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Phaneuf PV, Kim SH, Rychel K, Rode C, Beulig F, Palsson BO, Yang L. Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing. ACS Synth Biol 2024; 13:2045-2059. [PMID: 38934464 PMCID: PMC11264330 DOI: 10.1021/acssynbio.3c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 06/11/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
As the availability of data sets increases, meta-analysis leveraging aggregated and interoperable data types is proving valuable. This study leveraged a meta-analysis workflow to identify mutations that could improve robustness to reactive oxygen species (ROS) stresses using an industrially important melatonin production strain as an example. ROS stresses often occur during cultivation and negatively affect strain performance. Cellular response to ROS is also linked to the SOS response and resistance to pH fluctuations, which is important to strain robustness in large-scale biomanufacturing. This work integrated more than 7000 E. coli adaptive laboratory evolution (ALE) mutations across 59 experiments to statistically associate mutated genes to 2 ROS tolerance ALE conditions from 72 unique conditions. Mutant oxyR, fur, iscR, and ygfZ were significantly associated and hypothesized to contribute fitness in ROS stress. Across these genes, 259 total mutations were inspected in conjunction with transcriptomics from 46 iModulon experiments. Ten mutations were chosen for reintroduction based on mutation clustering and coinciding transcriptional changes as evidence of fitness impact. Strains with mutations reintroduced into oxyR, fur, iscR, and ygfZ exhibited increased tolerance to H2O2 and acid stress and reduced SOS response, all of which are related to ROS. Additionally, new evidence was generated toward understanding the function of ygfZ, an uncharacterized gene. This meta-analysis approach utilized aggregated and interoperable multiomics data sets to identify mutations conferring industrially relevant phenotypes with the least drawbacks, describing an approach for data-driven strain engineering to optimize microbial cell factories.
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Affiliation(s)
- PV Phaneuf
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - SH Kim
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - K Rychel
- Department
of Bioengineering, University of California,
San Diego, La Jolla ,California92093-0412 ,United States
| | - C Rode
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - F Beulig
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - BO Palsson
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
- Department
of Bioengineering, University of California,
San Diego, La Jolla ,California92093-0412 ,United States
- Bioinformatics
and Systems Biology Program, University
of California, San Diego, La Jolla ,California92093-0021, United States
- Department
of Pediatrics, University of California,
San Diego, La Jolla ,California 92093-0412, United States
| | - L Yang
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
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Plyuta VA, Sidorova DE, Koksharova OA, Khmel IA, Gnuchikh EY, Melkina OE. The effect of β-ionone on bacterial cells: the use of specific lux-biosensors. Res Microbiol 2024:104214. [PMID: 38740236 DOI: 10.1016/j.resmic.2024.104214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
The diversity of the biological activity of volatile organic compounds (VOCs), including unsaturated ketone β-ionone, promising pharmacological, biotechnological, and agricultural agent, has aroused considerable interest. However, the functional role and mechanisms of action of VOCs remain insufficiently studied. In this work, the response of bacterial cells to the action of β-ionone was studied using specific bioluminescent lux-biosensors containing stress-sensitive promoters. We determined that in Escherichia coli cells, β-ionone induces oxidative stress (PkatG and Pdps promoters) through a specific response mediated by the OxyR/OxyS regulon, but not SoxR/SoxS (PsoxS promoter). It has been shown that β-ionone at high concentrations (50 μM and above) causes a weak induction of the expression from the PibpA promoter and slightly induces the PcolD promoter in the E. coli biosensors; the observed effect is enhanced in the ΔoxyR mutants. This indicates the presence of some damage to proteins and DNA. β-Ionone was found to inhibit the bichaperone-dependent DnaKJE-ClpB refolding of heat-inactivated bacterial luciferase in E. coli wild-type and ΔibpB mutant strains. In the cells of the Gram-positive bacterium Bacillus subtilis 168 pNK-MrgA β-ionone does not cause oxidative stress. Thus, in this work, the specificity of bacterial cell stress responses to the action of β-ionone was shown.
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Affiliation(s)
- Vladimir A Plyuta
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Kurchatov Center for Genome Research, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Daria E Sidorova
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Kurchatov Center for Genome Research, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Olga A Koksharova
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1-40, 119991 Moscow, Russia.
| | - Inessa A Khmel
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Evgeniy Y Gnuchikh
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Kurchatov Center for Genome Research, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Olga E Melkina
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Kurchatov Center for Genome Research, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia.
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Xu G, Li P, Xue Z, Qi Y, Li X, Zhu D, Ma H, Kong L. RecA inhibitor epicatechin prolongs the development of fluoroquinolone resistance in Pasteurella multocida. Int J Biol Macromol 2024; 255:128026. [PMID: 37952805 DOI: 10.1016/j.ijbiomac.2023.128026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
Pasteurella multocida (P. multocida), a primary pathogen of bovine respiratory diseases, has become resistant to many antibiotics, including fluoroquinolones and aminoglycosides. A large number of studies have proved that SOS reaction plays a crucial role in the development of antibiotic resistance. We have shown that the deletion of SOS response-related genes (recA, recO) can delay the development of fluoroquinolone resistance in P. multocida, therefore, it can be used as potential targets for antibiotic resistance inhibitors. In this study, we have used molecular docking to screen RecA protein inhibitors with high throughput screening, and found that epicatechin as an inhibitor significantly inhibited the formation of fluoroquinolone resistance in P. multocida, while in vitro coadministration of epicatechin with and without ciprofloxacin improved the efficacy of the antimicrobial agent. In conclusion, our results indicate that epicatechin is an efficient RecA inhibitor, implying that combining it with ciprofloxacin is a highly promising method for treating P. multocida resistant to fluoroquinolones.
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Affiliation(s)
- Guanyi Xu
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun 130118, China.
| | - Penghui Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun 130118, China.
| | - Zhiyang Xue
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun 130118, China
| | - Yu Qi
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun 130118, China
| | - Xuesong Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun 130118, China
| | - Daomi Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun 130118, China
| | - Hongxia Ma
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun 130118, China; College of Life Sciences, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China.
| | - Lingcong Kong
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun 130118, China.
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Bulssico J, PapukashvilI I, Espinosa L, Gandon S, Ansaldi M. Phage-antibiotic synergy: Cell filamentation is a key driver of successful phage predation. PLoS Pathog 2023; 19:e1011602. [PMID: 37703280 PMCID: PMC10519598 DOI: 10.1371/journal.ppat.1011602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 09/25/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
Phages are promising tools to fight antibiotic-resistant bacteria, and as for now, phage therapy is essentially performed in combination with antibiotics. Interestingly, combined treatments including phages and a wide range of antibiotics lead to an increased bacterial killing, a phenomenon called phage-antibiotic synergy (PAS), suggesting that antibiotic-induced changes in bacterial physiology alter the dynamics of phage propagation. Using single-phage and single-cell techniques, each step of the lytic cycle of phage HK620 was studied in E. coli cultures treated with either ceftazidime, cephalexin or ciprofloxacin, three filamentation-inducing antibiotics. In the presence of sublethal doses of antibiotics, multiple stress tolerance and DNA repair pathways are triggered following activation of the SOS response. One of the most notable effects is the inhibition of bacterial division. As a result, a significant fraction of cells forms filaments that stop dividing but have higher rates of mutagenesis. Antibiotic-induced filaments become easy targets for phages due to their enlarged surface areas, as demonstrated by fluorescence microscopy and flow cytometry techniques. Adsorption, infection and lysis occur more often in filamentous cells compared to regular-sized bacteria. In addition, the reduction in bacterial numbers caused by impaired cell division may account for the faster elimination of bacteria during PAS. We developed a mathematical model to capture the interaction between sublethal doses of antibiotics and exposition to phages. This model shows that the induction of filamentation by sublethal doses of antibiotics can amplify the replication of phages and therefore yield PAS. We also use this model to study the consequences of PAS on the emergence of antibiotic resistance. A significant percentage of hyper-mutagenic filamentous bacteria are effectively killed by phages due to their increased susceptibility to infection. As a result, the addition of even a very low number of bacteriophages produced a strong reduction of the mutagenesis rate of the entire bacterial population. We confirm this prediction experimentally using reporters for bacterial DNA repair. Our work highlights the multiple benefits associated with the combination of sublethal doses of antibiotics with bacteriophages.
