101
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Lütticke C, Hauske P, Lewandrowski U, Sickmann A, Kaiser M, Ehrmann M. E. coli LoiP (YggG), a metalloprotease hydrolyzing Phe-Phe bonds. MOLECULAR BIOSYSTEMS 2012; 8:1775-82. [PMID: 22491786 DOI: 10.1039/c2mb05506f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
YggG is a conserved lipoprotein localized to the outer membrane of Gram negative bacteria. Even though the expressed open reading frame has been identified previously, the Escherichia coli protein remained uncharacterized. We report that YggG of E. coli is a metalloprotease that cleaves its targets preferentially between Phe-Phe residues. Since the yggG promoter is upregulated when bacteria are subjected to media of low osmolarity, YggG was named LoiP (low osmolarity induced protease). LoiP has an intramolecular disulfide (S-S) bond that is formed even in the absence of the periplasmic oxido-reductase DsbA and proper membrane localization of LoiP can depend on another putative metalloprotease, YfgC.
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Affiliation(s)
- Christiane Lütticke
- Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
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102
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Sandalakis V, Psaroulaki A, De Bock PJ, Christidou A, Gevaert K, Tsiotis G, Tselentis Y. Investigation of rifampicin resistance mechanisms in Brucella abortus using MS-driven comparative proteomics. J Proteome Res 2012; 11:2374-85. [PMID: 22360387 DOI: 10.1021/pr201122w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Mutations in the rpoB gene have already been shown to contribute to rifampicin resistance in many bacterial strains including Brucella species. Resistance against this antibiotic easily occurs and resistant strains have already been detected in human samples. We here present the first research project that combines proteomic, genomic, and microbiological analysis to investigate rifampicin resistance in an in vitro developed rifampicin resistant strain of Brucella abortus 2308. In silico analysis of the rpoB gene was performed and several antibiotics used in the therapy of Brucellosis were used for cross resistance testing. The proteomic profiles were examined and compared using MS-driven comparative proteomics. The resistant strain contained an already described mutation in the rpoB gene, V154F. A correlation between rifampicin resistance and reduced susceptibility on trimethoprim/sulfamethoxazole was detected by E-test and supported by the proteomics results. Using 12 836 MS/MS spectra we identified 6753 peptides corresponding to 456 proteins. The resistant strain presented 39 differentially regulated proteins most of which are involved in various metabolic pathways. Results from our research suggest that rifampicin resistance in Brucella mostly involves mutations in the rpoB gene, excitation of several metabolic processes, and perhaps the use of the already existing secretion mechanisms at a more efficient level.
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Affiliation(s)
- Vassilios Sandalakis
- Department of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, Medical School, University of Crete, GR-71110 Heraklion, Greece
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103
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Abstract
To help define the biological functions of nonessential genes of Francisella novicida, we measured the growth of arrayed members of a comprehensive transposon mutant library under a variety of nutrition and stress conditions. Mutant phenotypes were identified for 37% of the genes, corresponding to ten carbon source utilization pathways, nine amino acid- and nucleotide-biosynthetic pathways, ten intrinsic antibiotic resistance traits, and six other stress resistance traits. The greatest surprise of the analysis was the large number of genotype-phenotype relationships that were not predictable from studies of Escherichia coli and other model species. The study identified candidate genes for a missing glycolysis function (phosphofructokinase), an unusual proline-biosynthetic pathway, parallel outer membrane lipid asymmetry maintenance systems, and novel antibiotic resistance functions. The analysis provides an evaluation of annotation predictions, identifies cases in which fundamental processes differ from those in model species, and helps create an empirical foundation for understanding virulence and other complex processes. The value of genome sequences as foundations for analyzing complex traits in nonmodel organisms is limited by the need to rely almost exclusively on sequence similarities to predict gene functions in annotations. Many genes cannot be assigned functions, and some predictions are incorrect or incomplete. Due to these limitations, genome-scale experimental approaches that test and extend bioinformatics-based predictions are sorely needed. In this study, we describe such an approach based on phenotypic analysis of a comprehensive, sequence-defined transposon mutant library.
