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Saad MG, Beyenal H, Dong WJ. Dual roles of the conditional extracellular vesicles derived from Pseudomonas aeruginosa biofilms: Promoting and inhibiting bacterial biofilm growth. Biofilm 2024; 7:100183. [PMID: 38380422 PMCID: PMC10876606 DOI: 10.1016/j.bioflm.2024.100183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/19/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
Antibiotic-resistant biofilm infections have emerged as public health concerns because of their enhanced tolerance to high-dose antibiotic treatments. The biofilm life cycle involves multiple developmental stages, which are tightly regulated by active cell-cell communication via specific extracellular signal messengers such as extracellular vesicles. This study was aimed at exploring the roles of extracellular vesicles secreted by Pseudomonas aeruginosa at different developmental stages in controlling biofilm growth. Our results show that extracellular vesicles secreted by P. aeruginosa biofilms during their exponential growth phase (G-EVs) enhance biofilm growth. In contrast, extracellular vesicles secreted by P. aeruginosa biofilms during their death/survival phase (D-EVs) can effectively inhibit/eliminate P. aeruginosa PAO1 biofilms up to 4.8-log10 CFU/cm2. The inhibition effectiveness of D-EVs against P. aeruginosa biofilms grown for 96 h improved further in the presence of 10-50 μM Fe3+ ions. Proteomic analysis suggests the inhibition involves an iron-dependent ferroptosis mechanism. This study is the first to report the functional role of bacterial extracellular vesicles in bacterial growth, which depends on the developmental stage of the parent bacteria. The finding of D-EV-activated ferroptosis-based bacterial death may have significant implications for preventing antibiotic resistance in biofilms.
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Affiliation(s)
- Marwa Gamal Saad
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99164, USA
| | - Haluk Beyenal
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99164, USA
| | - Wen-Ji Dong
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99164, USA
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2
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Zhang H, Mou J, Ding J, Qin W. Rapid antibiotic screening based on E. coli apoptosis using a potentiometric sensor array. Anal Chim Acta 2024; 1297:342378. [PMID: 38438244 DOI: 10.1016/j.aca.2024.342378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/06/2024]
Abstract
Phenotypic antimicrobial susceptibility testing enables reliable antibiotic screening but requires multiple strategies to identify each phenotypic change induced by different bactericidal mechanisms. Bacteria apoptosis with typical phenotypic features has never been explored for antibiotic screening. Herein, we developed an antibiotic screening method based on the measurement of antibiotic-induced phosphatidylserine (PS) exposure of apoptotic bacteria. Phosphatidylserine externalization of E. coli that can be widely used as an apoptosis marker for antibiotics with different antibacterial mechanisms was explored. A positively charged PS-binding peptide was immobilized on magnetic beads (MBs) to recognize and capture apoptotic E. coli with PS externalization. Apoptotic E. coli binding led to the charge or charge density change of MBs-peptide, resulting in a potential change on a magneto-controlled polymeric membrane potentiometric sensor. Based on the detection of apoptotic E. coli killed by antibiotics, antibiotic screening for different classes of antibiotics and silver nanoparticles was achieved within 1.5 h using a potentiometric sensor array. This approach enables sensitive, general, and time-saving antibiotic screening, and may open up a new path for antibiotic susceptibility testing.
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Affiliation(s)
- Han Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Junsong Mou
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jiawang Ding
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, 266071, PR China.
| | - Wei Qin
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, 266071, PR China
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3
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Kwun MS, Lee DG. Ferroptosis-Like Death in Microorganisms: A Novel Programmed Cell Death Following Lipid Peroxidation. J Microbiol Biotechnol 2023; 33:992-997. [PMID: 37463851 PMCID: PMC10471485 DOI: 10.4014/jmb.2307.07002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/20/2023]
Abstract
Ferroptosis is a new kind of programmed cell death of which occurrence in microorganisms is not clearly verified. The elevated level of reactive oxygen species (ROS) influences cellular metabolisms through highly reactive hydroxyl radical formation under the iron-dependent Fenton reaction. Iron contributes to ROS production and acts as a cofactor for lipoxygenase to catalyze poly unsaturated fatty acid (PUFA) oxidation, exerting oxidative damage in cells. While ferroptosis is known to take place only in mammalian cells, recent studies discovered the possible ferroptosis-like death in few specific microorganisms. Capacity of integrating PUFA into intracellular membrane phospholipid has been considered as a key factor in bacterial or fungal ferroptosis-like death. Vibrio species in bacteria and Saccharomyces cerevisiae in fungi exhibited certain characteristics. Therefore, this review focus on introducing the occurrence of ferroptosis-like death in microorganisms and investigating the mode of action underlying the cells based on contribution of lipid peroxidation and iron-dependent reaction.
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Affiliation(s)
- Min Seok Kwun
- School of Life Sciences, BK 21 FOUR KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daehakro 80, Bukgu, Daegu 41566, Republic of Korea
| | - Dong Gun Lee
- School of Life Sciences, BK 21 FOUR KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daehakro 80, Bukgu, Daegu 41566, Republic of Korea
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4
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Zhang C, Kong Y, Xiang Q, Ma Y, Guo Q. Bacterial memory in antibiotic resistance evolution and nanotechnology in evolutionary biology. iScience 2023; 26:107433. [PMID: 37575196 PMCID: PMC10415926 DOI: 10.1016/j.isci.2023.107433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Bacterial memory refers to the phenomenon in which past experiences influence current behaviors in response to changing environments. It serves as a crucial process that enables adaptation and evolution. We first summarize the state-of-art approaches regarding history-dependent behaviors that impact growth dynamics and underlying mechanisms. Then, the phenotypic and genotypic origins of memory and how encoded memory modulates drug tolerance/resistance are reviewed. We also provide a summary of possible memory effects induced by antimicrobial nanoparticles. The regulatory networks and genetic underpinnings responsible for memory building partially overlap with nanoparticle and drug exposures, which may raise concerns about the impact of nanotechnology on adaptation. Finally, we provide a perspective on the use of nanotechnology to harness bacterial memory based on its unique mode of actions on information processing and transmission in bacteria. Exploring bacterial memory mechanisms provides valuable insights into acclimation, evolution, and the potential applications of nanotechnology in harnessing memory.
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Affiliation(s)
- Chengdong Zhang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yan Kong
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qingxin Xiang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yayun Ma
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Quanyi Guo
- School of Environment, Beijing Normal University, Beijing 100875, China
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5
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Kaźmierczak A, Tarkowská D, Plačková L, Doniak M, Doležal K. Hormonal crosstalk controls cell death induced by kinetin in roots of Vicia faba ssp. minor seedlings. Sci Rep 2023; 13:11661. [PMID: 37468550 DOI: 10.1038/s41598-023-38641-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023] Open
Abstract
Studies of vitality/mortality of cortex cells, as well as of the concentrations of ethylene (ETH), gibberellins (GAs), indolic compounds/auxins (ICs/AUXs) and cytokinins (CKs), were undertaken to explain the hormonal background of kinetin (Kin)-regulated cell death (RCD), which is induced in the cortex of the apical parts of roots of faba bean (Vicia faba ssp. minor) seedlings. Quantification was carried out with fluorescence microscopy, ETH sensors, spectrophotometry and ultrahigh-performance liquid chromatography tandem mass spectrometry (UHPLC‒MS/MS). The results indicated that Kin was metabolized to the transport form, i.e., kinetin-9-glucoside (Kin9G) and kinetin riboside (KinR). KinR was then converted to cis-zeatin (cZ) in apical parts of roots with meristems, to cis-zeatin riboside (cZR) in apical parts of roots without meristems and finally to cis-zeatin riboside 5'-monophosphate (cZR5'MP), which is indicated to be a ligand of cytokinin-dependent receptors inducing CD. The process may be enhanced by an increase in the amount of dihydrozeatin riboside (DHZR) as a byproduct of the pathway of zeatin metabolism. It seems that crosstalk of ETH, ICs/AUXs, GAs and CKs with the cZR5'MP, the cis-zeatin-dependent pathway, but not the trans-zeatin-dependent pathway, is responsible for Kin-RCD, indicating that the process is very specific and offers a useful model for studies of CD hallmarks in plants.
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Affiliation(s)
- Andrzej Kaźmierczak
- Department of Cytophysiology, Institute of Experimental Biology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland.
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany Academy of Sciences of the Czech Republic and Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Lenka Plačková
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, and Faculty of Science Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Magdalena Doniak
- Department of Cytophysiology, Institute of Experimental Biology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland
| | - Karel Doležal
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, and Faculty of Science Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
- Department of Chemical Biology and Genetics, Center of Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
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6
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Kaźmierczak A, Siatkowska E, Li R, Bothe S, Nick P. Kinetin induces microtubular breakdown, cell cycle arrest and programmed cell death in tobacco BY-2 cells. PROTOPLASMA 2023; 260:787-806. [PMID: 36239807 PMCID: PMC10125952 DOI: 10.1007/s00709-022-01814-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Plant cells can undergo regulated cell death in response to exogenous factors (often in a stress context), but also as regular element of development (often regulated by phytohormones). The cellular aspects of these death responses differ, which implies that the early signalling must be different. We use cytokinin-induced programmed cell death as paradigm to get insight into the role of the cytoskeleton for the regulation of developmentally induced cell death, using tobacco BY-2 cells as experimental model. We show that this PCD in response to kinetin correlates with an arrest of the cell cycle, a deregulation of DNA replication, a loss of plasma membrane integrity, a subsequent permeabilisation of the nuclear envelope, an increase of cytosolic calcium correlated with calcium depletion in the culture medium, an increase of callose deposition and the loss of microtubule and actin integrity. We discuss these findings in the context of a working model, where kinetin, mediated by calcium, causes the breakdown of the cytoskeleton, which, either by release of executing proteins or by mitotic catastrophe, will result in PCD.
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Affiliation(s)
- Andrzej Kaźmierczak
- Faculty of Biology and Environmental Protection, Institute of Experimental Biology, Department of Cytophysiology, University of Łódź, Pomorska 141/143, 90-236, Lodz, Poland
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Ewa Siatkowska
- Faculty of Biology and Environmental Protection, Institute of Experimental Biology, Department of Cytophysiology, University of Łódź, Pomorska 141/143, 90-236, Lodz, Poland
| | - Ruoxi Li
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Sophie Bothe
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Peter Nick
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.
