301
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Chemical Probes of Escherichia coli Uncovered through Chemical-Chemical Interaction Profiling with Compounds of Known Biological Activity. ACTA ACUST UNITED AC 2010; 17:852-62. [DOI: 10.1016/j.chembiol.2010.06.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 05/25/2010] [Accepted: 06/04/2010] [Indexed: 01/25/2023]
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302
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Cysteine biosynthesis, oxidative stress and antibiotic resistance in Salmonella typhimurium. Res Microbiol 2010; 161:643-50. [PMID: 20600858 DOI: 10.1016/j.resmic.2010.06.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/03/2010] [Accepted: 06/07/2010] [Indexed: 11/20/2022]
Abstract
The efficacy of antibiotics varies under different growth conditions due to the induction of specific or more general defense pathways, but the mechanisms are not completely understood. Actively swarming Salmonella show elevated resistance to many types of antibiotics. Previously, we had shown that cysteine biosynthesis was important for the induced antibiotic resistance phenotype of swarm cells. Here we examine the connection of cysteine to oxidative stress and demonstrate that the antioxidant properties of cysteine or cysteine-derived metabolites contribute to the antibiotic resistance in both vegetative and swarm cell populations. We observed that cys auxotrophs were oxidatively stressed, and in wild-type cells expression of the cys regulon was induced during periods of oxidative stress. In swarm cells, we found a 6-fold increase in reduced glutathione compared to swim cells and a corresponding increased resistance to oxidants. Wild-type and cys auxotrophs exhibited the same sensitivities to gentamicin, polymyxin and ciprofloxacin when grown anaerobically, suggesting that induced oxidative stress defense was contributing to elevated antibiotic resistance in swarm cells aerobically. Induction of the CysB regulon by addition of exogenous inducer resulted in elevated antibiotic resistance independently of swarming.
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303
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Daung-nkern J, Vattanaviboon P, Mongkolsuk S. Inactivation of nfuA enhances susceptibility of Pseudomonas aeruginosa to fluoroquinolone antibiotics. J Antimicrob Chemother 2010; 65:1831-2. [DOI: 10.1093/jac/dkq194] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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304
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Sissi C, Palumbo M. In front of and behind the replication fork: bacterial type IIA topoisomerases. Cell Mol Life Sci 2010; 67:2001-24. [PMID: 20165898 PMCID: PMC11115839 DOI: 10.1007/s00018-010-0299-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 01/26/2010] [Accepted: 02/01/2010] [Indexed: 01/03/2023]
Abstract
Topoisomerases are vital enzymes specialized in controlling DNA topology, in particular supercoiling and decatenation, to properly handle nucleic acid packing and cell dynamics. The type IIA enzymes act by cleaving both strands of a double helix and having another strand from the same or another molecule cross the DNA gate before a re-sealing event completes the catalytic cycle. Here, we will consider the two types of IIA prokaryotic topoisomerases, DNA Gyrase and Topoisomerase IV, as crucial regulators of bacterial cell cycle progression. Their synergistic action allows control of chromosome packing and grants occurrence of functional transcription and replication processes. In addition to displaying a fascinating molecular mechanism of action, which transduces chemical energy into mechanical energy by means of large conformational changes, these enzymes represent attractive pharmacological targets for antibacterial chemotherapy.
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Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131, Padua, Italy.
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305
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Abstract
Antibiotic drug-target interactions, and their respective direct effects, are generally well characterized. By contrast, the bacterial responses to antibiotic drug treatments that contribute to cell death are not as well understood and have proven to be complex as they involve many genetic and biochemical pathways. In this Review, we discuss the multilayered effects of drug-target interactions, including the essential cellular processes that are inhibited by bactericidal antibiotics and the associated cellular response mechanisms that contribute to killing. We also discuss new insights into these mechanisms that have been revealed through the study of biological networks, and describe how these insights, together with related developments in synthetic biology, could be exploited to create new antibacterial therapies.
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306
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Abstract
Early synthetic biology designs, namely the genetic toggle switch and repressilator, showed that regulatory components can be characterized and assembled to bring about complex, electronics-inspired behaviours in living systems (for example, memory storage and timekeeping). Through the characterization and assembly of genetic parts and biological building blocks, many more devices have been constructed, including switches, memory elements, oscillators, pulse generators, digital logic gates, filters and communication modules. Advances in the field are now allowing expansion beyond small gene networks to the realm of larger biological programs, which hold promise for a wide range of applications, including biosensing, therapeutics and the production of biofuels, pharmaceuticals and biomaterials. Synthetic biosensing circuits consist of sensitive elements that bind analytes and transducer modules that mobilize cellular responses. Balancing these two modules involves engineering modularity and specificity into the various circuits. Biosensor sensitive elements include environment-responsive promoters (transcriptional), RNA aptamers (translational) and protein receptors (post-translational). Biosensor transducer modules include engineered gene networks (transcriptional), non-coding regulatory RNAs (translational) and protein signal-transduction circuits (post-translational). The contributions of synthetic biology to therapeutics include: engineered networks and organisms for disease-mechanism elucidation, drug-target identification, drug-discovery platforms, therapeutic treatment, therapeutic delivery, and drug production and access. In the microbial production of biofuels and pharmaceuticals, synthetic biology has supplemented traditional genetic and metabolic engineering efforts by aiding the construction of optimized biosynthetic pathways. Optimizing metabolic flux through biosynthetic pathways is traditionally accomplished by driving the expression of pathway enzymes with strong, inducible promoters. New synthetic approaches include the rapid diversification of various pathway components, the rational and model-guided assembly of pathway components, and hybrid solutions.
Advances in the synthetic biology field are allowing an expansion beyond small gene networks towards larger biological programs that hold promise for a wide range of applications, including biosensing, therapeutics and the production of biofuels, pharmaceuticals and biomaterials. Synthetic biology is bringing together engineers and biologists to design and build novel biomolecular components, networks and pathways, and to use these constructs to rewire and reprogram organisms. These re-engineered organisms will change our lives over the coming years, leading to cheaper drugs, 'green' means to fuel our cars and targeted therapies for attacking 'superbugs' and diseases, such as cancer. The de novo engineering of genetic circuits, biological modules and synthetic pathways is beginning to address these crucial problems and is being used in related practical applications.
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Affiliation(s)
- Ahmad S Khalil
- Howard Hughes Medical Institute, Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, Massachusetts 02215, USA
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307
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Kohanski MA, DePristo MA, Collins JJ. Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Mol Cell 2010; 37:311-20. [PMID: 20159551 DOI: 10.1016/j.molcel.2010.01.003] [Citation(s) in RCA: 638] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 10/18/2009] [Accepted: 11/12/2009] [Indexed: 01/27/2023]
Abstract
Antibiotic resistance arises through mechanisms such as selection of naturally occurring resistant mutants and horizontal gene transfer. Recently, oxidative stress has been implicated as one of the mechanisms whereby bactericidal antibiotics kill bacteria. Here, we show that sublethal levels of bactericidal antibiotics induce mutagenesis, resulting in heterogeneous increases in the minimum inhibitory concentration for a range of antibiotics, irrespective of the drug target. This increase in mutagenesis correlates with an increase in ROS and is prevented by the ROS scavenger thiourea and by anaerobic conditions, indicating that sublethal concentrations of antibiotics induce mutagenesis by stimulating the production of ROS. We demonstrate that these effects can lead to mutant strains that are sensitive to the applied antibiotic but resistant to other antibiotics. This work establishes a radical-based molecular mechanism whereby sublethal levels of antibiotics can lead to multidrug resistance, which has important implications for the widespread use and misuse of antibiotics.