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104
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Xu T, Brown W, Marinus MG. Bleomycin sensitivity in Escherichia coli is medium-dependent. PLoS One 2012; 7:e33256. [PMID: 22438905 PMCID: PMC3305319 DOI: 10.1371/journal.pone.0033256] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/06/2012] [Indexed: 11/19/2022] Open
Abstract
Bleomycin (BLM) is a glycopeptide antibiotic and anti-tumor agent that targets primarily the furanose rings of DNA and in the presence of ferrous ions produces oxidative damage and DNA strand breaks. Escherichia coli cells growing in broth medium and exposed to low concentrations of BLM contain double-strand breaks and require homologous recombination to survive. To a lesser extent, the cells also require the abasic (AP) endonucleases associated with base excision repair, presumably to repair oxidative damage. As expected, there is strong induction of the SOS system in treated cells. In contrast, E. coli cells growing in glucose or glycerol minimal medium are resistant to the lethal action of BLM and do not require either homologous recombination functions or AP-endonucleases for survival. DNA ligase activity, however, is needed for cells growing in minimal medium to resist the lethal effects of BLM. There is weak SOS induction in such treated cells.
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Affiliation(s)
| | | | - Martin G. Marinus
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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105
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Hottes AK, Tavazoie S. Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries. Methods Mol Biol 2012; 765:83-97. [PMID: 21815088 DOI: 10.1007/978-1-61779-197-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Successful strain engineering involves perturbing key nodes within the cellular network. How the -network's connectivity affects the phenotype of interest and the ideal nodes to modulate, however, are frequently not readily apparent. To guide the generation of a list of candidate nodes for detailed investigation, designers often examine the behavior of a representative set of strains, such as a library of transposon insertion mutants, in the environment of interest. Here, we first present design principles for creating a maximally informative competitive selection. Then, we describe how to globally quantify the change in distribution of strains within a transposon library in response to a competitive selection by amplifying the DNA adjacent to the transposons and hybridizing it to a microarray. Finally, we detail strategies for analyzing the resulting hybridization data to identify genes and pathways that contribute both negatively and positively to fitness in the desired environment.
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Affiliation(s)
- Alison K Hottes
- Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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106
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Martínez JL. Bottlenecks in the transferability of antibiotic resistance from natural ecosystems to human bacterial pathogens. Front Microbiol 2012; 2:265. [PMID: 22319513 PMCID: PMC3249888 DOI: 10.3389/fmicb.2011.00265] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/12/2011] [Indexed: 11/17/2022] Open
Abstract
It is generally accepted that resistance genes acquired by human pathogens through horizontal gene transfer originated in environmental, non-pathogenic bacteria. As a consequence, there is increasing concern on the roles that natural, non-clinical ecosystems, may play in the evolution of resistance. Recent studies have shown that the variability of determinants that can provide antibiotic resistance on their expression in a heterologous host is much larger than what is actually found in human pathogens, which implies the existence of bottlenecks modulating the transfer, spread, and stability of antibiotic resistance genes. In this review, the role that different factors such as founder effects, ecological connectivity, fitness costs, or second-order selection may have on the establishment of a specific resistance determinant in a population of bacterial pathogens is analyzed.
