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Zeng X, Hu L, Ai Q, Liu CJ, Xiong LX, Yang WW, Zhang X, Liu L, Li GQ. Helicobacter macacae MazF interplays with Escherichia coli homologs and enhances antibiotic tolerance. Helicobacter 2023; 28:e13014. [PMID: 37559199 DOI: 10.1111/hel.13014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/17/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Toxin-antitoxin systems are highly variable, even among strains of the same bacterial species. The MazEF toxin-antitoxin system is found in many bacteria and plays important roles in various biological processes such as antibiotic tolerance and phage defense. However, no interplay of MazEF systems between different species was reported. MATERIALS AND METHODS MazEF toxin-antitoxin system of Helicobacter macacae was examined in three Escherichia coli strains with and without endogenous MazEF knockout. In vivo toxicity, antibiotic tolerance, and live/dead staining followed by flowcytometry analysis were performed to evaluate the functionality and interplay of the toxin-antitoxin system between the two species. RESULTS Controlled ectopic expression of MazF of H. macacae (MazFhm) in E. coli did not affect its growth. However, in endogenous MazEF knockout E. coli strains, MazFhm expression caused a sharp growth arrest. The toxicity of MazFhm could be neutralized by both the antitoxin of MazE homolog of H.macacae and the antitoxin of MazE of E. coli, indicating interplay of MazEF toxin-antitoxin systems between the two species. Induced expression of MazFhm enhanced tolerance to a lethal dose of levofloxacin, suggesting enhanced persister formation, which was further confirmed by live/dead cell staining. CONCLUSIONS The MazEF toxin-antitoxin system of H. macace enhances persister formation and thus antibiotic tolerance in E. coli. Our findings reveal an interplay between the MazEF systems of H. macacae and E. coli, emphasizing the need to consider this interaction while evaluating the toxicity and functionality of MazF homologs from different species in future studies.
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Affiliation(s)
- Xi Zeng
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
- Department of Gastroenterology, The First Affiliated Hospital of Shaoyang University, Shaoyang, China
| | - Limiao Hu
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Qi Ai
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Cai-Juan Liu
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Lu-Xi Xiong
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Wei-Wei Yang
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Xiaotuan Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Logen Liu
- Clinical Research Center, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
- Hunan Provincial Key Laboratory of Basic and Clinical Pharmacological Research on Gastrointestinal Tumors, University of South China, Hengyang, China
| | - Guo-Qing Li
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
- Hunan Provincial Key Laboratory of Basic and Clinical Pharmacological Research on Gastrointestinal Tumors, University of South China, Hengyang, China
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Lee KY, Lee BJ. Dynamics-Based Regulatory Switches of Type II Antitoxins: Insights into New Antimicrobial Discovery. Antibiotics (Basel) 2023; 12:antibiotics12040637. [PMID: 37106997 PMCID: PMC10135005 DOI: 10.3390/antibiotics12040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Type II toxin-antitoxin (TA) modules are prevalent in prokaryotes and are involved in cell maintenance and survival under harsh environmental conditions, including nutrient deficiency, antibiotic treatment, and human immune responses. Typically, the type II TA system consists of two protein components: a toxin that inhibits an essential cellular process and an antitoxin that neutralizes its toxicity. Antitoxins of type II TA modules typically contain the structured DNA-binding domain responsible for TA transcription repression and an intrinsically disordered region (IDR) at the C-terminus that directly binds to and neutralizes the toxin. Recently accumulated data have suggested that the antitoxin's IDRs exhibit variable degrees of preexisting helical conformations that stabilize upon binding to the corresponding toxin or operator DNA and function as a central hub in regulatory protein interaction networks of the type II TA system. However, the biological and pathogenic functions of the antitoxin's IDRs have not been well discussed compared with those of IDRs from the eukaryotic proteome. Here, we focus on the current state of knowledge about the versatile roles of IDRs of type II antitoxins in TA regulation and provide insights into the discovery of new antibiotic candidates that induce toxin activation/reactivation and cell death by modulating the regulatory dynamics or allostery of the antitoxin.