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Affiliation(s)
- Julián Bulssico
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Irina PapukashvilI
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
- Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Leon Espinosa
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Sylvain Gandon
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | - Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
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Hui CY, Hu SY, Yang XQ, Guo Y. A panel of visual bacterial biosensors for the rapid detection of genotoxic and oxidative damage: A proof of concept study. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 888:503639. [PMID: 37188434 DOI: 10.1016/j.mrgentox.2023.503639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
The emergence of new compounds during the past decade requires a high-throughput screening method for toxicity assay. The stress-responsive whole-cell biosensor is a powerful tool to evaluate direct or indirect damages of biological macromolecules induced by toxic chemicals. In this proof-of-concept study, nine well-characterized stress-responsive promoters were first selected to assemble a set of blue indigoidine-based biosensors. The PuspA-based, PfabA-based, and PgrpE-based biosensors were eliminated due to their high background. A dose-dependent increase of visible blue signal was observed in PrecA-, PkatG-, and PuvrA-based biosensors, responsive to potent mutagens, including mitomycin and nalidixic acid, but not to genotoxic lead and cadmium. The PrecA, PkatG, and Ppgi gene promoters were further fused to a purple deoxyviolacein synthetic enzyme cluster. Although high basal production of deoxyviolacein is unavoidable, an enhanced visible purple signal in response to mitomycin and nalidixic acid was observed as dose-dependent, especially in PkatG-based biosensors. The study shows that a set of stress-responsive biosensors employing visible pigment as a reporter is pre-validating in detecting extensive DNA damage and intense oxidative stress. Unlike widely-used fluorescent and bioluminescent biosensors, the visual pigment-based biosensor can become a novel, low-cost, mini-equipment, and high-throughput colorimetric device for the toxicity assessment of chemicals. However, combining multiple improvements can further improve the biosensing performance in future studies.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Shun-Yu Hu
- Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xue-Qin Yang
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
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Zhang X, Zhu Y, Li B, Tefsen B, Wang Z, Wells M. We need to plan streamlined environmental impact assessment for the future X-Press Pearl disasters. MARINE POLLUTION BULLETIN 2023; 188:114705. [PMID: 36791553 DOI: 10.1016/j.marpolbul.2023.114705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The X-Press Pearl disaster illustrates the urgent needs for streamlined environmental impact assessment to inform decision making. The environmental contamination caused by the disaster is complex, and the biological impact of different environmental stressors, and at different biological scales, needs to be determined. Traditional methods for analyzing complex environmental stressors are often inefficient and do not reflect the biological impact of pollution. The combination of chemical stressors and biological impacts is the key to environmental impact assessment based on integrated monitoring. Whole-cell bioreporters are tools for rapid, efficient and quantitative detection of the bioavailability, stressor effects, and toxicity of pollutants, i.e., spanning a wide range of applications. Here we propose the view that using whole-cell bioreporter technology to streamline short-term environmental impact assessment for maritime disasters such as the X-Press Pearl is more fit-for-purpose/practical than other approaches in use.
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Affiliation(s)
- Xiaokai Zhang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Yi Zhu
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Boling Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Boris Tefsen
- Department of Molecular Microbiology, Utrecht University, Padualaan 8, CH Utrecht 3584, Netherlands; Natural Sciences, Ronin Institute, Montclair, NJ 07043, USA
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Mona Wells
- Natural Sciences, Ronin Institute, Montclair, NJ 07043, USA; The Meadows Center for Water and the Environment, Texas State University, San Marcos, TX 78666, USA.
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Li H, Yang Y, Zhang D, Li Y, Zhang H, Luo J, Jones KC. Evaluating the simulated toxicities of metal mixtures and hydrocarbons using the alkane degrading bioreporter Acinetobacter baylyi ADPWH_recA. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126471. [PMID: 34216972 DOI: 10.1016/j.jhazmat.2021.126471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Oil spillages lead to the formation of hydrocarbon and metal mixtures possessing effects on alkane-degrading bacteria that are responsible for the bioremediation of oil-contaminated soils and waters. Studies of bacterial responses to the mixture of petroleum and metal can inform appropriate strategies for bioremediation. We employed a luminescent bioreporter Acinetobacter baylyi ADPWH_recA with alkane degradation capability to evaluate the combined effects from heavy metals (Cd, Pb and Cu) and alkanes (dodecane, tetradecane, hexadecane and octadecane). Bioluminescent ratios of ADPWH_recA in single Cd or Pb treatments ranged from 0.25 to 1.98, indicating both genotoxicity and cytotoxicity of these two metals, while ratios < 1.0 postexposure to Cu showed its cytotoxic impacts on ADPWH_recA bioreporter. Metal mixtures exhibited enhanced antagonistic effects (Ti>4.0) determined by the Toxic Unit model. With 100 mg/L alkane, the morbidity of ADPWH-recA reduced to < 20%, showing the inhibition of alkanes on Cd toxicity. Exposed to the metal mixture containing 10 mg/L Cu, the weak binding affinity of Cu with alkanes contributed to a high morbidity of > 85% in ADPWH_recA cells. This study provides a new way to understand the toxicity of mixture contaminants, which can help to optimize treatment efficiencies of bacterial remediation for oil contamination.
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Affiliation(s)
- Hanbing Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; Key Laboratory of Beijing on Regional Air Pollution Control, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yi Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100086, China
| | - Yanying Li
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Hao Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Jun Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Kevin C Jones
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK.
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Abilev SK, Kotova VY, Smirnova SV, Shapiro TN, Zavilgelsky GB. Specific Lux Biosensors of Escherichia coli Containing pRecA::lux, pColD::lux, and pDinI::lux Plasmids for Detection of Genotoxic Agents. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420060022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Shemer B, Shpigel E, Glozman A, Yagur-Kroll S, Kabessa Y, Agranat AJ, Belkin S. Genome-wide gene-deletion screening identifies mutations that significantly enhance explosives vapor detection by a microbial sensor. N Biotechnol 2020; 59:65-73. [PMID: 32622861 DOI: 10.1016/j.nbt.2020.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/16/2022]
Abstract
Genetically engineered microbial biosensors, capable of detecting traces of explosives residues above buried military ordnance and emitting an optical signal in response, may potentially serve for the standoff detection of buried landmines. A promising candidate for such an application is a previously reported Escherichia coli-based reporter strain that employs the yqjF gene promoter as its sensing element; however, for this sensor to be able to detect actual landmines reliably, it was necessary for its detection sensitivity and signal intensity to be enhanced. In this study, a high-throughput approach was employed to screen the effects of individual gene deletions on yqjF activation by 2,4-dinitrotoluene (DNT). Several genes were identified, the deletion of which elicited a significant enhancement of yqjF induction by DNT. The most promising of these mutations were introduced into the sensor strain, individually or in pairs, yielding a considerable increase in signal intensity and a lowering of the detection threshold. A strain harboring two of the identified mutations, ygdD and eutE, appears to be the most sensitive microbial biosensor currently described for the detection of traces of landmine explosives.
