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Sullivan GJ, Barquist L, Cain AK. A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria. mSystems 2024; 9:e0066523. [PMID: 38470252 PMCID: PMC11019837 DOI: 10.1128/msystems.00665-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Functional genomics techniques, such as transposon insertion sequencing and RNA-sequencing, are key to studying relative differences in bacterial mutant fitness or gene expression under selective conditions. However, certain stress conditions, mutations, or antibiotics can directly interfere with DNA synthesis, resulting in systematic changes in local DNA copy numbers along the chromosome. This can lead to artifacts in sequencing-based functional genomics data when comparing antibiotic treatment to an unstressed control. Further, relative differences in gene-wise read counts may result from alterations in chromosomal replication dynamics, rather than selection or direct gene regulation. We term this artifact "chromosomal location bias" and implement a principled statistical approach to correct it by calculating local normalization factors along the chromosome. These normalization factors are then directly incorporated into statistical analyses using standard RNA-sequencing analysis methods without modifying the read counts themselves, preserving important information about the mean-variance relationship in the data. We illustrate the utility of this approach by generating and analyzing a ciprofloxacin-treated transposon insertion sequencing data set in Escherichia coli as a case study. We show that ciprofloxacin treatment generates chromosomal location bias in the resulting data, and we further demonstrate that failing to correct for this bias leads to false predictions of mutant drug sensitivity as measured by minimum inhibitory concentrations. We have developed an R package and user-friendly graphical Shiny application, ChromoCorrect, that detects and corrects for chromosomal bias in read count data, enabling the application of functional genomics technologies to the study of antibiotic stress.IMPORTANCEAltered gene dosage due to changes in DNA replication has been observed under a variety of stresses with a variety of experimental techniques. However, the implications of changes in gene dosage for sequencing-based functional genomics assays are rarely considered. We present a statistically principled approach to correcting for the effect of changes in gene dosage, enabling testing for differences in the fitness effects or regulation of individual genes in the presence of confounding differences in DNA copy number. We show that failing to correct for these effects can lead to incorrect predictions of resistance phenotype when applying functional genomics assays to investigate antibiotic stress, and we provide a user-friendly application to detect and correct for changes in DNA copy number.
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Affiliation(s)
- Geraldine J. Sullivan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Lars Barquist
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Amy K. Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
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2
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Otto RM, Turska-Nowak A, Brown PM, Reynolds KA. A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment. Cell Syst 2024; 15:134-148.e7. [PMID: 38340730 PMCID: PMC10885703 DOI: 10.1016/j.cels.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/13/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Quantifying and predicting growth rate phenotype given variation in gene expression and environment is complicated by epistatic interactions and the vast combinatorial space of possible perturbations. We developed an approach for mapping expression-growth rate landscapes that integrates sparsely sampled experimental measurements with an interpretable machine learning model. We used mismatch CRISPRi across pairs and triples of genes to create over 8,000 titrated changes in E. coli gene expression under varied environmental contexts, exploring epistasis in up to 22 distinct environments. Our results show that a pairwise model previously used to describe drug interactions well-described these data. The model yielded interpretable parameters related to pathway architecture and generalized to predict the combined effect of up to four perturbations when trained solely on pairwise perturbation data. We anticipate this approach will be broadly applicable in optimizing bacterial growth conditions, generating pharmacogenomic models, and understanding the fundamental constraints on bacterial gene expression. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Ryan M Otto
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA
| | - Agata Turska-Nowak
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA
| | - Philip M Brown
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA
| | - Kimberly A Reynolds
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA; Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA.
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3
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Wallace VJ, Sakowski EG, Preheim SP, Prasse C. Bacteria exposed to antiviral drugs develop antibiotic cross-resistance and unique resistance profiles. Commun Biol 2023; 6:837. [PMID: 37573457 PMCID: PMC10423222 DOI: 10.1038/s42003-023-05177-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 07/25/2023] [Indexed: 08/14/2023] Open
Abstract
Antiviral drugs are used globally as treatment and prophylaxis for long-term and acute viral infections. Even though antivirals also have been shown to have off-target effects on bacterial growth, the potential contributions of antivirals to antimicrobial resistance remains unknown. Herein we explored the ability of different classes of antiviral drugs to induce antimicrobial resistance. Our results establish the previously unrecognized capacity of antivirals to broadly alter the phenotypic antimicrobial resistance profiles of both gram-negative and gram-positive bacteria Escherichia coli and Bacillus cereus. Bacteria exposed to antivirals including zidovudine, dolutegravir and raltegravir developed cross-resistance to commonly used antibiotics including trimethoprim, tetracycline, clarithromycin, erythromycin, and amoxicillin. Whole genome sequencing of antiviral-resistant E. coli isolates revealed numerous unique single base pair mutations, as well as multi-base pair insertions and deletions, in genes with known and suspected roles in antimicrobial resistance including those coding for multidrug efflux pumps, carbohydrate transport, and cellular metabolism. The observed phenotypic changes coupled with genotypic results indicate that bacteria exposed to antiviral drugs with antibacterial properties in vitro can develop multiple resistance mutations that confer cross-resistance to antibiotics. Our findings underscore the potential contribution of wide scale usage of antiviral drugs to the development and spread of antimicrobial resistance in humans and the environment.
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Affiliation(s)
- Veronica J Wallace
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Eric G Sakowski
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Science, Mount St. Mary's University, Emmitsburg, MD, USA
| | - Sarah P Preheim
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Carsten Prasse
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA.
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4
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Yan H, Ding M, Lin J, Zhao L, Han D, Hu Q. Folate-mediated one-carbon metabolism as a potential antifungal target for the sustainable cultivation of microalga Haematococcus pluvialis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:104. [PMID: 37330505 DOI: 10.1186/s13068-023-02353-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/29/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Microalgae are widely considered as multifunctional cell factories that are able to transform the photo-synthetically fixed CO2 to numerous high-value compounds, including lipids, carbohydrates, proteins and pigments. However, contamination of the algal mass culture with fungal parasites continues to threaten the production of algal biomass, which dramatically highlights the importance of developing effective measures to control the fungal infection. One viable solution is to identify potential metabolic pathways that are essential for fungal pathogenicity but are not obligate for algal growth, and to use inhibitors targeting such pathways to restrain the infection. However, such targets remain largely unknown, making it challenging to develop effective measures to mitigate the infection in algal mass culture. RESULTS In the present study, we conducted RNA-Seq analysis for the fungus Paraphysoderma sedebokerense, which can infect the astaxanthin-producing microalga Haematococcus pluvialis. It was found that many differentially expressed genes (DEGs) related to folate-mediated one-carbon metabolism (FOCM) were enriched in P. sedebokerense, which was assumed to produce metabolites required for the fungal parasitism. To verify this hypothesis, antifolate that hampered FOCM was applied to the culture systems. Results showed that when 20 ppm of the antifolate co-trimoxazole were added, the infection ratio decreased to ~ 10% after 9 days inoculation (for the control, the infection ratio was 100% after 5 days inoculation). Moreover, application of co-trimoxazole to H. pluvialis mono-culture showed no obvious differences in the biomass and pigment accumulation compared with the control, suggesting that this is a potentially algae-safe, fungi-targeted treatment. CONCLUSIONS This study demonstrated that applying antifolate to H. pluvialis culturing systems can abolish the infection of the fungus P. sedebokerense and the treatment shows no obvious disturbance to the algal culture, suggesting FOCM is a potential target for antifungal drug design in the microalgal mass culture industry.
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Affiliation(s)
- Hailong Yan
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Meng Ding
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Juan Lin
- Poyang Lake Eco-Economy Research Center, Jiujiang University, Jiujiang, 332005, China
| | - Liang Zhao
- Demeter Bio-Tech Co., Ltd, Zhuhai, 519000, China
| | - Danxiang Han
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Qiang Hu
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, 518060, China.
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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5
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Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI. Empowering drug off-target discovery with metabolic and structural analysis. Nat Commun 2023; 14:3390. [PMID: 37296102 PMCID: PMC10256842 DOI: 10.1038/s41467-023-38859-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/15/2023] [Indexed: 06/12/2023] Open
Abstract
Elucidating intracellular drug targets is a difficult problem. While machine learning analysis of omics data has been a promising approach, going from large-scale trends to specific targets remains a challenge. Here, we develop a hierarchic workflow to focus on specific targets based on analysis of metabolomics data and growth rescue experiments. We deploy this framework to understand the intracellular molecular interactions of the multi-valent dihydrofolate reductase-targeting antibiotic compound CD15-3. We analyse global metabolomics data utilizing machine learning, metabolic modelling, and protein structural similarity to prioritize candidate drug targets. Overexpression and in vitro activity assays confirm one of the predicted candidates, HPPK (folK), as a CD15-3 off-target. This study demonstrates how established machine learning methods can be combined with mechanistic analyses to improve the resolution of drug target finding workflows for discovering off-targets of a metabolic inhibitor.
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Affiliation(s)
- Sourav Chowdhury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Christopher Dalldorf
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Joao V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kongens Lyngby, Denmark
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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Park SK, Mohr G, Yao J, Russell R, Lambowitz AM. Group II intron-like reverse transcriptases function in double-strand break repair. Cell 2022; 185:3671-3688.e23. [PMID: 36113466 PMCID: PMC9530004 DOI: 10.1016/j.cell.2022.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/16/2022] [Accepted: 08/14/2022] [Indexed: 01/26/2023]
Abstract
Bacteria encode reverse transcriptases (RTs) of unknown function that are closely related to group II intron-encoded RTs. We found that a Pseudomonas aeruginosa group II intron-like RT (G2L4 RT) with YIDD instead of YADD at its active site functions in DNA repair in its native host and when expressed in Escherichia coli. G2L4 RT has biochemical activities strikingly similar to those of human DNA repair polymerase θ and uses them for translesion DNA synthesis and double-strand break repair (DSBR) via microhomology-mediated end-joining (MMEJ). We also found that a group II intron RT can function similarly in DNA repair, with reciprocal active-site substitutions showing isoleucine favors MMEJ and alanine favors primer extension in both enzymes. These DNA repair functions utilize conserved structural features of non-LTR-retroelement RTs, including human LINE-1 and other eukaryotic non-LTR-retrotransposon RTs, suggesting such enzymes may have inherent ability to function in DSBR in a wide range of organisms.
