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Purcarea C, Ruginescu R, Banciu RM, Vasilescu A. Extremozyme-Based Biosensors for Environmental Pollution Monitoring: Recent Developments. BIOSENSORS 2024; 14:143. [PMID: 38534250 DOI: 10.3390/bios14030143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Extremozymes combine high specificity and sensitivity with the ability to withstand extreme operational conditions. This work presents an overview of extremozymes that show potential for environmental monitoring devices and outlines the latest advances in biosensors utilizing these unique molecules. The characteristics of various extremozymes described so far are presented, underlining their stability and operational conditions that make them attractive for biosensing. The biosensor design is discussed based on the detection of photosynthesis-inhibiting herbicides as a case study. Several biosensors for the detection of pesticides, heavy metals, and phenols are presented in more detail to highlight interesting substrate specificity, applications or immobilization methods. Compared to mesophilic enzymes, the integration of extremozymes in biosensors faces additional challenges related to lower availability and high production costs. The use of extremozymes in biosensing does not parallel their success in industrial applications. In recent years, the "collection" of recognition elements was enriched by extremozymes with interesting selectivity and by thermostable chimeras. The perspectives for biosensor development are exciting, considering also the progress in genetic editing for the oriented immobilization of enzymes, efficient folding, and better electron transport. Stability, production costs and immobilization at sensing interfaces must be improved to encourage wider applications of extremozymes in biosensors.
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Affiliation(s)
- Cristina Purcarea
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Robert Ruginescu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Roberta Maria Banciu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania
- Department of Analytical and Physical Chemistry, University of Bucharest, 4-12 Regina Elisabeta Blvd., 030018 Bucharest, Romania
| | - Alina Vasilescu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania
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Sraphet S, Javadi B. Computational analysis of carboxylesterase genes and proteins in non-pathogenic food bacterium Alicyclobacillus acidocaldarius: insights from proteogenomics. World J Microbiol Biotechnol 2023; 39:348. [PMID: 37855845 DOI: 10.1007/s11274-023-03805-y] [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: 08/03/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Abstract
Over recent years, Alicyclobacillus acidocaldarius, a Gram-positive nonpathogenic rod-shaped thermo-acid-tolerant bacterium, has posed numerous challenges for the fruit juice industry. However, the bacterium's unique characteristics, particularly its nonpathogenic and thermophilic capabilities, offer significant opportunities for genetic exploration by biotechnologists. This study presents the computational proteogenomics report on the carboxylesterase (CE) enzyme in A. acidocaldarius, shedding light on structural and evolutional of CEs from this bacterium. Our analysis revealed that the average molecular weight of CEs in A. acidocaldarius was 41 kDa, with an isoelectric point around 5. The amino acid composition favored negative amino acids over positive ones. The aliphatic index and hydropathicity were approximately 88 and - 0.15, respectively. While the protein sequence showed no disulfide bonds in the CEs' structure, the presence of Cys amino acids was observed in the structure of CEs. Phylogenetic analysis presented more than 99% similarity between CEs, indicating their close evolutionary relationship. By applying homology modeling, the 3-dimensional structural models of the carboxylesterase were constructed, which with the help of structural conservation and solvent accessibility analysis highlighted key residues and regions responsible for enzyme stability and conformation. The specific patterns presented the total solvent accessibility of less than 25 (Å2) was in considerable position as well as Gly residues were noticeably have high accessibility to solvent in all structures. Ala was the more frequent amino acids in the conserved-SASA of carboxylesterases. Furthermore, unsupervised agglomerative hierarchical clustering based on solvent accessibility feature successfully clustered and even distinguished this enzyme from proteases from the same genome. These findings contribute to a deeper understanding of the nonpathogenic A. acidocaldarius carboxylesterase and its potential applications in biotechnology. Additionally, structural analysis of CEs would help to address potential solutions in fruit juice industry with utilization of computational structural biology.
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Affiliation(s)
- Supajit Sraphet
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Bagher Javadi
- Department of Sciences, Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand.