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7
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Gonçalves ASC, Leitão MM, Simões M, Borges A. The action of phytochemicals in biofilm control. Nat Prod Rep 2023; 40:595-627. [PMID: 36537821 DOI: 10.1039/d2np00053a] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2009 to 2021Antimicrobial resistance is now rising to dangerously high levels in all parts of the world, threatening the treatment of an ever-increasing range of infectious diseases. This has becoming a serious public health problem, especially due to the emergence of multidrug-resistance among clinically important bacterial species and their ability to form biofilms. In addition, current anti-infective therapies have low efficacy in the treatment of biofilm-related infections, leading to recurrence, chronicity, and increased morbidity and mortality. Therefore, it is necessary to search for innovative strategies/antibacterial agents capable of overcoming the limitations of conventional antibiotics. Natural compounds, in particular those obtained from plants, have been exhibiting promising properties in this field. Plant secondary metabolites (phytochemicals) can act as antibiofilm agents through different mechanisms of action from the available antibiotics (inhibition of quorum-sensing, motility, adhesion, and reactive oxygen species production, among others). The combination of different phytochemicals and antibiotics have revealed synergistic or additive effects in biofilm control. This review aims to bring together the most relevant reports on the antibiofilm properties of phytochemicals, as well as insights into their structure and mechanistic action against bacterial pathogens, spanning December 2008 to December 2021.
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Affiliation(s)
- Ariana S C Gonçalves
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal.
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
| | - Miguel M Leitão
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal.
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
| | - Manuel Simões
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal.
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
| | - Anabela Borges
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal.
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
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8
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Jaramillo D, Foxwell J, Burrows L, Snell A. Mycoplasma bovis testing for the screening of semen imported into New Zealand. N Z Vet J 2023:1-9. [PMID: 36866578 DOI: 10.1080/00480169.2023.2186506] [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: 03/04/2023]
Abstract
AIMS To evaluate the fitness of three PCR assays for the detection of Mycoplasma bovis in dilute (extended) bovine semen, and a reverse transcriptase-PCR (RT-PCR) adaptation as a proxy for viability. MATERIALS AND METHODS Four commercial kit-based methods for nucleic acid extraction were compared to test for the presence of PCR inhibitors in nucleic acid extracted from undiluted and diluted semen. Then, analytical sensitivity, analytical specificity, and diagnostic specificity of two real-time PCR and one conventional PCR were evaluated for the detection of M. bovis DNA in semen and compared against microbial culture. Furthermore, an RT-PCR was adapted to detect RNA only and tested on viable and non-viable M. bovis to establish its ability to discriminate between the two. RESULTS No significant PCR inhibition was detected from the dilute semen. All DNA extraction methods except one were equivalent, regardless of semen dilution. The analytical sensitivity of the real-time PCR assays was estimated as 45.6 cfu per 200 µL semen straw (2.2 × 102 cfu/mL). The conventional PCR was 10 times less sensitive. No cross-reactivity was observed for the real-time PCR for any of the bacteria tested and the diagnostic specificity was estimated as 100 (95% CI = 94.04-100) %. The RT-PCR was poor in distinguishing between viable and non-viable M. bovis. The mean quantification cycle (Cq) values for RNA extracted from different treatments to kill M. bovis remained unchanged 0-48 hours after inactivation. CONCLUSION AND CLINICAL RELEVANCE The real-time PCR were fit for the purpose of screening dilute semen for the detection of M. bovis to prevent incursion via importation of infected semen. The real-time PCR assays can be used interchangeably. The RT-PCR could not reliably indicate the viability of M. bovis. Based on the results from this study, a protocol and guidelines have been produced for laboratories elsewhere that wish to test bovine semen for M. bovis.
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Affiliation(s)
- D Jaramillo
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - J Foxwell
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - L Burrows
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - A Snell
- Biosecurity New Zealand, Ministry for Primary Industries, Wellington, New Zealand
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9
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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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10
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Rafeeq MM, Habib AH, Alzamami A, Alturki NA, Mashraqi MM, Alghamdi YS, Alshamrani S, Alharthi AA, Ahmad S. Effect of rifampicin combination-regimens against multi-drug resistant strains in North India. Bioinformation 2022; 18:482-487. [PMID: 36945223 PMCID: PMC10024775 DOI: 10.6026/97320630018482] [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: 04/02/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 11/23/2022] Open
Abstract
It is well-acknowledged that 'combination therapy' of antibiotics is indispensable for the treatment of patients suffering from serious bacterial infections. Therefore, it is of interest to collect data from the in vitro tests using 'rifampicin-cefotaxime' and 'rifampicin-tetracycline' combination regimens against multi drug resistant Escherichia coli and Klebsiella pneumoniae strains of nosocomial source in order to determine the effectiveness of the combination therapy. The minimum inhibitory concentration (MIC) values for cefotaxime, tetracycline and rifampicin antibiotics were found to be comparatively high for each of the antibiotics when given individually. However, carefully prepared combination-regimens exhibited significant inhibitory effect on the same bacterial isolates. DNA fragmentation study confirmed that 'rifampicin-cefotaxime' and 'rifampicin-tetracycline' combination-regimens could cause breakage of the bacterial DNA. Thus, we show that combination-regimens namely, 'rifampicin-cefotaxime' and 'rifampicin-tetracycline' were found to be capable of maintaining rifampicin susceptibility in the E. coli and K. pneumoniae strains. However, this susceptibility was not maintained by only rifampicin. More data using animal model experiments are needed for confirming and deriving translational benefits from these findings in future.
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Affiliation(s)
- Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Science, Shaqra University, AlQuwayiyah 11961, Saudi Arabia
| | - Norah A Alturki
- Clinical Laboratory Science Department, College of Applied Medical Science, King Saud University, Riyadh 11433, Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Youssef Saeed Alghamdi
- Department of Biology, Turabah University College, Taif University, P.O.BOX 11099, Taif 21944, Saudi Arabia
| | - Saleh Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Afaf Awwadh Alharthi
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, Taif University, Taif, Saudi Arabia
| | - Suhail Ahmad
- Department of Bioengineering, Integral University, Lucknow, India
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11
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The evolution of multicellularity and cancer: views and paradigms. Biochem Soc Trans 2021; 48:1505-1518. [PMID: 32677677 DOI: 10.1042/bst20190992] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022]
Abstract
Conceptually and mechanistically, the evolution of multicellularity required the integration of single cells into new functionally, reproductively and evolutionary stable multicellular individuals. As part of this process, a change in levels of selection occurred, with selection at the multicellular level overriding selection at the cell level. The stability of multicellular individuals is dependent on a combination of mechanisms that supress within-group evolution, by both reducing the occurrence of somatic mutations as well as supressing somatic selection. Nevertheless, mutations that, in a particular microenvironment, confer mutant lineages a fitness advantage relative to normal somatic cells do occur, and can result in cancer. This minireview highlights several views and paradigms that relate the evolution of multicellularity to cancer. As a phenomenon, cancer is generally understood as a failure of multicellular systems to suppress somatic evolution. However, as a disease, cancer is interpreted in different frameworks: (i) a breakdown of cooperative behaviors underlying the evolution of multicellularity, (ii) a disruption of molecular networks established during the emergence of multicellularity to impose constraints on single-celled units, or (iii) an atavistic state resulting from reactivating primitive programs that originated in the earliest unicellular species. A number of assumptions are common in all the views relating cancer as a disease to the evolution of multicellularity. For instance, cancer is considered a reversal to unicellularity, and cancer cells are thought to both resemble unicellular organisms and benefit from ancestral-like traits. Nevertheless, potential limitations of current paradigms should be acknowledged as different perspectives can provide novel insights with potential therapeutic implications.
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12
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Kahan R, Worm DJ, de Castro GV, Ng S, Barnard A. Modulators of protein-protein interactions as antimicrobial agents. RSC Chem Biol 2021; 2:387-409. [PMID: 34458791 PMCID: PMC8341153 DOI: 10.1039/d0cb00205d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-Protein interactions (PPIs) are involved in a myriad of cellular processes in all living organisms and the modulation of PPIs is already under investigation for the development of new drugs targeting cancers, autoimmune diseases and viruses. PPIs are also involved in the regulation of vital functions in bacteria and, therefore, targeting bacterial PPIs offers an attractive strategy for the development of antibiotics with novel modes of action. The latter are urgently needed to tackle multidrug-resistant and multidrug-tolerant bacteria. In this review, we describe recent developments in the modulation of PPIs in pathogenic bacteria for antibiotic development, including advanced small molecule and peptide inhibitors acting on bacterial PPIs involved in division, replication and transcription, outer membrane protein biogenesis, with an additional focus on toxin-antitoxin systems as upcoming drug targets.
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Affiliation(s)
- Rashi Kahan
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Dennis J Worm
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Guilherme V de Castro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Simon Ng
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Anna Barnard
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
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13
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Av Sá LGD, Silva CRD, de A Neto JB, Cândido TM, de Oliveira LC, do Nascimento FB, Barroso FD, da Silva LJ, de Mesquita JR, de Moraes MO, Cavalcanti BC, Júnior HV. Etomidate inhibits the growth of MRSA and exhibits synergism with oxacillin. Future Microbiol 2020; 15:1611-1619. [PMID: 33215536 DOI: 10.2217/fmb-2020-0078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Aim: The purpose of this study was to evaluate the antimicrobial activity of the anesthetic etomidate against strains of MRSA and biofilms. Materials & methods: The antibacterial effect of etomidate was assessed by the broth microdilution method. To investigate the probable action mechanism of the compound flow cytometry techniques were used. Results: MRSA strains showed MIC equal to 500 and 1000 μg/ml of etomidate. Four-fifths (80%) of the tested MRSA strains demonstrated synergistic effect with oxacillin. Etomidate also showed activity against MRSA biofilm at concentration of 250 μg/ml. Cytometric analysis revealed that the cells treated with etomidate leading to cell death, probably by apoptosis. Conclusion: Etomidate showed antibacterial activity against MRSA.
