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Pashirova T, Salah-Tazdaït R, Tazdaït D, Masson P. Applications of Microbial Organophosphate-Degrading Enzymes to Detoxification of Organophosphorous Compounds for Medical Countermeasures against Poisoning and Environmental Remediation. Int J Mol Sci 2024; 25:7822. [PMID: 39063063 PMCID: PMC11277490 DOI: 10.3390/ijms25147822] [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: 06/17/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Mining of organophosphorous (OPs)-degrading bacterial enzymes in collections of known bacterial strains and in natural biotopes are important research fields that lead to the isolation of novel OP-degrading enzymes. Then, implementation of strategies and methods of protein engineering and nanobiotechnology allow large-scale production of enzymes, displaying improved catalytic properties for medical uses and protection of the environment. For medical applications, the enzyme formulations must be stable in the bloodstream and upon storage and not susceptible to induce iatrogenic effects. This, in particular, includes the nanoencapsulation of bioscavengers of bacterial origin. In the application field of bioremediation, these enzymes play a crucial role in environmental cleanup by initiating the degradation of OPs, such as pesticides, in contaminated environments. In microbial cell configuration, these enzymes can break down chemical bonds of OPs and usually convert them into less toxic metabolites through a biotransformation process or contribute to their complete mineralization. In their purified state, they exhibit higher pollutant degradation efficiencies and the ability to operate under different environmental conditions. Thus, this review provides a clear overview of the current knowledge about applications of OP-reacting enzymes. It presents research works focusing on the use of these enzymes in various bioremediation strategies to mitigate environmental pollution and in medicine as alternative therapeutic means against OP poisoning.
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Affiliation(s)
- Tatiana Pashirova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya St., 420008 Kazan, Russia;
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Rym Salah-Tazdaït
- Bioengineering and Process Engineering Laboratory (BIOGEP), National Polytechnic School, 10 Rue des Frères Oudek, El Harrach, Algiers 16200, Algeria; (R.S.-T.); (D.T.)
| | - Djaber Tazdaït
- Bioengineering and Process Engineering Laboratory (BIOGEP), National Polytechnic School, 10 Rue des Frères Oudek, El Harrach, Algiers 16200, Algeria; (R.S.-T.); (D.T.)
- Department of Nature and Life Sciences, University of Algiers, Benyoucef Benkhedda, 2 Rue Didouche Mourad, Algiers 16000, Algeria
| | - Patrick Masson
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya St., 420008 Kazan, Russia;
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2
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Azman AA, Muhd Noor ND, Leow ATC, Mohd Noor SA, Mohamad Ali MS. Identification and characterization of a promiscuous metallohydrolase in metallo-β-lactamase superfamily from a locally isolated organophosphate-degrading Bacillus sp. strain S3wahi. Int J Biol Macromol 2024; 271:132395. [PMID: 38761915 DOI: 10.1016/j.ijbiomac.2024.132395] [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: 12/20/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
In this present study, characteristics and structure-function relationship of an organophosphate-degrading enzyme from Bacillus sp. S3wahi were described. S3wahi metallohydrolase, designated as S3wahi-MH (probable metallohydrolase YqjP), featured the conserved αβ/βα metallo-β-lactamase-fold (MBL-fold) domain and a zinc bimetal at its catalytic site. The metal binding site of S3wahi-MH also preserves the H-X-H-X-D-H motif, consisting of specific amino acids at Zn1 (Asp69, His70, Asp182, and His230) and Zn2 (His65, His67, and His137). The multifunctionality of S3wahi-MH was demonstrated through a steady-state kinetic study, revealing its highest binding affinity (KM) and catalytic efficiency (kcat/KM) for OP compound, paraoxon, with values of 8.09 × 10-6 M and 4.94 × 105 M-1 s-1, respectively. Using OP compound, paraoxon, as S3wahi-MH native substrate, S3wahi-MH exhibited remarkable stability over a broad temperature range, 20 °C - 60 °C and a broad pH tolerance, pH 6-10. Corresponded to S3wahi-MH thermal stability characterization, the estimated melting temperature (Tm) was found to be 72.12 °C. S3wahi-MH was also characterized with optimum catalytic activity at 30 °C and pH 8. Additionally, the activity of purified S3wahi-MH was greatly enhanced in the presence of 1 mM and 5 mM of manganese (Mn2+), showing relative activities of 1323.68 % and 2073.68 %, respectively. The activity of S3wahi-MH was also enhanced in the presence of DMSO and DMF, showing relative activities of 270.37 % and 307.41 %, respectively. The purified S3wahi-MH retained >60 % residual activity after exposure to non-ionic Tween series surfactants. Nevertheless, the catalytic activity of S3wahi-MH was severely impacted by the treatment of SDS, even at low concentrations. Considering its enzymatic properties and promiscuity, S3wahi-MH emerges as a promising candidate as a bioremediation tool in wide industrial applications, including agriculture industry.
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Affiliation(s)
- Ameera Aisyah Azman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Siti Aminah Mohd Noor
- Center for Defence Foundation Studies, National Defence University of Malaysia, Kem Perdana Sungai Besi, Kuala Lumpur 57000, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
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3
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Jacquet P, Billot R, Shimon A, Hoekstra N, Bergonzi C, Jenks A, Chabrière E, Daudé D, Elias MH. Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity. JACS AU 2024; 4:1941-1953. [PMID: 38818068 PMCID: PMC11134384 DOI: 10.1021/jacsau.4c00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 06/01/2024]
Abstract
Enzymatic promiscuity, the ability of enzymes to catalyze multiple, distinct chemical reactions, has been well documented and is hypothesized to be a major driver of the emergence of new enzymatic functions. Yet, the molecular mechanisms involved in the transition from one activity to another remain debated and elusive. Here, we evaluated the redesign of the active site binding cleft of lactonase SsoPox using structure-based design and combinatorial libraries. We created variants with largely improved catalytic abilities against phosphotriesters, the best ones being >1000-fold better compared to the wild-type enzyme. The observed shifts in activity specificity are large, and some variants completely lost their initial activity. The selected combinations of mutations have considerably reshaped the active site cavity via side chain changes but mostly through large rearrangements of the active site loops and changes to their conformations, as revealed by a suite of crystal structures. This suggests that a specific active site loop configuration is critical to the lactonase activity. Interestingly, analysis of high-resolution structures hints at the potential role of conformational sampling and its directionality in defining the enzyme activity profile.
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Affiliation(s)
| | - Raphaël Billot
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
| | - Amir Shimon
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Nathan Hoekstra
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Céline Bergonzi
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Anthony Jenks
- Department
of Biochemistry, Molecular Biology and Biophysics & Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Eric Chabrière
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
- Aix
Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
| | - David Daudé
- Gene&GreenTK, 19-21 Bd Jean Moulin, Marseille 13005, France
| | - Mikael H. Elias
- Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
- Department
of Biochemistry, Molecular Biology and Biophysics & Biotechnology
Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
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4
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Aberuagba A, Joel EB, Bello AJ, Igunnu A, Malomo SO, Olorunniji FJ. Thermophilic PHP Protein Tyrosine Phosphatases (Cap8C and Wzb) from Mesophilic Bacteria. Int J Mol Sci 2024; 25:1262. [PMID: 38279261 PMCID: PMC10816263 DOI: 10.3390/ijms25021262] [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: 10/29/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Protein tyrosine phosphatases (PTPs) of the polymerase and histidinol phosphatase (PHP) superfamily with characteristic phosphatase activity dependent on divalent metal ions are found in many Gram-positive bacteria. Although members of this family are co-purified with metal ions, they still require the exogenous supply of metal ions for full activation. However, the specific roles these metal ions play during catalysis are yet to be well understood. Here, we report the metal ion requirement for phosphatase activities of S. aureus Cap8C and L. rhamnosus Wzb. AlphaFold-predicted structures of the two PTPs suggest that they are members of the PHP family. Like other PHP phosphatases, the two enzymes have a catalytic preference for Mn2+, Co2+ and Ni2+ ions. Cap8C and Wzb show an unusual thermophilic property with optimum activities over 75 °C. Consistent with this model, the activity-temperature profiles of the two enzymes are dependent on the divalent metal ion activating the enzyme.
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Affiliation(s)
- Adepeju Aberuagba
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
| | - Enoch B. Joel
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos 930003, Nigeria
| | - Adebayo J. Bello
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
| | - Adedoyin Igunnu
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin 234031, Nigeria; (A.I.); (S.O.M.)
| | - Sylvia O. Malomo
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin 234031, Nigeria; (A.I.); (S.O.M.)
| | - Femi J. Olorunniji
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
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5
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Bhat N, Nutho B, Hanpaibool C, Hadsadee S, Vangnai A, Rungrotmongkol T. Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species. Proteins 2024; 92:96-105. [PMID: 37646471 DOI: 10.1002/prot.26579] [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: 03/06/2023] [Revised: 07/04/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Methyl parathion hydrolase (MPH) is an enzyme of the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphates (OPs). Recently, MPH has attracted attention as a promising enzymatic bioremediator. The crystal structure of MPH enzyme shows a dimeric form, with each subunit containing a binuclear metal ion center. MPH also demonstrates metal ion-dependent selectivity patterns. The origins of these patterns remain unclear but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. We aimed to investigate and compare the binding of different OP pesticides to MPH with cobalt(II) metal ions. In this study, MPH was modeled from Ochrobactrum sp. with different OP pesticides bound, including methyl paraoxon and dichlorvos and profenofos. The docked structures for each substrate optimized by DFT calculation were selected and subjected to atomistic molecular dynamics simulations for 500 ns. It was found that alpha metal ions did not coordinate with all the pesticides. Rather, the pesticides coordinated with less buried beta metal ions. It was also observed that the coordination of beta metal ions was perturbed to accommodate the pesticides. The binding free energy calculations and structure-based pharmacophore model revealed that all the three substrates could bind well at the active site. However, profenofos exhibit a stronger binding affinity to MPH in comparison to the other two substrates. Therefore, our findings provide molecular insight on the binding of different OP pesticides which could help us design the enzyme for OP pesticides degradation.
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Affiliation(s)
- Nayana Bhat
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Bodee Nutho
- Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Chonnikan Hanpaibool
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Sarinya Hadsadee
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Alisa Vangnai
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Hazardous Substance Management, Chulalongkorn University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
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6
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Porzio E, Andrenacci D, Manco G. Thermostable Lactonases Inhibit Pseudomonas aeruginosa Biofilm: Effect In Vitro and in Drosophila melanogaster Model of Chronic Infection. Int J Mol Sci 2023; 24:17028. [PMID: 38069351 PMCID: PMC10707464 DOI: 10.3390/ijms242317028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Pseudomonas aeruginosa is one of the six antimicrobial-resistant pathogens known as "ESKAPE" that represent a global threat to human health and are considered priority targets for the development of novel antimicrobials and alternative therapeutics. The virulence of P. aeruginosa is regulated by a four-chemicals communication system termed quorum sensing (QS), and one main class of QS signals is termed acylhomoserine lactones (acyl-HSLs), which includes 3-Oxo-dodecanoil homoserine lactone (3-Oxo-C12-HSL), which regulates the expression of genes implicated in virulence and biofilm formation. Lactonases, like Paraoxonase 2 (PON2) from humans and the phosphotriesterase-like lactonases (PLLs) from thermostable microorganisms, are able to hydrolyze acyl-HSLs. In this work, we explored in vitro and in an animal model the effect of some lactonases on the production of Pseudomonas virulence factors. This study presents a model of chronic infection in which bacteria were administered by feeding, and Drosophila adults were treated with enzymes and the antibiotic tobramycin, alone or in combination. In vitro, we observed significant effects of lactonases on biofilm formation as well as effects on bacterial motility and the expression of virulence factors. The treatment in vivo by feeding with the lactonase SacPox allowed us to significantly increase the biocidal effect of tobramycin in chronic infection.