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Garefalaki V, Manco G, Porzio E. Use of biosensors for rapid and sensitive detection of pesticides in food samples for food safety chemical risk assessment. EFSA J 2022; 20:e200922. [PMID: 36531285 PMCID: PMC9749373 DOI: 10.2903/j.efsa.2022.e200922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The utility of pesticides in the agricultural field is unquestionable, but at the same time pesticide use presents serious hazards to the environment and the human health. For that reason, detection of pesticides and their biotransformation products in food is of utmost importance. According to previous studies, esterase-based biosensors have been proposed as a viable and efficient solution for the detection of organophosphate pesticides. In this project, a double mutant of the thermostable esterase-2 (EST2) from Alicyclobacillus acidocaldarius was studied as a potential biosensor, for its ability to detect residual amounts of pesticides. Initial characterisation of the enzyme was performed, that included determination of optimal pH, thermophilicity, as well as kinetic analysis. Subsequently, the enzyme was studied by enzymatic activity assays with and without the presence of various organophosphate compounds. The effect of the organophosphates on the enzymatic activity was measured and complete inhibition of the enzyme was observed after incubation with paraoxon. These experiments were followed by an additional method involving labelling of the enzyme with a fluorescent probe. In this case, the effect of different pesticides on the EST2 enzyme was monitored by measuring the fluorescence quenching upon addition to the enzyme. Fourteen compounds were screened with this method and significant fluorescence quenching was observed in the presence of paraoxon and methyl-paraoxon when used in equimolar amounts with the enzyme in the range of nanomolar. This biosensor has been also used to test the presence of pesticides in real food samples, like fruits and juices. This research represents a starting point to develop effective fluorescence-based biosensors aiming at the screening of mutants with different pesticide selectivity profiles. The use of this enzyme-based biosensor can have applications in the field of food traceability as well as environmental monitoring, to control the presence of toxic chemicals, in particular organophosphate pesticides.
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Rodrigues ACM, Barbieri MV, Chino M, Manco G, Febbraio F. A 3D printable adapter for solid-state fluorescence measurements: the case of an immobilized enzymatic bioreceptor for organophosphate pesticides detection. Anal Bioanal Chem 2022; 414:1999-2008. [PMID: 35064794 PMCID: PMC8791905 DOI: 10.1007/s00216-021-03835-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/12/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022]
Abstract
The widespread use of pesticides in the last decades and their accumulation into the environment gave rise to major environmental and human health concerns. To address this topic, the scientific community pointed out the need to develop methodologies to detect and measure the presence of pesticides in different matrices. Biosensors have been recently explored as fast, easy, and sensitive methods for direct organophosphate pesticides monitoring. Thus, the present work aimed at designing and testing a 3D printed adapter useful on different equipment, and a membrane support to immobilize the esterase-2 from Alicyclobacillus acidocaldarius (EST2) bioreceptor. The latter is labelled with the IAEDANS, a bright fluorescent probe. EST2 was selected since it shows a high specificity toward paraoxon. Our results showed good stability and replicability, with an increasing linear fluorescent intensity recorded from 15 to 150 pmol of labelled EST2. Linearity of data was also observed when using the immobilized labelled EST2 to detect increasing amounts of paraoxon, with a limit of detection (LOD) of 0.09 pmol. This LOD value reveals the high sensitivity of our membrane support when mounted on the 3D adapter, comparable to modern methods using robotic workstations. Notably, the use of an independent support significantly simplified the manipulation of the membrane during experimental procedures and enabled it to match the specificities of different systems. In sum, this work emphasizes the advantages of using 3D printed accessories adapted to respond to the newest research needs.
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Affiliation(s)
- Andreia C M Rodrigues
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), 80131, Naples, Italy
| | - Maria Vittoria Barbieri
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), 80131, Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples "Federico II", 80126, Naples, Italy.
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), 80131, Naples, Italy
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), 80131, Naples, Italy.
