1
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Shi H, Li T, Xu J, Yu J, Yang S, Zhang XE, Tao S, Gu J, Deng JY. MgrB Inactivation Confers Trimethoprim Resistance in Escherichia coli. Front Microbiol 2021; 12:682205. [PMID: 34394028 PMCID: PMC8355897 DOI: 10.3389/fmicb.2021.682205] [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: 03/18/2021] [Accepted: 06/30/2021] [Indexed: 11/22/2022] Open
Abstract
After several decades of use, trimethoprim (TMP) remains one of the key access antimicrobial drugs listed by the World Health Organization. To circumvent the problem of trimethoprim resistance worldwide, a better understanding of drug-resistance mechanisms is required. In this study, we screened the single-gene knockout library of Escherichia coli, and identified mgrB and other several genes involved in trimethoprim resistance. Subsequent comparative transcriptional analysis between ΔmgrB and the wild-type strain showed that expression levels of phoP, phoQ, and folA were significantly upregulated in ΔmgrB. Further deleting phoP or phoQ could partially restore trimethoprim sensitivity to ΔmgrB, and co-overexpression of phoP/Q caused TMP resistance, suggesting the involvement of PhoP/Q in trimethoprim resistance. Correspondingly, MgrB and PhoP were shown to be able to modulated folA expression in vivo. After that, efforts were made to test if PhoP could directly modulate the expression of folA. Though phosphorylated PhoP could bind to the promotor region of folA in vitro, the former only provided a weak protection on the latter as shown by the DNA footprinting assay. In addition, deleting the deduced PhoP box in ΔmgrB could only slightly reverse the TMP resistance phenotype, suggesting that it is less likely for PhoP to directly modulate the transcription of folA. Taken together, our data suggested that, in E. coli, MgrB affects susceptibility to trimethoprim by modulating the expression of folA with the involvement of PhoP/Q. This work broadens our understanding of the regulation of folate metabolism and the mechanisms of TMP resistance in bacteria.
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Affiliation(s)
- Hongmei Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ting Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jintian Xu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jifang Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Jing Gu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jiao-Yu Deng
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan, China
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2
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Manna MS, Tamer YT, Gaszek I, Poulides N, Ahmed A, Wang X, Toprak FCR, Woodard DR, Koh AY, Williams NS, Borek D, Atilgan AR, Hulleman JD, Atilgan C, Tambar U, Toprak E. A trimethoprim derivative impedes antibiotic resistance evolution. Nat Commun 2021; 12:2949. [PMID: 34011959 PMCID: PMC8134463 DOI: 10.1038/s41467-021-23191-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/06/2021] [Indexed: 01/07/2023] Open
Abstract
The antibiotic trimethoprim (TMP) is used to treat a variety of Escherichia coli infections, but its efficacy is limited by the rapid emergence of TMP-resistant bacteria. Previous laboratory evolution experiments have identified resistance-conferring mutations in the gene encoding the TMP target, bacterial dihydrofolate reductase (DHFR), in particular mutation L28R. Here, we show that 4'-desmethyltrimethoprim (4'-DTMP) inhibits both DHFR and its L28R variant, and selects against the emergence of TMP-resistant bacteria that carry the L28R mutation in laboratory experiments. Furthermore, antibiotic-sensitive E. coli populations acquire antibiotic resistance at a substantially slower rate when grown in the presence of 4'-DTMP than in the presence of TMP. We find that 4'-DTMP impedes evolution of resistance by selecting against resistant genotypes with the L28R mutation and diverting genetic trajectories to other resistance-conferring DHFR mutations with catalytic deficiencies. Our results demonstrate how a detailed characterization of resistance-conferring mutations in a target enzyme can help identify potential drugs against antibiotic-resistant bacteria, which may ultimately increase long-term efficacy of antimicrobial therapies by modulating evolutionary trajectories that lead to resistance.
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Affiliation(s)
- Madhu Sudan Manna
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA ,grid.267313.20000 0000 9482 7121Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Yusuf Talha Tamer
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Ilona Gaszek
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Nicole Poulides
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Ayesha Ahmed
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Xiaoyu Wang
- grid.267313.20000 0000 9482 7121Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Furkan C. R. Toprak
- grid.264756.40000 0004 4687 2082Texas A&M University, College Station, TX USA
| | - DaNae R. Woodard
- grid.267313.20000 0000 9482 7121Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Andrew Y. Koh
- grid.267313.20000 0000 9482 7121Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX USA ,grid.267313.20000 0000 9482 7121Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Noelle S. Williams
- grid.267313.20000 0000 9482 7121Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Dominika Borek
- grid.267313.20000 0000 9482 7121Department of Molecular Biophysics, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Ali Rana Atilgan
- grid.5334.10000 0004 0637 1566Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - John D. Hulleman
- grid.267313.20000 0000 9482 7121Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX USA ,grid.267313.20000 0000 9482 7121Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Canan Atilgan
- grid.5334.10000 0004 0637 1566Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Uttam Tambar
- grid.267313.20000 0000 9482 7121Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX USA
| | - Erdal Toprak
- grid.267313.20000 0000 9482 7121Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX USA ,grid.267313.20000 0000 9482 7121Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX USA
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3
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Trimethoprim and other nonclassical antifolates an excellent template for searching modifications of dihydrofolate reductase enzyme inhibitors. J Antibiot (Tokyo) 2019; 73:5-27. [PMID: 31578455 PMCID: PMC7102388 DOI: 10.1038/s41429-019-0240-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/07/2019] [Accepted: 08/22/2019] [Indexed: 12/17/2022]
Abstract
The development of new mechanisms of resistance among pathogens, the occurrence and transmission of genes responsible for antibiotic insensitivity, as well as cancer diseases have been a serious clinical problem around the world for over 50 years. Therefore, intense searching of new leading structures and active substances, which may be used as new drugs, especially against strain resistant to all available therapeutics, is very important. Dihydrofolate reductase (DHFR) has attracted a lot of attention as a molecular target for bacterial resistance over several decades, resulting in a number of useful agents. Trimethoprim (TMP), (2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidine) is the well-known dihydrofolate reductase inhibitor and one of the standard antibiotics used in urinary tract infections (UTIs). This review highlights advances in design, synthesis, and biological evaluations in structural modifications of TMP as DHFR inhibitors. In addition, this report presents the differences in the active site of human and pathogen DHFR. Moreover, an excellent review of DHFR inhibition and their relevance to antimicrobial and parasitic chemotherapy was presented.
