1
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Zheng K, Lyu JC, Thomas EL, Schuster M, Sanguankiattichai N, Ninck S, Kaschani F, Kaiser M, van der Hoorn RAL. The proteome of Nicotiana benthamiana is shaped by extensive protein processing. THE NEW PHYTOLOGIST 2024; 243:1034-1049. [PMID: 38853453 DOI: 10.1111/nph.19891] [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: 02/12/2024] [Accepted: 04/29/2024] [Indexed: 06/11/2024]
Abstract
Processing by proteases irreversibly regulates the fate of plant proteins and hampers the production of recombinant proteins in plants, yet only few processing events have been described in agroinfiltrated Nicotiana benthamiana, which has emerged as the main transient protein expression platform in plant science and molecular pharming. Here, we used in-gel digests and mass spectrometry to monitor the migration and topography of 5040 plant proteins within a protein gel. By plotting the peptides over the gel slices, we generated peptographs that reveal where which part of each protein was detected within the protein gel. These data uncovered that 60% of the detected proteins have proteoforms that migrate at lower than predicted molecular weights, implicating extensive proteolytic processing. This analysis confirms the proteolytic removal and degradation of autoinhibitory prodomains of most but not all proteases, and revealed differential processing within pectinemethylesterase and lipase families. This analysis also uncovered intricate processing of glycosidases and uncovered that ectodomain shedding might be common for a diverse range of receptor-like kinases. Transient expression of double-tagged candidate proteins confirmed processing events in vivo. This large proteomic dataset implicates an elaborate proteolytic machinery shaping the proteome of N. benthamiana.
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Affiliation(s)
- Kaijie Zheng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, OX1 3RD, UK
| | - Joy C Lyu
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, OX1 3RD, UK
| | - Emma L Thomas
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, OX1 3RD, UK
| | - Mariana Schuster
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, OX1 3RD, UK
| | | | - Sabrina Ninck
- Chemical Biology, Center of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Essen, 45141, Germany
| | - Farnusch Kaschani
- Chemical Biology, Center of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Essen, 45141, Germany
| | - Markus Kaiser
- Chemical Biology, Center of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Essen, 45141, Germany
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford, OX1 3RD, UK
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2
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Li Z, Pickles IB, Sharma M, Melling B, Pallasdies L, Codée JDC, Williams SJ, Overkleeft HS, Davies GJ. Detection of Sulfoquinovosidase Activity in Cell Lysates Using Activity-Based Probes. Angew Chem Int Ed Engl 2024; 63:e202401358. [PMID: 38647177 DOI: 10.1002/anie.202401358] [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: 01/19/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
The sulfolipid sulfoquinovosyl diacylglycerol (SQDG), produced by plants, algae, and cyanobacteria, constitutes a major sulfur reserve in the biosphere. Microbial breakdown of SQDG is critical for the biological utilization of its sulfur. This commences through release of the parent sugar, sulfoquinovose (SQ), catalyzed by sulfoquinovosidases (SQases). These vanguard enzymes are encoded in gene clusters that code for diverse SQ catabolic pathways. To identify, visualize and isolate glycoside hydrolase CAZY-family 31 (GH31) SQases in complex biological environments, we introduce SQ cyclophellitol-aziridine activity-based probes (ABPs). These ABPs label the active site nucleophile of this enzyme family, consistent with specific recognition of the SQ cyclophellitol-aziridine in the active site, as evidenced in the 3D structure of Bacillus megaterium SQase. A fluorescent Cy5-probe enables visualization of SQases in crude cell lysates from bacteria harbouring different SQ breakdown pathways, whilst a biotin-probe enables SQase capture and identification by proteomics. The Cy5-probe facilitates monitoring of active SQase levels during different stages of bacterial growth which show great contrast to more traditional mRNA analysis obtained by RT-qPCR. Given the importance of SQases in global sulfur cycling and in human microbiota, these SQase ABPs provide a new tool with which to study SQase occurrence, activity and stability.