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Affiliation(s)
- Seung Kuk Park
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712, USA
| | - Georg Mohr
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jun Yao
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712, USA
| | - Rick Russell
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712, USA
| | - Alan M Lambowitz
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712, USA.
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TisB Protein Protects Escherichia coli Cells Suffering Massive DNA Damage from Environmental Toxic Compounds. mBio 2022; 13:e0038522. [PMID: 35377167 PMCID: PMC9040746 DOI: 10.1128/mbio.00385-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Toxin-antitoxin systems are genetic elements that are widespread in prokaryotes. Although molecular mode of action of many of these toxins has been identified, their biological functions are mostly unknown. We investigated the functional integration of the TisB/IstR toxin-antitoxin system in the Escherichia coli SOS genotoxic stress response network. We showed that the tisB gene is induced in cells exposed to high doses of the genotoxic antibiotic trimethoprim. However, we also found that TisB contributes to trimethoprim-induced lethality. This is a consequence of the TisB-induced drop in the proton motive force (PMF), which results in blocking the thymine import and therefore the functioning of the pyrimidine salvage pathway. Conversely, a TisB-induced PMF drop protects cells by preventing the import of some other toxic compounds, like the aminoglycoside antibiotic gentamicin and colicin M, in the SOS-induced cells. Colicins are cytotoxic molecules produced by Enterobacterales when they are exposed to strong genotoxic stresses in order to compete with other microbiota members. We indeed found that TisB contributes to E. coli’s fitness during mouse gut colonization. Based on the results obtained here, we propose that the primary biological role of the TisB toxin is to increase the probability of survival and maintenance in the mammalian gut of their bacterial hosts when they have to simultaneously deal with massive DNA damages and a fierce chemical warfare with other microbiota members.
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8
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Chen J, Gao T, Chang Y, Wei Y, Wang Y. Supramolecular complexation between cucurbit[7]uril and folate and analytical applications. JOURNAL OF CHEMICAL RESEARCH 2021. [DOI: 10.1177/17475198211066489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Folate (FA) plays a key role in the biosynthesis of amino acids, purines, and pyrimidines in the human body, and intracellular folate metabolism has become an attractive target of tumor chemotherapy. In this work, an inclusion interaction was found between FA and cucurbit[7]uril (CB[7]), and the formation of a CB[7]-FA 2:1 supramolecular inclusion complex was confirmed by fluorescence spectra, UV-Vis absorption spectroscopy, 1H NMR, and molecular modeling calculations. In addition, FA is generally determined through the indirect fluorescent method because it shows weak fluorescence in aqueous solution. Therefore, a simple, direct fluorescence probe method for rapidly measuring FA was investigated, and the linear equation of FA was ΔF = 14.691C + 37.366 within the concentration ranges of 0.82 ~ 18.31 µg mL–1. The proposed direct fluorescence method was applied to the determination of spiked plasma. We demonstrated that this method could provide an experimental basis for the targeted administration of the CB[7]-FA complex, and it could be extended as a promising fluorescence detection method for drugs in vivo.
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Affiliation(s)
- Jue Chen
- Shanxi University of Chinese Medicine, Taiyuan, P.R. China
| | - Tengmei Gao
- Shanxi University of Chinese Medicine, Taiyuan, P.R. China
| | - Yinxia Chang
- Shanxi University of Chinese Medicine, Taiyuan, P.R. China
| | - Yanming Wei
- Shanxi University of Chinese Medicine, Taiyuan, P.R. China
| | - Yonghui Wang
- Shanxi University of Chinese Medicine, Taiyuan, P.R. China
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9
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Qi Q, Angermayr SA, Bollenbach T. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Front Microbiol 2021; 12:760017. [PMID: 34745067 PMCID: PMC8564399 DOI: 10.3389/fmicb.2021.760017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions.
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Affiliation(s)
- Qin Qi
- Institute of Science and Technology Austria, Klosterneuburg, Austria.,Institute for Biological Physics, University of Cologne, Cologne, Germany
| | | | - Tobias Bollenbach
- Institute for Biological Physics, University of Cologne, Cologne, Germany.,Center for Data and Simulation Science, University of Cologne, Cologne, Germany
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10
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Oxidative damage blocks thymineless death and trimethoprim poisoning in Escherichia coli. J Bacteriol 2021; 204:e0037021. [PMID: 34633866 DOI: 10.1128/jb.00370-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cells that cannot synthesize one of the DNA precursors, dTTP, due to thyA mutation or metabolic poisoning, undergo thymineless death (TLD), - a chromosome-based phenomenon of unclear mechanisms. In E. coli, thymineless death is caused either by denying thyA mutants thymidine supplementation or by treating wild type cells with trimethoprim. Two recent reports promised a potential breakthrough in TLD understanding, suggesting significant oxidative damage during thymine starvation. Oxidative damage in vivo comes from Fenton's reaction, when hydrogen peroxide meets ferrous iron to produce hydroxyl radical. Therefore, TLD could kill via irreparable double-strand breaks behind replication forks, when starvation-caused single-strand DNA gaps are attacked by hydroxyl radicals. We tested the proposed Fenton-TLD connection, in both thyA mutants denied thymidine, as well as in trimethoprim-treated WT cells, under three conditions: 1) intracellular iron chelation; 2) mutational inactivation of hydrogen peroxide (HP) scavenging; 3) acute treatment with sublethal HP concentrations. We found that TLD kinetics are affected by neither iron chelation, nor HP stabilization in cultures, indicating no induction of oxidative damage during thymine starvation. Moreover, acute exogenous HP treatments completely block TLD, apparently by blocking cell division - which may be a novel TLD prerequisite. Separately, the acute trimethoprim sensitivity of the rffC and recBCD mutants demonstrates how bactericidal power of this antibiotic could be amplified by inhibiting the corresponding enzymes. Importance Mysterious thymineless death strikes cells that are starved for thymine and therefore replicating their chromosomal DNA without dTTP. After 67 years of experiments testing various obvious and not so obvious explanations, thymineless death is still without a mechanism. Recently, oxidative damage via in vivo Fenton's reaction was proposed as a critical contributor to the irreparable chromosome damage during thymine starvation. We have tested this idea by either blocking in vivo Fenton's reaction (expecting no thymineless death) or by amplifying oxidative damage (expecting hyper thymineless death). Instead, we found that blocking Fenton's reaction has no influence on thymineless death, while amplifying oxidative damage prevents thymineless death altogether. Thus, oxidative damage does not contribute to thymineless death, while the latter remains enigmatic.
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11
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Zhang Y, Chowdhury S, Rodrigues JV, Shakhnovich E. Development of antibacterial compounds that constrain evolutionary pathways to resistance. eLife 2021; 10:64518. [PMID: 34279221 PMCID: PMC8331180 DOI: 10.7554/elife.64518] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 07/13/2021] [Indexed: 01/27/2023] Open
Abstract
Antibiotic resistance is a worldwide challenge. A potential approach to block resistance is to simultaneously inhibit WT and known escape variants of the target bacterial protein. Here, we applied an integrated computational and experimental approach to discover compounds that inhibit both WT and trimethoprim (TMP) resistant mutants of E. coli dihydrofolate reductase (DHFR). We identified a novel compound (CD15-3) that inhibits WT DHFR and its TMP resistant variants L28R, P21L and A26T with IC50 50–75 µM against WT and TMP-resistant strains. Resistance to CD15-3 was dramatically delayed compared to TMP in in vitro evolution. Whole genome sequencing of CD15-3-resistant strains showed no mutations in the target folA locus. Rather, gene duplication of several efflux pumps gave rise to weak (about twofold increase in IC50) resistance against CD15-3. Altogether, our results demonstrate the promise of strategy to develop evolution drugs - compounds which constrain evolutionary escape routes in pathogens.
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Affiliation(s)
- Yanmin Zhang
- School of Science, China Pharmaceutical University, Nanjing, China.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Sourav Chowdhury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - João V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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12
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Bhattacharyya S, Bershtein S, Adkar BV, Woodard J, Shakhnovich EI. Metabolic response to point mutations reveals principles of modulation of in vivo enzyme activity and phenotype. Mol Syst Biol 2021; 17:e10200. [PMID: 34180142 PMCID: PMC8236904 DOI: 10.15252/msb.202110200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022] Open
Abstract
The relationship between sequence variation and phenotype is poorly understood. Here, we use metabolomic analysis to elucidate the molecular mechanism underlying the filamentous phenotype of E. coli strains that carry destabilizing mutations in dihydrofolate reductase (DHFR). We find that partial loss of DHFR activity causes reversible filamentation despite SOS response indicative of DNA damage, in contrast to thymineless death (TLD) achieved by complete inhibition of DHFR activity by high concentrations of antibiotic trimethoprim. This phenotype is triggered by a disproportionate drop in intracellular dTTP, which could not be explained by drop in dTMP based on the Michaelis-Menten-like in vitro activity curve of thymidylate kinase (Tmk), a downstream enzyme that phosphorylates dTMP to dTDP. Instead, we show that a highly cooperative (Hill coefficient 2.5) in vivo activity of Tmk is the cause of suboptimal dTTP levels. dTMP supplementation rescues filamentation and restores in vivo Tmk kinetics to Michaelis-Menten. Overall, this study highlights the important role of cellular environment in sculpting enzymatic kinetics with system-level implications for bacterial phenotype.
