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Font-Farre M, Brown D, Toth R, Mahadevan C, Brazier-Hicks M, Morimoto K, Kaschani F, Sinclair J, Dale R, Hall S, Morris M, Kaiser M, Wright AT, Burton J, van der Hoorn RAL. Discovery of active mouse, plant and fungal cytochrome P450s in endogenous proteomes and upon expression in planta. Sci Rep 2024; 14:10091. [PMID: 38698065 PMCID: PMC11066006 DOI: 10.1038/s41598-024-60333-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Eukaryotes produce a large number of cytochrome P450s that mediate the synthesis and degradation of diverse endogenous and exogenous metabolites. Yet, most of these P450s are uncharacterized and global tools to study these challenging, membrane-resident enzymes remain to be exploited. Here, we applied activity profiling of plant, mouse and fungal P450s with chemical probes that become reactive when oxidized by P450 enzymes. Identification by mass spectrometry revealed labeling of a wide range of active P450s, including six plant P450s, 40 mouse P450s and 13 P450s of the fungal wheat pathogen Zymoseptoria tritici. We next used transient expression of GFP-tagged P450s by agroinfiltration to show ER-targeting and NADPH-dependent, activity-based labeling of plant, mouse and fungal P450s. Both global profiling and transient expression can be used to detect a broad range of active P450s to study e.g. their regulation and discover selective inhibitors.
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Affiliation(s)
- Maria Font-Farre
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, UK
| | - Daniel Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Reka Toth
- Department of Biology, University of Oxford, Oxford, UK
| | | | | | - Kyoko Morimoto
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, UK
| | - Farnusch Kaschani
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - John Sinclair
- Bioscience, Syngenta, Jealotts Hill International Research Centre, Bracknell, UK
| | - Richard Dale
- Bioscience, Syngenta, Jealotts Hill International Research Centre, Bracknell, UK
| | - Samantha Hall
- Bioscience, Syngenta, Jealotts Hill International Research Centre, Bracknell, UK
| | - Melloney Morris
- Bioscience, Syngenta, Jealotts Hill International Research Centre, Bracknell, UK
| | - Markus Kaiser
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | | | - Jonathan Burton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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Aihara Y, Maeda B, Goto K, Takahashi K, Nomoto M, Toh S, Ye W, Toda Y, Uchida M, Asai E, Tada Y, Itami K, Sato A, Murakami K, Kinoshita T. Identification and improvement of isothiocyanate-based inhibitors on stomatal opening to act as drought tolerance-conferring agrochemicals. Nat Commun 2023; 14:2665. [PMID: 37188667 DOI: 10.1038/s41467-023-38102-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/16/2023] [Indexed: 05/17/2023] Open
Abstract
Stomatal pores in the plant epidermis open and close to regulate gas exchange between leaves and the atmosphere. Upon light stimulation, the plasma membrane (PM) H+-ATPase is phosphorylated and activated via an intracellular signal transduction pathway in stomatal guard cells, providing a primary driving force for the opening movement. To uncover and manipulate this stomatal opening pathway, we screened a chemical library and identified benzyl isothiocyanate (BITC), a Brassicales-specific metabolite, as a potent stomatal-opening inhibitor that suppresses PM H+-ATPase phosphorylation. We further developed BITC derivatives with multiple isothiocyanate groups (multi-ITCs), which demonstrate inhibitory activity on stomatal opening up to 66 times stronger, as well as a longer duration of the effect and negligible toxicity. The multi-ITC treatment inhibits plant leaf wilting in both short (1.5 h) and long-term (24 h) periods. Our research elucidates the biological function of BITC and its use as an agrochemical that confers drought tolerance on plants by suppressing stomatal opening.
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Affiliation(s)
- Yusuke Aihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- JST PRESTO, 7 Gobancho, Chiyoda, Tokyo, 102-0076, Japan
| | - Bumpei Maeda
- Department of Chemistry, School of Science, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
| | - Kanna Goto
- Department of Chemistry, School of Science, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
| | - Koji Takahashi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Mika Nomoto
- JST PRESTO, 7 Gobancho, Chiyoda, Tokyo, 102-0076, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- Center for Gene Research, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Shigeo Toh
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- Department of Environmental Bioscience, Meijo University, Nagoya, Japan
| | - Wenxiu Ye
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, 261325, Weifang, China
| | - Yosuke Toda
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- Phytometrics Co., Ltd., Hamamatsu, Shizuoka, 435-0036, Japan
| | - Mami Uchida
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Eri Asai
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Yasuomi Tada
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- Center for Gene Research, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Kei Murakami
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan.