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4
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Tamer YT, Gaszek IK, Abdizadeh H, Batur TA, Reynolds KA, Atilgan AR, Atilgan C, Toprak E. High-Order Epistasis in Catalytic Power of Dihydrofolate Reductase Gives Rise to a Rugged Fitness Landscape in the Presence of Trimethoprim Selection. Mol Biol Evol 2019; 36:1533-1550. [PMID: 30982891 PMCID: PMC6573477 DOI: 10.1093/molbev/msz086] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Evolutionary fitness landscapes of several antibiotic target proteins have been comprehensively mapped showing strong high-order epistasis between mutations, but understanding these effects at the biochemical and structural levels remained open. Here, we carried out an extensive experimental and computational study to quantitatively understand the evolutionary dynamics of Escherichia coli dihydrofolate reductase (DHFR) enzyme in the presence of trimethoprim-induced selection. To facilitate this, we developed a new in vitro assay for rapidly characterizing DHFR steady-state kinetics. Biochemical and structural characterization of resistance-conferring mutations targeting a total of ten residues spanning the substrate binding pocket of DHFR revealed distinct changes in the catalytic efficiencies of mutated DHFR enzymes. Next, we measured biochemical parameters (Km, Ki, and kcat) for a mutant library carrying all possible combinations of six resistance-conferring DHFR mutations and quantified epistatic interactions between them. We found that the high-order epistasis in catalytic power of DHFR (kcat and Km) creates a rugged fitness landscape under trimethoprim selection. Taken together, our data provide a concrete illustration of how epistatic coupling at the level of biochemical parameters can give rise to complex fitness landscapes, and suggest new strategies for developing mutant specific inhibitors.
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Affiliation(s)
- Yusuf Talha Tamer
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ilona K Gaszek
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Haleh Abdizadeh
- Faculty of Science and Engineering, University of Groningen, Groningen, Netherlands
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | | | - Kimberly A Reynolds
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ali Rana Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Erdal Toprak
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX
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5
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Baym M, Lieberman TD, Kelsic ED, Chait R, Gross R, Yelin I, Kishony R. Spatiotemporal microbial evolution on antibiotic landscapes. Science 2017; 353:1147-51. [PMID: 27609891 DOI: 10.1126/science.aag0822] [Citation(s) in RCA: 307] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/28/2016] [Indexed: 01/03/2023]
Abstract
A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front. While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front, we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behind more sensitive lineages. The MEGA-plate provides a versatile platform for studying microbial adaption and directly visualizing evolutionary dynamics.
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Affiliation(s)
- Michael Baym
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Tami D Lieberman
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Eric D Kelsic
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Remy Chait
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Rotem Gross
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Idan Yelin
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Roy Kishony
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA. Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel. Faculty of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel.
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6
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Liu PC, Lee YT, Wang CY, Yang YT. Design and Use of a Low Cost, Automated Morbidostat for Adaptive Evolution of Bacteria Under Antibiotic Drug Selection. J Vis Exp 2016. [PMID: 27768065 DOI: 10.3791/54426] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We describe a low cost, configurable morbidostat for characterizing the evolutionary pathway of antibiotic resistance. The morbidostat is a bacterial culture device that continuously monitors bacterial growth and dynamically adjusts the drug concentration to constantly challenge the bacteria as they evolve to acquire drug resistance. The device features a working volume of ~10 ml and is fully automated and equipped with optical density measurement and micro-pumps for medium and drug delivery. To validate the platform, we measured the stepwise acquisition of trimethoprim resistance in Escherichia coli MG 1655, and integrated the device with a multiplexed microfluidic platform to investigate cell morphology and antibiotic susceptibility. The approach can be up-scaled to laboratory studies of antibiotic drug resistance, and is extendible to adaptive evolution for strain improvements in metabolic engineering and other bacterial culture experiments.
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Affiliation(s)
- Po C Liu
- Electrical Engineering, National Tsing Hua University
| | - Yi T Lee
- Electrical Engineering, National Tsing Hua University
| | - Chun Y Wang
- Electrical Engineering, National Tsing Hua University
| | - Ya-Tang Yang
- Electrical Engineering, National Tsing Hua University;
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7
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Affiliation(s)
- C.J. Thomson
- Department of Medical Microbiology Medical School -University of Edinburgh Teviot Place Edinburgh EH8 9AG
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8
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Rabbers I, van Heerden JH, Nordholt N, Bachmann H, Teusink B, Bruggeman FJ. Metabolism at evolutionary optimal States. Metabolites 2015; 5:311-43. [PMID: 26042723 PMCID: PMC4495375 DOI: 10.3390/metabo5020311] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/20/2015] [Accepted: 05/25/2015] [Indexed: 01/13/2023] Open
Abstract
Metabolism is generally required for cellular maintenance and for the generation of offspring under conditions that support growth. The rates, yields (efficiencies), adaptation time and robustness of metabolism are therefore key determinants of cellular fitness. For biotechnological applications and our understanding of the evolution of metabolism, it is necessary to figure out how the functional system properties of metabolism can be optimized, via adjustments of the kinetics and expression of enzymes, and by rewiring metabolism. The trade-offs that can occur during such optimizations then indicate fundamental limits to evolutionary innovations and bioengineering. In this paper, we review several theoretical and experimental findings about mechanisms for metabolic optimization.