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Affiliation(s)
- Zirui Li
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Isabelle B Pickles
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Benjamin Melling
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Luise Pallasdies
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jeroen D C Codée
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Herman S Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
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3
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Sivaramakrishnan M, Veeraganti Naveen Prakash C, Chandrasekar B. Multifaceted roles of plant glycosyl hydrolases during pathogen infections: more to discover. PLANTA 2024; 259:113. [PMID: 38581452 DOI: 10.1007/s00425-024-04391-5] [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: 08/04/2023] [Accepted: 03/15/2024] [Indexed: 04/08/2024]
Abstract
MAIN CONCLUSION Carbohydrates are hydrolyzed by a family of carbohydrate-active enzymes (CAZymes) called glycosidases or glycosyl hydrolases. Here, we have summarized the roles of various plant defense glycosidases that possess different substrate specificities. We have also highlighted the open questions in this research field. Glycosidases or glycosyl hydrolases (GHs) are a family of carbohydrate-active enzymes (CAZymes) that hydrolyze glycosidic bonds in carbohydrates and glycoconjugates. Compared to those of all other sequenced organisms, plant genomes contain a remarkable diversity of glycosidases. Plant glycosidases exhibit activities on various substrates and have been shown to play important roles during pathogen infections. Plant glycosidases from different GH families have been shown to act upon pathogen components, host cell walls, host apoplastic sugars, host secondary metabolites, and host N-glycans to mediate immunity against invading pathogens. We could classify the activities of these plant defense GHs under eleven different mechanisms through which they operate during pathogen infections. Here, we have provided comprehensive information on the catalytic activities, GH family classification, subcellular localization, domain structure, functional roles, and microbial strategies to regulate the activities of defense-related plant GHs. We have also emphasized the research gaps and potential investigations needed to advance this topic of research.
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Affiliation(s)
| | | | - Balakumaran Chandrasekar
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani (BITS Pilani), Pilani, 333031, India.
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4
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Kong H, Song J, Ma S, Yang J, Shao Z, Li Q, Li Z, Xie Z, Yang P, Cao Y. Genome-wide identification and expression analysis of the glycosyl hydrolase family 1 genes in Medicago sativa revealed their potential roles in response to multiple abiotic stresses. BMC Genomics 2024; 25:20. [PMID: 38166654 PMCID: PMC10759430 DOI: 10.1186/s12864-023-09918-w] [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: 08/02/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs), are encoded by a large number of genes, which participate in the development and stress response of plants, particularly under biotic and abiotic stresses through the activation of phytohormones. However, there are few studies systematically analyzing stress or hormone-responsive BGLU genes in alfalfa. In this study, a total of 179 BGLU genes of the glycoside hydrolase family 1 were identified in the genome of alfalfa, and then were classified into five distinct clusters. Sequence alignments revealed several conserved and unique motifs among these MsBGLU proteins. Many cis-acting elements related to abiotic stresses and phytohormones were identified in the promoter of some MsBGLUs. Moreover, RNA-seq and RT-qPCR analyses showed that these MsBGLU genes exhibited distinct expression patterns in response to different abiotic stress and hormonal treatments. In summary, this study suggests that MsBGLU genes play crucial roles in response to various abiotic stresses and hormonal responses, and provides candidate genes for stress tolerance breeding in alfalfa.
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Affiliation(s)
- Haiming Kong
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jiaxing Song
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shihai Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jing Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zitong Shao
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qian Li
- College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zhongxing Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhiguo Xie
- Shaanxi Academy of Forestry, Xi'an, 710082, China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuman Cao
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, 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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Li Y, Wang Z, Zhu M, Niu Z, Li M, Zheng Z, Hu H, Lu Z, Zhang J, Wan D, Chen Q, Yang Y. A chromosome-scale Rhubarb (Rheum tanguticum) genome assembly provides insights into the evolution of anthraquinone biosynthesis. Commun Biol 2023; 6:867. [PMID: 37612424 PMCID: PMC10447539 DOI: 10.1038/s42003-023-05248-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Rhubarb is the collective name for various perennial plants from the genus Rheum L. and the Polygonaceae family. They are one of the most ancient, commonly used, and important herbs in traditional Chinese medicine. Rhubarb is a major source of anthraquinones, but how they are synthesized remains largely unknown. Here, we generate a genome sequence assembly of one important medicinal rhubarb R. tanguticum at the chromosome level, with 2.76 Gb assembled into 11 chromosomes. The genome is shaped by two recent whole-genome duplication events and recent bursts of retrotransposons. Metabolic analyses show that the major anthraquinones are mainly synthesized in its roots. Transcriptomic analysis reveals a co-expression module with a high correlation to anthraquinone biosynthesis that includes key chalcone synthase genes. One CHS, four CYP450 and two BGL genes involved in secondary metabolism show significantly upregulated expression levels in roots compared with other tissues and clustered in the co-expression module, which implies that they may also act as candidate genes for anthraquinone biosynthesis. This study provides valuable insights into the genetic bases of anthraquinone biosynthesis that will facilitate improved breeding practices and agronomic properties for rhubarb in the future.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhenyue Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhimin Niu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Minjie Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Jin Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Qiao Chen
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China.
