Y.); (S.F.M.)
- Department of Bacteriology, Mycology, and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
- Correspondence: (M.E.); (T.Z.S.); Tel.: +20-1220786861 (M.E.); +20-1014114122 (T.Z.S.)
| | - Tamer Z. Salem
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt; (B.W.); (A.Y.); (S.F.M.)
- Department of Microbial Genetics, AGERI, ARC, Giza 12619, Egypt
- Correspondence: (M.E.); (T.Z.S.); Tel.: +20-1220786861 (M.E.); +20-1014114122 (T.Z.S.)
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10
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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: 207] [Impact Index Per Article: 51.8] [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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11
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Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus. Genes (Basel) 2020; 11:genes11121392. [PMID: 33255299 PMCID: PMC7760498 DOI: 10.3390/genes11121392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/22/2022] Open
Abstract
Microorganisms used for the biohydrometallurgical extraction of metals from minerals must be able to survive high levels of metal and oxidative stress found in bioleaching environments. The Acidihalobacter genus consists of four species of halotolerant, iron–sulfur-oxidizing acidophiles that are unique in their ability to tolerate chloride and acid stress while simultaneously bioleaching minerals. This paper uses bioinformatic tools to predict the genes and mechanisms used by Acidihalobacter members in their defense against a wide range of metals and oxidative stress. Analysis revealed the presence of multiple conserved mechanisms of metal tolerance. Ac. yilgarnensis F5T, the only member of this genus that oxidizes the mineral chalcopyrite, contained a 39.9 Kb gene cluster consisting of 40 genes encoding mobile elements and an array of proteins with direct functions in copper resistance. The analysis also revealed multiple strategies that the Acidihalobacter members can use to tolerate high levels of oxidative stress. Three of the Acidihalobacter genomes were found to contain genes encoding catalases, which are not common to acidophilic microorganisms. Of particular interest was a rubrerythrin genomic cluster containing genes that have a polyphyletic origin of stress-related functions.
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12
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Park JY, Kim HJ, Pathak C, Yoon HJ, Kim DH, Park SJ, Lee BJ. Induced DNA bending by unique dimerization of HigA antitoxin. IUCRJ 2020; 7:748-760. [PMID: 32695421 PMCID: PMC7340258 DOI: 10.1107/s2052252520006466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
The bacterial toxin-antitoxin (TA) system regulates cell growth under various environmental stresses. Mycobacterium tuberculosis, the causative pathogen of tuberculosis (TB), has three HigBA type II TA systems with reverse gene organization, consisting of the toxin protein HigB and labile antitoxin protein HigA. Most type II TA modules are transcriptionally autoregulated by the antitoxin itself. In this report, we first present the crystal structure of the M. tuberculosis HigA3 antitoxin (MtHigA3) and MtHigA3 bound to its operator DNA complex. We also investigated the interaction between MtHigA3 and DNA using NMR spectroscopy. The MtHigA3 antitoxin structure is a homodimer that contains a structurally well conserved DNA-binding domain at the N-terminus and a dimerization domain at the C-terminus. Upon comparing the HigA homologue structures, a distinct difference was found in the C-terminal region that possesses the β-lid, and diverse orientations of two helix-turn-helix (HTH) motifs from HigA homologue dimers were observed. The structure of MtHigA3 bound to DNA reveals that the promoter DNA is bound to two HTH motifs of the MtHigA3 dimer presenting 46.5° bending, and the distance between the two HTH motifs of each MtHigA3 monomer was increased in MtHigA3 bound to DNA. The β-lid, which is found only in the tertiary structure of MtHigA3 among the HigA homologues, causes the formation of a tight dimerization network and leads to a unique arrangement for dimer formation that is related to the curvature of the bound DNA. This work could contribute to the understanding of the HigBA system of M. tuberculosis at the atomic level and may contribute to the development of new antibiotics for TB treatment.
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Affiliation(s)
- Jin-Young Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyo Jung Kim
- College of Pharmacy, Woosuk University, Wanju 55338, Republic of Korea
| | - Chinar Pathak
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Leicester Institute of Structural and Chemical Biology, University of Leicester, United Kingdom
| | - Hye-Jin Yoon
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Do-Hee Kim
- College of Pharmacy, Jeju National University, Jeju 63243, Republic of Korea
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, 534-2 Yeonsu-dong,Yeonsu-gu, Incheon 13120, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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13
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Balaure PC, Grumezescu AM. Recent Advances in Surface Nanoengineering for Biofilm Prevention and Control. Part I: Molecular Basis of Biofilm Recalcitrance. Passive Anti-Biofouling Nanocoatings. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1230. [PMID: 32599948 PMCID: PMC7353097 DOI: 10.3390/nano10061230] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/17/2022]
Abstract
Medical device-associated infections are becoming a leading cause of morbidity and mortality worldwide, prompting researchers to find new, more effective ways to control the bacterial colonisation of surfaces and biofilm development. Bacteria in biofilms exhibit a set of "emergent properties", meaning those properties that are not predictable from the study of free-living bacterial cells. The social coordinated behaviour in the biofilm lifestyle involves intricate signaling pathways and molecular mechanisms underlying the gain in resistance and tolerance (recalcitrance) towards antimicrobial agents as compared to free-floating bacteria. Nanotechnology provides powerful tools to disrupt the processes responsible for recalcitrance development in all stages of the biofilm life cycle. The present paper is a state-of-the-art review of the surface nanoengineering strategies currently used to design antibiofilm coatings. The review is structurally organised in two parts according to the targeted biofilm life cycle stages and molecular mechanisms intervening in recalcitrance development. Therefore, in the present first part, we begin with a presentation of the current knowledge of the molecular mechanisms responsible for increased recalcitrance that have to be disrupted. Further, we deal with passive surface nanoengineering strategies that aim to prevent bacterial cells from settling onto a biotic or abiotic surface. Both "fouling-resistant" and "fouling release" strategies are addressed as well as their synergic combination in a single unique nanoplatform.
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Affiliation(s)
- Paul Cătălin Balaure
- “Costin Nenitzescu” Department of Organic Chemistry, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, G. Polizu Street 1-7, 011061 Bucharest, Romania
| | - Alexandru Mihai Grumezescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, G. Polizu Street 1-7, 011061 Bucharest, Romania
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14
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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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15
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Bacterial persistence: Fundamentals and clinical importance. J Microbiol 2019; 57:829-835. [PMID: 31463787 DOI: 10.1007/s12275-019-9218-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/20/2022]
Abstract
The threat of antibiotic-resistant bacteria is increasing worldwide. Bacteria utilize persistence and resistance to survive antibiotic stress. For a long time, persistence has been studied only under laboratory conditions. Hence, studies of bacterial persistence are limited. Recently, however, the high incidence of infection relapses caused by persister cells in immunocompromised patients has emphasized the importance of persister research. Furthermore, persister pathogens are one of the causes of chronic infectious diseases, leading to the overuse of antibiotics and the emergence of antibiotic-resistant bacteria. Therefore, understanding the precise mechanism of persister formation is important for continued use of available antibiotics. In this review, we aimed to provide an overview of the persister studies published to date and the current knowledge of persister formation mechanisms. Recent studies of the features and mechanisms of persister formation are analyzed from the perspective of the nature of the persister cell.
