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Gholami A, Minai-Tehrani D, Farewell A, Eriksson LA. Discovery of novel inhibitors for Pseudomonas aeruginosa lipase enzyme from in silico and in vitro studies. J Biomol Struct Dyn 2024; 42:2197-2210. [PMID: 37098781 DOI: 10.1080/07391102.2023.2203258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/10/2023] [Indexed: 04/27/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen prone to developing drug-resistance and is a major cause of infection for burn patients and patients suffering from cystic fibrosis or are hospitalized in intensive care units. One of the virulence factors of this bacterium is the lipase enzyme that degrades the extracellular matrix of the host tissue and promotes invasion. Bromhexine is a mucolytic drug and has recently been reported to function as a competitive inhibitor of lipase with an IC50 value of 49 µM. In the present study, an attempt was made to identify stronger inhibitors from the ChEMBL database of bioactive compounds, as compared to the reference compound Bromhexine. Following docking and MD simulations, four hit compounds (N1-N4) were selected that showed promising binding modes and low RMSD values indicative of stable protein-ligand complexes. From subsequent binding pose metadynamics (BPMD) simulations, two of these (N2 and N4) stood out as more potent than Bromhexine, displaying stable interactions with residues in the catalytic site of the enzyme. Biological investigations were performed for all four compounds. Among them, the same two hit compounds were found to be the most effective binders with IC50 values of 22.1 and 27.5 µM, respectively; i.e. roughly twice as efficient as the reference Bromhexine. Taken together, our results show that these hits can be promising new candidates to use as leads for the development of drugs targeting the P. aeruginosa lipase enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asma Gholami
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Dariush Minai-Tehrani
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Anne Farewell
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
- Centre for Antibiotic Resistance Research, University of Gothenburg, Göteborg, Sweden
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
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2
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Abadikhah M, Liu M, Persson F, Wilén BM, Farewell A, Sun J, Modin O. Effect of anode material and dispersal limitation on the performance and biofilm community in microbial electrolysis cells. Biofilm 2023; 6:100161. [PMID: 37859795 PMCID: PMC10582064 DOI: 10.1016/j.bioflm.2023.100161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/05/2023] [Accepted: 10/08/2023] [Indexed: 10/21/2023] Open
Abstract
In a microbial electrolysis cell (MEC), the oxidization of organic compounds is facilitated by an electrogenic biofilm on the anode surface. The biofilm community composition determines the function of the system. Both deterministic and stochastic factors affect the community, but the relative importance of different factors is poorly understood. Anode material is a deterministic factor as materials with different properties may select for different microorganisms. Ecological drift is a stochastic factor, which is amplified by dispersal limitation between communities. Here, we compared the effects of three anode materials (graphene, carbon cloth, and nickel) with the effect of dispersal limitation on the function and biofilm community assembly. Twelve MECs were operated for 56 days in four hydraulically connected loops and shotgun metagenomic sequencing was used to analyse the microbial community composition on the anode surfaces at the end of the experiment. The anode material was the most important factor affecting the performance of the MECs, explaining 54-80 % of the variance observed in peak current density, total electric charge generation, and start-up lag time, while dispersal limitation explained 10-16 % of the variance. Carbon cloth anodes had the highest current generation and shortest lag time. However, dispersal limitation was the most important factor affecting microbial community structure, explaining 61-98 % of the variance in community diversity, evenness, and the relative abundance of the most abundant taxa, while anode material explained 0-20 % of the variance. The biofilms contained nine Desulfobacterota metagenome-assembled genomes (MAGs), which made up 64-89 % of the communities and were likely responsible for electricity generation in the MECs. Different MAGs dominated in different MECs. Particularly two different genotypes related to Geobacter benzoatilyticus competed for dominance on the anodes and reached relative abundances up to 83 %. The winning genotype was the same in all MECs that were hydraulically connected irrespective of anode material used.
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Affiliation(s)
- Marie Abadikhah
- Water Environment Technology, Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ming Liu
- Key Laboratory of Optoelectronics Technology, Beijing University of Technology, Beijing, 100124, China
| | - Frank Persson
- Water Environment Technology, Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Britt-Marie Wilén
- Water Environment Technology, Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Anne Farewell
- Chemistry and Molecular Biology, University of Gothenburg, Sweden
| | - Jie Sun
- College of Physics and Information Engineering, Fuzhou University, and Fujian Science and Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou, 350100, China
- Microtechnology and Nanoscience, Chalmers University of Technology, Gothenburg, Sweden
| | - Oskar Modin
- Water Environment Technology, Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
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3
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Park KS, Svennerholm K, Crescitelli R, Lässer C, Gribonika I, Andersson M, Boström J, Alalam H, Harandi AM, Farewell A, Lötvall J. Detoxified synthetic bacterial membrane vesicles as a vaccine platform against bacteria and SARS-CoV-2. J Nanobiotechnology 2023; 21:156. [PMID: 37208676 DOI: 10.1186/s12951-023-01928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/13/2023] [Indexed: 05/21/2023] Open
Abstract
The development of vaccines based on outer membrane vesicles (OMV) that naturally bud off from bacteria is an evolving field in infectious diseases. However, the inherent inflammatory nature of OMV limits their use as human vaccines. This study employed an engineered vesicle technology to develop synthetic bacterial vesicles (SyBV) that activate the immune system without the severe immunotoxicity of OMV. SyBV were generated from bacterial membranes through treatment with detergent and ionic stress. SyBV induced less inflammatory responses in macrophages and in mice compared to natural OMV. Immunization with SyBV or OMV induced comparable antigen-specific adaptive immunity. Specifically, immunization with Pseudomonas aeruginosa-derived SyBV protected mice against bacterial challenge, and this was accompanied by significant reduction in lung cell infiltration and inflammatory cytokines. Further, immunization with Escherichia coli-derived SyBV protected mice against E. coli sepsis, comparable to OMV-immunized group. The protective activity of SyBV was driven by the stimulation of B-cell and T-cell immunity. Also, SyBV were engineered to display the SARS-CoV-2 S1 protein on their surface, and these vesicles induced specific S1 protein antibody and T-cell responses. Collectively, these results demonstrate that SyBV may be a safe and efficient vaccine platform for the prevention of bacterial and viral infections.