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Affiliation(s)
- Lívia G do Av Sá
- Department of Clinical & Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceará, Fortaleza, CE, Brazil.,Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Cecília R da Silva
- Department of Clinical & Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceará, Fortaleza, CE, Brazil.,Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - João B de A Neto
- Department of Clinical & Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceará, Fortaleza, CE, Brazil.,Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil.,University Center Christus, Fortaleza, CE, Brazil
| | - Thiago M Cândido
- Department of Clinical & Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceará, Fortaleza, CE, Brazil.,Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Leilson C de Oliveira
- Department of Clinical & Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceará, Fortaleza, CE, Brazil.,Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Francisca Bsa do Nascimento
- Department of Clinical & Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceará, Fortaleza, CE, Brazil.,Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Fátima Dd Barroso
- Department of Clinical & Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceará, Fortaleza, CE, Brazil.,Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Lisandra J da Silva
- Department of Clinical & Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceará, Fortaleza, CE, Brazil.,Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | - Manoel O de Moraes
- Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Bruno C Cavalcanti
- Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Hélio Vn Júnior
- Department of Clinical & Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceará, Fortaleza, CE, Brazil.,Drug Research & Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
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14
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Zafar H, Saier MH. Comparative Genomics of the Transport Proteins of Ten Lactobacillus Strains. Genes (Basel) 2020; 11:genes11101234. [PMID: 33096690 PMCID: PMC7593918 DOI: 10.3390/genes11101234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/24/2022] Open
Abstract
The genus Lactobacillus includes species that may inhabit different anatomical locations in the human body, but the greatest percentage of its species are inhabitants of the gut. Lactobacilli are well known for their probiotic characteristics, although some species may become pathogenic and exert negative effects on human health. The transportome of an organism consists of the sum of the transport proteins encoded within its genome, and studies on the transportome help in the understanding of the various physiological processes taking place in the cell. In this communication we analyze the transport proteins and predict probable substrate specificities of ten Lactobacillus strains. Six of these strains (L. brevis, L. bulgaricus, L. crispatus, L. gasseri, L. reuteri, and L. ruminis) are currently believed to be only probiotic (OP). The remaining four strains (L. acidophilus, L. paracasei, L. planatarum, and L. rhamnosus) can play dual roles, being both probiotic and pathogenic (PAP). The characteristics of the transport systems found in these bacteria were compared with strains (E. coli, Salmonella, and Bacteroides) from our previous studies. Overall, the ten lactobacilli contain high numbers of amino acid transporters, but the PAP strains contain higher number of sugar, amino acid and peptide transporters as well as drug exporters than their OP counterparts. Moreover, some of the OP strains contain pore-forming toxins and drug exporters similar to those of the PAP strains, thus indicative of yet unrecognized pathogenic potential. The transportomes of the lactobacilli seem to be finely tuned according to the extracellular and probiotic lifestyles of these organisms. Taken together, the results of this study help to reveal the physiological and pathogenic potential of common prokaryotic residents in the human body.
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Affiliation(s)
- Hassan Zafar
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116, USA
- Department of Microbiology and Molecular Genetics, Faculty of Life Sciences, University of Okara, Okara, Punjab 56300, Pakistan
- Correspondence: (H.Z.); (M.H.S.J.); Tel.: +1-858-534-4084 (M.H.S.J.); Fax: +1-858-534-7108 (M.H.S.J.)
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116, USA
- Correspondence: (H.Z.); (M.H.S.J.); Tel.: +1-858-534-4084 (M.H.S.J.); Fax: +1-858-534-7108 (M.H.S.J.)
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15
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Sun XM, Zhang ZX, Wang LR, Wang JG, Liang Y, Yang HF, Tao RS, Jiang Y, Yang JJ, Yang S. Downregulation of T7 RNA polymerase transcription enhances pET-based recombinant protein production in Escherichia coli BL21 (DE3) by suppressing autolysis. Biotechnol Bioeng 2020; 118:153-163. [PMID: 32897579 DOI: 10.1002/bit.27558] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/25/2020] [Accepted: 08/30/2020] [Indexed: 12/15/2022]
Abstract
Escherichia coli BL21 (DE3) is an excellent and widely used host for recombinant protein production. Many variant hosts were developed from BL21 (DE3), but improving the expression of specific proteins remains a major challenge in biotechnology. In this study, we found that when BL21 (DE3) overexpressed glucose dehydrogenase (GDH), a significant industrial enzyme, severe cell autolysis was induced. Subsequently, we observed this phenomenon in the expression of 10 other recombinant proteins. This precludes a further increase of the produced enzyme activity by extending the fermentation time, which is not conducive to the reduction of industrial enzyme production costs. Analysis of membrane structure and messenger RNA expression analysis showed that cells could underwent a form of programmed cell death (PCD) during the autolysis period. However, blocking three known PCD pathways in BL21 (DE3) did not completely alleviate autolysis completely. Consequently, we attempted to develop a strong expression host resistant to autolysis by controlling the speed of recombinant protein expression. To find a more suitable protein expression rate, the high- and low-strength promoter lacUV5 and lac were shuffled and recombined to yield the promoter variants lacUV5-1A and lac-1G. The results showed that only one base in lac promoter needs to be changed, and the A at the +1 position was changed to a G, resulting in the improved host BL21 (DE3-lac1G), which resistant to autolysis. As a consequence, the GDH activity at 43 h was greatly increased from 37.5 to 452.0 U/ml. In scale-up fermentation, the new host was able to produce the model enzyme with a high rate of 89.55 U/ml/h at 43 h, compared to only 3 U/ml/h achieved using BL21 (DE3). Importantly, BL21 (DE3-lac1G) also successfully improved the production of 10 other enzymes. The engineered E. coli strain constructed in this study conveniently optimizes recombinant protein overexpression by suppressing cell autolysis, and shows great potential for industrial applications.
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Affiliation(s)
- Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Ling-Ru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu, China
| | | | - Yan Liang
- HuaRui Biotechnology Company, Huzhou, Zhejiang, China
| | - Hai-Feng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rong-Sheng Tao
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, Zhejiang, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, Zhejiang, China
| | - Jun-Jie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, Zhejiang, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, Zhejiang, China
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16
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González-Fernández S, Lozano-Iturbe V, García B, Andrés LJ, Menéndez MF, Rodríguez D, Vazquez F, Martín C, Quirós LM. Antibacterial effect of silver nanorings. BMC Microbiol 2020; 20:172. [PMID: 32560673 PMCID: PMC7304143 DOI: 10.1186/s12866-020-01854-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Background The emergence and expansion of antibiotic resistance makes it necessary to have alternative anti-infective agents, among which silver nanoparticles (AgNPs) display especially interesting properties. AgNPs carry out their antibacterial action through various molecular mechanisms, and the magnitude of the observed effect is dependent on multiple, not fully understood, aspects, particle shape being one of the most important. In this article, we conduct a study of the antibacterial effect of a recently described type of AgNP: silver nanorings (AgNRs), making comparisons with other alternative types of AgNP synthesized in parallel using the same methodology. Results When they act on planktonic forms, AgNRs produce a smaller effect on the viability of different bacteria than nanoparticles with other structures although their effect on growth is more intense over a longer period. When their action on biofilms is analyzed, AgNRs show a greater concentration-dependent effect. In both cases it was observed that the effect on inhibition depends on the microbial species, but not its Gram positive or negative nature. Growth patterns in silver-resistant Salmonella strains suggest that AgNRs work through different mechanisms to other AgNPs. The antibacterial effect is also produced to some extent by the conditioning of culture media or water by contact with AgNPs but, at least over short periods of time, this is not due to the release of Ag ions. Conclusions AgNRs constitute a new type of AgNP, whose antibacterial properties depend on their shape, and is capable of acting efficiently on both planktonic bacteria and biofilms.
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Affiliation(s)
- Sara González-Fernández
- Instituto Universitario Fernández-Vega, Instituto de Investigación Sanitaria del Principado de Asturias, and Departamento de Biología Funcional, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Víctor Lozano-Iturbe
- Instituto Universitario Fernández-Vega, Instituto de Investigación Sanitaria del Principado de Asturias, and Departamento de Biología Funcional, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Beatriz García
- Instituto Universitario Fernández-Vega, Instituto de Investigación Sanitaria del Principado de Asturias, and Departamento de Biología Funcional, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Luis J Andrés
- Departamento de Fotónica-ITMA Materials Technology, 33490, Avilés, Spain
| | - Mª Fe Menéndez
- Departamento de Fotónica-ITMA Materials Technology, 33490, Avilés, Spain
| | - David Rodríguez
- Instituto Universitario de Oncología del Principado de Asturias and Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Fernando Vazquez
- Instituto Universitario Fernández-Vega, Instituto de Investigación Sanitaria del Principado de Asturias, and Departamento de Biología Funcional, Universidad de Oviedo, 33006, Oviedo, Spain.,Servicio de Microbiología, Hospital Universitario Central de Asturias, 33011, Oviedo, Spain
| | - Carla Martín
- Instituto Universitario Fernández-Vega, Instituto de Investigación Sanitaria del Principado de Asturias, and Departamento de Biología Funcional, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Luis M Quirós
- Instituto Universitario Fernández-Vega, Instituto de Investigación Sanitaria del Principado de Asturias, and Departamento de Biología Funcional, Universidad de Oviedo, 33006, Oviedo, Spain.
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17
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Hernandez AJ, Lee SJ, Chang S, Lee JA, Loparo JJ, Richardson CC. Catalytically inactive T7 DNA polymerase imposes a lethal replication roadblock. J Biol Chem 2020; 295:9542-9550. [PMID: 32430399 DOI: 10.1074/jbc.ra120.013738] [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: 04/03/2020] [Revised: 05/18/2020] [Indexed: 11/06/2022] Open
Abstract
Bacteriophage T7 encodes its own DNA polymerase, the product of gene 5 (gp5). In isolation, gp5 is a DNA polymerase of low processivity. However, gp5 becomes highly processive upon formation of a complex with Escherichia coli thioredoxin, the product of the trxA gene. Expression of a gp5 variant in which aspartate residues in the metal-binding site of the polymerase domain were replaced by alanine is highly toxic to E. coli cells. This toxicity depends on the presence of a functional E. coli trxA allele and T7 RNA polymerase-driven expression but is independent of the exonuclease activity of gp5. In vitro, the purified gp5 variant is devoid of any detectable polymerase activity and inhibited DNA synthesis by the replisomes of E. coli and T7 in the presence of thioredoxin by forming a stable complex with DNA that prevents replication. On the other hand, the highly homologous Klenow fragment of DNA polymerase I containing an engineered gp5 thioredoxin-binding domain did not exhibit toxicity. We conclude that gp5 alleles encoding inactive polymerases, in combination with thioredoxin, could be useful as a shutoff mechanism in the design of a bacterial cell-growth system.
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Affiliation(s)
- Alfredo J Hernandez
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Seung-Joo Lee
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Seungwoo Chang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jaehun A Lee
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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18
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Bateman A. Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells. Biol Direct 2020; 15:8. [PMID: 32345370 PMCID: PMC7187495 DOI: 10.1186/s13062-020-00260-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Abstract Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the second model, two prokaryotes, probably an archaeon and a bacterial cell, engaged in prokaryotic endosymbiosis, with the species resident within the host becoming the mitochondrial progenitor. Both models have limitations. A search was therefore undertaken for alternative routes towards the origin of eukaryotic cells. The question was addressed by considering classes of potential pathways from prokaryotic to eukaryotic cells based on considerations of cellular topology. Among the solutions identified, one, called here the “third-space model”, has not been widely explored. A version is presented in which an extracellular space (the third-space), serves as a proxy cytoplasm for mixed populations of archaea and bacteria to “merge” as a transitionary complex without obligatory endosymbiosis or phagocytosis and to form a precursor cell. Incipient nuclei and mitochondria diverge by division of labour. The third-space model can accommodate the reorganization of prokaryote-like genomes to a more eukaryote-like genome structure. Nuclei with multiple chromosomes and mitosis emerge as a natural feature of the model. The model is compatible with the loss of archaeal lipid biochemistry while retaining archaeal genes and provides a route for the development of membranous organelles such as the Golgi apparatus and endoplasmic reticulum. Advantages, limitations and variations of the “third-space” models are discussed. Reviewers This article was reviewed by Damien Devos, Buzz Baum and Michael Gray.