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16
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Zavyalova E, Kopylov A. Energy Transfer as A Driving Force in Nucleic Acid⁻Protein Interactions. Molecules 2019; 24:molecules24071443. [PMID: 30979095 PMCID: PMC6480146 DOI: 10.3390/molecules24071443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/19/2022] Open
Abstract
Many nucleic acid–protein structures have been resolved, though quantitative structure-activity relationship remains unclear in many cases. Thrombin complexes with G-quadruplex aptamers are striking examples of a lack of any correlation between affinity, interface organization, and other common parameters. Here, we tested the hypothesis that affinity of the aptamer–protein complex is determined with the capacity of the interface to dissipate energy of binding. Description and detailed analysis of 63 nucleic acid–protein structures discriminated peculiarities of high-affinity nucleic acid–protein complexes. The size of the amino acid sidechain in the interface was demonstrated to be the most significant parameter that correlates with affinity of aptamers. This observation could be explained in terms of need of efficient energy transfer from interacting residues. Application of energy dissipation theory provided an illustrative tool for estimation of efficiency of aptamer–protein complexes. These results are of great importance for a design of efficient aptamers.
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Affiliation(s)
| | - Alexey Kopylov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia.
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17
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McVicker G, Hollingshead S, Pilla G, Tang CM. Maintenance of the virulence plasmid in Shigella flexneri is influenced by Lon and two functional partitioning systems. Mol Microbiol 2019; 111:1355-1366. [PMID: 30767313 PMCID: PMC6519299 DOI: 10.1111/mmi.14225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2019] [Indexed: 11/30/2022]
Abstract
Members of the genus Shigella carry a large plasmid, pINV, which is essential for virulence. In Shigella flexneri, pINV harbours three toxin‐antitoxin (TA) systems, CcdAB, GmvAT and VapBC that promote vertical transmission of the plasmid. Type II TA systems, such as those on pINV, consist of a toxic protein and protein antitoxin. Selective degradation of the antitoxin by proteases leads to the unopposed action of the toxin once genes encoding a TA system have been lost, such as following failure to inherit a plasmid harbouring a TA system. Here, we investigate the role of proteases in the function of the pINV TA systems and demonstrate that Lon, but not ClpP, is required for their activity during plasmid stability. This provides the first evidence that acetyltransferase family TA systems, such as GmvAT, can be regulated by Lon. Interestingly, S. flexneri pINV also harbours two putative partitioning systems, ParAB and StbAB. We show that both systems are functional for plasmid maintenance although their activity is masked by other systems on pINV. Using a model vector based on the pINV replicon, we observe temperature‐dependent differences between the two partitioning systems that contribute to our understanding of the maintenance of virulence in Shigella species.
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Affiliation(s)
- Gareth McVicker
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sarah Hollingshead
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Giulia Pilla
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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18
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Olson AT, Wang Z, Rico AB, Wiebe MS. A poxvirus pseudokinase represses viral DNA replication via a pathway antagonized by its paralog kinase. PLoS Pathog 2019; 15:e1007608. [PMID: 30768651 PMCID: PMC6395007 DOI: 10.1371/journal.ppat.1007608] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/28/2019] [Accepted: 01/31/2019] [Indexed: 12/26/2022] Open
Abstract
Poxviruses employ sophisticated, but incompletely understood, signaling pathways that engage cellular defense mechanisms and simultaneously ensure viral factors are modulated properly. For example, the vaccinia B1 protein kinase plays a vital role in inactivating the cellular antiviral factor BAF, and likely orchestrates other pathways as well. In this study, we utilized experimental evolution of a B1 deletion virus to perform an unbiased search for suppressor mutations and identify novel pathways involving B1. After several passages of the ΔB1 virus we observed a robust increase in viral titer of the adapted virus. Interestingly, our characterization of the adapted viruses reveals that mutations correlating with a loss of function of the vaccinia B12 pseudokinase provide a striking fitness enhancement to this virus. In support of predictions that reductive evolution is a driver of poxvirus adaptation, this is clear experimental evidence that gene loss can be of significant benefit. Next, we present multiple lines of evidence demonstrating that expression of full length B12 leads to a fitness reduction in viruses with a defect in B1, but has no apparent impact on wild-type virus or other mutant poxviruses. From these data we infer that B12 possesses a potent inhibitory activity that can be masked by the presence of the B1 kinase. Further investigation of B12 attributes revealed that it primarily localizes to the nucleus, a characteristic only rarely found among poxviral proteins. Surprisingly, BAF phosphorylation is reduced under conditions in which B12 is present in infected cells without B1, indicating that B12 may function in part by enhancing antiviral activity of BAF. Together, our studies of B1 and B12 present novel evidence that a paralogous kinase-pseudokinase pair can exhibit a unique epistatic relationship in a virus, perhaps serving to enhance B1 conservation during poxvirus evolution and to orchestrate yet-to-be-discovered nuclear events during infection.
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Affiliation(s)
- Annabel T. Olson
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States of America
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States of America
| | - Zhigang Wang
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States of America
| | - Amber B. Rico
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States of America
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, United States of America
| | - Matthew S. Wiebe
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States of America
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, United States of America
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19
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Rousset F, Cui L, Siouve E, Becavin C, Depardieu F, Bikard D. Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. PLoS Genet 2018; 14:e1007749. [PMID: 30403660 PMCID: PMC6242692 DOI: 10.1371/journal.pgen.1007749] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/19/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
High-throughput genetic screens are powerful methods to identify genes linked to a given phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be conveniently used to silence genes of interest in a method also known as CRISPRi. Here, we report a genome-wide CRISPR-dCas9 screen using a starting pool of ~ 92,000 sgRNAs which target random positions in the chromosome of E. coli. To benchmark our method, we first investigate its utility to predict gene essentiality in the genome of E. coli during growth in rich medium. We could identify 79% of the genes previously reported as essential and demonstrate the non-essentiality of some genes annotated as essential. In addition, we took advantage of the intermediate repression levels obtained when targeting the template strand of genes to show that cells are very sensitive to the expression level of a limited set of essential genes. Our data can be visualized on CRISPRbrowser, a custom web interface available at crispr.pasteur.fr. We then apply the screen to discover E. coli genes required by phages λ, T4 and 186 to kill their host, highlighting the involvement of diverse host pathways in the infection process of the three tested phages. We also identify colanic acid capsule synthesis as a shared resistance mechanism to all three phages. Finally, using a plasmid packaging system and a transduction assay, we identify genes required for the formation of functional λ capsids, thus covering the entire phage cycle. This study demonstrates the usefulness and convenience of pooled genome-wide CRISPR-dCas9 screens in bacteria and paves the way for their broader use as a powerful tool in bacterial genomics. Over the past few years, CRISPR-Cas technologies have emerged as powerful tools to edit genomes and modulate gene expression. They have been applied to perform high-throughput genetic screens with the purpose to understand the function of genes in a systematic manner, but the application of these screens to bacteria have so far remained limited. Here, we present the use of a library of ~92,000 guide RNAs directing the dCas9 protein to silence one by one all the genes in the chromosome of E. coli. To benchmark our method, we first investigate the performance of the technique to identify essential genes, highlighting several non-essential genes also found to be essential by other methods. We then apply our method to detect bacterial genes required by three different bacteriophages to kill E. coli and for the production of functional progeny by phage λ. Our screens highlight previously known and new genetic interactions between phages and their host’s pathways and emphasize the importance of bacterial capsule in the resistance to multiple phages. Altogether, our results demonstrate the usefulness of genome-wide CRISPR-dCas9 screens in bacteria to uncover genes involved in various phenotypes.
