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Ninck S, Klaus T, Kochetkova TV, Esser SP, Sewald L, Kaschani F, Bräsen C, Probst AJ, Kublanov IV, Siebers B, Kaiser M. Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities. ENVIRONMENTAL MICROBIOME 2024; 19:36. [PMID: 38831353 PMCID: PMC11145796 DOI: 10.1186/s40793-024-00577-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology. Different strategies for their uncovering such as bioprospecting, which relies mainly on metagenomic approaches in combination with sequence-based bioinformatic analyses, have emerged; yet accurate function prediction of their proteomes and deciphering the in vivo activity of an enzyme remains challenging. RESULTS Here, we present environmental activity-based protein profiling (eABPP), a multi-omics approach that extends genome-resolved metagenomics with mass spectrometry-based ABPP. This combination allows direct profiling of environmental community samples in their native habitat and the identification of active enzymes based on their function, even without sequence or structural homologies to annotated enzyme families. eABPP thus bridges the gap between environmental genomics, correct function annotation, and in vivo enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases from eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia. CONCLUSIONS By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms.
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Affiliation(s)
- Sabrina Ninck
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
| | - Thomas Klaus
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Sarah P Esser
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Leonard Sewald
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
- Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
- Centre of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany.
| | - Markus Kaiser
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
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2
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van Midden KP, Mantz M, Fonovič M, Gazvoda M, Svete J, Huesgen PF, van der Hoorn RAL, Klemenčič M. Mechanistic insights into CrCEP1: A dual-function cysteine protease with endo- and transpeptidase activity. Int J Biol Macromol 2024; 271:132505. [PMID: 38768911 DOI: 10.1016/j.ijbiomac.2024.132505] [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: 12/12/2023] [Revised: 04/05/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Proteases, essential regulators of plant stress responses, remain enigmatic in their precise functional roles. By employing activity-based probes for real-time monitoring, this study aimed to delve into protease activities in Chlamydomonas reinhardtii exposed to oxidative stress induced by hydrogen peroxide. However, our work revealed that the activity-based probes strongly labelled three non-proteolytic proteins-PsbO, PsbP, and PsbQ-integral components of photosystem II's oxygen-evolving complex. Subsequent biochemical assays and mass spectrometry experiments revealed the involvement of CrCEP1, a previously uncharacterized papain-like cysteine protease, as the catalyst of this labelling reaction. Further experiments with recombinant CrCEP1 and PsbO proteins replicated the reaction in vitro. Our data unveiled that endopeptidase CrCEP1 also has transpeptidase activity, ligating probes and peptides to the N-termini of Psb proteins, thereby expanding the repertoire of its enzymatic activities. The hitherto unknown transpeptidase activity of CrCEP1, working in conjunction with its proteolytic activity, unveils putative complex and versatile roles for proteases in cellular processes during stress responses.
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Affiliation(s)
- Katarina P van Midden
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Melissa Mantz
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany; CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany
| | - Marko Fonovič
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Martin Gazvoda
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Jurij Svete
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany; CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; CIBSS- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | | | - Marina Klemenčič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
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3
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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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4
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Chen MM, Kopittke PM, Zhao FJ, Wang P. Applications and opportunities of click chemistry in plant science. TRENDS IN PLANT SCIENCE 2024; 29:167-178. [PMID: 37612212 DOI: 10.1016/j.tplants.2023.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The Nobel Prize in Chemistry for 2022 was awarded to the pioneers of Lego-like 'click chemistry': combinatorial chemistry with remarkable modularity and diversity. It has been applied to a wide variety of biological systems, from microorganisms to plants and animals, including humans. Although click chemistry is a powerful chemical biology tool, comparatively few studies have examined its potential in plant science. Here, we review click chemistry reactions and their applications in plant systems, highlighting the activity-based probes and metabolic labeling strategies combined with bioorthogonal click chemistry to visualize plant biological processes. These applications offer new opportunities to explore and understand the underlying molecular mechanisms regulating plant composition, growth, metabolism, defense, and immune responses.
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Affiliation(s)
- Ming-Ming Chen
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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5
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Sueldo DJ, Godson A, Kaschani F, Krahn D, Kessenbrock T, Buscaill P, Schofield CJ, Kaiser M, van der Hoorn RAL. Activity-based proteomics uncovers suppressed hydrolases and a neo-functionalised antibacterial enzyme at the plant-pathogen interface. THE NEW PHYTOLOGIST 2024; 241:394-408. [PMID: 36866975 PMCID: PMC10952330 DOI: 10.1111/nph.18857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The extracellular space of plant tissues contains hundreds of hydrolases that might harm colonising microbes. Successful pathogens may suppress these hydrolases to enable disease. Here, we report the dynamics of extracellular hydrolases in Nicotiana benthamiana upon infection with Pseudomonas syringae. Using activity-based proteomics with a cocktail of biotinylated probes, we simultaneously monitored 171 active hydrolases, including 109 serine hydrolases (SHs), 49 glycosidases (GHs) and 13 cysteine proteases (CPs). The activity of 82 of these hydrolases (mostly SHs) increases during infection, while the activity of 60 hydrolases (mostly GHs and CPs) is suppressed during infection. Active β-galactosidase-1 (BGAL1) is amongst the suppressed hydrolases, consistent with production of the BGAL1 inhibitor by P. syringae. One of the other suppressed hydrolases, the pathogenesis-related NbPR3, decreases bacterial growth when transiently overexpressed. This is dependent on its active site, revealing a role for NbPR3 activity in antibacterial immunity. Despite being annotated as a chitinase, NbPR3 does not possess chitinase activity and contains an E112Q active site substitution that is essential for antibacterial activity and is present only in Nicotiana species. This study introduces a powerful approach to reveal novel components of extracellular immunity, exemplified by the discovery of the suppression of neo-functionalised Nicotiana-specific antibacterial NbPR3.
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Affiliation(s)
- Daniela J. Sueldo
- The Plant Chemetics Laboratory, Department of BiologyUniversity of OxfordOxfordOX1 3RBUK
| | - Alice Godson
- The Plant Chemetics Laboratory, Department of BiologyUniversity of OxfordOxfordOX1 3RBUK
| | - Farnusch Kaschani
- ZMB Chemical Biology, Faculty of BiologyUniversity of Duisburg‐Essen45117EssenGermany
| | - Daniel Krahn
- The Plant Chemetics Laboratory, Department of BiologyUniversity of OxfordOxfordOX1 3RBUK
- ZMB Chemical Biology, Faculty of BiologyUniversity of Duisburg‐Essen45117EssenGermany
| | - Till Kessenbrock
- ZMB Chemical Biology, Faculty of BiologyUniversity of Duisburg‐Essen45117EssenGermany
| | - Pierre Buscaill
- The Plant Chemetics Laboratory, Department of BiologyUniversity of OxfordOxfordOX1 3RBUK
| | - Christopher J. Schofield
- Chemistry Research LaboratoryDepartment of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchOxfordOX1 3TAUK
| | - Markus Kaiser
- ZMB Chemical Biology, Faculty of BiologyUniversity of Duisburg‐Essen45117EssenGermany
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6
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Barco-Antoñanzas M, Font-Farre M, Eceiza MV, Gil-Monreal M, van der Hoorn RAL, Royuela M, Zabalza A. Cysteine proteases are activated in sensitive Amaranthus palmeri populations upon treatment with herbicides inhibiting amino acid biosynthesis. PHYSIOLOGIA PLANTARUM 2023; 175:e13993. [PMID: 37882288 DOI: 10.1111/ppl.13993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 10/27/2023]
Abstract
The herbicides glyphosate and pyrithiobac inhibit the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in the aromatic amino acid biosynthetic pathway and acetolactate synthase (ALS) in the branched-chain amino acid biosynthetic pathway, respectively. Here we characterise the protease activity profiles of a sensitive (S), a glyphosate-resistant (GR) and a multiple-resistant (MR) population of Amaranthus palmeri in response to glyphosate and pyrithiobac. Amino acid accumulation and cysteine protease activities were induced with both herbicides in the S population and with pyrithiobac in the GR population, suggesting that the increase in cysteine proteases is responsible for the increased degradation of the available proteins and the observed increase in free amino acids. Herbicides did not induce any changes in the proteolytic activities in the populations with target-site resistance, indicating that this effect was only induced in sensitive plants.
