351
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Andersen JL, He GX, Kakarla P, K C R, Kumar S, Lakra WS, Mukherjee MM, Ranaweera I, Shrestha U, Tran T, Varela MF. Multidrug efflux pumps from Enterobacteriaceae, Vibrio cholerae and Staphylococcus aureus bacterial food pathogens. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:1487-547. [PMID: 25635914 PMCID: PMC4344678 DOI: 10.3390/ijerph120201487] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/15/2015] [Indexed: 02/07/2023]
Abstract
Foodborne illnesses caused by bacterial microorganisms are common worldwide and constitute a serious public health concern. In particular, microorganisms belonging to the Enterobacteriaceae and Vibrionaceae families of Gram-negative bacteria, and to the Staphylococcus genus of Gram-positive bacteria are important causative agents of food poisoning and infection in the gastrointestinal tract of humans. Recently, variants of these bacteria have developed resistance to medically important chemotherapeutic agents. Multidrug resistant Escherichia coli, Salmonella enterica, Vibrio cholerae, Enterobacter spp., and Staphylococcus aureus are becoming increasingly recalcitrant to clinical treatment in human patients. Of the various bacterial resistance mechanisms against antimicrobial agents, multidrug efflux pumps comprise a major cause of multiple drug resistance. These multidrug efflux pump systems reside in the biological membrane of the bacteria and actively extrude antimicrobial agents from bacterial cells. This review article summarizes the evolution of these bacterial drug efflux pump systems from a molecular biological standpoint and provides a framework for future work aimed at reducing the conditions that foster dissemination of these multidrug resistant causative agents through human populations.
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Affiliation(s)
- Jody L Andersen
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Gui-Xin He
- Department of Clinical Laboratory and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA.
| | - Prathusha Kakarla
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Ranjana K C
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Sanath Kumar
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India.
| | - Wazir Singh Lakra
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India.
| | - Mun Mun Mukherjee
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Indrika Ranaweera
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Ugina Shrestha
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Thuy Tran
- Department of Clinical Laboratory and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA.
| | - Manuel F Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
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Nguyen Le Minh P, de Cima S, Bervoets I, Maes D, Rubio V, Charlier D. Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli. FEBS Open Bio 2015; 5:76-84. [PMID: 25685666 PMCID: PMC4325133 DOI: 10.1016/j.fob.2015.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 02/01/2023] Open
Abstract
RutR, a TetR-family member in E. coli, exerts both positive and negative regulation. The crystal structure of the RutR mutant W167 protein without bound uracil is determined. Comparison of uracil-free and uracil-bound RutR reveal structural transitions. L74, W77, W167 and L78 are important for binding of the uracil effector. L78 is crucial for the specificity for uracil, preventing thymine binding.
RutR is a member of the large family of TetR transcriptional regulators in Escherichiacoli. It was originally discovered as the regulator of the rutABCDEFG operon encoding a novel pathway for pyrimidine utilization, but its highest affinity target is the control region of the carAB operon, encoding carbamoylphosphate synthase. Unlike most other TetR-like regulators, RutR exerts both positive and negative effects on promoter activity. Furthermore, RutR exhibits a very narrow ligand binding specificity, unlike the broad effector specificity that characterizes some of the well-studied multidrug resistance regulators of the family. Here we focus on ligand binding and ligand specificity of RutR. We construct single alanine substitution mutants of amino acid residues of the ligand-binding pocket, study their effect on in vitro DNA binding in absence and presence of potential ligands, and analyse their effect on positive regulation of the carP1 promoter and negative autoregulation in vivo. Although RutR structures have been determined previously, they were deposited in the Protein Data Bank without accompanying publications. All of them have uracil bound in the effector-binding site, representing the inactive form of the regulator. We determined the crystal structure of an unliganded mutant RutR protein and provide a structural basis for the use of uracil as sole effector molecule and the exclusion of the very similar thymine from the ligand-binding pocket.