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Affiliation(s)
- Benjamin Shemer
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Etai Shpigel
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Anat Glozman
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Sharon Yagur-Kroll
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Yosssef Kabessa
- Department of Applied Physics and the Brojde Center for Innovative Engineering and Computer Science, The Hebrew University of Jerusalem, Israel
| | - Aharon J Agranat
- Department of Applied Physics and the Brojde Center for Innovative Engineering and Computer Science, The Hebrew University of Jerusalem, Israel
| | - Shimshon Belkin
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.
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Bilal M, Iqbal HM. Microbial-derived biosensors for monitoring environmental contaminants: Recent advances and future outlook. PROCESS SAFETY AND ENVIRONMENTAL PROTECTION 2019. [DOI: 10.1016/j.psep.2019.01.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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A Combination of Linalool, Vitamin C, and Copper Synergistically Triggers Reactive Oxygen Species and DNA Damage and Inhibits Salmonella enterica subsp. enterica Serovar Typhi and Vibrio fluvialis. Appl Environ Microbiol 2019; 85:AEM.02487-18. [PMID: 30552187 DOI: 10.1128/aem.02487-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/26/2018] [Indexed: 11/20/2022] Open
Abstract
Inappropriate and disproportionate use of antibiotics is contributing immensely to the development of antibiotic resistance in bacterial species associated with food contamination. The use of natural products in combination can be a potent alternative hurdle strategy to inactivate foodborne pathogens. Here, we explored the pro-oxidant properties of essential oil linalool and vitamin C in combination with copper (LVC) in combating the foodborne pathogens Vibrio fluvialis and Salmonella enterica subsp. enterica serovar Typhi using a three-dimensional (3D) checkerboard microdilution assay. Antibacterial activity in terms of the MIC revealed that the triple combination exerted a synergistic effect compared to the effects of the individual constituents. The bactericidal effect of the triple combination was confirmed by a live/dead staining assay. Reactive oxygen species (ROS) measurements with the terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling assay and scanning electron microscopy imaging strongly suggested that the increase in ROS production is the underlying mechanism of the enhanced antibacterial potency of the LVC combination (linalool [1.298 mM], vitamin C [8 mM], copper [16.3 μM]). In addition, the hypersensitivity of oxidative stress regulator mutants (oxyR, katG, ahpC, and sodA mutants) toward LVC corroborated the involvement of ROS in cell death. Live/dead staining and changes in cellular morphology revealed that oxidative stress did not transform the cells into the viable but nonculturable (VBNC) state; rather, killing was associated with intracellular and extracellular oxidative burst. Furthermore, the LVC combination did not display toxicity to human cells, while it effectively reduced the pathogen levels in acidic fruit juices by 3 to 4 log CFU/ml without adversely altering the organoleptic properties. This study opens a new outlook for combinatorial antimicrobial therapy.IMPORTANCE There is a need to develop effective antibacterial therapies for mitigating bacterial pathogens in food systems. We used a 3D checkerboard assay to ascertain a safe synergistic combination of food-grade components: vitamin C, copper, and the essential oil linalool. Individually, these constituents have to be added in large amounts to exert their antibacterial effect, which leads to unwanted organoleptic properties. The triple combination could exceptionally inhibit foodborne Gram-negative pathogens like Vibrio fluvialis and Salmonella enterica subsp. enterica serovar Typhi at low concentrations (linalool, 1.298 mM; vitamin C, 8 mM; copper, 16.3 μM) and displayed potent microbial inhibition in acidic beverages. We found increased susceptibility in deletion mutants of oxidative stress regulators (oxyR, katG, ahpC, and sodA mutants) due to ROS generation by Fenton's chemistry. The results of this study show that it may be possible to use plant-based antimicrobials in synergistic combinations to control microbial contaminants.
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Yuan P, Dong J, Zhao W, Zhuo M, Li S, Huang S, Li J. Qualitative and quantitative assessment of genotoxins using SRRzlysis reporter under the control of a newly designed SOS responsive promoter in Escherichia coli. RSC Adv 2019; 9:35662-35670. [PMID: 35528065 PMCID: PMC9074414 DOI: 10.1039/c9ra06202e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/19/2019] [Indexed: 11/22/2022] Open
Abstract
A new bacterial genotoxicity detection strain was constructed, in which the cell lysis gene of SRRz from a lambda phage was controlled by a new designed SOS responsive element, designated as Escherichia coli BL21/pUC-PST. The biosensor responded only after 0.5 h contact with mutagens and the changes in cell culture turbidity could be easily differentiated with the naked eyes from the control sample. This SOS/SRRz system presented a dose-dependent manner to five model DNA-damaging agents with an improved detection sensitivity. The limits of detection (LODs) were 0.026 μM for mitomycin C, 320.4 μM for azinphos-methyl, 34.4 μM for methyl methanesulfonate, 4.6 μM for dithianone and 6.0 μM for dichlofluanid, which were much lower than previously reported. By performing binary and ternary mixture experiments, the toxic equivalency concept was validated in the E. coli SOS/SRRz system by comparison with bioanalytical equivalent concentrations (BEQ) and overall toxic equivalent concentration (TEQmixture) using Cr(vi) as the reference compound. Pearson analysis indicated that a strong correlation existed between the TEQmixture and BEQ values. Thus the TEQmixture could be presented as the Cr(vi) equivalent concentration from its dose–effect lysis profiles for the environmental sample. The proposed genotoxicity reporter strain allows for easier qualitative characterization and quantitative interpretation of the TEQmixture values using Cr(vi) as the reference for environmental water samples. A new bacterial genotoxicity detection strain was constructed, in which the cell lysis gene of SRRz from a lambda phage was controlled by a new designed SOS responsive element, designated as Escherichia coli BL21/pUC-PST.![]()
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Affiliation(s)
- Pengfei Yuan
- School of Biology and Biological Engineering
- South China University of Technology
- Higher Education Mega Center
- Guangzhou 510006
- China
| | - Junqing Dong
- School of Biology and Biological Engineering
- South China University of Technology
- Higher Education Mega Center
- Guangzhou 510006
- China
| | - Weibin Zhao
- School of Biology and Biological Engineering
- South China University of Technology
- Higher Education Mega Center
- Guangzhou 510006
- China
| | - Min Zhuo
- School of Biology and Biological Engineering
- South China University of Technology
- Higher Education Mega Center
- Guangzhou 510006
- China
| | - Shuang Li
- School of Biology and Biological Engineering
- South China University of Technology
- Higher Education Mega Center
- Guangzhou 510006
- China
| | - Shaobin Huang
- School of Environment and Energy
- South China University of Technology
- Higher Education Mega Center
- Guangzhou 510006
- China
| | - Jianjun Li
- State Key Laboratory of Applied Microbiology Southern China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application
- Guangdong Institute of Microbiology
- Guangzhou 510070
- China
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13
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Moreb EA, Hoover B, Yaseen A, Valyasevi N, Roecker Z, Menacho-Melgar R, Lynch MD. Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity. ACS Synth Biol 2017; 6:2209-2218. [PMID: 28915012 DOI: 10.1021/acssynbio.7b00174] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phage-derived "recombineering" methods are utilized for bacterial genome editing. Recombineering results in a heterogeneous population of modified and unmodified chromosomes, and therefore selection methods, such as CRISPR-Cas9, are required to select for edited clones. Cells can evade CRISPR-Cas-induced cell death through recA-mediated induction of the SOS response. The SOS response increases RecA dependent repair as well as mutation rates through induction of the umuDC error prone polymerase. As a result, CRISPR-Cas selection is more efficient in recA mutants. We report an approach to inhibiting the SOS response and RecA activity through the expression of a mutant dominant negative form of RecA, which incorporates into wild type RecA filaments and inhibits activity. Using a plasmid-based system in which Cas9 and recA mutants are coexpressed, we can achieve increased efficiency and consistency of CRISPR-Cas9-mediated selection and recombineering in E. coli, while reducing the induction of the SOS response. To date, this approach has been shown to be independent of recA genotype and host strain lineage. Using this system, we demonstrate increased CRISPR-Cas selection efficacy with over 10 000 guides covering the E. coli chromosome. The use of dominant negative RecA or homologues may be of broad use in bacterial CRISPR-Cas-based genome editing where the SOS pathways are present.