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Affiliation(s)
- François Rousset
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lun Cui
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Elise Siouve
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Christophe Becavin
- Hub Bioinformatique et Biostatistique, Institut Pasteur - C3BI, USR 3756 IP CNRS, Paris, France
| | - Florence Depardieu
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- * E-mail:
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20
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Tkachenko AG. Stress Responses of Bacterial Cells as Mechanism of Development of Antibiotic Tolerance (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818020114] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Butzin NC, Mather WH. Crosstalk between Diverse Synthetic Protein Degradation Tags in Escherichia coli. ACS Synth Biol 2018; 7:54-62. [PMID: 29193958 DOI: 10.1021/acssynbio.7b00122] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, a synthetic circuit in E. coli demonstrated that two proteins engineered with LAA tags targeted to the native protease ClpXP are susceptible to crosstalk due to competition for degradation between proteins. To understand proteolytic crosstalk beyond the single protease regime, we investigated in E. coli a set of synthetic circuits designed to probe the dynamics of existing and novel degradation tags fused to fluorescent proteins. These circuits were tested using both microplate reader and single-cell assays. We first quantified the degradation rates of each tag in isolation. We then tested if there was crosstalk between two distinguishable fluorescent proteins engineered with identical or different degradation tags. We demonstrated that proteolytic crosstalk was indeed not limited to the LAA degradation tag, but was also apparent between other diverse tags, supporting the complexity of the E. coli protein degradation system.
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Affiliation(s)
- Nicholas C. Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota 57007, United States
| | - William H. Mather
- Quantitative Biosciences, Inc., Solana Beach, California 92075, United States
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22
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Tajkarimi M, Wexler HM. CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome. Front Microbiol 2017; 8:2234. [PMID: 29218031 PMCID: PMC5704556 DOI: 10.3389/fmicb.2017.02234] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 10/31/2017] [Indexed: 12/29/2022] Open
Abstract
Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved. The CRISPR-Cas system is a multi-functional system described in prokaryotes that may be involved in control both of HGT and of gene regulation. Results: Clustered regularly interspaced short palindromic repeats (CRISPR) elements in all strains of B. fragilis (n = 109) with publically available genomes were identified. Three different CRISPR-Cas types, corresponding most closely to Type IB, Type IIIB, and Type IIC, were identified. Thirty-five strains had two CRISPR-Cas types, and three strains included all three CRISPR-Cas types in their respective genomes. The cas1 gene in the Type IIIB system encoded a reverse-transcriptase/Cas1 fusion protein rarely found in prokaryotes. We identified a short CRISPR (3 DR) with no associated cas genes present in most of the isolates; these CRISPRs were found immediately upstream of a hipA/hipB operon and we speculate that this element may be involved in regulation of this operon related to formation of persister cells during antimicrobial exposure. Also, blood isolates of B. fragilis did not have Type IIC CRISPR-Cas systems and had atypical Type IIIB CRISPR-Cas systems that were lacking adjacent cas genes. Conclusions: This is the first systematic report of CRISPR-Cas systems in a wide range of B. fragilis strains from a variety of sources. There are four apparent CRISPR-Cas systems in B. fragilis-three systems have adjacent cas genes. Understanding CRISPR/Cas function in B. fragilis will elucidate their role in gene expression, DNA repair and ability to survive exposure to antibiotics. Also, based on their unique CRISPR-Cas arrays, their phylogenetic clustering and their virulence potential, we are proposing that blood isolates of B. fragilis be viewed a separate subgroup.
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Affiliation(s)
- Mehrdad Tajkarimi
- Brentwood Biomedical Research Institute, Los Angeles, CA, United States
| | - Hannah M Wexler
- Brentwood Biomedical Research Institute, Los Angeles, CA, United States.,University of California, Los Angeles, Los Angeles, CA, United States.,GLAVA Health Care System, Los Angeles, CA, United States
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23
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Harms A, Maisonneuve E, Gerdes K. Mechanisms of bacterial persistence during stress and antibiotic exposure. Science 2017; 354:354/6318/aaf4268. [PMID: 27980159 DOI: 10.1126/science.aaf4268] [Citation(s) in RCA: 516] [Impact Index Per Article: 73.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bacterial persister cells avoid antibiotic-induced death by entering a physiologically dormant state and are considered a major cause of antibiotic treatment failure and relapsing infections. Such dormant cells form stochastically, but also in response to environmental cues, by various pathways that are usually controlled by the second messenger (p)ppGpp. For example, toxin-antitoxin modules have been shown to play a major role in persister formation in many model systems. More generally, the diversity of molecular mechanisms driving persister formation is increasingly recognized as the cause of physiological heterogeneity that underlies collective multistress and multidrug tolerance of persister subpopulations. In this Review, we summarize the current state of the field and highlight recent findings, with a focus on the molecular basis of persister formation and heterogeneity.
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Affiliation(s)
- Alexander Harms
- Center of Excellence for Bacterial Stress Response and Persistence (BASP), Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Etienne Maisonneuve
- Center of Excellence for Bacterial Stress Response and Persistence (BASP), Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Kenn Gerdes
- Center of Excellence for Bacterial Stress Response and Persistence (BASP), Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
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24
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Renbarger TL, Baker JM, Sattley WM. Slow and steady wins the race: an examination of bacterial persistence. AIMS Microbiol 2017; 3:171-185. [PMID: 31294156 PMCID: PMC6605009 DOI: 10.3934/microbiol.2017.2.171] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/21/2017] [Indexed: 12/02/2022] Open
Abstract
Bacterial persistence is a state of metabolic dormancy among a small fraction (<1%) of a genetically identical population of cells that, as a result, becomes transiently resistant to environmental stressors. Such cells, called persisters, are able to survive indeterminate periods of exposure to challenging and even hostile environmental conditions, including nutrient deprivation, oxidative stress, or the presence of an antibiotic to which the bacterium would normally be susceptible. Subpopulations of cells having the persister phenotype is also a common feature of biofilms, in which limited space, hypoxia, and nutrient deficiencies all contribute to the onset of persistence. Microbiologists have been aware of bacterial persistence since the early days of antibiotic development. However, in recent years the significance of this phenomenon has been brought into new focus, as persistent bacterial infections that require multiple rounds of antibiotic treatment are becoming a more widespread clinical challenge. Here, we provide an overview of the major features of bacterial persistence, including the various conditions that precipitate persister formation and a discussion of several of the better-characterized molecular mechanisms that trigger this distinctive mode of bacterial dormancy.