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Affiliation(s)
- Michael A Kohanski
- Howard Hughes Medical Institute, Boston University, Boston, MA 02215, USA
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308
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Many chromosomal genes modulate MarA-mediated multidrug resistance in Escherichia coli. Antimicrob Agents Chemother 2010; 54:2125-34. [PMID: 20211899 DOI: 10.1128/aac.01420-09] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug resistance (MDR) in clinical isolates of Escherichia coli can be associated with overexpression of marA, a transcription factor that upregulates multidrug efflux and downregulates membrane permeability. Using random transposome mutagenesis, we found that many chromosomal genes and environmental stimuli affected MarA-mediated antibiotic resistance. Seven genes affected resistance mediated by MarA in an antibiotic-specific way; these were mostly genes encoding unrelated enzymes, transporters, and unknown proteins. Other genes affected MarA-mediated resistance to all antibiotics tested. These genes were acrA, acrB, and tolC (which encode the major MarA-regulated multidrug efflux pump AcrAB-TolC), crp, cyaA, hns, and pcnB (four genes involved in global regulation of gene expression), and the unknown gene damX. The last five genes affected MarA-mediated MDR by altering marA expression or MarA function specifically on acrA. These findings demonstrate that MarA-mediated MDR is regulated at multiple levels by different genes and stimuli, which makes it both complex and fine-tuned and interconnects it with global cell regulation and metabolism. Such a regulation could contribute to the adaptation and spread of MDR strains and may be targeted to treat antibiotic-resistant E. coli and related pathogens.
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309
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Murphy KF, Adams RM, Wang X, Balázsi G, Collins JJ. Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res 2010; 38:2712-26. [PMID: 20211838 PMCID: PMC2860118 DOI: 10.1093/nar/gkq091] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Synthetic gene networks can be used to control gene expression and cellular phenotypes in a variety of applications. In many instances, however, such networks can behave unreliably due to gene expression noise. Accordingly, there is a need to develop systematic means to tune gene expression noise, so that it can be suppressed in some cases and harnessed in others, e.g. in cellular differentiation to create population-wide heterogeneity. Here, we present a method for controlling noise in synthetic eukaryotic gene expression systems, utilizing reduction of noise levels by TATA box mutations and noise propagation in transcriptional cascades. Specifically, we introduce TATA box mutations into promoters driving TetR expression and show that these mutations can be used to effectively tune the noise of a target gene while decoupling it from the mean, with negligible effects on the dynamic range and basal expression. We apply mathematical and computational modeling to explain the experimentally observed effects of TATA box mutations. This work, which highlights some important aspects of noise propagation in gene regulatory cascades, has practical implications for implementing gene expression control in synthetic gene networks.
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Affiliation(s)
- Kevin F Murphy
- Department of Biomedical Engineering, Howard Hughes Medical Institute, Center for BioDynamics & Center for Advanced Biotechnology, Department of Biology, Boston University, Boston, MA 02215, USA
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310
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Davies BW, Kohanski MA, Simmons LA, Winkler JA, Collins JJ, Walker GC. Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Mol Cell 2010; 36:845-60. [PMID: 20005847 DOI: 10.1016/j.molcel.2009.11.024] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2009] [Revised: 07/13/2009] [Accepted: 08/13/2009] [Indexed: 01/18/2023]
Abstract
Hydroxyurea (HU) specifically inhibits class I ribonucleotide reductase (RNR), depleting dNTP pools and leading to replication fork arrest. Although HU inhibition of RNR is well recognized, the mechanism by which it leads to cell death remains unknown. To investigate the mechanism of HU-induced cell death, we used a systems-level approach to determine the genomic and physiological responses of E. coli to HU treatment. Our results suggest a model by which HU treatment rapidly induces a set of protective responses to manage genomic instability. Continued HU stress activates iron uptake and toxins MazF and RelE, whose activity causes the synthesis of incompletely translated proteins and stimulation of envelope stress responses. These effects alter the properties of one of the cell's terminal cytochrome oxidases, causing an increase in superoxide production. The increased superoxide production, together with the increased iron uptake, fuels the formation of hydroxyl radicals that contribute to HU-induced cell death.
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Affiliation(s)
- Bryan W Davies
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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311
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Han X, Dorsey-Oresto A, Malik M, Wang JY, Drlica K, Zhao X, Lu T. Escherichia coli genes that reduce the lethal effects of stress. BMC Microbiol 2010; 10:35. [PMID: 20128927 PMCID: PMC2824699 DOI: 10.1186/1471-2180-10-35] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 02/04/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The continuing emergence of antimicrobial resistance requires the development of new compounds and/or enhancers of existing compounds. Genes that protect against the lethal effects of antibiotic stress are potential targets of enhancers. To distinguish such genes from those involved in drug uptake and efflux, a new susceptibility screen is required. RESULTS Transposon (Tn5)-mediated mutagenesis was used to create a library of Escherichia coli mutants that was screened for hypersensitivity to the lethal action of quinolones and counter-screened to have wild-type bacteriostatic susceptibility. Mutants with this novel "hyperlethal" phenotype were found. The phenotype was transferable to other E. coli strains by P1-mediated transduction, and for a subset of the mutants the phenotype was complemented by the corresponding wild-type gene cloned into a plasmid. Thus, the inactivation of these genes was responsible for hyperlethality. Nucleotide sequence analysis identified 14 genes, mostly of unknown function, as potential factors protecting from lethal effects of stress. The 14 mutants were killed more readily than wild-type cells by mitomycin C and hydrogen peroxide; nine were also more readily killed by UV irradiation, and several exhibited increased susceptibility to killing by sodium dodecyl sulfate. No mutant was more readily killed by high temperature. CONCLUSIONS A new screening strategy identified a diverse set of E. coli genes involved in the response to lethal antimicrobial and environmental stress, with some genes being involved in the response to multiple stressors. The gene set, which differed from sets previously identified with bacteriostatic assays, provides an entry point for obtaining small-molecule enhancers that will affect multiple antimicrobial agents.