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Affiliation(s)
- Andrew Bateman
- Division of Experimental Medicine, Department of Medicine, McGill University, Glen Site Pavilion E, 1001 Boulevard Decarie, Montreal, Quebec, H4A 3J1, Canada. .,Centre for Translational Biology, Research Institute of McGill University Health Centre, Glen Site Pavilion E, 1001 Boulevard Decarie, Montreal, Quebec, H4A 3J1, Canada.
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19
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Smith RP, Barraza I, Quinn RJ, Fortoul MC. The mechanisms and cell signaling pathways of programmed cell death in the bacterial world. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 352:1-53. [PMID: 32334813 DOI: 10.1016/bs.ircmb.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
While programmed cell death was once thought to be exclusive to eukaryotic cells, there are now abundant examples of well regulated cell death mechanisms in bacteria. The mechanisms by which bacteria undergo programmed cell death are diverse, and range from the use of toxin-antitoxin systems, to prophage-driven cell lysis. Moreover, some bacteria have learned how to coopt programmed cell death systems in competing bacteria. Interestingly, many of the potential reasons as to why bacteria undergo programmed cell death may parallel those observed in eukaryotic cells, and may be altruistic in nature. These include protection against infection, recycling of nutrients, to ensure correct morphological development, and in response to stressors. In the following chapter, we discuss the molecular and signaling mechanisms by which bacteria undergo programmed cell death. We conclude by discussing the current open questions in this expanding field.
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Affiliation(s)
- Robert P Smith
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States.
| | - Ivana Barraza
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Rebecca J Quinn
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Marla C Fortoul
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
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20
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Gao B, Chi L, Tu P, Gao N, Lu K. The Carbamate Aldicarb Altered the Gut Microbiome, Metabolome, and Lipidome of C57BL/6J Mice. Chem Res Toxicol 2019; 32:67-79. [PMID: 30406643 DOI: 10.1021/acs.chemrestox.8b00179] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The gut microbiome is highly involved in numerous aspects of host physiology, from energy harvest to stress response, and can confer many benefits to the host. The gut microbiome development could be affected by genetic and environmental factors, including pesticides. The carbamate insecticide aldicarb has been extensively used in agriculture, which raises serious public health concerns. However, the impact of aldicarb on the gut microbiome, host metabolome, and lipidome has not been well studied yet. Herein, we use multiomics approaches, including16S rRNA sequencing, shotgun metagenomics sequencing, metabolomics, and lipidomics, to elucidate aldicarb-induced toxicity in the gut microbiome and the host metabolic homeostasis. We demonstrated that aldicarb perturbed the gut microbiome development trajectory, enhanced gut bacterial pathogenicity, altered complex lipid profile, and induced oxidative stress, protein degradation, and DNA damage. The brain metabolism was also disturbed by the aldicarb exposure. These findings may provide a novel understanding of the toxicity of carbamate insecticides.
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Affiliation(s)
- Bei Gao
- Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.,NIH West Coast Metabolomics Center , University of California , Davis , California 95616 , United States
| | - Liang Chi
- Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Nan Gao
- National Engineering Research Center for Biotechnology, School of Biotechnology and Pharmaceutical Engineering , Nanjing Tech University , Nanjing 211816 , China
| | - Kun Lu
- Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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21
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Ning HQ, Li YQ, Tian QW, Wang ZS, Mo HZ. The apoptosis of Staphylococcus aureus induced by glycinin basic peptide through ROS oxidative stress response. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2018.09.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Batista de Andrade Neto J, Alexandre Josino MA, Rocha da Silva C, de Sousa Campos R, Aires do Nascimento FBS, Sampaio LS, Gurgel do Amaral Valente Sá L, de Sá Carneiro I, Dias Barroso FD, Juvêncio da Silva L, Lima de Mesquita JR, Cavalcanti BC, Odorico de Moraes M, Nobre Júnior HV. A mechanistic approach to the in-vitro resistance modulating effects of fluoxetine against meticillin resistant Staphylococcus aureus strains. Microb Pathog 2018; 127:335-340. [PMID: 30529514 DOI: 10.1016/j.micpath.2018.11.056] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 12/25/2022]
Abstract
Emergence of methicilin resistant Staphylococcus aureus (MRSA) strains is a major cause of infirmity worldwide and has limited our therapeutic options against these pathogens. In this regard, the search for candidates with an antimicrobial activity, with a greater efficacy and a lower toxicity, is necessary. As a result, there is greater need to search for resistance modifying agents which, in combination with existing drugs, will restore the efficacy of these drugs. The antibacterial effect of fluoxetine was determined by a broth microdilution method (the M07-A9 method of the Clinical and Laboratory Standard Institute) and flow cytometry techniques in which the probable mechanism of action of the compound was also assessed. The isolates used in the study belonged to the Laboratory of Bioprospecting of Antimicrobial Molecules (LABIMAN) of the Federal University of Ceará. After 24 h, Methicillin-resistant Sthaphylococcus aureus (MRSA) strains showed fluoxetine MICs equal to 64 μg/mL and 128 μg/mL, respectively. Cytometric analysis showed that treatment with fluoxetine caused alterations to the integrity of the plasma membranes and DNA damage, which led to cell death, probably by apoptosis.
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Affiliation(s)
- João Batista de Andrade Neto
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil
| | - Maria Aparecida Alexandre Josino
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil
| | - Cecília Rocha da Silva
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil; Christus University Center (UNICHRISTUS), Fortaleza, CE, Brazil
| | - Rosana de Sousa Campos
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil; Christus University Center (UNICHRISTUS), Fortaleza, CE, Brazil
| | | | - Letícia Serpa Sampaio
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil
| | - Lívia Gurgel do Amaral Valente Sá
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil
| | - Igor de Sá Carneiro
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil
| | - Fátima Daiana Dias Barroso
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil
| | - Lisandra Juvêncio da Silva
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil
| | | | - Bruno Coelho Cavalcanti
- Department of Physiology and Pharmacology, Federal University of Ceara, Fortaleza, CE, Brazil
| | | | - Hélio Vitoriano Nobre Júnior
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil.
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23
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Noor Mohammadi T, Maung A, Sato J, Sonoda T, Masuda Y, Honjoh K, Miyamoto T. Mechanism for antibacterial action of epigallocatechin gallate and theaflavin-3,3′-digallate on Clostridium perfringens. J Appl Microbiol 2018; 126:633-640. [DOI: 10.1111/jam.14134] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/12/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022]
Affiliation(s)
- T. Noor Mohammadi
- Division of Food Science and Biotechnology; Department of Bioscience and Biotechnology; Faculty of Agriculture; Graduate School; Kyushu University; Fukuoka Japan
| | - A.T. Maung
- Division of Food Science and Biotechnology; Department of Bioscience and Biotechnology; Faculty of Agriculture; Graduate School; Kyushu University; Fukuoka Japan
| | - J. Sato
- Safety Science Research; R&D; Kao Corporation; Ichikai-Machi Tochigi Japan
| | - T. Sonoda
- Safety Science Research; R&D; Kao Corporation; Ichikai-Machi Tochigi Japan
| | - Y. Masuda
- Division of Food Science and Biotechnology; Department of Bioscience and Biotechnology; Faculty of Agriculture; Graduate School; Kyushu University; Fukuoka Japan
| | - K. Honjoh
- Division of Food Science and Biotechnology; Department of Bioscience and Biotechnology; Faculty of Agriculture; Graduate School; Kyushu University; Fukuoka Japan
| | - T. Miyamoto
- Division of Food Science and Biotechnology; Department of Bioscience and Biotechnology; Faculty of Agriculture; Graduate School; Kyushu University; Fukuoka Japan
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24
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Xu J, Kiesel B, Kallies R, Jiang F, Liu Y, Maskow T. A fast and reliable method for monitoring of prophage-activating chemicals. Microb Biotechnol 2018; 11:1112-1120. [PMID: 29327434 PMCID: PMC6196395 DOI: 10.1111/1751-7915.13042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/17/2017] [Accepted: 11/27/2017] [Indexed: 12/03/2022] Open
Abstract
Bacteriophages, that is viruses that infect bacteria, either lyse bacteria directly or integrate their genome into the bacterial genome as so-called prophages, where they remain at a silent state. Both phages and bacteria are able to survive in this state. However, prophages can be reactivated with the introduction of chemicals, followed by the release of a high number of phage particles, which could infect other bacteria, thus harming ecosystems by a viral bloom. The basics for a fast, automatable analytical method for the detection of prophage-activating chemicals are developed and successfully tested here. The method exploits the differences in metabolic heat produced by Escherichia coli with (λ+) and without the lambda prophages (λ-). Since the metabolic heat primarily reflects opposing effects (i.e. the reduction of heat-producing cells by lysis and enhanced heat production to deliver the energetic costs for the synthesis of phages), a systematic analysis of the influence of the different conditions (experimentally and in silico) was performed and revealed anoxic conditions to be best suited. The main advantages of the suggested monitoring method are not only the possibility of obtaining fast results (after only few hours), but also the option for automation, the low workload (requires only few minutes) and the suitability of using commercially available instruments. The future challenge following this proof of principle is the development of thermal transducers which allow for the electronic subtraction of the λ+ from the λ- signal.