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Affiliation(s)
- Phu Nguyen Le Minh
- Research Group of Microbiology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussel, Belgium ; Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Cientificas (IBV-CSIC), Centro de Investigación Biomédicaen Red de Enfermedades Raras (CIBERER-ISCIII), C/Jaime Roig 11, E-46010 Valencia, Spain
| | - Sergio de Cima
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Cientificas (IBV-CSIC), Centro de Investigación Biomédicaen Red de Enfermedades Raras (CIBERER-ISCIII), C/Jaime Roig 11, E-46010 Valencia, Spain
| | - Indra Bervoets
- Research Group of Microbiology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussel, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussel, Belgium
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Cientificas (IBV-CSIC), Centro de Investigación Biomédicaen Red de Enfermedades Raras (CIBERER-ISCIII), C/Jaime Roig 11, E-46010 Valencia, Spain
| | - Daniel Charlier
- Research Group of Microbiology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussel, Belgium
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353
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Stanton BC, Siciliano V, Ghodasara A, Wroblewska L, Clancy K, Trefzer AC, Chesnut JD, Weiss R, Voigt CA. Systematic transfer of prokaryotic sensors and circuits to mammalian cells. ACS Synth Biol 2014; 3:880-91. [PMID: 25360681 PMCID: PMC4277766 DOI: 10.1021/sb5002856] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prokaryotic regulatory proteins respond to diverse signals and represent a rich resource for building synthetic sensors and circuits. The TetR family contains >10(5) members that use a simple mechanism to respond to stimuli and bind distinct DNA operators. We present a platform that enables the transfer of these regulators to mammalian cells, which is demonstrated using human embryonic kidney (HEK293) and Chinese hamster ovary (CHO) cells. The repressors are modified to include nuclear localization signals (NLS) and responsive promoters are built by incorporating multiple operators. Activators are also constructed by modifying the protein to include a VP16 domain. Together, this approach yields 15 new regulators that demonstrate 19- to 551-fold induction and retain both the low levels of crosstalk in DNA binding specificity observed between the parent regulators in Escherichia coli, as well as their dynamic range of activity. By taking advantage of the DAPG small molecule sensing mediated by the PhlF repressor, we introduce a new inducible system with 50-fold induction and a threshold of 0.9 μM DAPG, which is comparable to the classic Dox-induced TetR system. A set of NOT gates is constructed from the new repressors and their response function quantified. Finally, the Dox- and DAPG- inducible systems and two new activators are used to build a synthetic enhancer (fuzzy AND gate), requiring the coordination of 5 transcription factors organized into two layers. This work introduces a generic approach for the development of mammalian genetic sensors and circuits to populate a toolbox that can be applied to diverse applications from biomanufacturing to living therapeutics.
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Affiliation(s)
- Brynne C. Stanton
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Velia Siciliano
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amar Ghodasara
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Liliana Wroblewska
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kevin Clancy
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Axel C. Trefzer
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Jonathan D. Chesnut
- Synthetic Biology R&D, Life Science Solutions Group, Thermo Fisher Scientific, Carlsbad, California 92008, United States
| | - Ron Weiss
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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354
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Werten S, Dalm D, Palm GJ, Grimm CC, Hinrichs W. Tetracycline repressor allostery does not depend on divalent metal recognition. Biochemistry 2014; 53:7990-8. [PMID: 25432019 DOI: 10.1021/bi5012805] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genes that render bacteria resistant to tetracycline-derived antibiotics are tightly regulated by repressors of the TetR family. In their physiologically relevant, magnesium-complexed form, tetracyclines induce allosteric rearrangements in the TetR homodimer, leading to its release from the promoter and derepression of transcription. According to earlier crystallographic work, recognition of the tetracycline-associated magnesium ion by TetR is crucial and triggers the allosteric cascade. Nevertheless, the derivative 5a,6-anhydrotetracycline, which shows an increased affinity for TetR, causes promoter release even in the absence of magnesium. To resolve this paradox, it has been proposed that metal-free 5a,6-anhydrotetracycline acts via an exceptional, conformationally different induction mode that circumvents the normal magnesium requirement. We have tested this hypothesis by determining crystal structures of TetR-5a,6-anhydrotetracycline complexes in the presence of magnesium, ethylenediaminetetraacetic acid, or high concentrations of potassium. Analysis of these three structures reveals that, irrespective of the metal, the effects of 5a,6-anhydrotetracycline binding are indistinguishable from those of canonical induction by other tetracyclines. Together with a close scrutiny of the earlier evidence of a metal-triggered mechanism, these results demonstrate that magnesium recognition per se is not a prerequisite for tetracycline repressor allostery.