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Affiliation(s)
- Eirik Adim Moreb
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Benjamin Hoover
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Adam Yaseen
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Nisakorn Valyasevi
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Zoe Roecker
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Romel Menacho-Melgar
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Michael D. Lynch
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
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14
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Alhadrami HA. Biosensors: Classifications, medical applications, and future prospective. Biotechnol Appl Biochem 2017; 65:497-508. [DOI: 10.1002/bab.1621] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 09/22/2017] [Accepted: 09/30/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Hani A. Alhadrami
- Faculty of Applied Medical SciencesDepartment of Medical Laboratory TechnologyKing Abdulaziz University Jeddah Kingdom of Saudi Arabia
- Special Infectious Agent UnitKing Fahd Medical Research CentreKing Abdulaziz University Jeddah Kingdom of Saudi Arabia
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15
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Reporter Gene Assays in Ecotoxicology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 157:135-157. [PMID: 27928578 DOI: 10.1007/10_2016_47] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The need for simple and rapid means for evaluating the potential toxic effects of environmental samples has prompted the development of reporter gene assays, based on tester cells (bioreporters) genetically engineered to report on sample toxicity by producing a readily quantifiable signal. Bacteria are especially suitable to serve as bioreporters owing to their fast responses, low cost, convenient preservation, ease of handling, and amenability to genetic manipulations. Various bacterial bioreporters have been introduced for general toxicity and genotoxicity assessment, and the monitoring of endocrine disrupting and dioxin-like compounds has been mostly covered by similarly engineered eukaryotic cells. Some reporter gene assays have been validated, standardized, and accredited, and many others are under constant development. Efforts are aimed at broadening detection spectra, lowering detection thresholds, and combining toxicity identification capabilities with characterization of the toxic effects. Taking advantage of bacterial robustness, attempts are also being made to incorporate bacterial bioreporters into field instrumentation for online continuous monitoring or on-site spot checks. However, key hurdles concerning test validation, cell preservation, and regulatory issues related to the use of genetically modified organisms still remain to be overcome.
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16
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New methodologies in screening of antibiotic residues in animal-derived foods: Biosensors. Talanta 2017; 175:435-442. [PMID: 28842013 DOI: 10.1016/j.talanta.2017.07.044] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 05/15/2017] [Accepted: 07/13/2017] [Indexed: 01/05/2023]
Abstract
Antibiotics are leading medicine asset for fighting against microbial infection, but also one of the important causes of death worldwide. Many antibiotics used as therapeutics and growth promotion agents in animals can lead to antibiotic residues in animal-derived food which harm the health of people. Hence, it is vital to screen antibiotic residues in animal derived foods. Typical methods for screening antibiotic residues are based on microbiological growth inhibition and immunological analyses. However these two methods have some disadvantages, such as poor sensitive, lack of specificity and etc. Therefore, it is necessary to develop simple, more efficient and high sensitive screening methods of antibiotic residues. These assays have been introduced for the screening of numerous food samples. Biosensors are emerging methods, applied in screening antibiotic residues in animal-derived foods. Two types of biosensors, whole-cell based biosensors and surface plasmon resonance-based sensors have been extensively used. Their advantages include portability, small sample requirement, high sensitivity and good specificity over the traditional screening methods.
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17
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Design of synthetic epigenetic circuits featuring memory effects and reversible switching based on DNA methylation. Nat Commun 2017; 8:15336. [PMID: 28537256 PMCID: PMC5458116 DOI: 10.1038/ncomms15336] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/21/2017] [Indexed: 12/21/2022] Open
Abstract
Epigenetic systems store information in DNA methylation patterns in a durable but reversible manner, but have not been regularly used in synthetic biology. Here, we designed synthetic epigenetic memory systems using DNA methylation sensitive engineered zinc finger proteins to repress a memory operon comprising the CcrM methyltransferase and a reporter. Triggering by heat, nutrients, ultraviolet irradiation or DNA damaging compounds induces CcrM expression and DNA methylation. In the induced on-state, methylation in the operator of the memory operon prevents zinc finger protein binding leading to positive feedback and permanent activation. Using an mf-Lon protease degradable CcrM variant enables reversible switching. Epigenetic memory systems have numerous potential applications in synthetic biology, including life biosensors, death switches or induction systems for industrial protein production. The large variety of bacterial DNA methyltransferases potentially allows for massive multiplexing of signal storage and logical operations depending on more than one input signal. Recording systems would allow synthetic organisms to store a ‘memory' of a past event for future reference. Here the authors design an epigenetic memory system in E. coli that methylates DNA in response to exogenous and endogenous signals.
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18
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Bet-hedging in bacteriocin producing Escherichia coli populations: the single cell perspective. Sci Rep 2017; 7:42068. [PMID: 28165017 PMCID: PMC5292716 DOI: 10.1038/srep42068] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/03/2017] [Indexed: 11/08/2022] Open
Abstract
Production of public goods in biological systems is often a collaborative effort that may be detrimental to the producers. It is therefore sustainable only if a small fraction of the population shoulders the cost while the majority reap the benefits. We modelled this scenario using Escherichia coli populations producing colicins, an antibiotic that kills producer cells' close relatives. Colicin expression is a costly trait, and it has been proposed that only a small fraction of the population actively expresses the antibiotic. Colicinogenic populations were followed at the single-cell level using time-lapse microscopy, and showed two distinct, albeit dynamic, subpopulations: the majority silenced colicin expression, while a small fraction of elongated, slow-growing cells formed colicin-expressing hotspots, placing a significant burden on expressers. Moreover, monitoring lineages of individual colicinogenic cells showed stochastic switching between expressers and non-expressers. Hence, colicin expressers may be engaged in risk-reducing strategies-or bet-hedging-as they balance the cost of colicin production with the need to repel competitors. To test the bet-hedging strategy in colicin-mediated interactions, competitions between colicin-sensitive and producer cells were simulated using a numerical model, demonstrating a finely balanced expression range that is essential to sustaining the colicinogenic population.