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Affiliation(s)
- Elena Porzio
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy
| | - Davide Andrenacci
- CNR Institute of Molecular Genetics “Luigi-Luca Cavalli-Sforza” Unit of Bologna, 40136 Bologna, Italy
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy
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7
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Marone M, Porzio E, Lampitella EA, Manco G. A mesophilic phosphotriesterase-like lactonase shows high stability and proficiency as quorum quenching enzyme. Chem Biol Interact 2023; 383:110657. [PMID: 37573927 DOI: 10.1016/j.cbi.2023.110657] [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: 06/12/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
The problem of biofilm formation is a serious concern under various pathological conditions such as extensive burns, wounds in diabetic patients, bedsores, cystic fibrosis, nosocomial infections from implantable medical devices such as catheters, valves, etc. Environmental diffusion of biofilm (in pools, wet floors, industrial food plants) that could represent a reservoir of antibiotic resistant bacteria constitues an additional issue. In this work is described a lactonase from Rhodococcus erythropolis, a phosphotriesterase-like lactonase (PLL) enzyme, which has already been studied in the past and can be used for containment of biofilm formation. The protein is 28% and 40% identical with respect to the Pseudomonas diminuta PTE and the thermostable Saccharolobus solfataricus SsoPox respectively. The protein was obtained starting from a synthetic His-tagged gene, expressed in E. coli, purified and further characterized. New properties, not previously known or deducible from its sequence, have been highlighted. These properties are: the enzyme is thermophilic and thermostable even though it originates from a mesophilic bacterium; the enzyme has a long (months) shelf life at 4 °C; the enzyme is not only stable to low concentrations of the oxidant H2O2 but even activated by it at high concentrations; the enzyme proved to be a proficient quorum quenching enzyme, able to hydrolase acyl-homoserine lactones 3oxoC12-HSL and C4-HSL, and can inhibit up to 60% the formation of Pseudomonas aeruginosa (PAO1) biofilm. These different properties make the lactonase useful to fight resistant bacteria that induce inflammatory and infectious processes mediated by the quorum sensing mechanism.
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Affiliation(s)
- Maria Marone
- Institute of Biochemistry and Cell Biology. National Research Council of Italy, Via P. Castellino 111, Naples, Italy
| | - Elena Porzio
- Institute of Biochemistry and Cell Biology. National Research Council of Italy, Via P. Castellino 111, Naples, Italy
| | - Eros Antonio Lampitella
- Institute of Biochemistry and Cell Biology. National Research Council of Italy, Via P. Castellino 111, Naples, Italy
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology. National Research Council of Italy, Via P. Castellino 111, Naples, Italy.
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Huang S, Bergonzi C, Smith S, Hicks RE, Elias MH. Field testing of an enzymatic quorum quencher coating additive to reduce biocorrosion of steel. Microbiol Spectr 2023; 11:e0517822. [PMID: 37668433 PMCID: PMC10580884 DOI: 10.1128/spectrum.05178-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/27/2023] [Indexed: 09/06/2023] Open
Abstract
Microbial colonization can be detrimental to the integrity of metal surfaces and lead to microbiologically influenced corrosion. Biocorrosion is a serious problem for aquatic and marine industries in the world and severely affects the maritime transportation industry by destroying port infrastructure and increasing fuel usage and the time and cost required for maintenance of transport vessels. Here, we evaluate the potential of a stable quorum quenching lactonase enzyme to reduce biocorrosion in the field. Over the course of 21 months, steel samples coated with lactonase-containing acrylic paint were submerged at two different sites and depths in the Duluth-Superior Harbor (Lake Superior, MN, USA) and benchmarked against controls, including the biological biocide surfactin. In this experiment, the lactonase treatment outperformed the surfactin biocide treatment and significantly reduced the number of corrosion tubercles (37%; P < 0.01) and the corroded surface area (39%; P < 0.01) as compared to the acrylic-coated control coupons. In an attempt to evaluate the effects of signal disruption of surface microbial communities and the reasons for lower corrosion levels, 16S rRNA sequencing was performed and community populations were analyzed. Interestingly, surface communities were similar between all treatments, and only minor changes could be observed. Among these changes, several groups, including sulfate-reducing bacteria (SRB), appeared to correlate with corrosion levels, and more specifically, SRB abundance levels were lower on lactonase-treated steel coupons. We surmise that these minute community changes may have large impacts on corrosion rates. Overall, these results highlight the potential use of stable quorum quenching lactonases as an eco-friendly antifouling coating additive. IMPORTANCE Biocorrosion severely affects the maritime transportation industry by destroying port infrastructure and increasing fuel usage and the time and cost required to maintain transport vessels. Current solutions are partly satisfactory, and the antifouling coating still largely depends on biocide-containing products that are harmful to the environment. The importance of microbial signaling in biofouling and biocorrosion is not elucidated. We here take advantage of a highly stable lactonase that can interfere with N-acyl homoserine lactone-based quorum sensing and remain active in a coating base. The observed results show that an enzyme-containing coating can reduce biocorrosion over 21 months in the field. It also reveals subtle changes in the abundance of surface microbes, including sulfate-reducing bacteria. This work may contribute to pave the way for strategies pertaining to surface microbiome changes to reduce biocorrosion.
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Affiliation(s)
- Siqian Huang
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Biotechnology Institute, St. Paul, Minnesota, USA
| | - Celine Bergonzi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Biotechnology Institute, St. Paul, Minnesota, USA
| | - Sherry Smith
- Independant Scholar, Minneapolis, Minnesota, USA
| | - Randall E. Hicks
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Mikael H. Elias
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Biotechnology Institute, St. Paul, Minnesota, USA
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9
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Jacquet P, Billot R, Shimon A, Hoekstra N, Bergonzi C, Jenks A, Chabrière E, Daudé D, Elias MH. Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541809. [PMID: 37292757 PMCID: PMC10245850 DOI: 10.1101/2023.05.22.541809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enzymatic promiscuity, the ability of enzymes to catalyze multiple, distinct chemical reactions, has been well documented and is hypothesized to be a major driver for the emergence of new enzymatic functions. Yet, the molecular mechanisms involved in the transition from one activity to another remain debated and elusive. Here, we evaluated the redesign of the active site binding cleft of the lactonase SsoPox using structure-based design and combinatorial libraries. We created variants with largely improved catalytic abilities against phosphotriesters, the best ones being > 1,000-fold better compared to the wild-type enzyme. The observed shifts in activity specificity are large, ~1,000,000-fold and beyond, since some variants completely lost their initial activity. The selected combinations of mutations have considerably reshaped the active site cavity via side chain changes but mostly through large rearrangements of the active site loops, as revealed by a suite of crystal structures. This suggests that specific active site loop configuration is critical to the lactonase activity. Interestingly, analysis of high-resolution structures hints at the potential role of conformational sampling and its directionality in defining an enzyme activity profile.
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Affiliation(s)
- Pauline Jacquet
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Raphaël Billot
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Amir Shimon
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Nathan Hoekstra
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Céline Bergonzi
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Anthony Jenks
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Eric Chabrière
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
| | - David Daudé
- Gene&GreenTK, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Mikael H. Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
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10
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Fang L, Zhou Y, Chen T, Geng Y, Li Z, Zha W, Shi T, Hua R. Efficient biodegradation characteristics and detoxification pathway of organophosphorus insecticide profenofos via Cupriavidus nantongensis X1 T and enzyme OpdB. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160782. [PMID: 36513234 DOI: 10.1016/j.scitotenv.2022.160782] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Profenofos residues in the environment pose a high risk to mammals and non-target organisms. In this study, the biodegradation and detoxification of profenofos in an efficient degrading strain, Cupriavidus nantongensis X1T, was investigated. Strain X1T could degrade 88.82 % of 20 mg/L profenofos in 48 h. The optimum temperature and inoculation amount of strain X1T for the degradation of profenofos were 30-37 °C and 20 % (V/V), respectively. Metabolic pathway analysis showed that strain X1T could degrade both profenofos and its main metabolite 4-bromo-2-chlorophenol. Metabolite toxicity analysis results showed that dehalogenation was the main detoxification step in profenofos biodegradation. The key gene and enzyme for profenofos degradation in strain X1T were also explored. RT-qPCR shows that organophosphorus hydrolase (OpdB) was the key enzyme to control the hydrolysis process in strain X1T. The purified enzyme OpdB in vitro had the same degradation characteristics as strain X1T. Divalent metal cations could significantly enhance the hydrolysis activity of strain X1T and enzyme OpdB. Meanwhile, strain X1T could degrade 60.89 % of 20 mg/L profenofos in actual field soil within 72 h. This study provides an efficient biological resource for the remediation of profenofos residual pollution in the environment.
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Affiliation(s)
- Liancheng Fang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yujing Zhou
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Tianming Chen
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yuehan Geng
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zijing Li
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Wei Zha
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Taozhong Shi
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Rimao Hua
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China; Institute for Green Development, Anhui Agricultural University, Hefei, Anhui 230036, China.
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11
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De Luca V, Mandrich L, Manco G. Development of a Qualitative Test to Detect the Presence of Organophosphate Pesticides on Fruits and Vegetables. Life (Basel) 2023; 13:life13020490. [PMID: 36836850 PMCID: PMC9958579 DOI: 10.3390/life13020490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/23/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND In recent decades, the use of pesticides in agriculture has increased at a fast pace, highlighting safety problems for the environment and human health, which in turn has made it necessary to develop new detection and decontamination systems for pesticides. METHODS A new qualitative test capable of detecting the presence of pesticides on fruits and vegetables by using thermostable enzymes was discovered, and the test was carried out on apples and aubergines. The contaminating pesticides were extracted from fruits with acetonitrile and analyzed with a biosensor system based on the thermostable esterase EST2 immobilized on a nitrocellulose filter. This enzyme is irreversibly inhibited mainly in the presence of organophosphates pesticides. Therefore, by observing esterase activity inhibition, we revealed the presence of residual pesticides on the fruits and vegetables. RESULTS By analyzing the rate of esterase activity inhibition, we predicted that residual pesticides are present on the surface of the fruits. When we cleaned the fruits by washing them in the presence of the phosphotriesterase SsoPox before the detection of the esterase activity on filters, we observed a full recovery of the activity for apples and 30% for aubergines, indicating that the enzymatic decontamination of organophosphates pesticides took place. CONCLUSIONS The reported method permitted us to assess the pesticides present on the vegetables and their decontamination.
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Affiliation(s)
- Valentina De Luca
- Institute of Experimental Endocrinology and Oncology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Mandrich
- Research Institute on Terrestrial Ecosystems, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
- Correspondence: (L.M.); (G.M.)
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
- Correspondence: (L.M.); (G.M.)