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Affiliation(s)
- Iraes Rabbers
- Department of Systems Bioinformatics, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Johan H van Heerden
- Department of Systems Bioinformatics, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Niclas Nordholt
- Department of Systems Bioinformatics, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Herwig Bachmann
- Department of Systems Bioinformatics, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
- NIZO Food Research, 6718 ZB Ede, The Netherlands.
- Top Institute Food and Nutrition, 6700 AN Wageningen, The Netherlands.
| | - Bas Teusink
- Department of Systems Bioinformatics, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Frank J Bruggeman
- Department of Systems Bioinformatics, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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9
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Toprak E, Veres A, Michel JB, Chait R, Hartl DL, Kishony R. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet 2011; 44:101-5. [PMID: 22179135 PMCID: PMC3534735 DOI: 10.1038/ng.1034] [Citation(s) in RCA: 494] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 11/15/2011] [Indexed: 12/31/2022]
Abstract
Antibiotic resistance can evolve through the sequential accumulation of multiple mutations. To study such gradual evolution, we developed a selection device, the 'morbidostat', that continuously monitors bacterial growth and dynamically regulates drug concentrations, such that the evolving population is constantly challenged. We analyzed the evolution of resistance in Escherichia coli under selection with single drugs, including chloramphenicol, doxycycline and trimethoprim. Over a period of ∼20 days, resistance levels increased dramatically, with parallel populations showing similar phenotypic trajectories. Whole-genome sequencing of the evolved strains identified mutations both specific to resistance to a particular drug and shared in resistance to multiple drugs. Chloramphenicol and doxycycline resistance evolved smoothly through diverse combinations of mutations in genes involved in translation, transcription and transport. In contrast, trimethoprim resistance evolved in a stepwise manner, through mutations restricted to the gene encoding the enzyme dihydrofolate reductase (DHFR). Sequencing of DHFR over the time course of the experiment showed that parallel populations evolved similar mutations and acquired them in a similar order.
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Affiliation(s)
- Erdal Toprak
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Adrian Veres
- Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Jean-Baptiste Michel
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, USA
| | - Remy Chait
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Roy Kishony
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
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10
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Feng J, Grubbs J, Dave A, Goswami S, Horner CG, Howell EE. Radical redesign of a tandem array of four R67 dihydrofolate reductase genes yields a functional, folded protein possessing 45 substitutions. Biochemistry 2010; 49:7384-92. [PMID: 20684560 DOI: 10.1021/bi1005943] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
R67 dihydrofolate reductase (DHFR) is a plasmid-encoded, type II enzyme. Four monomers (78 amino acids long) assemble into a homotetramer possessing 222 symmetry. In previous studies, a tandem array of four R67 DHFR gene copies was fused in frame to generate a functional monomer named Quad1. This protein possessed the essential tertiary structure of the R67 "parent". To facilitate mutagenesis reactions, restriction enzyme sites were introduced in the tandem gene array. S59A and H362L mutations were also added to minimize possible folding topologies; this protein product, named Quad3, possesses 10 substitutions and is functional. Since R67 DHFR possesses a stable scaffold, a large jump in sequence space was performed by the further addition of 45 amino acid substitutions. The mutational design utilized alternate sequences from other type II DHFRs. In addition, most of the mutations were positioned on the surface of the protein as well as in the disordered N-terminal sequence, which serves as the linker between the fused domains. The resulting Quad4 protein is quite functional; however, it is less stable than Quad1, suffering a DeltaDeltaG loss of 5 kcal/mol at pH 5. One unexpected result was formation of Quad4 dimers and higher order oligomers at pH 8. R67 DHFR, and its derivative Quad proteins, possesses a robust scaffold, capable of withstanding introduction of >or=55 substitutions.
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Affiliation(s)
- Jian Feng
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, USA
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11
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Sikora AE, Zielke R, Datta K, Maddock JR. The Vibrio harveyi GTPase CgtAV is essential and is associated with the 50S ribosomal subunit. J Bacteriol 2006; 188:1205-10. [PMID: 16428430 PMCID: PMC1347350 DOI: 10.1128/jb.188.3.1205-1210.2006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It was previously reported that unlike the other obg/cgtA GTPases, the Vibrio harveyi cgtAV is not essential. Here we show that cgtAV was not disrupted in these studies and is, in fact, essential for viability. Depletion of CgtAV did not result in cell elongation. CgtAV is associated with the large ribosomal particle. In light of our results, we predict that the V. harveyi CgtAV protein plays a similar essential role to that seen for Obg/CgtA proteins in other bacteria.