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Affiliation(s)
- Tara L Renbarger
- Division of Natural Sciences, Indiana Wesleyan University, Marion, Indiana 46953, USA
| | - Jennifer M Baker
- Division of Natural Sciences, Indiana Wesleyan University, Marion, Indiana 46953, USA
| | - W Matthew Sattley
- Division of Natural Sciences, Indiana Wesleyan University, Marion, Indiana 46953, USA
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25
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Ruangprasert A, Maehigashi T, Miles SJ, Dunham CM. Importance of the E. coli DinJ antitoxin carboxy terminus for toxin suppression and regulated proteolysis. Mol Microbiol 2017; 104:65-77. [PMID: 28164393 DOI: 10.1111/mmi.13641] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2017] [Indexed: 11/26/2022]
Abstract
Toxin-antitoxin genes play important roles in the regulation of bacterial growth during stress. One response to stress is selective proteolysis of antitoxin proteins which releases their cognate toxin partners causing rapid inhibition of growth. The features of toxin-antitoxin complexes that are important to inhibit toxin activity as well as to release the active toxin remain elusive. Furthermore, it is unclear how antitoxins are selected for proteolysis by cellular proteases. Here, we test the minimal structural requirements of the Escherichia coli DinJ antitoxin to suppress its toxin partner, YafQ. We find that DinJ-YafQ complex formation is critically dependent on the last ten C-terminal residues of DinJ. However, deletion of these 10 DinJ residues has little effect on transcriptional autorepression suggesting that the YafQ toxin is not a critical component of the repression complex in contrast to other toxin-antitoxin systems. We further demonstrate that loop 5 preceding these ten C-terminal residues is important for Lon-mediated proteolysis. These results provide important insights into the critical interactions between toxin-antitoxin pairs necessary to inhibit toxin activity and the regulated proteolysis of antitoxins.
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Affiliation(s)
- Ajchareeya Ruangprasert
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Tatsuya Maehigashi
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Stacey J Miles
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA, 30322, USA
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26
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Van den Bergh B, Fauvart M, Michiels J. Formation, physiology, ecology, evolution and clinical importance of bacterial persisters. FEMS Microbiol Rev 2017; 41:219-251. [DOI: 10.1093/femsre/fux001] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/12/2017] [Indexed: 12/19/2022] Open
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27
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Bajaj RA, Arbing MA, Shin A, Cascio D, Miallau L. Crystal structure of the toxin Msmeg_6760, the structural homolog of Mycobacterium tuberculosis Rv2035, a novel type II toxin involved in the hypoxic response. Acta Crystallogr F Struct Biol Commun 2016; 72:863-869. [PMID: 27917833 PMCID: PMC5137462 DOI: 10.1107/s2053230x16017957] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 11/08/2016] [Indexed: 11/10/2022] Open
Abstract
The structure of Msmeg_6760, a protein of unknown function, has been determined. Biochemical and bioinformatics analyses determined that Msmeg_6760 interacts with a protein encoded in the same operon, Msmeg_6762, and predicted that the operon is a toxin-antitoxin (TA) system. Structural comparison of Msmeg_6760 with proteins of known function suggests that Msmeg_6760 binds a hydrophobic ligand in a buried cavity lined by large hydrophobic residues. Access to this cavity could be controlled by a gate-latch mechanism. The function of the Msmeg_6760 toxin is unknown, but structure-based predictions revealed that Msmeg_6760 and Msmeg_6762 are homologous to Rv2034 and Rv2035, a predicted novel TA system involved in Mycobacterium tuberculosis latency during macrophage infection. The Msmeg_6760 toxin fold has not been previously described for bacterial toxins and its unique structural features suggest that toxin activation is likely to be mediated by a novel mechanism.
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Affiliation(s)
- R. Alexandra Bajaj
- UCLA–DOE Institute and Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA
| | - Mark A. Arbing
- UCLA–DOE Institute and Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA
| | - Annie Shin
- UCLA–DOE Institute and Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA
| | - Duilio Cascio
- UCLA–DOE Institute and Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA
| | - Linda Miallau
- UCLA–DOE Institute and Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA
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28
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Abstract
Bacterial toxin–antitoxin (TA) systems, in which a labile antitoxin binds and inhibits the toxin, can promote adaptation and persistence by modulating bacterial growth in response to stress. Some atypical TA systems, known as tripartite toxin–antitoxin–chaperone (TAC) modules, include a molecular chaperone that facilitates folding and protects the antitoxin from degradation. Here we use a TAC module from Mycobacterium tuberculosis as a model to investigate the molecular mechanisms by which classical TAs can become ‘chaperone-addicted'. The chaperone specifically binds the antitoxin at a short carboxy-terminal sequence (chaperone addiction sequence, ChAD) that is not present in chaperone-independent antitoxins. In the absence of chaperone, the ChAD sequence destabilizes the antitoxin, thus preventing toxin inhibition. Chaperone–ChAD pairs can be transferred to classical TA systems or to unrelated proteins and render them chaperone-dependent. This mechanism might be used to optimize the expression and folding of heterologous proteins in bacterial hosts for biotechnological or medical purposes. Some bacterial toxin-antitoxin systems consist of a labile antitoxin that inhibits a toxin, and a chaperone that stabilizes the antitoxin. Here, Bordes et al. identify a sequence within the antitoxin to which the chaperone binds and which can be transferred to other proteins to make them chaperone-dependent.
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29
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Verstraeten N, Knapen W, Fauvart M, Michiels J. A Historical Perspective on Bacterial Persistence. Methods Mol Biol 2016; 1333:3-13. [PMID: 26468095 DOI: 10.1007/978-1-4939-2854-5_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Bactericidal antibiotics quickly kill the majority of a bacterial population. However, a small fraction of cells typically survive through entering the so-called persister state. Persister cells are increasingly being viewed as a major cause of the recurrence of chronic infectious disease and could be an important factor in the emergence of antibiotic resistance. The phenomenon of persistence was first described in the 1940s, but remained poorly understood for decades afterwards. Only recently, a series of breakthrough discoveries has started to shed light on persister physiology and the molecular and genetic underpinnings of persister formation. We here provide an overview of the key studies that have paved the way for the current boom in persistence research, with a special focus on the technological and methodological advances that have enabled this progress.
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Affiliation(s)
- Natalie Verstraeten
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, box 2460, 3001, Heverlee, Belgium
| | - Wouter Knapen
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, box 2460, 3001, Heverlee, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, box 2460, 3001, Heverlee, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, box 2460, 3001, Heverlee, Belgium.