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12
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Immobilization of a Broad Range of Polypeptides on the Frustule of the Diatom Thalassiosira pseudonana. Appl Environ Microbiol 2022; 88:e0115322. [PMID: 36226967 PMCID: PMC9642022 DOI: 10.1128/aem.01153-22] [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: 11/20/2022] Open
Abstract
Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in industrial processes. One recently developed technique, living diatom silica immobilization (LiDSI), has made it possible to immobilize proteins, including multimeric and redox enzymes, via a cellular excretion system onto the silica frustule of the marine diatom Thalassiosira pseudonana. However, the number of application examples so far is limited, and the type of proteins appropriate for the technique is still enigmatic. Here, we applied LiDSI to six industrially relevant polypeptides, including protamine, metallothionein, phosphotriesterase, choline oxidase, laccase, and polyamine synthase. Protamine and metallothionein were successfully immobilized on the frustule as protein fusions with green fluorescent protein (GFP) at the N terminus, indicating that LiDSI can be used for polypeptides which are rich in arginine and cysteine. In contrast, we obtained mutants for the latter four enzymes in forms without green fluorescent protein. Immobilized phosphotriesterase, choline oxidase, and laccase showed enzyme activities even after the purification of frustule in the presence of 1% (wt/vol) octylphenoxy poly(ethyleneoxy)ethanol. An immobilized branched-chain polyamine synthase changed the intracellular polyamine composition and silica nanomorphology. These results illustrate the possibility of LiDSI for industrial applications. IMPORTANCE Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in industrial processes. Living diatom silica immobilization (LiDSI) is a recently developed technique for in vivo protein immobilization on the diatom frustule. We aimed to explore the possibility of using LiDSI for industrial applications by successfully immobilizing six polypeptides: (i) protamine (Oncorhynchus keta), a stable antibacterial agent; (ii) metallothionein (Saccharomyces cerevisiae), a metal adsorption molecule useful for bioremediation; (iii) phosphotriesterase (Sulfolobus solfataricus), a scavenger for toxic organic phosphates; (iv) choline oxidase (Arthrobacter globiformis), an enhancer for photosynthetic activity and yield of plants; (v) laccase (Bacillus subtilis), a phenol oxidase utilized for delignification of lignocellulosic materials; and (vi) branched-chain polyamine synthase (Thermococcus kodakarensis), which produces branched-chain polyamines important for DNA and RNA stabilization at high temperatures. This study provides new insights into the field of applied biological materials.
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13
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Rehman ZU, Momin AA, Aldehaiman A, Irum T, Grünberg R, Arold ST. The exceptionally efficient quorum quenching enzyme LrsL suppresses Pseudomonas aeruginosa biofilm production. Front Microbiol 2022; 13:977673. [PMID: 36071959 PMCID: PMC9441902 DOI: 10.3389/fmicb.2022.977673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Quorum quenching (QQ) is the enzymatic degradation of molecules used by bacteria for synchronizing their behavior within communities. QQ has attracted wide attention due to its potential to inhibit biofilm formation and suppress the production of virulence factors. Through its capacity to limit biofouling and infections, QQ has applications in water treatment, aquaculture, and healthcare. Several different QQ enzymes have been described; however, they often lack the high stability and catalytic efficiency required for industrial applications. Previously, we identified genes from genome sequences of Red Sea sediment bacteria encoding potential QQ enzymes. In this study, we report that one of them, named LrsL, is a metallo-β-lactamase superfamily QQ enzyme with outstanding catalytic features. X-ray crystallography shows that LrsL is a zinc-binding dimer. LrsL has an unusually hydrophobic substrate binding pocket that can accommodate a broad range of acyl-homoserine lactones (AHLs) with exceptionally high affinity. In vitro, LrsL achieves the highest catalytic efficiency reported thus far for any QQ enzyme with a Kcat/KM of 3 × 107. LrsL effectively inhibited Pseudomonas aeruginosa biofilm formation without affecting bacterial growth. Furthermore, LrsL suppressed the production of exopolysaccharides required for biofilm production. These features, and its capacity to regain its function after prolonged heat denaturation, identify LrsL as a robust and unusually efficient QQ enzyme for clinical and industrial applications.
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Affiliation(s)
- Zahid Ur Rehman
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Environmental Science Program, Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Zahid Ur Rehman, ; Stefan T. Arold,
| | - Afaque A. Momin
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdullah Aldehaiman
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Tayyaba Irum
- Services Hospital, Services Institute of Medical Sciences, Lahore, Pakistan
| | - Raik Grünberg
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stefan T. Arold
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, Montpellier, France
- *Correspondence: Zahid Ur Rehman, ; Stefan T. Arold,
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14
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A Novel Organophosphorus Acid Anhydrolase from Deep Sea Sediment with High Degradation Efficiency for Organophosphorus Pesticides and Nerve Agent. Microorganisms 2022; 10:microorganisms10061112. [PMID: 35744629 PMCID: PMC9231299 DOI: 10.3390/microorganisms10061112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
Organophosphorus compounds (OPCs), including highly toxic nerve agents and pesticides, have been used widely in agricultural and military applications. However, they have aroused widespread concern because they persistently pollute the environment and threaten human life. Organophosphorus acid anhydrolase (OPAA) is a promising enzyme that can detoxify OPCs. Here, a novel OPAA (OPAA114644) was isolated and characterized from deep-sea sediment (−3104 m). It exhibited excellent alkaline stability, and the loss of activity was less than 20% in the pH range 5.0–9.0, even after being incubated for 30 d at 4 °C. It also exhibited high salt tolerance, and its enzymatic activity increased by approximately fourfold in the presence of 20% NaCl (w/v). Additionally, OPAA114644 exhibited high degradation efficiency for soman, dichlorvos, paraoxon, coumaphos, and chlorpyrifos with a concentration of up to 250 mg/L, with the degradation rate being 100%, 100%, 100%, 80% and 51%, respectively, in 20 min under optimal conditions. Notably, OPAA114644 dissolved in different solutions, such as 20% NaCl, 1 mM SDS, 0.05% soap, 10% methanol, and tap water, could efficiently decontaminate the residual paraoxon on the surfaces of glasses, cotton tissues, and apples. These results indicate that OPAA114644 has excellent potential for the biodegradation and bioremediation of OPCs pollution and represents a real application of OPAA in the decontamination and detoxification of foods and clothes, and in the remediation of sites such as floors. Deep-sea sediment might also be an abundant resource for various functional microorganisms and enzymes.
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15
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Vyas T, Singh V, Kodgire P, Joshi A. Insights in detection and analysis of organophosphates using organophosphorus acid anhydrolases (OPAA) enzyme-based biosensors. Crit Rev Biotechnol 2022; 43:521-539. [PMID: 35504858 DOI: 10.1080/07388551.2022.2052012] [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: 11/03/2022]
Abstract
The human population is dependent on agriculture for its food requirements and survival. Several insecticides and pesticides have found their use for improvements in agricultural yields. Organophosphates (OP) are one of the many compounds used as insecticides and pesticides. OPs have also been used to develop G and V-series chemicals which act as highly toxic nerve agents that can severely influence the normal function of the nervous system in all living beings. Thus, OP compounds utilized as insecticides/pesticides and nerve agents are hazardous to the environment, lethal for humans and other non-target animals. To avoid their toxicity, approaches to detect and neutralize them have become essential. A variety of analytical procedures such as electrochemical processes and chromatography methods, namely liquid and gas chromatography, have been employed to detect OPs. Though these techniques are sensitive and highly accurate they suffer from drawbacks, for instance: their bulky nature and expensive instrumentation, the difficulty of operation, long detection times, and they can yield unpredictable results with variable sample complexities. With the advent of several types of biosensors, the assay of OP compounds has become simpler, faster, cost-effective with improved sensitivity, and provides the capability for onsite detection. OP biosensor assays typically utilize several enzymes with the capability to hydrolyze/degrade OP compounds, such as organophosphate hydrolase (OPH) and organophosphate acid hydrolase (OPAA). This review focuses on discussing various aspects of OPAA as biological recognition unit in terms of its: structure, properties, activity enhancement methods, and utilization for developing OPAA-based biosensing technologies for insecticides, pesticides, and nerve agents.
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Affiliation(s)
- Tanmay Vyas
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Vinay Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Prashant Kodgire
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Abhijeet Joshi
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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16
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Mali H, Shah C, Rudakiya DM, Patel DH, Trivedi U, Subramanian RB. A novel organophosphate hydrolase from Arthrobacter sp. HM01: Characterization and applications. BIORESOURCE TECHNOLOGY 2022; 349:126870. [PMID: 35192947 DOI: 10.1016/j.biortech.2022.126870] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Bioremediation systems coupled to efficient microbial enzymes have emerged as an attractive approach for the in-situ removal of hazardous organophosphates (OPs) pesticides from the polluted environment. However, the role of engineered enzymes in OPs-degradation is rarely studied. In this study, the potential OPs-hydrolase (opdH) gene (Arthrobacter sp. HM01) was isolated, cloned, expressed, and purified. The recombinant organophosphate hydrolase (ropdH) was ∼29 kDa; which catalyzed a broad-range of OPs-pesticides in organic-solvent (∼99 % in 30 min), and was found to increase the catalytic efficiency by 10-folds over the native enzyme (kcat/Km: 107 M-1s-1). The degraded metabolites were analyzed using HPLC/GCMS. Through site-directed mutagenesis, it was confirmed that, conserved metal-bridged residue (Lys-127), plays a crucial role in OPs-degradation, which shows ∼18-folds decline in OPs-degradation. Furthermore, the catalytic activity and its stability has been enhanced by >2.0-fold through biochemical optimization. Thus, the study suggests that ropdH has all the required properties for OPs bioremediation.
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Affiliation(s)
- Himanshu Mali
- P. G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite Campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, Bakrol, Gujarat 388 315, India
| | - Chandni Shah
- P. G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite Campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, Bakrol, Gujarat 388 315, India
| | - Darshan M Rudakiya
- Synergy Cignpost Diagnostics, 3 Mills Studio, London, E3 3DU, United Kingdom
| | - Darshan H Patel
- Charotar Institute of Paramedical Sciences, Charotar University of Science and Technology, (CHARUSAT), Changa, Gujarat 388421, India
| | - Ujjval Trivedi
- P. G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite Campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, Bakrol, Gujarat 388 315, India
| | - R B Subramanian
- P. G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite Campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, Bakrol, Gujarat 388 315, India.