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Affiliation(s)
- Xiulin Han
- Yunnan Institute of Microbiology, Yunnan University, 52 Cui Hu Bei Lu, Kunming, Yunnan 650091, PR China
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312
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Thorenoor N, Lee JH, Lee SK, Cho SW, Kim YH, Kim KS, Lee C. Localization of the Death Effector Domain of Fas-Associated Death Domain Protein into the Membrane of Escherichia coli Induces Reactive Oxygen Species-Involved Cell Death. Biochemistry 2010; 49:1435-47. [DOI: 10.1021/bi901783s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nithyananda Thorenoor
- Life Sciences Division, Korea Institute of Science and Technology, 39-1 Hawolgok, Seongbuk, Seoul 136-791, Korea
- University of Science and Technology, 52, Eoeun, Yuseong, Daejeon 305-333, Korea
| | - Jin-Hee Lee
- Center for Neural Science, Korea Institute of Science and Technology, 39-1 Hawolgok, Seongbuk, Seoul 136-791, Korea
| | - Seong-Ki Lee
- Center for Neural Science, Korea Institute of Science and Technology, 39-1 Hawolgok, Seongbuk, Seoul 136-791, Korea
| | - Sung-Won Cho
- Center for Neural Science, Korea Institute of Science and Technology, 39-1 Hawolgok, Seongbuk, Seoul 136-791, Korea
| | - Yong-Hak Kim
- Functional Proteomics Center, Korea Institute of Science and Technology, 39-1 Hawolgok, Seongbuk, Seoul 136-791, Korea
| | - Key-Sun Kim
- Center for Neural Science, Korea Institute of Science and Technology, 39-1 Hawolgok, Seongbuk, Seoul 136-791, Korea
- University of Science and Technology, 52, Eoeun, Yuseong, Daejeon 305-333, Korea
| | - Cheolju Lee
- Life Sciences Division, Korea Institute of Science and Technology, 39-1 Hawolgok, Seongbuk, Seoul 136-791, Korea
- University of Science and Technology, 52, Eoeun, Yuseong, Daejeon 305-333, Korea
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313
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Wang X, Zhao X, Malik M, Drlica K. Contribution of reactive oxygen species to pathways of quinolone-mediated bacterial cell death. J Antimicrob Chemother 2010; 65:520-4. [PMID: 20067982 DOI: 10.1093/jac/dkp486] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Quinolone-mediated death of Escherichia coli has been proposed to occur by two pathways. One is blocked by inhibitors of protein synthesis; the other is not. It is currently unknown how these two pathways fit with the recent observation that hydroxyl radical accumulation is associated with quinolone lethality. METHODS E. coli was treated with thiourea plus 2,2'-bipyridyl to block hydroxyl radical accumulation, and the effect on quinolone lethality was measured for quinolones that distinguished the two lethal pathways: oxolinic acid requires protein synthesis to kill E. coli, while PD161144, a C-8-methoxy fluoroquinolone, does not. The lethal activity of another fluoroquinolone, moxifloxacin, was partially blocked by the presence of chloramphenicol, an inhibitor of protein synthesis. That feature made it possible to determine whether the effects of chloramphenicol and thiourea plus 2,2'-bipyridyl were additive. RESULTS Lethal activity of oxolinic acid was completely blocked by thiourea plus 2,2'-bipyridyl and by chloramphenicol. In contrast, PD161144 lethality was unaffected by these treatments. With moxifloxacin, both chloramphenicol and thiourea plus 2,2'-bipyridyl separately exhibited the same partial inhibition of quinolone lethality. No additivity in protection from moxifloxacin lethality was observed when thiourea, 2,2'-bipyridyl and chloramphenicol were combined and compared with the effect of chloramphenicol or thiourea plus 2,2'-bipyridyl used separately. CONCLUSIONS Inhibitor studies indicated that hydroxyl radical action contributes to quinolone-mediated cell death occurring via the chloramphenicol-sensitive lethal pathway but not via the chloramphenicol-insensitive pathway.
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Affiliation(s)
- Xiuhong Wang
- Public Health Research Institute, New Jersey Medical School, UMDNJ, 225 Warren Street, Newark, NJ 07103, USA
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314
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Bollenbach T, Quan S, Chait R, Kishony R. Nonoptimal microbial response to antibiotics underlies suppressive drug interactions. Cell 2009; 139:707-18. [PMID: 19914165 DOI: 10.1016/j.cell.2009.10.025] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 06/15/2009] [Accepted: 10/14/2009] [Indexed: 11/30/2022]
Abstract
Suppressive drug interactions, in which one antibiotic can actually help bacterial cells to grow faster in the presence of another, occur between protein and DNA synthesis inhibitors. Here, we show that this suppression results from nonoptimal regulation of ribosomal genes in the presence of DNA stress. Using GFP-tagged transcription reporters in Escherichia coli, we find that ribosomal genes are not directly regulated by DNA stress, leading to an imbalance between cellular DNA and protein content. To test whether ribosomal gene expression under DNA stress is nonoptimal for growth rate, we sequentially deleted up to six of the seven ribosomal RNA operons. These synthetic manipulations of ribosomal gene expression correct the protein-DNA imbalance, lead to improved survival and growth, and completely remove the suppressive drug interaction. A simple mathematical model explains the nonoptimal regulation in different nutrient environments. These results reveal the genetic mechanism underlying an important class of suppressive drug interactions.
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Affiliation(s)
- Tobias Bollenbach
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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315
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Páez PL, Becerra MC, Albesa I. Effect of the association of reduced glutathione and ciprofloxacin on the antimicrobial activity in Staphylococcus aureus. FEMS Microbiol Lett 2009; 303:101-5. [PMID: 20030722 DOI: 10.1111/j.1574-6968.2009.01867.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We report the effect of glutathione and the role of reactive oxygen species (ROS), assayed by a nitro blue tetrazolium reaction, on the antibacterial action of ciprofloxacin, gentamicin and chloramphenicol in Staphylococcus aureus 22 resistant to ciprofloxacin and gentamicin, and in S. aureus ATCC 29213 sensitive to the above three antibiotics. The association of glutathione with ciprofloxacin or gentamicin significantly reduced the value of the minimum inhibitory concentration (MIC) in resistant S. aureus 22, measured using the macrodilution method, with a concomitant increase of intracellular ROS and a decrease of extracellular ROS. However, glutathione did not induce modifications in MIC or ROS generated by chloramphenicol. Furthermore, in the sensitive S. aureus ATCC 29213, the association of glutathione with ciprofloxacin, gentamicin or chloramphenicol did not induce any significant variations of MIC or ROS. There was a correlation between the stimulus of intracellular ROS and the decrease of MIC caused by exogenous glutathione. According to the results obtained, it is possible to modify the sensitivity of resistant strains of S. aureus by the addition of exogenous glutathione.
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Affiliation(s)
- Paulina Laura Páez
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, Argentina
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316
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Dwyer DJ, Kohanski MA, Collins JJ. Role of reactive oxygen species in antibiotic action and resistance. Curr Opin Microbiol 2009; 12:482-9. [PMID: 19647477 PMCID: PMC2761529 DOI: 10.1016/j.mib.2009.06.018] [Citation(s) in RCA: 320] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 06/26/2009] [Accepted: 06/30/2009] [Indexed: 12/21/2022]
Abstract
The alarming spread of bacterial strains exhibiting resistance to current antibiotic therapies necessitates that we elucidate the specific genetic and biochemical responses underlying drug-mediated cell killing, so as to increase the efficacy of available treatments and develop new antibacterials. Recent research aimed at identifying such cellular contributions has revealed that antibiotics induce changes in metabolism that promote the formation of reactive oxygen species, which play a role in cell death. Here we discuss the relationship between drug-induced oxidative stress, the SOS response and their potential combined contribution to resistance development. Additionally, we describe ways in which these responses are being taken advantage to combat bacterial infections and arrest the rise of resistant strains.
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Affiliation(s)
- Daniel J Dwyer
- Howard Hughes Medical Institute, Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Boston University, 44 Cummington Street, Boston, MA 02215, USA.
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317
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Decorosi F, Tatti E, Mini A, Giovannetti L, Viti C. Characterization of two genes involved in chromate resistance in a Cr(VI)-hyper-resistant bacterium. Extremophiles 2009; 13:917-23. [PMID: 19768364 DOI: 10.1007/s00792-009-0279-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 08/26/2009] [Indexed: 11/30/2022]
Abstract
Mechanisms underlying chromate resistance in Cr(VI)-hyper-resistant Pseudomonas corrugata strain 28, isolated from a highly Cr(VI) polluted soil, were studied by analyzing its two Cr(VI)-sensitive mutants obtained by insertion mutagenesis. The mutants, namely Crg3 and Crg96, were characterized by the identification of disrupted genes, and by the high-throughput approach called Phenotype MicroArray (PM), which permitted the assay of 1,536 phenotypes simultaneously. Crg3 and Crg96 mutants were affected in a malic enzyme family gene and in a gene encoding for a RecG helicase, respectively. The application of PM provided a wealth of new information relating to the disrupted genes and permitted to establish that chromate resistance in P. corrugata strain 28 also depends on supply on NADPH required in repairing damage induced by chromate and on DNA integrity maintenance.