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Sergiev P, Osterman I, Golovina A, Laptev I, Pletnev P, Evfratov S, Marusich E, Leonov S, Ivanenkov Y, Bogdanov A, Dontsova O. Application of reporter strains for new antibiotic screening. ACTA ACUST UNITED AC 2016; 62:117-23. [DOI: 10.18097/pbmc20166202117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Screening for new antibiotics remains an important area of biology and medical science. Indispensable for this type of research is early identification of antibiotic mechanism of action. Preferentially, it should be studied quickly and cost-effectively, on the stage of primary screening. In this review we describe an application of reporter strains for rapid classification of antibiotics by its target, without prior purification of an active compound and determination of chemical structure
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Affiliation(s)
- P.V. Sergiev
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - I.A. Osterman
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - A.Ya. Golovina
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - I.G. Laptev
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - P.I. Pletnev
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - S.A. Evfratov
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - E.I. Marusich
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow region, Russia
| | - S.V. Leonov
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow region, Russia
| | - Ya.A. Ivanenkov
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow region, Russia
| | - A.A. Bogdanov
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - O.A. Dontsova
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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20
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21
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A novel high-throughput cell-based assay aimed at identifying inhibitors of DNA metabolism in bacteria. Antimicrob Agents Chemother 2014; 58:7264-72. [PMID: 25246396 DOI: 10.1128/aac.03475-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacterial biosensor strains can be useful tools for the discovery and characterization of antibacterial compounds. A plasmid-based reporter vector containing a transcriptional fusion between the recA promoter and green fluorescence protein gene was introduced into an Escherichia coli ΔtolC strain to create a biosensor strain that selectively senses inhibitors of DNA metabolism via the SOS response. The strain was used to develop a high-throughput assay to identify new inhibitors of DNA metabolism. Screening of the AstraZeneca compound library with this strain identified known inhibitors of DNA metabolism, as well as novel chemotypes. The cellular target of one novel series was elucidated as DNA gyrase through genetic characterization of laboratory-generated resistant mutants followed by 50% inhibitory concentration measurements in a DNA gyrase activity assay. These studies validated the use of this antibiotic biosensor strain to identify novel selective inhibitors of DNA metabolism by high-throughput screening.
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22
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Biosensors, antibiotics and food. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 145:153-85. [PMID: 25216955 DOI: 10.1007/978-3-662-43619-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Antibiotics are medicine's leading asset for fighting microbial infection, which is one of the leading causes of death worldwide. However, the misuse of antibiotics has led to the rapid spread of antibiotic resistance among bacteria and the development of multiple resistant pathogens. Therefore, antibiotics are rapidly losing their antimicrobial value. The use of antibiotics in food production animals is strictly controlled by the European Union (EU). Veterinary use is regulated to prevent the spread of resistance. EU legislation establishes maximum residue limits for veterinary medicinal products in foodstuffs of animal origin and enforces the establishment and execution of national monitoring plans. Among samples selected for monitoring, suspected noncompliant samples are screened and then subjected to confirmatory analysis to establish the identity and concentration of the contaminant. Screening methods for antibiotic residues are typically based on microbiological growth inhibition, whereas physico-chemical methods are used for confirmatory analysis. This chapter discusses biosensors, especially whole-cell based biosensors, as emerging screening methods for antibiotic residues. Whole-cell biosensors can offer highly sensitive and specific detection of residues. Applications demonstrating quantitative analysis and specific analyte identification further improve their potential as screening methods.
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23
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Ghazaryan L, Tonoyan L, Ashhab AA, Soares MIM, Gillor O. The role of stress in colicin regulation. Arch Microbiol 2014; 196:753-64. [PMID: 25048159 DOI: 10.1007/s00203-014-1017-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 07/05/2014] [Accepted: 07/11/2014] [Indexed: 12/28/2022]
Abstract
Bacteriocins produced by Enterobacteriaceae are high molecular weight toxic proteins that kill target cells through a variety of mechanisms, including pore formation and nucleic acid degradation. What is remarkable about these toxins is that their expression results in death to the producing cells and therefore bacteriocin induction have to be tightly regulated, often confined to times of stress. Information on the regulation of bacteriocins produced by enteric bacteria is sketchy as their expression has only been elucidated in a handful of bacteria. Here, we review the known regulatory mechanisms of enteric bacteriocins and explore the expression of 12 of them in response to various triggers: DNA-damaging agents, stringent response, catabolite repression, oxidative stress, growth phase, osmolarity, cold shock, nutrient deprivation, anaerobiosis and pH stress. Our results indicate that the expression of bacteriocins is mostly confined to mutagenic triggers, while all other triggers tested are limited inducers.
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Affiliation(s)
- Lusine Ghazaryan
- Zuckerberg Institute for Water Research, J. Blaustein Institutes for Desert Research, Ben-Gurion University, 84990, Midreshet Ben-Gurion, Israel
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24
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Date A, Pasini P, Daunert S. Fluorescent and bioluminescent cell-based sensors: strategies for their preservation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 117:57-75. [PMID: 20091290 DOI: 10.1007/10_2009_22] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Luminescent whole-cell biosensing systems have been developed for a variety of analytes of environmental, clinical, and biological interest. These analytical tools allow for sensitive, rapid, simple, and inexpensive quantitative detection of target analytes. Furthermore, they can be designed to be nonspecific, semispecific, or highly specific/selective. A notable feature of such sensing systems employing living cells is that they provide information on the analyte bioavailability and activity. These characteristics, along with their suitability to miniaturization, make cell-based sensors ideal for field applications. However, a major limitation to on-site use is their "shelf-life." To address this problem, various methods for preservation of sensing cells have been reported, including freeze-drying, immobilization in different types of matrices, and formation of spores. Among these, the use of spores emerged as a promising strategy for long-term storage of whole-cell sensing systems at room temperature as well as in extreme environmental conditions.
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Affiliation(s)
- Amol Date
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506-0055, USA
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25
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Environmental applications of photoluminescence-based biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014. [PMID: 19475374 DOI: 10.1007/10_2008_51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
For monitoring and treatment of soil and water, environmental scientists and engineers require measurements of the concentration of chemical contaminants. Although laboratory-based methods relying on gas or liquid chromatography can yield very accurate measurements, they are also complex, time consuming, expensive, and require sample pretreatment. Furthermore, they are not readily adapted for in situ measurements.Sensors are devices that can provide continuous, in situ measurements, ideally without the addition of reagents. A biosensor incorporates a biological component coupled to a transducer, which translates the interaction between the analyte and the biocomponent into a signal that can be processed and reported. A wide range of transducers have been employed in biosensors, the most common of which are electrochemical and optical. In this contribution, we focus on photoluminescence-based biosensors of potential use in the applications described above.Following a review of photoluminescence and a discussion of the optoelectronic hardware part of these biosensor systems, we provide explanations and examples of optical biosensors for specific chemical groups: hydrocarbons and alcohols, halogenated organics, nitro-, phospho-, sulfo-, and other substituted organics, and metals and other inorganics. We also describe approaches that have been taken to describe chemical mixtures as a whole (biological oxygen demand and toxicity) since most environmental samples contain mixtures of unknown (and changing) composition. Finally, we end with some thoughts on future research directions that are necessary to achieve the full potential of environmental biosensors.
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26
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Detection of induced synthesis of colicin E9 using ColE9p::gfpmut2 based reporter system. World J Microbiol Biotechnol 2014; 30:2091-9. [PMID: 24652519 DOI: 10.1007/s11274-014-1635-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
The majority of colicin operons are regulated by an SOS response inducible promoter (SOS promoter), located at upstream of the colicin operons. Therefore, colicin synthesis is induced by DNA damaging agents like mitomycin C (MMC) because the resulting DNA damage switches on the SOS response in bacteria. In this study, we have described the strategy for fusion of the SOS promoter of the colicin E9 operon (ColE9p) with a promoterless green fluorescent reporter gene (gfpmut2). We observed that the ColE9p-gfpmut2 is inducible by MMC which confirmed that the ColE9p-gfpmut2 is sensitive to SOS response inducing agents. The data implies that the ColE9p-gfpmut2 based reporter system is suitable for monitoring the ColE9 synthesis induced by SOS response inducing agents including antibiotics. Using green fluorescent protein expression from the ColE9p-gfpmut2 as an indicator of ColE9 synthesis; we have investigated, first time, the inducing effects of cephalexin antibiotic on ColE9 synthesis. Our data demonstrated that the cephalexin has potential to induce ColE9 synthesis from E. coli JM83 host cells albeit the level of this induction is very low hence its detection required a highly sensitive method.