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Affiliation(s)
- Maria Barco-Antoñanzas
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus de Arrosadía, Pamplona, Spain
| | - Maria Font-Farre
- The Plant Chemetics Laboratory, Department of Biology Sciences, University of Oxford, Oxford, UK
| | - Mikel V Eceiza
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus de Arrosadía, Pamplona, Spain
| | - Miriam Gil-Monreal
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus de Arrosadía, Pamplona, Spain
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Biology Sciences, University of Oxford, Oxford, UK
| | - Mercedes Royuela
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus de Arrosadía, Pamplona, Spain
| | - Ana Zabalza
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus de Arrosadía, Pamplona, Spain
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7
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Porta EO, Steel PG. Activity-based protein profiling: A graphical review. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2023; 5:100164. [PMID: 37692766 PMCID: PMC10484978 DOI: 10.1016/j.crphar.2023.100164] [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: 04/17/2023] [Revised: 08/06/2023] [Accepted: 08/23/2023] [Indexed: 09/12/2023] Open
Abstract
Activity-based protein profiling (ABPP) is a chemoproteomic technology that employs small chemical probes to directly interrogate protein function within complex proteomes. Since its initial application almost 25 years ago, ABPP has proven to be a powerful and versatile tool for addressing numerous challenges in drug discovery, including the development of highly selective small-molecule inhibitors, the discovery of new therapeutic targets, and the illumination of target proteins in tissues and organisms. This graphical review provides an overview of the rapid evolution of ABPP strategies, highlighting the versatility of the approach with selected examples of its successful application.
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Affiliation(s)
| | - Patrick G. Steel
- Department of Chemistry, Durham University, Durham, DH1 3LE, United Kingdom
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8
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Stael S, Sabljić I, Audenaert D, Andersson T, Tsiatsiani L, Kumpf RP, Vidal-Albalat A, Lindgren C, Vercammen D, Jacques S, Nguyen L, Njo M, Fernández-Fernández ÁD, Beunens T, Timmerman E, Gevaert K, Van Montagu M, Ståhlberg J, Bozhkov PV, Linusson A, Beeckman T, Van Breusegem F. Structure-function study of a Ca 2+-independent metacaspase involved in lateral root emergence. Proc Natl Acad Sci U S A 2023; 120:e2303480120. [PMID: 37216519 PMCID: PMC10235996 DOI: 10.1073/pnas.2303480120] [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: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Metacaspases are part of an evolutionarily broad family of multifunctional cysteine proteases, involved in disease and normal development. As the structure-function relationship of metacaspases remains poorly understood, we solved the X-ray crystal structure of an Arabidopsis thaliana type II metacaspase (AtMCA-IIf) belonging to a particular subgroup not requiring calcium ions for activation. To study metacaspase activity in plants, we developed an in vitro chemical screen to identify small molecule metacaspase inhibitors and found several hits with a minimal thioxodihydropyrimidine-dione structure, of which some are specific AtMCA-IIf inhibitors. We provide mechanistic insight into the basis of inhibition by the TDP-containing compounds through molecular docking onto the AtMCA-IIf crystal structure. Finally, a TDP-containing compound (TDP6) effectively hampered lateral root emergence in vivo, probably through inhibition of metacaspases specifically expressed in the endodermal cells overlying developing lateral root primordia. In the future, the small compound inhibitors and crystal structure of AtMCA-IIf can be used to study metacaspases in other species, such as important human pathogens, including those causing neglected diseases.
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Affiliation(s)
- Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Igor Sabljić
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Dominique Audenaert
- VIB Screening Core, VIB,9052Ghent, Belgium
- Centre for Bioassay Development and Screening, Ghent University,9000Ghent, Belgium
| | | | - Liana Tsiatsiani
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | | | | | | | - Dominique Vercammen
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Silke Jacques
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Long Nguyen
- VIB Screening Core, VIB,9052Ghent, Belgium
- Centre for Bioassay Development and Screening, Ghent University,9000Ghent, Belgium
| | - Maria Njo
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Álvaro D. Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Tine Beunens
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Evy Timmerman
- Department of Biomolecular Medicine, Ghent University,9052Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9052Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University,9052Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9052Ghent, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Peter V. Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Anna Linusson
- Department of Chemistry, Umeå University,90187Umeå, Sweden
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
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9
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Kiselev A, Camborde L, Carballo LO, Kaschani F, Kaiser M, van der Hoorn RAL, Gaulin E. The root pathogen Aphanomyces euteiches secretes modular proteases in pea apoplast during host infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1140101. [PMID: 37051076 PMCID: PMC10084794 DOI: 10.3389/fpls.2023.1140101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
To successfully colonize the host, phytopathogens have developed a large repertoire of components to both combat the host plant defense mechanisms and to survive in adverse environmental conditions. Microbial proteases are predicted to be crucial components of these systems. In the present work, we aimed to identify active secreted proteases from the oomycete Aphanomyces euteiches, which causes root rot diseases on legumes. Genome mining and expression analysis highlighted an overrepresentation of microbial tandemly repeated proteases, which are upregulated during host infection. Activity Based Protein Profiling and mass spectrometry (ABPP-MS) on apoplastic fluids isolated from pea roots infected by the pathogen led to the identification of 35 active extracellular microbial proteases, which represents around 30% of the genes expressed encoding serine and cysteine proteases during infection. Notably, eight of the detected active secreted proteases carry an additional C-terminal domain. This study reveals novel active modular extracellular eukaryotic proteases as potential pathogenicity factors in Aphanomyces genus.
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Affiliation(s)
- Andrei Kiselev
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Laura Ossorio Carballo
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Farnusch Kaschani
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Renier A. L. van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
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10
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Krammer L, Breinbauer R. Activity‐Based Protein Profiling of Oxidases and Reductases. Isr J Chem 2023. [DOI: 10.1002/ijch.202200086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Leo Krammer
- Institute of Organic Chemistry Graz University of Technology Stremayrgasse 9 A-8010 Graz Austria
| | - Rolf Breinbauer
- Institute of Organic Chemistry Graz University of Technology Stremayrgasse 9 A-8010 Graz Austria
- BIOTECHMED Graz A-8010 Graz Austria
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11
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Wright AT, Hudson LA, Garcia WL. Activity‐Based Protein Profiling – Enabling Phenotyping of Host‐Associated and Environmental Microbiomes. Isr J Chem 2023. [DOI: 10.1002/ijch.202200099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Aaron T. Wright
- Department of Biology Baylor University Waco Texas 76798 USA
- Department of Chemistry and Biochemistry Baylor University Waco Texas 76798 USA
| | - LaRae A. Hudson
- Department of Biology Baylor University Waco Texas 76798 USA
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12
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Identification of fungal lignocellulose-degrading biocatalysts secreted by Phanerochaete chrysosporium via activity-based protein profiling. Commun Biol 2022; 5:1254. [DOI: 10.1038/s42003-022-04141-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
AbstractActivity-based protein profiling (ABPP) has emerged as a versatile biochemical method for studying enzyme activity under various physiological conditions, with applications so far mainly in biomedicine. Here, we show the potential of ABPP in the discovery of biocatalysts from the thermophilic and lignocellulose-degrading white rot fungus Phanerochaete chrysosporium. By employing a comparative ABPP-based functional screen, including a direct profiling of wood substrate-bound enzymes, we identify those lignocellulose-degrading carbohydrate esterase (CE1 and CE15) and glycoside hydrolase (GH3, GH5, GH16, GH17, GH18, GH25, GH30, GH74 and GH79) enzymes specifically active in presence of the substrate. As expression of fungal enzymes remains challenging, our ABPP-mediated approach represents a preselection procedure for focusing experimental efforts on the most promising biocatalysts. Furthermore, this approach may also allow the functional annotation of domains-of-unknown functions (DUFs). The ABPP-based biocatalyst screening described here may thus allow the identification of active enzymes in a process of interest and the elucidation of novel biocatalysts that share no sequence similarity to known counterparts.