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17
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Mali H, Shah C, Patel DH, Trivedi U, Subramanian RB. Bio-catalytic system of metallohydrolases for remediation of neurotoxin organophosphates and applications with a future vision. J Inorg Biochem 2022; 231:111771. [DOI: 10.1016/j.jinorgbio.2022.111771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 12/29/2022]
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18
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Thakur M, Dean SN, Moore M, Spangler JR, Johnson BJ, Medintz IL, Walper SA. Packaging of Diisopropyl Fluorophosphatase (DFPase) in Bacterial Outer Membrane Vesicles Protects Its Activity at Extreme Temperature. ACS Biomater Sci Eng 2022; 8:493-501. [DOI: 10.1021/acsbiomaterials.1c01192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Meghna Thakur
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
- College of Science, George Mason University, 4400 University Drive, Fairfax, Virginia 22030, United States
| | - Scott N. Dean
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Martin Moore
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Joseph R. Spangler
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Brandy J. Johnson
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
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19
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Ruan X, Yang Y, Liu W, Ma X, Zhang C, Meng Q, Wang Z, Cui F, Feng J, Cai F, Yuan Y, Zhu G. Mechanical Bond Approach to Introducing Self-Adaptive Active Sites in Covalent Organic Frameworks for Zinc-Catalyzed Organophosphorus Degradation. ACS CENTRAL SCIENCE 2021; 7:1698-1706. [PMID: 34729413 PMCID: PMC8554822 DOI: 10.1021/acscentsci.1c00941] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Indexed: 05/11/2023]
Abstract
Mechanically interlocked molecules (MIMs) with discrete molecular components linked through a mechanical bond in space can be harnessed for the operation of molecular switches and machines, which shows huge potential to imitate the dynamic response of natural enzymes. In this work, rotaxane compounds were adopted as building monomers for the synthesis of a crown-ether ring mechanically intercalated covalence organic framework (COF). This incorporation of MIMs into open architecture implemented large amplitude motions, whose wheel slid along the axle in response to external stimulation. After impregnation with Zn2+ ions, the relative locations of two zinc active sites (crown-ether coordinated Zn(II) and bipyridine coordinated Zn(II)) are endowed with great flexibility to fit the conformational transformation of an organophosphorus agent during the hydrolytic process. Notably, the resulting self-adaptive binuclear zinc center in a crown-ether-threaded COF network is endowed with a record catalytic ability, with a rate over 85.5 μM min-1 for organophosphorus degradation. The strategy of synthesis for porous artificial enzymes through the introduction of mechanically bound crown ether will enable significant breakthroughs and new synthetic concepts for the development of advanced biomimetic catalysts.
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20
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Overview of a bioremediation tool: organophosphorus hydrolase and its significant application in the food, environmental, and therapy fields. Appl Microbiol Biotechnol 2021; 105:8241-8253. [PMID: 34665276 DOI: 10.1007/s00253-021-11633-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 12/14/2022]
Abstract
In the past decades, the organophosphorus compounds had been widely used in the environment and food industries as pesticides. Owing to the life-threatening and long-lasting problems of organophosphorus insecticide (OPs), an effective detection and removal of OPs have garnered growing attention both in the scientific and practical fields in recent years. Bacterial organophosphorus hydrolases (OPHs) have been extensively studied due to their high specific activity against OPs. OPH could efficiently hydrolyze a broad range of substrates both including the OP pesticides and some nerve agents, suggesting a great potential for the remediation of OPs. In this review, the microbial identification, molecular modification, and practical application of OPHs were comprehensively discussed.Key points• Microbial OPH is a significant bioremediation tool against OPs.• Identification and molecular modification of OPH was discussed in detail.• The applications of OPH in food, environmental, and therapy fields are presented.
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21
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Paidi MK, Satapute P, Haider MS, Udikeri SS, Ramachandra YL, Vo DVN, Govarthanan M, Jogaiah S. Mitigation of organophosphorus insecticides from environment: Residual detoxification by bioweapon catalytic scavengers. ENVIRONMENTAL RESEARCH 2021; 200:111368. [PMID: 34081974 DOI: 10.1016/j.envres.2021.111368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/09/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Organophosphorus insecticides (OPIs) have low persistence and are easily biodegradable in nature. The United States and India are the major countries producing OPIs of about 25% and 17% of the world, respectively. OPIs commonly used for agricultural practices occupy a major share in the global market, which leads to the increasing contamination of OPIs residues in various food chains. To overcome this issue, an enzymatic degradation method has been approved by several environmental toxic, and controlling agencies, including United States Environmental Protection Agency (USEPA). Different catalytic enzymes have been isolated and identified from various microbial sources to neutralize the toxic pesticides and/or insecticides. In this review, we have gathered information on OPIs biotransformation and their residual toxicity in the environment. Particularly, it focuses on OPIs degrading enzymes such as chlorpyrifos hydrolase, diisopropylfluorophosphatase, organophosphate acid anhydrolase, organophosphate hydrolases, and phosphotriesterases like lactonasesspecific activity either P-O link group type or P-S link group of pesticides. To summarize, the catalytic degradation of organophosphorus insecticides is not only profitable but also environmentally friendly. Hence, the enzymatic catalyst is an ultimate and super bio-weapon to mitigate or decontaminate various OPIs residues in both terrestrial and aqueous environments.
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Affiliation(s)
- Murali Krishna Paidi
- AcSIR, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Gijubhai Badheka Marg, Bhavnagar, Gujarat, 364002, India
| | - Praveen Satapute
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad, Karnataka, 580003, India
| | - Muhammad Salman Haider
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Shashikant Shiddappa Udikeri
- Agricultural Research Station, Dharwad Farm, University of Agricultural Sciences, Dharwad, 580005, Karnataka, India
| | | | - Dai-Viet N Vo
- Center of Excellence for Green Energy and Environmental Nanomaterials (CE@GrEEN), Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, South Korea.
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad, Karnataka, 580003, India.
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22
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Transitioning from Oxime to the Next Potential Organophosphorus Poisoning Therapy Using Enzymes. J CHEM-NY 2021. [DOI: 10.1155/2021/7319588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
For years, organophosphorus poisoning has been a major concern of health problems throughout the world. An estimated 200,000 acute pesticide poisoning deaths occur each year, many in developing countries. Apart from the agricultural pesticide poisoning, terrorists have used these organophosphorus compounds to attack civilian populations in some countries. Recent misuses of sarin in the Syrian conflict had been reported in 2018. Since the 1950s, the therapy to overcome this health problem is to utilize a reactivator to reactivate the inhibited acetylcholinesterase by these organophosphorus compounds. However, many questions remain unanswered regarding the efficacy and toxicity of this reactivator. Pralidoxime, MMB-4, TMB-4, obidoxime, and HI-6 are the examples of the established oximes, yet they are of insufficient effectiveness in some poisonings and only a limited spectrum of the different nerve agents and pesticides are being covered. Alternatively, an option in the treatment of organophosphorus poisoning that has been explored is through the use of enzyme therapy. Organophosphorus hydrolases are a group of enzymes that look promising for detoxifying organophosphorus compounds and have recently gained much interest. These enzymes have demonstrated remarkable protective and antidotal value against some different organophosphorus compounds in vivo in animal models. Apart from that, enzyme treatments have also been applied for decontamination purposes. In this review, the restrictions and obstacles in the therapeutic development of oximes, along with the new strategies to overcome the problems, are discussed. The emerging interest in enzyme treatment with its advantages and disadvantages is described as well.
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23
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Low CX, Tan LTH, Ab Mutalib NS, Pusparajah P, Goh BH, Chan KG, Letchumanan V, Lee LH. Unveiling the Impact of Antibiotics and Alternative Methods for Animal Husbandry: A Review. Antibiotics (Basel) 2021; 10:578. [PMID: 34068272 PMCID: PMC8153128 DOI: 10.3390/antibiotics10050578] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 02/07/2023] Open
Abstract
Since the 1950s, antibiotics have been used in the field of animal husbandry for growth promotion, therapy and disease prophylaxis. It is estimated that up to 80% of the antibiotics produced by the pharmaceutical industries are used in food production. Most of the antibiotics are used as feed additives at sub-therapeutic levels to promote growth. However, studies show the indiscriminate use of antibiotics has led to the emergence of multidrug-resistant pathogens that threaten both animal health and human health, including vancomycin-resistant Enterococcus (VRE), Methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacteriaceae (CRE). This scenario is further complicated by the slow progress in achieving scientific breakthroughs in uncovering novel antibiotics following the 1960s. Most of the pharmaceutical industries have long diverted research funds away from the field of antibiotic discovery to more lucrative areas of drug development. If this situation is allowed to continue, humans will return to the pre-antibiotics era and potentially succumb to huge health and economic consequences. Fortunately, studies investigating various alternatives to antibiotics use in livestock show promising results. These alternatives include the application of bacteriophages and phage derived peptidoglycan degrading enzymes, engineered peptides, egg yolk antibodies, probiotics, prebiotics and synbiotics, as well as quorum quenching molecules. Therefore, this review aims to discuss the use of growth-promoting antibiotics and their impact on livestock and provide insights on the alternative approaches for animal husbandry.
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Affiliation(s)
- Chuen Xian Low
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor Darul Ehsan 47500, Malaysia; (C.X.L.); (L.T.-H.T.); (N.-S.A.M.); (P.P.)
| | - Loh Teng-Hern Tan
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor Darul Ehsan 47500, Malaysia; (C.X.L.); (L.T.-H.T.); (N.-S.A.M.); (P.P.)
- Clinical School Johor Bahru, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Johor Bahru 80100, Malaysia
| | - Nurul-Syakima Ab Mutalib
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor Darul Ehsan 47500, Malaysia; (C.X.L.); (L.T.-H.T.); (N.-S.A.M.); (P.P.)
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Universiti Kebangsaan Malaysia, Kuala Lumpur 50603, Malaysia
| | - Priyia Pusparajah
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor Darul Ehsan 47500, Malaysia; (C.X.L.); (L.T.-H.T.); (N.-S.A.M.); (P.P.)
| | - Bey-Hing Goh
- Biofunctional Molecule Exploratory Research Group (BMEX), School of Pharmacy, Monash University Malaysia, Selangor Darul Ehsan 47500, Malaysia;
- College of Pharmaceutical Sciences, Zhenjiang University, Hangzhou 310058, China
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang 212013, China
| | - Vengadesh Letchumanan
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor Darul Ehsan 47500, Malaysia; (C.X.L.); (L.T.-H.T.); (N.-S.A.M.); (P.P.)
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery (NBDD) Research Group, Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor Darul Ehsan 47500, Malaysia; (C.X.L.); (L.T.-H.T.); (N.-S.A.M.); (P.P.)
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Catalytic Performance of a Recombinant Organophosphate-Hydrolyzing Phosphotriesterase from Brevundimonas diminuta in the Presence of Surfactants. Catalysts 2021. [DOI: 10.3390/catal11050597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Phosphotriestease (PTE), also known as parathion hydrolase, has the ability to hydrolyze the triester linkage of organophosphate (OP) pesticides and chemical warfare nerve agents, making it highly suitable for environment remediation. Here, we studied the effects of various surfactants and commercial detergents on the esterase activity of a recombinant PTE (His6-tagged BdPTE) from Brevundimonas diminuta. Enzymatic assays indicated that His6-tagged BdPTE was severely inactivated by SDS even at lower concentrations and, conversely, the other three surfactants (Triton X-100, Tween 20, and Tween 80) had a stimulatory effect on the activity, especially at a pre-incubating temperature of 40 °C. The enzyme exhibited a good compatibility with several commercial detergents, such as Dr. Formula® and Sugar Bubble®. The evolution results of pyrene fluorescence spectroscopy showed that the enzyme molecules participated in the formation of SDS micelles but did not alter the property of SDS micelles above the critical micelle concentration (CMC). Structural analyses revealed a significant change in the enzyme’s secondary structure in the presence of SDS. Through the use of the intentionally fenthion-contaminated Chinese cabbage leaves as the model experiment, enzyme–Joy® washer solution could remove the pesticide from the contaminated sample more efficiently than detergent alone. Overall, our data promote a better understanding of the links between the esterase activity of His6-tagged BdPTE and surfactants, and they offer valuable information about its potential applications in liquid detergent formulations.