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Affiliation(s)
| | - Shimon Bershtein
- Department of Life SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Bharat V Adkar
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeMAUSA
| | - Jaie Woodard
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeMAUSA
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13
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The Small RNAs PA2952.1 and PrrH as Regulators of Virulence, Motility, and Iron Metabolism in Pseudomonas aeruginosa. Appl Environ Microbiol 2021; 87:AEM.02182-20. [PMID: 33158897 DOI: 10.1128/aem.02182-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that undergoes swarming motility in response to semisolid conditions with amino acids as a nitrogen source. With a genome encoding hundreds of potential intergenic small RNAs (sRNAs), P. aeruginosa can easily adapt to different conditions and stresses. We previously identified 20 sRNAs that were differentially expressed (DE) under swarming conditions. Here, these sRNAs were overexpressed in strain PAO1 and were subjected to an array of phenotypic screens. Overexpression of the PrrH sRNA resulted in decreased swimming motility, whereas a ΔprrH mutant had decreased cytotoxicity and increased pyoverdine production. Overexpression of the previously uncharacterized PA2952.1 sRNA resulted in decreased swarming and swimming motilities, increased gentamicin and tobramycin resistance under swarming conditions, and increased trimethoprim susceptibility. Transcriptome sequencing (RNA-Seq) and proteomic analysis were performed on the wild type (WT) overexpressing PA2952.1 compared to the empty vector control under swarming conditions, and these revealed the differential expression (absolute fold change [FC] ≥ 1.5) of 784 genes and the differential abundance (absolute FC ≥ 1.25) of 59 proteins. Among these were found 73 transcriptional regulators, two-component systems, and sigma and anti-sigma factors. Downstream effectors included downregulated pilus and flagellar genes, the upregulated efflux pump MexGHI-OpmD, and the upregulated arn operon. Genes involved in iron and zinc uptake were generally upregulated, and certain pyoverdine genes were upregulated. Overall, the sRNAs PA2952.1 and PrrH appeared to be involved in regulating virulence-related programs in P. aeruginosa, including iron acquisition and motility.IMPORTANCE Due to the rising incidence of multidrug-resistant (MDR) strains and the difficulty of eliminating P. aeruginosa infections, it is important to understand the regulatory mechanisms that allow this bacterium to adapt to and thrive under a variety of conditions. Small RNAs (sRNAs) are one regulatory mechanism that allows bacteria to change the amount of protein synthesized. In this study, we overexpressed 20 different sRNAs in order to investigate how this might affect different bacterial behaviors. We found that one of the sRNAs, PrrH, played a role in swimming motility and virulence phenotypes, indicating a potentially important role in clinical infections. Another sRNA, PA2952.1, affected other clinically relevant phenotypes, including motility and antibiotic resistance. RNA-Seq and proteomics of the strain overexpressing PA2952.1 revealed the differential expression of 784 genes and 59 proteins, with a total of 73 regulatory factors. This substantial dysregulation indicates an important role for the sRNA PA2952.1.
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Effect of Coptis chinensis on Biofilm Formation and Antibiotic Susceptibility in Mycobacterium abscessus. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:9754357. [PMID: 33224261 PMCID: PMC7671804 DOI: 10.1155/2020/9754357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 11/18/2022]
Abstract
Mycobacterium abscessus infections are notoriously difficult to be treated and newer treatment options are required. Coptis chinensis (C. chinensis) and its main compound berberine are frequently used to treat bacterial and viral infections. In this study, the susceptibility of M. abscessus to C. chinensis extract and berberine was assessed by minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) evaluation. The effects of C. chinensis and berberine on biofilm formation and antibiotic susceptibility in M. abscessus were observed. C. chinensis at concentrations of MIC (1.5 mg/mL) and 2 × MIC (3.0 mg/mL) and berberine at ½ × MIC (0.125 mg/mL) demonstrated a strong inhibition of biofilm formation. Concentration of C. chinensis at ½ × MIC resulted in a significant reduction in MICs of trimethoprim/sulfamethoxazole (TMP/SXT), clarithromycin (CLA), and linezolid (LZD). Similarly, ½ × MIC berberine had a significant effect on the MIC reductions of nine antibiotics including TMP/SXT, CLA, and LZD. Notably, the resistance level MIC of LZD against M. abscessus was reversed to a susceptible level by treatment with either C. chinensis or berberine. Therefore, C. chinensis and berberine have the potential to produce a synergistic antimycobacterial effect, reduce biofilm formation, and decrease antibacterial resistance to LZD in M. abscessus.
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Henrikus SS, Henry C, McGrath AE, Jergic S, McDonald J, Hellmich Y, Bruckbauer ST, Ritger ML, Cherry M, Wood EA, Pham PT, Goodman MF, Woodgate R, Cox MM, van Oijen AM, Ghodke H, Robinson A. Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair. Nucleic Acids Res 2020; 48:8490-8508. [PMID: 32687193 PMCID: PMC7470938 DOI: 10.1093/nar/gkaa597] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 06/30/2020] [Accepted: 07/16/2020] [Indexed: 01/09/2023] Open
Abstract
Several functions have been proposed for the Escherichia coli DNA polymerase IV (pol IV). Although much research has focused on a potential role for pol IV in assisting pol III replisomes in the bypass of lesions, pol IV is rarely found at the replication fork in vivo. Pol IV is expressed at increased levels in E. coli cells exposed to exogenous DNA damaging agents, including many commonly used antibiotics. Here we present live-cell single-molecule microscopy measurements indicating that double-strand breaks induced by antibiotics strongly stimulate pol IV activity. Exposure to the antibiotics ciprofloxacin and trimethoprim leads to the formation of double strand breaks in E. coli cells. RecA and pol IV foci increase after treatment and exhibit strong colocalization. The induction of the SOS response, the appearance of RecA foci, the appearance of pol IV foci and RecA-pol IV colocalization are all dependent on RecB function. The positioning of pol IV foci likely reflects a physical interaction with the RecA* nucleoprotein filaments that has been detected previously in vitro. Our observations provide an in vivo substantiation of a direct role for pol IV in double strand break repair in cells treated with double strand break-inducing antibiotics.
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Affiliation(s)
- Sarah S Henrikus
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Camille Henry
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706, USA
| | - Amy E McGrath
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Slobodan Jergic
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yvonne Hellmich
- Institute of Biochemistry, Goethe Universität, Frankfurt 3MR4+W2, Germany
| | | | - Matthew L Ritger
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706, USA
| | - Megan E Cherry
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706, USA
| | - Phuong T Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706, USA
| | - Antoine M van Oijen
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Harshad Ghodke
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
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Wang D, Li H, Khan WU, Ma X, Tang H, Tang Y, Huang D, Liu Z. SmpB and tmRNA Orchestrate Purine Pathway for the Trimethoprim Resistance in Aeromonas veronii. Front Cell Infect Microbiol 2020; 10:239. [PMID: 32547961 PMCID: PMC7270562 DOI: 10.3389/fcimb.2020.00239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/27/2020] [Indexed: 11/24/2022] Open
Abstract
Small protein B(SmpB) cooperates with transfer-messenger RNA (tmRNA) for trans-translation to ensure the quality control of protein synthesis in prokaryotes. Furthermore, they regulate cell metabolism separately. According to research, SmpB functions as a transcription factor, and tmRNA acts as a small RNA. Purine pathway has been reported to be related to trimethoprim resistance, including hypoxanthine synthesis, adenosine metabolism and guanosine metabolism. Another reason of drug tolerance is the efflux pump of the bacterium. In transcriptomic data, it was shown that the expression of some related enzymes in adenosine metabolism were raised significantly in smpB deletion strain than that of wild type, which led to the differential trimethoprim resistance of Aeromonas veronii (A. veronii). Furthermore, the metabolic products of adenosine AMP, cAMP, and deoxyadenosine were accumulated significantly. However, the expressions of the enzymes related to hypoxanthine synthesis and guanosine metabolism were elevated significantly in ssrA (small stable RNA, tmRNA) deletion strain, which eventually caused an augmented metabolic product xanthine. In addition, the deletion of ssrA also affected the significant downregulations of efflux pump acrA/acrB. The minimal inhibitory concentrations (MIC) were overall decreased after the trimethoprim treatment to the wild type, ΔsmpB and ΔssrA. And the difference in sensitivity between ΔsmpB and ΔssrA was evident. The MIC of ΔsmpB was descended significantly than those of wild type and ΔssrA in M9 medium supplemented with 1 mM adenosine, illustrating that the adenosine metabolism pathway was principally influenced by SmpB. Likewise, the strain ΔssrA conferred more sensitivity than wild type and ΔsmpB in M9 medium supplemented with 1mM guanosine. By overexpressing acrA/acrB, the tolerance to trimethoprim was partially recovered in ΔssrA. These results revealed that SmpB and tmRNA acted on different branches in purine metabolism, conferring the diverse trimethoprim resistance to A. veronii. This study suggests that the trans-translation system might be an effective target in clinical treatment of A. veronii and other multi-antibiotic resistance bacteria with trimethoprim.
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Affiliation(s)
- Dan Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Science, Hainan University, Haikou, China.,Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops Hainan University, Haikou, China
| | - Hong Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Science, Hainan University, Haikou, China
| | - Wasi Ullah Khan
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops Hainan University, Haikou, China
| | - Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Science, Hainan University, Haikou, China
| | - Hongqian Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Science, Hainan University, Haikou, China
| | - Yanqiong Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Science, Hainan University, Haikou, China
| | - Dongyi Huang
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops Hainan University, Haikou, China
| | - Zhu Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Science, Hainan University, Haikou, China
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Bhosle A, Datey A, Chandrasekharan G, Singh D, Chakravortty D, Chandra N. A Strategic Target Rescues Trimethoprim Sensitivity in Escherichia coli. iScience 2020; 23:100986. [PMID: 32240953 PMCID: PMC7115098 DOI: 10.1016/j.isci.2020.100986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/09/2020] [Accepted: 03/10/2020] [Indexed: 01/03/2023] Open
Abstract
Trimethoprim, a preferred treatment for urinary tract infections, is becoming obsolete owing to the rapid dissemination of resistant E. coli. Although direct resistance mechanisms such as overexpression of a mutant FolA and dfr enzymes are well characterized, associated alterations that drive or sustain resistance are unknown. We identify the repertoire of resistance-associated perturbations by constructing and interrogating a transcriptome-integrated functional interactome. From the cross talk between perturbations in stress-response and metabolic pathways, we identify the critical dependence on serine hydroxymethyltransferase (GlyA) as an emergent vulnerability. Through its deletion, we demonstrate that GlyA is necessary to sustain high levels of resistance in both laboratory-evolved resistant E. coli and a multidrug-resistant clinical isolate. Through comparative evolution, we show that the absence of GlyA activity decelerates the acquisition of resistance in E. coli. Put together, our results identify GlyA as a promising target, providing a basis for the rational design of drug combinations. TMP-resistant E. coli show cross talk between stress response and metabolic pathways Dependence on glyA is an emergent vulnerability associated with TMP resistance Knockout of glyA partially rescues sensitivity to TMP in E. coli
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Affiliation(s)
- Amrisha Bhosle
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Akshay Datey
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Giridhar Chandrasekharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Deepshikha Singh
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Dipshikha Chakravortty
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India; Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India.