- JST PRESTO, 7 Gobancho, Chiyoda, Tokyo, 102-0076, Japan.
- Department of Chemistry, School of Science, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan.
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan.
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan.
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3
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Grosse‐Holz F, Kelly S, Blaskowski S, Kaschani F, Kaiser M, van der Hoorn RA. The transcriptome, extracellular proteome and active secretome of agroinfiltrated Nicotiana benthamiana uncover a large, diverse protease repertoire. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1068-1084. [PMID: 29055088 PMCID: PMC5902771 DOI: 10.1111/pbi.12852] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/06/2017] [Accepted: 10/15/2017] [Indexed: 05/06/2023]
Abstract
Infiltration of disarmed Agrobacterium tumefaciens into leaves of Nicotiana benthamiana (agroinfiltration) facilitates quick and safe production of antibodies, vaccines, enzymes and metabolites for industrial use (molecular farming). However, yield and purity of proteins produced by agroinfiltration are hampered by unintended proteolysis, restricting industrial viability of the agroinfiltration platform. Proteolysis may be linked to an immune response to agroinfiltration, but understanding of the response to agroinfiltration is limited. To identify the proteases, we studied the transcriptome, extracellular proteome and active secretome of agroinfiltrated leaves over a time course, with and without the P19 silencing inhibitor. Remarkably, the P19 expression had little effect on the leaf transcriptome and no effect on the extracellular proteome. 25% of the detected transcripts changed in abundance upon agroinfiltration, associated with a gradual up-regulation of immunity at the expense of photosynthesis. By contrast, 70% of the extracellular proteins increased in abundance, in many cases associated with increased efficiency of extracellular delivery. We detect a dynamic reprogramming of the proteolytic machinery upon agroinfiltration by detecting transcripts encoding for 975 different proteases and protease homologs. The extracellular proteome contains peptides derived from 196 proteases and protease homologs, and activity-based proteomics displayed 17 active extracellular Ser and Cys proteases in agroinfiltrated leaves. We discuss unique features of the N. benthamiana protease repertoire and highlight abundant extracellular proteases in agroinfiltrated leaves, being targets for reverse genetics. This data set increases our understanding of the plant response to agroinfiltration and indicates ways to improve a key expression platform for both plant science and molecular farming.
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Affiliation(s)
| | - Steven Kelly
- Department of Plant SciencesUniversity of OxfordOxfordUK
| | - Svenja Blaskowski
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenEssenGermany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenEssenGermany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenEssenGermany
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Liu C, Moschou PN. Cutting in the middleman: hidden substrates at the interface between proteases and plant development. THE NEW PHYTOLOGIST 2018; 218:916-922. [PMID: 28262953 DOI: 10.1111/nph.14501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/21/2017] [Indexed: 06/06/2023]
Abstract
Contents Summary 916 I. Introduction 916 II. DEK1: towards identification of protease substrates 917 III. Separases: when proteolytic modules attain nonproteolytic functions 918 IV. The peculiar case of a nonredundant subtilisin 919 V. Towards a solution to the protease redundancy problem 920 VI. Matters arising and closing remarks 921 Acknowledgements 921 References 921 SUMMARY: Proteases are integral components of proteome remodelling networks that regulate turnover of proteins and expand their functional diversity. Accumulating evidence highlights the importance of proteases as being central hubs of developmental programs. Yet the molecular pathways that many proteases act on, their natural substrates and their putative nonproteolytic functions remain largely elusive. Here, we discuss recent findings on proteases with functions that converge into plant development regulation, such as DEFECTIVE KERNEL 1 (DEK1), separase and subtilisins, to highlight conspicuous but unexplored aspects of protease biology. We also suggest an exploratory framework for addressing protease functions.
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Affiliation(s)
- Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
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Zhou Y, Li W, You W, Di Z, Wang M, Zhou H, Yuan S, Wong NK, Xiao Y. Discovery of Arabidopsis UGT73C1 as a steviol-catalyzing UDP-glycosyltransferase with chemical probes. Chem Commun (Camb) 2018; 54:7179-7182. [DOI: 10.1039/c7cc09951g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A strategy for rapidly mining biological parts from plants for synthetic biology utilizing natural product-derived chemical probes has been reported.
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Affiliation(s)
- Yiqing Zhou
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Wenjing You
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Zhengao Di
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Mingli Wang
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Haiyan Zhou
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Shuguang Yuan
- Laboratory of Physical Chemistry of Polymers and Membranes
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Switzerland
| | - Nai-Kei Wong
- State Key Discipline of Infection Diseases
- Shenzhen Third People's Hospital
- The Second Affiliated Hospital
- Shenzhen University
- Shenzhen 518112
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
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