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Affiliation(s)
- Francesca Decorosi
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Florence, Italy
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318
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Heisig P. Type II topoisomerases--inhibitors, repair mechanisms and mutations. Mutagenesis 2009; 24:465-9. [PMID: 19762349 DOI: 10.1093/mutage/gep035] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Type II topoisomerases are ubiquitous enzymes that play an essential role in the control of replicative DNA synthesis and share structural and functional homology among different prokaryotic and eukaryotic organisms. Antibacterial fluoroquinolones target prokaryotic topoisomerases at concentrations 100- to 1000-fold lower than mammalian enzymes, the preferred targets of anticancer drugs such as etoposide. The mechanisms of action of both of these types of inhibitors involve the fixation of an intermediate reaction step, where the enzyme is covalently bound to an enzyme-mediated DNA double-strand break (DSB). The resulting ternary drug-enzyme-DNA complexes can then be converted to cleavage complexes that block further movement of the DNA replication fork, subsequently inducing stress responses. In haploid prokaryotic cells, stress responses include error-free and error-prone DNA damage repair pathways, such as homologous recombination and translesion synthesis, respectively. The latter can result in the acquisition of point mutations. Diploid mammalian cells are assumed to preferentially use recombination mechanisms for the repair of DSBs, an example of which, non-homologous end joining, is a major error-prone repair mechanism associated with an increased frequency of detectable small deletions, insertions and translocations. However, results obtained from safety testing of novel fluoroquinolones at high concentrations indicate that point mutations may also occur in mammalian cells. Recent data provide evidence for translesion synthesis catalysed by error-prone repair polymerases as a damage-tolerance repair mechanism of DSBs in eukaryotic cells. This paper discusses possible roles of different mechanisms for the repair of DSBs operating in both eukaryotic and prokaryotic cells that result in recombinational rearrangements, deletions/insertions as well as point mutations.
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Affiliation(s)
- Peter Heisig
- Pharmaceutical Biology and Microbiology, Department of Chemistry, University of Hamburg, Bundesstrasse 45, 20146 Hamburg, Germany.
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319
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Giannakis M, Bäckhed HK, Chen SL, Faith JJ, Wu M, Guruge JL, Engstrand L, Gordon JI. Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis. J Biol Chem 2009; 284:30383-94. [PMID: 19723631 PMCID: PMC2781593 DOI: 10.1074/jbc.m109.052738] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Helicobacter pylori infection is associated with gastric adenocarcinoma in some humans, especially those that develop an antecedent condition, chronic atrophic gastritis (ChAG). Gastric epithelial progenitors (GEPs) in transgenic gnotobiotic mice with a ChAG-like phenotype harbor intracellular collections of H. pylori. To characterize H. pylori adaptations to ChAG, we sequenced the genomes of 24 isolates obtained from 6 individuals, each sampled over a 4-year interval, as they did or did not progress from normal gastric histology to ChAG and/or adenocarcinoma. H. pylori populations within study participants were largely clonal and remarkably stable regardless of disease state. GeneChip studies of the responses of a cultured mouse gastric stem cell-like line (mGEPs) to infection with sequenced strains yielded a 695-member dataset of transcripts that are (i) differentially expressed after infection with ChAG-associated isolates, but not with a “normal” or a heat-killed ChAG isolate, and (ii) enriched in genes and gene functions associated with tumorigenesis in general and gastric carcinogenesis in specific cases. Transcriptional profiling of a ChAG strain during mGEP infection disclosed a set of responses, including up-regulation of hopZ, an adhesin belonging to a family of outer membrane proteins. Expression profiles of wild-type and ΔhopZ strains revealed a number of pH-regulated genes modulated by HopZ, including hopP, which binds sialylated glycans produced by GEPs in vivo. Genetic inactivation of hopZ produced a fitness defect in the stomachs of gnotobiotic transgenic mice but not in wild-type littermates. This study illustrates an approach for identifying GEP responses specific to ChAG-associated H. Pylori strains and bacterial genes important for survival in a model of the ChAG gastric ecosystem.
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Affiliation(s)
- Marios Giannakis
- Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
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320
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Malmström J, Beck M, Schmidt A, Lange V, Deutsch EW, Aebersold R. Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 2009; 460:762-5. [PMID: 19606093 PMCID: PMC2723184 DOI: 10.1038/nature08184] [Citation(s) in RCA: 330] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 05/29/2009] [Indexed: 12/01/2022]
Abstract
Mass-spectrometry-based methods for relative proteome quantification have broadly affected life science research. However, important research directions, particularly those involving mathematical modelling and simulation of biological processes, also critically depend on absolutely quantitative data--that is, knowledge of the concentration of the expressed proteins as a function of cellular state. Until now, absolute protein concentration measurements of a considerable fraction of the proteome (73%) have only been derived from genetically altered Saccharomyces cerevisiae cells, a technique that is not directly portable from yeast to other species. Here we present a mass-spectrometry-based strategy to determine the absolute quantity, that is, the average number of protein copies per cell in a cell population, for a large fraction of the proteome in genetically unperturbed cells. Applying the technology to the human pathogen Leptospira interrogans, a spirochete responsible for leptospirosis, we generated an absolute protein abundance scale for 83% of the mass-spectrometry-detectable proteome, from cells at different states. Taking advantage of the unique cellular dimensions of L. interrogans, we used cryo-electron tomography morphological measurements to verify, at the single-cell level, the average absolute abundance values of selected proteins determined by mass spectrometry on a population of cells. Because the strategy is relatively fast and applicable to any cell type, we expect that it will become a cornerstone of quantitative biology and systems biology.
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Affiliation(s)
- Johan Malmström
- Institute of Molecular Systems Biology, ETH Zurich (Swiss Federal Institute of Technology), Wolfgang Pauli-Str. 16, CH-8093 Zurich, Switzerland
| | - Martin Beck
- Institute of Molecular Systems Biology, ETH Zurich (Swiss Federal Institute of Technology), Wolfgang Pauli-Str. 16, CH-8093 Zurich, Switzerland
| | - Alexander Schmidt
- Institute of Molecular Systems Biology, ETH Zurich (Swiss Federal Institute of Technology), Wolfgang Pauli-Str. 16, CH-8093 Zurich, Switzerland
- Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
| | - Vinzenz Lange
- Institute of Molecular Systems Biology, ETH Zurich (Swiss Federal Institute of Technology), Wolfgang Pauli-Str. 16, CH-8093 Zurich, Switzerland
- Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
| | - Eric W. Deutsch
- Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich (Swiss Federal Institute of Technology), Wolfgang Pauli-Str. 16, CH-8093 Zurich, Switzerland
- Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA
- Faculty of Science, University of Zurich, Switzerland
- Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
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321
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Superoxide protects Escherichia coli from bleomycin mediated lethality. J Inorg Biochem 2009; 103:1273-7. [PMID: 19679357 DOI: 10.1016/j.jinorgbio.2009.07.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 07/01/2009] [Accepted: 07/13/2009] [Indexed: 11/23/2022]
Abstract
Superoxide and its products, especially hydroxyl radical, were recently proposed to be instrumental in cell death following treatment with a wide range of antimicrobials. Surprisingly, bleomycin lethality to Escherichia coli was ameliorated by a genetic deficiency of superoxide dismutase or by furnishing the superoxide generator plumbagin. Rescue by plumbagin was similar in strains containing or lacking recA or with inactive, inducible, or constitutive soxRS regulons. Thus, superoxide interferes with bleomycin cytotoxicity in ways not readily explained by genetic pathways expected to protect from oxidative damage.