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Affiliation(s)
- A E Sikora
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
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12
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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14
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Adrian PV, Klugman KP. Mutations in the dihydrofolate reductase gene of trimethoprim-resistant isolates of Streptococcus pneumoniae. Antimicrob Agents Chemother 1997; 41:2406-13. [PMID: 9371341 PMCID: PMC164136 DOI: 10.1128/aac.41.11.2406] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Streptococcus pneumoniae isolates resistant to several antimicrobial agent classes including trimethoprim-sulfamethoxazole have been reported with increasing frequency throughout the world. The MICs of trimethoprim, sulfamethoxazole, and trimethoprim-sulfamethoxazole (1:19) for 259 clinical isolates from South Africa were determined, and 166 of these 259 (64%) isolates were resistant to trimethoprim-sulfamethoxazole (MICs > or =20 mg/liter). Trimethoprim resistance was found to be more strongly correlated with trimethoprim-sulfamethoxazole resistance (correlation coefficient, 0.744) than was sulfamethoxazole resistance (correlation coefficient, 0.441). The dihydrofolate reductase genes from 11 trimethoprim-resistant (MICs, 64 to 512 microg/ml) clinical isolates of Streptococcus pneumoniae were amplified by PCR, and the nucleotide sequences were determined. Two main groups of mutations to the dihydrofolate reductase gene were found. Both groups shared six amino acid changes (Glu20-Asp, Pro70-Ser, Gln81-His, Asp92-Ala, Ile100-Leu, and Leu135-Phe). The first group included two extra changes (Lys60-Gln and Pro111-Ser), and the second group was characterized by six additional amino acid changes (Glu14-Asp, Ile74-Leu, Gln91-His, Glu94-Asp, Phe147-Ser, and Ala149-Thr). Chromosomal DNA from resistant isolates and cloned PCR products of the genes encoding resistant dihydrofolate reductases were capable of transforming a susceptible strain of S. pneumoniae to trimethoprim resistance. The inhibitor profiles of recombinant dihydrofolate reductase from resistant and susceptible isolates revealed that the dihydrofolate reductase from trimethoprim-resistant isolates was 50-fold more resistant (50% inhibitory doses [ID50s], 3.9 to 7.3 microM) than that from susceptible strains (ID50s, 0.15 microM). Site-directed mutagenesis experiments revealed that one mutation, Ile100-Leu, resulted in a 50-fold increase in the ID50 of trimethoprim. The resistant dihydrofolate reductases were characterized by highly conserved redundant changes in the nucleotide sequence, suggesting that the genes encoding resistant dihydrofolate reductases may have evolved as a result of inter- or intraspecies recombination by transformation.
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Affiliation(s)
- P V Adrian
- Pneumococcal Diseases Research Unit of South African Institute for Medical Research, University of the Witwatersrand, and Medical Research Council, Johannesburg.
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15
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Lee H, Reyes VM, Kraut J. Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4. Biochemistry 1996; 35:7012-20. [PMID: 8679526 DOI: 10.1021/bi960028g] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The crystal structure of Escherichia coli dihydrofolate reductase (ecDHFR, EC 1.5.1.3) as a binary complex with folinic acid (5-formyl-5,6,7,8-tetrahydrofolate; also called leucovorin or citrovorum factor) has been solved in two space groups, P6(1) and P6(5), with, respectively, two molecules and one molecule per asymmetric unit. The crystal structures have been refined to an R-factor of 14.2% at resolutions of 2.0 and 1.9 A. The P6(1) structure is isomorphous with several previously reported ecDHFR binary complexes [Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C., & Kraut, J. (1982) J. Biol. Chem. 257, 13650-13662; Reyes, V.M., Sawaya, M.R., Brown, K.A., & Kraut, J. (1995) Biochemistry 34, 2710-2723]; enzyme and ligand conformations are very similar to the P6(1) 5,10-dideazatetrahydrofolate complex. While the two enzyme subdomains of the P6(1) structure are nearly in the closed conformation, exemplified by the methotrexate P6(1) binary complex, in the P6(5) structure they are in an intermediate conformation, halfway between the closed and the fully open conformation of the apoenzyme [Bystroff, C., Oatley, S.J., & Kraut, J. (1990) Biochemistry 29, 3263-3277]. Thus crystal packing strongly influences this aspect of the enzyme structure. In contrast to the P6(1) structure, in which the Met-20 loop (residues 9-23) is turned away from the substrate binding pocket, in the P6(5) structure the Met-20 loop blocks the pocket and protrudes into the cofactor binding site. In this respect, the P6(5) structure is unique. Additionally, positioning of a Ca2+ ion (a component of the crystallization medium) is different in the two crystal packings: in the P6(1) structure it lies at the boundary between the two molecules of the asymmetric unit, while in P6(5) it coordinates two water molecules, the hydroxyl group of an ethanol molecule, and the backbone carbonyl oxygens of Glu-17, Asn-18, and Met-20. The Ca2+ ion thus stabilizes a single turn of 3(10) helix (residues 16-18 in the Met-20 loop), a second unique feature of the P6(5) crystal structure. The disposition of the N5-formyl group in these structures indicates formation, at least half of the time, of an intramolecular hydrogen bond between the formyl oxygen and O4 of the tetrahydropterin ring. This observation is consistent with the existence of an enol-keto equilibrium in which the enolic tautomer is favored when a hydrogen-bond acceptor is present between O4 and N5. Such would be the case whenever a water molecule occupies that site as part of a hypothetical proton-relay mechanism. Two arginine side chains, Arg-52 in the P6(5) structure and Arg-44 in molecule A of the P6(1) structure, are turned away drastically from the ligand (p-aminobenzoyl)glutamic acid moiety as compared with previously reported DHFR binary complex structures. As in the ecDHFR dideazatetrahydrofolate complex, in both the P6(1) and P6(5) structures a water molecule bridges pteridine O4 and Trp-22(N epsilon 1) with ideal geometry for hydrogen bonding, perhaps contributing to the slow release of 5,6,7,8-tetrahydrofolate from the enzyme-product complex. When either the P6(1) or the P6(5) structures are superimposed with the NADPH holoenzyme [Sawaya, M. R. (1994) Ph.D. Dissertation, University of California, San Diego], we find that the distances between the nicotinamide C4 and pteridine C6 and C7 are very short, 2.1 and 1.7 A in the P6(1) case and 2.0 and 1.4 A in the P6(5) case, perhaps in part explaining the more rapid release of tetrahydrofolate from the enzyme-product complex when NADPH is bound.