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Rodrigues ACM, Barbieri MV, Chino M, Manco G, Febbraio F. A FRET Approach to Detect Paraoxon among Organophosphate Pesticides Using a Fluorescent Biosensor. SENSORS (BASEL, SWITZERLAND) 2022; 22:561. [PMID: 35062524 PMCID: PMC8778994 DOI: 10.3390/s22020561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/09/2022] [Indexed: 02/01/2023]
Abstract
The development of faster, sensitive and real-time methods for detecting organophosphate (OP) pesticides is of utmost priority in the in situ monitoring of these widespread compounds. Research on enzyme-based biosensors is increasing, and a promising candidate as a bioreceptor is the thermostable enzyme esterase-2 from Alicyclobacillus acidocaldarius (EST2), with a lipase-like Ser-His-Asp catalytic triad with a high affinity for OPs. This study aimed to evaluate the applicability of Förster resonance energy transfer (FRET) as a sensitive and reliable method to quantify OPs at environmentally relevant concentrations. For this purpose, the previously developed IAEDANS-labelled EST2-S35C mutant was used, in which tryptophan and IAEDANS fluorophores are the donor and the acceptor, respectively. Fluorometric measurements showed linearity with increased EST2-S35C concentrations. No significant interference was observed in the FRET measurements due to changes in the pH of the medium or the addition of other organic components (glucose, ascorbic acid or yeast extract). Fluorescence quenching due to the presence of paraoxon was observed at concentrations as low as 2 nM, which are considered harmful for the ecosystem. These results pave the way for further experiments encompassing more complex matrices.
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Affiliation(s)
- Andreia C. M. Rodrigues
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy; (M.V.B.); (G.M.)
| | - Maria Vittoria Barbieri
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy; (M.V.B.); (G.M.)
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, 80126 Naples, Italy;
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy; (M.V.B.); (G.M.)
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy; (M.V.B.); (G.M.)
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Cetrangolo GP, Rusko J, Gori C, Carullo P, Manco G, Chino M, Febbraio F. Highly Sensitive Detection of Chemically Modified Thio-Organophosphates by an Enzymatic Biosensing Device: An Automated Robotic Approach. SENSORS 2020; 20:s20051365. [PMID: 32131482 PMCID: PMC7085774 DOI: 10.3390/s20051365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/28/2020] [Accepted: 02/28/2020] [Indexed: 12/28/2022]
Abstract
Pesticides represent some of the most common man-made chemicals in the world. Despite their unquestionable utility in the agricultural field and in the prevention of pest infestation in public areas of cities, pesticides and their biotransformation products are toxic to the environment and hazardous to human health. Esterase-based biosensors represent a viable alternative to the expensive and time-consuming systems currently used for their detection. In this work, we used the esterase-2 from Alicyclobacillus acidocaldarius as bioreceptor for a biosensing device based on an automated robotic approach. Coupling the robotic system with a fluorescence inhibition assay, in only 30 s of enzymatic assay, we accomplished the detection limit of 10 pmol for 11 chemically oxidized thio-organophosphates in solution. In addition, we observed differences in the shape of the inhibition curves determined measuring the decrease of esterase-2 residual activity over time. These differences could be used for the characterization and identification of thio-organophosphate pesticides, leading to a pseudo fingerprinting for each of these compounds. This research represents a starting point to develop technologies for automated screening of toxic compounds in samples from industrial sectors, such as the food industry, and for environmental monitoring.
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Affiliation(s)
- Giovanni Paolo Cetrangolo
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
| | - Janis Rusko
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
- Institute of Food Safety, Animal Health and Environment “BIOR”, Lejupes Street 3, LV-1076 Riga, Latvia
| | - Carla Gori
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
| | - Paola Carullo
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
- Correspondence: (G.M.); (F.F.); Tel.: +39-081-6132-296 (G.M.); +39-081-6132-611 (F.F.)
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”. Via Cintia, 80126 Napoli, Italy;
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
- Correspondence: (G.M.); (F.F.); Tel.: +39-081-6132-296 (G.M.); +39-081-6132-611 (F.F.)