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Toxin-Antitoxin Modules Are Pliable Switches Activated by Multiple Protease Pathways. Toxins (Basel) 2016; 8:toxins8070214. [PMID: 27409636 PMCID: PMC4963847 DOI: 10.3390/toxins8070214] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 02/06/2023] Open
Abstract
Toxin-antitoxin (TA) modules are bacterial regulatory switches that facilitate conflicting outcomes for cells by promoting a pro-survival phenotypic adaptation and/or by directly mediating cell death, all through the toxin activity upon degradation of antitoxin. Intensive study has revealed specific details of TA module functions, but significant gaps remain about the molecular details of activation via antitoxin degradation used by different bacteria and in different environments. This review summarizes the current state of knowledge about the interaction of antitoxins with cellular proteases Lon and ClpP to mediate TA module activation. An understanding of these processes can answer long-standing questions regarding stochastic versus specific activation of TA modules and provide insight into the potential for manipulation of TA modules to alter bacterial growth.
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Desperate times call for desperate measures: benefits and costs of toxin-antitoxin systems. Curr Genet 2016; 63:69-74. [PMID: 27276988 DOI: 10.1007/s00294-016-0622-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/03/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022]
Abstract
Toxin-antitoxin (TA) loci were first described as killing systems for plasmid maintenance. The surprisingly abundant presence of TA loci in bacterial chromosomes has stimulated an extensive research in the recent decade aimed to understand the biological importance of these potentially deadly systems. Accumulating evidence suggests that the evolutionary success of genomic TA systems could be explained by their ability to increase bacterial fitness under stress conditions. While TA systems remain quiescent under favorable growth conditions, the toxins can be activated in response to stress resulting in growth suppression and development of stress-tolerant dormant state. Yet, several studies suggest that the TA-mediated stress protection is costly and traded off against decreased fitness under normal growth conditions. Here, we give an overview of the fitness benefits of the chromosomal TA systems, and discuss the costs of TA-mediated stress protection.
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Interconnection of post-transcriptional regulation: The RNA-binding protein Hfq is a novel target of the Lon protease in Pseudomonas aeruginosa. Sci Rep 2016; 6:26811. [PMID: 27229357 PMCID: PMC4882532 DOI: 10.1038/srep26811] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/09/2016] [Indexed: 01/22/2023] Open
Abstract
Besides being a major opportunistic human pathogen, Pseudomonas aeruginosa can be found in a wide range of environments. This versatility is linked to complex regulation, which is achieved through the action of transcriptional regulators, and post-transcriptional regulation by intracellular proteases including Lon. Indeed, lon mutants in this species show defects in motility, biofilm formation, pathogenicity and fluoroquinolone resistance. Here, the proteomic approach stable isotope labeling by amino acids in cell culture (SILAC) was used to search for novel proteolytic targets. One of the proteins that accumulated in the lon mutant was the RNA-binding protein Hfq. Further experiments demonstrated the ability of Lon to degrade Hfq in vitro. Also, overexpression of the hfq gene in the wild-type strain led to partial inhibition of swarming, swimming and twitching motilities, indicating that Hfq accumulation could contribute to the phenotypes displayed by Lon mutants. Hfq overexpression also led to the upregulation of the small regulatory RNA PhrS. Analysis of the phenotypes of strains lacking or overexpressing this sRNA indicated that the Lon protease might be indirectly regulating the levels and activity of sRNAs via Hfq. Overall, this study revealed new links in the complex regulatory chain that controls multicellular behaviours in P. aeruginosa.
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Abstract
A major factor complicating efforts to control the tuberculosis epidemic is the long duration of treatment required to successfully clear the infection. One reason that long courses of treatment are required may be the fact that mycobacterial cells arise during the course of infection that are less susceptible to antibiotics. Here we describe the paradigms of phenotypic drug tolerance and resistance as they apply to mycobacteria. We then discuss the mechanisms by which phenotypically drug-tolerant and -resistant cells arise both at a population level and in specialized subpopulations of cells that may be especially important in allowing the bacterium to survive in the face of treatment. These include general mechanisms that have been shown to alter the susceptibility of mycobacteria to antibiotics including growth arrest, efflux pump induction, and biofilm formation. In addition, we discuss emerging data from single-cell studies of mycobacteria that have identified unique ways in which specialized subpopulations of cells arise that vary in their frequency, in their susceptibility to drug, and in their stability over time.
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Rowe SE, Conlon BP, Keren I, Lewis K. Persisters: Methods for Isolation and Identifying Contributing Factors--A Review. Methods Mol Biol 2016; 1333:17-28. [PMID: 26468096 DOI: 10.1007/978-1-4939-2854-5_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Persister cells are phenotypic variants surviving a lethal dose of antibiotic, sufficient to kill the bulk of an exponential phase population. In this chapter we summarize current techniques to isolate persisters and discuss limitations associated with identifying mechanisms of persister formation.
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Affiliation(s)
- Sarah E Rowe
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Brian P Conlon
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Iris Keren
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave., Boston, MA, 02115, USA.
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Stability of the GraA Antitoxin Depends on Growth Phase, ATP Level, and Global Regulator MexT. J Bacteriol 2015; 198:787-96. [PMID: 26668267 DOI: 10.1128/jb.00684-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/10/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Bacterial type II toxin-antitoxin systems consist of a potentially poisonous toxin and an antitoxin that inactivates the toxic protein by binding to it. Most of the toxins regulate stress survival, but their activation depends on the stability of the antitoxin that has to be degraded in order for the toxin to be able to attack its cellular targets. The degradation of antitoxins is usually rapid and carried out by ATP-dependent protease Lon or Clp, which is activated under stress conditions. The graTA system of Pseudomonas putida encodes the toxin GraT, which can affect the growth rate and stress tolerance of bacteria but is under most conditions inactivated by the unusually stable antitoxin GraA. Here, we aimed to describe the stability features of the antitoxin GraA by analyzing its degradation rate in total cell lysates of P. putida. We show that the degradation rate of GraA depends on the growth phase of bacteria being fastest in the transition from exponential to stationary phase. In accordance with this, higher ATP levels were shown to stabilize GraA. Differently from other antitoxins, the main cellular proteases Lon and Clp are not involved in GraA stability. Instead, GraA seems to be degraded through a unique pathway involving an endoprotease that cleaves the antitoxin into two unequal parts. We also identified the global transcriptional regulator MexT as a factor for destabilization of GraA, which indicates that the degradation of GraA may be induced by conditions similar to those that activate MexT. IMPORTANCE Toxin-antitoxin (TA) modules are widespread in bacterial chromosomes and have important roles in stress tolerance. As activation of a type II toxin is triggered by proteolytic degradation of the antitoxin, knowledge about the regulation of the antitoxin stability is critical for understanding the activation of a particular TA module. Here, we report on the unusual degradation pathway of the antitoxin GraA of the recently characterized GraTA system. While GraA is uncommonly stable in the exponential and late-stationary phases, its degradation increases in the transition phase. The degradation pathway of GraA involves neither Lon nor Clp, which usually targets antitoxins, but rather an unknown endoprotease and the global regulator MexT, suggesting a new type of regulation of antitoxin stability.