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Affiliation(s)
- José L Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Cientificas Madrid, Spain
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107
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Toprak E, Veres A, Michel JB, Chait R, Hartl DL, Kishony R. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet 2011; 44:101-5. [PMID: 22179135 PMCID: PMC3534735 DOI: 10.1038/ng.1034] [Citation(s) in RCA: 493] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 11/15/2011] [Indexed: 12/31/2022]
Abstract
Antibiotic resistance can evolve through the sequential accumulation of multiple mutations. To study such gradual evolution, we developed a selection device, the 'morbidostat', that continuously monitors bacterial growth and dynamically regulates drug concentrations, such that the evolving population is constantly challenged. We analyzed the evolution of resistance in Escherichia coli under selection with single drugs, including chloramphenicol, doxycycline and trimethoprim. Over a period of ∼20 days, resistance levels increased dramatically, with parallel populations showing similar phenotypic trajectories. Whole-genome sequencing of the evolved strains identified mutations both specific to resistance to a particular drug and shared in resistance to multiple drugs. Chloramphenicol and doxycycline resistance evolved smoothly through diverse combinations of mutations in genes involved in translation, transcription and transport. In contrast, trimethoprim resistance evolved in a stepwise manner, through mutations restricted to the gene encoding the enzyme dihydrofolate reductase (DHFR). Sequencing of DHFR over the time course of the experiment showed that parallel populations evolved similar mutations and acquired them in a similar order.
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Affiliation(s)
- Erdal Toprak
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Adrian Veres
- Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Jean-Baptiste Michel
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, USA
| | - Remy Chait
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Roy Kishony
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
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108
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Abstract
The serendipitous discovery of penicillin inspired intensive research into how small molecules affect basic cellular processes and their potential to treat disease. Biochemical and genetic approaches have been fundamental for clarifying small-molecule modes of action. Genomic technologies have permitted the use of chemical-genetic strategies that comprehensively study compound-target relationships in the context of a living cell, providing a systems biology view of both the cellular targets and the interdependent networks that respond to chemical stress. These studies highlight the fact that in vitro determinations of mechanism rarely translate into a complete understanding of drug behavior in the cell. Here, we review key discoveries that gave rise to the field of chemical genetics, with particular attention to chemical-genetic strategies developed for bakers' yeast, their extension to clinically relevant microbial pathogens, and the potential of these approaches to affect antimicrobial drug discovery.
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109
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Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet 2011; 7:e1002377. [PMID: 22125496 PMCID: PMC3219608 DOI: 10.1371/journal.pgen.1002377] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 09/24/2011] [Indexed: 12/28/2022] Open
Abstract
As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. Proper assembly of the cell envelope is essential for bacterial growth, environmental adaptation, and drug resistance. Yet, while the biological roles of the many genes and pathways involved in biosynthesis of the cell envelope have been studied extensively in isolation, how the myriad components intersect functionally to maintain envelope integrity under different growth conditions has not been explored systematically. Genome-scale genetic interaction screens have increasingly been performed to great impact in yeast; no analogous comprehensive studies have yet been reported for bacteria despite their prominence in human health and disease. We addressed this by using a synthetic genetic array technology to generate quantitative maps of genetic interactions encompassing virtually all the components of the cell envelope biosynthetic machinery of the classic model bacterium E. coli in two common laboratory growth conditions (rich and minimal medium). From the resulting networks of high-confidence genetic interactions, we identify condition-specific functional dependencies underlying envelope assembly and global remodeling of genetic backup mechanisms that ensure envelope integrity under environmental challenge.