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7
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Cetrangolo GP, Gori C, Rusko J, Terreri S, Manco G, Cimmino A, Febbraio F. Determination of Picomolar Concentrations of Paraoxon in Human Urine by Fluorescence-Based Enzymatic Assay. SENSORS 2019; 19:s19224852. [PMID: 31703397 PMCID: PMC6891394 DOI: 10.3390/s19224852] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/28/2019] [Accepted: 11/06/2019] [Indexed: 01/31/2023]
Abstract
Organophosphate (OP) pesticides are widely used in the agricultural field and in the prevention of pest infestation in private and public areas of cities. Despite their unquestionable utility, several of these compounds demonstrate toxic effects to the environment and human health. In particular, the occurrence of some organophosphate pesticides is correlated to the incidence of nervous system disorders, especially in children. The detection of pesticide residues in the human body represents an important task to preserve human health. In our work we propose the use of esterase-based biosensors as a viable alternative to the expensive and time-consuming systems currently used for their detection in human fluids. Using the esterase-2 activity, coupled with a fluorescence inhibition assay, we are able to detect very low concentration levels of diethyl (4-nitrophenyl) phosphate (paraoxon) in the range of the femtomole (fmol). Method robustness tests indicate the stability of esterase-2 in a diluted solution of 4% human urine, and we are able to accurately determine concentration levels of paraoxon in the range from 0.1 to 2 picomoles (pmol). The system sensitivity for OP detection is calculated at 524 ± 14.15 fmol of paraoxon recognized at 10% of inhibition, with an estimated limit of quantification of 262 ± 8.12 pmol mL-1. These values are comparable with the most recent analysis methods based on mass spectrometry carried out on human samples for pesticide detection. This research represents a starting point to develop cheap and fast testing methods for a rapid screening of toxic substances in human samples.
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Affiliation(s)
- Giovanni Paolo Cetrangolo
- Institute of Biochemistry and Cellular Biology – National Research Council (CNR), via Pietro Castellino 111, 80131 Naples, Italy; (G.P.C.); (C.G.); (J.R.)
| | - Carla Gori
- Institute of Biochemistry and Cellular Biology – National Research Council (CNR), via Pietro Castellino 111, 80131 Naples, Italy; (G.P.C.); (C.G.); (J.R.)
| | - Janis Rusko
- Institute of Biochemistry and Cellular Biology – National Research Council (CNR), via Pietro Castellino 111, 80131 Naples, Italy; (G.P.C.); (C.G.); (J.R.)
- Institute of Food Safety, Animal Health and Environment “BIOR”, Lejupes street 3, LV-1076 Riga, Latvia
| | - Sara Terreri
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”–National Research Council (CNR), via Pietro Castellino 111, 80131 Naples, Italy; (S.T.); (A.C.)
| | - Giuseppe Manco
- Institute of Biochemistry and Cellular Biology – National Research Council (CNR), via Pietro Castellino 111, 80131 Naples, Italy; (G.P.C.); (C.G.); (J.R.)
- Correspondence: (G.M.); (F.F.); Tel.: +39-081-613-2296 (G.M.); +39-081-613-2611 (F.F.)
| | - Amelia Cimmino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”–National Research Council (CNR), via Pietro Castellino 111, 80131 Naples, Italy; (S.T.); (A.C.)
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cellular Biology – National Research Council (CNR), via Pietro Castellino 111, 80131 Naples, Italy; (G.P.C.); (C.G.); (J.R.)
- Correspondence: (G.M.); (F.F.); Tel.: +39-081-613-2296 (G.M.); +39-081-613-2611 (F.F.)
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Rusko J, Febbraio F. Development of an automated multienzymatic biosensor for risk assessment of pesticide contamination in water and food. EFSA J 2018; 16:e16084. [PMID: 32626055 PMCID: PMC7015495 DOI: 10.2903/j.efsa.2018.e16084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The goal of this research is to better address the problems related to the widespread presence of pesticides in the environment. Despite the unquestionable utility of the pesticides against various pests in the agricultural field, most pesticides and the corresponding pesticide residues are toxic to the environment and hazardous to human health. The recent literature on organophosphate compounds emphasises a clear correlation between their use and the occurrence of disorders in the nervous system, especially in children. The conventional systems for the detection and analysis of these compounds are expensive, time‐consuming and require highly specialised operators; moreover, no online automated screening systems are yet available, that would allow the identification and quantification of the presence of these chemicals in samples from industrial sectors such as the food industry. Esterase‐based biosensors represent a viable alternative to this problem. In this fellowship programme, we aim to develop a robust and sensitive methodology that enables the screening of toxic compounds using a streamlined process, using an automated robotic system to achieve a continuous monitoring for risk assessment of pesticides.