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13
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Husaini AM, Haq SAU, Jiménez AJL. Understanding saffron biology using omics- and bioinformatics tools: stepping towards a better Crocus phenome. Mol Biol Rep 2022; 49:5325-5340. [PMID: 35106686 PMCID: PMC8807023 DOI: 10.1007/s11033-021-07053-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022]
Abstract
Saffron is a unique plant in many aspects, and its cellular processes are regulated at multiple levels. The genetic makeup in the form of eight chromosome triplets (2n = 3x = 24) with a haploid genetic content (genome size) of 3.45 Gbp is decoded into different types of RNA by transcription. The RNA then translates into peptides and functional proteins, sometimes involving post-translational modifications too. The interactions of the genome, transcriptome, proteome and other regulatory molecules ultimately result in the complex set of primary and secondary metabolites of saffron metabolome. These complex interactions manifest in the form of a set of traits 'phenome' peculiar to saffron. The phenome responds to the environmental changes occurring in and around saffron and modify its response in respect of growth, development, disease response, stigma quality, apocarotenoid biosynthesis, and other processes. Understanding these complex relations between different yet interconnected biological activities is quite challenging in saffron where classical genetics has a very limited role owing to its sterility, and the absence of a whole-genome sequence. Omics-based technologies are immensely helpful in overcoming these limitations and developing a better understanding of saffron biology. In addition to creating a comprehensive picture of the molecular mechanisms involved in apocarotenoid synthesis, stigma biogenesis, corm activity, and flower development, omics-technologies will ultimately lead to the engineering of saffron plants with improved phenome.
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Affiliation(s)
- Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar Campus, Srinagar, Jammu and Kashmir, 190025, India.
| | - Syed Anam Ul Haq
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar Campus, Srinagar, Jammu and Kashmir, 190025, India
| | - Alberto José López Jiménez
- Departamento de Ciencia y Tecnología Agroforestal y Genética, Escuela Técnica Superior de Ingenieros Agrónomos y de Montes, Universidad de Castilla-La Mancha, Albacete, Spain
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14
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Klaus T, Ninck S, Albersmeier A, Busche T, Wibberg D, Jiang J, Elcheninov AG, Zayulina KS, Kaschani F, Bräsen C, Overkleeft HS, Kalinowski J, Kublanov IV, Kaiser M, Siebers B. Activity-Based Protein Profiling for the Identification of Novel Carbohydrate-Active Enzymes Involved in Xylan Degradation in the Hyperthermophilic Euryarchaeon Thermococcus sp. Strain 2319x1E. Front Microbiol 2022; 12:734039. [PMID: 35095781 PMCID: PMC8790579 DOI: 10.3389/fmicb.2021.734039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/22/2021] [Indexed: 12/02/2022] Open
Abstract
Activity-based protein profiling (ABPP) has so far scarcely been applied in Archaea in general and, especially, in extremophilic organisms. We herein isolated a novel Thermococcus strain designated sp. strain 2319x1E derived from the same enrichment culture as the recently reported Thermococcus sp. strain 2319x1. Both strains are able to grow with xylan as the sole carbon and energy source, and for Thermococcus sp. strain 2319x1E (optimal growth at 85°C, pH 6–7), the induction of xylanolytic activity in the presence of xylan was demonstrated. Since the solely sequence-based identification of xylanolytic enzymes is hardly possible, we established a complementary approach by conducting comparative full proteome analysis in combination with ABPP using α- or β-glycosidase selective probes and subsequent mass spectrometry (MS)-based analysis. This complementary proteomics approach in combination with recombinant protein expression and classical enzyme characterization enabled the identification of a novel bifunctional maltose-forming α-amylase and deacetylase (EGDIFPOO_00674) belonging to the GH57 family and a promiscuous β-glycosidase (EGIDFPOO_00532) with β-xylosidase activity. We thereby further substantiated the general applicability of ABPP in archaea and expanded the ABPP repertoire for the identification of glycoside hydrolases in hyperthermophiles.
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Affiliation(s)
- Thomas Klaus
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Faculty of Chemistry, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Sabrina Ninck
- Department of Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Andreas Albersmeier
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jianbing Jiang
- Section of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Kseniya S Zayulina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Farnusch Kaschani
- Department of Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Faculty of Chemistry, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Herman S Overkleeft
- Section of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Markus Kaiser
- Department of Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Faculty of Chemistry, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
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15
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Passarge A, Doehlemann G, Misas Villamil JC. Detection of Apoplastic Protease Inhibitors Using Convolution Activity-Based Protein Profiling. Methods Mol Biol 2022; 2447:95-104. [PMID: 35583775 DOI: 10.1007/978-1-0716-2079-3_8] [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] [Indexed: 06/15/2023]
Abstract
Activity-based protein profiling (ABPP) is a powerful tool in biological chemistry to monitor protein activity using chemical probes that bind covalently and irreversible to active site of enzymes such as proteases. To date, there are three different ways to experimentally use ABPP: comparative, competitive, and convolution ABPP. Here we use and describe the convolution ABPP approach, a method used to detect changes in protease inhibitor abundance in different proteomes. We have applied this method to monitor the activity of Lolium perenne apoplastic cysteine proteases during the interaction with the fungal endophyte Epichloë festucae. We describe the method to isolate apoplastic fluids from infected and uninfected L. perenne ryegrass leaves and the protocol to perform a convolution ABPP experiment. Furthermore, we report how to quantify and analyze fluorescent gels obtained from the ABPP labeling.
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Affiliation(s)
- Andrea Passarge
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Johana C Misas Villamil
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany.
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16
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In Planta Labeling Using a Clickable ER-Disrupting Probe Suggests a Role for Oleosins in Arabidopsis Seedling ER Integrity. ACS Chem Biol 2021; 16:2151-2157. [PMID: 34505514 DOI: 10.1021/acschembio.1c00607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several small-molecule perturbagens of the plant endomembrane system are known, but few selectively disrupt endoplasmic reticulum (ER) structure and function. We conducted a microscopy-based screen for small-molecule disruptors of ER structure and discovered eroonazole, a 1,2-4-triazole that induces extensive ER vesiculation in Arabidopsis seedlings. To identify eroonazole targets, we synthesized a clickable photoaffinity derivative and used it for whole-seedling labeling experiments. These reveal that the probe labels multiple oleosins, plant membrane proteins that stabilize ER-derived lipid droplets. Oleosin labeling is absent in an oleosin1234 quadruple mutant and reduced using an inactive analog. Cellular analyses of the ER in the quadruple mutant demonstrate that oleosins are required for normal ER structure during seed germination and suggest that perturbation of oleosin function by eroonazole underlies its effects on seedling ER structure.
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17
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Elmore JM, Griffin BD, Walley JW. Advances in functional proteomics to study plant-pathogen interactions. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102061. [PMID: 34102449 DOI: 10.1016/j.pbi.2021.102061] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 05/20/2023]
Abstract
Pathogen infection triggers complex signaling networks in plant cells that ultimately result in either susceptibility or resistance. We have made substantial progress in dissecting many of these signaling events, and it is becoming clear that changes in proteome composition and protein activity are major drivers of plant-microbe interactions. Here, we highlight different approaches to analyze the functional proteomes of hosts and pathogens and discuss how they have been used to further our understanding of plant disease. Global proteome profiling can quantify the dynamics of proteins, posttranslational modifications, and biological pathways that contribute to immune-related outcomes. In addition, emerging techniques such as enzyme activity-based profiling, proximity labeling, and kinase-substrate profiling are being used to dissect biochemical events that operate during infection. Finally, we discuss how these functional approaches can be integrated with other profiling data to gain a mechanistic, systems-level view of plant and pathogen signaling.
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Affiliation(s)
- James M Elmore
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50014, USA.
| | - Brianna D Griffin
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50014, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50014, USA.
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18
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Bleau JR, Spoel SH. Selective redox signaling shapes plant-pathogen interactions. PLANT PHYSIOLOGY 2021; 186:53-65. [PMID: 33793940 PMCID: PMC8154045 DOI: 10.1093/plphys/kiaa088] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
A review of recent progress in understanding the mechanisms whereby plants utilize selective and reversible redox signaling to establish immunity.