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Affiliation(s)
- Juan Xu
- State Key Laboratory of VirologyCollege of Chemistry and Molecule SciencesWuhan UniversityWuhan430072China
| | - Bärbel Kiesel
- Department of Environmental MicrobiologyUFZ – Helmholtz Centre for Environmental ResearchPermoserstrasse 1504318LeipzigGermany
| | - René Kallies
- Department of Environmental MicrobiologyUFZ – Helmholtz Centre for Environmental ResearchPermoserstrasse 1504318LeipzigGermany
| | - Feng‐Lei Jiang
- State Key Laboratory of VirologyCollege of Chemistry and Molecule SciencesWuhan UniversityWuhan430072China
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecule SciencesWuhan UniversityWuhan430072China
| | - Yi Liu
- State Key Laboratory of VirologyCollege of Chemistry and Molecule SciencesWuhan UniversityWuhan430072China
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecule SciencesWuhan UniversityWuhan430072China
| | - Thomas Maskow
- Department of Environmental MicrobiologyUFZ – Helmholtz Centre for Environmental ResearchPermoserstrasse 1504318LeipzigGermany
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25
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Li J, Ma L, Liao X, Liu D, Lu X, Chen S, Ye X, Ding T. Ultrasound-Induced Escherichia coli O157:H7 Cell Death Exhibits Physical Disruption and Biochemical Apoptosis. Front Microbiol 2018; 9:2486. [PMID: 30459727 PMCID: PMC6232819 DOI: 10.3389/fmicb.2018.02486] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/28/2018] [Indexed: 12/30/2022] Open
Abstract
Ultrasound has attracted great interest of both industry and scientific communities for its potential use as a physical processing and preservation tool. In this study, Escherichia coli O157:H7 was selected as the model microbe to investigate the ultrasound-induced cell death. Slight variations in membrane potential and ion exchanges across membrane induced by low-intensity ultrasound increased the membrane permeability of E. coli O157:H7, and this reversible sublethal effect can preserve the viability of E. coli O157:H7 and meanwhile be beneficial for bioprocessing application. In comparison, high-intensity ultrasound resulted in irreversible lethal effect on E. coli O157:H7, which can be applied in the field of microbial inactivation. In addition, both low- and high-intensity ultrasound induced either physical destruction or trigger genetically encoded apoptosis of E. coli O157:H7. Accumulation of reactive oxygen species and decrease of adenosine tri-phosphate might be related to the physiological and biochemical hallmarks of apoptosis, including exposed phosphatidylserine and activated caspases in E. coli O157:H7. The result provides novel insight into the mechanisms of non-thermal physical treatment on the inactivation of bacteria and lays foundation for the further research on the cell signaling and metabolic pathway in apoptotic bacteria.
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Affiliation(s)
- Jiao Li
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, China.,Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, China
| | - Luyao Ma
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Xinyu Liao
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, China.,Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, China
| | - Donghong Liu
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, China.,Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, China
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Shiguo Chen
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, China.,Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, China
| | - Xingqian Ye
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, China.,Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, China
| | - Tian Ding
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, China.,Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, China
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26
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Wen X, Langevin AM, Dunlop MJ. Antibiotic export by efflux pumps affects growth of neighboring bacteria. Sci Rep 2018; 8:15120. [PMID: 30310093 PMCID: PMC6181935 DOI: 10.1038/s41598-018-33275-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/25/2018] [Indexed: 12/19/2022] Open
Abstract
Cell-cell interactions play an important role in bacterial antibiotic resistance. Here, we asked whether neighbor proximity is sufficient to generate single-cell variation in antibiotic resistance due to local differences in antibiotic concentrations. To test this, we focused on multidrug efflux pumps because recent studies have revealed that expression of pumps is heterogeneous across populations. Efflux pumps can export antibiotics, leading to elevated resistance relative to cells with low or no pump expression. In this study, we co-cultured cells with and without AcrAB-TolC pump expression and used single-cell time-lapse microscopy to quantify growth rate as a function of a cell’s neighbors. In inhibitory concentrations of chloramphenicol, we found that cells lacking functional efflux pumps (ΔacrB) grow more slowly when they are surrounded by cells with AcrAB-TolC pumps than when surrounded by ΔacrB cells. To help explain our experimental results, we developed an agent-based mathematical model, which demonstrates the impact of neighbors based on efflux efficiency. Our findings hold true for co-cultures of Escherichia coli with and without pump expression and also in co-cultures of E. coli and Salmonella typhumirium. These results show how drug export and local microenvironments play a key role in defining single-cell level antibiotic resistance.
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Affiliation(s)
- Xi Wen
- Biomedical Engineering Department, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Ariel M Langevin
- Biomedical Engineering Department, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Mary J Dunlop
- Biomedical Engineering Department, Boston University, Boston, MA, 02215, USA. .,Biological Design Center, Boston University, Boston, MA, 02215, USA.
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27
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Robertson J, Gizdavic-Nikolaidis M, Nieuwoudt MK, Swift S. The antimicrobial action of polyaniline involves production of oxidative stress while functionalisation of polyaniline introduces additional mechanisms. PeerJ 2018; 6:e5135. [PMID: 29967756 PMCID: PMC6026458 DOI: 10.7717/peerj.5135] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/08/2018] [Indexed: 12/31/2022] Open
Abstract
Polyaniline (PANI) and functionalised polyanilines (fPANI) are novel antimicrobial agents whose mechanism of action was investigated. Escherichia coli single gene deletion mutants revealed that the antimicrobial mechanism of PANI likely involves production of hydrogen peroxide while homopolymer poly(3-aminobenzoic acid), P3ABA, used as an example of a fPANI, disrupts metabolic and respiratory machinery, by targeting ATP synthase and causes acid stress. PANI was more active against E. coli in aerobic, compared to anaerobic, conditions, while this was apparent for P3ABA only in rich media. Greater activity in aerobic conditions suggests involvement of reactive oxygen species. P3ABA treatment causes an increase in intracellular free iron, which is linked to perturbation of metabolic enzymes and could promote reactive oxygen species production. Addition of exogenous catalase protected E. coli from PANI antimicrobial action; however, this was not apparent for P3ABA treated cells. The results presented suggest that PANI induces production of hydrogen peroxide, which can promote formation of hydroxyl radicals causing biomolecule damage and potentially cell death. P3ABA is thought to act as an uncoupler by targeting ATP synthase resulting in a futile cycle, which precipitates dysregulation of iron homeostasis, oxidative stress, acid stress, and potentially the fatal loss of proton motive force.
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Affiliation(s)
- Julia Robertson
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | | | | | - Simon Swift
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
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28
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Fate of nuclear material during subsequent steps of the kinetin-induced PCD in apical parts of Vicia faba ssp. minor seedling roots. Micron 2018; 110:79-87. [PMID: 29772476 DOI: 10.1016/j.micron.2018.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 10/17/2022]
Abstract
In animals during apoptosis, the best examined type of programmed cell death (PCD), three main phases are distinguished: (i) specification (signaling), (ii) killing and (iii) execution one. It has bean postulated that plant PCD also involves three subsequent phases: (i) transmission of death signals to cells (signaling), (ii) initiation of killing processes and (iii) destruction of cells. One of the most important hallmarks of animal and plant PCD are those regarding nucleus, not thoroughly studied in plants so far. To study kinetin-induced PCD (Kin-PCD) in the context of nuclear material faith, 2-cm apical parts of Vicia faba ssp. minor seedling roots were used. Applied assays involving spectrophotometry, transmission electron microscopy, fluorescence and white light microscopy allowed to examine metabolic and cytomorphologic hallmarks such as changes in DNA content, ssDNA formation and activity of acidic and basic nucleases (DNases and RNases) as well as malformations and fragmentation of nucleoli and nuclei. The obtained results concerning the PCD hallmarks and influence of ZnSO4 on Kin-PCD allowed us to confirmed presence of specification/signaling, killing and execution/degradation phases of the process and broaden the knowledge about processes affecting nuclei during PCD.
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29
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Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria. PLoS Biol 2018; 16:e2005056. [PMID: 29750784 PMCID: PMC5966242 DOI: 10.1371/journal.pbio.2005056] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/23/2018] [Accepted: 04/12/2018] [Indexed: 11/29/2022] Open
Abstract
The stress-induced mutagenesis hypothesis postulates that in response to stress, bacteria increase their genome-wide mutation rate, in turn increasing the chances that a descendant is able to better withstand the stress. This has implications for antibiotic treatment: exposure to subinhibitory doses of antibiotics has been reported to increase bacterial mutation rates and thus probably the rate at which resistance mutations appear and lead to treatment failure. More generally, the hypothesis posits that stress increases evolvability (the ability of a population to generate adaptive genetic diversity) and thus accelerates evolution. Measuring mutation rates under stress, however, is problematic, because existing methods assume there is no death. Yet subinhibitory stress levels may induce a substantial death rate. Death events need to be compensated by extra replication to reach a given population size, thus providing more opportunities to acquire mutations. We show that ignoring death leads to a systematic overestimation of mutation rates under stress. We developed a system based on plasmid segregation that allows us to measure death and division rates simultaneously in bacterial populations. Using this system, we found that a substantial death rate occurs at the tested subinhibitory concentrations previously reported to increase mutation rate. Taking this death rate into account lowers and sometimes removes the signal for stress-induced mutagenesis. Moreover, even when antibiotics increase mutation rate, we show that subinhibitory treatments do not increase genetic diversity and evolvability, again because of effects of the antibiotics on population dynamics. We conclude that antibiotic-induced mutagenesis is overestimated because of death and that understanding evolvability under stress requires accounting for the effects of stress on population dynamics as much as on mutation rate. Our goal here is dual: we show that population dynamics and, in particular, the numbers of cell divisions are crucial but neglected parameters in the evolvability of a population, and we provide experimental and computational tools and methods to study evolvability under stress, leading to a reassessment of the magnitude and significance of the stress-induced mutagenesis paradigm. The effect of environmental stress on bacterial mutagenesis has been a paradigm-shift discovery. Recent developments include evidence that various antibiotics increase mutation rates in bacteria when used at subinhibitory concentrations. It is therefore suggested that such treatments promote resistance evolution because they increase the generation of genetic variation on which natural selection can act. However, existing methods to compute mutation rate neglect the effect of stress on death and population dynamics. Developing new experimental and computational tools, we find that taking death into account significantly lowers the signal for stress-induced mutagenesis. Moreover, we show that treatments that increase mutation rate do not always lead to increased genetic diversity, which questions the standard paradigm of increased evolvability under stress.
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30
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Lee AJ, Wang S, Meredith HR, Zhuang B, Dai Z, You L. Robust, linear correlations between growth rates and β-lactam-mediated lysis rates. Proc Natl Acad Sci U S A 2018; 115:4069-4074. [PMID: 29610312 PMCID: PMC5910845 DOI: 10.1073/pnas.1719504115] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is widely acknowledged that faster-growing bacteria are killed faster by β-lactam antibiotics. This notion serves as the foundation for the concept of bacterial persistence: dormant bacterial cells that do not grow are phenotypically tolerant against β-lactam treatment. Such correlation has often been invoked in the mathematical modeling of bacterial responses to antibiotics. Due to the lack of thorough quantification, however, it is unclear whether and to what extent the bacterial growth rate can predict the lysis rate upon β-lactam treatment under diverse conditions. Enabled by experimental automation, here we measured >1,000 growth/killing curves for eight combinations of antibiotics and bacterial species and strains, including clinical isolates of bacterial pathogens. We found that the lysis rate of a bacterial population linearly depends on the instantaneous growth rate of the population, regardless of how the latter is modulated. We further demonstrate that this predictive power at the population level can be explained by accounting for bacterial responses to the antibiotic treatment by single cells. This linear dependence of the lysis rate on the growth rate represents a dynamic signature associated with each bacterium-antibiotic pair and serves as the quantitative foundation for designing combination antibiotic therapy and predicting the population-structure change in a population with mixed phenotypes.