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Affiliation(s)
- Kyong-Su Park
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Kristina Svennerholm
- Department of Anesthesiology and Intensive Care Medicine, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Rossella Crescitelli
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Surgery, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Cecilia Lässer
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Inta Gribonika
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Mickael Andersson
- Department of Chemistry and Molecular Biology, Centre for Antibiotic Resistance, University of Gothenburg, Gothenburg, Sweden
| | - Jonas Boström
- Department of Chemistry and Molecular Biology, Centre for Antibiotic Resistance, University of Gothenburg, Gothenburg, Sweden
| | - Hanna Alalam
- Department of Chemistry and Molecular Biology, Centre for Antibiotic Resistance, University of Gothenburg, Gothenburg, Sweden
| | - Ali M Harandi
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- BC Children's Hospital Research Institute, Vaccine Evaluation Center, University of British Columbia, Columbia, Canada
| | - Anne Farewell
- Department of Chemistry and Molecular Biology, Centre for Antibiotic Resistance, University of Gothenburg, Gothenburg, Sweden
| | - Jan Lötvall
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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Gamfeldt L, Hagan JG, Farewell A, Palm M, Warringer J, Roger F. Scaling‐up the biodiversity–ecosystem functioning relationship: the effect of environmental heterogeneity on transgressive overyielding. OIKOS 2023. [DOI: 10.1111/oik.09652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lars Gamfeldt
- Dept of Marine Sciences, Univ. of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
- Centre for Sea and Society Gothenburg Sweden
| | - James G. Hagan
- Dept of Marine Sciences, Univ. of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
| | - Anne Farewell
- Dept of Chemistry and Molecular Biology, Univ. of Gothenburg Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe), Univ. of Gothenburg Gothenburg Sweden
| | - Martin Palm
- Dept of Chemistry and Molecular Biology, Univ. of Gothenburg Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe), Univ. of Gothenburg Gothenburg Sweden
| | - Jonas Warringer
- Dept of Chemistry and Molecular Biology, Univ. of Gothenburg Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe), Univ. of Gothenburg Gothenburg Sweden
| | - Fabian Roger
- Centre for Environmental and Climate Research, Lund Univ. Lund Sweden
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5
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Abadikhah M, Rodriguez MDC, Persson F, Wilén BM, Farewell A, Modin O. Evidence of competition between electrogens shaping electroactive microbial communities in microbial electrolysis cells. Front Microbiol 2022; 13:959211. [PMID: 36590422 PMCID: PMC9800620 DOI: 10.3389/fmicb.2022.959211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
In single-chamber microbial electrolysis cells (MECs), organic compounds are oxidized at the anode, liberating electrons that are used for hydrogen evolution at the cathode. Microbial communities on the anode and cathode surfaces and in the bulk liquid determine the function of the MEC. The communities are complex, and their assembly processes are poorly understood. We investigated MEC performance and community composition in nine MECs with a carbon cloth anode and a cathode of carbon nanoparticles, titanium, or stainless steel. Differences in lag time during the startup of replicate MECs suggested that the initial colonization by electrogenic bacteria was stochastic. A network analysis revealed negative correlations between different putatively electrogenic Deltaproteobacteria on the anode. Proximity to the conductive anode surface is important for electrogens, so the competition for space could explain the observed negative correlations. The cathode communities were dominated by hydrogen-utilizing taxa such as Methanobacterium and had a much lower proportion of negative correlations than the anodes. This could be explained by the diffusion of hydrogen throughout the cathode biofilms, reducing the need to compete for space.
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Affiliation(s)
- Marie Abadikhah
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden,*Correspondence: Marie Abadikhah, ✉
| | - Miguel de Celis Rodriguez
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Britt-Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Anne Farewell
- Institute of Chemistry and Molecular Biology and the Center for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Guzman-Otazo J, Joffré E, Agramont J, Mamani N, Jutkina J, Boulund F, Hu YOO, Jumilla-Lorenz D, Farewell A, Larsson DGJ, Flach CF, Iñiguez V, Sjöling Å. Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli. Front Microbiol 2022; 13:997849. [DOI: 10.3389/fmicb.2022.997849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.
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7
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Bourgard C, Rodríguez-Hernández D, Rudenko A, Rutgersson C, Palm M, Larsson DGJ, Farewell A, Grøtli M, Sunnerhagen P. Development of Dicationic Bisguanidine-Arylfuran Derivatives as Potent Agents against Gram-Negative Bacteria. Antibiotics (Basel) 2022; 11:antibiotics11081115. [PMID: 36009984 PMCID: PMC9404985 DOI: 10.3390/antibiotics11081115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Antibiotic resistance among bacteria is a growing global challenge. A major reason for this is the limited progress in developing new classes of antibiotics active against Gram-negative bacteria. Here, we investigate the antibacterial activity of a dicationic bisguanidine-arylfuran, originally developed as an antitrypanosomal agent, and new derivatives thereof. The compounds showed good activity (EC50 2–20 µM) against antibiotic-resistant isolates of the Gram-negative members of the ESKAPE group (Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) and Escherichia coli with different antibiotic susceptibility patterns, including ESBL isolates. Cytotoxicity was moderate, and several of the new derivatives were less cytotoxic than the lead molecule, offering better selectivity indices (40–80 for several ESKAPE isolates). The molecular mechanism for the antibacterial activity of these molecules is unknown, but sensitivity profiling against human ESKAPE isolates and E. coli collections with known susceptibility patterns against established antibiotics indicates that it is distinct from lactam and quinolone antibiotics.
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Affiliation(s)
- Catarina Bourgard
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Diego Rodríguez-Hernández
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Anastasia Rudenko
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Carolin Rutgersson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, S-413 46 Gothenburg, Sweden
| | - Martin Palm
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
| | - D. G. Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, S-413 46 Gothenburg, Sweden
| | - Anne Farewell
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Correspondence: (M.G.); (P.S.)
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, S-405 30 Gothenburg, Sweden
- Correspondence: (M.G.); (P.S.)
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8
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Thomsen H, Agnes M, Uwangue O, Persson L, Mattsson M, Graf FE, Kasimati EM, Yannakopoulou K, Ericson MB, Farewell A. Increased antibiotic efficacy and noninvasive monitoring of Staphylococcus epidermidis biofilms using per-cysteamine-substituted γ-cyclodextrin - A delivery effect validated by fluorescence microscopy. Int J Pharm 2020; 587:119646. [PMID: 32679261 DOI: 10.1016/j.ijpharm.2020.119646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022]
Abstract
Limited and poor delivery of antibiotics is cited as one reason for the difficulty in treating antibiotic-resistant biofilms associated with chronic infections. We investigate the effectiveness of a positively charged, single isomer cyclodextrin derivative, octakis[6-(2-aminoethylthio)-6-deoxy]-γ-CD (γCys) to improve the delivery of antibiotics to biofilms. Using multiphoton laser scanning microscopy complemented with super-resolution fluorescence microscopy, we showed that γCys tagged with fluorescein (FITC) is uniformly distributed throughout live S. epidermidis biofilm cultures in vitro and results suggest it is localized extracellularly in the biofilm matrix. NMR spectroscopic data in aqueous solution confirm that γCys forms inclusion complexes with both the antibiotics oxacillin and rifampicin. Efficacy of γCys/antibiotic (oxacillin and rifampicin) was measured in the biofilms. While treatment with γCys/oxacillin had little improvement over oxacillin alone, γCys/rifampicin reduced the biofilm viability to background levels demonstrating a remarkable improvement over rifampicin alone. The strong synergistic effect for γCys/rifampicin is at this stage not clearly understood, but plausible explanations are related to increased solubility of rifampicin upon complexation and/or synergistic interference with components of the biofilm. The results demonstrate that designed cyclodextrin nanocarriers, like γCys, efficiently deliver suitable antibiotics to biofilms and that fluorescence microscopy offers a novel approach for mechanistic investigations.
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Affiliation(s)
- Hanna Thomsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Sweden; CARe, Centre for Antibiotic Resistance Research, University of Gothenburg, Sweden
| | - Marco Agnes
- Institute of Nanoscience & Nanotechnology, National Center for Scientific Research " Demokritos", Aghia Paraskevi Attikis 15341, Greece
| | - Owens Uwangue
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Sweden
| | - Linnéa Persson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Sweden
| | - Matilda Mattsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Sweden
| | - Fabrice E Graf
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Sweden; CARe, Centre for Antibiotic Resistance Research, University of Gothenburg, Sweden
| | - Eleni-Marina Kasimati
- Institute of Nanoscience & Nanotechnology, National Center for Scientific Research " Demokritos", Aghia Paraskevi Attikis 15341, Greece
| | - Konstantina Yannakopoulou
- Institute of Nanoscience & Nanotechnology, National Center for Scientific Research " Demokritos", Aghia Paraskevi Attikis 15341, Greece
| | - Marica B Ericson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Sweden
| | - Anne Farewell
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Sweden; CARe, Centre for Antibiotic Resistance Research, University of Gothenburg, Sweden.