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Affiliation(s)
- Jade R Bleau
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Steven H Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
- Author for communication:
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19
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Godson A, van der Hoorn RAL. The front line of defence: a meta-analysis of apoplastic proteases in plant immunity. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3381-3394. [PMID: 33462613 PMCID: PMC8042752 DOI: 10.1093/jxb/eraa602] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/23/2020] [Indexed: 05/13/2023]
Abstract
Secreted proteases act at the front line of defence and play pivotal roles in disease resistance. However, the criteria for apoplastic immune proteases are not always defined and followed. Here, we critically reviewed 46 apoplastic proteases that function in plant defence. We found that most apoplastic immune proteases are induced upon infection, and 17 proteases are genetically required for the immune response. Proteolytic activity has been confirmed for most of the proteases but is rarely shown to be required for biological function, and the apoplastic location of proteases can be subjective and dynamic. Pathogen-derived inhibitors have only been described for cysteine and serine proteases, and the selection pressure acting on immune proteases is rarely investigated. We discuss six different mechanisms by which these proteases mediate plant immunity and summarize the challenges for future research.
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Affiliation(s)
- Alice Godson
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, UK
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20
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Lentz CS. What you see is what you get: activity-based probes in single-cell analysis of enzymatic activities. Biol Chem 2021; 401:233-248. [PMID: 31939273 DOI: 10.1515/hsz-2019-0262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/25/2019] [Indexed: 11/15/2022]
Abstract
Molecular imaging methods can provide spatio-temporal information about the distribution of biomolecules or biological processes, such as certain enzymatic activities, in single cells. Within a cell, it is possible to define the subcellular location of a target, its trafficking through the cell, colocalization with other biomolecules of interest and involvement in certain cell biological processes. On the other hand, single-cell imaging promises to distinguish cells that are phenotypically different from each other. The corresponding cellular diversity comprises the presence of functionally distinct cells in a population ('phenotypic heterogeneity'), as well as dynamic cellular responses to external stimuli ('phenotypic plasticity'), which is highly relevant, e.g. during cell differentiation, activation (of immune cells), or cell death. This review focuses on applications of a certain class of chemical probes, the so-called activity-based probes (ABPs), for visualization of enzymatic activities in the single-cell context. It discusses the structure of ABPs and other chemical probes, exemplary applications of ABPs in single-cell studies in human, mouse and bacterial systems and considerations to be made with regard to data interpretation.
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Affiliation(s)
- Christian S Lentz
- Department of Chemical Biology (CBIO), Helmholtz-Centre for Infection Research, Inhoffenstr. 7, D-38102 Braunschweig, Germany
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21
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Fuerst R, Breinbauer R. Activity-Based Protein Profiling (ABPP) of Oxidoreductases. Chembiochem 2021; 22:630-638. [PMID: 32881211 PMCID: PMC7894341 DOI: 10.1002/cbic.202000542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/02/2020] [Indexed: 12/20/2022]
Abstract
Over the last two decades, activity-based protein profiling (ABPP) has been established as a tremendously useful proteomic tool for measuring the activity of proteins in their cellular context, annotating the function of uncharacterized proteins, and investigating the target profile of small-molecule inhibitors. Unlike hydrolases and other enzyme classes, which exhibit a characteristic nucleophilic residue, oxidoreductases have received much less attention in ABPP. In this minireview, the state of the art of ABPP of oxidoreductases is described and the scope and limitations of the existing approaches are discussed. It is noted that several ABPP probes have been described for various oxidases, but none so far for a reductase, which gives rise to opportunities for future research.
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Affiliation(s)
- Rita Fuerst
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Rolf Breinbauer
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
- BIOTECHMEDGrazAustria
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22
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Interrogating Plant-Microbe Interactions with Chemical Tools: Click Chemistry Reagents for Metabolic Labeling and Activity-Based Probes. Molecules 2021; 26:molecules26010243. [PMID: 33466477 PMCID: PMC7796436 DOI: 10.3390/molecules26010243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 01/01/2021] [Indexed: 01/22/2023] Open
Abstract
Continued expansion of the chemical biology toolbox presents many new and diverse opportunities to interrogate the fundamental molecular mechanisms driving complex plant-microbe interactions. This review will examine metabolic labeling with click chemistry reagents and activity-based probes for investigating the impacts of plant-associated microbes on plant growth, metabolism, and immune responses. While the majority of the studies reviewed here used chemical biology approaches to examine the effects of pathogens on plants, chemical biology will also be invaluable in future efforts to investigate mutualistic associations between beneficial microbes and their plant hosts.
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23
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Parthasarathy A, Mantravadi PK, Kalesh K. Detectives and helpers: Natural products as resources for chemical probes and compound libraries. Pharmacol Ther 2020; 216:107688. [PMID: 32980442 DOI: 10.1016/j.pharmthera.2020.107688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023]
Abstract
About 70% of the drugs in use are derived from natural products, either used directly or in chemically modified form. Among all possible small molecules (not greater than 5 kDa), only a few of them are biologically active. Natural product libraries may have a higher rate of finding "hits" than synthetic libraries, even with the use of fewer compounds. This is due to the complementarity between the "chemical space" of small molecules and biological macromolecules such as proteins, DNA and RNA, in addition to the three-dimensional complexity of NPs. Chemical probes are molecules which aid in the elucidation of the biological mechanisms behind the action of drugs or drug-like molecules by binding with macromolecular/cellular interaction partners. Probe development and application have been spurred by advancements in photoaffinity label synthesis, affinity chromatography, activity based protein profiling (ABPP) and instrumental methods such as cellular thermal shift assay (CETSA) and advanced/hyphenated mass spectrometry (MS) techniques, as well as genome sequencing and bioengineering technologies. In this review, we restrict ourselves to a survey of natural products (including peptides/mini-proteins and excluding antibodies), which have been applied largely in the last 5 years for the target identification of drugs/drug-like molecules used in research on infectious diseases, and the description of their mechanisms of action.
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Affiliation(s)
- Anutthaman Parthasarathy
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, 85 Lomb Memorial Dr, Rochester, NY 14623, USA
| | | | - Karunakaran Kalesh
- Department of Chemistry, Durham University, Lower Mount Joy, South Road, Durham DH1 3LE, UK.
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24
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Steiger AK, Fansler SJ, Whidbey C, Miller CJ, Wright AT. Probe-enabled approaches for function-dependent cell sorting and characterization of microbiome subpopulations. Methods Enzymol 2020; 638:89-107. [PMID: 32416923 DOI: 10.1016/bs.mie.2020.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Understanding the roles that individual species or communities play within a microbiome is a significant challenge. The complexity and heterogeneity of microbiomes presents a challenge to researchers looking to unravel the function that microbiomes serve within larger environments. While identification of the species and proteins present in a microbiome can be accomplished through genomics approaches, strategies that report on enzyme activity are limited. In this chapter, we describe the application of small molecule chemical probes in the isolation and subsequent characterization of microbiome subpopulations based on enzymatic function. We will cover protocols for labeling microbes with appropriate probes, microbiome sample preparation, and using fluorescence-activated cell sorting to isolate subpopulations based on function. We hope that the strategies outlined here will serve as a resource for researchers studying the functional role that microbiomes play in the gut and soil.
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Affiliation(s)
- Andrea K Steiger
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Christopher Whidbey
- Department of Chemistry, Seattle University, Seattle, Washington, United States
| | - Carson J Miller
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Aaron T Wright
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States; The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States.
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25
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Kytidou K, Artola M, Overkleeft HS, Aerts JMFG. Plant Glycosides and Glycosidases: A Treasure-Trove for Therapeutics. FRONTIERS IN PLANT SCIENCE 2020; 11:357. [PMID: 32318081 PMCID: PMC7154165 DOI: 10.3389/fpls.2020.00357] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/11/2020] [Indexed: 05/10/2023]
Abstract
Plants contain numerous glycoconjugates that are metabolized by specific glucosyltransferases and hydrolyzed by specific glycosidases, some also catalyzing synthetic transglycosylation reactions. The documented value of plant-derived glycoconjugates to beneficially modulate metabolism is first addressed. Next, focus is given to glycosidases, the central theme of the review. The therapeutic value of plant glycosidases is discussed as well as the present production in plant platforms of therapeutic human glycosidases used in enzyme replacement therapies. The increasing knowledge on glycosidases, including structure and catalytic mechanism, is described. The novel insights have allowed the design of functionalized highly specific suicide inhibitors of glycosidases. These so-called activity-based probes allow unprecedented visualization of glycosidases cross-species. Here, special attention is paid on the use of such probes in plant science that promote the discovery of novel enzymes and the identification of potential therapeutic inhibitors and chaperones.