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India; Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India.
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Multi-Omic Analyses Provide Links between Low-Dose Antibiotic Treatment and Induction of Secondary Metabolism in Burkholderia thailandensis. mBio 2020; 11:mBio.03210-19. [PMID: 32098820 PMCID: PMC7042699 DOI: 10.1128/mbio.03210-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Low doses of antibiotics can trigger secondary metabolite biosynthesis in bacteria, but the underlying mechanisms are generally unknown. We sought to better understand this phenomenon by studying how the antibiotic trimethoprim activates the synthesis of the virulence factor malleilactone in Burkholderia thailandensis Using transcriptomics, quantitative multiplexed proteomics, and primary metabolomics, we systematically mapped the changes induced by trimethoprim. Surprisingly, even subinhibitory doses of the antibiotic resulted in broad transcriptional and translational alterations, with ∼8.5% of the transcriptome and ∼5% of the proteome up- or downregulated >4-fold. Follow-up studies with genetic-biochemical experiments showed that the induction of malleilactone synthesis can be sufficiently explained by the accumulation of methionine biosynthetic precursors, notably homoserine, as a result of inhibition of the folate pathway. Homoserine activated the malleilactone gene cluster via the transcriptional regulator MalR and gave rise to a secondary metabolome which was very similar to that generated by trimethoprim. Our work highlights the expansive changes that low-dose trimethoprim induces on bacterial physiology and provides insights into its stimulatory effect on secondary metabolism.IMPORTANCE The discovery of antibiotics ranks among the most significant accomplishments of the last century. Although the targets of nearly all clinical antibiotics are known, our understanding regarding their natural functions and the effects of subinhibitory concentrations is in its infancy. Stimulatory rather than inhibitory functions have been attributed to low-dose antibiotics. Among these, we previously found that antibiotics activate silent biosynthetic genes and thereby enhance the metabolic output of bacteria. The regulatory circuits underlying this phenomenon are unknown. We take a first step toward elucidating these circuits and show that low doses of trimethoprim (Tmp) have cell-wide effects on the saprophyte Burkholderia thailandensis Most importantly, inhibition of one-carbon metabolic processes by Tmp leads to an accumulation of homoserine, which induces the production of an otherwise silent cytotoxin via a LuxR-type transcriptional regulator. These results provide a starting point for uncovering the molecular basis of the hormetic effects of antibiotics.
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19
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Multidrug Adaptive Resistance of Pseudomonas aeruginosa Swarming Cells. Antimicrob Agents Chemother 2020; 64:AAC.01999-19. [PMID: 31844008 DOI: 10.1128/aac.01999-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/10/2019] [Indexed: 01/25/2023] Open
Abstract
Swarming surface motility is a complex adaptation leading to multidrug antibiotic resistance and virulence factor production in Pseudomonas aeruginosa Here, we expanded previous studies to demonstrate that under swarming conditions, P. aeruginosa PA14 is more resistant to multiple antibiotics, including aminoglycosides, β-lactams, chloramphenicol, ciprofloxacin, tetracycline, trimethoprim, and macrolides, than swimming cells, but is not more resistant to polymyxin B. We investigated the mechanism(s) of swarming-mediated antibiotic resistance by examining the transcriptomes of swarming cells and swarming cells treated with tobramycin by transcriptomics (RNA-Seq) and reverse transcriptase quantitative PCR (qRT-PCR). RNA-Seq of swarming cells (versus swimming) revealed 1,581 dysregulated genes, including 104 transcriptional regulators, two-component systems, and sigma factors, numerous upregulated virulence and iron acquisition factors, and downregulated ribosomal genes. Strain PA14 mutants in resistome genes that were dysregulated under swarming conditions were tested for their ability to swarm in the presence of tobramycin. In total, 41 mutants in genes dysregulated under swarming conditions were shown to be more resistant to tobramycin under swarming conditions, indicating that swarming-mediated tobramycin resistance was multideterminant. Focusing on two genes downregulated under swarming conditions, both prtN and wbpW mutants were more resistant to tobramycin, while the prtN mutant was additionally resistant to trimethoprim under swarming conditions; complementation of these mutants restored susceptibility. RNA-Seq of swarming cells treated with subinhibitory concentrations of tobramycin revealed the upregulation of the multidrug efflux pump MexXY and downregulation of virulence factors.
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20
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Dunn LL, Smith DM, Critzer FJ. Transcriptomic Behavior of Salmonella enterica Newport in Response to Oxidative Sanitizers. J Food Prot 2020; 83:221-232. [PMID: 31934775 DOI: 10.4315/0362-028x.jfp-19-299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/04/2019] [Indexed: 11/11/2022]
Abstract
ABSTRACT Agricultural water is a known source of contamination to fresh produce and can contain foodborne pathogens including Salmonella enterica, pathogenic Escherichia coli, Listeria monocytogenes, and Campylobacter jejuni. To mitigate such risks, antimicrobial agents such as hypochlorites and peroxyacetic acid (PAA) can be applied to in-line irrigation systems as well as to water used in postharvest washing. Although these compounds are effective and widely used, some pathogenic bacteria adapt to survive exposure. RNA sequencing was used to analyze the Salmonella Newport transcriptome after exposure to sodium hypochlorite (NaOCl) and PAA in a simulated agricultural water system. Overall cellular adaptive response was determined quantitatively as a function of overall gene expression of the >4,000 genes in the Salmonella Newport genome. Differentially expressed genes ranged from 11 due to 10-ppm NaOCl treatment, 316 due to 20-ppm NaOCl treatment, 1,719 due to 10-ppm PAA treatment, and 2,010 due to 20-ppm PAA treatment compared with that of the controls (water only). Differentially expressed transcripts included cellular functions such as biosynthesis, degradation, energy generation, and nonmetabolically linked functions. Oxidative exposure upregulated genes associated with key virulence, attachment, and gene transfer. Amino acid biosynthesis was upregulated due to NaOCl exposure but primarily downregulated when Salmonella Newport was exposed to PAA. Slight upregulation occurred in nucleoside and nucleotide biosynthesis, a known DNA repair mechanism seen during exposure to sanitizers. Our results indicate that Salmonella Newport reacts differently when exposed to NaOCl versus PAA, despite oxidative activity being the primary modes of antimicrobial action of both compounds. HIGHLIGHTS
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Affiliation(s)
- Laurel L Dunn
- Department of Food Science and Technology, Food Science Building, University of Georgia, 100 Cedar Street, Athens, Georgia 30602 (ORCID: https://orcid.org/0000-0003-0786-5253 [L.L.D.])
| | - Dara M Smith
- Department of Food Science, University of Tennessee, 2600 River Drive, Knoxville, Tennessee 37996
| | - Faith J Critzer
- School of Food Science, Irrigated Agriculture Research and Extension Center, Washington State University, 24106 North Bunn Road, Prosser, Washington 99350, USA
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21
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Galán-Vásquez E, Perez-Rueda E. Identification of Modules With Similar Gene Regulation and Metabolic Functions Based on Co-expression Data. Front Mol Biosci 2019; 6:139. [PMID: 31921888 PMCID: PMC6929668 DOI: 10.3389/fmolb.2019.00139] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/18/2019] [Indexed: 12/16/2022] Open
Abstract
Biological systems respond to environmental perturbations and to a large diversity of compounds through gene interactions, and these genetic factors comprise complex networks. In particular, a wide variety of gene co-expression networks have been constructed in recent years thanks to the dramatic increase of experimental information obtained with techniques, such as microarrays and RNA sequencing. These networks allow the identification of groups of co-expressed genes that can function in the same process and, in turn, these networks may be related to biological functions of industrial, medical and academic interest. In this study, gene co-expression networks for 17 bacterial organisms from the COLOMBOS database were analyzed via weighted gene co-expression network analysis and clustered into modules of genes with similar expression patterns for each species. These networks were analyzed to determine relevant modules through a hypergeometric approach based on a set of transcription factors and enzymes for each genome. The richest modules were characterized using PFAM families and KEGG metabolic maps. Additionally, we conducted a Gene Ontology analysis for enrichment of biological functions. Finally, we identified modules that shared similarity through all the studied organisms by using comparative genomics.
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Affiliation(s)
- Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Ciudad Universitaria, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Mexico.,Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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22
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Sub-Inhibitory concentrations of SOS-Response inducing antibiotics stimulate integrase expression and excision of pathogenicity islands in uropathogenic Escherichia coli strain 536. Int J Med Microbiol 2019; 310:151361. [PMID: 31640923 DOI: 10.1016/j.ijmm.2019.151361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/26/2019] [Accepted: 09/29/2019] [Indexed: 01/24/2023] Open
Abstract
Urinary tract infections are one of the most common bacterial infections and a major public health problem. The predominant causative agents are uropathogenic Escherichia coli. These strains differ from commensal E. coli by the presence of additional horizontally acquired chromosomal material, so-called pathogenicity islands, which encode traits that promote efficient bacterial colonization of the urinary tract. Uropathogenic model strain E. coli 536 possesses six archetypal pathogenicity islands. Bacteriophage-like integrases encoded by each pathogenicity island contribute to island instability. To learn more about the stability of these six islands and factors controlling their stability we constructed two chromosomal reporter systems for the measurement of island loss, as well as for the measurement of the promoter activity of the six island-associated integrase genes at the population level. We used these reporter gene modules to analyze the role of SOS response in island instability. Tests with subinhibitory concentrations of different antibiotics, including many drugs commonly used for the treatment of urinary tract infection, indicated that only SOS response-inducing antibiotics led to an increased loss of islands which was always associated with an increase in the bacterial subpopulations showing high integrase promoter activity. This suggests that island excision correlates with the expression of the cognate integrase. Our reporter modules are valuable tools to investigate the impact of various growth conditions on genome plasticity. Furthermore, a better understanding of the conditions, which affect bacterial integrase expression may open ways to specifically manipulate the genome content of bacterial pathogens by increasing pathogenicity island deletion rates in infecting or colonizing bacteria, thus leading to the attenuation of bacterial pathogens.