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322
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Nanduri B, Shack LA, Burgess SC, Lawrence ML. The transcriptional response of Pasteurella multocida to three classes of antibiotics. BMC Genomics 2009; 10 Suppl 2:S4. [PMID: 19607655 PMCID: PMC2966327 DOI: 10.1186/1471-2164-10-s2-s4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pasteurella multocida is a gram-negative bacterial pathogen that has a broad host range. One of the diseases it causes is fowl cholera in poultry. The availability of the genome sequence of avian P. multocida isolate Pm70 enables the application of functional genomics for observing global gene expression in response to a given stimulus. We studied the effects of three classes of antibiotics on the P. multocida transcriptome using custom oligonucleotide microarrays from NimbleGen Systems. Hybridizations were conducted with RNA isolated from three independent cultures of Pm70 grown in the presence or absence of sub-minimum inhibitory concentration (sub-MIC) of antibiotics. Differentially expressed (DE) genes were identified by ANOVA and Dunnett's test. Biological modeling of the differentially expressed genes (DE) was conducted based on Clusters of Orthologous (COG) groups and network analysis in Pathway Studio. RESULTS The three antibiotics used in this study, amoxicillin, chlortetracycline, and enrofloxacin, collectively influenced transcription of 25% of the P. multocida Pm70 genome. Some DE genes identified were common to more than one antibiotic. The overall transcription signatures of the three antibiotics differed at the COG level of the analysis. Network analysis identified differences in the SOS response of P. multocida in response to the antibiotics. CONCLUSION This is the first report of the transcriptional response of an avian strain of P. multocida to sub-lethal concentrations of three different classes of antibiotics. We identified common adaptive responses of P. multocida to antibiotic stress. The observed changes in gene expression of known and putative P. multocida virulence factors establish the molecular basis for the therapeutic efficacy of sub-MICs. Our network analysis demonstrates the feasibility and limitations of applying systems modeling to high throughput datasets in 'non-model' bacteria.
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Affiliation(s)
- Bindu Nanduri
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.
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323
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At the crossroads of bacterial metabolism and virulence factor synthesis in Staphylococci. Microbiol Mol Biol Rev 2009; 73:233-48. [PMID: 19487727 DOI: 10.1128/mmbr.00005-09] [Citation(s) in RCA: 281] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacteria live in environments that are subject to rapid changes in the availability of the nutrients that are necessary to provide energy and biosynthetic intermediates for the synthesis of macromolecules. Consequently, bacterial survival depends on the ability of bacteria to regulate the expression of genes coding for enzymes required for growth in the altered environment. In pathogenic bacteria, adaptation to an altered environment often includes activating the transcription of virulence genes; hence, many virulence genes are regulated by environmental and nutritional signals. Consistent with this observation, the regulation of most, if not all, virulence determinants in staphylococci is mediated by environmental and nutritional signals. Some of these external signals can be directly transduced into a regulatory response by two-component regulators such as SrrAB; however, other external signals require transduction into intracellular signals. Many of the external environmental and nutritional signals that regulate virulence determinant expression can also alter bacterial metabolic status (e.g., iron limitation). Altering the metabolic status results in the transduction of external signals into intracellular metabolic signals that can be "sensed" by regulatory proteins (e.g., CodY, Rex, and GlnR). This review uses information derived primarily using Bacillus subtilis and Escherichia coli to articulate how gram-positive pathogens, with emphasis on Staphylococcus aureus and Staphylococcus epidermidis, regulate virulence determinant expression in response to a changing environment.
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324
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Delineating bacteriostatic and bactericidal targets in mycobacteria using IPTG inducible antisense expression. PLoS One 2009; 4:e5923. [PMID: 19526063 PMCID: PMC2691988 DOI: 10.1371/journal.pone.0005923] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 04/16/2009] [Indexed: 02/02/2023] Open
Abstract
In order to identify novel high value antibacterial targets it is desirable to delineate whether the inactivation of the target enzyme will lead to bacterial death or stasis. This knowledge is particularly important in slow growing organisms, like mycobacteria, where most of the viable anti-tubercular agents are bactericidal. A bactericidal target can be identified through the conditional deletion or inactivation of the target gene at a relatively high cell number and subsequently following the time course of survival for the bacteria. A simple protocol to execute conditional inactivation of a gene is by antisense expression. We have developed a mycobacteria specific IPTG inducible vector system and monitored the effect of antisense inhibition of several known essential genes in mycobacteria by following their survival kinetics. By this method, we could differentiate between genes whose down regulation lead to bacteriostatic or bactericidal effect. Targets for standard anti-tubercular drugs like inhA for isoniazid, rpoB and C for rifampicin, and gyr A/B for flouroquinolones were shown to be bactericidal. In contrast targets like FtsZ behaved in a bacteriostatic manner. Induction of antisense expression in embB and ribosomal RNA genes, viz., rplJ and rpsL showed only a marginal growth inhibition. The specificity of the antisense inhibition was conclusively shown in the case of auxotrophic gene ilvB. The bactericidal activity following antisense expression of ilvB was completely reversed when the growth media was supplemented with the isoleucine, leucine, valine and pantothenate. Additionally, under these conditions the expression of several genes in branched chain amino acid pathway was severely suppressed indicating targeted gene inactivation.
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325
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Hydroxyl radicals are involved in cell killing by the bacterial topoisomerase I cleavage complex. J Bacteriol 2009; 191:5315-9. [PMID: 19525344 DOI: 10.1128/jb.00559-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli expressing SOS-inducing mutant topoisomerase I was utilized to demonstrate that covalent protein-DNA complex accumulation results in oxidative damage. Hydroxyl radicals were detected following mutant topoisomerase induction. The presence of the Fe(2+) chelator 2,2'-dipyridyl and an iscS mutation affecting Fe-S cluster formation protect against topoisomerase I cleavage complex-mediated cell killing.
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326
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Mukherjee P, Sureka K, Datta P, Hossain T, Barik S, Das KP, Kundu M, Basu J. Novel role of Wag31 in protection of mycobacteria under oxidative stress. Mol Microbiol 2009; 73:103-19. [PMID: 19496931 DOI: 10.1111/j.1365-2958.2009.06750.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Wag31 of Mycobacterium tuberculosis belongs to the DivIVA family of proteins known to regulate cell morphology in Gram-positive bacteria. Here we demonstrate an unrecognized, novel role of Wag31 in oxidatively stressed mycobacteria. We report the cleavage of penicillin-binding protein 3 (PBP3) by the intramembrane metalloprotease Rv2869c (MSMEG_2579) in oxidatively stressed cells. Amino acids (102)A and (103)A of PBP3 are required for Rv2869c-mediated cleavage. Wag31(MTB), by virtue of its interaction with PBP3 through amino acid residues (46)NSD(48), protects it from oxidative stress-induced cleavage. PBP3 undergoes cleavage in Mycobacterium smegmatis (strain PM2) harbouring wag31(Delta(46)NSD(48)) instead of the wild type, with concomitant reduction in ability to withstand oxidative stress. Overexpression of Wag31(Delta(46)NSD(48)) attenuates the survival of M. tuberculosis in macrophages with concomitant cleavage of PBP3, and renders the organism more susceptible towards hydrogen peroxide as well as drugs which generate reactive oxygen species, namely isoniazid and ofloxacin. We propose that targeting Wag31 could enhance the activity of mycobactericidal drugs which are known to generate reactive oxygen species.
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Affiliation(s)
- Partha Mukherjee
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra, Road, Kolkata 700009, India
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327
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Fernández-Reyes M, Rodríguez-Falcón M, Chiva C, Pachón J, Andreu D, Rivas L. The cost of resistance to colistin in Acinetobacter baumannii: a proteomic perspective. Proteomics 2009; 9:1632-45. [PMID: 19253303 DOI: 10.1002/pmic.200800434] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Colistin resistance in Acinetobacter baumannii, a pathogen of clinical concern, was induced in the susceptible strain ATCC 19606 by growth under increasing pressure of the antibiotic, the only drug universally active against multi-resistant clinical strains. In 2-D difference gel electrophoresis (DIGE) experiments, 35 proteins with differences in expression between both phenotypes were identified, most of them appearing as down regulated in the colistin-resistant strain. These include outer membrane (OM) proteins, chaperones, protein biosynthesis factors, and metabolic enzymes, all suggesting substantial loss of biological fitness in the resistant phenotype, as substantiated by complementary experiments in the absence of colistin. Results shed light on the scarcity of widespread clinical outbreaks for resistant phenotypes.