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25
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Xu W, Zhao S, Zhang W, Wu H, Guang C, Mu W. Recent advances and future prospective of organophosphorus-degrading enzymes: identification, modification, and application. Crit Rev Biotechnol 2021; 41:1096-1113. [PMID: 33906533 DOI: 10.1080/07388551.2021.1898331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The organophosphorus-based OPs) nerve agents and pesticides have been applied in the agriculture industry for a long time. However, they were found to have a persistent effect on the environment and threaten human health. Traditional methods, including incineration and landfilling, could not thoroughly remove these organophosphorus compounds (OPs). Meanwhile, chemical hydrolysis for decontamination was also inhibited due to the presence of corrosive materials and high costs. Biological remediation for OPs employing microorganisms and organophosphorus-degrading enzymes is promising due to a mild and controllable procedure, environmental-friendly reactions, and high efficacy. A wide variety of enzymes have shown latent ability in degrading OPs hazards like organophosphorus hydrolase (OPH), organophosphorus acid anhydrolase (OPAA), the diisopropylfluorophosphatase (DFPase), and mammalian paraoxonase 1 (PON 1). To this end, increasing efforts have been made on these intriguing enzymes to increase their expression level, enhance the catalytic activity, modify the optimal substrate, and expand the practical application. In this review, the enzyme resource, crystal structure, molecular modification, and industry application were compared and discussed in detail. Moreover, the proposed ideas and positive results could be useful for the other relevant OPs-degrading enzymes.
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Affiliation(s)
- Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Sumao Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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26
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Zhao S, Xu W, Zhang W, Wu H, Guang C, Mu W. In-depth biochemical identification of a novel methyl parathion hydrolase from Azohydromonas australica and its high effectiveness in the degradation of various organophosphorus pesticides. BIORESOURCE TECHNOLOGY 2021; 323:124641. [PMID: 33429316 DOI: 10.1016/j.biortech.2020.124641] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Organophosphorus pesticides are highly toxic phosphate compounds with the general structure of O = P(OR)3 and threaten human health seriously. Methyl parathion hydrolase from microbial is an important enzyme to degrade organophosphorus pesticides (OPs) into less toxic or nontoxic compounds like. p-nitrophenol and diethyl phosphate. Here, a gene encoding methyl parathion hydrolase from Azohydromonas australica was firstly cloned and expressed in Escherichia coli. The recombinant hydrolase showed its optimal pH and temperature at pH 9.5 and 50 °C. Leveraging 1 mM Mn2+, the enzyme activity was significantly enhanced by 29.3-fold, and the thermostability at 40 and 50 °C was also improved. The recombinant MPH showed the specific activity of 4.94 and 16.0 U/mg towards methyl parathion and paraoxon, respectively. Moreover, A. australica MPH could effectively degrade various of OPs pesticides including methyl parathion, paraoxon, dichlorvos and chlorpyrifos in a few minutes, suggesting a great potential in the bioremediation of OPs pesticides.
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Affiliation(s)
- Sumao Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
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27
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Verma S, Meghwanshi GK, Kumar R. Current perspectives for microbial lipases from extremophiles and metagenomics. Biochimie 2021; 182:23-36. [PMID: 33421499 DOI: 10.1016/j.biochi.2020.12.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/21/2020] [Accepted: 12/31/2020] [Indexed: 01/21/2023]
Abstract
Microbial lipases are most broadly used biocatalysts for environmental and industrial applications. Lipases catalyze the hydrolysis and synthesis of long acyl chain esters and have a characteristic folding pattern of α/β hydrolase with highly conserved catalytic triad (Serine, Aspartic/Glutamic acid and Histidine). Mesophilic lipases (optimal activity in neutral pH range, mesophilic temperature range, atmospheric pressure, normal salinity, non-radio-resistant, and instability in organic solvents) have been in use for many industrial biotransformation reactions. However, lipases from extremophiles can be used to design biotransformation reactions with higher yields, less byproducts or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. The extremophile lipase perform activity at extremes of temperature, pH, salinity, and pressure which can be screened from metagenome and de novo lipase design using computational approaches. Despite structural similarity, they exhibit great diversity at the sequence level. This diversity is broader when lipases from the bacterial, archaeal, plant, and animal domains/kingdoms are compared. Furthermore, a great diversity of novel lipases exists and can be discovered from the analysis of the dark matter - the unexplored nucleotide/metagenomic databases. This review is an update on extremophilic microbial lipases, their diversity, structure, and classification. An overview on novel lipases which have been detected through analysis of the genomic dark matter (metagenome) has also been presented.
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Affiliation(s)
- Swati Verma
- Department of Microbiology, Maharaja Ganga Singh University, Bikaner, 334004, India
| | | | - Rajender Kumar
- Department of Clinical Microbiology, Umeå University, SE-90185, Umeå, Sweden.
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28
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Yang J, Xiao Y, Liu Y, Li R, Long L. Structure-based redesign of the bacterial prolidase active-site pocket for efficient enhancement of methyl-parathion hydrolysis. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00490e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutagenesis at four residues surrounding the active-site pocket of an old bacterial prolidase scaffold led to a 10 000-fold increase in methyl-parathion hydrolysis and broadening substrate specificity against organophosphorus compounds.
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Affiliation(s)
- Jian Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
- Guangzhou 510301
| | - Yunzhu Xiao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
- Guangzhou 510301
| | - Yu Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
- Guangzhou 510301
| | - Ru Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
- Guangzhou 510301
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology
- Guangdong Key Laboratory of Marine Materia Medica
- South China Sea Institute of Oceanology
- Chinese Academy of Sciences
- Guangzhou 510301
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29
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De Luca V, Mandrich L. Enzyme Promiscuous Activity: How to Define it and its Evolutionary Aspects. Protein Pept Lett 2020; 27:400-410. [PMID: 31868141 DOI: 10.2174/0929866527666191223141205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 11/22/2022]
Abstract
Enzymes are among the most studied biological molecules because better understanding enzymes structure and activity will shed more light on their biological processes and regulation; from a biotechnological point of view there are many examples of enzymes used with the aim to obtain new products and/or to make industrial processes less invasive towards the environment. Enzymes are known for their high specificity in the recognition of a substrate but considering the particular features of an increasing number of enzymes this is not completely true, in fact, many enzymes are active on different substrates: this ability is called enzyme promiscuity. Usually, promiscuous activities have significantly lower kinetic parameters than to that of primary activity, but they have a crucial role in gene evolution. It is accepted that gene duplication followed by sequence divergence is considered a key evolutionary mechanism to generate new enzyme functions. In this way, promiscuous activities are the starting point to increase a secondary activity in the main activity and then get a new enzyme. The primary activity can be lost or reduced to a promiscuous activity. In this review we describe the differences between substrate and enzyme promiscuity, and its rule in gene evolution. From a practical point of view the knowledge of promiscuity can facilitate the in vitro progress of proteins engineering, both for biomedical and industrial applications. In particular, we report cases regarding esterases, phosphotriesterases and cytochrome P450.
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Affiliation(s)
- Valentina De Luca
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 111, 80131, Naples, Italy
| | - Luigi Mandrich
- Research Institute on Terrestrial Ecosystems, National Research Council, Via Pietro Castellino, 111, 80131, Naples, Italy
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30
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Billot R, Plener L, Jacquet P, Elias M, Chabrière E, Daudé D. Engineering acyl-homoserine lactone-interfering enzymes toward bacterial control. J Biol Chem 2020; 295:12993-13007. [PMID: 32690609 DOI: 10.1074/jbc.rev120.013531] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/17/2020] [Indexed: 12/20/2022] Open
Abstract
Enzymes able to degrade or modify acyl-homoserine lactones (AHLs) have drawn considerable interest for their ability to interfere with the bacterial communication process referred to as quorum sensing. Many proteobacteria use AHL to coordinate virulence and biofilm formation in a cell density-dependent manner; thus, AHL-interfering enzymes constitute new promising antimicrobial candidates. Among these, lactonases and acylases have been particularly studied. These enzymes have been isolated from various bacterial, archaeal, or eukaryotic organisms and have been evaluated for their ability to control several pathogens. Engineering studies on these enzymes were carried out and successfully modulated their capacity to interact with specific AHL, increase their catalytic activity and stability, or enhance their biotechnological potential. In this review, special attention is paid to the screening, engineering, and applications of AHL-modifying enzymes. Prospects and future opportunities are also discussed with a view to developing potent candidates for bacterial control.
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Affiliation(s)
- Raphaël Billot
- Gene&GreenTK, Marseille, France; IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | | | | | - Mikael Elias
- Molecular Biology and Biophysics and Biotechnology Institute, Department of Biochemistry, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric Chabrière
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France.
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31
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Carusone TM, Cardiero G, Cerreta M, Mandrich L, Moran O, Porzio E, Catara G, Lacerra G, Manco G. WTAP and BIRC3 are involved in the posttranscriptional mechanisms that impact on the expression and activity of the human lactonase PON2. Cell Death Dis 2020; 11:324. [PMID: 32382056 PMCID: PMC7206036 DOI: 10.1038/s41419-020-2504-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 12/15/2022]
Abstract
The activity of human paraoxonase 2 (PON2) is rapidly reduced in cells incubated with the bacterial quorormone 3-Oxo-dodecanoyl Homoserine Lactone (3OC12HSL), an observation that led to hypothesize a fast PON2 post-translational modification (PTM). Recently, we detected a 3OC12HSL-induced PTM in a cell-free system in which a crude extract from 3OC12HSL-treated HeLa cells was able to inactivate and ubiquitinate at position 144 a recombinant PON2. Here we show the occurrence of this and new PTMs on PON2 in HeLa cells. PTMs were found to gather nearby the two SNPs, A148G, and S311C, that are related to type-2 diabetes and its complications. Furthermore, we detected a PTM nearby a 12 amino acids region that is deleted in PON2 Isoform 2. An in vitro mutation analysis showed that the SNPs and the deletion are involved in PON2 activity and suggested a role of PTMs on its modulation, while a SAXS analysis pointed to Isoform 2 as being largely unstructured, compared to the wild type. Besides, we discovered a control of PON2 expression via a putative mRNA operon involving the Wilms tumor 1 associated protein (WTAP) and the E3 ubiquitin ligase (E3UbL) baculoviral IAP repeat-containing 3 (BIRC3).
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Affiliation(s)
- Teresa Maria Carusone
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy
| | - Giovanna Cardiero
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", (IGB-ABT, CNR), National Research Council, Naples, Italy
| | - Mariangela Cerreta
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy
| | - Luigi Mandrich
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy
| | - Oscar Moran
- Institute of Biophysics (IBF, CNR), National Research Council, Genoa, Italy
| | - Elena Porzio
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy
| | - Giuliana Catara
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy
| | - Giuseppina Lacerra
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", (IGB-ABT, CNR), National Research Council, Naples, Italy.
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology (IBBC, CNR), National Research Council, Naples, Italy.