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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7
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Pernis M, Salaj T, Bellová J, Danchenko M, Baráth P, Klubicová K. Secretome analysis revealed that cell wall remodeling and starch catabolism underlie the early stages of somatic embryogenesis in Pinus nigra. FRONTIERS IN PLANT SCIENCE 2023; 14:1225424. [PMID: 37600183 PMCID: PMC10436561 DOI: 10.3389/fpls.2023.1225424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
Somatic embryogenesis is an efficient mean for rapid micropropagation and preservation of the germplasm of valuable coniferous trees. Little is known about how the composition of secretome tracks down the level of embryogenic capacity. Unlike embryogenic tissue on solid medium, suspension cell cultures enable the study of extracellular proteins secreted into a liquid cultivation medium, avoiding contamination from destructured cells. Here, we present proteomic data of the secretome of Pinus nigra cell lines with contrasting embryogenic capacity, accounting for variability between genotypes. Our results showed that cell wall-related and carbohydrate-acting proteins were the most differentially accumulated. Peroxidases, extensin, α-amylase, plant basic secretory family protein (BSP), and basic secretory protease (S) were more abundant in the medium from the lines with high embryogenic capacity. In contrast, the medium from the low embryogenic capacity cell lines contained a higher amount of polygalacturonases, hothead protein, and expansin, which are generally associated with cell wall loosening or softening. These results corroborated the microscopic findings in cell lines with low embryogenic capacity-long suspensor cells without proper assembly. Furthermore, proteomic data were subsequently validated by peroxidase and α-amylase activity assays, and hence, we conclude that both tested enzyme activities can be considered potential markers of high embryogenic capacity.
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Affiliation(s)
- Miroslav Pernis
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Nitra, Slovakia
| | - Terézia Salaj
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Nitra, Slovakia
| | - Jana Bellová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Maksym Danchenko
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Nitra, Slovakia
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Katarína Klubicová
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Nitra, Slovakia
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8
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Vilen Z, Reeves AE, Huang ML. (Glycan Binding) Activity‐Based Protein Profiling in Cells Enabled by Mass Spectrometry‐Based Proteomics. Isr J Chem 2023; 63. [PMID: 37131487 PMCID: PMC10150848 DOI: 10.1002/ijch.202200097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The presence of glycan modifications at the cell surface and other locales positions them as key regulators of cell recognition and function. However, due to the complexity of glycosylation, the annotation of which proteins bear glycan modifications, which glycan patterns are present, and which proteins are capable of binding glycans is incomplete. Inspired by activity-based protein profiling to enrich for proteins in cells based on select characteristics, these endeavors have been greatly advanced by the development of appropriate glycan-binding and glycan-based probes. Here, we provide context for these three problems and describe how the capability of molecules to interact with glycans has enabled the assignment of proteins with specific glycan modifications or of proteins that bind glycans. Furthermore, we discuss how the integration of these probes with high resolution mass spectrometry-based technologies has greatly advanced glycoscience.
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Affiliation(s)
- Zak Vilen
- Skaggs Graduate School of Chemical and Biological Sciences Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- Department of Molecular Medicine Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037, USA
| | - Abigail E. Reeves
- Skaggs Graduate School of Chemical and Biological Sciences Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- Department of Molecular Medicine Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037, USA
| | - Mia L. Huang
- Skaggs Graduate School of Chemical and Biological Sciences Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- Department of Molecular Medicine Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037, USA
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9
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Zhang X, Zheng F, Zhao C, Li Z, Li C, Xia Y, Zheng S, Wang X, Sun X, Zhao X, Lin X, Lu X, Xu G. Novel Method for Comprehensive Annotation of Plant Glycosides Based on Untargeted LC-HRMS/MS Metabolomics. Anal Chem 2022; 94:16604-16613. [DOI: 10.1021/acs.analchem.2c02362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Xiuqiong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Fujian Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Zaifang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Chao Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- Dalian University of Technology, Dalian116024, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Yueyi Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Sijia Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Xinxin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Xiaoshan Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Xiaohui Lin
- Dalian University of Technology, Dalian116024, P. R. China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian116023, P. R. China
- University of Chinese Academy of Sciences, Beijing100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian116023, P. R. China
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10
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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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11