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Carraro N, Poulin D, Burrus V. Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner. PLoS Genet 2015; 11:e1005298. [PMID: 26061412 PMCID: PMC4489591 DOI: 10.1371/journal.pgen.1005298] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/23/2015] [Indexed: 02/07/2023] Open
Abstract
Integrative and Conjugative Elements (ICEs) of the SXT/R391 family disseminate multidrug resistance among pathogenic Gammaproteobacteria such as Vibrio cholerae. SXT/R391 ICEs are mobile genetic elements that reside in the chromosome of their host and eventually self-transfer to other bacteria by conjugation. Conjugative transfer of SXT/R391 ICEs involves a transient extrachromosomal circular plasmid-like form that is thought to be the substrate for single-stranded DNA translocation to the recipient cell through the mating pore. This plasmid-like form is thought to be non-replicative and is consequently expected to be highly unstable. We report here that the ICE R391 of Providencia rettgeri is impervious to loss upon cell division. We have investigated the genetic determinants contributing to R391 stability. First, we found that a hipAB-like toxin/antitoxin system improves R391 stability as its deletion resulted in a tenfold increase of R391 loss. Because hipAB is not a conserved feature of SXT/R391 ICEs, we sought for alternative and conserved stabilization mechanisms. We found that conjugation itself does not stabilize R391 as deletion of traG, which abolishes conjugative transfer, did not influence the frequency of loss. However, deletion of either the relaxase-encoding gene traI or the origin of transfer (oriT) led to a dramatic increase of R391 loss correlated with a copy number decrease of its plasmid-like form. This observation suggests that replication initiated at oriT by TraI is essential not only for conjugative transfer but also for stabilization of SXT/R391 ICEs. Finally, we uncovered srpMRC, a conserved locus coding for two proteins distantly related to the type II (actin-type ATPase) parMRC partitioning system of plasmid R1. R391 and plasmid stabilization assays demonstrate that srpMRC is active and contributes to reducing R391 loss. While partitioning systems usually stabilizes low-copy plasmids, srpMRC is the first to be reported that stabilizes a family of ICEs.
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Affiliation(s)
- Nicolas Carraro
- Laboratory of bacterial molecular genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dominique Poulin
- Laboratory of bacterial molecular genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Laboratory of bacterial molecular genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Hauryliuk V, Atkinson GC, Murakami KS, Tenson T, Gerdes K. Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nat Rev Microbiol 2015; 13:298-309. [PMID: 25853779 PMCID: PMC4659695 DOI: 10.1038/nrmicro3448] [Citation(s) in RCA: 548] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppGpp) are involved in regulating growth and several different stress responses in bacteria. In recent years, substantial progress has been made in our understanding of the molecular mechanisms of (p)ppGpp metabolism and (p)ppGpp-mediated regulation. In this Review, we summarize these recent insights, with a focus on the molecular mechanisms governing the activity of the RelA/SpoT homologue (RSH) proteins, which are key players that regulate the cellular levels of (p)ppGpp. We also discuss the structural basis of transcriptional regulation by (p)ppGpp and the role of (p)ppGpp in GTP metabolism and in the emergence of bacterial persisters.
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Affiliation(s)
- Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87 Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87 Umeå, Sweden
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Gemma C. Atkinson
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87 Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87 Umeå, Sweden
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Katsuhiko S. Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Kenn Gerdes
- Department of Biology, Section for Molecular Microbiology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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Wei YX, Ye L, Liu DB, Zhang ZY, Liu C, Guo XK. Activation of the chromosomally encoded mazEF(Bif) locus of Bifidobacterium longum under acid stress. Int J Food Microbiol 2015; 207:16-22. [PMID: 25950853 DOI: 10.1016/j.ijfoodmicro.2015.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 02/18/2015] [Accepted: 04/19/2015] [Indexed: 01/15/2023]
Abstract
Toxin-antitoxin (TA) systems are distributed within the genomes of almost all free-living bacteria. Although the roles of chromosomally encoded TA systems are still under debate, they are suspected to be involved in various stress responses. Here, we provide the first report of a type II TA system in the probiotic bacterium Bifidobacterium longum. Bioinformatic analysis of the B. longum JDM301 genome identified a pair of linked genes encoding a MazEF-like TA system at the locus BLJ_811-BLJ_812. Our results showed that B. longum mazEF(Bif) genes form a bicistronic operon. The over-expression of MazF(Bif) was toxic to Escherichia coli and could be neutralized by the co-expression of its cognate antitoxin MazE(Bif). We demonstrated that MazEF(Bif) was activated during acid stress, which would most likely be encountered in the gastrointestinal tract. In addition, we found that the protease ClpPX(Bif), in addition to MazEF(Bif), was induced under acid stress. Furthermore, we examined antitoxin levels over time for MazEF(Bif) and observed that the antitoxin MazE(Bif) was degraded by ClpPX(Bif), which suggested that MazEF(Bif) was activated through the hydrolysis of MazE(Bif) by ClpP1X(Bif) and ClpP2X(Bif) under acid stress. Our results suggest that the MazEF(Bif) TA module may play an important role in cell physiology and may represent a cell growth modulator that helps bacteria to cope with acid stress in the gastrointestinal tract and environment.
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Affiliation(s)
- Yan-Xia Wei
- Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity/School of Stomatology, Xuzhou Medical College, Xuzhou, Jiangsu 221004, China; Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lu Ye
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dian-Bin Liu
- Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity/School of Stomatology, Xuzhou Medical College, Xuzhou, Jiangsu 221004, China
| | - Zhuo-Yang Zhang
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chang Liu
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Xiao-Kui Guo
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Biofilm-related infections: bridging the gap between clinical management and fundamental aspects of recalcitrance toward antibiotics. Microbiol Mol Biol Rev 2015; 78:510-43. [PMID: 25184564 DOI: 10.1128/mmbr.00013-14] [Citation(s) in RCA: 762] [Impact Index Per Article: 84.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Surface-associated microbial communities, called biofilms, are present in all environments. Although biofilms play an important positive role in a variety of ecosystems, they also have many negative effects, including biofilm-related infections in medical settings. The ability of pathogenic biofilms to survive in the presence of high concentrations of antibiotics is called "recalcitrance" and is a characteristic property of the biofilm lifestyle, leading to treatment failure and infection recurrence. This review presents our current understanding of the molecular mechanisms of biofilm recalcitrance toward antibiotics and describes how recent progress has improved our capacity to design original and efficient strategies to prevent or eradicate biofilm-related infections.