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Affiliation(s)
- Kassiani Kytidou
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Marta Artola
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
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26
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Jutras PV, Dodds I, van der Hoorn RA. Proteases of Nicotiana benthamiana: an emerging battle for molecular farming. Curr Opin Biotechnol 2020; 61:60-65. [PMID: 31765962 DOI: 10.1016/j.copbio.2019.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/19/2022]
Abstract
Molecular farming increasingly uses the tobacco relative Nicotiana benthamiana for production of recombinant proteins through transient expression. Several proteins are produced efficiently with this expression platform, but yields for other proteins are often very low. These low yields are frequently due to endogenous proteases. The latest genome annotations indicate that N. benthamiana encodes for at least 1243 putative proteases that probably act redundantly and consecutively on substrates in different subcellular compartments. Here, we discuss the N. benthamiana protease repertoire that may affect recombinant protein production and recent advances in protease depletion strategies to increase recombinant protein production in N. benthamiana.
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Affiliation(s)
- Philippe V Jutras
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, UK
| | - Isobel Dodds
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, UK
| | - Renier Al van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, UK.
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27
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Jutras PV, Grosse‐Holz F, Kaschani F, Kaiser M, Michaud D, van der Hoorn RA. Activity-based proteomics reveals nine target proteases for the recombinant protein-stabilizing inhibitor SlCYS8 in Nicotiana benthamiana. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1670-1678. [PMID: 30742730 PMCID: PMC6662110 DOI: 10.1111/pbi.13092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 05/23/2023]
Abstract
Co-expression of protease inhibitors like the tomato cystatin SlCYS8 is useful to increase recombinant protein production in plants, but key proteases involved in protein proteolysis are still unknown. Here, we performed activity-based protein profiling to identify proteases that are inhibited by SlCYS8 in agroinfiltrated Nicotiana benthamiana. We discovered that SlCYS8 selectively suppresses papain-like cysteine protease (PLCP) activity in both apoplastic fluids and total leaf extracts, while not affecting vacuolar-processing enzyme and serine hydrolase activity. A robust concentration-dependent inhibition of PLCPs occurred in vitro when purified SlCYS8 was added to leaf extracts, indicating direct cystatin-PLCP interactions. Activity-based proteomics revealed that nine different Cathepsin-L/-F-like PLCPs are strongly inhibited by SlCYS8 in leaves. By contrast, the activity of five other Cathepsin-B/-H-like PLCPs, as well as 87 Ser hydrolases, was unaffected by SlCYS8. SlCYS8 expression prevented protein degradation by inhibiting intermediate and mature isoforms of granulin-containing proteases from the Resistant-to-Desiccation-21 (RD21) PLCP subfamily. Our data underline the key role of endogenous PLCPs on recombinant protein degradation and reveal candidate proteases for depletion strategies.
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Affiliation(s)
- Philippe V. Jutras
- Department of Plant SciencesPlant Chemetics LaboratoryUniversity of OxfordOxfordUK
| | | | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenEssenGermany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenEssenGermany
| | - Dominique Michaud
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuébecCanada
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Fernández-Fernández ÁD, Van der Hoorn RAL, Gevaert K, Van Breusegem F, Stael S. Caught green-handed: methods for in vivo detection and visualization of protease activity. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2125-2141. [PMID: 30805604 DOI: 10.1093/jxb/erz076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Proteases are enzymes that cleave peptide bonds of other proteins. Their omnipresence and diverse activities make them important players in protein homeostasis and turnover of the total cell proteome as well as in signal transduction in plant stress responses and development. To understand protease function, it is of paramount importance to assess when and where a specific protease is active. Here, we review the existing methods to detect in vivo protease activity by means of imaging chemical activity-based probes and genetically encoded sensors. We focus on the diverse fluorescent and luminescent sensors at the researcher's disposal and evaluate the potential of imaging techniques to deliver in vivo spatiotemporal detail of protease activity. We predict that in the coming years, revised techniques will help to elucidate plant protease activity and functions and hence expand the current status of the field.
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Affiliation(s)
- Álvaro Daniel Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
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29
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Paulus JK, Van der Hoorn RAL. Do proteolytic cascades exist in plants? JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1997-2002. [PMID: 30668744 PMCID: PMC6460957 DOI: 10.1093/jxb/erz016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/15/2018] [Accepted: 01/08/2019] [Indexed: 05/10/2023]
Affiliation(s)
- Judith K Paulus
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, UK
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30
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Stael S, Van Breusegem F, Gevaert K, Nowack MK. Plant proteases and programmed cell death. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1991-1995. [PMID: 31222306 PMCID: PMC6460956 DOI: 10.1093/jxb/erz126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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31
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Dynamic hydrolase labelling as a marker for seed quality in Arabidopsis seeds. Biochem J 2019; 476:843-857. [PMID: 30782971 DOI: 10.1042/bcj20180911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 12/27/2022]
Abstract
Seed quality is affected by different constituents of the seed. In general, seed lots are considered to be of high quality when they exhibit fast and homogeneous germination. When seeds are stored, they undergo different degrees of damage that have detrimental effects on their quality. Therefore, accurate prediction of the seed quality and viability levels of a seed lot is of high importance in the seed-producing industry. Here, we describe the use of activity-based protein profiling of proteases to evaluate the quality of artificially and naturally aged seeds of Arabidopsis thaliana Using this approach, we have identified two protease activities with opposite behaviours in aged seeds of Arabidopsis that correlate with the quality status of the seeds. We show that vacuolar processing enzymes (VPEs) become more active during the ageing process, in both artificial and natural ageing treatments. Secondly, we demonstrate that serine hydrolases are active at the beginning of our artificial ageing treatment, but their labelling decreases along with seed viability. We present a list of candidate hydrolases active during seed germination and propose that these protease activities can be used in combination with VPEs to develop novel markers of seed quality.
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32
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Ormancey M, Thuleau P, van der Hoorn RAL, Grat S, Testard A, Kamal KY, Boudsocq M, Cotelle V, Mazars C. Sphingolipid-induced cell death in Arabidopsis is negatively regulated by the papain-like cysteine protease RD21. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:12-17. [PMID: 30823989 DOI: 10.1016/j.plantsci.2018.10.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 05/12/2023]
Abstract
It is now well established that sphingoid Long Chain Bases (LCBs) are crucial mediators of programmed cell death. In plants, the mycotoxin fumonisin B1 (FB1) produced by the necrotrophic fungus Fusarium moniliforme disrupts the sphingolipid biosynthesis pathway by inhibiting the ceramide synthase leading to an increase in the amount of phytosphingosine (PHS) and dihydrosphingosine (DHS), the two major LCBs in Arabidopsis thaliana. To date, the signaling pathway involved in FB1-induced cell death remains largely uncharacterized. It is also well acknowledged that plant proteases such as papain-like cysteine protease are largely involved in plant immunity. Here, we show that the papain-like cysteine protease RD21 (responsive-to-desiccation-21) is activated in response to PHS and FB1 in Arabidopsis cultured cells and leaves, respectively. Using two allelic null mutants of RD21, and two different PCD bioassays, we demonstrate that the protein acts as a negative regulator of FB1-induced cell death in Arabidopsis.
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Affiliation(s)
- Mélanie Ormancey
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France.
| | - Patrice Thuleau
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France.
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
| | - Sabine Grat
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France.
| | - Ambroise Testard
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France.
| | - Khaled Y Kamal
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France; Agronomy Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
| | - Marie Boudsocq
- Institute of Plant Sciences Paris Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry Val d'Essonne, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192, Gif-sur-Yvette, France.
| | - Valérie Cotelle
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France.
| | - Christian Mazars
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France.