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Affiliation(s)
- Anna J Lee
- Department of Biomedical Engineering, Duke University, Durham, NC 27708
| | - Shangying Wang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708
| | - Hannah R Meredith
- Department of Biomedical Engineering, Duke University, Durham, NC 27708
| | - Bihan Zhuang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708
| | - Zhuojun Dai
- Department of Biomedical Engineering, Duke University, Durham, NC 27708
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708;
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710
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31
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Libby E, Driscoll WW, Ratcliff WC. Programmed cell death can increase the efficacy of microbial bet -hedging. Sci Rep 2018; 8:1120. [PMID: 29348455 PMCID: PMC5773525 DOI: 10.1038/s41598-017-18687-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/13/2017] [Indexed: 11/09/2022] Open
Abstract
Programmed cell death (PCD) occurs in both unicellular and multicellular organisms. While PCD plays a key role in the development and maintenance of multicellular organisms, explaining why single-celled organisms would evolve to actively commit suicide has been far more challenging. Here, we explore the potential for PCD to act as an accessory to microbial bet-hedging strategies that utilize stochastic phenotype switching. We consider organisms that face unpredictable and recurring disasters, in which fitness depends on effective phenotypic diversification. We show that when reproductive opportunities are limited by carrying capacity, PCD drives population turnover, providing increased opportunities for phenotypic diversification through stochastic phenotype switching. The main cost of PCD, providing resources for growth to a PCD(−) competitor, is ameliorated by genetic assortment in spatially structured populations. Using agent -based simulations, we explore how basic demographic factors, namely bottlenecks and local dispersal, can generate sufficient spatial structure to favor the evolution of high PCD rates.
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Affiliation(s)
- Eric Libby
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - William W Driscoll
- Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, 55108, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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32
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Identification of Staphylococcus aureus Cellular Pathways Affected by the Stilbenoid Lead Drug SK-03-92 Using a Microarray. Antibiotics (Basel) 2017; 6:antibiotics6030017. [PMID: 28892020 PMCID: PMC5617981 DOI: 10.3390/antibiotics6030017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/25/2017] [Accepted: 09/07/2017] [Indexed: 12/16/2022] Open
Abstract
The mechanism of action for a new lead stilbene compound coded SK-03-92 with bactericidal activity against methicillin-resistant Staphylococcus aureus (MRSA) is unknown. To gain insight into the killing process, transcriptional profiling was performed on SK-03-92 treated vs. untreated S. aureus. Fourteen genes were upregulated and 38 genes downregulated by SK-03-92 treatment. Genes involved in sortase A production, protein metabolism, and transcriptional regulation were upregulated, whereas genes encoding transporters, purine synthesis proteins, and a putative two-component system (SACOL2360 (MW2284) and SACOL2361 (MW2285)) were downregulated by SK-03-92 treatment. Quantitative real-time polymerase chain reaction analyses validated upregulation of srtA and tdk as well as downregulation of the MW2284/MW2285 and purine biosynthesis genes in the drug-treated population. A quantitative real-time polymerase chain reaction analysis of MW2284 and MW2285 mutants compared to wild-type cells demonstrated that the srtA gene was upregulated by both putative two-component regulatory gene mutants compared to the wild-type strain. Using a transcription profiling technique, we have identified several cellular pathways regulated by SK-03-92 treatment, including a putative two-component system that may regulate srtA and other genes that could be tied to the SK-03-92 mechanism of action, biofilm formation, and drug persisters.
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33
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Srikumar A, Krishna PS, Sivaramakrishna D, Kopfmann S, Hess WR, Swamy MJ, Lin-Chao S, Prakash JSS. The Ssl2245-Sll1130 Toxin-Antitoxin System Mediates Heat-induced Programmed Cell Death in Synechocystis sp. PCC6803. J Biol Chem 2017; 292:4222-4234. [PMID: 28104802 DOI: 10.1074/jbc.m116.748178] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 01/17/2017] [Indexed: 12/13/2022] Open
Abstract
Two putative heat-responsive genes, ssl2245 and sll1130, constitute an operon that also has characteristics of a toxin-antitoxin system, thus joining several enigmatic features. Closely related orthologs of Ssl2245 and Sll1130 exist in widely different bacteria, which thrive under environments with large fluctuations in temperature and salinity, among which some are thermo-epilithic biofilm-forming cyanobacteria. Transcriptome analyses revealed that the clustered regularly interspaced short palindromic repeats (CRISPR) genes as well as several hypothetical genes were commonly up-regulated in Δssl2245 and Δsll1130 mutants. Genes coding for heat shock proteins and pilins were also induced in Δsll1130 We observed that the majority of cells in a Δsll1130 mutant strain remained unicellular and viable after prolonged incubation at high temperature (50 °C). In contrast, the wild type formed large cell clumps of dead and live cells, indicating the attempt to form biofilms under harsh conditions. Furthermore, we observed that Sll1130 is a heat-stable ribonuclease whose activity was inhibited by Ssl2245 at optimal temperatures but not at high temperatures. In addition, we demonstrated that Ssl2245 is physically associated with Sll1130 by electrostatic interactions, thereby inhibiting its activity at optimal growth temperature. This association is lost upon exposure to heat, leaving Sll1130 to exhibit its ribonuclease activity. Thus, the activation of Sll1130 leads to the degradation of cellular RNA and thereby heat-induced programmed cell death that in turn supports the formation of a more resistant biofilm for the surviving cells. We suggest to designate Ssl2245 and Sll1130 as MazE and MazF, respectively.
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Affiliation(s)
- Afshan Srikumar
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
| | - Pilla Sankara Krishna
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
| | | | - Stefan Kopfmann
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany, and
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany, and
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Sue Lin-Chao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Jogadhenu S S Prakash
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
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34
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Silva LN, Zimmer KR, Macedo AJ, Trentin DS. Plant Natural Products Targeting Bacterial Virulence Factors. Chem Rev 2016; 116:9162-236. [PMID: 27437994 DOI: 10.1021/acs.chemrev.6b00184] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Decreased antimicrobial efficiency has become a global public health issue. The paucity of new antibacterial drugs is evident, and the arsenal against infectious diseases needs to be improved urgently. The selection of plants as a source of prototype compounds is appropriate, since plant species naturally produce a wide range of secondary metabolites that act as a chemical line of defense against microorganisms in the environment. Although traditional approaches to combat microbial infections remain effective, targeting microbial virulence rather than survival seems to be an exciting strategy, since the modulation of virulence factors might lead to a milder evolutionary pressure for the development of resistance. Additionally, anti-infective chemotherapies may be successfully achieved by combining antivirulence and conventional antimicrobials, extending the lifespan of these drugs. This review presents an updated discussion of natural compounds isolated from plants with chemically characterized structures and activity against the major bacterial virulence factors: quorum sensing, bacterial biofilms, bacterial motility, bacterial toxins, bacterial pigments, bacterial enzymes, and bacterial surfactants. Moreover, a critical analysis of the most promising virulence factors is presented, highlighting their potential as targets to attenuate bacterial virulence. The ongoing progress in the field of antivirulence therapy may therefore help to translate this promising concept into real intervention strategies in clinical areas.
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Affiliation(s)
- Laura Nunes Silva
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Rio Grande do Sul 90610-000, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Rio Grande do Sul 91501-970, Brazil
| | - Karine Rigon Zimmer
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre , Porto Alegre, Rio Grande do Sul 90050-170, Brazil
| | - Alexandre José Macedo
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Rio Grande do Sul 90610-000, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Rio Grande do Sul 91501-970, Brazil.,Instituto Nacional do Semiárido , Campina Grande, Paraı́ba 58429-970, Brazil
| | - Danielle Silva Trentin
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Rio Grande do Sul 90610-000, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Rio Grande do Sul 91501-970, Brazil
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35
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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: 72] [Impact Index Per Article: 9.0] [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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36
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Asplund-Samuelsson J, Sundh J, Dupont CL, Allen AE, McCrow JP, Celepli NA, Bergman B, Ininbergs K, Ekman M. Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem. Front Microbiol 2016; 7:1043. [PMID: 27458440 PMCID: PMC4933709 DOI: 10.3389/fmicb.2016.01043] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/22/2016] [Indexed: 11/13/2022] Open
Abstract
Metacaspases are distant homologs of metazoan caspase proteases, implicated in stress response, and programmed cell death (PCD) in bacteria and phytoplankton. While the few previous studies on metacaspases have relied on cultured organisms and sequenced genomes, no studies have focused on metacaspases in a natural setting. We here present data from the first microbial community-wide metacaspase survey; performed by querying metagenomic and metatranscriptomic datasets from the brackish Baltic Sea, a water body characterized by pronounced environmental gradients and periods of massive cyanobacterial blooms. Metacaspase genes were restricted to ~4% of the bacteria, taxonomically affiliated mainly to Bacteroidetes, Alpha- and Betaproteobacteria and Cyanobacteria. The gene abundance was significantly higher in larger or particle-associated bacteria (>0.8 μm), and filamentous Cyanobacteria dominated metacaspase gene expression throughout the bloom season. Distinct seasonal expression patterns were detected for the three metacaspase genes in Nodularia spumigena, one of the main bloom-formers. Clustering of normalized gene expression in combination with analyses of genomic and assembly data suggest functional diversification of these genes, and possible roles of the metacaspase genes related to stress responses, i.e., sulfur metabolism in connection to oxidative stress, and nutrient stress induced cellular differentiation. Co-expression of genes encoding metacaspases and nodularin toxin synthesis enzymes was also observed in Nodularia spumigena. The study shows that metacaspases represent an adaptation of potentially high importance for several key organisms in the Baltic Sea, most prominently Cyanobacteria, and open up for further exploration of their physiological roles in microbes and assessment of their ecological impact in aquatic habitats.
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Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - John Sundh
- Science for Life Laboratory, Department of Biology and Environmental Science, Linnaeus UniversitySolna, Sweden
| | - Chris L. Dupont
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Andrew E. Allen
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - John P. McCrow
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Narin A. Celepli
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Birgitta Bergman
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Karolina Ininbergs
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Martin Ekman
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
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Durand P, Sym S, Michod R. Programmed Cell Death and Complexity in Microbial Systems. Curr Biol 2016; 26:R587-R593. [DOI: 10.1016/j.cub.2016.05.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Ramisetty BCM, Raj S, Ghosh D. Escherichia coli MazEF toxin-antitoxin system does not mediate programmed cell death. J Basic Microbiol 2016; 56:1398-1402. [PMID: 27259116 DOI: 10.1002/jobm.201600247] [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] [Received: 04/20/2016] [Accepted: 05/20/2016] [Indexed: 11/06/2022]
Abstract
Toxin-antitoxins systems (TAS) are prokaryotic operons containing two small overlapping genes which encode two components referred to as toxin and antitoxin. Involvement of TAS in bacterial programmed cell death (PCD) is highly controversial. MazEF, a typical type II TAS, is particularly implicated in mediating PCD in Escherichia coli. Hence, we compared the metabolic fitness and stress tolerance of E. coli strains (MC4100 and its mazEF-derivative) which were extensively used by proponents of mazEF-mediated PCD. We found that both the strains are deficient in relA gene and that the ΔmazEF strain has lower fitness and stress tolerance compared to wild type MC4100. We could not reproduce mazEF mediated PCD which emphasizes the need for skeptic approach to the PCD hypothesis.