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27
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Transcription termination controls prophage maintenance in Escherichia coli genomes. Proc Natl Acad Sci U S A 2013; 110:14414-9. [PMID: 23940369 DOI: 10.1073/pnas.1303400110] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Prophages represent a large fraction of prokaryotic genomes and often provide new functions to their hosts, in particular virulence and fitness. How prokaryotic cells maintain such gene providers is central for understanding bacterial genome evolution by horizontal transfer. Prophage excision occurs through site-specific recombination mediated by a prophage-encoded integrase. In addition, a recombination directionality factor (or excisionase) directs the reaction toward excision and prevents the phage genome from being reintegrated. In this work, we describe the role of the transcription termination factor Rho in prophage maintenance through control of the synthesis of transcripts that mediate recombination directionality factor expression and, thus, excisive recombination. We show that Rho inhibition by bicyclomycin allows for the expression of prophage genes that lead to excisive recombination. Thus, besides its role in the silencing of horizontally acquired genes, Rho also maintains lysogeny of defective and functional prophages.
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28
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ParA encoded on chromosome II of Deinococcus radiodurans binds to nucleoid and inhibits cell division in Escherichia coli. J Biosci 2013; 38:487-97. [DOI: 10.1007/s12038-013-9352-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Xu T, Close DM, Sayler GS, Ripp S. Genetically modified whole-cell bioreporters for environmental assessment. ECOLOGICAL INDICATORS 2013; 28:125-141. [PMID: 26594130 PMCID: PMC4649933 DOI: 10.1016/j.ecolind.2012.01.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Living whole-cell bioreporters serve as environmental biosentinels that survey their ecosystems for harmful pollutants and chemical toxicants, and in the process act as human and other higher animal proxies to pre-alert for unfavorable, damaging, or toxic conditions. Endowed with bioluminescent, fluorescent, or colorimetric signaling elements, bioreporters can provide a fast, easily measured link to chemical contaminant presence, bioavailability, and toxicity relative to a living system. Though well tested in the confines of the laboratory, real-world applications of bioreporters are limited. In this review, we will consider bioreporter technologies that have evolved from the laboratory towards true environmental applications, and discuss their merits as well as crucial advancements that still require adoption for more widespread utilization. Although the vast majority of environmental monitoring strategies rely upon bioreporters constructed from bacteria, we will also examine environmental biosensing through the use of less conventional eukaryotic-based bioreporters, whose chemical signaling capacity facilitates a more human-relevant link to toxicity and health-related consequences.
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Affiliation(s)
- Tingting Xu
- The University of Tennessee Center for Environmental Biotechnology, 676 Dabney Hall, Knoxville, TN 37996, USA
| | - Dan M. Close
- The Joint Institute for Biological Sciences, Oak Ridge National Laboratory, PO Box 2008, MS6342 Oak Ridge, TN 37831, USA
| | - Gary S. Sayler
- The University of Tennessee Center for Environmental Biotechnology, 676 Dabney Hall, Knoxville, TN 37996, USA
- The Joint Institute for Biological Sciences, Oak Ridge National Laboratory, PO Box 2008, MS6342 Oak Ridge, TN 37831, USA
| | - Steven Ripp
- The University of Tennessee Center for Environmental Biotechnology, 676 Dabney Hall, Knoxville, TN 37996, USA
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30
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Lawrence JG, Butela K, Atzinger A. A likelihood approach to classifying fluorescent events collected by multicolor flow cytometry. J Microbiol Methods 2013; 94:1-12. [PMID: 23588324 DOI: 10.1016/j.mimet.2013.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 04/04/2013] [Accepted: 04/04/2013] [Indexed: 11/19/2022]
Abstract
Flow cytometry is an effective tool for enumerating fluorescently-labeled microbes recovered from natural environments. However, low signal strength and the presence of fluorescent, non-cellular particles complicate the separation of cellular events from noise. Existing classification methods rely on the arbitrary placement of noise thresholds, resulting in potentially high rates of misclassification of fluorescent cells, thus precluding the robust estimation of the proportions of classes of fluorescent cells. Here we present a method for objectively separating signal from noise. Rather than setting an arbitrary noise threshold, the Z-scoring approach uses the Gaussian distribution of signal strength (a) to locate noise threshold for individual fluorophores, (b) to predict the likelihood of different fluorescent genotypes in producing the signal observed, and (c) to normalize the fraction of cellular events count for each fluorescent cell class. The likelihood framework allows rejection of alternative genotypes, leading to robust and reliable classification of fluorescent cells. Use of Z-scoring in classification of cells expressing multiple fluorophores, use of spillover in actively scoring events, and the successful classification of multiple fluorophores using a single detector within a flow cytometer are discussed. A software package that performs Z-scoring for cells labeled with one or more fluorophores is described.
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31
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Osterman IA, Prokhorova IV, Sysoev VO, Boykova YV, Efremenkova OV, Svetlov MS, Kolb VA, Bogdanov AA, Sergiev PV, Dontsova OA. Attenuation-based dual-fluorescent-protein reporter for screening translation inhibitors. Antimicrob Agents Chemother 2012; 56:1774-83. [PMID: 22252829 PMCID: PMC3318315 DOI: 10.1128/aac.05395-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 12/28/2011] [Indexed: 11/20/2022] Open
Abstract
A reporter construct was created on the basis of the transcription attenuator region of the Escherichia coli tryptophan operon. Dual-fluorescent-protein genes for red fluorescent protein and cerulean fluorescent protein were used as a sensor and internal control of gene expression. The sequence of the attenuator was modified to avoid tryptophan sensitivity while preserving sensitivity to ribosome stalling. Antimicrobial compounds which cause translation arrest at the stage of elongation induce the reporter both in liquid culture and on an agar plate. This reporter could be used for high-throughput screening of translation inhibitors.
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Affiliation(s)
- Ilya A. Osterman
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Irina V. Prokhorova
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Vasily O. Sysoev
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Yulia V. Boykova
- G. F. Gauze Institute for Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Olga V. Efremenkova
- G. F. Gauze Institute for Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Maxim S. Svetlov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Vyacheslav A. Kolb
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey A. Bogdanov
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Olga A. Dontsova
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
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Chen Z, Lu M, Zou D, Wang H. An E. coli SOS-EGFP biosensor for fast and sensitive detection of DNA damaging agents. J Environ Sci (China) 2012; 24:541-549. [PMID: 22655371 DOI: 10.1016/s1001-0742(11)60722-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
An E. coli SOS-EGFP biosensor which expresses enhanced green fluorescent protein as a reporter protein under the control of recA gene promoter in SOS response was constructed for detection of DNA damage and evaluation of DNA damaging chemicals. The chemicals that may cause substantial DNA damage will trigger SOS response in the constructed bacterial biosensor, and then the reporter egfp gene under the control of recA promoter is stimulated to express as a fluorescent protein, allowing fast and sensitive fluorescence detection. Interestingly, this biosensor can be simultaneously applied for evaluation of genotoxicity and cytotoxicity. The SOS-EGFP bacterial biosensor provides a sensitive, specific and simple method for detecting known and potential DNA damaging chemicals.