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Morimoto K, Krahn D, Kaschani F, Hopkinson‐Woolley D, Gee A, Buscaill P, Mohammed S, Sieber SA, Cravatt BF, Schofield CJ, van der Hoorn RAL. Broad-range metalloprotease profiling in plants uncovers immunity provided by defence-related metalloenzyme. THE NEW PHYTOLOGIST 2022; 235:1287-1301. [PMID: 35510806 PMCID: PMC9322406 DOI: 10.1111/nph.18200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Plants encode > 100 metalloproteases representing > 19 different protein families. Tools to study this large and diverse class of proteases have not yet been introduced into plant research. We describe the use of hydroxamate-based photoaffinity probes to explore plant proteomes for metalloproteases. We detected labelling of 23 metalloproteases in leaf extracts of the model plant Arabidopsis thaliana that belong to nine different metalloprotease families and localize to different subcellular compartments. The probes identified several chloroplastic FtsH proteases, vacuolar aspartyl aminopeptidase DAP1, peroxisomal metalloprotease PMX16, extracellular matrix metalloproteases and many cytosolic metalloproteases. We also identified nonproteolytic metallohydrolases involved in the release of auxin and in the urea cycle. Studies on tobacco plants (Nicotiana benthamiana) infected with the bacterial plant pathogen Pseudomonas syringae uncovered the induced labelling of PRp27, a secreted protein with implicated metalloprotease activity. PRp27 overexpression increases resistance, and PRp27 mutants lacking metal binding site are no longer labelled, but still show increased immunity. Collectively, these studies reveal the power of broad-range metalloprotease profiling in plants using hydroxamate-based probes.
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Affiliation(s)
- Kyoko Morimoto
- The Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Daniel Krahn
- The Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
- Department of Chemistry and the Ineos Oxford Institute for Antimcrobial ResearchUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Farnusch Kaschani
- The Plant Chemetics LaboratoryMax Planck Institute for Plant Breeding ResearchCologne50829Germany
| | - Digby Hopkinson‐Woolley
- The Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Anna Gee
- The Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Pierre Buscaill
- The Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Shabaz Mohammed
- Department of BiochemistryUniversity of OxfordOxfordOX1 3QUUK
| | - Stephan A. Sieber
- Department of ChemistryThe Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCA92037USA
| | - Benjamin F. Cravatt
- Department of ChemistryThe Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCA92037USA
| | - Christopher J. Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimcrobial ResearchUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Renier A. L. van der Hoorn
- The Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
- The Plant Chemetics LaboratoryMax Planck Institute for Plant Breeding ResearchCologne50829Germany
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12
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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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13
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Abreha KB, Alexandersson E, Resjö S, Lankinen Å, Sueldo D, Kaschani F, Kaiser M, van der Hoorn RAL, Levander F, Andreasson E. Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling. Int J Mol Sci 2021; 22:12033. [PMID: 34769464 PMCID: PMC8584485 DOI: 10.3390/ijms222112033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/11/2023] Open
Abstract
Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June-August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June-August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July-August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and β-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and β-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses.
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Affiliation(s)
- Kibrom B. Abreha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Åsa Lankinen
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Daniela Sueldo
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Farnusch Kaschani
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Markus Kaiser
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Renier A. L. van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, SE-221 00 Lund, Sweden;
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
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14
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Yan C, Yang N, Wang X, Wang Y. VqBGH40a isolated from Chinese wild Vitis quinquangularis degrades trans-piceid and enhances trans-resveratrol. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110989. [PMID: 34315603 DOI: 10.1016/j.plantsci.2021.110989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/31/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Resveratrol (3,5,4'-trihydroxy-stilbene) is a phytoalexin that can prevent plants from pathogen attacks. Piceid is the glycosylation product of resveratrol and the main storage form of stilbenes in grapevines. Here, we reported the function of a β-glycoside hydrolase gene, VqBGH40a, from the Chinese wild grapevine Vitis quinquangularis accession Danfeng-2 in the regulation of plant resistance to powdery mildew (Uncinula necator). VqBGH40a belonging to β-glycoside hydrolase family 1 encoded 506 amino acids and was located on the cytomembrane. Its optimal induction condition was 28 or 30℃, for 4 h, with 0.1 mM IPTG in a prokaryotic expression system. Enzyme activity detection showed that purified VqBGH40a could hydrolyze trans-piceid to form trans-resveratrol in vitro. VqBGH40a was transiently overexpressed in Danfeng-2 leaves and then artificially inoculated with powdery mildew showed that VqBGH40a protein could hydrolyze trans-piceid in vivo. Additionally, a comparative family analysis between VqBGH40a and 38 VviBGHs was performed. Overall, these results demonstrate that VqBGH40a can hydrolyze trans-piceid, enhance trans-resveratrol content, and participate in the defense mechanism of grapevine against powdery mildew.