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Hidese R, Ataka K, Bill E, Shima S. Cu I and H 2 O 2 Inactivate and Fe II Inhibits [Fe]-Hydrogenase at Very Low Concentrations. Chembiochem 2015; 16:1861-1865. [PMID: 26136368 DOI: 10.1002/cbic.201500318] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 11/09/2022]
Abstract
[Fe]-Hydrogenase (Hmd) catalyzes reversible hydride transfer from H2 . It harbors an iron-guanylylpyridinol as a cofactor with an FeII that is ligated to one thiolate, two COs, one acyl-C, one pyridinol-N, and solvent. Here, we report that CuI and H2 O2 inactivate Hmd (half-maximal rates at 1 μM CuI and 20 μM H2 O2 ) and that FeII inhibits the enzyme with very high affinity (Ki =40 nM). Infrared and EPR studies together with competitive inhibition studies with isocyanide indicated that CuI exerts its inhibitory effect most probably by binding to the active site iron-thiolate ligand. Using the same methods, it was found that H2 O2 binds to the active-site iron at the solvent-binding site and oxidizes FeII to FeIII . Also it was shown that FeII reversibly binds away from the active site iron, with binding being competitive to the organic hydride acceptor; this inhibition is specific for FeII and is reminiscent of that for the [FeFe]-hydrogenase second iron, which specifically interacts with H2 .
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Affiliation(s)
- Ryota Hidese
- Max-Planck-Institute für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse 10, 35043 Marburg (Germany)
| | - Kenichi Ataka
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin (Germany)
| | - Eckhard Bill
- Max Planck Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr (Germany)
| | - Seigo Shima
- Max-Planck-Institute für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse 10, 35043 Marburg (Germany).,PRESTO, Japan Science and Technology Agency (JST), Saitama 332-0012 (Japan)
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Fluorescence spectroscopy approaches for the development of a real-time organophosphate detection system using an enzymatic sensor. SENSORS 2015; 15:3932-51. [PMID: 25671511 PMCID: PMC4367393 DOI: 10.3390/s150203932] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/02/2015] [Indexed: 01/28/2023]
Abstract
Organophosphates are organic substances that contain a phosphoryl or a thiophosphoryl bond. They are mainly used around the world as pesticides, but can also be used as chemical warfare agents. Their detection is normally entrusted to techniques like GC- and LC-MS that, although sensitive, do not allow their identification on site and in real time. We have approached their identification by exploiting the high-affinity binding of these compounds with the esterase 2 from Alicyclobacillus acidocaldarius. Using an in silico analysis to evaluate the binding affinities of the enzyme with organophosphate inhibitors, like paraoxon, and other organophosphate compounds, like parathion, chlorpyriphos, and other organophosphate thio-derivatives, we have designed fluorescence spectroscopy experiments to study the quenching of the tryptophan residues after esterase 2 binding with the organophosphate pesticides. The changes in the fluorescence signals permitted an immediate and quantitative identification of these compounds from nano- to picomolar concentrations. A fluorescence based polarity-sensitive probe (ANS) was also employed as a means to understand the extent of the interactions involved, as well as to explore other ways to detect organophosphate pesticides. Finally, we designed a framework for the development of a biosensor that exploits fluorescence technology in combination with a sensitive and very stable bio-receptor.