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40
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Chan WT, Balsa D, Espinosa M. One cannot rule them all: Are bacterial toxins-antitoxins druggable? FEMS Microbiol Rev 2015; 39:522-40. [PMID: 25796610 PMCID: PMC4487406 DOI: 10.1093/femsre/fuv002] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2015] [Indexed: 01/31/2023] Open
Abstract
Type II (proteic) toxin–antitoxin (TA) operons are widely spread in bacteria and archaea. They are organized as operons in which, usually, the antitoxin gene precedes the cognate toxin gene. The antitoxin generally acts as a transcriptional self-repressor, whereas the toxin acts as a co-repressor, both proteins constituting a harmless complex. When bacteria encounter a stressful environment, TAs are triggered. The antitoxin protein is unstable and will be degraded by host proteases, releasing the free toxin to halt essential processes. The result is a cessation of cell growth or even death. Because of their ubiquity and the essential processes targeted, TAs have been proposed as good candidates for development of novel antimicrobials. We discuss here the possible druggability of TAs as antivirals and antibacterials, with focus on the potentials and the challenges that their use may find in the ‘real’ world. We present strategies to develop TAs as antibacterials in view of novel technologies, such as the use of very small molecules (fragments) as inhibitors of protein–protein interactions. Appropriate fragments could disrupt the T:A interfaces leading to the release of the targeted TA pair. Possible ways of delivery and formulation of Tas are also discussed. We consider various approaches to develop the toxins of the type II family as possible candidates to drug discovery; druggability of toxins-antitoxins could be possible as antivirals. As antibacterials, they might be considered as druggable but delivery and formulation may not be simple so far.
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Affiliation(s)
- Wai Ting Chan
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28006-Madrid, Spain
| | - Dolors Balsa
- Immunology & Vaccines, Laboratorios LETI, Gran Via de les Corts Catalanes 184. 08034-Barcelona, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28006-Madrid, Spain
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Hadži S, Garcia-Pino A, Gerdes K, Lah J, Loris R. Crystallization of two operator complexes from the Vibrio cholerae HigBA2 toxin-antitoxin module. Acta Crystallogr F Struct Biol Commun 2015; 71:226-33. [PMID: 25664801 PMCID: PMC4321481 DOI: 10.1107/s2053230x15000746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/13/2015] [Indexed: 11/11/2022] Open
Abstract
The HigA2 antitoxin and the HigBA2 toxin-antitoxin complex from Vibrio cholerae were crystallized in complex with their operator box. Screening of 22 different DNA duplexes led to two crystal forms of HigA2 complexes and one crystal form of a HigBA2 complex. Crystals of HigA2 in complex with a 17 bp DNA duplex belong to space group P3221, with unit-cell parameters a = b = 94.0, c = 123.7 Å, and diffract to 2.3 Å resolution. The second form corresponding to HigA2 in complex with a 19 bp duplex belong to space group P43212 and only diffract to 3.45 Å resolution. Crystals of the HigBA2 toxin-antitoxin were obtained in complex with a 31 bp duplex and belonged to space group P41212, with unit-cell parameters a = b = 113.6, c = 121.1 Å. They diffract to 3.3 Å resolution.
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Affiliation(s)
- San Hadži
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ascerceva 5, 1000 Ljubljana, Slovenia
| | - Abel Garcia-Pino
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Kenn Gerdes
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ascerceva 5, 1000 Ljubljana, Slovenia
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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Persister Cells in Biofilm Associated Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 831:1-9. [DOI: 10.1007/978-3-319-09782-4_1] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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43
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Conlon BP. Staphylococcus aureus chronic and relapsing infections: Evidence of a role for persister cells: An investigation of persister cells, their formation and their role in S. aureus disease. Bioessays 2014; 36:991-6. [PMID: 25100240 DOI: 10.1002/bies.201400080] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Staphylococcus aureus is an opportunistic pathogen capable of causing a variety of diseases including osteomyelitis, endocarditis, infections of indwelling devices and wound infections. These infections are often chronic and highly recalcitrant to antibiotic treatment. Persister cells appear to be central to this recalcitrance. A multitude of factors contribute to S. aureus virulence and high levels of treatment failure. These include its ability to colonize the skin and nares of the host, its ability to evade the host immune system and its development of resistance to a variety of antibiotics. Less understood is the phenomenon of persister cells and their role in S. aureus infections and treatment outcome. Persister cells occur as a sub-population of phenotypic variants that are tolerant to antibiotic treatment. This review examines the importance of persisters in chronic and relapsing S. aureus infections and proposes methods for their eradication.
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Affiliation(s)
- Brian P Conlon
- Antimicrobial Discovery Center, Northeastern University, Boston, MA, USA
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44
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Wen Y, Behiels E, Felix J, Elegheert J, Vergauwen B, Devreese B, Savvides SN. The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence. Nucleic Acids Res 2014; 42:10134-47. [PMID: 25056321 PMCID: PMC4150777 DOI: 10.1093/nar/gku665] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nearly all bacteria exhibit a type of phenotypic growth described as persistence that is thought to underlie antibiotic tolerance and recalcitrant chronic infections. The chromosomally encoded high-persistence (Hip) toxin–antitoxin proteins HipASO and HipBSO from Shewanella oneidensis, a proteobacterium with unusual respiratory capacities, constitute a type II toxin–antitoxin protein module. Here we show that phosphorylated HipASO can engage in an unexpected ternary complex with HipBSO and double-stranded operator DNA that is distinct from the prototypical counterpart complex from Escherichia coli. The structure of HipBSO in complex with operator DNA reveals a flexible C-terminus that is sequestered by HipASO in the ternary complex, indicative of its role in binding HipASO to abolish its function in persistence. The structure of HipASO in complex with a non-hydrolyzable ATP analogue shows that HipASO autophosphorylation is coupled to an unusual conformational change of its phosphorylation loop. However, HipASO is unable to phosphorylate the translation factor Elongation factor Tu, contrary to previous reports, but in agreement with more recent findings. Our studies suggest that the phosphorylation state of HipA is an important factor in persistence and that the structural and mechanistic diversity of HipAB modules as regulatory factors in bacterial persistence is broader than previously thought.
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Affiliation(s)
- Yurong Wen
- Unit for Biological Mass Spectrometry and Proteomics, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Unit for Structural Biology, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ester Behiels
- Unit for Biological Mass Spectrometry and Proteomics, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Jan Felix
- Unit for Structural Biology, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Jonathan Elegheert
- Unit for Structural Biology, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Bjorn Vergauwen
- Unit for Structural Biology, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Bart Devreese
- Unit for Biological Mass Spectrometry and Proteomics, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Savvas N Savvides
- Unit for Structural Biology, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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45
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Liang Y, Gao Z, Wang F, Zhang Y, Dong Y, Liu Q. Structural and functional characterization of Escherichia coli toxin-antitoxin complex DinJ-YafQ. J Biol Chem 2014; 289:21191-202. [PMID: 24923448 DOI: 10.1074/jbc.m114.559773] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Toxin YafQ functions as a ribonuclease in the dinJ-yafQ toxin-antitoxin system of Escherichia coli. Antitoxin DinJ neutralizes YafQ-mediated toxicity by forming a stable protein complex. Here, crystal structures of the (DinJ)2-(YafQ)2 complex and the isolated YafQ toxin have been determined. The structure of the heterotetrameric complex (DinJ)2-(YafQ)2 revealed that the N-terminal region of DinJ folds into a ribbon-helix-helix motif and dimerizes for DNA recognition, and the C-terminal portion of each DinJ exclusively wraps around a YafQ molecule. Upon incorporation into the heterotetrameric complex, a conformational change of YafQ in close proximity to the catalytic site of the typical microbial ribonuclease fold was observed and validated. Mutagenesis experiments revealed that a DinJ mutant restored YafQ RNase activity in a tetramer complex in vitro but not in vivo. An electrophoretic mobility shift assay showed that one of the palindromic sequences present in the upstream intergenic region of DinJ served as a binding sequences for both the DinJ-YafQ complex and the antitoxin DinJ alone. Based on structure-guided and site-directed mutagenesis of DinJ-YafQ, we showed that two pairs of amino acids in DinJ were important for DNA binding; the R8A and K16A substitutions and the S31A and R35A substitutions in DinJ abolished the DNA binding ability of the DinJ-YafQ complex.