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33
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Recent progress in synthesis and characterization of metal chalcone complexes and their potential as bioactive agents. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.05.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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34
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Grosse‐Holz F, Madeira L, Zahid MA, Songer M, Kourelis J, Fesenko M, Ninck S, Kaschani F, Kaiser M, van der Hoorn RA. Three unrelated protease inhibitors enhance accumulation of pharmaceutical recombinant proteins in Nicotiana benthamiana. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1797-1810. [PMID: 29509983 PMCID: PMC6131417 DOI: 10.1111/pbi.12916] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/25/2018] [Accepted: 02/28/2018] [Indexed: 05/21/2023]
Abstract
Agroinfiltrated Nicotiana benthamiana is a flexible and scalable platform for recombinant protein (RP) production, but its great potential is hampered by plant proteases that degrade RPs. Here, we tested 29 candidate protease inhibitors (PIs) in agroinfiltrated N. benthamiana leaves for enhancing accumulation of three unrelated RPs: glycoenzyme α-Galactosidase; glycohormone erythropoietin (EPO); and IgG antibody VRC01. Of the previously described PIs enhancing RP accumulation, we found only cystatin SlCYS8 to be effective. We identified three additional new, unrelated PIs that enhance RP accumulation: N. benthamiana NbPR4, NbPot1 and human HsTIMP, which have been reported to inhibit cysteine, serine and metalloproteases, respectively. Remarkably, accumulation of all three RPs is enhanced by each PI similarly, suggesting that the mechanism of degradation of unrelated RPs follows a common pathway. Inhibitory functions HsTIMP and SlCYS8 are required to enhance RP accumulation, suggesting that their target proteases may degrade RPs. Different PIs additively enhance RP accumulation, but the effect of each PI is dose-dependent. Activity-based protein profiling (ABPP) revealed that the activities of papain-like Cys proteases (PLCPs), Ser hydrolases (SHs) or vacuolar processing enzymes (VPEs) in leaves are unaffected upon expression of the new PIs, whereas SlCYS8 expression specifically suppresses PLCP activity only. Quantitative proteomics indicates that the three new PIs affect agroinfiltrated tissues similarly and that they all increase immune responses. NbPR4, NbPot1 and HsTIMP can be used to study plant proteases and improve RP accumulation in molecular farming.
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Affiliation(s)
| | - Luisa Madeira
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Muhammad Awais Zahid
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Molly Songer
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Jiorgos Kourelis
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Mary Fesenko
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstrEssenGermany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstrEssenGermany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstrEssenGermany
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35
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Niu L, Xu X, Liu H, Wu X, Wang W. On the Promising Role of Enzyme Activity Assay in Interpreting Comparative Proteomic Data in Plants. Proteomics 2018; 18:e1800234. [PMID: 30179302 DOI: 10.1002/pmic.201800234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/18/2018] [Indexed: 11/09/2022]
Abstract
Comparative proteomics is widely used to detect protein changes, especially differential abundance proteins (DAPs) that are involved in plant responses to development, disease, or environment. Once DAPs are identified, it is essential to validate any change in their abundance, and their role in the biological process under study. In addition to common confirmation by quantitative RT-PCR, immunoblot, and multiple reaction monitoring analysis, it has been proposed that enzyme activity assay (EAA) can be complementary to the standard proteomics results, especially regarding the elucidation of protein (enzyme) function and the mechanism of enzyme-associated biochemical or metabolic pathways. The enzymes discussed here are the DAPs identified in comparative plant proteomics. Despite the small number of enzymes in a proteome, they often make up a substantial proportion of the DAPs identified in comparative studies. Currently, only a few studies have performed EAA to complement the interpretation of proteomic data, especially activity-based protein profiling. This viewpoint aims to arouse the attention of proteomic researchers on the promising role of EAA in plant proteomics and highlights the need for high-throughput assays of enzyme activities in comparative plant proteomics.
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Affiliation(s)
- Liangjie Niu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangru Xu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hui Liu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaolin Wu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wei Wang
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China.,College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
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36
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Demir F, Niedermaier S, Villamor JG, Huesgen PF. Quantitative proteomics in plant protease substrate identification. THE NEW PHYTOLOGIST 2018; 218:936-943. [PMID: 28493421 DOI: 10.1111/nph.14587] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/07/2017] [Indexed: 05/17/2023]
Abstract
Contents Summary 936 I. Introduction 936 II. The quest for plant protease substrates - proteomics to the rescue? 937 III. Quantitative proteome comparison reveals candidate substrates 938 IV. Dynamic metabolic stable isotope labeling to measure protein turnover in vivo 938 V. Terminomics - large-scale identification of protease cleavage sites 939 VI. Substrate or not substrate, that is the question 940 VII. Concluding remarks 941 Acknowledgements 941 References 941 SUMMARY: Proteolysis is a central regulatory mechanism of protein homeostasis and protein function that affects all aspects of plant life. Higher plants encode for hundreds of proteases, but their physiological substrates and hence their molecular functions remain mostly unknown. Current quantitative mass spectrometry-based proteomics enables unbiased large-scale interrogation of the proteome and its modifications. Here we provide an overview of proteomics techniques that allow profiling of changes in protein abundance, measurement of proteome turnover rates, identification of protease cleavage sites in vivo and in vitro and determination of protease sequence specificity. We discuss how these techniques can help to reveal protease substrates and determine plant protease function, illustrated by recent studies on selected plant proteases.
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Affiliation(s)
- Fatih Demir
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Stefan Niedermaier
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Joji Grace Villamor
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Pitter Florian Huesgen
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
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37
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Gregor R, David S, Meijler MM. Chemical strategies to unravel bacterial-eukaryotic signaling. Chem Soc Rev 2018; 47:1761-1772. [PMID: 29260158 DOI: 10.1039/c7cs00606c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The common language of bacteria and higher life forms is a lexicon of small molecules that the research community is only beginning to decipher. While many new signaling molecules have been discovered in recent years, the identification of their targets is mostly lagging. This review will focus on the latest chemical-probe based research aimed at understanding how bacteria interact chemically with mammals and plants. In general, chemical biology strategies remain under-utilized in this complex field of research, with a few key exceptions, and we hope that this review encourages others to implement these techniques in their research. Specifically, we highlight the chemical biology techniques used in recent studies, especially activity-based protein profiling, that have been applied to unravel the chemical mechanisms of interkingdom interactions.
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Affiliation(s)
- R Gregor
- Department of Chemistry and National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, 84105, Israel.
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38
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Santos RB, Chandrasekar B, Mandal MK, Kaschani F, Kaiser M, Both L, van der Hoorn RAL, Schiermeyer A, Abranches R. Low Protease Content in Medicago truncatula Cell Cultures Facilitates Recombinant Protein Production. Biotechnol J 2018. [PMID: 29528190 DOI: 10.1002/biot.201800050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Medicago truncatula is an established model for studying legume biology. More recently, it has also been exploited as a Molecular Farming platform for the production of recombinant proteins, with the successful expression of fungal and human proteins in plants and cell suspension cultures of this species. One of the challenges that now must be overcome is the degradation of final products during production and downstream processing stages. In the M. truncatula genome, there are more than 400 putative protease-encoding genes, but to date, the proteolytic content of Medicago cell cultures has not been studied. In this report, the proteolytic activities that can potentially hamper the successful production of recombinant proteins in this system are evaluated. The potential proteases responsible for the degradation of target proteins are identified. Interestingly, the number of proteases found in Medicago spent medium is considerably lower than that of the well-established tobacco bright yellow 2 (BY-2) system. Papain-like cysteine proteases are found to be the major contributors to recombinant protein degradation in Medicago. This knowledge is used to engineer a cell line with reduced endogenous protease activity by expressing a selective protease inhibitor, further improving this expression platform.