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Affiliation(s)
- H Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0506, USA
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16
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Asselbergs FA, Widmer R. Use of the Escherichia coli chromosomal DHFR gene as selection marker in mammalian cells. J Biotechnol 1995; 43:133-8. [PMID: 8562018 DOI: 10.1016/0168-1656(95)00131-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The folA gene, the chromosomal dhfr gene of Escherichia coli, was engineered for expression in mammalian cells. In contrast to plasmid-derived bacterial dhfr genes previously used as selection markers in mammalian cells, the folA gene product is inhibitable by methotrexate (MTX) and trimethoprim (TMP). Therefore, this dhfr may present an alternative to mammalian dhfr species currently used as amplifiable selection markers. Transfected E. coli folA dhfr could complement the lack of endogenous DHFR in Chinese hamster ovary (CHO) cells lacking a functional dhfr gene. Both MTX and TMP inhibited growth of E. coli folA dhfr-transfected CHO cells. Expression of E. coli folA DHFR could be visualized by incubating the transfected cells with a fluorescent methotrexate derivative (F-MTX). Binding of F-MTX to E. coli folA DHFR was inhibitable as by both MTX and TMP, whereas MTX but not TMP blocked binding of F-MTX to recombinant mouse DHFR.
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Affiliation(s)
- F A Asselbergs
- Pharma Research Department, CIBA-GEIGY Ltd., Basel, Switzerland
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17
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Huovinen P, Sundström L, Swedberg G, Sköld O. Trimethoprim and sulfonamide resistance. Antimicrob Agents Chemother 1995; 39:279-89. [PMID: 7726483 PMCID: PMC162528 DOI: 10.1128/aac.39.2.279] [Citation(s) in RCA: 300] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- P Huovinen
- Antimicrobial Research Laboratory, National Public Health Institute, Turku, Finland
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18
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Leszczyńska K, Bolhuis A, Leenhouts K, Venema G, Cegłowski P. Cloning and molecular analysis of the dihydrofolate reductase gene from Lactococcus lactis. Appl Environ Microbiol 1995; 61:561-6. [PMID: 7574597 PMCID: PMC167319 DOI: 10.1128/aem.61.2.561-566.1995] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The Lactococcus lactis gene encoding trimethoprim resistance has been cloned and expressed in Escherichia coli and Bacillus subtilis. Several lines of evidence indicate that the cloned gene encodes dihydrofolate reductase (DHFR). (i) It fully complements the fol "null" mutation in E. coli. (ii) Nucleotide sequencing of the cloned fragment revealed the presence of one open reading frame encoding a protein that shares homology with the family of bacterial DHFR enzymes. (iii) Overexpression of this open reading frame in E. coli resulted in the appearance in cell extracts of a protein of the expected size as well as in a dramatic increase of DHFR activity. In cell extracts, the DHFR activity was not inhibited by low trimethoprim concentration. By Northern (RNA) blotting and primer extension analyses, the size and the start point of the dhfr transcript, respectively, have been determined. Results of these experiments indicate that in L. lactis the dhfr gene represents part of a larger transcription unit.
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Affiliation(s)
- K Leszczyńska
- Institute of Biochemistry and Biophysics, Warsaw, Poland
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19
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Dion A, Linn CE, Bradrick TD, Georghiou S, Howell EE. How do mutations at phenylalanine-153 and isoleucine-155 partially suppress the effects of the aspartate-27-->serine mutation in Escherichia coli dihydrofolate reductase? Biochemistry 1993; 32:3479-87. [PMID: 8461309 DOI: 10.1021/bi00064a036] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Several second-site suppressors of the D27S lesion in Escherichia coli dihydrofolate reductase (DHFR) have been identified. The activity of the primary mutant, D27S DHRF, was found to be greatly decreased at pH 7.0, consistent with aspartic acid-27 being critically involved in proton donation during catalysis. Partial suppressors of the D27S mutation have been selected by their ability to confer an increased resistance to trimethoprim upon host E. coli; the suppressors have been identified as F153S or I155N substitutions. D27S+F153S and D27S+I155N DHFRs display 2-3-fold increases in kcat over D27S DHFR values, but only the F153S mutation decreases the Km for dihydrofolate by a factor of 2. Neither double mutant approaches wild-type DHFR activity. Unexpectedly, Phe153 and Ile155 occur on the surface of the protein and are approximately 8 and 14 A distant from the active site. Ile155 is a member of a beta-bulge. A previously identified suppressing mutation, F137S, occurs nearby and is also a member of the same beta-bulge [Howell et al. (1990) Biochemistry 29, 8561-8569]. Clustering of these three second-site mutations indicates this area of the structure may be important in protein function. Conformational changes due to the presence of these suppressing mutations are likely as the F153S and I155N mutations do not affect hydride-transfer rates upon introduction in wild-type DHFR and alterations in circular dichroism spectra are associated with the double-mutant DHFRs.