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328
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Increased antibiotic resistance of Escherichia coli in mature biofilms. Appl Environ Microbiol 2009; 75:4093-100. [PMID: 19376922 DOI: 10.1128/aem.02949-08] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilms are considered to be highly resistant to antimicrobial agents. Several mechanisms have been proposed to explain this high resistance of biofilms, including restricted penetration of antimicrobial agents into biofilms, slow growth owing to nutrient limitation, expression of genes involved in the general stress response, and emergence of a biofilm-specific phenotype. However, since combinations of these factors are involved in most biofilm studies, it is still difficult to fully understand the mechanisms of biofilm resistance to antibiotics. In this study, the antibiotic susceptibility of Escherichia coli cells in biofilms was investigated with exclusion of the effects of the restricted penetration of antimicrobial agents into biofilms and the slow growth owing to nutrient limitation. Three different antibiotics, ampicillin (100 microg/ml), kanamycin (25 microg/ml), and ofloxacin (10 microg/ml), were applied directly to cells in the deeper layers of mature biofilms that developed in flow cells after removal of the surface layers of the biofilms. The results of the antibiotic treatment analyses revealed that ofloxacin and kanamycin were effective against biofilm cells, whereas ampicillin did not kill the cells, resulting in regrowth of the biofilm after the ampicillin treatment was discontinued. LIVE/DEAD staining revealed that a small fraction of resistant cells emerged in the deeper layers of the mature biofilms and that these cells were still alive even after 24 h of ampicillin treatment. Furthermore, to determine which genes in the biofilm cells are induced, allowing increased resistance to ampicillin, global gene expression was analyzed at different stages of biofilm formation, the attachment, colony formation, and maturation stages. The results showed that significant changes in gene expression occurred during biofilm formation, which were partly induced by rpoS expression. Based on the experimental data, it is likely that the observed resistance of biofilms can be attributed to formation of ampicillin-resistant subpopulations in the deeper layers of mature biofilms but not in young colony biofilms and that the production and resistance of the subpopulations were aided by biofilm-specific phenotypes, like slow growth and induction of rpoS-mediated stress responses.
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329
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Tamayo M, Santiso R, Gosalvez J, Bou G, Fernández JL. Rapid assessment of the effect of ciprofloxacin on chromosomal DNA from Escherichia coli using an in situ DNA fragmentation assay. BMC Microbiol 2009; 9:69. [PMID: 19364397 PMCID: PMC2670838 DOI: 10.1186/1471-2180-9-69] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Accepted: 04/13/2009] [Indexed: 12/29/2022] Open
Abstract
Background Fluoroquinolones are extensively used antibiotics that induce DNA double-strand breaks (DSBs) by trapping DNA gyrase and topoisomerase IV on DNA. This effect is usually evaluated using biochemical or molecular procedures, but these are not effective at the single-cell level. We assessed ciprofloxacin (CIP)-induced chromosomal DNA breakage in single-cell Escherichia coli by direct visualization of the DNA fragments that diffused from the nucleoid obtained after bacterial lysis in an agarose microgel on a slide. Results Exposing the E. coli strain TG1 to CIP starting at a minimum inhibitory concentration (MIC) of 0.012 μg/ml and at increasing doses for 40 min increased the DNA fragmentation progressively. DNA damage started to be detectable at the MIC dose. At a dose of 1 μg/ml of CIP, DNA damage was visualized clearly immediately after processing, and the DNA fragmentation increased progressively with the antibiotic incubation time. The level of DNA damage was much higher when the bacteria were taken from liquid LB broth than from solid LB agar. CIP treatment produced a progressively slower rate of DNA damage in bacteria in the stationary phase than in the exponentially growing phase. Removing the antibiotic after the 40 min incubation resulted in progressive DSB repair activity with time. The magnitude of DNA repair was inversely related to CIP dose and was noticeable after incubation with CIP at 0.1 μg/ml but scarce after 10 μg/ml. The repair activity was not strictly related to viability. Four E. coli strains with identified mechanisms of reduced sensitivity to CIP were assessed using this procedure and produced DNA fragmentation levels that were inversely related to MIC dose, except those with very high MIC dose. Conclusion This procedure for determining DNA fragmentation is a simple and rapid test for studying and evaluating the effect of quinolones.
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Affiliation(s)
- María Tamayo
- INIBIC-Complejo Hospitalario Universitario A Coruña, Unidad de Genética, A Coruña, Spain.
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330
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Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc Natl Acad Sci U S A 2009; 106:4629-34. [PMID: 19255432 DOI: 10.1073/pnas.0800442106] [Citation(s) in RCA: 346] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial drug development is increasingly lagging behind the evolution of antibiotic resistance, and as a result, there is a pressing need for new antibacterial therapies that can be readily designed and implemented. In this work, we engineered bacteriophage to overexpress proteins and attack gene networks that are not directly targeted by antibiotics. We show that suppressing the SOS network in Escherichia coli with engineered bacteriophage enhances killing by quinolones by several orders of magnitude in vitro and significantly increases survival of infected mice in vivo. In addition, we demonstrate that engineered bacteriophage can enhance the killing of antibiotic-resistant bacteria, persister cells, and biofilm cells, reduce the number of antibiotic-resistant bacteria that arise from an antibiotic-treated population, and act as a strong adjuvant for other bactericidal antibiotics (e.g., aminoglycosides and beta-lactams). Furthermore, we show that engineering bacteriophage to target non-SOS gene networks and to overexpress multiple factors also can produce effective antibiotic adjuvants. This work establishes a synthetic biology platform for the rapid translation and integration of identified targets into effective antibiotic adjuvants.
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331
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Contribution of oxidative damage to antimicrobial lethality. Antimicrob Agents Chemother 2009; 53:1395-402. [PMID: 19223646 DOI: 10.1128/aac.01087-08] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A potential pathway linking hydroxyl radicals to antimicrobial lethality was examined by using mutational and chemical perturbations of Escherichia coli. Deficiencies of sodA or sodB had no effect on norfloxacin lethality; however, the absence of both genes together reduced lethal activity, consistent with rapid conversion of excessive superoxide to hydrogen peroxide contributing to quinolone lethality. Norfloxacin was more lethal with a mutant deficient in katG than with its isogenic parent, suggesting that detoxification of peroxide to water normally reduces quinolone lethality. An iron chelator (bipyridyl) and a hydroxyl radical scavenger (thiourea) reduced the lethal activity of norfloxacin, indicating that norfloxacin-stimulated accumulation of peroxide affects lethal activity via hydroxyl radicals generated through the Fenton reaction. Ampicillin and kanamycin, antibacterials unrelated to fluoroquinolones, displayed behavior similar to that of norfloxacin except that these two agents showed hyperlethality with an ahpC (alkyl hydroperoxide reductase) mutant rather than with a katG mutant. Collectively, these data are consistent with antimicrobial stress increasing the production of superoxide, which then undergoes dismutation to peroxide, from which a highly toxic hydroxyl radical is generated. Hydroxyl radicals then enhance antimicrobial lethality, as suggested by earlier work. Such findings indicate that oxidative stress networks may provide targets for antimicrobial potentiation.