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Affiliation(s)
- Ki-Young Lee
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si 11160, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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ArsR Family Regulator MSMEG_6762 Mediates the Programmed Cell Death by Regulating the Expression of HNH Nuclease in Mycobacteria. Microorganisms 2022; 10:microorganisms10081535. [PMID: 36013953 PMCID: PMC9416677 DOI: 10.3390/microorganisms10081535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Programmed cell death (PCD) is the result of an intracellular program and is accomplished by a regulated process in both prokaryotic and eukaryotic organisms. Here, we report a programed cell death process in Mycobacterium smegmatis, an Actinobacteria species which involves a transcription factor and a DNase of the HNH family. We found that over-expression of an ArsR family member of the transcription factor, MSMEG_6762, leads to cell death. Transcriptome analysis revealed an increase in the genes' transcripts involved in DNA repair and homologous recombination, and in three members of HNH family DNases. Knockout of one of the DNase genes, MSMEG_1275, alleviated cell death and its over-expression of programmed cell death. Purified MSMEG_1275 cleaved the M. smegmatis DNA at multiple sites. Overall, our results indicate that the MSMEG_6762 affects cell death and is mediated, at least partially, by activation of the HNH nuclease expression under a stress condition.
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Abstract
Toxin-antitoxin systems are widespread in bacterial genomes. They are usually composed of two elements: a toxin that inhibits an essential cellular process and an antitoxin that counteracts its cognate toxin. In the past decade, a number of new toxin-antitoxin systems have been described, bringing new growth inhibition mechanisms to light as well as novel modes of antitoxicity. However, recent advances in the field profoundly questioned the role of these systems in bacterial physiology, stress response and antimicrobial persistence. This shifted the paradigm of the functions of toxin-antitoxin systems to roles related to interactions between hosts and their mobile genetic elements, such as viral defence or plasmid stability. In this Review, we summarize the recent progress in understanding the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin-antitoxin systems.
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Dai J, Chen Z, Hou J, Wang Y, Guo M, Cao J, Wang L, Xu H, Tian B, Zhao Y. MazEF Toxin-Antitoxin System-Mediated DNA Damage Stress Response in Deinococcus radiodurans. Front Genet 2021; 12:632423. [PMID: 33679894 PMCID: PMC7933679 DOI: 10.3389/fgene.2021.632423] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/12/2021] [Indexed: 01/01/2023] Open
Abstract
Deinococcus radiodurans shows marked resistance to various types of DNA-damaging agents, including mitomycin C (MMC). A type II toxin-antitoxin (TA) system that responds to DNA damage stress was identified in D. radiodurans, comprising the toxin MazF-dr and the antitoxin MazE-dr. The cleavage specificity of MazF-dr, an endoribonuclease, was previously characterized. Here, we further investigated the regulatory role of the MazEF system in the response to DNA damage stress in D. radiodurans. The crystal structure of D. radiodurans MazF (MazF-dr) was determined at a resolution of 1.3 Å and is the first structure of the toxin of the TA system of D. radiodurans. MazF-dr forms a dimer mediated by the presence of interlocked loops. Transcriptional analysis revealed 650 downregulated genes in the wild-type (WT) strain, but not in the mazEF mutant strain, which are potentially regulated by MazEF-dr in response to MMC treatment. Some of these genes are involved in membrane trafficking and metal ion transportation. Subsequently, compared with the WT strain, the mazEF mutant strain exhibited much lower MMC-induced intracellular iron concentrations, reactive oxygen species (ROS), and protein carbonylation levels. These results provide evidence that MazEF-mediated cell death in D. radiodurans might be caused by an increase in ROS accumulation upon DNA damage stress.