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Mamedov I, Naghiyev F, Maharramov A, Uwangue O, Farewell A, Sunnerhagen P, Erdelyi M. Antibacterial activity of 2-amino-3-cyanopyridine derivatives. Mendeleev Communications 2020. [DOI: 10.1016/j.mencom.2020.07.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Kvint K, Palm M, Farewell A. Teaching about antibiotic resistance to a broad audience: a multidisciplinary approach. FEMS Microbiol Lett 2020; 367:5865125. [PMID: 32602885 PMCID: PMC8962684 DOI: 10.1093/femsle/fnaa111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/26/2020] [Indexed: 12/17/2022] Open
Abstract
Education for the general public about antibiotic resistance is advocated as a key component of our response to this crisis. Since this is a multidisciplinary problem encompassing natural, medical and social sciences, it is an educational challenge as both students and lecturers will have vastly different backgrounds in the topics. Here we describe an online multidisciplinary course on antibiotic resistance spanning topics as diverse as chemistry and practical philosophy. The target group was any post-secondary school student and the participating students had different occupations and educational experience. Although as many as 38% of the students were currently studying natural sciences at university, the course included a diverse group with medical professionals (16%) and teachers (6%) making up a significant fraction of the class. The outcomes based on examination and the course evaluations were very positive and we have indications that the information students gained from this course has been spread to others. Unlike other online courses addressing antibiotic resistance, this course is both accessible to a wide range of students and covers a broad range of topics. We advocate courses like ours as an effective tool in educating the public about this crisis.
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Affiliation(s)
- Kristian Kvint
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Guldhedsdsgatan 10A, SE-413 46, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden
| | - Martin Palm
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9E, SE-405 30, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden
| | - Anne Farewell
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9E, SE-405 30, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden
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11
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Dimovska Nilsson K, Palm M, Hood J, Sheriff J, Farewell A, Fletcher JS. Chemical Changes On, and Through, The Bacterial Envelope in Escherichia coli Mutants Exhibiting Impaired Plasmid Transfer Identified Using Time-of-Flight Secondary Ion Mass Spectrometry. Anal Chem 2019; 91:11355-11361. [PMID: 31359753 DOI: 10.1021/acs.analchem.9b02533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) using a (CO2)6k+ gas cluster ion beam (GCIB) was used to analyze Escherichia coli mutants previously identified as having impaired plasmid transfer capability related to the spread of antibiotic resistance. The subset of mutants selected were expected to result in changes in the bacterial envelope composition through the deletion of genes encoding for FabF, DapF, and Lpp, where the surface sensitivity of ToF-SIMS can be most useful. Analysis of arrays of spotted bacteria allowed changes in the lipid composition of the bacteria to be elucidated using multivariate analysis and confirmed through imaging of individual ion signals. Significant changes in chemical composition were observed, including a surprising loss of cyclopropanated fatty acids in the fabF mutant where FabF is associated with the elongation of FA(16:1) to FA(18:1) and not cyclopropane formation. The ability of the GCIB to generate increased higher mass signals from biological samples allowed intact lipid A (m/z 1796) to be detected on the bacteria and, despite a 40 keV impact energy, depth profiled through the bacterial envelope along with other high mass ions including species at m/z 1820 and 2428, attributed to ECACYC, that were only observed below the surface of the bacteria and were notably absent in the depth profile of the lpp mutant. The analysis provides new insights into the action of the specific pathways targeted in this study and paves the way for whole new avenues for the characterization of intact molecules within the bacterial envelope.
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Affiliation(s)
- Kelly Dimovska Nilsson
- Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg 405 30 , Sweden
| | - Martin Palm
- Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg 405 30 , Sweden.,Centre for Antibiotic Resistance Research , University of Gothenburg , Gothenburg 405 30 , Sweden
| | - James Hood
- School of Engineering , Newcastle University , Newcastle upon Tyne NE1 7RU , United Kingdom
| | - Jake Sheriff
- School of Engineering , Newcastle University , Newcastle upon Tyne NE1 7RU , United Kingdom
| | - Anne Farewell
- Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg 405 30 , Sweden.,Centre for Antibiotic Resistance Research , University of Gothenburg , Gothenburg 405 30 , Sweden
| | - John S Fletcher
- Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg 405 30 , Sweden
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12
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Moradigaravand D, Palm M, Farewell A, Mustonen V, Warringer J, Parts L. Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data. PLoS Comput Biol 2018; 14:e1006258. [PMID: 30550564 PMCID: PMC6310291 DOI: 10.1371/journal.pcbi.1006258] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 12/28/2018] [Accepted: 11/18/2018] [Indexed: 12/17/2022] Open
Abstract
The emergence of microbial antibiotic resistance is a global health threat. In clinical settings, the key to controlling spread of resistant strains is accurate and rapid detection. As traditional culture-based methods are time consuming, genetic approaches have recently been developed for this task. The detection of antibiotic resistance is typically made by measuring a few known determinants previously identified from genome sequencing, and thus requires the prior knowledge of its biological mechanisms. To overcome this limitation, we employed machine learning models to predict resistance to 11 compounds across four classes of antibiotics from existing and novel whole genome sequences of 1936 E. coli strains. We considered a range of methods, and examined population structure, isolation year, gene content, and polymorphism information as predictors. Gradient boosted decision trees consistently outperformed alternative models with an average accuracy of 0.91 on held-out data (range 0.81-0.97). While the best models most frequently employed gene content, an average accuracy score of 0.79 could be obtained using population structure information alone. Single nucleotide variation data were less useful, and significantly improved prediction only for two antibiotics, including ciprofloxacin. These results demonstrate that antibiotic resistance in E. coli can be accurately predicted from whole genome sequences without a priori knowledge of mechanisms, and that both genomic and epidemiological data can be informative. This paves way to integrating machine learning approaches into diagnostic tools in the clinic.
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Affiliation(s)
- Danesh Moradigaravand
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Martin Palm
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research at the University of Gothenburg, Gothenburg, Sweden
| | - Anne Farewell
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research at the University of Gothenburg, Gothenburg, Sweden
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology HIIT, Helsinki, Finland
| | - Jonas Warringer
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research at the University of Gothenburg, Gothenburg, Sweden
| | - Leopold Parts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Department of Computer Science, University of Tartu, Tartu, Estonia
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13
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Graf FE, Palm M, Warringer J, Farewell A. Inhibiting conjugation as a tool in the fight against antibiotic resistance. Drug Dev Res 2018; 80:19-23. [DOI: 10.1002/ddr.21457] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Fabrice E. Graf
- Department of Chemistry and Molecular Biology; University of Gothenburg; Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe); University of Gothenburg; Gothenburg Sweden
| | - Martin Palm
- Department of Chemistry and Molecular Biology; University of Gothenburg; Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe); University of Gothenburg; Gothenburg Sweden
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology; University of Gothenburg; Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe); University of Gothenburg; Gothenburg Sweden
| | - Anne Farewell
- Department of Chemistry and Molecular Biology; University of Gothenburg; Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe); University of Gothenburg; Gothenburg Sweden
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14
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Thomsen H, Graf FE, Farewell A, Ericson MB. Exploring photoinactivation of microbial biofilms using laser scanning microscopy and confined 2-photon excitation. J Biophotonics 2018; 11:e201800018. [PMID: 29785840 DOI: 10.1002/jbio.201800018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
One pertinent complication in bacterial infection is the growth of biofilms, that is, communities of surface-adhered bacteria resilient to antibiotics. Photodynamic inactivation (PDI) has been proposed as an alternative to antibiotic treatment; however, novel techniques complementing standard efficacy measures are required. Herein, we present an approach employing multiphoton microscopy complemented with Airyscan super-resolution microscopy, to visualize the distribution of curcumin in Staphylococcus epidermidis biofilms. The effects of complexation of curcumin with hydroxypropyl-γ-cyclodextrin (HPγCD) were studied. It was shown that HPγCD curcumin demonstrated higher bioavailability in the biofilms compared to curcumin, without affecting the subcellular uptake. Spectral quantification following PDI demonstrates a method for monitoring elimination of biofilms in real time using noninvasive 3D imaging. Additionally, spatially confined 2-photon inactivation was demonstrated for the first time in biofilms. These results support the feasibility of advanced optical microscopy as a sensitive tool for evaluating treatment efficacy in biofilms toward improved mechanistic studies of PDI.