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Affiliation(s)
- Zhilan Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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33
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Etoh H, Yasuda M, Akimoto T. Signal enhancement by a multi-layered substrate for mutagen detection using an SOS response-induced green fluorescent protein in genetically modified Escherichia coli. ANAL SCI 2011; 27:1179-83. [PMID: 22156243 DOI: 10.2116/analsci.27.1179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this paper, we describe a method to enhance the fluorescence signal of mutagen detection using SOS response-induced green fluorescence protein (GFP) in genetically modified Escherichia coli using a multi-layered substrate. To generate E. coli that express SOS response-induced GFP, we constructed a plasmid carrying the RecA promoter located upstream of the GFP gene and used it to transform E. coli BL21. The transformed strain was incubated with mitomycin C (MMC), a typical mutagen, and then immobilized on a multi-layered substrate with Ag and a thin Al(2)O(3) layer on a glass slide. Since the multi-layered substrate technique is an optical technique with potential to enhance the fluorescence of fluorophore placed on top of the substrate, the multi-layered substrate was expected to improve the fluorescence signal of mutagen detection. We obtained an average 14-fold fluorescence enhancement of MMC-induced GFP in the concentration range 1 to 1000 ng/ml. In addition, the lower detection limit of MMC was improved using this technique, and was estimated to be 1 ng/ml because of an enlargement of the difference between the blank and the signal of 1 ng/ml of MMC.
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Affiliation(s)
- Hiroki Etoh
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachiouji, Tokyo 192–0982, Japan
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34
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Experimental methods and modeling techniques for description of cell population heterogeneity. Biotechnol Adv 2011; 29:575-99. [DOI: 10.1016/j.biotechadv.2011.03.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/04/2011] [Accepted: 03/31/2011] [Indexed: 11/24/2022]
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35
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Green fluorescent protein-based biosensor to detect and quantify stress responses induced by DNA-degrading colicins. Appl Environ Microbiol 2011; 77:6691-3. [PMID: 21803919 DOI: 10.1128/aem.00534-11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here we report the development of a whole-cell biosensor to detect and quantify the induction of the SOS response activated by DNA-degrading colicins. This biosensor utilizes the SOS-responsive cda promoter to regulate the expression of green fluorescent protein. The biosensor assay revealed induction of stress for all DNA-degrading reference colicins (E2, E7, and E8).
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36
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Abstract
The coming of age of whole‐cell biosensors, combined with the continuing advances in array technologies, has prepared the ground for the next step in the evolution of both disciplines – the whole‐cell array. In the present review, we highlight the state‐of‐the‐art in the different disciplines essential for a functional bacterial array. These include the genetic engineering of the biological components, their immobilization in different polymers, technologies for live cell deposition and patterning on different types of solid surfaces, and cellular viability maintenance. Also reviewed are the types of signals emitted by the reporter cell arrays, some of the transduction methodologies for reading these signals and the mathematical approaches proposed for their analysis. Finally, we review some of the potential applications for bacterial cell arrays, and list the future needs for their maturation: a richer arsenal of high‐performance reporter strains, better methodologies for their incorporation into hardware platforms, design of appropriate detection circuits, the continuing development of dedicated algorithms for multiplex signal analysis and – most importantly – enhanced long‐term maintenance of viability and activity on the fabricated biochips.
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Affiliation(s)
- Tal Elad
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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37
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Yagur-Kroll S, Bilic B, Belkin S. Strategies for enhancing bioluminescent bacterial sensor performance by promoter region manipulation. Bioeng Bugs 2011; 1:151-3. [PMID: 21326942 DOI: 10.4161/bbug.1.2.11104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Accepted: 01/04/2010] [Indexed: 11/19/2022] Open
Abstract
Genetically engineered microbial reporter strains are based upon the fusion of an inducible sensing element upstream of a reporting element, so that the construct emits a dose-dependent signal when exposed to the inducing compound(s) or stress factor(s). In this communication we described several general approaches undertaken in order to enhance the sensing performance of such promoter::reporter fusions. Significant improvements in detection sensitivity, response kinetics and signal intensity were achieved by modification of the length of the promoter-containing DNA fragment, by random or site-directed mutagenesis and by promoter duplication. The general nature of these genetics manipulations makes them applicable to other types of promoter::reporter fusions.
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Affiliation(s)
- Sharon Yagur-Kroll
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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38
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39
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Kotova VY, Manukhov IV, Zavilgelskii GB. Lux-biosensors for detection of SOS-response, heat shock, and oxidative stress. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810080089] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Shin HJ. Genetically engineered microbial biosensors for in situ monitoring of environmental pollution. Appl Microbiol Biotechnol 2010; 89:867-77. [DOI: 10.1007/s00253-010-2990-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 10/27/2010] [Accepted: 10/27/2010] [Indexed: 10/18/2022]
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41
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Identification of Vibrio natriegens uvrA and uvrB genes and analysis of gene regulation using transcriptional reporter plasmids. J Microbiol 2010; 48:644-56. [DOI: 10.1007/s12275-010-9370-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 05/16/2010] [Indexed: 01/14/2023]
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42
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Escherichia coli as a bioreporter in ecotoxicology. Appl Microbiol Biotechnol 2010; 88:1007-25. [PMID: 20803141 DOI: 10.1007/s00253-010-2826-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 08/02/2010] [Accepted: 08/03/2010] [Indexed: 01/30/2023]
Abstract
Ecotoxicological assessment relies to a large extent on the information gathered with surrogate species and the extrapolation of test results across species and different levels of biological organisation. Bacteria have long been used as a bioreporter for genotoxic testing and general toxicity. Today, it is clear that bacteria have the potential for screening of other toxicological endpoints. Escherichia coli has been studied for years; in-depth knowledge of its biochemistry and genetics makes it the most proficient prokaryote for the development of new toxicological assays. Several assays have been designed with E. coli as a bioreporter, and the recent trend to develop novel, better advanced reporters makes bioreporter development one of the most dynamic in ecotoxicology. Based on in-depth knowledge of E. coli, new assays are being developed or existing ones redesigned, thanks to the availability of new reporter genes and new or improved substrates. The technological evolution towards easier and more sensitive detection of different gene products is another important aspect. Often, this requires the redesign of the bacterium to make it compatible with the novel measuring tests. Recent advances in surface chemistry and nanoelectronics open the perspective for advanced reporter based on novel measuring platforms and with an online potential. In this article, we will discuss the use of E. coli-based bioreporters in ecotoxicological applications as well as some innovative sensors awaited for the future.