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Affiliation(s)
- Jingli Dai
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, China
| | - Zijing Chen
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, China
| | - Jinfeng Hou
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, China
| | - Yudong Wang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, China
| | - Miao Guo
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, China
| | - Jiajia Cao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, China
| | - Hong Xu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, China
| | - Bing Tian
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, China
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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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Targeting Type II Toxin-Antitoxin Systems as Antibacterial Strategies. Toxins (Basel) 2020; 12:toxins12090568. [PMID: 32899634 PMCID: PMC7551001 DOI: 10.3390/toxins12090568] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
The identification of novel targets for antimicrobial agents is crucial for combating infectious diseases caused by evolving bacterial pathogens. Components of bacterial toxin–antitoxin (TA) systems have been recognized as promising therapeutic targets. These widespread genetic modules are usually composed of two genes that encode a toxic protein targeting an essential cellular process and an antitoxin that counteracts the activity of the toxin. Uncontrolled toxin expression may elicit a bactericidal effect, so they may be considered “intracellular molecular bombs” that can lead to elimination of their host cells. Based on the molecular nature of antitoxins and their mode of interaction with toxins, TA systems have been classified into six groups. The most prevalent are type II TA systems. Due to their ubiquity among clinical isolates of pathogenic bacteria and the essential processes targeted, they are promising candidates for the development of novel antimicrobial strategies. In this review, we describe the distribution of type II TA systems in clinically relevant human pathogens, examine how these systems could be developed as the targets for novel antibacterials, and discuss possible undesirable effects of such therapeutic intervention, such as the induction of persister cells, biofilm formation and toxicity to eukaryotic cells.
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Ramisetty BCM, Sudhakari PA. 'Bacterial Programmed Cell Death': cellular altruism or genetic selfism? FEMS Microbiol Lett 2020; 367:5895326. [PMID: 32821912 DOI: 10.1093/femsle/fnaa141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023] Open
Abstract
Cell-dependent propagation of the 'self' is the driver of all species, organisms and even genes. Conceivably, elimination of these entities is caused by cellular death. Then, how can genes that cause the death of the same cell evolve? Programmed cell death (PCD) is the gene-dependent self-inflicted death. In multicellular organisms, PCD of a cell confers fitness to the surviving rest of the organism, which thereby allows the selection of genes responsible for PCD. However, PCD in free-living bacteria is intriguing; the death of the cell is the death of the organism. How can such PCD genes be selected in unicellular organisms? The bacterial PCD in a population is proposed to confer fitness to the surviving kin in the form of sporulation, nutrition, infection-containment and matrix materials. While the cell-centred view leading to propositions of 'altruism' is enticing, the gene-centred view of 'selfism' is neglected. In this opinion piece, we reconceptualize the PCD propositions as genetic selfism (death due to loss/mutation of selfish genes) rather than cellular altruism (death for the conferment of fitness to kin). Within the scope and the available evidence, we opine that some of the PCD-like observations in bacteria seem to be the manifestation of genetic selfism by Restriction-Modification systems and Toxin-Antitoxin systems.
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Affiliation(s)
- Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India 613401
| | - Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India 613401
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Reassessing the Role of the Type II MqsRA Toxin-Antitoxin System in Stress Response and Biofilm Formation: mqsA Is Transcriptionally Uncoupled from mqsR. mBio 2019; 10:mBio.02678-19. [PMID: 31848281 PMCID: PMC6918082 DOI: 10.1128/mbio.02678-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Toxin-antitoxin (TA) systems are broadly distributed modules whose biological roles remain mostly unknown. The mqsRA system is a noncanonical TA system in which the toxin and antitoxins genes are organized in operon but with the particularity that the toxin gene precedes that of the antitoxin. This system was shown to regulate global processes such as resistance to bile salts, motility, and biofilm formation. In addition, the MqsA antitoxin was shown to be a master regulator that represses the transcription of the csgD, cspD, and rpoS global regulator genes, thereby displaying a pleiotropic regulatory role. Here, we identified two promoters located in the toxin sequence driving the constitutive expression of mqsA, allowing thereby excess production of the MqsA antitoxin compared to the MqsR toxin. Our results show that both antitoxin-specific and operon promoters are not regulated by stresses such as amino acid starvation, oxidative shock, or bile salts. Moreover, we show that the MqsA antitoxin is not a global regulator as suggested, since the expression of csgD, cspD and rpoS is similar in wild-type and ΔmqsRA mutant strains. Moreover, these two strains behave similarly in terms of biofilm formation and sensitivity to oxidative stress or bile salts.IMPORTANCE There is growing controversy regarding the role of chromosomal toxin-antitoxin systems in bacterial physiology. mqsRA is a peculiar toxin-antitoxin system, as the gene encoding the toxin precedes that of the antitoxin. This system was previously shown to play a role in stress response and biofilm formation. In this work, we identified two promoters specifically driving the constitutive expression of the antitoxin, thereby decoupling the expression of antitoxin from the toxin. We also showed that mqsRA contributes neither to the regulation of biofilm formation nor to the sensitivity to oxidative stress and bile salts. Finally, we were unable to confirm that the MqsA antitoxin is a global regulator. Altogether, our data are ruling out the involvement of the mqsRA system in Escherichia coli regulatory networks.