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Affiliation(s)
- Sebastiaan Werten
- Department of Molecular Structural Biology, Institute for Biochemistry, University of Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
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355
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Crowe AM, Stogios PJ, Casabon I, Evdokimova E, Savchenko A, Eltis LD. Structural and functional characterization of a ketosteroid transcriptional regulator of Mycobacterium tuberculosis. J Biol Chem 2014; 290:872-82. [PMID: 25406313 DOI: 10.1074/jbc.m114.607481] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catabolism of host cholesterol is critical to the virulence of Mycobacterium tuberculosis and is a potential target for novel therapeutics. KstR2, a TetR family repressor (TFR), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (HIP). Binding of KstR2 to its operator sequences is relieved upon binding of HIP-CoA. A 1.6-Å resolution crystal structure of the KstR2(Mtb)·HIP-CoA complex reveals that the KstR2(Mtb) dimer accommodates two molecules of HIP-CoA. Each ligand binds in an elongated cleft spanning the dimerization interface such that the HIP and CoA moieties interact with different KstR2(Mtb) protomers. In isothermal titration calorimetry studies, the dimer bound 2 eq of HIP-CoA with high affinity (K(d) = 80 ± 10 nm) but bound neither HIP nor CoASH. Substitution of Arg-162 or Trp-166, residues that interact, respectively, with the diphosphate and HIP moieties of HIP-CoA, dramatically decreased the affinity of KstR2(Mtb) for HIP-CoA but not for its operator sequence. The variant of R162M that decreased the affinity for HIP-CoA (ΔΔG = 13 kJ mol(-1)) is consistent with the loss of three hydrogen bonds as indicated in the structural data. A 24-bp operator sequence bound two dimers of KstR2. Structural comparisons with a ligand-free rhodococcal homologue and a DNA-bound homologue suggest that HIP-CoA induces conformational changes of the DNA-binding domains of the dimer that preclude their proper positioning in the major groove of DNA. The results provide insight into KstR2-mediated regulation of expression of steroid catabolic genes and the determinants of ligand binding in TFRs.
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Affiliation(s)
- Adam M Crowe
- From the Departments of Biochemistry and Molecular Biology and
| | - Peter J Stogios
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and
| | - Israël Casabon
- Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Elena Evdokimova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and The Midwest Center for Structural Genomics (MCSG), Argonne National Laboratory, Argonne, Illinois 60439
| | - Alexei Savchenko
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and The Midwest Center for Structural Genomics (MCSG), Argonne National Laboratory, Argonne, Illinois 60439
| | - Lindsay D Eltis
- From the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada,
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356
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Wu H, Chen M, Mao Y, Li W, Liu J, Huang X, Zhou Y, Ye BC, Zhang L, Weaver DT, Zhang B. Dissecting and engineering of the TetR family regulator SACE_7301 for enhanced erythromycin production in Saccharopolyspora erythraea. Microb Cell Fact 2014; 13:158. [PMID: 25391994 PMCID: PMC4258057 DOI: 10.1186/s12934-014-0158-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 10/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saccharopolyspora erythraea was extensively utilized for the industrial-scale production of erythromycin A (Er-A), a macrolide antibiotic commonly used in human medicine. Yet, S. erythraea lacks regulatory genes in the erythromycin biosynthetic gene (ery) cluster, hampering efforts to enhance Er-A production via the engineering of regulatory genes. RESULTS By the chromosome gene inactivation technique based on homologous recombination with linearized DNA fragments, we have inactivated a number of candidate TetR family transcriptional regulators (TFRs) and identified one TFR (SACE_7301) positively controlling erythromycin biosynthesis in S. erythraea A226. qRT-PCR and EMSA analyses