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Affiliation(s)
- Rita B Santos
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Balakumaran Chandrasekar
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
| | - Manoj K Mandal
- Department of Plant Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Faculty of Biology, University of Duisburg-Essen, ZMB, Universitätsstraße 2, 45117 Essen, Germany
| | - Markus Kaiser
- Chemical Biology, Faculty of Biology, University of Duisburg-Essen, ZMB, Universitätsstraße 2, 45117 Essen, Germany
| | - Leonard Both
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
| | - Andreas Schiermeyer
- Department of Plant Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany
| | - Rita Abranches
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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39
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Havé M, Balliau T, Cottyn-Boitte B, Dérond E, Cueff G, Soulay F, Lornac A, Reichman P, Dissmeyer N, Avice JC, Gallois P, Rajjou L, Zivy M, Masclaux-Daubresse C. Increases in activity of proteasome and papain-like cysteine protease in Arabidopsis autophagy mutants: back-up compensatory effect or cell-death promoting effect? JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1369-1385. [PMID: 29281085 PMCID: PMC6037082 DOI: 10.1093/jxb/erx482] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/14/2017] [Indexed: 05/18/2023]
Abstract
Autophagy is essential for protein degradation, nutrient recycling, and nitrogen remobilization. Autophagy is induced during leaf ageing and in response to nitrogen starvation, and is known to play a fundamental role in nutrient recycling for remobilization and seed filling. Accordingly, ageing leaves of Arabidopsis autophagy mutants (atg) have been shown to over-accumulate proteins and peptides, possibly because of a reduced protein degradation capacity. Surprisingly, atg leaves also displayed higher protease activities. The work reported here aimed at identifying the nature of the proteases and protease activities that accumulated differentially (higher or lower) in the atg mutants. Protease identification was performed using shotgun LC-MS/MS proteome analyses and activity-based protein profiling (ABPP). The results showed that the chloroplast FTSH (FILAMENTATION TEMPERATURE SENSITIVE H) and DEG (DEGRADATION OF PERIPLASMIC PROTEINS) proteases and several extracellular serine proteases [subtilases (SBTs) and serine carboxypeptidase-like (SCPL) proteases] were less abundant in atg5 mutants. By contrast, proteasome-related proteins and cytosolic or vacuole cysteine proteases were more abundant in atg5 mutants. Rubisco degradation assays and ABPP showed that the activities of proteasome and papain-like cysteine protease were increased in atg5 mutants. Whether these proteases play a back-up role in nutrient recycling and remobilization in atg mutants or act to promote cell death is discussed in relation to their accumulation patterns in the atg5 mutant compared with the salicylic acid-depleted atg5/sid2 double-mutant, and in low nitrate compared with high nitrate conditions. Several of the proteins identified are indeed known as senescence- and stress-related proteases or as spontaneous cell-death triggering factors.
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Affiliation(s)
- Marien Havé
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, France
| | - Thierry Balliau
- UMR GQE- le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, France
| | | | - Emeline Dérond
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, France
| | - Gwendal Cueff
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, France
| | | | - Aurélia Lornac
- UCBN, INRA, UMR INRA-UBCN 950 Ecophysiologie Végétale, Agronomie & Nutrition N.C.S., Université de Caen Normandie, France
| | - Pavel Reichman
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, Halle (Saale), Germany and Science Campus Halle – Plant-based Bioeconomy, Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, Halle (Saale), Germany and Science Campus Halle – Plant-based Bioeconomy, Germany
| | - Jean-Christophe Avice
- UCBN, INRA, UMR INRA-UBCN 950 Ecophysiologie Végétale, Agronomie & Nutrition N.C.S., Université de Caen Normandie, France
| | - Patrick Gallois
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Loïc Rajjou
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, France
| | - Michel Zivy
- UMR GQE- le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, France
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40
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Zhuang C, Zhang W, Sheng C, Zhang W, Xing C, Miao Z. Chalcone: A Privileged Structure in Medicinal Chemistry. Chem Rev 2017; 117:7762-7810. [PMID: 28488435 PMCID: PMC6131713 DOI: 10.1021/acs.chemrev.7b00020] [Citation(s) in RCA: 757] [Impact Index Per Article: 108.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Privileged structures have been widely used as an effective template in medicinal chemistry for drug discovery. Chalcone is a common simple scaffold found in many naturally occurring compounds. Many chalcone derivatives have also been prepared due to their convenient synthesis. These natural products and synthetic compounds have shown numerous interesting biological activities with clinical potentials against various diseases. This review aims to highlight the recent evidence of chalcone as a privileged scaffold in medicinal chemistry. Multiple aspects of chalcone will be summarized herein, including the isolation of novel chalcone derivatives, the development of new synthetic methodologies, the evaluation of their biological properties, and the exploration of the mechanisms of action as well as target identification. This review is expected to be a comprehensive, authoritative, and critical review of the chalcone template to the chemistry community.
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Affiliation(s)
- Chunlin Zhuang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Wen Zhang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Wannian Zhang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
- School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan 750004, China
| | - Chengguo Xing
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Drive,
Gainesville, Florida 32610, United States
| | - Zhenyuan Miao
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
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41
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Havé M, Marmagne A, Chardon F, Masclaux-Daubresse C. Nitrogen remobilization during leaf senescence: lessons from Arabidopsis to crops. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2513-2529. [PMID: 27707774 DOI: 10.1093/jxb/erw365] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
As a result of climate changes, land use and agriculture have to adapt to new demands. Agriculture is responsible for a large part of the greenhouse gas (GHG) emissions that have to be urgently reduced in order to protect the environment. At the same time, agriculture has to cope with the challenges of sustainably feeding a growing world population. Reducing the use of the ammonia-nitrate fertilizers that are responsible for a large part of the GHGs released and that have a negative impact on carbon balance is one of the objectives of precision agriculture. One way to reduce N fertilizers without dramatically affecting grain yields is to improve the nitrogen recycling and remobilization performances of plants. Mechanisms involved in nitrogen recycling, such as autophagy, are essential for nutrient remobilization at the whole-plant level and for seed quality. Studies on leaf senescence and nutrient recycling provide new perspectives for improvement. The aim of this review is to give an overview of the mechanisms involved in nitrogen recycling and remobilization during leaf senescence and to present the different approaches undertaken to improve nitrogen remobilization efficiency using both model plants and crop species.
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Affiliation(s)
- Marien Havé
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Anne Marmagne
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Fabien Chardon
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Céline Masclaux-Daubresse
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
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Preston GM. Profiling the extended phenotype of plant pathogens: Challenges in Bacterial Molecular Plant Pathology. MOLECULAR PLANT PATHOLOGY 2017; 18:443-456. [PMID: 28026146 PMCID: PMC6638297 DOI: 10.1111/mpp.12530] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 05/18/2023]
Abstract
One of the most fundamental questions in plant pathology is what determines whether a pathogen grows within a plant? This question is frequently studied in terms of the role of elicitors and pathogenicity factors in the triggering or overcoming of host defences. However, this focus fails to address the basic question of how the environment in host tissues acts to support or restrict pathogen growth. Efforts to understand this aspect of host-pathogen interactions are commonly confounded by several issues, including the complexity of the plant environment, the artificial nature of many experimental infection systems and the fact that the physiological properties of a pathogen growing in association with a plant can be very different from the properties of the pathogen in culture. It is also important to recognize that the phenotype and evolution of pathogen and host are inextricably linked through their interactions, such that the environment experienced by a pathogen within a host, and its phenotype within the host, is a product of both its interaction with its host and its evolutionary history, including its co-evolution with host plants. As the phenotypic properties of a pathogen within a host cannot be defined in isolation from the host, it may be appropriate to think of pathogens as having an 'extended phenotype' that is the product of their genotype, host interactions and population structure within the host environment. This article reflects on the challenge of defining and studying this extended phenotype, in relation to the questions posed below, and considers how knowledge of the phenotype of pathogens in the host environment could be used to improve disease control. What determines whether a pathogen grows within a plant? What aspects of pathogen biology should be considered in describing the extended phenotype of a pathogen within a host? How can we study the extended phenotype in ways that provide insights into the phenotypic properties of pathogens during natural infections?