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Wang Y, Li B, Han W, Yang G, Zhang Z, Feng Y. Redesigning the active site of a carboxyl esterase from the archaeon Archaeoglobus fulgidus to improve sensitivity to organophosphorus compounds. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.08.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Ašler IL, Kovačić F, Marchetti-Deschmann M, Allmaier G, Štefanić Z, Kojić-Prodić B. Inhibition of extracellular lipase from Streptomyces rimosus with 3,4-dichloroisocoumarin. J Enzyme Inhib Med Chem 2012; 28:1094-104. [DOI: 10.3109/14756366.2012.716834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ivana Leščić Ašler
- Rudjer Bošković Institute, Department for Physical Chemistry,
Zagreb, Croatia
| | - Filip Kovačić
- Institute of Molecular Enzyme Technology, Heinrich-Heine University Düsseldorf, Research Center Jülich,
Jülich, Germany
| | | | - Günter Allmaier
- Vienna University of Technology, Institute for Chemical Technologies and Analytics,
Vienna, Austria
| | - Zoran Štefanić
- Rudjer Bošković Institute, Department for Physical Chemistry,
Zagreb, Croatia
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Levisson M, Han GW, Deller MC, Xu Q, Biely P, Hendriks S, Ten Eyck LF, Flensburg C, Roversi P, Miller MD, McMullan D, von Delft F, Kreusch A, Deacon AM, van der Oost J, Lesley SA, Elsliger MA, Kengen SWM, Wilson IA. Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima. Proteins 2012; 80:1545-59. [PMID: 22411095 DOI: 10.1002/prot.24041] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/10/2012] [Accepted: 01/18/2012] [Indexed: 11/06/2022]
Abstract
TM0077 from Thermotoga maritima is a member of the carbohydrate esterase family 7 and is active on a variety of acetylated compounds, including cephalosporin C. TM0077 esterase activity is confined to short-chain acyl esters (C2-C3), and is optimal around 100°C and pH 7.5. The positional specificity of TM0077 was investigated using 4-nitrophenyl-β-D-xylopyranoside monoacetates as substrates in a β-xylosidase-coupled assay. TM0077 hydrolyzes acetate at positions 2, 3, and 4 with equal efficiency. No activity was detected on xylan or acetylated xylan, which implies that TM0077 is an acetyl esterase and not an acetyl xylan esterase as currently annotated. Selenomethionine-substituted and native structures of TM0077 were determined at 2.1 and 2.5 Å resolution, respectively, revealing a classic α/β-hydrolase fold. TM0077 assembles into a doughnut-shaped hexamer with small tunnels on either side leading to an inner cavity, which contains the six catalytic centers. Structures of TM0077 with covalently bound phenylmethylsulfonyl fluoride and paraoxon were determined to 2.4 and 2.1 Å, respectively, and confirmed that both inhibitors bind covalently to the catalytic serine (Ser188). Upon binding of inhibitor, the catalytic serine adopts an altered conformation, as observed in other esterase and lipases, and supports a previously proposed catalytic mechanism in which Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction.
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Affiliation(s)
- Mark Levisson
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
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The crystal structure of the cephalosporin deacetylating enzyme acetyl xylan esterase bound to paraoxon explains the low sensitivity of this serine hydrolase to organophosphate inactivation. Biochem J 2011; 436:321-30. [DOI: 10.1042/bj20101859] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Organophosphorus insecticides and nerve agents irreversibly inhibit serine hydrolase superfamily enzymes. One enzyme of this superfamily, the industrially important (for β-lactam antibiotic synthesis) AXE/CAH (acetyl xylan esterase/cephalosporin acetyl hydrolase) from the biotechnologically valuable organism Bacillus pumilus, exhibits low sensitivity to the organophosphate paraoxon (diethyl-p-nitrophenyl phosphate, also called paraoxon-ethyl), reflected in a high Ki for it (~5 mM) and in a slow formation (t½~1 min) of the covalent adduct of the enzyme and for DEP (E-DEP, enzyme–diethyl phosphate, i.e. enzyme–paraoxon). The crystal structure of the E-DEP complex determined at 2.7 Å resolution (1 Å=0.1 nm) reveals strain in the active Ser181-bound organophosphate as a likely cause for the limited paraoxon sensitivity. The strain results from active-site-size limitation imposed by bulky conserved aromatic residues that may exclude as substrates esters having acyl groups larger than acetate. Interestingly, in the doughnut-like homohexamer of the enzyme, the six active sites are confined within a central chamber formed between two 60°-staggered trimers. The exclusive access to this chamber through a hole around the three-fold axis possibly limits the size of the xylan natural substrates. The enzyme provides a rigid scaffold for catalysis, as reflected in the lack of movement associated with paraoxon adduct formation, as revealed by comparing this adduct structure with that also determined in the present study at 1.9 Å resolution for the paraoxon-free enzyme.