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Affiliation(s)
- Hanna Thomsen
- Biomedical Photonics, Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- CARe, Center for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Fabrice E Graf
- CARe, Center for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anne Farewell
- CARe, Center for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Marica B Ericson
- Biomedical Photonics, Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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15
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Thomsen H, Benkovics G, Fenyvesi É, Farewell A, Malanga M, Ericson MB. Delivery of cyclodextrin polymers to bacterial biofilms — An exploratory study using rhodamine labelled cyclodextrins and multiphoton microscopy. Int J Pharm 2017; 531:650-657. [DOI: 10.1016/j.ijpharm.2017.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/29/2017] [Accepted: 06/03/2017] [Indexed: 01/07/2023]
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16
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Wehrli PM, Angerer TB, Farewell A, Fletcher JS, Gottfries J. Investigating the Role of the Stringent Response in Lipid Modifications during the Stationary Phase in E. coli by Direct Analysis with Time-of-Flight-Secondary Ion Mass Spectrometry. Anal Chem 2016; 88:8680-8. [DOI: 10.1021/acs.analchem.6b01981] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Patrick M. Wehrli
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
- Centre for Antibiotic
Resistance Research (CARe), University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Tina B. Angerer
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Anne Farewell
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
- Centre for Antibiotic
Resistance Research (CARe), University of Gothenburg, 405 30, Gothenburg, Sweden
| | - John S. Fletcher
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Johan Gottfries
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
- Centre for Antibiotic
Resistance Research (CARe), University of Gothenburg, 405 30, Gothenburg, Sweden
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17
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Persson Ö, Nyström T, Farewell A. UspB, a member of the sigma-S regulon, facilitates RuvC resolvase function. DNA Repair (Amst) 2010; 9:1162-9. [DOI: 10.1016/j.dnarep.2010.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 08/09/2010] [Accepted: 08/09/2010] [Indexed: 10/19/2022]
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18
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Jansson K, Warringer J, Farewell A, Park HO, Hoe KL, Kim DU, Hayles J, Sunnerhagen P. The tumor suppressor homolog in fission yeast, myh1(+), displays a strong interaction with the checkpoint gene rad1(+). Mutat Res 2008; 644:48-55. [PMID: 18675827 DOI: 10.1016/j.mrfmmm.2008.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 06/02/2008] [Accepted: 07/03/2008] [Indexed: 11/25/2022]
Abstract
The DNA glycosylase MutY is strongly conserved in evolution, and homologs are found in most eukaryotes and prokaryotes examined. This protein is implicated in repair of oxidative DNA damage, in particular adenine mispaired opposite 7,8-dihydro-8-oxoguanine. Previous investigations in Escherichia coli, fission yeast, and mammalian cells show an association of mutations in MutY homologs with a mutator phenotype and carcinogenesis. Eukaryotic MutY homologs physically associate with several proteins with a role in replication, DNA repair, and checkpoint signaling, specifically the trimeric 9-1-1 complex. In a genetic investigation of the fission yeast MutY homolog, myh1(+), we show that the myh1 mutation confers a moderately increased UV sensitivity alone and in combination with mutations in several DNA repair genes. The myh1 rad1, and to a lesser degree myh1 rad9, double mutants display a synthetic interaction resulting in enhanced sensitivity to DNA damaging agents and hydroxyurea. UV irradiation of myh1 rad1 double mutants results in severe chromosome segregation defects and visible DNA fragmentation, and a failure to activate the checkpoint. Additionally, myh1 rad1 double mutants exhibit morphological defects in the absence of DNA damaging agents. We also found a moderate suppression of the slow growth and UV sensitivity of rhp51 mutants by the myh1 mutation. Our results implicate fission yeast Myh1 in repair of a wider range of DNA damage than previously thought, and functionally link it to the checkpoint pathway.
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Affiliation(s)
- Kristina Jansson
- Department of Cell and Molecular Biology, Lundberg Laboratory, Göteborg University, P.O. Box 462, Göteborg SE-405 30, Sweden
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19
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Abstract
The universal stress protein (Usp) superfamily encompasses a conserved group of proteins involved in stress resistance, adaptation to energy deficiency, cell motility and adhesion, and is found in all kingdoms of life. The paradigm usp gene, uspA, of Escherichia coli is transcriptionally activated by a large variety of stresses, and the alarmone ppGpp is required for this activation. Here, we show that the uspA gene is also regulated by an intermediate of the glycolytic/gluconeogenic pathways. Specifically, mutations and conditions resulting in fructose-6-phosphate (F-6-P) accumulation elicit superinduction of uspA upon carbon starvation, whereas genetic manipulations reducing the pool size of F-6-P have the opposite effect. This metabolic control of uspA does not act via ppGpp. Other, but not all, usp genes of the usp superfamily are similarly affected by alterations in F-6-P levels. We suggest that alterations in the pool size of phosphorylated sugars of the upper glycolytic pathway may ensure accumulation of required survival proteins preceding the complete depletion of the external carbon source. Indeed, we show that uspA is, in fact, induced before the carbon source is depleted from the medium.
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Affiliation(s)
- Orjan Persson
- Department of Cell and Molecular Biology-Microbiology, Göteborg University, Box 462, 405 30 Göteborg, Sweden
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20
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Magnusson LU, Gummesson B, Joksimović P, Farewell A, Nyström T. Identical, independent, and opposing roles of ppGpp and DksA in Escherichia coli. J Bacteriol 2007; 189:5193-202. [PMID: 17496080 PMCID: PMC1951846 DOI: 10.1128/jb.00330-07] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recent discovery that the protein DksA acts as a coregulator of genes controlled by ppGpp led us to investigate the similarities and differences between the relaxed phenotype of a ppGpp-deficient mutant and the phenotype of a strain lacking DksA. We demonstrate that the absence of DksA and ppGpp has similar effects on many of the observed phenotypes but that DksA and ppGpp also have independent and sometimes opposing roles in the cell. Specifically, we show that overexpression of DksA can compensate for the loss of ppGpp with respect to transcription of the promoters P(uspA), P(livJ), and P(rrnBP1) as well as amino acid auxotrophy, cell-cell aggregation, motility, filamentation, and stationary phase morphology, suggesting that DksA can function without ppGpp in regulating gene expression. In addition, ppGpp and DksA have opposing effects on adhesion. In the course of our analysis, we also discovered new features of the relaxed mutant, namely, defects in cell-cell aggregation and motility.