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Affiliation(s)
| | - Swati Raj
- School of Chemical and Biotechnology, SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Dimpy Ghosh
- School of Chemical and Biotechnology, SASTRA University, Thirumalaisamudram, Thanjavur, India
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Chan WT, Espinosa M, Yeo CC. Keeping the Wolves at Bay: Antitoxins of Prokaryotic Type II Toxin-Antitoxin Systems. Front Mol Biosci 2016; 3:9. [PMID: 27047942 PMCID: PMC4803016 DOI: 10.3389/fmolb.2016.00009] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/04/2016] [Indexed: 12/21/2022] Open
Abstract
In their initial stages of discovery, prokaryotic toxin-antitoxin (TA) systems were confined to bacterial plasmids where they function to mediate the maintenance and stability of usually low- to medium-copy number plasmids through the post-segregational killing of any plasmid-free daughter cells that developed. Their eventual discovery as nearly ubiquitous and repetitive elements in bacterial chromosomes led to a wealth of knowledge and scientific debate as to their diversity and functionality in the prokaryotic lifestyle. Currently categorized into six different types designated types I–VI, type II TA systems are the best characterized. These generally comprised of two genes encoding a proteic toxin and its corresponding proteic antitoxin, respectively. Under normal growth conditions, the stable toxin is prevented from exerting its lethal effect through tight binding with the less stable antitoxin partner, forming a non-lethal TA protein complex. Besides binding with its cognate toxin, the antitoxin also plays a role in regulating the expression of the type II TA operon by binding to the operator site, thereby repressing transcription from the TA promoter. In most cases, full repression is observed in the presence of the TA complex as binding of the toxin enhances the DNA binding capability of the antitoxin. TA systems have been implicated in a gamut of prokaryotic cellular functions such as being mediators of programmed cell death as well as persistence or dormancy, biofilm formation, as defensive weapons against bacteriophage infections and as virulence factors in pathogenic bacteria. It is thus apparent that these antitoxins, as DNA-binding proteins, play an essential role in modulating the prokaryotic lifestyle whilst at the same time preventing the lethal action of the toxins under normal growth conditions, i.e., keeping the proverbial wolves at bay. In this review, we will cover the diversity and characteristics of various type II TA antitoxins. We shall also look into some interesting deviations from the canonical type II TA systems such as tripartite TA systems where the regulatory role is played by a third party protein and not the antitoxin, and a unique TA system encoding a single protein with both toxin as well as antitoxin domains.
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Affiliation(s)
- Wai Ting Chan
- Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Manuel Espinosa
- Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Chew Chieng Yeo
- Faculty of Medicine, Biomedical Research Centre, Universiti Sultan Zainal Abidin Kuala Terengganu, Malaysia
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40
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Li T, Zhai S, Xu M, Shang M, Gao Y, Liu G, Wang Q, Zheng L. SpxB-mediated H2 O2 induces programmed cell death in Streptococcus sanguinis. J Basic Microbiol 2016; 56:741-52. [PMID: 26879582 DOI: 10.1002/jobm.201500617] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/31/2016] [Indexed: 12/17/2022]
Abstract
Streptococcus sanguinis (S. sanguinis) is a commensal oral streptococci that produces hydrogen peroxide (H2 O2 ), and this production is dependent on pyruvate oxidase (SpxB) activity. In addition to its well-known role in intraspecies or interspecies competitions, recent studies have shown that H2 O2 produced by S. sanguinis under aerobic conditions not only upregulates biofilm formation and eDNA release but also regulates cell death without obvious cell lysis. Here, we report that S. sanguinis exhibits characteristic hallmarks of eukaryotic apoptosis when it encounters endogenous and exogenous H2 O2 . As the most common mode of programmed cell death (PCD), apoptosis is accompanied by a series of biochemical and morphological events, including DNA fragmentation, chromosome condensation, membrane potential depolarization, phosphatidylserine (PS) exposure, and caspase substrate binding protein activity changes. In addition, we also provide genetic evidence that there is decreased expression of the related DNA repair genes comEA, recA, dnaC, dinG, and pcrA in the wild-type compared to the isogenic spxB mutant in S. sanguinis. Our data suggest that endogenous H2 O2 is the most important agent in this development process in S. sanguinis.
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Affiliation(s)
- Ting Li
- Department of Pathogen Biology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Shuheng Zhai
- Department of Clinical Medicine English Class, China Medical University, Shenyang, China
| | - Mengya Xu
- Department of Pathogen Biology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Mengmeng Shang
- Department of Pathogen Biology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Yu Gao
- Department of Pathogen Biology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Gangshan Liu
- Department of Clinical Medicine English Class, China Medical University, Shenyang, China
| | - Qingxuan Wang
- Department of Dental Medicine, China Medical University, Shenyang, China
| | - Lanyan Zheng
- Department of Pathogen Biology, College of Basic Medical Sciences, China Medical University, Shenyang, China
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Hazan R, Que YA, Maura D, Strobel B, Majcherczyk PA, Hopper LR, Wilbur DJ, Hreha TN, Barquera B, Rahme LG. Auto Poisoning of the Respiratory Chain by a Quorum-Sensing-Regulated Molecule Favors Biofilm Formation and Antibiotic Tolerance. Curr Biol 2016; 26:195-206. [PMID: 26776731 DOI: 10.1016/j.cub.2015.11.056] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/24/2015] [Accepted: 11/24/2015] [Indexed: 01/05/2023]
Abstract
Bacterial programmed cell death and quorum sensing are direct examples of prokaryote group behaviors, wherein cells coordinate their actions to function cooperatively like one organism for the benefit of the whole culture. We demonstrate here that 2-n-heptyl-4-hydroxyquinoline-N-oxide (HQNO), a Pseudomonas aeruginosa quorum-sensing-regulated low-molecular-weight excreted molecule, triggers autolysis by self-perturbing the electron transfer reactions of the cytochrome bc1 complex. HQNO induces specific self-poisoning by disrupting the flow of electrons through the respiratory chain at the cytochrome bc1 complex, causing a leak of reducing equivalents to O2 whereby electrons that would normally be passed to cytochrome c are donated directly to O2. The subsequent mass production of reactive oxygen species (ROS) reduces membrane potential and disrupts membrane integrity, causing bacterial cell autolysis and DNA release. DNA subsequently promotes biofilm formation and increases antibiotic tolerance to beta-lactams, suggesting that HQNO-dependent cell autolysis is advantageous to the bacterial populations. These data identify both a new programmed cell death system and a novel role for HQNO as a critical inducer of biofilm formation and antibiotic tolerance. This newly identified pathway suggests intriguing mechanistic similarities with the initial mitochondrial-mediated steps of eukaryotic apoptosis.
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Affiliation(s)
- Ronen Hazan
- Department of Surgery and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, Boston, MA 02114, USA; Shriners Hospitals for Children Boston, Boston, MA 02114, USA
| | - Yok Ai Que
- Department of Surgery and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, Boston, MA 02114, USA; Shriners Hospitals for Children Boston, Boston, MA 02114, USA
| | - Damien Maura
- Department of Surgery and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, Boston, MA 02114, USA; Shriners Hospitals for Children Boston, Boston, MA 02114, USA
| | - Benjamin Strobel
- Department of Surgery and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Laura Rose Hopper
- Department of Surgery and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David J Wilbur
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Teri N Hreha
- Department of Biological Sciences, CBIS, Rensselaer Polytechnic Institute, 110 8(th) Street, Troy, NY 12180, USA
| | - Blanca Barquera
- Department of Biological Sciences, CBIS, Rensselaer Polytechnic Institute, 110 8(th) Street, Troy, NY 12180, USA
| | - Laurence G Rahme
- Department of Surgery and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Surgery, Center for Surgery, Innovation and Bioengineering, Massachusetts General Hospital, Boston, MA 02114, USA; Shriners Hospitals for Children Boston, Boston, MA 02114, USA.
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42
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Cell Differentiation and Spatial Organization in Yeast Colonies: Role of Cell-Wall Integrity Pathway. Genetics 2015; 201:1427-38. [PMID: 26510787 DOI: 10.1534/genetics.115.180919] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/10/2015] [Indexed: 11/18/2022] Open
Abstract
Many microbial communities contain organized patterns of cell types, yet relatively little is known about the mechanism or function of this organization. In colonies of the budding yeast Saccharomyces cerevisiae, sporulation occurs in a highly organized pattern, with a top layer of sporulating cells sharply separated from an underlying layer of nonsporulating cells. A mutant screen identified the Mpk1 and Bck1 kinases of the cell-wall integrity (CWI) pathway as specifically required for sporulation in colonies. The CWI pathway was induced as colonies matured, and a target of this pathway, the Rlm1 transcription factor, was activated specifically in the nonsporulating cell layer, here termed feeder cells. Rlm1 stimulates permeabilization of feeder cells and promotes sporulation in an overlying cell layer through a cell-nonautonomous mechanism. The relative fraction of the colony apportioned to feeder cells depends on nutrient environment, potentially buffering sexual reproduction against suboptimal environments.
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43
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Leung V, Dufour D, Lévesque CM. Death and survival in Streptococcus mutans: differing outcomes of a quorum-sensing signaling peptide. Front Microbiol 2015; 6:1176. [PMID: 26557114 PMCID: PMC4615949 DOI: 10.3389/fmicb.2015.01176] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/12/2015] [Indexed: 11/13/2022] Open
Abstract
Bacteria are considered "social" organisms able to communicate with one another using small hormone-like molecules (pheromones) in a process called quorum-sensing (QS). These signaling molecules increase in concentration as a function of bacterial cell density. For most human pathogens, QS is critical for virulence and biofilm formation, and the opportunity to interfere with bacterial QS could provide a sophisticated means for manipulating the composition of pathogenic biofilms, and possibly eradicating the infection. Streptococcus mutans is a well-characterized resident of the dental plaque biofilm, and is the major pathogen of dental caries (cavities). In S. mutans, its CSP QS signaling peptide does not act as a classical QS signal by accumulating passively in proportion to cell density. In fact, particular stresses such as those encountered in the oral cavity, induce the production of the CSP pheromone, suggesting that the pheromone most probably functions as a stress-inducible alarmone by triggering the signaling to the bacterial population to initiate an adaptive response that results in different phenotypic outcomes. This mini-review discusses two different CSP-induced phenotypes, bacterial "suicide" and dormancy, and the underlying mechanisms by which S. mutans utilizes the same QS signaling peptide to regulate two opposite phenotypes.