demonstrated that SACE_7301 activated the transcription of erythromycin biosynthetic gene eryAI and the resistance gene ermE by interacting with their promoter regions with low affinities, similar to BldD (SACE_2077) previously identified to regulate erythromycin biosynthesis and morphological differentiation. Therefore, we designed a strategy for overexpressing SACE_7301 with 1 to 3 extra copies under the control of PermE* in A226. Following up-regulated transcriptional expression of SACE_7301, eryAI and ermE, the SACE_7301-overexpressed strains all increased Er-A production over A226 proportional to the number of copies. Likewise, when SACE_7301 was overexpressed in an industrial S. erythraea WB strain, Er-A yields of the mutants WB/7301, WB/2×7301 and WB/3×7301 were respectively increased by 17%, 29% and 42% relative to that of WB. In a 5 L fermentor, Er-A accumulation increased to 4,230 mg/L with the highest-yield strain WB/3×7301, an approximately 27% production improvement over WB (3,322 mg/L). CONCLUSIONS We have identified and characterized a TFR, SACE_7301, in S. erythraea that positively regulated erythromycin biosynthesis, and overexpression of SACE_7301 in wild-type and industrial S. erythraea strains enhanced Er-A yields. This study markedly improves our understanding of the unusual regulatory mechanism of erythromycin biosynthesis, and provides a novel strategy towards Er-A overproduction by engineering transcriptional regulators of S. erythraea.
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Affiliation(s)
- Hang Wu
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Meng Chen
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Yongrong Mao
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Weiwei Li
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Jingtao Liu
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China. .,Beijing Institute of Cell Biotechnology, Beijing, 100043, China.
| | - Xunduan Huang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Ying Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China.
| | - Bang-Ce Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China.
| | - Lixin Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China. .,CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - David T Weaver
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
| | - Buchang Zhang
- Institute of Health Sciences, School of Life Sciences, Anhui University, Hefei, 230601, China.
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357
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Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis. Proc Natl Acad Sci U S A 2014; 111:E4697-705. [PMID: 25339443 DOI: 10.1073/pnas.1413128111] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coenzyme Q (CoQ) is an isoprenylated quinone that is essential for cellular respiration and is synthesized in mitochondria by the combined action of at least nine proteins (COQ1-9). Although most COQ proteins are known to catalyze modifications to CoQ precursors, the biochemical role of COQ9 remains unclear. Here, we report that a disease-related COQ9 mutation leads to extensive disruption of the CoQ protein biosynthetic complex in a mouse model, and that COQ9 specifically interacts with COQ7 through a series of conserved residues. Toward understanding how COQ9 can perform these functions, we solved the crystal structure of Homo sapiens COQ9 at 2.4 Å. Unexpectedly, our structure reveals that COQ9 has structural homology to the TFR family of bacterial transcriptional regulators, but that it adopts an atypical TFR dimer orientation and is not predicted to bind DNA. Our structure also reveals a lipid-binding site, and mass spectrometry-based analyses of purified COQ9 demonstrate that it associates with multiple lipid species, including CoQ itself. The conserved COQ9 residues necessary for its interaction with COQ7 comprise a surface patch around the lipid-binding site, suggesting that COQ9 might serve to present its bound lipid to COQ7. Collectively, our data define COQ9 as the first, to our knowledge, mammalian TFR structural homolog and suggest that its lipid-binding capacity and association with COQ7 are key features for enabling CoQ biosynthesis.