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Affiliation(s)
- Chaohui Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Ministry of Agriculture of China, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture of China, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Na Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Ministry of Agriculture of China, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture of China, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xinqi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Ministry of Agriculture of China, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture of China, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Ministry of Agriculture of China, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture of China, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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15
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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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16
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Chen X, Xu J, Wong NK, Zhong S, Yang M, Liu Z, Lu Y, Li W, Zhou Y. Chemoproteomic Profiling of Cobalamin-Independent Methionine Synthases in Plants with a Covalent Probe. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8050-8056. [PMID: 32618189 DOI: 10.1021/acs.jafc.0c03301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cobalamin-independent methionine synthases (MS) are zinc-binding methyltransferases that catalyze de novo methionine biosynthesis in higher plants, which are enzymes critically involved in seed germination and plant growth. Here, we report a highly selective sulfonyl fluoride-based probe for chemoproteomic profiling of MS enzymes in living systems of the model plant Arabidopsis thaliana, as implemented in in-gel-, mass spectrometry-, and imaging-based platforms. This probe holds promise for facilitating and accelerating fundamental research and industrial application of MS enzymes, particularly in the contexts of MS1/2-targeting herbicide screening and design.
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Affiliation(s)
- Xin Chen
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingyuan Xu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Nai-Kei Wong
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Suyun Zhong
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Mengquan Yang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhen Liu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Yan Lu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiqing Zhou
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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17
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Kriechbaum R, Ziaee E, Grünwald‐Gruber C, Buscaill P, van der Hoorn RAL, Castilho A. BGAL1 depletion boosts the level of β-galactosylation of N- and O-glycans in N. benthamiana. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1537-1549. [PMID: 31837192 PMCID: PMC7292537 DOI: 10.1111/pbi.13316] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 05/18/2023]
Abstract
Glyco-design of proteins is a powerful tool in fundamental studies of structure-function relationship and in obtaining profiles optimized for efficacy of therapeutic glycoproteins. Plants, particularly Nicotiana benthamiana, are attractive hosts to produce recombinant glycoproteins, and recent advances in glyco-engineering facilitate customized N-glycosylation of plant-derived glycoproteins. However, with exception of monoclonal antibodies, homogenous human-like β1,4-galactosylation is very hard to achieve in recombinant glycoproteins. Despite significant efforts to optimize the expression of β1,4-galactosyltransferase, many plant-derived glycoproteins still exhibit incomplete processed N-glycans with heterogeneous terminal galactosylation. The most obvious suspects to be involved in trimming terminal galactose residues are β-galactosidases (BGALs) from the glycosyl hydrolase family GH35. To elucidate the so far uncharacterized mechanisms leading to the trimming of terminal galactose residues from glycans of secreted proteins, we studied a N. benthamiana BGAL known to be active in the apoplast (NbBGAL1). Here, we determined the NbBGAL1 subcellular localization, substrate specificity and in planta biological activity. We show that NbBGAL1 can remove β1,4- and β1,3-galactose residues on both N- and O-glycans. Transient BGAL1 down-regulation by RNA interference (RNAi) and BGAL1 depletion by genome editing drastically reduce β-galactosidase activity in N. benthamiana and increase the amounts of fully galactosylated complex N-glycans on several plant-produced glycoproteins. Altogether, our data demonstrate that NbBGAL1 acts on galactosylated complex N-glycans of plant-produced glycoproteins.