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Affiliation(s)
- Lisa U Magnusson
- Department of Cell and Molecular Biology-Microbiology, Göteborg University, Box 462, 405 30 Göteborg, Sweden.
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21
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Abstract
The small nucleotide ppGpp acts as a global regulator of gene expression in bacteria. Proteomic analysis of cells lacking ppGpp has shown that this nucleotide might affect many more genes than previously anticipated. These findings and others suggest that ppGpp causes a redirection of transcription so that genes important for starvation survival and virulence are favoured at the expense of those required for growth and proliferation. In addition, new insights into the mechanism by which ppGpp affects gene expression have been achieved owing to in vitro studies of ppGpp function, complemented by structural studies of the ppGpp-RNA polymerase complex.
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Affiliation(s)
- Lisa U Magnusson
- Department of Cell and Molecular Biology-Microbiology, Göteborg University, Box 462, 405 30 Göteborg, Sweden
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22
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Aertsen A, Vanoirbeek K, De Spiegeleer P, Sermon J, Hauben K, Farewell A, Nyström T, Michiels CW. Heat shock protein-mediated resistance to high hydrostatic pressure in Escherichia coli. Appl Environ Microbiol 2004; 70:2660-6. [PMID: 15128516 PMCID: PMC404417 DOI: 10.1128/aem.70.5.2660-2666.2004] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A random library of Escherichia coli MG1655 genomic fragments fused to a promoterless green fluorescent protein (GFP) gene was constructed and screened by differential fluorescence induction for promoters that are induced after exposure to a sublethal high hydrostatic pressure stress. This screening yielded three promoters of genes belonging to the heat shock regulon (dnaK, lon, clpPX), suggesting a role for heat shock proteins in protection against, and/or repair of, damage caused by high pressure. Several further observations provide additional support for this hypothesis: (i). the expression of rpoH, encoding the heat shock-specific sigma factor sigma(32), was also induced by high pressure; (ii). heat shock rendered E. coli significantly more resistant to subsequent high-pressure inactivation, and this heat shock-induced pressure resistance followed the same time course as the induction of heat shock genes; (iii). basal expression levels of GFP from heat shock promoters, and expression of several heat shock proteins as determined by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteins extracted from pulse-labeled cells, was increased in three previously isolated pressure-resistant mutants of E. coli compared to wild-type levels.
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Affiliation(s)
- Abram Aertsen
- Laboratory of Food Microbiology, Katholieke Universiteit Leuven, Leuven, Belgium
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23
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Prytz I, Sandén AM, Nyström T, Farewell A, Wahlström A, Förberg C, Pragai Z, Barer M, Harwood C, Larsson G. Fed-batch production of recombinant beta-galactosidase using the universal stress promoters uspA and uspB in high cell density cultivations. Biotechnol Bioeng 2003; 83:595-603. [PMID: 12827701 DOI: 10.1002/bit.10716] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A high-level production system using the universal stress promoters uspA and uspB in a fed-batch cultivation based on minimal medium was designed. In development it was shown that a standard industrial fed-batch protocol could not be used for this purpose since it failed to induce the levels of product as compared to the basal level. Instead, a batch protocol followed by a low constant feed of glucose was shown to give full induction. The levels of the product protein, beta-galactosidase, corresponded to approximately 25% of the total protein. Higher levels were found using the uspA than uspB vectors where uspA showed considerably higher basal level. The data indicate that the sigma(70) regulated promoter, uspA, although affected by the alarmone guanosine tetraphosphate, ppGpp, worked partly in a similar manner to constitutive promoters. An industrial high cell density fed-batch cultivation on the basis of the suggested fed-batch protocol and the uspA promoter gave a final beta-galatosidase concentration of 7 g/L and a final cell concentration of 65 g/L. The heterogeneity in production of the individual cell was measured by fluorescence microscopy. The data show that there is a process time independent heterogeneity in production, which is suggested to be caused by heterogeneity in the substrate uptake rate of the individual cell.
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Affiliation(s)
- Ingela Prytz
- The Swedish Centre for Bioprocess Technology, Stockholm Centre for Physics, Astronomy and Biotechnology, SE-106 91 Stockholm, Sweden
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24
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Mergulhão FJM, Monteiro GA, Larsson G, Bostrom M, Farewell A, Nyström T, Cabral JMS, Taipa MA. Evaluation of inducible promoters on the secretion of a ZZ-proinsulin fusion protein in Escherichia coli. Biotechnol Appl Biochem 2003; 38:87-93. [PMID: 12740005 DOI: 10.1042/ba20030043] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2003] [Revised: 04/11/2003] [Accepted: 05/09/2003] [Indexed: 11/17/2022]
Abstract
Four inducible promoters, uspA, uspB, lacUV5 and malK, were evaluated in the expression of the fusion protein ZZ-proinsulin by Escherichia coli. The aim was to select for their effects on the most appropriate expression system (promoter and culture medium) for secretion of ZZ-proinsulin to the periplasmic space and culture medium. All the expression vectors contained the RNase III cleavage site to ensure that the mRNA translation rate remained independent of 5'-untranslated regions thus making promoter strength comparisons more accurate. The highest ZZ-proinsulin secretion yields were 6.2 mg/g of dry cell weight in the periplasmic space and 2.6 mg/g of dry cell weight in the culture medium using the malK promoter. It was also demonstrated that the use of M9 minimal medium favours secretion.
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Affiliation(s)
- Filipe J M Mergulhão
- Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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25
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Mergulhão FJM, Monteiro GA, Larsson G, Sandén AM, Farewell A, Nystrom T, Cabral JMS, Taipa MA. Medium and copy number effects on the secretion of human proinsulin in Escherichia coli using the universal stress promoters uspA and uspB. Appl Microbiol Biotechnol 2003; 61:495-501. [PMID: 12764564 DOI: 10.1007/s00253-003-1232-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2002] [Revised: 12/17/2002] [Accepted: 12/19/2002] [Indexed: 10/25/2022]
Abstract
The use of the uspA and uspB promoters (universal stress promoters) for heterologous protein production in Escherichia coli is described. Best results were obtained with a moderate copy number vector (15-60 copies) bearing the uspA promoter, reaching 4.6 mg/g dry cell weight (DCW) of ZZ-proinsulin secreted to the periplasm and 1.9 mg/g DCW secreted to the culture medium. These values are about 1.7-fold higher than those previously reported with the same ZZ fusion tag and the SpA leader peptide showing that these stress promoters are potentially valuable for recombinant protein secretion in E. coli. It is further demonstrated that the use of M9 minimal medium is advantageous for protein secretion as compared to LB rich medium.