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43
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Where microbiology meets microengineering: design and applications of reporter bacteria. Nat Rev Microbiol 2010; 8:511-22. [DOI: 10.1038/nrmicro2392] [Citation(s) in RCA: 404] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Tecon R, Beggah S, Czechowska K, Sentchilo V, Chronopoulou PM, McGenity TJ, van der Meer JR. Development of a multistrain bacterial bioreporter platform for the monitoring of hydrocarbon contaminants in marine environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:1049-55. [PMID: 20000678 DOI: 10.1021/es902849w] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Petroleum hydrocarbons are common contaminants in marine and freshwater aquatic habitats, often occurring as a result of oil spillage. Rapid and reliable on-site tools for measuring the bioavailable hydrocarbon fractions, i.e., those that are most likely to cause toxic effects or are available for biodegradation, would assist in assessing potential ecological damage and following the progress of cleanup operations. Here we examined the suitability of a set of different rapid bioassays (2-3 h) using bacteria expressing the LuxAB luciferase to measure the presence of short-chain linear alkanes, monoaromatic and polyaromatic compounds, biphenyls, and DNA-damaging agents in seawater after a laboratory-scale oil spill. Five independent spills of 20 mL of NSO-1 crude oil with 2 L of seawater (North Sea or Mediterranean Sea) were carried out in 5 L glass flasks for periods of up to 10 days. Bioassays readily detected ephemeral concentrations of short-chain alkanes and BTEX (i.e., benzene, toluene, ethylbenzene, and xylenes) in the seawater within minutes to hours after the spill, increasing to a maximum of up to 80 muM within 6-24 h, after which they decreased to low or undetectable levels. The strong decrease in short-chain alkanes and BTEX may have been due to their volatilization or biodegradation, which was supported by changes in the microbial community composition. Two- and three-ring PAHs appeared in the seawater phase after 24 h with a concentration up to 1 muM naphthalene equivalents and remained above 0.5 muM for the duration of the experiment. DNA-damage-sensitive bioreporters did not produce any signal with the oil-spilled aqueous-phase samples, whereas bioassays for (hydroxy)biphenyls showed occasional responses. Chemical analysis for alkanes and PAHs in contaminated seawater samples supported the bioassay data, but did not show the typical ephemeral peaks observed with the bioassays. We conclude that bacterium-based bioassays can be a suitable alternative for rapid on-site quantitative measurement of hydrocarbons in seawater.
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Affiliation(s)
- Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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45
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Buchinger S, Grill P, Morosow V, Ben-Yoav H, Shacham-Diamand Y, Biran A, Pedahzur R, Belkin S, Reifferscheid G. Evaluation of chrono-amperometric signal detection for the analysis of genotoxicity by a whole cell biosensor. Anal Chim Acta 2010; 659:122-8. [DOI: 10.1016/j.aca.2009.11.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 11/05/2009] [Accepted: 11/10/2009] [Indexed: 01/08/2023]
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46
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Elad T, Lee JH, Gu MB, Belkin S. Microbial cell arrays. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 117:85-108. [PMID: 20625955 DOI: 10.1007/10_2009_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The coming of age of whole-cell biosensors, combined with the continuing advances in array technologies, has prepared the ground for the next step in the evolution of both disciplines - the whole cell array. In the present chapter, we highlight the state-of-the-art in the different disciplines essential for a functional bacterial array. These include the genetic engineering of the biological components, their immobilization in different polymers, technologies for live cell deposition and patterning on different types of solid surfaces, and cellular viability maintenance. Also reviewed are the types of signals emitted by the reporter cell arrays, some of the transduction methodologies for reading these signals, and the mathematical approaches proposed for their analysis. Finally, we review some of the potential applications for bacterial cell arrays, and list the future needs for their maturation: a richer arsenal of high-performance reporter strains, better methodologies for their incorporation into hardware platforms, design of appropriate detection circuits, the continuing development of dedicated algorithms for multiplex signal analysis, and - most importantly - enhanced long term maintenance of viability and activity on the fabricated biochips.
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Affiliation(s)
- Tal Elad
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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47
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Biran A, Yagur-Kroll S, Pedahzur R, Buchinger S, Reifferscheid G, Ben-Yoav H, Shacham-Diamand Y, Belkin S. Bacterial genotoxicity bioreporters. Microb Biotechnol 2009; 3:412-27. [PMID: 21255340 PMCID: PMC3815808 DOI: 10.1111/j.1751-7915.2009.00160.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Ever since the introduction of the Salmonella typhimurium mammalian microsome mutagenicity assay (the ‘Ames test’) over three decades ago, there has been a constant development of additional genotoxicity assays based upon the use of genetically engineered microorganisms. Such assays rely either on reversion principles similar to those of the Ames test, or on promoter–reporter fusions that generate a quantifiable dose‐dependent signal in the presence of potential DNA damaging compounds and the induction of repair mechanisms; the latter group is the subject of the present review. Some of these assays were only briefly described in the scientific literature, whereas others have been developed all the way to commercial products. Out of these, only one, the umu‐test, has been fully validated and ISO‐ and OECD standardized. Here we review the main directions undertaken in the construction and testing of bacterial‐based genotoxicity bioassays, including the attempts to incorporate at least a partial metabolic activation capacity into the molecular design. We list the genetic modifications introduced into the tester strains, compare the performance of the different assays, and briefly describe the first attempts to incorporate such bacterial reporters into actual genotoxicity testing devices.
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Affiliation(s)
- Alva Biran
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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48
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Martineau R, Stout V, Towe B. Whole cell biosensing via recA::mCherry and LED-based flow-through fluorometry. Biosens Bioelectron 2009; 25:759-66. [DOI: 10.1016/j.bios.2009.08.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 08/14/2009] [Accepted: 08/15/2009] [Indexed: 10/20/2022]
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49
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Yagur-Kroll S, Bilic B, Belkin S. Strategies for enhancing bioluminescent bacterial sensor performance by promoter region manipulation. Microb Biotechnol 2009; 3:300-10. [PMID: 21255329 PMCID: PMC3815372 DOI: 10.1111/j.1751-7915.2009.00149.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bioluminescent bacterial sensors are based upon the fusion of bacterial bioluminescence (lux) genes, acting as a reporter element, to selected bacterial stress‐response gene promoters. Depending upon the nature of the promoter, the resulting constructs react to diverse types of environmental stress, including the presence of toxic chemicals, by dose‐dependant light emission. Two bacterial sensors, harbouring sulA::luxCDABE and grpE::luxCDABE fusions, activated by the model chemicals nalidixic acid (NA) and ethanol, respectively, were subjected to molecular manipulations of the promoter region, in order to enhance the intensity and speed of their response and lower their detection thresholds. By manipulating the length of the promoter‐containing segment (both promoters), by introducing random or specific mutations in the promoter sequence or by duplicating the promoter sequence (sulA only), major improvements in sensor performance were obtained. Improvements included significantly enhanced sensitivity, earlier response times and an increase in signal intensity. The general approaches described herein may be of general applicability for optimizing bacterial sensor performance, regardless of the sensing or reporting elements employed.
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Affiliation(s)
- Sharon Yagur-Kroll
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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50
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Onnis-Hayden A, Weng H, He M, Hansen S, Ilyin V, Lewis K, Guc AZ. Prokaryotic real-time gene expression profiling for toxicity assessment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2009; 43:4574-4581. [PMID: 19603679 DOI: 10.1021/es803227z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Examining global effects of toxins on gene expression profiles is proving to be a powerful method for toxicity assessment and for investigating mechanisms of toxicity. This study demonstrated the application of prokaryotic real-time gene expression profiling in Escherichia coli for toxicity assessment of environmental pollutants in water samples, by use of a cell-array library of 93 E. coli K12 strains with transcriptional green fluorescent protein (GFP) fusions covering most known stress response genes. The high-temporal-resolution gene expression data, for the first time, revealed complex and time-dependent transcriptional activities of various stress-associated genes in response to mercury and mitomycin (MMC) exposure and allowed for gene clustering analysis based on temporal response patterns. Compound-specific and distinctive gene expression profiles were obtained for MMC and mercury at different concentrations. MMC (genotoxin) induced not only the SOS response, which regulates DNA damage and repair, but also many other stress genes associated with drug resistance/sensitivity and chemical detoxification. A number of genes belonging to the P-type ATPase family and the MerR family were identified to be related to mercury resistance, among which zntA was found to be up-regulated at an increasing level as the mercury concentration increased. A mechanism-based evaluation of toxins based on real-time gene expression profiles promises, to be an efficient and informative method for toxicity assessment in environmental samples.
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Affiliation(s)
- Annalisa Onnis-Hayden
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, USA
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