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Affiliation(s)
- A Dion
- Department of Biochemistry, University of Tennessee, Knoxville 37996-0840
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20
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Silver LL, Bostian KA. Discovery and development of new antibiotics: the problem of antibiotic resistance. Antimicrob Agents Chemother 1993; 37:377-83. [PMID: 8460908 PMCID: PMC187680 DOI: 10.1128/aac.37.3.377] [Citation(s) in RCA: 134] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- L L Silver
- Department of Microbiology and Molecular Genetics, Merck Research Laboratory, Rahway, New Jersey 07065-0900
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21
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Reece LJ, Nichols R, Ogden RC, Howell EE. Construction of a synthetic gene for an R-plasmid-encoded dihydrofolate reductase and studies on the role of the N-terminus in the protein. Biochemistry 1991; 30:10895-904. [PMID: 1932013 DOI: 10.1021/bi00109a013] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
R67 dihydrofolate reductase (DHFR) is a novel protein that provides clinical resistance to the antibacterial drug trimethoprim. The crystal structure of a dimeric form of R67 DHFR indicates the first 16 amino acids are disordered [Matthews et al. (1986) Biochemistry 25, 4194-4204]. To investigate whether these amino acids are necessary for protein function, the first 16 N-terminal residues have been cleaved off by chymotrypsin. The truncated protein is fully active with kcat = 1.3 s-1, Km(NADPH) = 3.0 microM, and Km(dihydrofolate) = 5.8 microM. This result suggests the functional core of the protein resides in the beta-barrel structure defined by residues 27-78. To study this protein further, synthetic genes coding for full-length and truncated R67 DHFRs were constructed. Surprisingly, the gene coding for truncated R67 DHFR does not produce protein in vivo or confer trimethoprim resistance upon Escherichia coli. Therefore, the relative stabilities of native and truncated R67 DHFR were investigated by equilibrium unfolding studies. Unfolding of dimeric native R67 DHFR is protein concentration dependent and can be described by a two-state model involving native dimer and unfolded monomer. Using absorbance, fluorescence, and circular dichroism techniques, an average delta GH2O of 13.9 kcal mol-1 is found for native R67 DHFR. In contrast, an average delta GH2O of 11.3 kcal mol-1 is observed for truncated R67 DHFR. These results indicate native R67 DHFR is 2.6 kcal mol-1 more stable than truncated protein. This stability difference may be part of the reason why protein from the truncated gene is not found in vivo in E. coli.
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Affiliation(s)
- L J Reece
- Department of Biochemistry, University of Tennessee, Knoxville 37996-0840
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22
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Rohlman CE, Matthews RG. Role of purine biosynthetic intermediates in response to folate stress in Escherichia coli. J Bacteriol 1990; 172:7200-10. [PMID: 2254281 PMCID: PMC210845 DOI: 10.1128/jb.172.12.7200-7210.1990] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Folic acid plays a central role in anabolic metabolism by supplying single-carbon units at varied levels of oxidation for both nucleotide and amino acid biosyntheses. It has been proposed that 5-amino-4-imidazole carboxamide riboside 5'-triphosphate (ZTP), an intermediate in de novo purine biosynthesis, serves as a signal of cellular folate stress and mediates a physiologically beneficial response to folate stress in Salmonella typhimurium (B. R. Bochner, and B. N. Ames, Cell 29:929-937, 1982). We examined the physiological response of Escherichia coli to folate stress induced by the drugs psicofuranine, trimethoprim, and sodium sulfathiazole or by p-aminobenzoic acid (pABA) starvation. Analysis of nucleotide pools showed that psicofuranine or trimethoprim treatment of a prototrophic strain or growth of a pABA auxotroph on limiting pABA induced the production of the nucleotide ZTP, as previously observed in S. typhimurium by Bochner and Ames. Accumulation of ZTP and its precursor 5-amino-4-imidazole carboxamide riboside 5'-monophosphate (ZMP) did not correlate well with folate stress in E. coli, as measured by determination of the folate/protein ratios of extracts of treated cells. Treatment of cells with psicofuranine caused a marked accumulation of 5-amino-4-imidazole carboxamide ribonucleotides (Z-ribonucleotides) but a statistically insignificant drop in the folate/protein ratio of cell extracts. Sodium sulfathiazole treatment at a drug concentration that led to a threefold drop in the growth rate and in the folate/protein ratio of treated cells led to little accumulation of Z-ribonucleotides in E. coli A purF his+ strain which produces ZTP and ZMP when treated with trimethoprim was constructed. In this strain, histidine represses the synthesis of both ZMP and ZTP. Treatment of cells of this strain with trimethoprim resulted in a decrease in the folate/protein ratio of cell extracts, but a blockade of Z-ribonucleotide accumulation did not affect the extent of folate depletion seen in treated cells and had only a small effect on the resistance of this strain to growth inhibition by trimethoprim. The patterns of protein expression induced by treatment of this strain with trimethoprim or psicofuranine were examined by two-dimensional electrophoretic resolution of the total cellular proteins. No differences in protein expression were seen when the treatment were performed in media containing or lacking histidine. These studies failed to provide evidence in E. coli for a folate stress regulon controlled by ZTP.
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Affiliation(s)
- C E Rohlman
- Department of Biological Chemistry, University of Michigan, Ann Arbor 48109
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23
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Howell EE, Booth C, Farnum M, Kraut J, Warren MS. A second-site mutation at phenylalanine-137 that increases catalytic efficiency in the mutant aspartate-27----serine Escherichia coli dihydrofolate reductase. Biochemistry 1990; 29:8561-9. [PMID: 2271539 DOI: 10.1021/bi00489a009] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The adaptability of Escherichia coli dihydrofolate reductase (DHFR) is being explored by identifying second-site mutations that can partially suppress the deleterious effect associated with removal of the active-site proton donor aspartic acid-27. The Asp27----serine mutant DHFR (D27S) was previously characterized and the catalytic activity found to be greatly decreased at pH 7.0 [Howell et al. (1986) Science 231, 1123-1128]. Using resistance to trimethoprim (a DHFR inhibitor) in a genetic selection procedure, we have isolated a double-mutant DHFR gene containing Asp27----Ser and Phe137----Ser mutations (D27S+F137S). The presence of the F137S mutation increases kcat approximately 3-fold and decreases Km(DHF) approximately 2-fold over D27S DHFR values. The overall effect on kcat/Km(DHF) is a 7-fold increase. The D27S+F137S double-mutant DHFR is still 500-fold less active than wild-type DHFR at pH 7. Surprisingly, Phe137 is approximately 15 A from residue 27 in the active site and is part of a beta-bulge. We propose the F137S mutation likely causes its catalytic effect by slightly altering the conformation of D27S DHFR. This supposition is supported by the observation that the F137S mutation does not have the same kinetic effect when introduced into the wild-type and D27S DHFRs, by the altered distribution of two conformers of free enzyme [see Dunn et al. (1990)] and by a preliminary difference Fourier map comparing the D27S and D27S+F137S DHFR crystal structures.