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32
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Rémy B, Plener L, Decloquement P, Armstrong N, Elias M, Daudé D, Chabrière É. Lactonase Specificity Is Key to Quorum Quenching in Pseudomonas aeruginosa. Front Microbiol 2020; 11:762. [PMID: 32390993 PMCID: PMC7193897 DOI: 10.3389/fmicb.2020.00762] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/30/2020] [Indexed: 12/31/2022] Open
Abstract
The human opportunistic pathogen Pseudomonas aeruginosa orchestrates the expression of many genes in a cell density-dependent manner by using quorum sensing (QS). Two acyl-homoserine lactones (AHLs) are involved in QS circuits and contribute to the regulation of virulence factors production, biofilm formation, and antimicrobial sensitivity. Disrupting QS, a strategy referred to as quorum quenching (QQ) can be achieved using exogenous AHL-degrading lactonases. However, the importance of enzyme specificity on quenching efficacy has been poorly investigated. Here, we used two lactonases both targeting the signal molecules N-(3-oxododecanoyl)-L-homoserine lactone (3-oxo-C12 HSL) and butyryl-homoserine lactone (C4 HSL) albeit with different efficacies on C4 HSL. Interestingly, both lactonases similarly decreased AHL concentrations and comparably impacted the expression of AHL-based QS genes. However, strong variations were observed in Pseudomonas Quinolone Signal (PQS) regulation depending on the lactonase used. Both lactonases were also found to decrease virulence factors production and biofilm formation in vitro, albeit with different efficiencies. Unexpectedly, only the lactonase with lower efficacy on C4 HSL was able to inhibit P. aeruginosa pathogenicity in vivo in an amoeba infection model. Similarly, proteomic analysis revealed large variations in protein levels involved in antibiotic resistance, biofilm formation, virulence and diverse cellular mechanisms depending on the chosen lactonase. This global analysis provides evidences that QQ enzyme specificity has a significant impact on the modulation of QS-associated behavior in P. aeruginosa PA14.
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Affiliation(s)
- Benjamin Rémy
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France.,Gene&GreenTK, Marseille, France
| | | | - Philippe Decloquement
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics - BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | | | - Éric Chabrière
- Aix Marseille University, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
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Nascimento FX, Hernández AG, Glick BR, Rossi MJ. Plant growth-promoting activities and genomic analysis of the stress-resistant Bacillus megaterium STB1, a bacterium of agricultural and biotechnological interest. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 25:e00406. [PMID: 31886139 PMCID: PMC6920507 DOI: 10.1016/j.btre.2019.e00406] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/05/2019] [Accepted: 12/01/2019] [Indexed: 12/14/2022]
Abstract
In this work, the stress-resistant Bacillus megaterium STB1 is characterized and its ability to promote plant growth under normal and stress conditions is demonstrated. The genomic sequence of this bacterium, and a detailed analysis of the genes involved in facilitating its stress resistance and plant growth-promoting activities is also reported. The B. megaterium STB1 genome is rich in genetic elements involved in multiple stress resistance, xenobiotic degradation, pathogen antagonistic activities, and other traits related to soil and rhizosphere colonization. Moreover, genes participating in the biosynthesis of auxins and cytokinins, the modulation of polyamines, GABA, brassinosteroids and ethylene levels were also found. Ultimately, this study brings new insights into the role of B. megaterium as a plant growth-promoting bacterium and opens new opportunities for the development of novel strategies for agriculture and biotechnology.
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Affiliation(s)
- Francisco X. Nascimento
- IBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, 2780-157, Portugal
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Anabel G. Hernández
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Márcio J. Rossi
- Laboratório de Microbiologia e Bioprocessos, MIP-CCB, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-900, Brazil
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34
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Structural and Functional Characterization of New SsoPox Variant Points to the Dimer Interface as a Driver for the Increase in Promiscuous Paraoxonase Activity. Int J Mol Sci 2020; 21:ijms21051683. [PMID: 32121487 PMCID: PMC7084321 DOI: 10.3390/ijms21051683] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/02/2020] [Accepted: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
Increasing attention is more and more directed toward the thermostable Phosphotriesterase-Like-Lactonase (PLL) family of enzymes, for the efficient and reliable decontamination of toxic nerve agents. In the present study, the DNA Staggered Extension Process (StEP) technique was utilized to obtain new variants of PLL enzymes. Divergent homologous genes encoding PLL enzymes were utilized as templates for gene recombination and yielded a new variant of SsoPox from Saccharolobus solfataricus. The new mutant, V82L/C258L/I261F/W263A (4Mut) exhibited catalytic efficiency of 1.6 × 105 M−1 s−1 against paraoxon hydrolysis at 70°C, which is more than 3.5-fold and 42-fold improved in comparison with C258L/I261F/W263A (3Mut) and wild type SsoPox, respectively. 4Mut was also tested with chemical warfare nerve agents including tabun, sarin, soman, cyclosarin and VX. In particular, 4Mut showed about 10-fold enhancement in the hydrolysis of tabun and soman with respect to 3Mut. The crystal structure of 4Mut has been solved at the resolution of 2.8 Å. We propose that, reorganization of dimer conformation that led to increased central groove volume and dimer flexibility could be the major determinant for the improvement in hydrolytic activity in the 4Mut.
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AidB, a Novel Thermostable N-Acylhomoserine Lactonase from the Bacterium Bosea sp. Appl Environ Microbiol 2019; 85:AEM.02065-19. [PMID: 31604771 DOI: 10.1128/aem.02065-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/04/2019] [Indexed: 11/20/2022] Open
Abstract
Many Gram-negative bacteria employ N-acylhomoserine lactones (AHLs) as quorum-sensing (QS) signal molecules to regulate virulence expression in a density-dependent manner. Quorum quenching (QQ) via enzymatic inactivation of AHLs is a promising strategy to reduce bacterial infections and drug resistance. Herein, a thermostable AHL lactonase (AidB), which could degrade different AHLs, with or without a substitution of carbonyl or hydroxyl at the C-3 position, was identified from the soil bacterium Bosea sp. strain F3-2. Ultrahigh-performance liquid chromatography analysis demonstrated that AidB is an AHL lactonase that hydrolyzes the ester bond of the homoserine lactone (HSL) ring. AidB was thermostable in the range 30 to 80°C and showed maximum activity after preincubation at 60°C for 30 min. The optimum temperature of AidB was 60°C, and the enzyme could be stably stored in double-distilled water (ddH2O) at 4°C or room temperature. AidB homologs were found only in Rhizobiales and Rhodospirillales of the Alphaproteobacteria AidB from Agrobacterium tumefaciens and AidB from Rhizobium multihospitium (with amino acid identities of 50.6% and 52.8% to AidB, respectively) also showed thermostable AHL degradation activity. When introduced into bacteria, plasmid-expressed AidB attenuated pyocyanin production by Pseudomonas aeruginosa PAO1 and the pathogenicity of Pectobacterium carotovorum subsp. carotovorum Z3-3, suggesting that AidB is a potential therapeutic agent by degrading AHLs.IMPORTANCE A quorum-sensing system using AHLs as the signal in many bacterial pathogens is a critical virulence regulator and an attractive target for anti-infective drugs. In this work, we identified a novel AHL lactonase, AidB, from a soil bacterial strain, Bosea sp. F3-2. The expression of aidB reduced the production of AHL signals and QS-dependent virulence factors in Pseudomonas aeruginosa and Pectobacterium carotovorum The homologs of AidB with AHL-degrading activities were found only in several genera belonging to the Alphaproteobacteria Remarkably, AidB is a thermostable enzyme that retained its catalytic activity after treatment at 80°C for 30 min and exhibits reliable storage stability at both 4°C and room temperature. These properties might make it more suitable for practical application.
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Thakur M, Medintz IL, Walper SA. Enzymatic Bioremediation of Organophosphate Compounds-Progress and Remaining Challenges. Front Bioeng Biotechnol 2019; 7:289. [PMID: 31781549 PMCID: PMC6856225 DOI: 10.3389/fbioe.2019.00289] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Organophosphate compounds are ubiquitously employed as agricultural pesticides and maintained as chemical warfare agents by several nations. These compounds are highly toxic, show environmental persistence and accumulation, and contribute to numerous cases of poisoning and death each year. While their use as weapons of mass destruction is rare, these never fully disappear into obscurity as they continue to be tools of fear and control by governments and terrorist organizations. Beyond weaponization, their wide-scale dissemination as agricultural products has led to environmental accumulation and intoxication of soil and water across the globe. Therefore, there is a dire need for rapid and safe agents for environmental bioremediation, personal decontamination, and as therapeutic detoxicants. Organophosphate hydrolyzing enzymes are emerging as appealing targets to satisfy decontamination needs owing to their ability to hydrolyze both pesticides and nerve agents using biologically-derived materials safe for both the environment and the individual. As the release of genetically modified organisms is not widely accepted practice, researchers are exploring alternative strategies of organophosphate bioremediation that focus on cell-free enzyme systems. In this review, we first discuss several of the more prevalent organophosphorus hydrolyzing enzymes along with research and engineering efforts that have led to an enhancement in their activity, substrate tolerance, and stability. In the later half we focus on advances achieved through research focusing on enhancing the catalytic activity and stability of phosphotriesterase, a model organophosphate hydrolase, using various approaches such as nanoparticle display, DNA scaffolding, and outer membrane vesicle encapsulation.
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Affiliation(s)
- Meghna Thakur
- College of Science, George Mason University, Fairfax, VA, United States
| | - Igor L Medintz
- Center for Bio/Molecular Sciences, U.S. Naval Research Laboratory, Washington, DC, United States
| | - Scott A Walper
- Center for Bio/Molecular Sciences, U.S. Naval Research Laboratory, Washington, DC, United States
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Murugayah SA, Gerth ML. Engineering quorum quenching enzymes: progress and perspectives. Biochem Soc Trans 2019; 47:793-800. [PMID: 31064863 PMCID: PMC6599154 DOI: 10.1042/bst20180165] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Abstract
Quorum sensing is a key contributor to the virulence of many important plant, animal and human pathogens. The disruption of this signalling-a process referred to as 'quorum quenching'-is a promising new approach for controlling microbial pathogens. In this mini-review, we have focused on efforts to engineer enzymes that disrupt quorum sensing by inactivating acyl-homoserine lactone signalling molecules. We review different approaches for protein engineering and provide examples of how these engineering approaches have been used to tailor the stability, specificity and activities of quorum quenching enzymes. Finally, we grapple with some of the issues around these approaches-including the disconnect between in vitro biochemistry and potential in vivo applications.
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Affiliation(s)
- Shereen A Murugayah
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Monica L Gerth
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Wang TN, Guan QT, Pain A, Kaksonen AH, Hong PY. Discovering, Characterizing, and Applying Acyl Homoserine Lactone-Quenching Enzymes to Mitigate Microbe-Associated Problems Under Saline Conditions. Front Microbiol 2019; 10:823. [PMID: 31057524 PMCID: PMC6479171 DOI: 10.3389/fmicb.2019.00823] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/01/2019] [Indexed: 11/13/2022] Open
Abstract
Quorum quenching (QQ) is proposed as a new strategy for mitigating microbe-associated problems (e.g., fouling, biocorrosion). However, most QQ agents reported to date have not been evaluated for their quenching efficacies under conditions representative of seawater desalination plants, cooling towers or marine aquaculture. In this study, bacterial strains were isolated from Saudi Arabian coastal environments and screened for acyl homoserine lactone (AHL)-quenching activities. Five AHL quenching bacterial isolates from the genera Pseudoalteromonas, Pontibacillus, and Altererythrobacter exhibited high AHL-quenching activity at a salinity level of 58 g/L and a pH of 7.8 at 50°C. This result demonstrates the potential use of these QQ bacteria in mitigating microbe-associated problems under saline and alkaline conditions at high (>37°C) temperatures. Further characterizations of the QQ efficacies revealed two bacterial isolates, namely, Pseudoalteromonas sp. L11 and Altererythrobacter sp. S1-5, which could possess enzymatic QQ activity. The genome sequences of L11 and S1-5 with a homologous screening against reported AHL quenching genes suggest the existence of four possible QQ coding genes in each strain. Specifically, two novel AHL enzymes, AiiAS1-5 and EstS1-5 from Altererythrobacter sp. S1-5, both contain signal peptides and exhibit QQ activity over a broad range of pH, salinity, and temperature values. In particular, AiiAS1-5 demonstrated activity against a wide spectrum of AHL molecules. When tested against three bacterial species, namely, Aeromonas hydrophila, Pseudomonas aeruginosa, and Vibrio alginolyticus, AiiAS1-5 was able to inhibit the motility of all three species under saline conditions. The biofilm formation associated with P. aeruginosa was also significantly inhibited by AiiAS1-5. AiiAS1-5 also reduced the quorum sensing-mediated virulence traits of A. hydrophila, P. aeruginosa, and V. alginolyticus during the mid and late exponential phases of cell growth. The enzyme did not impose any detrimental effects on cell growth, suggesting a lower potential for the target bacterium to develop resistance over long-term exposure. Overall, this study suggested that some QQ enzymes obtained from the bacteria that inhabit saline environments under high temperatures have potential applications in the mitigation of microbe-associated problems.