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Affiliation(s)
- Ricarda Kriechbaum
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Esmaiel Ziaee
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
- Department of Food Science and TechnologyCollege of AgricultureShiraz UniversityShirazIran
| | | | - Pierre Buscaill
- The Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | | | - Alexandra Castilho
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesViennaAustria
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18
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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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19
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Ghorashi AC, Kohler JJ. Not All Quiet on the Sugar Front: Glycan Combatants in Host-Pathogen Interactions. Biochemistry 2019; 59:3061-3063. [PMID: 31589414 DOI: 10.1021/acs.biochem.9b00524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Atossa C Ghorashi
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Jennifer J Kohler
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
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20
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Montero-Morales L, Maresch D, Crescioli S, Castilho A, Ilieva KM, Mele S, Karagiannis SN, Altmann F, Steinkellner H. In Planta Glycan Engineering and Functional Activities of IgE Antibodies. Front Bioeng Biotechnol 2019; 7:242. [PMID: 31632959 PMCID: PMC6781838 DOI: 10.3389/fbioe.2019.00242] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/12/2019] [Indexed: 12/22/2022] Open
Abstract
Human immunoglobulin E (IgE) is the most extensively glycosylated antibody isotype so glycans attached to the seven N-glycosites (NGS) in its Fab and Fc domains may modulate its functions. However, targeted modification of glycans in multiply glycosylated proteins remains a challenge. Here, we applied an in vivo approach that allows the manipulation of IgE N-glycans, using a trastuzumab equivalent IgE (HER2-IgE) as a model. Taking advantage of plant inherent features, i.e., synthesis of largely homogeneous complex N-glycans and susceptibility to glycan engineering, we generated targeted glycoforms of HER2-IgE largely resembling those found in serum IgE. Plant-derived HER2-IgE exhibited N-glycans terminating with GlcNAc, galactose or sialic acid, lacking, or carrying core fucose and xylose. We were able to not only modulate the five NGSs naturally decorated with complex N-glycans, but to also induce targeted glycosylation at the usually unoccupied NGS6, thus increasing the overall glycosylation content of HER2-IgE. Recombinant human cell-derived HER2-IgE exhibited large N-glycan heterogeneity. All HER2-IgE variants demonstrated glycosylation-independent binding to the target antigen and the high affinity receptor FcεRI, and subsequent similar capacity to trigger mast cell degranulation. In contrast, binding to the low affinity receptor CD23 (FcεRII) was modulated by the glycan profile, with increased binding to IgE variants with glycans terminating with GlcNAc residues. Here we offer an efficient in planta approach to generate defined glycoforms on multiply glycosylated IgE, allowing the precise exploration of glycosylation-dependent activities.
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Affiliation(s)
- Laura Montero-Morales
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Silvia Crescioli
- School of Basic and Medical Biosciences, King's College London, St. John's Institute of Dermatology, Guy's Hospital, London, United Kingdom
| | - Alexandra Castilho
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kristina M Ilieva
- School of Basic and Medical Biosciences, King's College London, St. John's Institute of Dermatology, Guy's Hospital, London, United Kingdom.,Breast Cancer Now Research Unit, Guy's Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Silvia Mele
- School of Basic and Medical Biosciences, King's College London, St. John's Institute of Dermatology, Guy's Hospital, London, United Kingdom
| | - Sophia N Karagiannis
- School of Basic and Medical Biosciences, King's College London, St. John's Institute of Dermatology, Guy's Hospital, London, United Kingdom.,Breast Cancer Now Research Unit, Guy's Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Friedrich Altmann
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Herta Steinkellner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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21
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Morimoto K, Cole KS, Kourelis J, Witt CH, Brown D, Krahn D, Stegmann M, Kaschani F, Kaiser M, Burton J, Mohammed S, Yamaguchi-Shinozaki K, Weerapana E, van der Hoorn RAL. Triazine Probes Target Ascorbate Peroxidases in Plants. PLANT PHYSIOLOGY 2019; 180:1848-1859. [PMID: 31138623 PMCID: PMC6670103 DOI: 10.1104/pp.19.00481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
Though they are rare in nature, anthropogenic 1,3,5-triazines have been used in herbicides as chemically stable scaffolds. Here, we show that small 1,3,5-triazines selectively target ascorbate peroxidases (APXs) in Arabidopsis (Arabidopsis thaliana), tomato (Solanum lycopersicum), rice (Oryza sativa), maize (Zea mays), liverwort (Marchantia polymorpha), and other plant species. The alkyne-tagged 2-chloro-4-methyl-1,3,5-triazine probe KSC-3 selectively binds APX enzymes, both in crude extracts and in living cells. KSC-3 blocks APX activity, thereby reducing photosynthetic activity under moderate light stress, even in apx1 mutant plants. This suggests that APX enzymes in addition to APX1 protect the photosystem against reactive oxygen species. Profiling APX1 with KCS-3 revealed that the catabolic products of atrazine (a 1,3,5-triazine herbicide), which are common soil pollutants, also target APX1. Thus, KSC-3 is a powerful chemical probe to study APX enzymes in the plant kingdom.
