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Van Fossen EM, Kroll JO, Anderson LN, McNaughton AD, Herrera D, Oda Y, Wilson AJ, Nelson WC, Kumar N, Frank AR, Elmore JR, Handakumbura P, Lin VS, Egbert RG. Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in Acinetobacter pittii. Appl Environ Microbiol 2024:e0102624. [PMID: 39248464 DOI: 10.1128/aem.01026-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 08/15/2024] [Indexed: 09/10/2024] Open
Abstract
Interactions between plants and soil microbial communities that benefit plant growth and enhance nutrient acquisition are driven by the selective release of metabolites from plant roots, or root exudation. To investigate these plant-microbe interactions, we developed a photoaffinity probe based on sorgoleone (sorgoleone diazirine alkyne for photoaffinity labeling, SoDA-PAL), a hydrophobic secondary metabolite and allelochemical produced in Sorghum bicolor root exudates. We applied SoDA-PAL to the identification of sorgoleone-binding proteins in Acinetobacter pittii SO1, a potential plant growth-promoting microbe isolated from sorghum rhizosphere soil. Competitive photoaffinity labeling of A. pittii whole cell lysates with SoDA-PAL identified 137 statistically enriched proteins, including putative transporters, transcriptional regulators, and a subset of proteins with predicted enzymatic functions. We performed computational protein modeling and docking with sorgoleone to prioritize candidates for experimental validation and then confirmed binding of sorgoleone to four of these proteins in vitro: the α/β fold hydrolase SrgB (OH685_09420), a fumarylacetoacetase (OH685_02300), a lysophospholipase (OH685_14215), and an unannotated hypothetical protein (OH685_18625). Our application of this specialized sorgoleone-based probe coupled with structural bioinformatics streamlines the identification of microbial proteins involved in metabolite recognition, metabolism, and toxicity, widening our understanding of the range of cellular pathways that can be affected by a plant secondary metabolite.IMPORTANCEHere, we demonstrate that a photoaffinity-based chemical probe modeled after sorgoleone, an important secondary metabolite released by sorghum roots, can be used to identify microbial proteins that directly interact with sorgoleone. We applied this probe to the sorghum-associated bacterium Acinetobacter pittii and showed that probe labeling is dose-dependent and sensitive to competition with purified sorgoleone. Coupling the probe with proteomics and computational analysis facilitated the identification of putative sorgoleone binders, including a protein implicated in a conserved pathway essential for sorgoleone catabolism. We anticipate that discoveries seeded by this workflow will expand our understanding of the molecular mechanisms by which specific metabolites in root exudates shape the sorghum rhizosphere microbiome.
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Affiliation(s)
- Elise M Van Fossen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jared O Kroll
- Energy Processes and Materials Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lindsey N Anderson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Andrew D McNaughton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Daisy Herrera
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Yasuhiro Oda
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Andrew J Wilson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - William C Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Neeraj Kumar
- Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Andrew R Frank
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Joshua R Elmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Pubudu Handakumbura
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Vivian S Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Robert G Egbert
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
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Ibrahim AE, Ghantarchyan H, Le T, Bhagat A, Maknouni B, Arabian S. A Rare Presentation of Severe Organophosphate Poisoning: A Case Report and Review of Literature. Cureus 2022; 14:e31497. [DOI: 10.7759/cureus.31497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
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Cannon J, Tang S, Yang K, Harrison R, Choi SK. Dual acting oximes designed for therapeutic decontamination of reactive organophosphates via catalytic inactivation and acetylcholinesterase reactivation. RSC Med Chem 2021; 12:1592-1603. [PMID: 34671741 DOI: 10.1039/d1md00194a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/04/2021] [Indexed: 01/24/2023] Open
Abstract
A conventional approach in the therapeutic decontamination of reactive organophosphate (OP) relies on chemical OP degradation by oxime compounds. However, their efficacy is limited due to their lack of activity in the reactivation of acetylcholinesterase (AChE), the primary target of OP. Here, we describe a set of α-nucleophile oxime derivatives which are newly identified for such dual modes of action. Thus, we prepared a 9-member oxime library, each composed of an OP-reactive oxime core linked to an amine-terminated scaffold, which varied through an N-alkyl functionalization. This library was screened by enzyme assays performed with human and electric eel subtypes of OP-inactivated AChE, which led to identifying three oxime leads that displayed significant enhancements in reactivation activity comparable to 2-PAM. They were able to reactivate both enzymes inactivated by three OP types including paraoxon, chlorpyrifos and malaoxon, suggesting their broad spectrum of OP susceptibility. All compounds in the library were able to retain catalytic reactivity in paraoxon inactivation by rates increased up to 5 or 8-fold relative to diacetylmonoxime (DAM) under controlled conditions at pH (8.0, 10.5) and temperature (17, 37 °C). Finally, selected lead compounds displayed superb efficacy in paraoxon decontamination on porcine skin in vitro. In summary, we addressed an unmet need in therapeutic OP decontamination by designing and validating a series of congeneric oximes that display dual modes of action.