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RexAB is essential for the mutagenic repair of Staphylococcus aureus DNA damage caused by co-trimoxazole. Antimicrob Agents Chemother 2019:AAC.00944-19. [PMID: 31591116 PMCID: PMC6879246 DOI: 10.1128/aac.00944-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Co-trimoxazole (SXT) is a combination therapeutic that consists of sulfamethoxazole and trimethoprim that is increasingly used to treat skin and soft-tissue infections caused by methicillin-resistant Staphylococcus aureus (MRSA). However, the use of SXT is limited to the treatment of low-burden, superficial S. aureus infections and its therapeutic value is compromised by the frequent emergence of resistance. As a first step towards the identification of approaches to enhance the efficacy of SXT, we examined the role of bacterial DNA repair in antibiotic susceptibility and mutagenesis. We found that mutants lacking the DNA repair complex RexAB had a modest 2-fold lower SXT MIC than wild-type strains but were killed 50-5000-fold more efficiently by the combination antibiotic at the breakpoint concentration. SXT-mediated DNA damage occurred via both thymidine limitation and the generation of reactive oxygen species, and triggered induction of the SOS response in a RexAB-dependent manner. SOS induction was associated with a 50% increase in the mutation rate, which may contribute to emergence of resistant strains during SXT therapy. In summary, this work determined that SXT caused DNA damage in S. aureus via both thymidine limitation and oxidative stress, which was repaired by the RexAB complex, leading to induction of the mutagenic SOS response. Small molecule inhibitors of RexAB could therefore have therapeutic value by increasing the efficacy of SXT and decreasing the emergence of drug-resistance during treatment of infections caused by S. aureus.
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Rodrigues JV, Shakhnovich EI. Adaptation to mutational inactivation of an essential gene converges to an accessible suboptimal fitness peak. eLife 2019; 8:50509. [PMID: 31573512 PMCID: PMC6828540 DOI: 10.7554/elife.50509] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022] Open
Abstract
The mechanisms of adaptation to inactivation of essential genes remain unknown. Here we inactivate E. coli dihydrofolate reductase (DHFR) by introducing D27G,N,F chromosomal mutations in a key catalytic residue with subsequent adaptation by an automated serial transfer protocol. The partial reversal G27- > C occurred in three evolutionary trajectories. Conversely, in one trajectory for D27G and in all trajectories for D27F,N strains adapted to grow at very low metabolic supplement (folAmix) concentrations but did not escape entirely from supplement auxotrophy. Major global shifts in metabolome and proteome occurred upon DHFR inactivation, which were partially reversed in adapted strains. Loss-of-function mutations in two genes, thyA and deoB, ensured adaptation to low folAmix by rerouting the 2-Deoxy-D-ribose-phosphate metabolism from glycolysis towards synthesis of dTMP. Multiple evolutionary pathways of adaptation converged to a suboptimal solution due to the high accessibility to loss-of-function mutations that block the path to the highest, yet least accessible, fitness peak. Predicting how viruses and bacteria evolve remains a challenge. The ability to anticipate when and how bacteria might develop drug resistance would make treating life-threatening diseases easier and could potentially help prevent drug resistance altogether. Studying bacterial evolution under different conditions and cataloguing all possible DNA mutations that allow these bacteria to survive are crucial steps in predicting the appearance of drug resistance. Studies have revealed that bacteria can adapt to sources of stress, such as antibiotics, in different ways – each involving mutations in distinct genes. However, not all the mutations provide the same benefits to the organism, and the factors that influence how bacteria will adapt are unclear. Now, Rodrigues and Shakhnovich have used a new approach to push the adaptation ability of the bacterium Escherichia coli to the limit. First, they genetically engineered different E. coli strains by introducing distinct mutations to an enzyme the bacterium needs to make DNA. These mutations make the resulting strains dependent on external molecules to synthesize new DNA. Next, the cells were grown in conditions where the supply of these DNA precursors was progressively decreased, forcing them to adapt. The obvious way for bacteria to adapt to these conditions would be to ‘revert’ the mutations that Rodrigues and Shakhnovich introduced in the first place. By using this approach, Rodrigues and Shakhnovich were able to test how often the obvious evolutionary solution happens compared with presumably less-preferred alternative routes. In rare cases, a specific mutation did restore the activity of the enzyme that enabled DNA synthesis. However, in most cases the bacteria found a different evolutionary solution whereby they all adapt to the decrease in external DNA precursors in the same way, but not by reverting the original mutation. Instead, further mutations disrupt the activity of two metabolic genes, allowing the cells to use the external DNA precursors more efficiently, and keep building DNA. These cells are therefore able to survive even when the levels of the external DNA components are very low, but they will die in the complete absence of these precursor molecules. This evolutionary solution leads to a non-optimal effect: mutations that restore the activity of the original enzyme, which are the best solution when the two metabolic genes are intact, are no longer as effective. This finding represents a clear example of interactions between genes determining evolutionary outcomes. Rodrigues and Shakhnovich showed that, since it is more likely for a random mutation to disrupt a gene than to revert a previous mutation, adaptations that are less-than-optimal but still work might predominate simply because they happen faster. Understanding why certain evolutionary adaptations prevail is an important step in predicting evolution and may lead to breakthroughs in many areas. For example, if scientists can identify mutations likely to make bacteria resistant to drugs, it may be possible to act proactively against the bacterial strains that carry those mutations. Eventually, if the factors that lead to specific adaptations are known, it may be possible to exploit this knowledge to create weaknesses in the bacteria’s own defences.
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Affiliation(s)
- João V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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Blázquez J, Rodríguez-Beltrán J, Matic I. Antibiotic-Induced Genetic Variation: How It Arises and How It Can Be Prevented. Annu Rev Microbiol 2019; 72:209-230. [PMID: 30200850 DOI: 10.1146/annurev-micro-090817-062139] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
By targeting essential cellular processes, antibiotics provoke metabolic perturbations and induce stress responses and genetic variation in bacteria. Here we review current knowledge of the mechanisms by which these molecules generate genetic instability. They include production of reactive oxygen species, as well as induction of the stress response regulons, which lead to enhancement of mutation and recombination rates and modulation of horizontal gene transfer. All these phenomena influence the evolution and spread of antibiotic resistance. The use of strategies to stop or decrease the generation of resistant variants is also discussed.
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Affiliation(s)
- Jesús Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain; .,Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain.,Red Española de Investigacion en Patologia Infecciosa, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ivan Matic
- Faculté de Médecine Paris Descartes, INSERM 1001, CNRS, Université Paris-Descartes-Sorbonne Paris Cité, 75014 Paris, France;
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26
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Muthuramalingam M, White JC, Murphy T, Ames JR, Bourne CR. The toxin from a ParDE toxin-antitoxin system found in Pseudomonas aeruginosa offers protection to cells challenged with anti-gyrase antibiotics. Mol Microbiol 2019; 111:441-454. [PMID: 30427086 PMCID: PMC6368863 DOI: 10.1111/mmi.14165] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2018] [Indexed: 12/13/2022]
Abstract
Toxin-antitoxin systems are mediators of diverse activities in bacterial physiology. For the ParE-type toxins, their reported role of gyrase inhibition utilized during plasmid-segregation killing indicates they are toxic. However, their location throughout chromosomes leads to questions about function, including potential non-toxic outcomes. The current study has characterized a ParDE system from the opportunistic human pathogen Pseudomonas aeruginosa (Pa). We identified a protective function for this ParE toxin, PaParE, against effects of quinolone and other antibiotics. However, higher concentrations of PaParE are themselves toxic to cells, indicating the phenotypic outcome can vary based on its concentration. Our assays confirmed PaParE inhibition of gyrase-mediated supercoiling of DNA with an IC50 value in the low micromolar range, a species-specificity that resulted in more efficacious inhibition of Escherichia coli derived gyrase versus Pa gyrase, and overexpression in the absence of antitoxin yielded an expected filamentous morphology with multi-foci nucleic acid material. Additional data revealed that the PaParE toxin is monomeric and interacts with dimeric PaParD antitoxin with a KD in the lower picomolar range, yielding a heterotetramer. This work provides novel insights into chromosome-encoded ParE function, whereby its expression can impart partial protection to cultures from selected antibiotics.
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Affiliation(s)
- Meenakumari Muthuramalingam
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
- Present address:
Department of Pharmaceutical ChemistryUniversity of KansasLawrence66047 KSUSA
| | - John C. White
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
| | - Tamiko Murphy
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
| | - Jessica R. Ames
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
| | - Christina R. Bourne
- The University of Oklahoma, Department of Chemistry and BiochemistryNorman73019OKUSA
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27
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Gruber CC, Walker GC. Incomplete base excision repair contributes to cell death from antibiotics and other stresses. DNA Repair (Amst) 2018; 71:108-117. [PMID: 30181041 DOI: 10.1016/j.dnarep.2018.08.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Numerous lethal stresses in bacteria including antibiotics, thymineless death, and MalE-LacZ expression trigger an increase in the production of reactive oxygen species. This results in the oxidation of the nucleotide pool by radicals produced by Fenton chemistry. Following the incorporation of these oxidized nucleotides into the genome, the cell's unsuccessful attempt to repair these lesions through base excision repair (BER) contributes causally to the lethality of these stresses. We review the evidence for this phenomenon of incomplete BER-mediated cell death and discuss how better understanding this pathway could contribute to the development of new antibiotics.
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Affiliation(s)
- Charley C Gruber
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States.
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28
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AlRabiah H, Allwood JW, Correa E, Xu Y, Goodacre R. pH plays a role in the mode of action of trimethoprim on Escherichia coli. PLoS One 2018; 13:e0200272. [PMID: 30005078 PMCID: PMC6044521 DOI: 10.1371/journal.pone.0200272] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/20/2018] [Indexed: 01/08/2023] Open
Abstract
Metabolomics-based approaches were applied to understand interactions of trimethoprim with Escherichia coli K-12 at sub-minimum inhibitory concentrations (MIC≈0.2, 0.03 and 0.003 mg L-1). Trimethoprim inhibits dihydrofolate reductase and thereby is an indirect inhibitor of nucleic acid synthesis. Due to the basicity of trimethoprim, two pH levels (5 and 7) were selected which mimicked healthy urine pH. This also allowed investigation of the effect on bacterial metabolism when trimethoprim exists in different ionization states. UHPLC-MS was employed to detect trimethoprim molecules inside the bacterial cell and this showed that at pH 7 more of the drug was recovered compared to pH 5; this correlated with classical growth curve measurements. FT-IR spectroscopy was used to establish recovery of reproducible phenotypes under all 8 conditions (3 drug levels and control in 2 pH levels) and GC-MS was used to generate global metabolic profiles. In addition to finding direct mode-of-action effects where nucleotides were decreased at pH 7 with increasing trimethoprim levels, off-target pH-related effects were observed for many amino acids. Additionally, stress-related effects were observed where the osmoprotectant trehalose was higher at increased antibiotic levels at pH 7. This correlated with glucose and fructose consumption and increase in pyruvate-related products as well as lactate and alanine. Alanine is a known regulator of sugar metabolism and this increase may be to enhance sugar consumption and thus trehalose production. These results provide a wider view of the action of trimethoprim. Metabolomics indicated alternative metabolism areas to be investigated to further understand the off-target effects of trimethoprim.