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Physiological, Genetic, and Transcriptomic Analysis of Alcohol-Induced Delay of Escherichia coli Death. Appl Environ Microbiol 2019; 85:AEM.02113-18. [PMID: 30389772 DOI: 10.1128/aem.02113-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/27/2018] [Indexed: 11/20/2022] Open
Abstract
When Escherichia coli K-12 is inoculated into rich medium in batch culture, cells experience five phases. While the lag and logarithmic phases are mechanistically fairly well defined, the stationary phase, death phase, and long-term stationary phase are less well understood. Here, we characterize a mechanism of delaying death, a phenomenon we call the "alcohol effect," where the addition of small amounts of certain alcohols prolongs stationary phase for at least 10 days longer than in untreated conditions. We show that the stationary phase is extended when ethanol is added above a minimum threshold concentration. Once ethanol levels fall below a threshold concentration, cells enter the death phase. We also show that the effect is conferred by the addition of straight-chain alcohols 1-propanol, 1-butanol, 1-pentanol, and, to a lesser degree, 1-hexanol. However, methanol, isopropanol, 1-heptanol, and 1-octanol do not delay entry into death phase. Though modulated by RpoS, the alcohol effect does not require RpoS activity or the activities of the AdhE or AdhP alcohol dehydrogenases. Further, we show that ethanol is capable of extending the life span of stationary-phase cultures for non-K-12 E. coli strains and that this effect is caused in part by genes of the glycolate degradation pathway. These data suggest a model where ethanol and other shorter 1-alcohols can serve as signaling molecules, perhaps by modulating patterns of gene expression that normally regulate the transition from stationary phase to death phase.IMPORTANCE In one of the most well-studied organisms in the life sciences, Escherichia coli, we still do not fully understand what causes populations to die. This is largely due to the technological difficulties of studying bacterial cell death. This study provides an avenue to studying how and why E. coli populations, and perhaps other microbes, transition from stationary phase to death phase by exploring how ethanol and other alcohols delay the onset of death. Here, we demonstrate that alcohols are acting as signaling molecules to achieve the delay in death phase. This study not only offers a better understanding of a fundamental process but perhaps also provides a gateway to studying the dynamics between ethanol and microbes in the human gastrointestinal tract.