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Affiliation(s)
- E E Howell
- Department of Biochemistry, University of Tennessee, Knoxville 37996-0840
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24
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Burns JL, Lien DM, Hedin LA. Isolation and characterization of dihydrofolate reductase from trimethoprim-susceptible and trimethoprim-resistant Pseudomonas cepacia. Antimicrob Agents Chemother 1989; 33:1247-51. [PMID: 2802552 PMCID: PMC172634 DOI: 10.1128/aac.33.8.1247] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Trimethoprim resistance was investigated in cystic fibrosis isolates of Pseudomonas cepacia. Determination of the MIC of trimethoprim for 111 strains revealed at least two populations of resistant organisms, suggesting the presence of more than one mechanism of resistance. Investigation of the antibiotic target, dihydrofolate reductase, was undertaken in both a susceptible strain and a strain with high-level resistance (MIC, greater than 1,000 micrograms/ml). The enzyme was purified by using ammonium sulfate precipitation, gel filtration, and ion-exchange chromatography. Specific activities, molecular weights, isoelectric points, and substrate kinetics were similar for both enzymes. However, the dihydrofolate reductase from the trimethoprim-resistant strain demonstrated decreased susceptibility to inhibition by trimethoprim and increased susceptibility to inhibition by methotrexate, suggesting that these two enzymes are not identical. We conclude that the mechanism of trimethoprim resistance in this strain with high-level resistance is production of a trimethoprim-resistant dihydrofolate reductase.
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Affiliation(s)
- J L Burns
- Division of Infectious Disease, Children's Hospital and Medical Center, Seattle, Washington
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25
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Tripathi G. Biocatalysis made to order. Appl Biochem Biotechnol 1988; 19:33-59. [PMID: 3060014 DOI: 10.1007/bf02921464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Recombinant DNA technology is now being explored to engineer enzyme molecules. It has many far-reaching applications in biocatalytic processes of enzyme engineering. The facts have pursued certain important industrial, biomedical, and environmental problems. These current excitements are mainly focused on the basis of gene cloning and in vitro mutagenesis for overproduction and redesigning of enzymes, as well as their probable implications in industry, antibiotic research, and waste degradation.
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Affiliation(s)
- G Tripathi
- Department of Zoology, Banaras Hindu University, Varanasi, India
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26
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Howell EE, Foster PG, Foster LM. Construction of a dihydrofolate reductase-deficient mutant of Escherichia coli by gene replacement. J Bacteriol 1988; 170:3040-5. [PMID: 2838456 PMCID: PMC211246 DOI: 10.1128/jb.170.7.3040-3045.1988] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The dihydrofolate reductase (fol) gene in Escherichia coli has been deleted and replaced by a selectable marker. Verification of the delta fol::kan strain has been accomplished using genetic and biochemical criteria, including Southern analysis of the chromosomal DNA. The delta fol::kan mutation is stable in E. coli K549 [thyA polA12 (Ts)] and can be successfully transduced to other E. coli strains providing they have mutations in their thymidylate synthetase (thyA) genes. A preliminary investigation of the relationship between fol and thyA gene expression suggests that a Fol- cell (i.e., a dihydrofolate reductase deficiency phenotype) is not viable unless thymidylate synthetase activity is concurrently eliminated. This observation indicates that either the nonproductive accumulation of dihydrofolate or the depletion of tetrahydrofolate cofactor pools is lethal in a Fol- ThyA+ strain. Strains containing the thyA delta fol::kan lesions require the presence of Fol end products for growth, and these lesions typically increase the doubling time of the strain by a factor of 2.5 in rich medium.
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Affiliation(s)
- E E Howell
- Agouron Institute, La Jolla, California 92037
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27
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Barclay BJ, Huang T, Nagel MG, Misener VL, Game JC, Wahl GM. Mapping and sequencing of the dihydrofolate reductase gene (DFR1) of Saccharomyces cerevisiae. Gene 1988; 63:175-85. [PMID: 2838386 DOI: 10.1016/0378-1119(88)90523-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The dihydrofolate reductase gene (DFR1) from Saccharomyces cerevisiae has been mapped and sequenced. The gene was isolated on an 8.8-kb BamHI fragment from a yeast genomic library by screening of Escherichia coli transformants for resistance to trimethoprim. A 1.8-kb SalI-BamHI fragment which was able to confer methotrexate resistance in yeast also complemented an E. coli DHFR-deficient (folA) mutant. Nucleotide sequence analysis revealed that the yeast DFR1 gene encoded a polypeptide with a predicted Mr of 24230. The deduced sequence of 211 amino acid residues showed considerable homology with DHFRs from both bacterial and animal sources. The codon bias index of the DFR1 coding region is 0.0083, which indicates a random pattern of codon usage. The upstream region contains two consensus sequences required for binding of the yeast's positive regulatory factor, GCN4, suggesting that the DFR1 gene might be subject to the amino acid general control. Several potential 'TATA' boxes are located in the sequence 5' to the gene. Located in the 3' flanking region are homologies with several canonical sequences thought to be required for efficient transcription termination in yeast. We also mapped the DFR1 gene to a position 1.4 cM proximal to the MET7 locus on chromosome XV.