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Affiliation(s)
- F J M Mergulhão
- Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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26
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Sandén AM, Prytz I, Tubulekas I, Förberg C, Le H, Hektor A, Neubauer P, Pragai Z, Harwood C, Ward A, Picon A, De Mattos JT, Postma P, Farewell A, Nyström T, Reeh S, Pedersen S, Larsson G. Limiting factors in Escherichia coli fed-batch production of recombinant proteins. Biotechnol Bioeng 2003; 81:158-66. [PMID: 12451552 DOI: 10.1002/bit.10457] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Fed-batch production of recombinant beta-galactosidase in E. coli was studied with respect to the specific growth rate at induction. The cultivations were designed to induce protein production by IPTG at a glucose feed rate corresponding to high mu = 0.5 h(-1)) or low (mu = 0.1 h(-1)) specific growth rate. Protein production rate was approximately 100% higher at the higher specific growth rate, resulting in the accumulation of beta-galactosidase up to 30% of the total cell protein. Transcription analysis showed that beta-galactosidase-specific messenger RNA was immediately formed after induction (<5 min), but the amount was the same in both cases and was thus not the initial limiting factor. The content of ribosomes, as represented by rRNA, rapidly decreased with specific growth rate from a relative level of 100%, at the high specific growth rate, to 20% at the low specific growth rate. At high specific growth rate, ribosomes were additionally degraded upon induction due to the high production level. Translation therefore seemed to be the initial limiting factor of the protein synthesis capacity. The alarmone guanosine tetraphosphate increased at both high and low feed level inductions, indicating an induction-forced starvation of charged tRNA and/or glucose. The altered physiological status was also detected by the formation of acetic acid. However, the higher production rate resulted in high-level accumulation of acetic acid, which was absent at low feed rate production. Acetic acid production is thus coupled to the high product formation rate and is proposed to be due either to a precursor drain of Krebs cycle intermediates and a time lag before induction of the glyoxalate shunt, or to single amino acid overflow, since the model product is relatively poor in glycin and alanin. In conclusion, it is proposed that production at high specific growth rate becomes precursor-limited, while production at low specific growth rate is carbon- and/or energy-limited.
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Affiliation(s)
- Anna Maria Sandén
- The Swedish Centre for Bioprocess Technology, Stockholm Center for Physics, Astronomy and Biotechnology, SE-106 91, Stockholm, Sweden
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27
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Abstract
When Escherichia coli cells enter stationary phase due to carbon starvation the synthesis of ribosomal proteins is rapidly repressed. In a DeltarelA DeltaspoT mutant, defective in the production of the alarmone guanosine tetraphosphate (ppGpp), this regulation of the levels of the protein synthesizing system is abolished. Using a proteomic approach we demonstrate that the production of the vast majority of detected E. coli proteins are decontrolled during carbon starvation in the DeltarelA DeltaspoT strain and that the starved cells behave as if they were growing exponentially. In addition we show that the inhibition of ribosome synthesis by the stringent response can be qualitatively mimicked by artificially lowering the levels of the housekeeping sigma factor, sigma(70). In other words, genes encoding the protein-synthesizing system are especially sensitive to reduced availability of sigma(70) programmed RNA polymerase. This effect is not dependent on ppGpp since lowering the levels of sigma(70) gives a similar but less pronounced effect in a ppGpp(0) strain. The data is discussed in view of the models advocating for a passive control of gene expression during stringency based on alterations in RNA polymerase availability.
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Affiliation(s)
- Lisa U Magnusson
- Department of Cell and Molecular Biology-Microbiology, Göteborg University, Box 462, Sweden
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28
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Puškarova A, Ferianc P, Kormanec J, Homerova D, Farewell A, Nyström T. Regulation of yodA encoding a novel cadmium-induced protein in Escherichia coli. Microbiology (Reading) 2002; 148:3801-3811. [PMID: 12480884 DOI: 10.1099/00221287-148-12-3801] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial accommodation to moderate concentrations of cadmium is accompanied by transient activation of general stress proteins as well as a sustained induction of other proteins of hitherto unknown functions. One of the latter proteins was previously identified as the product of the Escherichia coli yodA ORF. The yodA ORF encodes 216 aa residues (the YodA protein) and the increased synthesis of YodA during cadmium stress was found probably to be a result of transcriptional activation from one single promoter upstream of the structural yodA gene. Analysis of a transcriptional gene fusion, P(yodA)-lacZ, demonstrated that basal expression of yodA is low during exponential growth and expression is increased greater than 50-fold by addition of cadmium to growing cells. However, challenging cells with additional metals such as zinc, copper, cobalt and nickel did not increase the level of yodA expression. In addition, hydrogen peroxide also increased yodA expression whereas the superoxide-generating agent paraquat failed to do so. Surprisingly, cadmium-induced transcription of yodA is dependent on soxS and fur, but independent of oxyR. Moreover, a double relA spoT mutation abolished induction of yodA during cadmium exposure but ppGpp is not sufficient to induce yodA since expression of the gene is not elevated during stationary phase. After 45 min of cadmium exposure the YodA protein was primarily detected in the cytoplasmic fraction but was later (150 min) found in both the cytoplasmic and periplasmic compartments.
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Affiliation(s)
- A Puškarova
- Institute of Molecular Biology of the Slovak Academy of Sciences, Dúbravská cesta 21, SK-84251 Bratislava, Slovak Republic1
| | - P Ferianc
- Institute of Molecular Biology of the Slovak Academy of Sciences, Dúbravská cesta 21, SK-84251 Bratislava, Slovak Republic1
| | - J Kormanec
- Institute of Molecular Biology of the Slovak Academy of Sciences, Dúbravská cesta 21, SK-84251 Bratislava, Slovak Republic1
| | - D Homerova
- Institute of Molecular Biology of the Slovak Academy of Sciences, Dúbravská cesta 21, SK-84251 Bratislava, Slovak Republic1
| | - A Farewell
- Department of Cell and Molecular Biology, Göteborg University, Medicinaregatan 9C, SE-41390 Göteborg, Sweden2
| | - T Nyström
- Institute of Molecular Biology of the Slovak Academy of Sciences, Dúbravská cesta 21, SK-84251 Bratislava, Slovak Republic1
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Dukan S, Farewell A, Ballesteros M, Taddei F, Radman M, Nyström T. Protein oxidation in response to increased transcriptional or translational errors. Proc Natl Acad Sci U S A 2000; 97:5746-9. [PMID: 10811907 PMCID: PMC18504 DOI: 10.1073/pnas.100422497] [Citation(s) in RCA: 221] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, we show a correlation between synthesis of aberrant proteins and their oxidative modification. The level of aberrant proteins was elevated in Escherichia coli cultures by decreasing transcriptional or translational fidelity using specific mutations or drugs. Protein carbonylation, an oxidative modification, increased in parallel to the induction of the heat shock chaperone GroEL. As the protein turnover rates and level of intracellular oxidative stress remained unchanged, it appears that carbonylation results from the increased susceptibility of the misfolded proteins. These studies show that the cellular protein oxidation is not limited only by available reactive oxygen species, but by the levels of aberrant proteins. Thus, protein oxidation seen in aging cells may be the consequence also of reduced transcriptional/translational fidelity, and protein structures appear to have evolved to minimize oxidative damage. In addition, we discuss the possibility that carbonylation, being an unrepairable protein modification, may serve as a tagging system to shunt misfolded proteins between pathways of refolding by chaperones or the proteolytic apparatus.
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Affiliation(s)
- S Dukan
- Department of Cell and Molecular Biology-Microbiology, Göteborg University, Box 462, 405 30 Göteborg, Sweden
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Kvint K, Farewell A, Nyström T. RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigma(s). J Biol Chem 2000; 275:14795-8. [PMID: 10747855 DOI: 10.1074/jbc.c000128200] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RpoS-dependent promoters require ppGpp for induction in the stationary phase. This has been thought to be a simple consequence of final sigma(S) itself requiring ppGpp for its production. By using four model promoters requiring final sigma(S) for normal induction in the stationary phase, we demonstrate that final sigma(S)-dependent promoters require ppGpp even in the presence of high levels of final sigma(S) produced ectopically. Similar to final sigma(70)-dependent promoters under positive control by ppGpp, the requirement of final sigma(S)-dependent promoters for this alarmone is bypassed by specific "stringent" mutations in the beta-subunit of RNA polymerase. The results suggest that stationary phase induction of both final sigma(S)- and final sigma(70)-dependent genes requires the stringent control modulon and that stringency confers dual control on the RpoS regulon by affecting promoter activity and the levels of the required final sigma-factor.