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110
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Deutschbauer A, Price MN, Wetmore KM, Shao W, Baumohl JK, Xu Z, Nguyen M, Tamse R, Davis RW, Arkin AP. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet 2011; 7:e1002385. [PMID: 22125499 PMCID: PMC3219624 DOI: 10.1371/journal.pgen.1002385] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 09/30/2011] [Indexed: 11/21/2022] Open
Abstract
Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility. We find that 2,350 genes have a pattern of fitness that is significantly different from random and 1,230 of these genes (37% of our total assayed genes) have enough signal to show strong biological correlations. We find that genes in all functional categories have phenotypes, including hundreds of hypotheticals, and that potentially redundant genes (over 50% amino acid identity to another gene in the genome) are also likely to have distinct phenotypes. Using fitness patterns, we were able to propose specific molecular functions for 40 genes or operons that lacked specific annotations or had incomplete annotations. In one example, we demonstrate that the previously hypothetical gene SO_3749 encodes a functional acetylornithine deacetylase, thus filling a missing step in S. oneidensis metabolism. Additionally, we demonstrate that the orphan histidine kinase SO_2742 and orphan response regulator SO_2648 form a signal transduction pathway that activates expression of acetyl-CoA synthase and is required for S. oneidensis to grow on acetate as a carbon source. Lastly, we demonstrate that gene expression and mutant fitness are poorly correlated and that mutant fitness generates more confident predictions of gene function than does gene expression. The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes. Many computationally predicted gene annotations in bacteria are incomplete or wrong. Consequently, experimental methods to systematically determine gene function in bacteria are required. Here, we describe a genetic approach to meet this challenge. We constructed a large transposon mutant library in the metal-reducing bacterium Shewanella oneidensis MR-1 and profiled the fitness of this collection in more than 100 diverse experimental conditions. In addition to identifying a phenotype for more than 2,000 genes, we demonstrate that mutant fitness profiles can be used to assign “evidence-based” gene annotations for enzymes, signaling proteins, transporters, and transcription factors, a subset of which we verify experimentally.
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Affiliation(s)
- Adam Deutschbauer
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Morgan N. Price
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Kelly M. Wetmore
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Wenjun Shao
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jason K. Baumohl
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Zhuchen Xu
- Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America
| | - Michelle Nguyen
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Raquel Tamse
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Ronald W. Davis
- Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Adam P. Arkin
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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111
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Lee S, Jarantow L, Wang H, Sillaots S, Cheng H, Meredith T, Thompson J, Roemer T. Antagonism of Chemical Genetic Interaction Networks Resensitize MRSA to β-Lactam Antibiotics. ACTA ACUST UNITED AC 2011; 18:1379-89. [DOI: 10.1016/j.chembiol.2011.08.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/19/2011] [Accepted: 08/22/2011] [Indexed: 02/07/2023]
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112
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Amini S, Hottes AK, Smith LE, Tavazoie S. Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms. PLoS Pathog 2011; 7:e1002298. [PMID: 22028649 PMCID: PMC3197603 DOI: 10.1371/journal.ppat.1002298] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Accepted: 08/18/2011] [Indexed: 12/23/2022] Open
Abstract
Bacteria in biofilms have higher antibiotic tolerance than their planktonic counterparts. A major outstanding question is the degree to which the biofilm-specific cellular state and its constituent genetic determinants contribute to this hyper-tolerant phenotype. Here, we used genome-wide functional profiling of a complex, heterogeneous mutant population of Pseudomonas aeruginosa MPAO1 in biofilm and planktonic growth conditions with and without tobramycin to systematically quantify the contribution of each locus to antibiotic tolerance under these two states. We identified large sets of mutations that contribute to antibiotic tolerance predominantly in the biofilm or planktonic setting only, offering global insights into the differences and similarities between biofilm and planktonic antibiotic tolerance. Our mixed population-based experimental design recapitulated the complexity of natural biofilms and, unlike previous studies, revealed clinically observed behaviors including the emergence of quorum sensing-deficient mutants. Our study revealed a substantial contribution of the cellular state to the antibiotic tolerance of biofilms, providing a rational foundation for the development of novel therapeutics against P. aeruginosa biofilm-associated infections. Biofilms, matrix-enclosed surface-colonized communities of bacteria, are extremely resistant to antimicrobial agents, withstanding concentrations of antibiotics orders of magnitude higher compared to free-swimming planktonic cells. This is a well-established characteristic of infections caused by the opportunistic pathogen Pseudomonas aeruginosa, the major cause of morbidity in cystic fibrosis patients and a frequent cause of nosocomial infections, and Pseudomonas infections generally persist despite the use of long-term antibiotic therapy. Nonetheless, the genetic basis of the hyper-tolerance of biofilms to antimicrobial agents is poorly understood. In this study, we use a genome-wide genetic footprinting technology to systematically quantify the contribution of each locus in P. aeruginosa to antibiotic tolerance in both biofilm and planktonic states. Comparing and contrasting the genome-wide genetic profile of these two physiological states revealed that large sets of genes modulate antibiotic tolerance as a function of the cellular state.