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358
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Hayashi T, Tanaka Y, Sakai N, Okada U, Yao M, Watanabe N, Tamura T, Tanaka I. Structural and genomic DNA analysis of the putative TetR transcriptional repressor SCO7518 from Streptomyces coelicolor A3(2). FEBS Lett 2014; 588:4311-8. [PMID: 25305383 DOI: 10.1016/j.febslet.2014.09.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/18/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
Abstract
SCO7518 is a protein of unknown function from Streptomyces coelicolor A3(2) that has been classified into the TetR transcriptional regulator family. In this study, a crystal structure of SCO7518 was determined at 2.29Å resolution. The structure is a homodimer of protomers that comprise an N-terminal DNA-binding domain and a C-terminal dimerization and regulatory domain, and possess a putative ligand-binding cavity. Genomic systematic evolution of ligands by exponential enrichment and electrophoretic mobility shift assays revealed that SCO7518 specifically binds to an operator sequence located upstream of the sco7519 gene, which encodes a maltose O-acetyltransferase. These results suggest that SCO7518 is a transcriptional repressor of sco7519 expression.
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Affiliation(s)
- Takeshi Hayashi
- Department of Food and Fermentation Science, Faculty of Food and Nutrition, Beppu University, Beppu, Oita 874-8501, Japan; Food Science and Nutrition, Graduate School of Food Science and Nutrition, Beppu University, Beppu, Oita 874-8501, Japan
| | - Yoshikazu Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Sakai
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ui Okada
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nobuhisa Watanabe
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomohiro Tamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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359
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Nodwell JR. Are you talking to me? A possible role for γ-butyrolactones in interspecies signalling. Mol Microbiol 2014; 94:483-5. [PMID: 25200025 DOI: 10.1111/mmi.12787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2014] [Indexed: 12/17/2022]
Abstract
The secreted γ-butyrolactone signalling molecule SVB1 regulates the biosynthesis of jadomycin in Streptomyces venezuelae. Interestingly, this molecule is identical to SCB3, a secreted regulator of secondary metabolism in Streptomyces coelicolor. This is a departure for this class of signalling molecules as there are no previous reports of identical signalling molecules produced in different species. One implication of this work is that different species of bacteria could use shared extracellular signals to co-ordinate secondary metabolism when and if it is advantageous to do so.
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Affiliation(s)
- Justin R Nodwell
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
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360
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A γ-butyrolactone autoregulator-receptor system involved in the regulation of auricin production in Streptomyces aureofaciens CCM 3239. Appl Microbiol Biotechnol 2014; 99:309-25. [DOI: 10.1007/s00253-014-6057-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/15/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
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361
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Zou Z, Du D, Zhang Y, Zhang J, Niu G, Tan H. A γ-butyrolactone-sensing activator/repressor, JadR3, controls a regulatory mini-network for jadomycin biosynthesis. Mol Microbiol 2014; 94:490-505. [PMID: 25116816 DOI: 10.1111/mmi.12752] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2014] [Indexed: 01/12/2023]
Abstract
Two regulatory genes, jadR2 and jadR3, in the jadomycin (jad) biosynthetic gene cluster of Streptomyces venezuelae encode homologues of γ-butyrolactone receptor. JadR2 was previously shown to be a pseudo γ-butyrolactone receptor. jadR3 is situated at the upstream of jadW123 encoding putative enzymes for γ-butyrolactone biosynthesis. Disruption of jadR3 resulted in markedly decreased production of jadomycin. Transcriptional analysis revealed that JadR3 represses jadW1, jadR2 and jadR3 but activates jadR1, the key activator gene for jadomycin biosynthesis. DNase I footprinting showed that JadR3 has four binding sites in the intergenic regions of jadR2-jadR1 and jadR3-jadW1. A JadR3 interactive molecule, SVB1, was purified from a large-scale fermentation and its structure found to be the same as SCB3, a γ-butyrolactone from Streptomyces coelicolor, and was absent from a jadW123 mutant lacking jadomycin production. Addition of SVB1 or extract from S. coelicolor to the mutant restored jadomycin production. Overall, our results revealed that the association of JadR3 and SVB1 plays an important role in controlling a regulatory mini-network governing jadomycin biosynthesis, providing new insights into the ways in which γ-butyrolactone/receptor systems modulate antibiotic biosynthesis in Streptomyces.