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Affiliation(s)
- K Kvint
- Department of Cell and Molecular Biology-Microbiology, Göteborg University, Box 462, 405 30 Göteborg, Sweden
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Kvint K, Hosbond C, Farewell A, Nybroe O, Nyström T. Emergency derepression: stringency allows RNA polymerase to override negative control by an active repressor. Mol Microbiol 2000; 35:435-43. [PMID: 10652104 DOI: 10.1046/j.1365-2958.2000.01714.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The uspA promoter, driving production of the universal stress protein A in response to diverse stresses, is demonstrated to be under dual control. One regulatory pathway involves activation of the promoter by the alarmone guanosine 3',5'-bisphosphate, via the beta-subunit of RNA polymerase, whereas the other consists of negative control by the FadR repressor. In contrast to canonical dual control by activation and repression circuits, which depends on concomitant activation and derepression for induction to occur, the ppGpp-dependent activation of the uspA promoter overrides repression by an active FadR under conditions of severe cellular stress (starvation). The ability of RNA polymerase to overcome repression during stringency depends, in part, on the strength of the FadR operator. This emergency derepression is operative on other FadR-regulated genes induced by starvation and is argued to be an essential regulatory mechanism operating during severe stress.
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Affiliation(s)
- K Kvint
- Department of Cell and Molecular Biology - Microbiology, Göteborg University, Box 462, 405 30 Göteborg, Sweden
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Abstract
The open reading frame immediately upstream of uspA is demonstrated to encode a 14-kDa protein which we named UspB (universal stress protein B) because of its general responsiveness to different starvation and stress conditions. UspB is predicted to be an integral membrane protein with at least one and perhaps two membrane-spanning domains. Overexpression of UspB causes cell death in stationary phase, whereas mutants of uspB are sensitive to exposure to ethanol but not heat in stationary phase. In contrast to uspA, stationary-phase induction of uspB requires the sigma factor sigmaS. The expression of uspB is modulated by H-NS, consistent with the role of H-NS in altering sigmaS levels. Our results demonstrate that a gene of the RpoS regulon is involved in the development of stationary-phase resistance to ethanol, in addition to the regulon's previously known role in thermotolerance, osmotolerance, and oxidative stress resistance.
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Affiliation(s)
- A Farewell
- Department of Microbiology, Lund University, Lund, Sweden.
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Abstract
In this report, we examine the effect of temperature on protein synthesis. The rate of protein accumulation is determined by three factors: the number of working ribosomes, the rate at which ribosomes are working, and the rate of protein degradation. Measurements of RNA/protein ratios and the levels of individual ribosomal proteins and rRNA show that the cellular amount of ribosomal machinery in Escherichia coli is constant between 25 and 37 degreesC. Within this range, in a given medium, temperature affects ribosomal function the same as it affects overall growth. Two independent methodologies show that the peptide chain elongation rate increases as a function of temperature identically to growth rate up to 37 degreesC. Unlike the growth rate, however, the elongation rate continues to increase up to 44 degreesC at the same rate as between 25 and 37 degreesC. Our results show that the peptide elongation rate is not rate limiting for growth at high temperature. Taking into consideration the number of ribosomes per unit of cell mass, there is an apparent excess of protein synthetic capacity in these cells, indicating a dramatic increase in protein degradation at high temperature. Temperature shift experiments show that peptide chain elongation rate increases immediately, which supports a mechanism of heat shock response induction in which an increase in unfolded, newly translated protein induces this response. In addition, we find that at low temperature (15 degreesC), cells contain a pool of nontranslating ribosomes which do not contribute to cell growth, supporting the idea that there is a defect in initiation at low temperature.
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Affiliation(s)
- A Farewell
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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Abstract
A mutation in the Escherichia coli gene encoding the stationary phase-inducible sigma factor (sigmaS, RpoS) not only abolishes transcription of some genes in stationary phase, but also causes superinduction of other stationary phase-induced genes. We have examined this phenomenon of repression by sigmaS using as a model system the divergently transcribed stationary phase-inducible genes, uspA and uspB. uspA is transcribed by sigma70-programmed RNA polymerase and is superinduced in an rpoS mutant, while uspB induction is sigmaS dependent. The data suggest that the superinduction of uspA is caused by an increased amount of sigma70 bound to RNA polymerase in the absence of the competing sigmaS. Increasing the ability of sigma70 to compete against sigmaS by overproducing sigma70 mimics the effect of an rpoS mutation by causing superinduction of sigma70-dependent stationary phase-inducible genes (uspA and fadD), silencing of sigmaS-dependent genes (uspB, bolAp1 and fadL) and inhibiting the development of sigmaS-dependent phenotypes, such as hydrogen peroxide resistance in stationary phase. In addition, overproduction of sigmaS markedly reduced stationary phase expression of a sigma70-dependent promoter. Thus, we conclude that sigma factors compete for a limiting amount of RNA polymerase during stationary phase. The implications of this competition in the passive control of promoter activity is discussed.
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Affiliation(s)
- A Farewell
- Department of Microbiology, Lund University, Sweden
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Glatz E, Farewell A, Rutberg B. The Bacillus subtilis glpD leader and antiterminator protein GlpP provide a target for glucose repression in Escherichia coli. FEMS Microbiol Lett 1998; 162:93-6. [PMID: 9595668 DOI: 10.1111/j.1574-6968.1998.tb12983.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Expression of the Bacillus subtilis glpD gene which encodes glycerol-3-phosphate (G3P) dehydrogenase is regulated by the GlpP protein which, in the presence of G3P, causes antitermination of transcription of glpD. The glpD gene leader fused to lacZ was integrated into the chromosome of Escherichia coli deleted for the lac operon and carrying the B. subtilis glpP gene on a plasmid. beta-Galactosidase activity of this strain was increased by the addition of G3P. When G3P and glucose, glucose-6-phosphate or fructose-6-phosphate were added, beta-galactosidase activity was reduced showing that GlpP mediates catabolite repression of transcription from the glpD leader in the absence of any other B. subtilis protein.
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Affiliation(s)
- E Glatz
- Department of Microbiology, Lund University, Sweden.
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Abstract
The influence of cadmium on stress protein production in Escherichia coli K-12 (strain MG1655) was analysed using two-dimensional polyacrylamide gel electrophoresis and the gene-protein database of E. coli K-12. Cadmium (273 microM) caused complete but transient inhibition of growth accompanied by the synthesis of cadmium-induced proteins (CDPs). It was found that some CDPs induced during the growth-arrested phase belong to the heat-shock, oxidation stress, SOS and stringent response regulons, while others are general stress inducible proteins (e.g. H-NS, UspA). In addition, trigger factor, adenylate kinase, W-protein, the cold shock protein G041.2, and seven unknown proteins whose synthesis is not known to be controlled by a global regulator, were identified as immediate responders to cadmium exposure. The rate of synthesis of most of the immediate responders to cadmium exposure decreased when the growth of the cells resumed. However, seven CDPs, including those encoded by argI, tyrA and xthA, maintained a high production rate during growth in the presence of cadmium. Two of the unidentified proteins were N-terminally sequenced by Edman degradation. The N-terminal amino acid sequence of one of these proteins (designated F023.3) matches the E. coli open reading frame o216. This ORF is similar to the N-terminal third of the copper-binding protein amine oxidases (encoded by maoA) of both E. coli and Klebsiella pneumoniae (K. aerogenes). The other N-terminally sequenced protein (designated C044.6) matches perfectly the product of the metK gene, S-adenosylmethionine synthetase I. In comparison to untreated cells, cadmium-stressed cells were found to recover more rapidly during subsequent stress conditions, such as ethanol, osmotic, heat shock, and nalidixic acid treatment. The role of the CDPs is discussed in view of their physiological assignments in the cell.