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Affiliation(s)
- Jayme Cannon
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School Ann Arbor Michigan 48109 USA .,Department of Internal Medicine, University of Michigan Medical School Ann Arbor Michigan 48109 USA
| | - Shengzhuang Tang
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School Ann Arbor Michigan 48109 USA .,Department of Internal Medicine, University of Michigan Medical School Ann Arbor Michigan 48109 USA
| | - Kelly Yang
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School Ann Arbor Michigan 48109 USA
| | - Racquel Harrison
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School Ann Arbor Michigan 48109 USA
| | - Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School Ann Arbor Michigan 48109 USA .,Department of Internal Medicine, University of Michigan Medical School Ann Arbor Michigan 48109 USA
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Choi SK. Nanomaterial-Enabled Sensors and Therapeutic Platforms for Reactive Organophosphates. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:224. [PMID: 33467113 PMCID: PMC7830340 DOI: 10.3390/nano11010224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 12/29/2020] [Accepted: 01/14/2021] [Indexed: 01/15/2023]
Abstract
Unintended exposure to harmful reactive organophosphates (OP), which comprise a group of nerve agents and agricultural pesticides, continues to pose a serious threat to human health and ecosystems due to their toxicity and prolonged stability. This underscores an unmet need for developing technologies that will allow sensitive OP detection, rapid decontamination and effective treatment of OP intoxication. Here, this article aims to review the status and prospect of emerging nanotechnologies and multifunctional nanomaterials that have shown considerable potential in advancing detection methods and treatment modalities. It begins with a brief introduction to OP types and their biochemical basis of toxicity followed by nanomaterial applications in two topical areas of primary interest. One topic relates to nanomaterial-based sensors which are applicable for OP detection and quantitative analysis by electrochemical, fluorescent, luminescent and spectrophotometric methods. The other topic is directed on nanotherapeutic platforms developed as OP remedies, which comprise nanocarriers for antidote drug delivery and nanoscavengers for OP inactivation and decontamination. In summary, this article addresses OP-responsive nanomaterials, their design concepts and growing impact on advancing our capability in the development of OP sensors, decontaminants and therapies.
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Affiliation(s)
- Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA;
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Verhelst SHL, Bonger KM, Willems LI. Bioorthogonal Reactions in Activity-Based Protein Profiling. Molecules 2020; 25:E5994. [PMID: 33352858 PMCID: PMC7765892 DOI: 10.3390/molecules25245994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/27/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions.
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Affiliation(s)
- Steven H. L. Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Herestr. 49, Box 802, 3000 Leuven, Belgium
- AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Kimberly M. Bonger
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Lianne I. Willems
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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Korram J, Dewangan L, Karbhal I, Nagwanshi R, Vaishanav SK, Ghosh KK, Satnami ML. CdTe QD-based inhibition and reactivation assay of acetylcholinesterase for the detection of organophosphorus pesticides. RSC Adv 2020; 10:24190-24202. [PMID: 35516221 PMCID: PMC9055098 DOI: 10.1039/d0ra03055d] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
An enzyme immobilized glutathione (GSH)-capped CdTe quantum dot (QD)-based fluorescence assay has been developed for monitoring organophosphate pesticides.
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Affiliation(s)
- Jyoti Korram
- School of Studies in Chemistry
- Pt. Ravishankar Shukla University
- Raipur
- India
| | - Lakshita Dewangan
- School of Studies in Chemistry
- Pt. Ravishankar Shukla University
- Raipur
- India
| | - Indrapal Karbhal
- School of Studies in Chemistry
- Pt. Ravishankar Shukla University
- Raipur
- India
| | - Rekha Nagwanshi
- Department of Chemistry
- Govt. Madhav Science P. G. College
- Ujjain
- India
| | - Sandeep K. Vaishanav
- School of Studies in Chemistry
- Pt. Ravishankar Shukla University
- Raipur
- India
- State Forensic Science Laboratory
| | - Kallol K. Ghosh
- School of Studies in Chemistry
- Pt. Ravishankar Shukla University
- Raipur
- India
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