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Affiliation(s)
- Sasan Amini
- Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Alison K. Hottes
- Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Lincoln E. Smith
- Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Saeed Tavazoie
- Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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113
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Amini S, Tavazoie S. Antibiotics and the post-genome revolution. Curr Opin Microbiol 2011; 14:513-8. [PMID: 21816663 DOI: 10.1016/j.mib.2011.07.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 12/28/2022]
Abstract
The emergence of pathogenic bacteria resistant to multiple antimicrobial agents is turning into a major crisis in human and veterinary medicine. This necessitates a serious re-evaluation of our approaches toward antibacterial drug discovery and use. Concurrent advances in genomics including whole-genome sequencing, genotyping, and gene expression profiling have the potential to transform our basic understanding of antimicrobial pathways and lead to the discovery of novel targets and therapeutics.
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Affiliation(s)
- Sasan Amini
- Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
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114
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Baquero F, Coque TM, de la Cruz F. Ecology and evolution as targets: the need for novel eco-evo drugs and strategies to fight antibiotic resistance. Antimicrob Agents Chemother 2011; 55:3649-60. [PMID: 21576439 PMCID: PMC3147629 DOI: 10.1128/aac.00013-11] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In recent years, the explosive spread of antibiotic resistance determinants among pathogenic, commensal, and environmental bacteria has reached a global dimension. Classical measures trying to contain or slow locally the progress of antibiotic resistance in patients on the basis of better antibiotic prescribing policies have clearly become insufficient at the global level. Urgent measures are needed to directly confront the processes influencing antibiotic resistance pollution in the microbiosphere. Recent interdisciplinary research indicates that new eco-evo drugs and strategies, which take ecology and evolution into account, have a promising role in resistance prevention, decontamination, and the eventual restoration of antibiotic susceptibility. This minireview summarizes what is known and what should be further investigated to find drugs and strategies aiming to counteract the "four P's," penetration, promiscuity, plasticity, and persistence of rapidly spreading bacterial clones, mobile genetic elements, or resistance genes. The term "drug" is used in this eco-evo perspective as a tool to fight resistance that is able to prevent, cure, or decrease potential damage caused by antibiotic resistance, not necessarily only at the individual level (the patient) but also at the ecological and evolutionary levels. This view offers a wealth of research opportunities for science and technology and also represents a large adaptive challenge for regulatory agencies and public health officers. Eco-evo drugs and interventions constitute a new avenue for research that might influence not only antibiotic resistance but the maintenance of a healthy interaction between humans and microbial systems in a rapidly changing biosphere.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Institute Ramón and Cajal for Health Research (IRYCIS), CIBER Research Network in Epidemiology and Public Health (CIBERESP), Ramón y Cajal University Hospital, Madrid, Spain.
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115
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Abstract
We present genetic studies that help define the functional network underlying intrinsic aminoglycoside resistance in Pseudomonas aeruginosa. Our analysis shows that proteolysis, particularly that controlled by the membrane protease FtsH, is a major determinant of resistance. First, we examined the consequences of inactivating genes controlled by AmgRS, a two-component regulator required for intrinsic tobramycin resistance. Three of the gene products account for resistance: a modulator of FtsH protease (YccA), a membrane protease (HtpX), and a membrane protein of unknown function (PA5528). Second, we screened mutations inactivating 66 predicted proteases and related functions. Insertions inactivating two FtsH protease accessory factors (HflK and HflC) and a cytoplasmic protease (HslUV) increased tobramycin sensitivity. Finally, we generated an ftsH deletion mutation. The mutation dramatically increased aminoglycoside sensitivity. Many of the functions whose inactivation increased sensitivity appeared to act independently, since multiple mutations led to additive or synergistic effects. Up to 500-fold increases in tobramycin sensitivity were observed. Most of the mutations also were highly pleiotropic, increasing sensitivity to a membrane protein hybrid, several classes of antibiotics, alkaline pH, NaCl, and other compounds. We propose that the network of proteases provides robust protection from aminoglycosides and other substances through the elimination of membrane-disruptive mistranslation products.