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Affiliation(s)
- Gail M. Preston
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
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Misas-Villamil JC, van der Burgh AM, Grosse-Holz F, Bach-Pages M, Kovács J, Kaschani F, Schilasky S, Emon AEK, Ruben M, Kaiser M, Overkleeft HS, van der Hoorn RAL. Subunit-selective proteasome activity profiling uncovers uncoupled proteasome subunit activities during bacterial infections. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:418-430. [PMID: 28117509 DOI: 10.1111/tpj.13494] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
The proteasome is a nuclear-cytoplasmic proteolytic complex involved in nearly all regulatory pathways in plant cells. The three different catalytic activities of the proteasome can have different functions, but tools to monitor and control these subunits selectively are not yet available in plant science. Here, we introduce subunit-selective inhibitors and dual-color fluorescent activity-based probes for studying two of the three active catalytic subunits of the plant proteasome. We validate these tools in two model plants and use this to study the proteasome during plant-microbe interactions. Our data reveal that Nicotiana benthamiana incorporates two different paralogs of each catalytic subunit into active proteasomes. Interestingly, both β1 and β5 activities are significantly increased upon infection with pathogenic Pseudomonas syringae pv. tomato DC3000 lacking hopQ1-1 [PtoDC3000(ΔhQ)] whilst the activity profile of the β1 subunit changes. Infection with wild-type PtoDC3000 causes proteasome activities that range from strongly induced β1 and β5 activities to strongly suppressed β5 activities, revealing that β1 and β5 activities can be uncoupled during bacterial infection. These selective probes and inhibitors are now available to the plant science community, and can be widely and easily applied to study the activity and role of the different catalytic subunits of the proteasome in different plant species.
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Affiliation(s)
- Johana C Misas-Villamil
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Botanical Institute and Cluster of Excellence on Plant Sciences, University of Cologne, 50674, Cologne, Germany
| | - Aranka M van der Burgh
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Friederike Grosse-Holz
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Lane, Oxford, OX1 3RB, UK
| | - Marcel Bach-Pages
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Lane, Oxford, OX1 3RB, UK
| | - Judit Kovács
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Department of Plant Biology, University of Szeged, Szeged, Hungary
| | - Farnusch Kaschani
- Chemical Biology, Universität Duisburg-Essen, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universitätsstr. 2, 45117, Essen, Germany
| | - Sören Schilasky
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Asif E K Emon
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Mark Ruben
- Gorlaeus Laboratories, Institute of Chemistry and Netherlands Proteomics Centre, 2333 CC, Leiden, The Netherlands
| | - Markus Kaiser
- Chemical Biology, Universität Duisburg-Essen, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universitätsstr. 2, 45117, Essen, Germany
| | - Hermen S Overkleeft
- Gorlaeus Laboratories, Institute of Chemistry and Netherlands Proteomics Centre, 2333 CC, Leiden, The Netherlands
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Lane, Oxford, OX1 3RB, UK
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Kovács J, Poór P, Kaschani F, Chandrasekar B, Hong TN, Misas-Villamil JC, Xin BT, Kaiser M, Overkleeft HS, Tari I, van der Hoorn RAL. Proteasome Activity Profiling Uncovers Alteration of Catalytic β2 and β5 Subunits of the Stress-Induced Proteasome during Salinity Stress in Tomato Roots. FRONTIERS IN PLANT SCIENCE 2017; 8:107. [PMID: 28217134 PMCID: PMC5289967 DOI: 10.3389/fpls.2017.00107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 01/18/2017] [Indexed: 05/20/2023]
Abstract
The stress proteasome in the animal kingdom facilitates faster conversion of oxidized proteins during stress conditions by incorporating different catalytic β subunits. Plants deal with similar kind of stresses and also carry multiple paralogous genes encoding for each of the three catalytic β subunits. Here, we investigated the existence of stress proteasomes upon abiotic stress (salt stress) in tomato roots. In contrast to Arabidopsis thaliana, tomato has a simplified proteasome gene set with single genes encoding each β subunit except for two genes encoding β2. Using proteasome activity profiling on tomato roots during salt stress, we discovered a transient modification of the catalytic subunits of the proteasome coinciding with a loss of cell viability. This stress-induced active proteasome disappears at later time points and coincides with the need to degrade oxidized proteins during salt stress. Subunit-selective proteasome probes and MS analysis of fluorescent 2D gels demonstrated that the detected stress-induced proteasome is not caused by an altered composition of subunits in active proteasomes, but involves an increased molecular weight of both labeled β2 and β5 subunits, and an additional acidic pI shift for labeled β5, whilst labeled β1 remains mostly unchanged. Treatment with phosphatase or glycosidases did not affect the migration pattern. This stress-induced proteasome may play an important role in PCD during abiotic stress.
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Affiliation(s)
- Judit Kovács
- Department of Plant Biology, University of SzegedSzeged, Hungary
| | - Péter Poór
- Department of Plant Biology, University of SzegedSzeged, Hungary
| | - Farnusch Kaschani
- Chemical Biology, Fakultät für Biologie, Zentrum für Medizinische Biotechnologie, Universität Duisburg-EssenEssen, Germany
| | - Balakumaran Chandrasekar
- Plant Chemetics Laboratory, Department of Plant Sciences, University of OxfordOxford, UK
- Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Tram N. Hong
- Plant Chemetics Laboratory, Department of Plant Sciences, University of OxfordOxford, UK
- Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Johana C. Misas-Villamil
- Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Botanical Institute and Cluster of Excellence on Plant Sciences, University of CologneCologne, Germany
| | - Bo T. Xin
- Leiden Institute of Chemistry, Leiden UniversityLeiden, Netherlands
| | - Markus Kaiser
- Chemical Biology, Fakultät für Biologie, Zentrum für Medizinische Biotechnologie, Universität Duisburg-EssenEssen, Germany
| | | | - Irma Tari
- Department of Plant Biology, University of SzegedSzeged, Hungary
| | - Renier A. L. van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of OxfordOxford, UK
- Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding ResearchCologne, Germany
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45
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Pružinská A, Shindo T, Niessen S, Kaschani F, Tóth R, Millar AH, van der Hoorn RAL. Major Cys protease activities are not essential for senescence in individually darkened Arabidopsis leaves. BMC PLANT BIOLOGY 2017; 17:4. [PMID: 28061816 PMCID: PMC5217659 DOI: 10.1186/s12870-016-0955-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 12/19/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND Papain-like Cys Proteases (PLCPs) and Vacuolar Processing Enzymes (VPEs) are amongst the most highly expressed proteases during leaf senescence in Arabidopsis. Using activity-based protein profiling (ABPP), a method that enables detection of active enzymes within a complex sample using chemical probes, the activities of PLCPs and VPEs were investigated in individually darkened leaves of Arabidopsis, and their role in senescence was tested in null mutants. RESULTS ABPP and mass spectrometry revealed an increased activity of several PLCPs, particularly RD21A and AALP. By contrast, despite increased VPE transcript levels, active VPE decreased in individually darkened leaves. Eight protease knock-out lines and two protease over expressing lines were subjected to senescence phenotype analysis to determine the importance of individual protease activities to senescence. Unexpectedly, despite the absence of dominating PLCP activities in these plants, the rubisco and chlorophyll decline in individually darkened leaves and the onset of whole plant senescence were unaltered. However, a significant delay in progression of whole plant senescence was observed in aalp-1 and rd21A-1/aalp-1 mutants, visible in the reduced number of senescent leaves. CONCLUSIONS Major Cys protease activities are not essential for dark-induced and developmental senescence and only a knock out line lacking AALP shows a slight but significant delay in plant senescence.
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Affiliation(s)
- Adriana Pružinská
- The Plant Chemetics laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA Australia
| | - Takayuki Shindo
- The Plant Chemetics laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Sherry Niessen
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Center for Physiological Proteomics, The Scripps Research Institute, La Jolla, 92037 California USA
| | - Farnusch Kaschani
- The Plant Chemetics laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Réka Tóth
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - A. Harvey Millar
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA Australia
| | - Renier A. L. van der Hoorn
- The Plant Chemetics laboratory, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, UK
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46
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Daneri-Castro SN, Chandrasekar B, Grosse-Holz FM, van der Hoorn RAL, Roberts TH. Activity-based protein profiling of hydrolytic enzymes induced by gibberellic acid in isolated aleurone layers of malting barley. FEBS Lett 2016; 590:2956-62. [DOI: 10.1002/1873-3468.12320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/14/2016] [Accepted: 07/16/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Sergio N. Daneri-Castro
- Faculty of Agriculture and Environment; Plant Breeding Institute; University of Sydney; Eveleigh Australia
| | | | | | | | - Thomas H. Roberts
- Faculty of Agriculture and Environment; Plant Breeding Institute; University of Sydney; Eveleigh Australia
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