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Affiliation(s)
- Kyoko Morimoto
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Kyle S Cole
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467
| | - Jiorgos Kourelis
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Collin H Witt
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467
| | - Daniel Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Daniel Krahn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Monika Stegmann
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Farnusch Kaschani
- Zentrum für Medizinische Biotechnologie, Chemical Biology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Markus Kaiser
- Zentrum für Medizinische Biotechnologie, Chemical Biology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jonathan Burton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Shabaz Mohammed
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
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22
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Buscaill P, Chandrasekar B, Sanguankiattichai N, Kourelis J, Kaschani F, Thomas EL, Morimoto K, Kaiser M, Preston GM, Ichinose Y, van der Hoorn RAL. Glycosidase and glycan polymorphism control hydrolytic release of immunogenic flagellin peptides. Science 2019; 364:eaav0748. [PMID: 30975858 DOI: 10.1126/science.aav0748] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/12/2019] [Indexed: 11/02/2022]
Abstract
Plants and animals recognize conserved flagellin fragments as a signature of bacterial invasion. These immunogenic elicitor peptides are embedded in the flagellin polymer and require hydrolytic release before they can activate cell surface receptors. Although much of flagellin signaling is understood, little is known about the release of immunogenic fragments. We discovered that plant-secreted β-galactosidase 1 (BGAL1) of Nicotiana benthamiana promotes hydrolytic elicitor release and acts in immunity against pathogenic Pseudomonas syringae strains only when they carry a terminal modified viosamine (mVio) in the flagellin O-glycan. In counter defense, P. syringae pathovars evade host immunity by using BGAL1-resistant O-glycans or by producing a BGAL1 inhibitor. Polymorphic glycans on flagella are common to plant and animal pathogenic bacteria and represent an important determinant of host immunity to bacterial pathogens.
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Affiliation(s)
- Pierre Buscaill
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | | | | | - Farnusch Kaschani
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Emma L Thomas
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Kyoko Morimoto
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Markus Kaiser
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Yuki Ichinose
- The Graduate School of Environmental and Life Science, Okayama University, Japan
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23
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Genome-Wide Analysis of Glycoside Hydrolase Family 1 β-glucosidase Genes in Brassica rapa and Their Potential Role in Pollen Development. Int J Mol Sci 2019; 20:ijms20071663. [PMID: 30987159 PMCID: PMC6480273 DOI: 10.3390/ijms20071663] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/03/2022] Open
Abstract
Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs) are encoded by a large number of genes, and are involved in many developmental processes and stress responses in plants. Due to their importance in plant growth and development, genome-wide analyses have been conducted in model plants (Arabidopsis and rice) and maize, but not in Brassica species, which are important vegetable crops. In this study, we systematically analyzed B. rapaBGLUs (BrBGLUs), and demonstrated the involvement of several genes in pollen development. Sixty-four BrBGLUs were identified in Brassica databases, which were anchored onto 10 chromosomes, with 10 tandem duplications. Phylogenetic analysis revealed that 64 genes were classified into 10 subgroups, and each subgroup had relatively conserved intron/exon structures. Clustering with Arabidopsis BGLUs (AtBGLUs) facilitated the identification of several important subgroups for flavonoid metabolism, the production of glucosinolates, the regulation of abscisic acid (ABA) levels, and other defense-related compounds. At least six BrBGLUs might be involved in pollen development. The expression of BrBGLU10/AtBGLU20, the analysis of co-expressed genes, and the examination of knocked down Arabidopsis plants strongly suggests that BrBGLU10/AtBGLU20 has an indispensable function in pollen development. The results that are obtained from this study may provide valuable information for the further understanding of β-glucosidase function and Brassica breeding, for nutraceuticals-rich Brassica crops.