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Affiliation(s)
- Yajing Liang
- From the School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China, the Multidiscipline Research Center, Institute of High Energy Physics of the Chinese Academy of Sciences, 19B Yuequan Road, Beijing 100049, China, and
| | - Zengqiang Gao
- the Multidiscipline Research Center, Institute of High Energy Physics of the Chinese Academy of Sciences, 19B Yuequan Road, Beijing 100049, China, and
| | - Fei Wang
- the Multidiscipline Research Center, Institute of High Energy Physics of the Chinese Academy of Sciences, 19B Yuequan Road, Beijing 100049, China, and
| | - Yangli Zhang
- the Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, YiXueYuanlu-1, Chongqing 400016, China
| | - Yuhui Dong
- the Multidiscipline Research Center, Institute of High Energy Physics of the Chinese Academy of Sciences, 19B Yuequan Road, Beijing 100049, China, and
| | - Quansheng Liu
- the Multidiscipline Research Center, Institute of High Energy Physics of the Chinese Academy of Sciences, 19B Yuequan Road, Beijing 100049, China, and
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Loris R, Garcia-Pino A. Disorder- and Dynamics-Based Regulatory Mechanisms in Toxin–Antitoxin Modules. Chem Rev 2014; 114:6933-47. [DOI: 10.1021/cr400656f] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Remy Loris
- Molecular
Recognition Unit, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural
Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Abel Garcia-Pino
- Molecular
Recognition Unit, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural
Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
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47
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Sterckx YGJ, Volkov AN, Vranken WF, Kragelj J, Jensen MR, Buts L, Garcia-Pino A, Jové T, Van Melderen L, Blackledge M, van Nuland NAJ, Loris R. Small-angle X-ray scattering- and nuclear magnetic resonance-derived conformational ensemble of the highly flexible antitoxin PaaA2. Structure 2014; 22:854-65. [PMID: 24768114 DOI: 10.1016/j.str.2014.03.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/14/2014] [Accepted: 03/15/2014] [Indexed: 11/26/2022]
Abstract
Antitoxins from prokaryotic type II toxin-antitoxin modules are characterized by a high degree of intrinsic disorder. The description of such highly flexible proteins is challenging because they cannot be represented by a single structure. Here, we present a combination of SAXS and NMR data to describe the conformational ensemble of the PaaA2 antitoxin from the human pathogen E. coli O157. The method encompasses the use of SAXS data to filter ensembles out of a pool of conformers generated by a custom NMR structure calculation protocol and the subsequent refinement by a block jackknife procedure. The final ensemble obtained through the method is validated by an established residual dipolar coupling analysis. We show that the conformational ensemble of PaaA2 is highly compact and that the protein exists in solution as two preformed helices, connected by a flexible linker, that probably act as molecular recognition elements for toxin inhibition.
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Affiliation(s)
- Yann G J Sterckx
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Wim F Vranken
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Jaka Kragelj
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel CNRS-CEA-UJF UMR 5075, 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Malene Ringkjøbing Jensen
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel CNRS-CEA-UJF UMR 5075, 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Lieven Buts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Abel Garcia-Pino
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Thomas Jové
- Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires Faculté des Sciences, Université Libre de Bruxelles, 12 Rue des Professeurs Jeener et Brachet, B-6041 Gosselies, Belgium
| | - Laurence Van Melderen
- Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires Faculté des Sciences, Université Libre de Bruxelles, 12 Rue des Professeurs Jeener et Brachet, B-6041 Gosselies, Belgium
| | - Martin Blackledge
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel CNRS-CEA-UJF UMR 5075, 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Nico A J van Nuland
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Molecular Recognition Unit and Jean Jeener NMR Centre, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussels, Belgium.
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48
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Maisonneuve E, Gerdes K. Molecular Mechanisms Underlying Bacterial Persisters. Cell 2014; 157:539-48. [DOI: 10.1016/j.cell.2014.02.050] [Citation(s) in RCA: 389] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/20/2014] [Accepted: 02/25/2014] [Indexed: 10/25/2022]
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Multiple toxin-antitoxin systems in Mycobacterium tuberculosis. Toxins (Basel) 2014; 6:1002-20. [PMID: 24662523 PMCID: PMC3968373 DOI: 10.3390/toxins6031002] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/20/2014] [Accepted: 02/24/2014] [Indexed: 12/26/2022] Open
Abstract
The hallmark of Mycobacterium tuberculosis is its ability to persist for a long-term in host granulomas, in a non-replicating and drug-tolerant state, and later awaken to cause disease. To date, the cellular factors and the molecular mechanisms that mediate entry into the persistence phase are poorly understood. Remarkably, M. tuberculosis possesses a very high number of toxin-antitoxin (TA) systems in its chromosome, 79 in total, regrouping both well-known (68) and novel (11) families, with some of them being strongly induced in drug-tolerant persisters. In agreement with the capacity of stress-responsive TA systems to generate persisters in other bacteria, it has been proposed that activation of TA systems in M. tuberculosis could contribute to its pathogenesis. Herein, we review the current knowledge on the multiple TA families present in this bacterium, their mechanism, and their potential role in physiology and virulence.
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50
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Brzozowska I, Zielenkiewicz U. The ClpXP protease is responsible for the degradation of the Epsilon antidote to the Zeta toxin of the streptococcal pSM19035 plasmid. J Biol Chem 2014; 289:7514-23. [PMID: 24492616 DOI: 10.1074/jbc.m113.519488] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most bacterial genomes contain different types of toxin-antitoxin (TA) systems. The ω-ε-ζ proteinaceous type II TA cassette from the streptococcal pSM19035 plasmid is a member of the ε/ζ family, which is commonly found in multiresistance plasmids and chromosomes of various human pathogens. Regulation of type II TA systems relies on the proteolysis of antitoxin proteins. Under normal conditions, the Epsilon antidote neutralizes the Zeta toxin through the formation of a tight complex. In this study, we show, using both in vivo and in vitro analyses, that the ClpXP protease is responsible for Epsilon antitoxin degradation. Using in vivo studies, we examined the stability of the plasmids with active or inactive ω-ε-ζ TA cassettes in B. subtilis mutants that were defective for different proteases. Using in vitro assays, the degradation of purified His6-Epsilon by the His6-LonBs, ClpPBs, and ClpXBs proteases from B. subtilis was analyzed. Additionally, we showed that purified Zeta toxin protects the Epsilon protein from rapid ClpXP-catalyzed degradation.
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Affiliation(s)
- Iwona Brzozowska
- From the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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