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Affiliation(s)
- Haitham AlRabiah
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - J. William Allwood
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Invergowrie, Dundee, Scotland United Kingdom
| | - Elon Correa
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Yun Xu
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
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29
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Sulfamethoxazole - Trimethoprim represses csgD but maintains virulence genes at 30°C in a clinical Escherichia coli O157:H7 isolate. PLoS One 2018; 13:e0196271. [PMID: 29718957 PMCID: PMC5931665 DOI: 10.1371/journal.pone.0196271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 04/10/2018] [Indexed: 12/22/2022] Open
Abstract
The high frequency of prophage insertions in the mlrA gene of clinical serotype O157:H7 isolates renders such strains deficient in csgD-dependent biofilm formation but prophage induction may restore certain mlrA properties. In this study we used transcriptomics to study the effect of high and low sulfamethoxazole–trimethoprim (SMX-TM) concentrations on prophage induction, biofilm regulation, and virulence gene expression in strain PA20 under environmental conditions following 5-hour and 12-hour exposures in broth or on agar. SMX-TM at a sub-lethal concentration induced strong RecA expression resulting in concentration- and time-dependent major transcriptional shifts with emphasis on up-regulation of genes within horizontally-transferred chromosomal regions (HTR). Neither high or low levels of SMX-TM stimulated csgD expression at either time point, but both levels resulted in slight repression. Full expression of Ler-dependent genes paralleled expression of group 1 pch homologues in the presence of high glrA. Finally, stx2 expression, which is strongly dependent on prophage induction, was enhanced at 12 hours but repressed at five hours, in spite of early SOS initiation by the high SMX-TM concentration. Our findings indicate that, similar to host conditions, exposure to environmental conditions increased the expression of virulence genes in a clinical isolate but genes involved in the protective biofilm response were repressed.
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30
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Wegener M, Hansen MJ, Driessen AJM, Szymanski W, Feringa BL. Photocontrol of Antibacterial Activity: Shifting from UV to Red Light Activation. J Am Chem Soc 2017; 139:17979-17986. [PMID: 29136373 PMCID: PMC5730949 DOI: 10.1021/jacs.7b09281] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 12/24/2022]
Abstract
The field of photopharmacology aims to introduce smart drugs that, through the incorporation of molecular photoswitches, allow for the remote spatial and temporal control of bioactivity by light. This concept could be particularly beneficial in the treatment of bacterial infections, by reducing the systemic and environmental side effects of antibiotics. A major concern in the realization of such light-responsive drugs is the wavelength of the light that is applied. Studies on the photocontrol of biologically active agents mostly rely on UV light, which is cytotoxic and poorly suited for tissue penetration. In our efforts to develop photoswitchable antibiotics, we introduce here antibacterial agents whose activity can be controlled by visible light, while getting into the therapeutic window. For that purpose, a UV-light-responsive core structure based on diaminopyrimidines with suitable antibacterial properties was identified. Subsequent modification of an azobenzene photoswitch moiety led to structures that allowed us to control their activity against Escherichia coli in both directions with light in the visible region. For the first time, full in situ photocontrol of antibacterial activity in the presence of bacteria was attained with green and violet light. Most remarkably, one of the diaminopyrimidines revealed an at least 8-fold difference in activity before and after irradiation with red light at 652 nm, showcasing the effective "activation" of a biological agent otherwise inactive within the investigated concentration range, and doing so with red light in the therapeutic window.
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Affiliation(s)
- Michael Wegener
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
| | - Mickel J. Hansen
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Molecular
Microbiology, Groningen Biomolecular Sciences
and Biotechnology Institute, Nijenborgh 7 9747 AG Groningen, The Netherlands
| | - Wiktor Szymanski
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
- Department
of Radiology, University of Groningen, University
Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Ben L. Feringa
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
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31
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Maladaptive DNA repair is the ultimate contributor to the death of trimethoprim-treated cells under aerobic and anaerobic conditions. Proc Natl Acad Sci U S A 2017; 114:11512-11517. [PMID: 29073080 PMCID: PMC5664507 DOI: 10.1073/pnas.1706236114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Antibiotic resistance leads to substantial mortality and morbidity and significant economic cost because it seriously undermines our ability to treat bacterial infections. Therefore, a better understanding of the effect of antibiotics on bacteria is needed to increase the effectiveness of treatments and slow the emergence of resistance. The bactericidal effects of antibiotics are triggered by target-specific interactions, but there is growing evidence that an important part of their cytotoxicity results from metabolic disturbances induced by treatment. In this article, we report that the perturbation of DNA replication by a wide-spectrum antibiotic, trimethoprim, affects bacterial metabolism, which provokes the production of genotoxic agents and DNA damage, whose processing ultimately contributes to cell death under both aerobic and anaerobic conditions. The bactericidal effects of antibiotics are undoubtedly triggered by target-specific interactions, but there is growing evidence that an important aspect of cytotoxicity results from treatment-induced metabolic perturbations. In this study, we characterized molecular mechanisms whereby trimethoprim treatment results in cell death, using Escherichia coli as the model organism. E. coli cells grown in rich medium that contained all amino acids and low amounts of thymidine were treated with trimethoprim under aerobic and anaerobic conditions. Under these growth conditions, accelerated thymine depletion is the primary trigger of the processes leading to cell death. Thymine depletion-induced DNA replication stress leads to the production of reactive oxygen species under aerobic conditions and of the DNA-damaging byproducts of nitrate respiration under anaerobic conditions. Lowering the DNA replication initiation rate by introducing the dnaA(Sx) allele or by overexpressing Hda protein reduces the number of active replication forks, which reduces the consumption of thymidine and increases resistance to trimethoprim under both aerobic and anaerobic conditions. Analysis of the involvement of DNA repair enzymes in trimethoprim-induced cytotoxicity clearly indicates that different amounts and/or different types of DNA lesions are produced in the presence or absence of oxygen. Maladaptive processing of the DNA damage by DNA repair enzymes, in particular by MutM and MutY DNA glycosylases, ultimately contributes to cell death.
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32
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Defois C, Ratel J, Denis S, Batut B, Beugnot R, Peyretaillade E, Engel E, Peyret P. Environmental Pollutant Benzo[ a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota. Front Microbiol 2017; 8:1562. [PMID: 28861070 PMCID: PMC5559432 DOI: 10.3389/fmicb.2017.01562] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/02/2017] [Indexed: 01/23/2023] Open
Abstract
Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding, metatranscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota. B[a]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dose-dependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[a]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[a]P induces a specific deviation in the microbial metabolism.
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Affiliation(s)
- Clémence Defois
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Jérémy Ratel
- UR370 QuaPA, MASS Team, Institut National de la Recherche AgronomiqueSaint-Genes-Champanelle, France
| | - Sylvain Denis
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Bérénice Batut
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Réjane Beugnot
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Eric Peyretaillade
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
| | - Erwan Engel
- UR370 QuaPA, MASS Team, Institut National de la Recherche AgronomiqueSaint-Genes-Champanelle, France
| | - Pierre Peyret
- MEDIS, Institut National de la Recherche Agronomique, Université Clermont AuvergneClermont-Ferrand, France
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33
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Noisy Response to Antibiotic Stress Predicts Subsequent Single-Cell Survival in an Acidic Environment. Cell Syst 2017; 4:393-403.e5. [PMID: 28342718 DOI: 10.1016/j.cels.2017.03.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/14/2016] [Accepted: 03/01/2017] [Indexed: 11/23/2022]
Abstract
Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to "cross-protect" bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors.
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34
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Bhattacharyya S, Bershtein S, Yan J, Argun T, Gilson AI, Trauger SA, Shakhnovich EI. Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity. eLife 2016; 5. [PMID: 27938662 PMCID: PMC5176355 DOI: 10.7554/elife.20309] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/09/2016] [Indexed: 12/31/2022] Open
Abstract
Gene dosage toxicity (GDT) is an important factor that determines optimal levels of protein abundances, yet its molecular underpinnings remain unknown. Here, we demonstrate that overexpression of DHFR in E. coli causes a toxic metabolic imbalance triggered by interactions with several functionally related enzymes. Though deleterious in the overexpression regime, surprisingly, these interactions are beneficial at physiological concentrations, implying their functional significance in vivo. Moreover, we found that overexpression of orthologous DHFR proteins had minimal effect on all levels of cellular organization - molecular, systems, and phenotypic, in sharp contrast to E. coli DHFR. Dramatic difference of GDT between 'E. coli's self' and 'foreign' proteins suggests the crucial role of evolutionary selection in shaping protein-protein interaction (PPI) networks at the whole proteome level. This study shows how protein overexpression perturbs a dynamic metabolon of weak yet potentially functional PPI, with consequences for the metabolic state of cells and their fitness.