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Febbraio F, Merone L, Cetrangolo GP, Rossi M, Nucci R, Manco G. Thermostable Esterase 2 from Alicyclobacillus acidocaldarius as Biosensor for the Detection of Organophosphate Pesticides. Anal Chem 2011; 83:1530-6. [DOI: 10.1021/ac102025z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ferdinando Febbraio
- Istituto di Biochimica delle Proteine, CNR. Via P. Castellino 111, 80131 Naples, Italy
| | - Luigia Merone
- Istituto di Biochimica delle Proteine, CNR. Via P. Castellino 111, 80131 Naples, Italy
| | | | - Mosè Rossi
- Istituto di Biochimica delle Proteine, CNR. Via P. Castellino 111, 80131 Naples, Italy
| | - Roberto Nucci
- Istituto di Biochimica delle Proteine, CNR. Via P. Castellino 111, 80131 Naples, Italy
| | - Giuseppe Manco
- Istituto di Biochimica delle Proteine, CNR. Via P. Castellino 111, 80131 Naples, Italy
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Merone L, Mandrich L, Porzio E, Rossi M, Müller S, Reiter G, Worek F, Manco G. Improving the promiscuous nerve agent hydrolase activity of a thermostable archaeal lactonase. BIORESOURCE TECHNOLOGY 2010; 101:9204-9212. [PMID: 20667718 DOI: 10.1016/j.biortech.2010.06.102] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/16/2010] [Accepted: 06/24/2010] [Indexed: 05/29/2023]
Abstract
The thermostable Phosphotriesterase-Like Lactonase from Sulfolobus solfataricus (SsoPox) hydrolyzes lactones and, at a lower rate, neurotoxic organophosphorus compounds. The persistent demand of detoxification tools in the field of agricultural wastes and restoring of conditions after terrorist acts prompted us to exploit SsoPox as a "starter" to evolve its ancillary nerve agents hydrolytic capability. A directed evolution strategy yielded, among several variants, the single mutant W263F with k(cat) and specificity constant against paraoxon 16- and 6-fold enhanced, respectively, compared to the wild type. Furthermore, a phenomenon of enzyme activation by SDS has been observed, which allowed to increase those values 150- and 28-fold, respectively. The activity of SsoPox against the deadly nerve gas Cyclosarin has been reported for the first time and proved to be substantially unaffected for variant W263F. Finally, outperforming efficiency of W263F was demonstrated, under severe stressing conditions, with respect to the best known phosphotriesterase PTE from Brevundimonas diminuta.
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Affiliation(s)
- Luigia Merone
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy
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Levisson M, Sun L, Hendriks S, Swinkels P, Akveld T, Bultema JB, Barendregt A, van den Heuvel RHH, Dijkstra BW, van der Oost J, Kengen SWM. Crystal structure and biochemical properties of a novel thermostable esterase containing an immunoglobulin-like domain. J Mol Biol 2008; 385:949-62. [PMID: 19013466 DOI: 10.1016/j.jmb.2008.10.075] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 10/24/2008] [Accepted: 10/27/2008] [Indexed: 11/26/2022]
Abstract
Comparative analysis of the genome of the hyperthermophilic bacterium Thermotoga maritima revealed a hypothetical protein (EstA) with typical esterase features. The EstA protein was functionally produced in Escherichia coli and purified to homogeneity. It indeed displayed esterase activity with optima at or above 95 degrees C and at pH 8.5, with a preference for esters with short acyl chains (C2-C10). Its 2.6-A-resolution crystal structure revealed a classical alpha/beta hydrolase domain with a catalytic triad consisting of a serine, an aspartate, and a histidine. EstA is irreversibly inhibited by the organophosphate paraoxon. A 3.0-A-resolution structure confirmed that this inhibitor binds covalently to the catalytic serine residue of EstA. Remarkably, the structure also revealed the presence of an N-terminal immunoglobulin (Ig)-like domain, which is unprecedented among esterases. EstA forms a hexamer both in the crystal and in solution. Electron microscopy showed that the hexamer in solution is identical with the hexamer in the crystal, which is formed by two trimers, with the N-terminal domains facing each other. Mutational studies confirmed that residues Phe89, Phe112, Phe116, Phe246, and Trp377 affect enzyme activity. A truncated mutant of EstA, in which the Ig-like domain was removed, showed only 5% of wild-type activity, had lower thermostability, and failed to form hexamers. These data suggest that the Ig-like domain plays an important role in the enzyme multimerization and activity of EstA.
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Affiliation(s)
- Mark Levisson
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
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