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Affiliation(s)
- Zhengzhong Zou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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362
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Bhukya H, Bhujbalrao R, Bitra A, Anand R. Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2). Nucleic Acids Res 2014; 42:10122-33. [PMID: 25092919 PMCID: PMC4150764 DOI: 10.1093/nar/gku587] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Antibiotic production and resistance pathways in Streptomyces are dictated by the interplay of transcriptional regulatory proteins that trigger downstream responses via binding to small diffusible molecules. To decipher the mode of DNA binding and the associated allosteric mechanism in the sub-class of transcription factors that are induced by γ-butyrolactones, we present the crystal structure of CprB in complex with the consensus DNA element to a resolution of 3.25 Å. Binding of the DNA results in the restructuring of the dimeric interface of CprB, inducing a pendulum-like motion of the helix-turn-helix motif that inserts into the major groove. The crystal structure revealed that, CprB is bound to DNA as a dimer of dimers with the mode of binding being analogous to the broad spectrum multidrug transporter protein QacR from the antibiotic resistant strain Staphylococcus aureus. It was demonstrated that the CprB displays a cooperative mode of DNA binding, following a clamp and click model. Experiments performed on a subset of DNA sequences from Streptomyces coelicolor A3(2) suggest that CprB is most likely a pleiotropic regulator. Apart from serving as an autoregulator, it is potentially a part of a network of proteins that modulates the γ-butyrolactone synthesis and antibiotic regulation pathways in S. coelicolor A3(2).
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Affiliation(s)
- Hussain Bhukya
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India IITB-Monash Research Academy, Mumbai 400076, Maharashtra, India
| | - Ruchika Bhujbalrao
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Aruna Bitra
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
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363
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Mak S, Xu Y, Nodwell JR. The expression of antibiotic resistance genes in antibiotic-producing bacteria. Mol Microbiol 2014; 93:391-402. [PMID: 24964724 DOI: 10.1111/mmi.12689] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2014] [Indexed: 12/01/2022]
Abstract
Antibiotic-producing bacteria encode antibiotic resistance genes that protect them from the biologically active molecules that they produce. The expression of these genes needs to occur in a timely manner: either in advance of or concomitantly with biosynthesis. It appears that there have been at least two general solutions to this problem. In many cases, the expression of resistance genes is tightly linked to that of antibiotic biosynthetic genes. In others, the resistance genes can be induced by their cognate antibiotics or by intermediate molecules from their biosynthetic pathways. The regulatory mechanisms that couple resistance to antibiotic biosynthesis are mechanistically diverse and potentially relevant to the origins of clinical antibiotic resistance.
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Affiliation(s)
- Stefanie Mak
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
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364
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Wu P, Pan H, Zhang C, Wu H, Yuan L, Huang X, Zhou Y, Ye BC, Weaver DT, Zhang L, Zhang B. SACE_3986, a TetR family transcriptional regulator, negatively controls erythromycin biosynthesis in Saccharopolyspora erythraea. ACTA ACUST UNITED AC 2014; 41:1159-67. [DOI: 10.1007/s10295-014-1449-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 04/17/2014] [Indexed: 11/29/2022]
Abstract
Abstract
Erythromycin, a medically important antibiotic, is produced by Saccharopolyspora erythraea. Unusually, the erythromycin biosynthetic gene cluster lacks a regulatory gene, and the regulation of its biosynthesis remains largely unknown. In this study, through gene deletion, complementation and overexpression experiments, we identified a novel TetR family transcriptional regulator SACE_3986 negatively regulating erythromycin biosynthesis in S. erythraea A226. When SACE_3986 was further inactivated in an industrial strain WB, erythromycin A yield of the mutant was increased by 54.2 % in average compared with that of its parent strain, displaying the universality of SACE_3986 as a repressor for erythromycin production in S. erythraea. qRT-PCR analysis indicated that SACE_3986 repressed the transcription of its adjacent gene SACE_3985 (which encodes a short-chain dehydrogenase/reductase), erythromycin biosynthetic gene eryAI and the resistance gene ermE. As determined by EMSA analysis, purified SACE_3986 protein specifically bound to the intergenic region between SACE_3985 and SACE_3986, whereas it did not bind to the promoter regions of eryAI and ermE. Furthermore, overexpression of SACE_3985 in A226 led to enhanced erythromycin A yield by at least 32.6 %. These findings indicate that SACE_3986 is a negative regulator of erythromycin biosynthesis, and the adjacent gene SACE_3985 is one of its target genes. The present study provides a basis to increase erythromycin production by engineering of SACE_3986 and SACE_3985 in S. erythraea.