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116
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Abstract
It is generally assumed that antibiotics and resistance determinants are the task forces of a biological warfare in which each resistance determinant counteracts the activity of a specific antibiotic. According to this view, antibiotic resistance might be considered as a specific response to an injury, not necessarily linked to bacterial metabolism, except for the burden that the acquisition of resistance might impose on the bacteria (fitness costs). Nevertheless, it is known that changes in bacterial metabolism, such as those associated with dormancy or biofilm formation, modulate bacterial susceptibility to antibiotics (phenotypic resistance), indicating that there exists a linkage between bacterial metabolism and antibiotic resistance. The analyses of the intrinsic resistomes of bacterial pathogens also demonstrate that the building up of intrinsic resistance requires the concerted action of many elements, several of which play a relevant role in the bacterial metabolism. In this article, we will review the current knowledge on the linkage between bacterial metabolism and antibiotic resistance and will discuss the role of global metabolic regulators such as Crc in bacterial susceptibility to antibiotics. Given that growing into the human host requires a metabolic adaptation, we will discuss whether this adaptation might trigger resistance even in the absence of selective pressure by antibiotics.
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Affiliation(s)
- José L Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid, Spain.
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117
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Blaby-Haas CE, de Crécy-Lagard V. Mining high-throughput experimental data to link gene and function. Trends Biotechnol 2011; 29:174-82. [PMID: 21310501 DOI: 10.1016/j.tibtech.2011.01.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/21/2010] [Accepted: 01/04/2011] [Indexed: 12/25/2022]
Abstract
Nearly 2200 genomes that encode around 6 million proteins have now been sequenced. Around 40% of these proteins are of unknown function, even when function is loosely and minimally defined as 'belonging to a superfamily'. In addition to in silico methods, the swelling stream of high-throughput experimental data can give valuable clues for linking these unknowns with precise biological roles. The goal is to develop integrative data-mining platforms that allow the scientific community at large to access and utilize this rich source of experimental knowledge. To this end, we review recent advances in generating whole-genome experimental datasets, where this data can be accessed, and how it can be used to drive prediction of gene function.
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Affiliation(s)
- Crysten E Blaby-Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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118
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Castaneda-Garcia A, Do TT, Blazquez J. The K+ uptake regulator TrkA controls membrane potential, pH homeostasis and multidrug susceptibility in Mycobacterium smegmatis. J Antimicrob Chemother 2011; 66:1489-98. [DOI: 10.1093/jac/dkr165] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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119
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Babu M, Aoki H, Chowdhury WQ, Gagarinova A, Graham C, Phanse S, Laliberte B, Sunba N, Jessulat M, Golshani A, Emili A, Greenblatt JF, Ganoza MC. Ribosome-dependent ATPase interacts with conserved membrane protein in Escherichia coli to modulate protein synthesis and oxidative phosphorylation. PLoS One 2011; 6:e18510. [PMID: 21556145 PMCID: PMC3083400 DOI: 10.1371/journal.pone.0018510] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 03/09/2011] [Indexed: 01/15/2023] Open
Abstract
Elongation factor RbbA is required for ATP-dependent deacyl-tRNA release presumably after each peptide bond formation; however, there is no information about the cellular role. Proteomic analysis in Escherichia coli revealed that RbbA reciprocally co-purified with a conserved inner membrane protein of unknown function, YhjD. Both proteins are also physically associated with the 30S ribosome and with members of the lipopolysaccharide transport machinery. Genome-wide genetic screens of rbbA and yhjD deletion mutants revealed aggravating genetic interactions with mutants deficient in the electron transport chain. Cells lacking both rbbA and yhjD exhibited reduced cell division, respiration and global protein synthesis as well as increased sensitivity to antibiotics targeting the ETC and the accuracy of protein synthesis. Our results suggest that RbbA appears to function together with YhjD as part of a regulatory network that impacts bacterial oxidative phosphorylation and translation efficiency.