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Affiliation(s)
- Sanchari Bhattacharyya
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Shimon Bershtein
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Jin Yan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,College of Chemical Engineering, Sichuan University, Chengdu, China
| | - Tijda Argun
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Amy I Gilson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Sunia A Trauger
- Small Molecule Mass Spectrometry, Northwest Laboratories, Harvard University, Cambridge, United States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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35
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Stepanek JJ, Schäkermann S, Wenzel M, Prochnow P, Bandow JE. Purine biosynthesis is the bottleneck in trimethoprim-treated Bacillus subtilis. Proteomics Clin Appl 2016; 10:1036-1048. [PMID: 27329548 DOI: 10.1002/prca.201600039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 06/01/2016] [Accepted: 06/15/2016] [Indexed: 11/11/2022]
Abstract
PURPOSE Trimethoprim is a folate biosynthesis inhibitor. Tetrahydrofolates are essential for the transfer of C1 units in several biochemical pathways including purine, thymine, methionine, and glycine biosynthesis. This study addressed the effects of folate biosynthesis inhibition on bacterial physiology. EXPERIMENTAL DESIGN Two complementary proteomic approaches were employed to analyze the response of Bacillus subtilis to trimethoprim. Acute changes in protein synthesis rates were monitored by radioactive pulse labeling of newly synthesized proteins and subsequent 2DE analysis. Changes in protein levels were detected using gel-free quantitative MS. RESULTS Proteins involved in purine and histidine biosynthesis, the σB -dependent general stress response, and sporulation were upregulated. Most prominently, the PurR-regulon required for de novo purine biosynthesis was derepressed indicating purine depletion. The general stress response was activated energy dependently and in a subpopulation of treated cultures an early onset of sporulation was observed, most likely triggered by low guanosine triphosphate levels. Supplementation of adenosine triphosphate, adenosine, and guanosine to the medium substantially decreased antibacterial activity, showing that purine depletion becomes the bottleneck in trimethoprim-treated B. subtilis. CONCLUSIONS AND CLINICAL RELEVANCE The frequently prescribed antibiotic trimethoprim causes purine depletion in B. subtilis, which can be complemented by supplementing purines to the medium.
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Affiliation(s)
| | | | - Michaela Wenzel
- Ruhr-Universität Bochum, Applied Microbiology, Bochum, Germany
| | - Pascal Prochnow
- Ruhr-Universität Bochum, Applied Microbiology, Bochum, Germany
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36
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Microscale insights into pneumococcal antibiotic mutant selection windows. Nat Commun 2015; 6:8773. [PMID: 26514094 PMCID: PMC4632196 DOI: 10.1038/ncomms9773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/30/2015] [Indexed: 11/26/2022] Open
Abstract
The human pathogen Streptococcus pneumoniae shows alarming rates of antibiotic resistance emergence. The basic requirements for de novo resistance emergence are poorly understood in the pneumococcus. Here we systematically analyse the impact of antibiotics on S. pneumoniae at concentrations that inhibit wild type cells, that is, within the mutant selection window. We identify discrete growth-inhibition profiles for bacteriostatic and bactericidal compounds, providing a predictive framework for distinction between the two classifications. Cells treated with bacteriostatic agents show continued gene expression activity, and real-time mutation assays link this activity to the development of genotypic resistance. Time-lapse microscopy reveals that antibiotic-susceptible pneumococci display remarkable growth and death bistability patterns in response to many antibiotics. We furthermore capture the rise of subpopulations with decreased susceptibility towards cell wall synthesis inhibitors (heteroresisters). We show that this phenomenon is epigenetically inherited, and that heteroresistance potentiates the accumulation of genotypic resistance. The emergence of antibiotic resistance in bacteria is driven by inhibitory but non-lethal antibiotic concentrations. Here, Sorg and Veening study the effects of different antibiotics on the pneumococcus, with a focus on inhibition dynamics, metabolic activity and processes at the single-cell level.
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37
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Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria. PLoS Genet 2015; 11:e1005612. [PMID: 26484862 PMCID: PMC4618355 DOI: 10.1371/journal.pgen.1005612] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/25/2015] [Indexed: 01/02/2023] Open
Abstract
Horizontal gene transfer (HGT) plays a central role in bacterial evolution, yet the molecular and cellular constraints on functional integration of the foreign genes are poorly understood. Here we performed inter-species replacement of the chromosomal folA gene, encoding an essential metabolic enzyme dihydrofolate reductase (DHFR), with orthologs from 35 other mesophilic bacteria. The orthologous inter-species replacements caused a marked drop (in the range 10–90%) in bacterial growth rate despite the fact that most orthologous DHFRs are as stable as E.coli DHFR at 37°C and are more catalytically active than E. coli DHFR. Although phylogenetic distance between E. coli and orthologous DHFRs as well as their individual molecular properties correlate poorly with growth rates, the product of the intracellular DHFR abundance and catalytic activity (kcat/KM), correlates strongly with growth rates, indicating that the drop in DHFR abundance constitutes the major fitness barrier to HGT. Serial propagation of the orthologous strains for ~600 generations dramatically improved growth rates by largely alleviating the fitness barriers. Whole genome sequencing and global proteome quantification revealed that the evolved strains with the largest fitness improvements have accumulated mutations that inactivated the ATP-dependent Lon protease, causing an increase in the intracellular DHFR abundance. In one case DHFR abundance increased further due to mutations accumulated in folA promoter, but only after the lon inactivating mutations were fixed in the population. Thus, by apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products. Once this barrier is alleviated, more fine-tuned evolution occurs to adjust the function/expression of the transferred proteins to the constraints imposed by the intracellular environment of the host organism. Horizontal gene transfer (HGT) is central to bacterial evolution. The outcome of an HGT event (fixation in a population, elimination, or separation as a subdominant clone) depends not only on the availability of a new gene but crucially on the fitness cost or benefit of the genomic incorporation of the foreign gene and its expression in recipient bacteria. Here we studied the fitness landscape for inter-species chromosomal replacement of an essential protein, dihydrofolate reductase (DHFR) encoded by the folA gene, by its orthologs from other mesophilic bacteria. We purified and biochemically characterized 33 out of 35 orthologous DHFRs and found that most of them are stable and more catalytically active than E. coli DHFR. However, the inter-species replacement of DHFR caused significant fitness loss for most transgenic strains due to low abundance of orthologous DHFRs in E. coli cytoplasm. Laboratory evolution resulted in an increase in orthologous DHFR abundance leading to a dramatic fitness improvement. Genomic and proteomic analyses of “naive” and evolved strains suggest a new function of protein homeostasis to discriminate between “self” and “non-self” proteins, thus creating fitness barriers to HGT.
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38
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Khodursky A, Guzmán EC, Hanawalt PC. Thymineless Death Lives On: New Insights into a Classic Phenomenon. Annu Rev Microbiol 2015; 69:247-63. [PMID: 26253395 DOI: 10.1146/annurev-micro-092412-155749] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The primary mechanisms by which bacteria lose viability when deprived of thymine have been elusive for over half a century. Early research focused on stalled replication forks and the deleterious effects of uracil incorporation into DNA from thymidine-deficient nucleotide pools. The initiation of the replication cycle and origin-proximal DNA degradation during thymine starvation have now been quantified via whole-genome microarrays and other approaches. These advances have fostered innovative models and informative experiments in bacteria since this topic was last reviewed. Given that thymineless death is similar in mammalian cells and that certain antibacterial and chemotherapeutic drugs elicit thymine deficiency, a mechanistic understanding of this phenomenon might have valuable biomedical applications.
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Affiliation(s)
- Arkady Khodursky
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108;
| | - Elena C Guzmán
- Departamento de Bioquímica Biología Molecular y Genética, Universidad de Extremadura, 06071 Badajoz, Spain;
| | - Philip C Hanawalt
- Department of Biology, Stanford University, Stanford, California 94305;
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Ostrer L, Hamann BL, Khodursky A. Perturbed states of the bacterial chromosome: a thymineless death case study. Front Microbiol 2015; 6:363. [PMID: 25964781 PMCID: PMC4408854 DOI: 10.3389/fmicb.2015.00363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/10/2015] [Indexed: 11/24/2022] Open
Abstract
Spatial patterns of transcriptional activity in the living genome of Escherichia coli represent one of the more peculiar aspects of the E. coli chromosome biology. Spatial transcriptional correlations can be observed throughout the chromosome, and their formation depends on the state of replication in the cell. The condition of thymine starvation leading to thymineless death (TLD) is at the "cross-roads" of replication and transcription. According to a current view, e.g., (Cagliero et al., 2014), one of the cellular objectives is to segregate the processes of transcription and replication in time and space. An ultimate segregation would take place when one process is inhibited and another is not, as it happens during thymine starvation, which results in numerous molecular and physiological abnormalities associated with TLD. One of such abnormalities is the loss of spatial correlations in the vicinity of the origin of replication. We review the transcriptional consequences of replication inhibition by thymine starvation in a context of the state of DNA template in the starved cells and opine about a possible significance of normal physiological coupling between the processes of replication and transcription.
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Affiliation(s)
| | | | - Arkady Khodursky
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, St. Paul, MN, USA
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Bershtein S, Choi JM, Bhattacharyya S, Budnik B, Shakhnovich E. Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship. Cell Rep 2015; 11:645-56. [PMID: 25892240 DOI: 10.1016/j.celrep.2015.03.051] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 02/20/2015] [Accepted: 03/23/2015] [Indexed: 11/18/2022] Open
Abstract
Linking the molecular effects of mutations to fitness is central to understanding evolutionary dynamics. Here, we establish a quantitative relation between the global effect of mutations on the E. coli proteome and bacterial fitness. We created E. coli strains with specific destabilizing mutations in the chromosomal folA gene encoding dihydrofolate reductase (DHFR) and quantified the ensuing changes in the abundances of 2,000+ E. coli proteins in mutant strains using tandem mass tags with subsequent LC-MS/MS. mRNA abundances in the same E. coli strains were also quantified. The proteomic effects of mutations in DHFR are quantitatively linked to phenotype: the SDs of the distributions of logarithms of relative (to WT) protein abundances anticorrelate with bacterial growth rates. Proteomes hierarchically cluster first by media conditions, and within each condition, by the severity of the perturbation to DHFR function. These results highlight the importance of a systems-level layer in the genotype-phenotype relationship.