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Affiliation(s)
- Panpan Wu
- grid.252245.6 0000000100854987 Institute of Health Sciences, School of Life Sciences Anhui University Hefei 230601 China
| | - Hui Pan
- grid.252245.6 0000000100854987 Institute of Health Sciences, School of Life Sciences Anhui University Hefei 230601 China
| | - Congming Zhang
- grid.252245.6 0000000100854987 Institute of Health Sciences, School of Life Sciences Anhui University Hefei 230601 China
| | - Hang Wu
- grid.252245.6 0000000100854987 Institute of Health Sciences, School of Life Sciences Anhui University Hefei 230601 China
| | - Li Yuan
- grid.252245.6 0000000100854987 Institute of Health Sciences, School of Life Sciences Anhui University Hefei 230601 China
| | - Xunduan Huang
- grid.252245.6 0000000100854987 Institute of Health Sciences, School of Life Sciences Anhui University Hefei 230601 China
| | - Ying Zhou
- grid.28056.39 0000000121634895 State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 200237 Shanghai China
| | - Bang-ce Ye
- grid.28056.39 0000000121634895 State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 200237 Shanghai China
| | - David T Weaver
- grid.252245.6 0000000100854987 Institute of Health Sciences, School of Life Sciences Anhui University Hefei 230601 China
| | - Lixin Zhang
- grid.252245.6 0000000100854987 Institute of Health Sciences, School of Life Sciences Anhui University Hefei 230601 China
- grid.9227.e 0000000119573309 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology Chinese Academy of Sciences 100101 Beijing China
| | - Buchang Zhang
- grid.252245.6 0000000100854987 Institute of Health Sciences, School of Life Sciences Anhui University Hefei 230601 China
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365
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Genetic and metabolic analysis of the carbofuran catabolic pathway in Novosphingobium sp. KN65.2. Appl Microbiol Biotechnol 2014; 98:8235-52. [DOI: 10.1007/s00253-014-5858-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/27/2014] [Accepted: 05/27/2014] [Indexed: 12/12/2022]
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366
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Baucheron S, Nishino K, Monchaux I, Canepa S, Maurel MC, Coste F, Roussel A, Cloeckaert A, Giraud E. Bile-mediated activation of the acrAB and tolC multidrug efflux genes occurs mainly through transcriptional derepression of ramA in Salmonella enterica serovar Typhimurium. J Antimicrob Chemother 2014; 69:2400-6. [PMID: 24816212 DOI: 10.1093/jac/dku140] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES In Salmonella Typhimurium, the genes encoding the AcrAB-TolC multidrug efflux system are mainly regulated by the ramRA locus, composed of the divergently transcribed ramA and ramR genes. The acrAB and tolC genes are transcriptionally activated by RamA, the gene for which is itself transcriptionally repressed by RamR. Previous studies have reported that bile induces acrAB in a ramA-dependent manner, but none provided evidence for an induction of ramA expression by bile. Therefore, the objective of this study was to clarify the regulatory mechanism by which bile activates acrAB and tolC. METHODS qRT-PCR was used to address the effects of bile (using choleate, an ox-bile extract) on the expression of ramA, ramR, acrB and tolC. Electrophoretic mobility shift assays and surface plasmon resonance experiments were used to measure the effect of bile on RamR binding to the ramA promoter (PramA) region. RESULTS We show that ramA is transcriptionally activated by bile and is strictly required for the bile-mediated activation of acrB and tolC. Additionally, bile is shown to specifically inhibit the binding of RamR to the PramA region, which overlaps the putative divergent ramR promoter, thereby explaining our observation that bile also activates ramR transcription. CONCLUSIONS We propose a regulation model whereby the bile-mediated activation of the acrAB and tolC multidrug efflux genes occurs mainly through the transcriptional derepression of the ramA activator gene.