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Affiliation(s)
- Mohan Babu
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Hiroyuki Aoki
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Wasimul Q. Chowdhury
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Alla Gagarinova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Chris Graham
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Sadhna Phanse
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Ben Laliberte
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Canada
| | - Noor Sunba
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Canada
| | - Matthew Jessulat
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jack F. Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - M. Clelia Ganoza
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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120
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Amaral L, Fanning S, Pagès JM. Efflux pumps of gram-negative bacteria: genetic responses to stress and the modulation of their activity by pH, inhibitors, and phenothiazines. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2011; 77:61-108. [PMID: 21692367 DOI: 10.1002/9780470920541.ch2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Leonard Amaral
- Unit of Mycobacteriology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
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121
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Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA. Phenotypic landscape of a bacterial cell. Cell 2010; 144:143-56. [PMID: 21185072 DOI: 10.1016/j.cell.2010.11.052] [Citation(s) in RCA: 501] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/07/2010] [Accepted: 11/24/2010] [Indexed: 01/09/2023]
Abstract
The explosion of sequence information in bacteria makes developing high-throughput, cost-effective approaches to matching genes with phenotypes imperative. Using E. coli as proof of principle, we show that combining large-scale chemical genomics with quantitative fitness measurements provides a high-quality data set rich in discovery. Probing growth profiles of a mutant library in hundreds of conditions in parallel yielded > 10,000 phenotypes that allowed us to study gene essentiality, discover leads for gene function and drug action, and understand higher-order organization of the bacterial chromosome. We highlight new information derived from the study, including insights into a gene involved in multiple antibiotic resistance and the synergy between a broadly used combinatory antibiotic therapy, trimethoprim and sulfonamides. This data set, publicly available at http://ecoliwiki.net/tools/chemgen/, is a valuable resource for both the microbiological and bioinformatic communities, as it provides high-confidence associations between hundreds of annotated and uncharacterized genes as well as inferences about the mode of action of several poorly understood drugs.
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122
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PoxA, yjeK, and elongation factor P coordinately modulate virulence and drug resistance in Salmonella enterica. Mol Cell 2010; 39:209-21. [PMID: 20670890 DOI: 10.1016/j.molcel.2010.06.021] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 03/03/2010] [Accepted: 05/14/2010] [Indexed: 11/21/2022]
Abstract
We report an interaction between poxA, encoding a paralog of lysyl tRNA-synthetase, and the closely linked yjeK gene, encoding a putative 2,3-beta-lysine aminomutase, that is critical for virulence and stress resistance in Salmonella enterica. Salmonella poxA and yjeK mutants share extensive phenotypic pleiotropy, including attenuated virulence in mice, an increased ability to respire under nutrient-limiting conditions, hypersusceptibility to a variety of diverse growth inhibitors, and altered expression of multiple proteins, including several encoded on the SPI-1 pathogenicity island. PoxA mediates posttranslational modification of bacterial elongation factor P (EF-P), analogous to the modification of the eukaryotic EF-P homolog, eIF5A, with hypusine. The modification of EF-P is a mechanism of regulation whereby PoxA acts as an aminoacyl-tRNA synthetase that attaches an amino acid to a protein resembling tRNA rather than to a tRNA.