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Mets T, Kasvandik S, Saarma M, Maiväli Ü, Tenson T, Kaldalu N. Fragmentation of Escherichia coli mRNA by MazF and MqsR. Biochimie 2019; 156:79-91. [DOI: 10.1016/j.biochi.2018.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/06/2018] [Indexed: 01/21/2023]
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Li T, Weng Y, Ma X, Tian B, Dai S, Jin Y, Liu M, Li J, Yu J, Hua Y. Deinococcus radiodurans Toxin-Antitoxin MazEF-dr Mediates Cell Death in Response to DNA Damage Stress. Front Microbiol 2017; 8:1427. [PMID: 28798741 PMCID: PMC5526972 DOI: 10.3389/fmicb.2017.01427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/14/2017] [Indexed: 01/30/2023] Open
Abstract
Here we identified a functional MazEF-dr system in the exceptionally stress-resistant bacterium D. radiodurans. We showed that overexpression of the toxin MazF-dr inhibited the growth of Escherichia coli. The toxic effect of MazF-dr was due to its sequence-specific endoribonuclease activity on RNAs containing a consensus 5′ACA3′, and it could be neutralized by MazE-dr. The MazF-dr showed a special cleavage preference for the nucleotide present before the ACA sequence with the order by U>A>G>C. MazEF-dr mediated the death of D. radiodurans cells under sub-lethal dose of stresses. The characteristics of programmed cell death (PCD) including membrane blebbing, loss of membrane integrity and cytoplasm condensation occurred in a fraction of the wild-type population at sub-lethal concentration of the DNA damaging agent mitomycin C (MMC); however, a MazEF-dr mutation relieved the cell death, suggesting that MazEF-dr mediated cell death through its endoribonuclease activity in response to DNA damage stress. The MazEF-dr-mediated cell death of a fraction of the population might serve as a survival strategy for the remaining population of D. radiodurans under DNA damage stress.
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Affiliation(s)
- Tao Li
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Yulan Weng
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Xiaoqiong Ma
- Central Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhou, China
| | - Bing Tian
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Shang Dai
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Ye Jin
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Mengjia Liu
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Jiulong Li
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Jiangliu Yu
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
| | - Yuejin Hua
- Key Laboratory of Nuclear Agricultural Science of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang UniversityHangzhou, China
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Ramisetty BCM, Santhosh RS. Endoribonuclease type II toxin-antitoxin systems: functional or selfish? MICROBIOLOGY-SGM 2017; 163:931-939. [PMID: 28691660 DOI: 10.1099/mic.0.000487] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Most bacterial genomes have multiple type II toxin-antitoxin systems (TAs) that encode two proteins which are referred to as a toxin and an antitoxin. Toxins inhibit a cellular process, while the interaction of the antitoxin with the toxin attenuates the toxin's activity. Endoribonuclease-encoding TAs cleave RNA in a sequence-dependent fashion, resulting in translational inhibition. To account for their prevalence and retention by bacterial genomes, TAs are credited with clinically significant phenomena, such as bacterial programmed cell death, persistence, biofilms and anti-addiction to plasmids. However, the programmed cell death and persistence hypotheses have been challenged because of conceptual, methodological and/or strain issues. In an alternative view, chromosomal TAs seem to be retained by virtue of addiction at two levels: via a poison-antidote combination (TA proteins) and via transcriptional reprogramming of the downstream core gene (due to integration). Any perturbation in the chromosomal TA operons could cause fitness loss due to polar effects on the downstream genes and hence be detrimental under natural conditions. The endoribonucleases encoding chromosomal TAs are most likely selfish DNA as they are retained by bacterial genomes, even though TAs do not confer a direct advantage via the TA proteins. TAs are likely used by various replicons as 'genetic arms' that allow the maintenance of themselves and associated genetic elements. TAs seem to be the 'selfish arms' that make the best use of the 'arms race' between bacterial genomes and plasmids.