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Affiliation(s)
- Sylvie Baucheron
- INRA, UMR1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, F-37000 Tours, France
| | - Kunihiko Nishino
- Laboratory of Microbiology and Infectious Diseases, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
| | - Isabelle Monchaux
- INRA, UMR1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, F-37000 Tours, France
| | - Sylvie Canepa
- INRA, UMR7247, Plateforme d'Analyse Intégrative des Biomolécules et de Phénomique des Animaux d'Intérêt Bio-agronomique, Nouzilly, France
| | - Marie-Christine Maurel
- INRA, UMR7247, Plateforme d'Analyse Intégrative des Biomolécules et de Phénomique des Animaux d'Intérêt Bio-agronomique, Nouzilly, France
| | - Franck Coste
- Centre de Biophysique Moléculaire CNRS, UPR4301, Orléans, France
| | - Alain Roussel
- Centre de Biophysique Moléculaire CNRS, UPR4301, Orléans, France
| | - Axel Cloeckaert
- INRA, UMR1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, F-37000 Tours, France
| | - Etienne Giraud
- INRA, UMR1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, F-37000 Tours, France
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367
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Santos MR, Marques AT, Becker JD, Moreira LM. The Sinorhizobium meliloti EmrR regulator is required for efficient colonization of Medicago sativa root nodules. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:388-399. [PMID: 24593245 DOI: 10.1094/mpmi-09-13-0284-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The nitrogen-fixing bacterium Sinorhizobium meliloti must adapt to diverse conditions encountered during its symbiosis with leguminous plants. We characterized a new symbiotically relevant gene, emrR (SMc03169), whose product belongs to the TetR family of repressors and is divergently transcribed from emrAB genes encoding a putative major facilitator superfamily-type efflux pump. An emrR deletion mutant produced more succinoglycan, displayed increased cell-wall permeability, and exhibited higher tolerance to heat shock. It also showed lower tolerance to acidic conditions, a reduced production of siderophores, and lower motility and biofilm formation. The simultaneous deletion of emrA and emrR genes restored the mentioned traits to the wild-type phenotype, except for survival under heat shock, which was lower than that displayed by the wild-type strain. Furthermore, the ΔemrR mutant as well as the double ΔemrAR mutant was impaired in symbiosis with Medicago sativa; it formed fewer nodules and competed poorly with the wild-type strain for nodule colonization. Expression profiling of the ΔemrR mutant showed decreased expression of genes involved in Nod-factor and rhizobactin biosynthesis and in stress responses. Expression of genes directing the biosynthesis of succinoglycan and other polysaccharides were increased. EmrR may therefore be involved in a regulatory network targeting membrane and cell wall modifications in preparation for colonization of root hairs during symbiosis.
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368
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Wang L, Tang H, Yu H, Yao Y, Xu P. An unusual repressor controls the expression of a crucial nicotine-degrading gene cluster inPseudomonas putida S16. Mol Microbiol 2014; 91:1252-69. [DOI: 10.1111/mmi.12533] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Lijuan Wang
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Hao Yu
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Yuxiang Yao
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
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369
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Sidda JD, Song L, Poon V, Al-Bassam M, Lazos O, Buttner MJ, Challis GL, Corre C. Discovery of a family of γ-aminobutyrate ureas via rational derepression of a silent bacterial gene cluster. Chem Sci 2014. [DOI: 10.1039/c3sc52536h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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370
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Rhodococcus erythropolis and Its γ-Lactone Catabolic Pathway: An Unusual Biocontrol System That Disrupts Pathogen Quorum Sensing Communication. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3040816] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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