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123
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Genetic determinants involved in the susceptibility of Pseudomonas aeruginosa to beta-lactam antibiotics. Antimicrob Agents Chemother 2010; 54:4159-67. [PMID: 20679510 DOI: 10.1128/aac.00257-10] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The resistome of P. aeruginosa for three β-lactam antibiotics, namely, ceftazidime, imipenem, and meropenem, was deciphered by screening a comprehensive PA14 mutant library for mutants with increased or reduced susceptibility to these antimicrobials. Confirmation of the phenotypes of all selected mutants was performed by Etest. Of the total of 78 confirmed mutants, 41 demonstrated a reduced susceptibility phenotype and 37 a supersusceptibility (i.e., altered intrinsic resistance) phenotype, with 6 mutants demonstrating a mixed phenotype, depending on the antibiotic. Only three mutants demonstrated reduced (PA0908) or increased (glnK and ftsK) susceptibility to all three antibiotics. Overall, the mutant profiles of susceptibility suggested distinct mechanisms of action and resistance for the three antibiotics despite their similar structures. More detailed analysis indicated important roles for novel and known β-lactamase regulatory genes, for genes with likely involvement in barrier function, and for a range of regulators of alginate biosynthesis.
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124
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Staphylococcus aureus TargetArray: comprehensive differential essential gene expression as a mechanistic tool to profile antibacterials. Antimicrob Agents Chemother 2010; 54:3659-70. [PMID: 20547796 DOI: 10.1128/aac.00308-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The widespread emergence of antibiotic-resistant bacteria and a lack of new pharmaceutical development have catalyzed a need for new and innovative approaches for antibiotic drug discovery. One bottleneck in antibiotic discovery is the lack of a rapid and comprehensive method to identify compound mode of action (MOA). Since a hallmark of antibiotic action is as an inhibitor of essential cellular targets and processes, we identify a set of 308 essential genes in the clinically important pathogen Staphylococcus aureus. A total of 446 strains differentially expressing these genes were constructed in a comprehensive platform of sensitized and resistant strains. A subset of strains allows either target underexpression or target overexpression by heterologous promoter replacements with a suite of tetracycline-regulatable promoters. A further subset of 236 antisense RNA-expressing clones allows knockdown expression of cognate targets. Knockdown expression confers selective antibiotic hypersensitivity, while target overexpression confers resistance. The antisense strains were configured into a TargetArray in which pools of sensitized strains were challenged in fitness tests. A rapid detection method measures strain responses toward antibiotics. The TargetArray antibiotic fitness test results show mechanistically informative biological fingerprints that allow MOA elucidation.
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125
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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: 628] [Impact Index Per Article: 44.9] [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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126
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Kempf I, Zeitouni S. [The cost of antibiotic resistance: analysis and consequences]. ACTA ACUST UNITED AC 2009; 60:e9-14. [PMID: 19942376 DOI: 10.1016/j.patbio.2009.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 10/27/2009] [Indexed: 11/16/2022]
Abstract
Antimicrobial resistance, either by mutation or acquisition of resistance determinants harbored by mobile genetic elements, may confer a biological cost for the bacteria. This biological cost can be evaluated by comparing the resistant mutant to the wild susceptible strain, in the absence of antibiotic selection. This fitness cost can affect the growth rate in vitro or the survival in the host or in the environment or the virulence capacity. Various studies have evidenced this cost, either in vitro or in vivo, in different analysis models. However, bacteria can evolve and adapt to reduce this cost, by compensatory mutations or fine regulation of resistance expression. This compensatory evolution allows resistant bacteria to persist even in the absence of antibiotic selection pressure.
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Affiliation(s)
- I Kempf
- Unite´ mycoplasmologie-bacteriologie, Zoopole-les-Croix, 22440 Ploufragan, France.
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127
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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: 313] [Impact Index Per Article: 20.9] [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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