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Affiliation(s)
- Peter Ferianc
- 1 Institute of Microbiology of the Slovak Academy of Sciences, Štefánikova 3, SK-81434 Bratislava,Slovak Republic
| | - Anne Farewell
- 2 Department of Microbiology, University of Lund, Sweden
| | - Thomas Nyström
- 2 Department of Microbiology, University of Lund, Sweden
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Diez AA, Farewell A, Nannmark U, Nyström T. A mutation in the ftsK gene of Escherichia coli affects cell-cell separation, stationary-phase survival, stress adaptation, and expression of the gene encoding the stress protein UspA. J Bacteriol 1997; 179:5878-83. [PMID: 9294448 PMCID: PMC179480 DOI: 10.1128/jb.179.18.5878-5883.1997] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
An insertional mutation in ftsK, encoding an Escherichia coli product similar to the sporulation protein SpoIIIE of Bacillus subtilis, results in uspA overexpression in stationary phase and impairs cell division. The ftsK1::cat insertion mutant forms chains which are the result of inhibited cell-cell separation, while chromosome synthesis and partitioning appear to be normal as judged by flow cytometry and electron and light microscopy in combination with DNA staining. The cells of the chains are attached to each other by a small envelope structure, and unlike in a spoIIIE mutant of B. subtilis, there is no DNA trapped in the division plane. In addition, plasmids harboring a truncated ftsK allele lacking the last 195 bp of the gene cause chain formation in wild-type cells. While the mutant cells grow at essentially the same rate as the parent in complex and defined minimal media, they are sensitive to stresses. Specifically, the mutant failed to grow at elevated salt concentrations and survived stationary phase poorly. The phenotypes of the ftsK1::cat mutant are complemented by the 3' end (spoIIIE-like half) of the ftsK locus. In contrast, the 5' end of the ftsK locus reported to complement ftsK44(Ts) phenotypes does not complement the phenotypes of the ftsK1::cat mutant.
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Affiliation(s)
- A A Diez
- Department of Microbiology, Lund University, Sweden
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Farewell A, Diez AA, DiRusso CC, Nyström T. Role of the Escherichia coli FadR regulator in stasis survival and growth phase-dependent expression of the uspA, fad, and fab genes. J Bacteriol 1996; 178:6443-50. [PMID: 8932299 PMCID: PMC178529 DOI: 10.1128/jb.178.22.6443-6450.1996] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The increased expression of the uspA gene of Escherichia coli is an essential part of the cell's response to growth arrest. We demonstrate that stationary-phase activation of the uspA promoter is in part dependent on growth phase-dependent inactivation or repression of the FadR regulator. Transcription of uspA is derepressed during exponential growth in fadR null mutants or by including the fatty acid oleate in the growth medium of FadR+ cells. The results of DNA footprinting analysis show that FadR binds downstream of the uspA promoter in the noncoding region. Thus, uspA is a member of the fadR regulon. All the fad-lacZ fusions examined (fadBA, fadL, and fadD) are increasingly expressed in stationary phase with kinetics similar to that of the increased expression of uspA. In contrast, beta-galactosidase levels decrease during stationary phase in a fabA-lacZ lysogen, consistent with the role of FadR as an activator of fabA. The growth phase-dependent increased and decreased transcription of fad genes and fabA, respectively, is dependent on the status of the fadR gene. Cells carrying a mutation in the FadR gene (fadRS219N) that makes it nonderepressible exhibit a weak stationary-phase induction of uspA and fad genes. In addition, cells carrying fadRS219N survive long-term stasis poorly, indicating that FadR-dependent alterations in fatty acid metabolism are an integral and important part of the adaptation to stationary phase.
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Affiliation(s)
- A Farewell
- Department of Microbiology, Lund University, Sweden
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Abstract
The response of exponentially growing cultures of Escherichia coli to abrupt shifts in hydrostatic pressure was studied. A pressure upshift to 546 atm (55,304 kPa) of hydrostatic pressure profoundly perturbed cell division, nucleoid structure, and the total rate of protein synthesis. The number of polypeptides synthesized at increased pressure was greatly reduced, and many proteins exhibited elevated rates of synthesis relative to total protein synthesis. We designated the latter proteins pressure-induced proteins (PIPs). The PIP response was transient, with the largest induction occurring approximately 60 to 90 min postshift. Fifty-five PIPs were identified. Many of these proteins are also induced by heat shock or cold shock. The PIP demonstrating the greatest pressure induction was a basic protein of 15.6 kDa. High pressure inhibits growth but does not inhibit the synthesis of stringently controlled proteins. Cold shock is the only additional signal which has been found to elicit this type of response. These data indicate that elevated pressure induces a unique stress response in E. coli, the further characterization of which could be useful in delineating its inhibitory nature.
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Affiliation(s)
- T J Welch
- Center for Marine Biomedicine and Biotechnology, Scripps Institution of Oceanography, University of California, San Diego, La Jolla 92093-0202
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40
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Abstract
The transcriptional organization of the rfaGBIJ gene cluster of Salmonella typhimurium was studied by using lacZ and cat transcriptional probes. The results indicated that the leftward end of the gene cluster (rfaG-rfaB-rfaI) is an operon that is transcribed from one or more promoters that lie upstream of rfaG. The results further indicated that the product of the rfaH (sfrB) gene acts as a positive regulator of transcription of the entire rfaGBIJ cluster. At least one site required for the RfaH-mediated transcriptional regulation lies within or very close to the upstream promoter.
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Affiliation(s)
- R Brazas
- Department of Microbiology, University of Connecticut Health Center, Farmington 06032
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Farewell A, Brazas R, Davie E, Mason J, Rothfield LI. Suppression of the abnormal phenotype of Salmonella typhimurium rfaH mutants by mutations in the gene for transcription termination factor Rho. J Bacteriol 1991; 173:5188-93. [PMID: 1860828 PMCID: PMC208212 DOI: 10.1128/jb.173.16.5188-5193.1991] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mutations in the rfaH gene have previously been shown to cause premature termination of transcription of the traYZ operon of the F factor and also to prevent expression of the rfaGBIJ gene cluster of Salmonella typhimurium. In the present study, mutants were selected for their ability to restore the normal pattern of rfaGBIJ function. On the basis of this initial section, several classes of extragenic suppressor mutants were isolated that completely or partially corrected the Tra- and Rfa- phenotypes of the prototype rfaH mutant. The suppressor mutations included mutations in rho and mutations that mapped in or close to rpoBC. Other suppressor mutations were located elsewhere on the chromosome, presumably identifying other genes that play a role in the RfaH-mediated transcriptional regulation.
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Affiliation(s)
- A Farewell
- Department of Microbiology, University of Connecticut Health Center, Farmington 06030
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