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Affiliation(s)
- Shimon Bershtein
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA; Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
| | - Jeong-Mo Choi
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Sanchari Bhattacharyya
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Bogdan Budnik
- MSPRL, Center of Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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Mitosch K, Bollenbach T. Bacterial responses to antibiotics and their combinations. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:545-557. [PMID: 25756107 DOI: 10.1111/1758-2229.12190] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Antibiotics affect bacterial cell physiology at many levels. Rather than just compensating for the direct cellular defects caused by the drug, bacteria respond to antibiotics by changing their morphology, macromolecular composition, metabolism, gene expression and possibly even their mutation rate. Inevitably, these processes affect each other, resulting in a complex response with changes in the expression of numerous genes. Genome-wide approaches can thus help in gaining a comprehensive understanding of bacterial responses to antibiotics. In addition, a combination of experimental and theoretical approaches is needed for identifying general principles that underlie these responses. Here, we review recent progress in our understanding of bacterial responses to antibiotics and their combinations, focusing on effects at the levels of growth rate and gene expression. We concentrate on studies performed in controlled laboratory conditions, which combine promising experimental techniques with quantitative data analysis and mathematical modeling. While these basic research approaches are not immediately applicable in the clinic, uncovering the principles and mechanisms underlying bacterial responses to antibiotics may, in the long term, contribute to the development of new treatment strategies to cope with and prevent the rise of resistant pathogenic bacteria.
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Li J, Liu F, Wang Q, Ge P, Woo PCY, Yan J, Zhao Y, Gao GF, Liu CH, Liu C. Genomic and transcriptomic analysis of NDM-1 Klebsiella pneumoniae in spaceflight reveal mechanisms underlying environmental adaptability. Sci Rep 2014; 4:6216. [PMID: 25163721 PMCID: PMC4147364 DOI: 10.1038/srep06216] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/07/2014] [Indexed: 01/10/2023] Open
Abstract
The emergence and rapid spread of New Delhi Metallo-beta-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae strains has caused a great concern worldwide. To better understand the mechanisms underlying environmental adaptation of those highly drug-resistant K. pneumoniae strains, we took advantage of the China's Shenzhou 10 spacecraft mission to conduct comparative genomic and transcriptomic analysis of a NDM-1 K. pneumoniae strain (ATCC BAA-2146) being cultivated under different conditions. The samples were recovered from semisolid medium placed on the ground (D strain), in simulated space condition (M strain), or in Shenzhou 10 spacecraft (T strain) for analysis. Our data revealed multiple variations underlying pathogen adaptation into different environments in terms of changes in morphology, H2O2 tolerance and biofilm formation ability, genomic stability and regulation of metabolic pathways. Additionally, we found a few non-coding RNAs to be differentially regulated. The results are helpful for better understanding the adaptive mechanisms of drug-resistant bacterial pathogens.
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Affiliation(s)
- Jia Li
- 1] Nanlou Respiratory Diseases Department, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing 100853, China [2] School of medicine, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Fei Liu
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Qi Wang
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Pupu Ge
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, University Pathology Building, Compound Pokfulam Road, Hong Kong, China
| | - Jinghua Yan
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbei Road, Changping District, Beijing 102206, China
| | - George F Gao
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Cui Hua Liu
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Changting Liu
- Nanlou Respiratory Diseases Department, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing 100853, China
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43
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Antibiotic-induced replication stress triggers bacterial competence by increasing gene dosage near the origin. Cell 2014; 157:395-406. [PMID: 24725406 DOI: 10.1016/j.cell.2014.01.068] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 12/01/2013] [Accepted: 01/29/2014] [Indexed: 12/12/2022]
Abstract
Streptococcus pneumoniae (pneumococcus) kills nearly 1 million children annually, and the emergence of antibiotic-resistant strains poses a serious threat to human health. Because pneumococci can take up DNA from their environment by a process called competence, genes associated with antibiotic resistance can rapidly spread. Remarkably, competence is activated in response to several antibiotics. Here, we demonstrate that antibiotics targeting DNA replication cause an increase in the copy number of genes proximal to the origin of replication (oriC). As the genes required for competence initiation are located near oriC, competence is thereby activated. Transcriptome analyses show that antibiotics targeting DNA replication also upregulate origin-proximal gene expression in other bacteria. This mechanism is a direct, intrinsic consequence of replication fork stalling. Our data suggest that evolution has conserved the oriC-proximal location of important genes in bacteria to allow for a robust response to replication stress without the need for complex gene-regulatory pathways. PAPERCLIP:
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Nixon MR, Saionz KW, Koo MS, Szymonifka MJ, Jung H, Roberts JP, Nandakumar M, Kumar A, Liao R, Rustad T, Sacchettini JC, Rhee KY, Freundlich JS, Sherman DR. Folate pathway disruption leads to critical disruption of methionine derivatives in Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2014; 21:819-30. [PMID: 24954008 DOI: 10.1016/j.chembiol.2014.04.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 04/11/2014] [Accepted: 04/23/2014] [Indexed: 01/08/2023]
Abstract
In this study, we identified antifolates with potent, targeted activity against whole-cell Mycobacterium tuberculosis (MTB). Liquid chromatography-mass spectrometry analysis of antifolate-treated cultures revealed metabolic disruption, including decreased pools of methionine and S-adenosylmethionine. Transcriptomic analysis highlighted altered regulation of genes involved in the biosynthesis and utilization of these two compounds. Supplementation with amino acids or S-adenosylmethionine was sufficient to rescue cultures from antifolate treatment. Instead of the "thymineless death" that characterizes folate pathway inhibition in a wide variety of organisms, these data suggest that MTB is vulnerable to a critical disruption of the reactions centered around S-adenosylmethionione, the activated methyl cycle.
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Affiliation(s)
- Molly R Nixon
- Interdisciplinary Program in Pathobiology, Department of Global Health, University of Washington, Seattle, WA 98195, USA; Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Kurt W Saionz
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Mi-Sun Koo
- Department of Pharmacology and Physiology and Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ 07103, USA
| | - Michael J Szymonifka
- Department of Pharmacology and Physiology and Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ 07103, USA
| | - Hunmin Jung
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Justin P Roberts
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Madhumita Nandakumar
- Departments of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Anuradha Kumar
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Reiling Liao
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Tige Rustad
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Kyu Y Rhee
- Departments of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Joel S Freundlich
- Department of Pharmacology and Physiology and Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ 07103, USA
| | - David R Sherman
- Interdisciplinary Program in Pathobiology, Department of Global Health, University of Washington, Seattle, WA 98195, USA; Seattle Biomedical Research Institute, Seattle, WA 98109, USA.
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45
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Martín CM, Viguera E, Guzmán EC. Rifampicin suppresses thymineless death by blocking the transcription-dependent step of chromosome initiation. DNA Repair (Amst) 2014; 18:10-7. [PMID: 24742961 DOI: 10.1016/j.dnarep.2014.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/25/2014] [Accepted: 03/07/2014] [Indexed: 11/19/2022]
Abstract
Thymineless death (TLD), a phenomenon in which thymine auxotrophy becomes lethal when cells are starved of thymine, can be prevented by the presence of rifampicin, an RNA polymerase inhibitor. Several lines of evidence link TLD to chromosome initiation events. This suggests that rifampicin-mediated TLD suppression could be due to the inhibition of RNA synthesis required for DNA chromosomal initiation at oriC, although other mechanisms cannot be discarded. In this work, we show that the addition of different rifampicin concentrations to thymine-starved cells modulates TLD and chromosomal initiation capacity (ChIC). Time-lapse experiments find increasing levels of ChIC during thymine starvation correlated with the accumulation of simple-Y, double-Y and bubble arc replication intermediates at the oriC region as visualized by two-dimensional DNA agarose gel electrophoresis. None of these structures were observed following rifampicin addition or under genetic-physiological conditions that suppress TLD, indicating that abortive chromosome replication initiations under thymine starvation are crucial for this lethality. Significantly, the introduction of mioC and gid mutations which alter transcription levels around oriC, reduces ChIC and alleviates TLD. These results show that the impairment of transcription-dependent initiation caused by rifampicin addition, is responsible for TLD suppression. Our findings here may provide new avenues for the development of improved antibacterial treatments and chemotherapies based on thymine starvation-induced cell death.
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Affiliation(s)
- Carmen Mata Martín
- Departamento de Bioquímica, Biología Molecular y Genética, Universidad de Extremadura, 06071 Badajoz, Spain
| | - Enrique Viguera
- Área de Genética, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Elena C Guzmán
- Departamento de Bioquímica, Biología Molecular y Genética, Universidad de Extremadura, 06071 Badajoz, Spain.
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46
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Edwards AL, Sangurdekar DP, Jeong KS, Khodursky AB, Rybenkov VV. Transient growth arrest in Escherichia coli induced by chromosome condensation. PLoS One 2013; 8:e84027. [PMID: 24376785 PMCID: PMC3871593 DOI: 10.1371/journal.pone.0084027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 11/18/2013] [Indexed: 11/21/2022] Open
Abstract
MukB is a bacterial SMC (structural maintenance of chromosome) protein that regulates the global folding of the Escherichia coli chromosome by bringing distant DNA segments together. We report that moderate overproduction of MukB may lead, depending on strain and growth conditions, to transient growth arrest. In DH5α cells, overproduction of MukB or MukBEF using pBAD expression system triggered growth arrest 2.5 h after induction. The exit from growth arrest was accompanied by the loss of the overproducing plasmid and a decline in the abundance of MukBEF. The arrested cells showed a compound gene expression profile which can be characterized by the following features: (i) a broad and deep downregulation of ribosomal proteins (up to 80-fold); (ii) downregulation of groups of genes encoding enzymes involved in nucleotide metabolism, respiration, and central metabolism; (iii) upregulation of some of the genes responsive to general stress; and (iv) degradation of the patterns of spatial correlations in the transcriptional activity of the chromosome. The transcriptional state of the MukB induced arrest is most similar to stationary cells and cells recovered from stationary phase into a nutrient deprived medium, to amino acid starved cells and to the cells shifting from glucose to acetate. The mukB++ state is dissimilar from all examined transcriptional states generated by protein overexpression with the possible exception of RpoE and RpoH overexpression. Thus, the transcription profile of MukB-arrested cells can be described as a combination of responses typical for other growth-arrested cells and those for overproducers of DNA binding proteins with a particularly deep down-regulation of ribosomal genes.
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MESH Headings
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Bacterial/chemistry
- Chromosomes, Bacterial/genetics
- Chromosomes, Bacterial/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Escherichia coli/cytology
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Gene Expression Regulation, Bacterial
- Time Factors
- Transcription, Genetic
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Affiliation(s)
- Andrea L. Edwards
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Dipen P. Sangurdekar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, Minnesota, United States of America
| | - Kyeong S. Jeong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, Minnesota, United States of America
| | - Arkady B. Khodursky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, Minnesota, United States of America
| | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, United States of America
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