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Hall AMJ, Gollan B, Helaine S. Toxin–antitoxin systems: reversible toxicity. Curr Opin Microbiol 2017; 36:102-110. [DOI: 10.1016/j.mib.2017.02.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/06/2017] [Accepted: 02/04/2017] [Indexed: 10/20/2022]
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Cho J, Carr AN, Whitworth L, Johnson B, Wilson KS. MazEF toxin-antitoxin proteins alter Escherichia coli cell morphology and infrastructure during persister formation and regrowth. Microbiology (Reading) 2017; 163:308-321. [DOI: 10.1099/mic.0.000436] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Junho Cho
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Anita Nicole Carr
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Lisa Whitworth
- Microscopy Laboratory, Oklahoma State University, Stillwater, OK 74078, USA
| | - Brent Johnson
- Microscopy Laboratory, Oklahoma State University, Stillwater, OK 74078, USA
| | - Kevin Scott Wilson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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Ramisetty BCM, Ghosh D, Roy Chowdhury M, Santhosh RS. What Is the Link between Stringent Response, Endoribonuclease Encoding Type II Toxin-Antitoxin Systems and Persistence? Front Microbiol 2016; 7:1882. [PMID: 27933045 PMCID: PMC5120126 DOI: 10.3389/fmicb.2016.01882] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 11/09/2016] [Indexed: 11/21/2022] Open
Abstract
Persistence is a transient and non-inheritable tolerance to antibiotics by a small fraction of a bacterial population. One of the proposed determinants of bacterial persistence is toxin–antitoxin systems (TASs) which are also implicated in a wide range of stress-related phenomena. Maisonneuve E, Castro-Camargo M, Gerdes K. 2013. Cell 154:1140–1150 reported an interesting link between ppGpp mediated stringent response, TAS, and persistence. It is proposed that accumulation of ppGpp enhances the accumulation of inorganic polyphosphate which modulates Lon protease to degrade antitoxins. The decrease in the concentration of antitoxins supposedly activated the toxin to increase in the number of persisters during antibiotic treatment. In this study, we show that inorganic polyphosphate is not required for transcriptional activation of yefM/yoeB TAS, which is an indirect indication of Lon-dependent degradation of YefM antitoxin. The Δ10 strain, an Escherichia coli MG1655 derivative in which the 10 TAS are deleted, is more sensitive to ciprofloxacin compared to wild type MG1655. Furthermore, we show that the Δ10 strain has relatively lower fitness compared to the wild type and hence, we argue that the persistence related implications based on Δ10 strain are void. We conclude that the transcriptional regulation and endoribonuclease activity of YefM/YoeB TAS is independent of ppGpp and inorganic polyphosphate. Therefore, we urge for thorough inspection and debate on the link between chromosomal endoribonuclease TAS and persistence.
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Affiliation(s)
- Bhaskar C M Ramisetty
- School of Chemical and Biotechnology, SASTRA UniversityThanjavur, India; Department of Biochemistry and Molecular Biology, University of Southern DenmarkOdense, Denmark
| | - Dimpy Ghosh
- School of Chemical and Biotechnology, SASTRA University Thanjavur, India
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Gao EB, Huang Y, Ning D. Metabolic Genes within Cyanophage Genomes: Implications for Diversity and Evolution. Genes (Basel) 2016; 7:genes7100080. [PMID: 27690109 PMCID: PMC5083919 DOI: 10.3390/genes7100080] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/30/2016] [Accepted: 09/15/2016] [Indexed: 11/16/2022] Open
Abstract
Cyanophages, a group of viruses specifically infecting cyanobacteria, are genetically diverse and extensively abundant in water environments. As a result of selective pressure, cyanophages often acquire a range of metabolic genes from host genomes. The host-derived genes make a significant contribution to the ecological success of cyanophages. In this review, we summarize the host-derived metabolic genes, as well as their origin and roles in cyanophage evolution and important host metabolic pathways, such as the light-dependent reactions of photosynthesis, the pentose phosphate pathway, nutrient acquisition and nucleotide biosynthesis. We also discuss the suitability of the host-derived metabolic genes as potential diagnostic markers for the detection of genetic diversity of cyanophages in natural environments.
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Affiliation(s)
- E-Bin Gao
- School of The Environment and Safety Engineering, Jiangsu University, No. 301, Xuefu Road, Zhenjiang 212013, Jiangsu Province, China.
| | - Youhua Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No. 164, Xingangxi Road, Haizhu District, Guangzhou 5103401, Guangdong Province, China.
| | - Degang Ning
- ACS Key Laboratory of Algae Biology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7, Donghu South Road, Wuchang District, Wuhan 430072, Hubei Province, China.
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