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Affiliation(s)
- B J Barclay
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
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28
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Flensburg J, Sköld O. Massive overproduction of dihydrofolate reductase in bacteria as a response to the use of trimethoprim. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 162:473-6. [PMID: 3549289 DOI: 10.1111/j.1432-1033.1987.tb10664.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Among several observations of greatly increased levels of chromosomal dihydrofolate reductase as a cause of resistance to high concentrations of the antifolate drug trimethoprim, in clinically isolated bacteria, one is described here of a strain of Escherichia coli overproducing dihydrofolate reductase several hundredfold. The chromosomally located resistance gene of this strain was isolated, inserted into a plasmid vector, and analyzed for its nucleotide sequence. The structural gene for the overproduced dihydrofolate reductase was found to be identical to that of E. coli K12, with nine exceptions, of which seven resulted in synonymous codon usage. Two transversions resulted in a substitution of Gly or Trp at amino acid position 30, and of Gln for Glu at position 154. Six of the nine base changes resulted in codons more frequently used. The Gly substitution which leads to a less commonly used codon, was thought to relate to the observed threefold increase in Ki for trimethoprim. Furthermore, a C----T transition was found in the -35 region of the promoter, increasing its homology with the E. coli consensus promoter sequence. In the ribosome-binding area of the resistant strain, finally, seven base changes were observed, two of which resulted in a five-base sequence of complementarity with the 3'-end of ribosomal 16S RNA. The distance between the -10 site of the promoter and the start codon for translation was finally increased one base pair by the insertion of an A at position +9 in the resistant strain. These genetic changes towards more efficient transcriptional and translational start sequences and towards increased mRNA expressivity are interpreted to reflect an evolutionary adaptation to the presence of antifolates.
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29
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Flensburg J, Sköld O. Regulatory changes in the formation of chromosomal dihydrofolate reductase causing resistance to trimethoprim. J Bacteriol 1984; 159:184-90. [PMID: 6330028 PMCID: PMC215611 DOI: 10.1128/jb.159.1.184-190.1984] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
High resistance to trimethoprim mediated by the several hundredfold overproduction of the drug target enzyme, dihyrofolate reductase, in a clinically isolated Escherichia coli strain, 1810, was cloned onto several vector plasmids and seemed to be comprised of a single dihydrofolate reductase gene, which by DNA-DNA hybridization and restriction enzyme digestion mapping was very similar to the corresponding gene of E. coli K-12. Determination of mRNA formation in the originally isolated resistant strain and strains with cloned trimethoprim resistance determinant demonstrated an about 15-fold increase in production of dihydrofolate reductase mRNA compared with that in E. coli K-12. This was explained by the occurrence of a promoter up mutation in the resistant isolate accompanied by changes in the restriction enzyme digestion pattern found by comparison with the corresponding pattern from E. coli K-12.
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30
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Villafranca JE, Howell EE, Voet DH, Strobel MS, Ogden RC, Abelson JN, Kraut J. Directed mutagenesis of dihydrofolate reductase. Science 1983; 222:782-8. [PMID: 6356360 DOI: 10.1126/science.6356360] [Citation(s) in RCA: 165] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Three mutations of the enzyme dihydrofolate reductase were constructed by oligonucleotide-directed mutagenesis of the cloned Escherichia coli gene. The mutations--at residue 27, aspartic acid replaced with asparagine; at residue 39, proline replaced with cysteine; and at residue 95, glycine replaced with alanine--were designed to answer questions about the relations between molecular structure and function that were raised by the x-ray crystal structures. Properties of the mutant proteins show that Asp-27 is important for catalysis and that perturbation of the local structure at a conserved cis peptide bond following Gly-95 abolishes activity. Substitution of cysteine for proline at residue 39 results in the appearance of new forms of the enzyme that correspond to various oxidation states of the cysteine. One of these forms probably represents a species cross-linked by an intrachain disulfide bridge between the cysteine at position 85 and the new cysteine at position 39.
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31
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Gronenborn AM, Clore GM. Characterization of the DNA binding region recognized by dihydrofolate reductase from lactobacillus casei. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44411-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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32
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Mukhopadhyay P, Syrowik U, Palchaudhuri S. Trimethoprim-induced DNA polymerase I deficiency in Escherichia coli K-12. J Bacteriol 1983; 154:1098-103. [PMID: 6343343 PMCID: PMC217579 DOI: 10.1128/jb.154.3.1098-1103.1983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Curing of the mini-ColE1 plasmid pML21 was observed among cells of Escherichia coli K-12 strain C600(pML21) grown under subinhibitory conditions in the presence of trimethoprim, a specific inhibitor of dihydrofolate reductase. Some of the cured colonies showed (i) a reduction in frequency of transformation with pML21 compared with those of isogenic strains not treated with trimethoprim, (ii) loss of viability after acquisition of a recA mutation, and (iii) UV sensitivity greater than that of the original isogenic strain. These colonies therefore had PolA- phenotypes. Moreover, they were found to be deficient in DNA polymerase I activity in the in vitro assays, indicating the occurrence of a polA mutation in them. Many of the colonies with PolA- phenotypes were also thyA deoC mutants, and these mutations, in addition to the polA mutations, appeared to be involved in the expression of the PolA- phenotypes.
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