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332
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Construction of a functional network for common DNA damage responses in Escherichia coli. Genomics 2009; 93:514-24. [PMID: 19232389 DOI: 10.1016/j.ygeno.2009.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 01/15/2009] [Accepted: 01/31/2009] [Indexed: 11/24/2022]
Abstract
In this study, we aim to identify a common, general mode of toxic action in Escherichia coli when experiencing DNA damage, irrespective of the agents used. We conducted or collected 69 microarray data from seven different DNA damaging agents. In a quantitative manner, we constructed a probable DNA damage stress network, entitled the 'Functional Linked Network (FLN)', which consists of 399 significantly perturbed genes and the 1283 interactions among them. The SOS response related genes (LexA modules) were found to be dominantly activated by DNA damage, irrespective of the agents. Several minor, plausible modules were also implicated in this network, and appear to be related with the metabolic inhibition response to DNA damage or mediate the induction of SOS response. This systems and comparison approach across a variety of genotoxic agents may serve as a starting point to specify some of the unknown and common features of DNA damage responses in bacteria.
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333
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Hongsthong A, Sirijuntarut M, Prommeenate P, Lertladaluck K, Porkaew K, Cheevadhanarak S, Tanticharoen M. Proteome analysis at the subcellular level of the cyanobacterium Spirulina platensis in response to low-temperature stress conditions. FEMS Microbiol Lett 2009; 288:92-101. [PMID: 18764876 DOI: 10.1111/j.1574-6968.2008.01330.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The present study addresses the differential expression of Spirulina platensis proteins detected during cold-induced stress, analyzed at the subcellular level. In performing differential expression analysis, the results revealed upregulated proteins in every subcellular fraction, including two-component response systems, DNA repair, molecular chaperones, stress-induced proteins and proteins involved in other biological processes such as secretion systems and nitrogen assimilation. The chlorophyll biosynthetic proteins, protochlorophyllide oxidoreductase and ChlI, had unique expression patterns as detected in the thylakoid membrane; the levels of these proteins immediately decreased during the first 45 min of low-temperature exposure. In contrast, their expression levels significantly increased after low-temperature exposure, indicating the relevance of the chlorophyll biosynthesis in Spirulina in response to low-temperature stress in the light condition. In addition, this is the first report in which genome-based protein identification in S. platensis by peptide mass fingerprinting was performed using the database derived from the unpublished Spirulina genome sequence.
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334
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Palecková P, Bobek J, Mikulík K. tmRNA of Streptomyces collinus and Streptomyces griseus during the growth and in the presence of antibiotics. Microb Biotechnol 2009; 2:114-22. [PMID: 21261886 PMCID: PMC3815426 DOI: 10.1111/j.1751-7915.2008.00066.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Streptomycetes are soil microorganisms with the potential to produce a broad spectrum of secondary metabolities. The production of antibiotics is accompanied by a decrease in protein synthesis, which raises the question of how these bacteria survived the transition from the primary to the secondary metabolism. Translating ribosomes incapable to properly elongate or terminate polypeptide chain activate bacterial trans‐translation system. Abundance and stability of the tmRNA during growth of Streptomyces collinus and Streptomyces griseus producing kirromycin and streptomycin, respectively, was analysed. The level of tmRNA is mostly proportional to the activity of the translational system. We demonstrate that the addition of sub‐inhibitory concentrations of produced antibiotics to the cultures from the beginning of the exponential phase of growth leads to an increase in tmRNA levels and to an incorporation of amino acids into the tag‐peptides at trans‐translation of stalled ribosomes. These findings suggest that produced antibiotics induce tmRNA that facilitate reactivation of stalled complex of ribosomes and maintain viability. The effect of antibiotics that inhibit the cell‐wall turnover, DNA, RNA or protein synthesis on the level of tmRNA was examined. Antibiotics interfering with ribosomal target sites are more effective at stimulation of the tmRNA level in streptomycetes examined than those affecting the synthesis of DNA, RNA or the cell wall.
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Affiliation(s)
- Petra Palecková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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335
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Drlica K, Hiasa H, Kerns R, Malik M, Mustaev A, Zhao X. Quinolones: action and resistance updated. Curr Top Med Chem 2009; 9:981-98. [PMID: 19747119 PMCID: PMC3182077 DOI: 10.2174/156802609789630947] [Citation(s) in RCA: 235] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 07/30/2009] [Indexed: 11/22/2022]
Abstract
The quinolones trap DNA gyrase and DNA topoisomerase IV on DNA as complexes in which the DNA is broken but constrained by protein. Early studies suggested that drug binding occurs largely along helix-4 of the GyrA (gyrase) and ParC (topoisomerase IV) proteins. However, recent X-ray crystallography shows drug intercalating between the -1 and +1 nucleotides of cut DNA, with only one end of the drug extending to helix-4. These two models may reflect distinct structural steps in complex formation. A consequence of drug-enzyme-DNA complex formation is reversible inhibition of DNA replication; cell death arises from subsequent events in which bacterial chromosomes are fragmented through two poorly understood pathways. In one pathway, chromosome fragmentation stimulates excessive accumulation of highly toxic reactive oxygen species that are responsible for cell death. Quinolone resistance arises stepwise through selective amplification of mutants when drug concentrations are above the MIC and below the MPC, as observed with static agar plate assays, dynamic in vitro systems, and experimental infection of rabbits. The gap between MIC and MPC can be narrowed by compound design that should restrict the emergence of resistance. Resistance is likely to become increasingly important, since three types of plasmid-borne resistance have been reported.
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Affiliation(s)
- Karl Drlica
- Public Health Research Institute, New Jersey Medical School, UMDNJ, 225 Warren Street, Newark, NJ 07103, USA.
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336
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Viti C, Decorosi F, Mini A, Tatti E, Giovannetti L. Involvement of the oscA gene in the sulphur starvation response and in Cr(VI) resistance in Pseudomonas corrugata 28. Microbiology (Reading) 2009; 155:95-105. [DOI: 10.1099/mic.0.021873-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas corrugata28 is a Cr(VI)-hyper-resistant bacterium. A Cr(VI)-sensitive mutant was obtained by insertional mutagenesis using EZ-Tn5<R6Kγori/KAN-2>Tnp. The mutant strain was impaired in a gene, here namedoscA(organosulphurcompounds), which encoded a hypothetical small protein of unknown function. The gene was located upstream of a gene cluster that encodes the components of the sulphate ABC transporter, and it formed a transcriptional unit withsbp, which encoded the periplasmic binding protein of the transporter. TheoscA–sbptranscriptional unit was strongly and quickly overexpressed after chromate exposure, suggesting the involvement ofoscAin chromate resistance, which was further confirmed by means of a complementation experiment. Phenotype MicroArray (PM) analysis made it possible to assay 1536 phenotypes and also indicated that theoscAgene was involved in the utilization of organosulphur compounds as a sole source of sulphur. This is believed to be the first evidence thatoscAplays a role in activating a sulphur starvation response, which is required to cope with oxidative stress induced by chromate.
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Affiliation(s)
- Carlo Viti
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Francesca Decorosi
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Annalisa Mini
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Enrico Tatti
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Luciana Giovannetti
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
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Pisani F, Italiano F, de Leo F, Gallerani R, Rinalducci S, Zolla L, Agostiano A, Ceci L, Trotta M. Soluble proteome investigation of cobalt effect on the carotenoidless mutant ofRhodobacter sphaeroides. J Appl Microbiol 2009; 106:338-49. [DOI: 10.1111/j.1365-2672.2008.04007.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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338
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Kohanski MA, Dwyer DJ, Wierzbowski J, Cottarel G, Collins JJ. Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell 2008; 135:679-90. [PMID: 19013277 DOI: 10.1016/j.cell.2008.09.038] [Citation(s) in RCA: 403] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Revised: 07/14/2008] [Accepted: 09/15/2008] [Indexed: 12/24/2022]
Abstract
Aminoglycoside antibiotics, such as gentamicin and kanamycin, directly target the ribosome, yet the mechanisms by which these bactericidal drugs induce cell death are not fully understood. Recently, oxidative stress has been implicated as one of the mechanisms whereby bactericidal antibiotics kill bacteria. Here, we use systems-level approaches and phenotypic analyses to provide insight into the pathway whereby aminoglycosides ultimately trigger hydroxyl radical formation. We show, by disabling systems that facilitate membrane protein traffic, that mistranslation and misfolding of membrane proteins are central to aminoglycoside-induced oxidative stress and cell death. Signaling through the envelope stress-response two-component system is found to be a key player in this process, and the redox-responsive two-component system is shown to have an associated role. Additionally, we show that these two-component systems play a general role in bactericidal antibiotic-mediated oxidative stress and cell death, expanding our understanding of the common mechanism of killing induced by bactericidal antibiotics.