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Affiliation(s)
- Tian-Nyu Wang
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Qing-Tian Guan
- Pathogen Genomics Laboratory, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Arnab Pain
- Pathogen Genomics Laboratory, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Pei-Ying Hong
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Schwab M, Bergonzi C, Sakkos J, Staley C, Zhang Q, Sadowsky MJ, Aksan A, Elias M. Signal Disruption Leads to Changes in Bacterial Community Population. Front Microbiol 2019; 10:611. [PMID: 30984139 PMCID: PMC6449428 DOI: 10.3389/fmicb.2019.00611] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/11/2019] [Indexed: 01/02/2023] Open
Abstract
The disruption of bacterial signaling (quorum quenching) has been proven to be an innovative approach to influence the behavior of bacteria. In particular, lactonase enzymes that are capable of hydrolyzing the N-acyl homoserine lactone (AHL) molecules used by numerous bacteria, were reported to inhibit biofilm formation, including those of freshwater microbial communities. However, insights and tools are currently lacking to characterize, understand and explain the effects of signal disruption on complex microbial communities. Here, we produced silica capsules containing an engineered lactonase that exhibits quorum quenching activity. Capsules were used to design a filtration cartridge to selectively degrade AHLs from a recirculating bioreactor. The growth of a complex microbial community in the bioreactor, in the presence or absence of lactonase, was monitored over a 3-week period. Dynamic population analysis revealed that signal disruption using a quorum quenching lactonase can effectively reduce biofilm formation in the recirculating bioreactor system and that biofilm inhibition is concomitant to drastic changes in the composition, diversity and abundance of soil bacterial communities within these biofilms. Effects of the quorum quenching lactonase on the suspension community also affected the microbial composition, suggesting that effects of signal disruption are not limited to biofilm populations. This unexpected finding is evidence for the importance of signaling in the competition between bacteria within communities. This study provides foundational tools and data for the investigation of the importance of AHL-based signaling in the context of complex microbial communities.
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Affiliation(s)
- Michael Schwab
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Celine Bergonzi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Jonathan Sakkos
- Department of Mechanical Engineering, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Christopher Staley
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Surgery, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Qian Zhang
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Michael J Sadowsky
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Alptekin Aksan
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Mechanical Engineering, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States
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40
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Vitola G, Mazzei R, Poerio T, Porzio E, Manco G, Perrotta I, Militano F, Giorno L. Biocatalytic membrane reactor development for organophosphates degradation. JOURNAL OF HAZARDOUS MATERIALS 2019; 365:789-795. [PMID: 30476802 DOI: 10.1016/j.jhazmat.2018.11.063] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Organophosphates (OPs) are highly toxic compounds used as pesticides and nerve agents. The devastating effects, reported in different studies, on the environment and human health indicate a serious scenario for both instantaneous and long terms effects. Bio-based strategies for OPs degradation seem the most promising solutions, particularly when extremophiles enzymes are used. These systems permit OPs degradation with high efficiency and specificity under mild conditions. However, as frequently observed, enzymes can easily lose activity in batch systems, so that a strategy to improve biocatalyst stability is highly needed, in order to develop continuous systems. In this work, for the first time, a continuous biocatalytic system for organophosphates (OPs) detoxification has been proposed by using a triple mutant of the thermostable phosphotriesterase (named SsoPox) isolated from the hyperthermophilic archaeon Sulfolobus solfataricus. The enzyme was covalently immobilized on polymeric membranes to develop a biocatalytic membrane reactor (BMR) able to hydrolyse a pesticide (paraoxon) contained in water. High paraoxon degradation (about 90%) and long term stability (1 year) were obtained when the enzyme was covalently immobilized on hydrophilic membranes. On the contrary, the enzyme in batch system completely loses its activity within few months after its solubilisation in buffer.
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Affiliation(s)
- G Vitola
- Institute on Membrane Technology, National Research Council, ITM-CNR, via P. Bucci, 17/C, 87036 Rende, Cosenza, Italy
| | - R Mazzei
- Institute on Membrane Technology, National Research Council, ITM-CNR, via P. Bucci, 17/C, 87036 Rende, Cosenza, Italy.
| | - T Poerio
- Institute on Membrane Technology, National Research Council, ITM-CNR, via P. Bucci, 17/C, 87036 Rende, Cosenza, Italy
| | - E Porzio
- Institute of Protein Biochemistry, National Research Council, IBP-CNR, via P. Castellino 111, 80131 Naples, Italy
| | - G Manco
- Institute of Protein Biochemistry, National Research Council, IBP-CNR, via P. Castellino 111, 80131 Naples, Italy
| | - I Perrotta
- Centre for Microscopy and Microanalysis (CM2), Dept. of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Cosenza, Italy
| | - F Militano
- Institute on Membrane Technology, National Research Council, ITM-CNR, via P. Bucci, 17/C, 87036 Rende, Cosenza, Italy
| | - L Giorno
- Institute on Membrane Technology, National Research Council, ITM-CNR, via P. Bucci, 17/C, 87036 Rende, Cosenza, Italy
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41
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Straub CT, Counts JA, Nguyen DMN, Wu CH, Zeldes BM, Crosby JR, Conway JM, Otten JK, Lipscomb GL, Schut GJ, Adams MWW, Kelly RM. Biotechnology of extremely thermophilic archaea. FEMS Microbiol Rev 2018; 42:543-578. [PMID: 29945179 DOI: 10.1093/femsre/fuy012] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022] Open
Abstract
Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.
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Affiliation(s)
- Christopher T Straub
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James A Counts
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James R Crosby
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan M Conway
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan K Otten
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
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Nemmara VV, Xiang DF, Fedorov AA, Fedorov EV, Bonanno JB, Almo SC, Raushel FM. Substrate Profile of the Phosphotriesterase Homology Protein from Escherichia coli. Biochemistry 2018; 57:6219-6227. [PMID: 30277746 PMCID: PMC6643279 DOI: 10.1021/acs.biochem.8b00935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The phosphotriesterase homology protein (PHP) from Escherichia coli is a member of a family of proteins that is related to phosphotriestrase (PTE), a bacterial enzyme from cog1735 with unusual substrate specificity toward the hydrolysis of synthetic organic phosphates and phosphonates. PHP was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of PHP was determined at a resolution of 1.84 Å with zinc and phosphate in the active site. The protein folds as a distorted (β/α)8-barrel and possesses a binuclear metal center in the active site. The catalytic function and substrate profile of PHP were investigated using a structure-guided approach that combined bioinformatics, computational docking, organic synthesis, and steady-state enzyme kinetics. PHP was found to catalyze the hydrolysis of phosphorylated glyceryl acetates. The best substrate was 1,2-diacetyl glycerol-3-phosphate with a kcat/ Km of 4.9 × 103 M-1 s-1. The presence of a phosphate group in the substrate was essential for enzymatic hydrolysis by the enzyme. It was surprising, however, to find that PHP was unable to hydrolyze any of the lactones tested as potential substrates, unlike most of the other enzymes from cog1735.
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Affiliation(s)
- Venkatesh V Nemmara
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Dao Feng Xiang
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - A A Fedorov
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - E V Fedorov
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Jeffrey B Bonanno
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Steven C Almo
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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Porzio E, Bettazzi F, Mandrich L, Del Giudice I, Restaino OF, Laschi S, Febbraio F, De Luca V, Borzacchiello MG, Carusone TM, Worek F, Pisanti A, Porcaro P, Schiraldi C, De Rosa M, Palchetti I, Manco G. Innovative Biocatalysts as Tools to Detect and Inactivate Nerve Agents. Sci Rep 2018; 8:13773. [PMID: 30214052 PMCID: PMC6137069 DOI: 10.1038/s41598-018-31751-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/25/2018] [Indexed: 11/13/2022] Open
Abstract
Pesticides and warfare nerve agents are frequently organophosphates (OPs) or related compounds. Their acute toxicity highlighted more than ever the need to explore applicable strategies for the sensing, decontamination and/or detoxification of these compounds. Herein, we report the use of two different thermostable enzyme families capable to detect and inactivate OPs. In particular, mutants of carboxylesterase-2 from Alicyclobacillus acidocaldarius and of phosphotriesterase-like lactonases from Sulfolobus solfataricus and Sulfolobus acidocaldarius, have been selected and assembled in an optimized format for the development of an electrochemical biosensor and a decontamination formulation, respectively. The features of the developed tools have been tested in an ad-hoc fabricated chamber, to mimic an alarming situation of exposure to a nerve agent. Choosing ethyl-paraoxon as nerve agent simulant, a limit of detection (LOD) of 0.4 nM, after 5 s of exposure time was obtained. Furthermore, an optimized enzymatic formulation was used for a fast and efficient environmental detoxification (>99%) of the nebulized nerve agent simulants in the air and on surfaces. Crucial, large-scale experiments have been possible thanks to production of grams amounts of pure (>90%) enzymes.
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Affiliation(s)
- Elena Porzio
- Institute of Protein Biochemistry, National Research Council of Italy, Naples, Italy
| | - Francesca Bettazzi
- Department of Chemistry, University of Florence, Sesto Fiorentino (FI), Italy
| | - Luigi Mandrich
- Institute of Protein Biochemistry, National Research Council of Italy, Naples, Italy
| | | | | | | | - Ferdinando Febbraio
- Institute of Protein Biochemistry, National Research Council of Italy, Naples, Italy
| | - Valentina De Luca
- Institute of Protein Biochemistry, National Research Council of Italy, Naples, Italy
| | | | - Teresa M Carusone
- Institute of Protein Biochemistry, National Research Council of Italy, Naples, Italy
| | - Franz Worek
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | | | | | | | - Mario De Rosa
- University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Ilaria Palchetti
- Department of Chemistry, University of Florence, Sesto Fiorentino (FI), Italy
| | - Giuseppe Manco
- Institute of Protein Biochemistry, National Research Council of Italy, Naples, Italy.