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Affiliation(s)
- Vincent Leung
- Dental Research Institute, Faculty of Dentistry, University of Toronto , Toronto, ON, Canada
| | - Delphine Dufour
- Dental Research Institute, Faculty of Dentistry, University of Toronto , Toronto, ON, Canada
| | - Céline M Lévesque
- Dental Research Institute, Faculty of Dentistry, University of Toronto , Toronto, ON, Canada
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44
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Iranzo J, Lobkovsky AE, Wolf YI, Koonin EV. Virus-host arms race at the joint origin of multicellularity and programmed cell death. Cell Cycle 2015; 13:3083-8. [PMID: 25486567 PMCID: PMC4615056 DOI: 10.4161/15384101.2014.949496] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Unicellular eukaryotes and most prokaryotes possess distinct mechanisms of programmed cell death (PCD). How an “altruistic” trait, such as PCD, could evolve in unicellular organisms? To address this question, we developed a mathematical model of the virus-host co-evolution that involves interaction between immunity, PCD and cellular aggregation. Analysis of the parameter space of this model shows that under high virus load and imperfect immunity, joint evolution of cell aggregation and PCD is the optimal evolutionary strategy. Given the abundance of viruses in diverse habitats and the wide spread of PCD in most organisms, these findings imply that multiple instances of the emergence of multicellularity and its essential attribute, PCD, could have been driven, at least in part, by the virus-host arms race.
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Affiliation(s)
- Jaime Iranzo
- a National Center for Biotechnology Information; National Library of Medicine; National Institutes of Health ; Bethesda , MD USA
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45
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Meredith HR, Lopatkin AJ, Anderson DJ, You L. Bacterial temporal dynamics enable optimal design of antibiotic treatment. PLoS Comput Biol 2015; 11:e1004201. [PMID: 25905796 PMCID: PMC4407907 DOI: 10.1371/journal.pcbi.1004201] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/19/2015] [Indexed: 01/08/2023] Open
Abstract
There is a critical need to better use existing antibiotics due to the urgent threat of antibiotic resistant bacteria coupled with the reduced effort in developing new antibiotics. β-lactam antibiotics represent one of the most commonly used classes of antibiotics to treat a broad spectrum of Gram-positive and -negative bacterial pathogens. However, the rise of extended spectrum β-lactamase (ESBL) producing bacteria has limited the use of β-lactams. Due to the concern of complex drug responses, many β-lactams are typically ruled out if ESBL-producing pathogens are detected, even if these pathogens test as susceptible to some β-lactams. Using quantitative modeling, we show that β-lactams could still effectively treat pathogens producing low or moderate levels of ESBLs when administered properly. We further develop a metric to guide the design of a dosing protocol to optimize treatment efficiency for any antibiotic-pathogen combination. Ultimately, optimized dosing protocols could allow reintroduction of a repertoire of first-line antibiotics with improved treatment outcomes and preserve last-resort antibiotics. Antibiotic resistance is a growing problem that the World Health Organization describes as “one of the top three threats to global health.” To date, bacteria have developed resistance to all antibiotics used in clinical settings. Unfortunately, the evolution of antibiotic resistant bacteria is accelerating, as antibiotics continue to be misused and overused. As the antibiotic pipeline is drying up, it becomes increasingly critical to utilize the antibiotics already on the market more effectively. The key to designing better regimens lies in the ability to predict how bacteria will respond to a particular antibiotic treatment. Because of this, we need a simple metric that characterizes this pathogen-antibiotic interaction that can be easily measured and used to design dosing protocols that will effectively clear an infection. To help guide the design of effective protocols, we use quantitative modeling to develop a metric that is easy to measure and quantifies the pathogen-antibiotic interaction. Through optimized antibiotic regimens, our strategy could extend the use of first-line antibiotics, improve treatment outcome, and preserve last-resort antibiotics.
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Affiliation(s)
- Hannah R. Meredith
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Allison J. Lopatkin
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Deverick J. Anderson
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Infection Control Outreach Network, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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46
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Andrukov BG, Somova LM, Timchenko NF. STRATEGY OF PROGRAMMED CELL DEATH IN PROKARYOTES. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2015. [DOI: 10.15789/2220-7619-2015-1-15-26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Programmed cell death (PCD) was first studied in eukaryotic organisms. This system also operates in the development life cycle of prokaryotes. The system PCD in microorganisms is activated a wide range of signals in response to the stresses associated with adverse environmental conditions or exposure to antibacterial agents. The results of numerous studies in the past decade allow considering the system PCD in prokaryotes as an evolutionary conservation of the species. These results significantly expanded understanding of the role of PCD in microorganisms and opened a number of important areas of research of the morphological and molecular genetic approaches to the study of death strategies for the survival in bacterial populations. The purpose of the review is to summarize the morphological and molecular genetic characteristics of PCD in prokaryotes which are real manifestations of the mechanisms of this phenomenon.
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47
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Collective antibiotic tolerance: mechanisms, dynamics and intervention. Nat Chem Biol 2015; 11:182-8. [PMID: 25689336 DOI: 10.1038/nchembio.1754] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/12/2015] [Indexed: 12/14/2022]
Abstract
Bacteria have developed resistance against every antibiotic at a rate that is alarming considering the timescale at which new antibiotics are developed. Thus, there is a critical need to use antibiotics more effectively, extend the shelf life of existing antibiotics and minimize their side effects. This requires understanding the mechanisms underlying bacterial drug responses. Past studies have focused on survival in the presence of antibiotics by individual cells, as genetic mutants or persisters. Also important, however, is the fact that a population of bacterial cells can collectively survive antibiotic treatments lethal to individual cells. This tolerance can arise by diverse mechanisms, including resistance-conferring enzyme production, titration-mediated bistable growth inhibition, swarming and interpopulation interactions. These strategies can enable rapid population recovery after antibiotic treatment and provide a time window during which otherwise susceptible bacteria can acquire inheritable genetic resistance. Here, we emphasize the potential for targeting collective antibiotic tolerance behaviors as an antibacterial treatment strategy.
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48
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Die for the community: an overview of programmed cell death in bacteria. Cell Death Dis 2015; 6:e1609. [PMID: 25611384 PMCID: PMC4669768 DOI: 10.1038/cddis.2014.570] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 11/25/2014] [Accepted: 12/01/2014] [Indexed: 02/07/2023]
Abstract
Programmed cell death is a process known to have a crucial role in many aspects of eukaryotes physiology and is clearly essential to their life. As a consequence, the underlying molecular mechanisms have been extensively studied in eukaryotes and we now know that different signalling pathways leading to functionally and morphologically different forms of death exist in these organisms. Similarly, mono-cellular organism can activate signalling pathways leading to death of a number of cells within a colony. The reason why a single-cell organism would activate a program leading to its death is apparently counterintuitive and probably for this reason cell death in prokaryotes has received a lot less attention in the past years. However, as summarized in this review there are many reasons leading to prokaryotic cell death, for the benefit of the colony. Indeed, single-celled organism can greatly benefit from multicellular organization. Within this forms of organization, regulation of death becomes an important issue, contributing to important processes such as: stress response, development, genetic transformation, and biofilm formation.
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49
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Aouacheria A. [From dualism to multiplicity: seeing BCL-2 family proteins and cell death with new eyes]. Biol Aujourdhui 2015; 209:331-55. [PMID: 27021052 DOI: 10.1051/jbio/2016003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Indexed: 11/15/2022]
Abstract
The concept of cell death has many links to the concept of death itself, defined as the opposite of life. Achievements obtained through research on apoptosis have apparently allowed us to transcend this Manichean view. Death is no longer outside, but rather inside living systems, as a constitutive force at work within the living matter. Whereas the death of cells can be positive and breed "creation" (e.g. during morphogenesis), its dysregulation can also cause or contribute to fatal diseases including cancer. It is tempting to apply this biological discourse to illuminate the relations between life and death, taken in general terms, but does this generalization actually hold? Is this discourse not essentially a metaphor? If cell death is considered as a vital aspect of various biological processes, then are we not faced with some vitalistic conception of death? Are there one or more meanings to the word "death"? Does the power to self-destruct act in opposition to other key features of living entities, or rather in juxtaposition to them? In this article, we first describe how the field of cell death has been developed on the basis of perceived and built dichotomies, mirroring the original opposition between life and death. We detail the limitations of the current paradigm of apoptosis regulation by BCL-2 family proteins, which nicely illustrate the problem of binary thinking in biology. Last, we try to show a way out of this dualistic matrix, by drawing on the notions of multiplicity, complexity, diversity, evolution and contingency.
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Affiliation(s)
- Abdel Aouacheria
- LBMC - Laboratoire de Biologie Moléculaire de la Cellule, École Normale Supérieure de Lyon, UMR 5239, CNRS, Université Lyon 1, HCL, 46 Allée d'Italie, 69364 Lyon Cedex 07, France - ISEM - Institut des Sciences de l'Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier, France
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50
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Lafleur JE, Rice SA. Induction of resistance to S. aureus in an environmental marine biofilm grown in Sydney Harbor, NSW, Australia. World J Microbiol Biotechnol 2014; 31:353-8. [PMID: 25526959 DOI: 10.1007/s11274-014-1787-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/08/2014] [Indexed: 12/01/2022]
Abstract
The study of environmental biofilms is complicated by the difficulty of working with them under lab conditions. Nonetheless, knowledge of cellular activity and interactions within environmental biofilms could lead to novel biomedical applications. To address this problem we previously proposed a new technique for inducing resistance to Staphylococcus aureus in an intact environmental biofilm. In the current follow-up study we applied the new technique in a biogeographically distinct environment using a different strain of S. aureus. The proposed technique for inducing resistance to S. aureus in an environmental biofilm involves growing the environmental biofilms over several days in media reflecting their natural habitat on agar that contains spent culture supernatant from S. aureus over-night culture. We found in this second study that it was possible to induce resistance to S. aureus in an environmental biofilm from a biogeographically distinct environment, though not in the same way as we had previously observed. Environmental consortia from Sydney Harbor, Australia display an ability to inhibit biofilm formation by S. aureus; only in the case where the environmental biofilms were pretreated with UV radiation was there a difference in activity between environmental consortia grown on plain agar, and that grown on S. aureus agar. Application of the new technique in the current study also differs in that significant killing of cells within an established S. aureus biofilm by environmental consortia grown on S. aureus agar was possible.
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Affiliation(s)
- John E Lafleur
- Department of Emergency Medicine, Alpert School of Medicine of Brown University, Providence, RI, USA,
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