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Affiliation(s)
- Michael A Kohanski
- Department of Biomedical Engineering, Center for BioDynamics, and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
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339
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Kolodkin-Gal I, Sat B, Keshet A, Kulka HE. The communication factor EDF and the toxin-antitoxin module mazEF determine the mode of action of antibiotics. PLoS Biol 2008; 6:e319. [PMID: 19090622 PMCID: PMC2602726 DOI: 10.1371/journal.pbio.0060319] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 11/07/2008] [Indexed: 12/03/2022] Open
Abstract
It was recently reported that the production of Reactive Oxygen Species (ROS) is a common mechanism of cell death induced by bactericidal antibiotics. Here we show that triggering the Escherichia coli chromosomal toxin-antitoxin system mazEF is an additional determinant in the mode of action of some antibiotics. We treated E. coli cultures by antibiotics belonging to one of two groups: (i) Inhibitors of transcription and/or translation, and (ii) DNA damaging. We found that antibiotics of both groups caused: (i) mazEF-mediated cell death, and (ii) the production of ROS through MazF action. However, only antibiotics of the first group caused mazEF-mediated cell death that is ROS-dependent, whereas those of the second group caused mazEF-mediated cell death by an ROS-independent pathway. Furthermore, our results showed that the mode of action of antibiotics was determined by the ability of E. coli cells to communicate through the signaling molecule Extracellular Death Factor (EDF) participating in mazEF induction.
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340
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Known Bioactive Small Molecules Probe the Function of a Widely Conserved but Enigmatic Bacterial ATPase, YjeE. ACTA ACUST UNITED AC 2008; 15:1287-95. [DOI: 10.1016/j.chembiol.2008.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 09/30/2008] [Accepted: 10/14/2008] [Indexed: 11/22/2022]
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341
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Tse-Dinh YC. Bacterial topoisomerase I as a target for discovery of antibacterial compounds. Nucleic Acids Res 2008; 37:731-7. [PMID: 19042977 PMCID: PMC2647297 DOI: 10.1093/nar/gkn936] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacterial topoisomerase I is a potential target for discovery of new antibacterial compounds. Mutant topoisomerases identified by SOS induction screening demonstrated that accumulation of the DNA cleavage complex formed by type IA topoisomerases is bactericidal. Characterization of these mutants of Yersinia pestis and Escherichia coli topoisomerase I showed that DNA religation can be inhibited while maintaining DNA cleavage activity by decreasing the binding affinity of Mg(II) ions. This can be accomplished either by mutation of the TOPRIM motif involved directly in Mg(II) binding or by altering the charge distribution of the active site region. Besides being used to elucidate the key elements for the control of the cleavage-religation equilibrium, the SOS-inducing mutants of Y. pestis and E. coli topoisomerase I have also been utilized as models to study the cellular response following the accumulation of bacterial topoisomerase I cleavage complex. Bacterial topoisomerase I is required for preventing hypernegative supercoiling of DNA during transcription. It plays an important role in transcription of stress genes during bacterial stress response. Topoisomerase I targeting poisons may be particularly effective when the bacterial pathogen is responding to host defense, or in the presence of other antibiotics that induce the bacterial stress response.
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Affiliation(s)
- Yuk-Ching Tse-Dinh
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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342
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Complex ciprofloxacin resistome revealed by screening a Pseudomonas aeruginosa mutant library for altered susceptibility. Antimicrob Agents Chemother 2008; 52:4486-91. [PMID: 18824609 DOI: 10.1128/aac.00222-08] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa offers substantial therapeutic challenges due to its high intrinsic resistance to many antibiotics and its propensity to develop mutational and/or adaptive resistance. The PA14 comprehensive mutant library was screened for mutants exhibiting either two- to eightfold increased susceptibilities (revealing genes involved in intrinsic resistance) or decreased susceptibilities (mutational resistance) to the fluoroquinolone ciprofloxacin. Thirty-five and 79 mutants with increased and decreased susceptibilities, respectively, were identified, as confirmed by broth dilution.
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343
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Cosgrove EJ, Zhou Y, Gardner TS, Kolaczyk ED. Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia. ACTA ACUST UNITED AC 2008; 24:2482-90. [PMID: 18779235 DOI: 10.1093/bioinformatics/btn476] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION DNA microarrays are routinely applied to study diseased or drug-treated cell populations. A critical challenge is distinguishing the genes directly affected by these perturbations from the hundreds of genes that are indirectly affected. Here, we developed a sparse simultaneous equation model (SSEM) of mRNA expression data and applied Lasso regression to estimate the model parameters, thus constructing a network model of gene interaction effects. This inferred network model was then used to filter data from a given experimental condition of interest and predict the genes directly targeted by that perturbation. RESULTS Our proposed SSEM-Lasso method demonstrated substantial improvement in sensitivity compared with other tested methods for predicting the targets of perturbations in both simulated datasets and microarray compendia. In simulated data, for two different network types, and over a wide range of signal-to-noise ratios, our algorithm demonstrated a 167% increase in sensitivity on average for the top 100 ranked genes, compared with the next best method. Our method also performed well in identifying targets of genetic perturbations in microarray compendia, with up to a 24% improvement in sensitivity on average for the top 100 ranked genes. The overall performance of our network-filtering method shows promise for identifying the direct targets of genetic dysregulation in cancer and disease from expression profiles. AVAILABILITY Microarray data are available at the Many Microbe Microarrays Database (M3D, http://m3d.bu.edu). Algorithm scripts are available at the Gardner Lab website (http://gardnerlab.bu.edu/SSEMLasso).
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Affiliation(s)
- Elissa J Cosgrove
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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344
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Potts RG, Lujan SA, Redinbo MR. Winning the asymmetric war: new strategies for combating antibacterial resistance. Future Microbiol 2008; 3:119-23. [PMID: 18366330 DOI: 10.2217/17460913.3.2.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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345
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346
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Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA, Collins JJ. A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics. Cell 2007; 130:797-810. [PMID: 17803904 DOI: 10.1016/j.cell.2007.06.049] [Citation(s) in RCA: 1984] [Impact Index Per Article: 116.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Revised: 05/18/2007] [Accepted: 06/27/2007] [Indexed: 11/30/2022]
Abstract
Antibiotic mode-of-action classification is based upon drug-target interaction and whether the resultant inhibition of cellular function is lethal to bacteria. Here we show that the three major classes of bactericidal antibiotics, regardless of drug-target interaction, stimulate the production of highly deleterious hydroxyl radicals in Gram-negative and Gram-positive bacteria, which ultimately contribute to cell death. We also show, in contrast, that bacteriostatic drugs do not produce hydroxyl radicals. We demonstrate that the mechanism of hydroxyl radical formation induced by bactericidal antibiotics is the end product of an oxidative damage cellular death pathway involving the tricarboxylic acid cycle, a transient depletion of NADH, destabilization of iron-sulfur clusters, and stimulation of the Fenton reaction. Our results suggest that all three major classes of bactericidal drugs can be potentiated by targeting bacterial systems that remediate hydroxyl radical damage, including proteins involved in triggering the DNA damage response, e.g., RecA.
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Affiliation(s)
- Michael A Kohanski
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
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