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44
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Catalytic bioscavengers as countermeasures against organophosphate nerve agents. Chem Biol Interact 2018; 292:50-64. [DOI: 10.1016/j.cbi.2018.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 12/30/2022]
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45
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Bergonzi C, Schwab M, Naik T, Daudé D, Chabrière E, Elias M. Structural and Biochemical Characterization of AaL, a Quorum Quenching Lactonase with Unusual Kinetic Properties. Sci Rep 2018; 8:11262. [PMID: 30050039 PMCID: PMC6062542 DOI: 10.1038/s41598-018-28988-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/29/2018] [Indexed: 11/10/2022] Open
Abstract
Quorum quenching lactonases are enzymes that are capable of disrupting bacterial signaling based on acyl homoserine lactones (AHL) via their enzymatic degradation. In particular, lactonases have therefore been demonstrated to inhibit bacterial behaviors that depend on these chemicals, such as the formation of biofilms or the expression of virulence factors. Here we characterized biochemically and structurally a novel representative from the metallo-β-lactamase superfamily, named AaL that was isolated from the thermoacidophilic bacterium Alicyclobacillus acidoterrestris. AaL is a potent quorum quenching enzyme as demonstrated by its ability to inhibit the biofilm formation of Acinetobacter baumannii. Kinetic studies demonstrate that AaL is both a proficient and a broad spectrum enzyme, being capable of hydrolyzing a wide range of lactones with high rates (kcat/KM > 105 M-1.s-1). Additionally, AaL exhibits unusually low KM values, ranging from 10 to 80 µM. Analysis of AaL structures bound to phosphate, glycerol, and C6-AHL reveals a unique hydrophobic patch (W26, F87 and I237), involved in substrate binding, possibly accounting for the enzyme's high specificity. Identifying the specificity determinants will aid the development of highly specific quorum quenching enzymes as potential therapeutics.
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Affiliation(s)
- Celine Bergonzi
- Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA
| | - Michael Schwab
- Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA
| | - Tanushree Naik
- Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA
| | - David Daudé
- Gene&GreenTK, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Eric Chabrière
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Mikael Elias
- Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA.
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Manoharan P, Sridhar J. Computational protein design and protein-ligand interaction studies for the improvement of organophosphorus degrading potential of Deinococcus radiodurans. J Mol Graph Model 2018; 83:12-16. [PMID: 29753940 DOI: 10.1016/j.jmgm.2018.04.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/06/2018] [Accepted: 04/26/2018] [Indexed: 11/28/2022]
Abstract
The organophosphorus hydrolase enzyme is involved in the catalyzing reaction that involve hydrolysis of organophosphate toxic compounds. An enzyme from Deinococcus radiodurans reported as homologous to phosphotriesterase and show activity against organophosphate. In the past activity of this enzyme is low and efforts made to improve the activity by experimental mutation study. However only very few organophosphates tested against very few catalytic site mutations. In order to improve the catalytic power of the organophosphorus hydrolase enzyme, we carried out systematic functional hotspot based protein engineering strategy. The mutants tested against 46 know organophosphate compounds using molecular docking study. Finally, we carried out an extensive molecular docking study to predict the binding of 46 organophosphate compounds to wild-type protein and mutant organophosphorus hydrolase enzyme. At the end we are able to improve the degrading potential of organophosphorus hydrolase enzyme against organophosphate toxic compounds. This preliminary study and the outcome would be useful guide for the experimental scientist involved in the bioremediation of toxic organophosphate compounds.
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Affiliation(s)
- Prabu Manoharan
- Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai 625021, India
| | - J Sridhar
- Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai 625021, India.
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Restaino OF, Borzacchiello MG, Scognamiglio I, Fedele L, Alfano A, Porzio E, Manco G, De Rosa M, Schiraldi C. High yield production and purification of two recombinant thermostable phosphotriesterase-like lactonases from Sulfolobus acidocaldarius and Sulfolobus solfataricus useful as bioremediation tools and bioscavengers. BMC Biotechnol 2018; 18:18. [PMID: 29558934 PMCID: PMC5861644 DOI: 10.1186/s12896-018-0427-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/09/2018] [Indexed: 02/01/2023] Open
Abstract
Background Thermostable phosphotriesterase-like lactonases (PLLs) are able to degrade organophosphates and could be potentially employed as bioremediation tools and bioscavengers. But nowadays their manufacturing in high yields is still an issue that limits their industrial applications. In this work we aimed to set up a high yield production and purification biotechnological process of two recombinant PLLs expressed in E. coli, the wild type SacPox from Sulfolobus acidocaldarius and a triple mutated SsoPox C258L/I261F/W263A, originally from Sulfolobus solfataricus. To follow this aim new induction approaches were investigated to boost the enzyme production, high cell density fermentation strategies were set-up to reach higher and higher enzyme yields up to 22-L scale, a downstream train was studied to meet the requirements of an efficient industrial purification process. Results Physiological studies in shake flasks demonstrated that the use of galactose as inducer increased the enzyme concentrations up to 4.5 folds, compared to the production obtained by induction with IPTG. Optimising high cell density fed-batch strategies the production and the productivity of both enzymes were further enhanced of 26 folds, up to 2300 U·L− 1 and 47.1 U·L− 1·h− 1 for SacPox and to 8700 U·L− 1 and 180.6 U·L− 1·h− 1 for SsoPox C258L/I261F/W263A, and the fermentation processes resulted scalable from 2.5 to 22.0 L. After being produced and extracted from the cells, the enzymes were first purified by a thermo-precipitation step, whose conditions were optimised by response surface methodology. A following ultra-filtration process on 100 and 5 KDa cut-off membranes drove to a final pureness and a total recovery of both enzymes of 70.0 ± 2.0%, suitable for industrial applications. Conclusions In this paper, for the first time, a high yield biotechnological manufacturing process of the recombinant enzymes SacPox and SsoPox C258L/I261F/W263A was set-up. The enzyme production was boosted by combining a new galactose induction approach with high cell density fed-batch fermentation strategies. An efficient enzyme purification protocol was designed coupling a thermo-precipitation step with a following membrane-based ultra-filtration process. Electronic supplementary material The online version of this article (10.1186/s12896-018-0427-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Odile Francesca Restaino
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, University of Campania "Luigi Vanvitelli"-ex Second University of Naples, Naples, Italy.
| | - Maria Giovanna Borzacchiello
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, University of Campania "Luigi Vanvitelli"-ex Second University of Naples, Naples, Italy
| | - Ilaria Scognamiglio
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, University of Campania "Luigi Vanvitelli"-ex Second University of Naples, Naples, Italy
| | - Luigi Fedele
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, University of Campania "Luigi Vanvitelli"-ex Second University of Naples, Naples, Italy
| | - Alberto Alfano
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, University of Campania "Luigi Vanvitelli"-ex Second University of Naples, Naples, Italy
| | - Elena Porzio
- Institute of Protein Biochemistry, National Research Council of Italy, Naples, Italy
| | - Giuseppe Manco
- Institute of Protein Biochemistry, National Research Council of Italy, Naples, Italy
| | - Mario De Rosa
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, University of Campania "Luigi Vanvitelli"-ex Second University of Naples, Naples, Italy
| | - Chiara Schiraldi
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, University of Campania "Luigi Vanvitelli"-ex Second University of Naples, Naples, Italy
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Alejo-González K, Hanson-Viana E, Vazquez-Duhalt R. Enzymatic detoxification of organophosphorus pesticides and related toxicants. JOURNAL OF PESTICIDE SCIENCE 2018; 43:1-9. [PMID: 30363124 PMCID: PMC6140661 DOI: 10.1584/jpestics.d17-078] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/08/2018] [Indexed: 05/20/2023]
Abstract
Millions of cases of pesticide intoxication occur yearly and represent a public health problem. In addition, pesticide poisoning is the preferred suicidal method in rural areas. The use of enzymes for the treatment of intoxication due to organophosphorus pesticides was proposed decades ago. Several enzymes are able to transform organophosphorus compounds such as pesticides and nerve agents. Some specific enzymatic treatments have been proposed, including direct enzyme injection, liposome and erythrocytes carriers, PEGylated preparations and extracorporeal enzymatic treatments. Nevertheless, no enzymatic treatments are currently available. In this work, the use of enzymes for treating of organophosphorus pesticide intoxication is critically reviewed and the remaining challenges are discussed.
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Affiliation(s)
- Karla Alejo-González
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera Tijuana-Ensenada, Ensenada, Baja California 22760 México
| | - Erik Hanson-Viana
- Facultad de Medicina, Universidad Autónoma de Baja California, Mexicali, Mexico
| | - Rafael Vazquez-Duhalt
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera Tijuana-Ensenada, Ensenada, Baja California 22760 México
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49
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Quehenberger J, Shen L, Albers SV, Siebers B, Spadiut O. Sulfolobus - A Potential Key Organism in Future Biotechnology. Front Microbiol 2017; 8:2474. [PMID: 29312184 PMCID: PMC5733018 DOI: 10.3389/fmicb.2017.02474] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/28/2017] [Indexed: 11/13/2022] Open
Abstract
Extremophilic organisms represent a potentially valuable resource for the development of novel bioprocesses. They can act as a source for stable enzymes and unique biomaterials. Extremophiles are capable of carrying out microbial processes and biotransformations under extremely hostile conditions. Extreme thermoacidophilic members of the well-characterized genus Sulfolobus are outstanding in their ability to thrive at both high temperatures and low pH. This review gives an overview of the biological system Sulfolobus including its central carbon metabolism and the development of tools for its genetic manipulation. We highlight findings of commercial relevance and focus on potential industrial applications. Finally, the current state of bioreactor cultivations is summarized and we discuss the use of Sulfolobus species in biorefinery applications.
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Affiliation(s)
- Julian Quehenberger
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Faculty of Chemistry – Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Faculty of Chemistry – Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
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Jacquet P, Hiblot J, Daudé D, Bergonzi C, Gotthard G, Armstrong N, Chabrière E, Elias M. Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase. Sci Rep 2017; 7:16745. [PMID: 29196634 PMCID: PMC5711954 DOI: 10.1038/s41598-017-16841-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
The redesign of enzyme active sites to alter their function or specificity is a difficult yet appealing challenge. Here we used a structure-based design approach to engineer the lactonase SsoPox from Sulfolobus solfataricus into a phosphotriesterase. The five best variants were characterized and their structure was solved. The most active variant, αsD6 (V27A-Y97W-L228M-W263M) demonstrates a large increase in catalytic efficiencies over the wild-type enzyme, with increases of 2,210-fold, 163-fold, 58-fold, 16-fold against methyl-parathion, malathion, ethyl-paraoxon, and methyl-paraoxon, respectively. Interestingly, the best mutants are also capable of degrading fensulfothion, which is reported to be an inhibitor for the wild-type enzyme, as well as others that are not substrates of the starting template or previously reported W263 mutants. The broad specificity of these engineered variants makes them promising candidates for the bioremediation of organophosphorus compounds. Analysis of their structures reveals that the increase in activity mainly occurs through the destabilization of the active site loop involved in substrate binding, and it has been observed that the level of disorder correlates with the width of the enzyme specificity spectrum. This finding supports the idea that active site conformational flexibility is essential to the acquisition of broader substrate specificity.
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Affiliation(s)
- Pauline Jacquet
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Julien Hiblot
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
- MPI for Medical Research, Chemical Biology department (EPFL), Heidelberg, Germany
| | - David Daudé
- Gene&GreenTK, IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Céline Bergonzi
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Guillaume Gotthard
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Nicholas Armstrong
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Eric Chabrière
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France.
| | - Mikael Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA.
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