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24
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Poret M, Chandrasekar B, van der Hoorn RAL, Déchaumet S, Bouchereau A, Kim TH, Lee BR, Macquart F, Hara-Nishimura I, Avice JC. A Genotypic Comparison Reveals That the Improvement in Nitrogen Remobilization Efficiency in Oilseed Rape Leaves Is Related to Specific Patterns of Senescence-Associated Protease Activities and Phytohormones. FRONTIERS IN PLANT SCIENCE 2019; 10:46. [PMID: 30778361 PMCID: PMC6369165 DOI: 10.3389/fpls.2019.00046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/14/2019] [Indexed: 05/24/2023]
Abstract
Oilseed rape (Brassica napus L.) is an oleoproteaginous crop characterized by low N use efficiency (NUE) that is mainly related to a weak Nitrogen Remobilization Efficiency (NRE) during the sequential leaf senescence of the vegetative stages. Based on the hypothesis that proteolysis efficiency is crucial for the improvement of leafNRE, our objective was to characterize key senescence-associated proteolytic mechanisms of two genotypes (Ténor and Samouraï) previously identified with contrasting NREs. To reach this goal, biochemical changes, protease activities and phytohormone patterns were studied in mature leaves undergoing senescence in two genotypes with contrasting NRE cultivated in a greenhouse under limiting or ample nitrate supply. The genotype with the higher NRE (Ténor) possessed enhanced senescence processes in response to nitrate limitation, and this led to greater degradation of soluble proteins compared to the other genotype (Samouraï). This efficient proteolysis is associated with (i) an increase in serine and cysteine protease (CP) activities and (ii) the appearance of new CP activities (RD21-like, SAG12-like, RD19-like, cathepsin-B, XBCP3-like and aleurain-like proteases) during senescence induced by N limitation. Compared to Samouraï, Ténor has a higher hormonal ratio ([salicylic acid] + [abscisic acid])/([cytokinins]) that promotes senescence, particularly under low N conditions, and this is correlated with the stronger protein degradation and serine/CP activities observed during senescence. Short statement: The improvement in N recycling during leaf senescence in a genotype of Brassica napus L. characterized by a high nitrogen remobilization efficiency is related to a high phytohormonal ratio ([salicylic acid] + [abscisic acid])/([cytokinins]) that promotes leaf senescence and is correlated with an increase or the induction of specific serine and cysteine protease activities.
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Affiliation(s)
- Marine Poret
- Université de Caen Normandie, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., FED 4277 Normandie Végétal, Caen, France
| | - Balakumaran Chandrasekar
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Sylvain Déchaumet
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France
| | - Alain Bouchereau
- INRA, UMR 1349 Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France
| | - Tae-Hwan Kim
- Department of Animal Science, Institute of Agricultural Science and Technology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Bok-Rye Lee
- Department of Animal Science, Institute of Agricultural Science and Technology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Flavien Macquart
- Université de Caen Normandie, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., FED 4277 Normandie Végétal, Caen, France
| | - Ikuko Hara-Nishimura
- Laboratory of Plant Cell Biology, Faculty of Science and Engineering, Konan University Okamoto, Kobe, Japan
| | - Jean-Christophe Avice
- Université de Caen Normandie, UMR INRA–UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., FED 4277 Normandie Végétal, Caen, France
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25
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Rugen MD, Vernet MMJL, Hantouti L, Soenens A, Andriotis VME, Rejzek M, Brett P, van den Berg RJBHN, Aerts JMFG, Overkleeft HS, Field RA. A chemical genetic screen reveals that iminosugar inhibitors of plant glucosylceramide synthase inhibit root growth in Arabidopsis and cereals. Sci Rep 2018; 8:16421. [PMID: 30401902 PMCID: PMC6219604 DOI: 10.1038/s41598-018-34749-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/19/2018] [Indexed: 01/11/2023] Open
Abstract
Iminosugars are carbohydrate mimics that are useful as molecular probes to dissect metabolism in plants. To analyse the effects of iminosugar derivatives on germination and seedling growth, we screened a library of 390 N-substituted iminosugar analogues against Arabidopsis and the small cereal Eragrostis tef (Tef). The most potent compound identified in both systems, N-5-(adamantane-1-yl-ethoxy)pentyl- L-ido-deoxynojirimycin (L-ido-AEP-DNJ), inhibited root growth in agar plate assays by 92% and 96% in Arabidopsis and Tef respectively, at 10 µM concentration. Phenocopying the effect of L-ido-AEP-DNJ with the commercial inhibitor (PDMP) implicated glucosylceramide synthase as the target responsible for root growth inhibition. L-ido-AEP-DNJ was twenty-fold more potent than PDMP. Liquid chromatography-mass spectrometry (LC-MS) analysis of ceramide:glucosylceramide ratios in inhibitor-treated Arabidopsis seedlings showed a decrease in the relative quantity of the latter, confirming that glucosylceramide synthesis is perturbed in inhibitor-treated plants. Bioinformatic analysis of glucosylceramide synthase indicates gene conservation across higher plants. Previous T-DNA insertional inactivation of glucosylceramide synthase in Arabidopsis caused seedling lethality, indicating a role in growth and development. The compounds identified herein represent chemical alternatives that can overcome issues caused by genetic intervention. These inhibitors offer the potential to dissect the roles of glucosylceramides in polyploid crop species.
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Affiliation(s)
- Michael D Rugen
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mathieu M J L Vernet
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Laila Hantouti
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Amalia Soenens
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Vasilios M E Andriotis
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- School of Natural and Environmental Sciences, Devonshire Building, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Paul Brett
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Richard J B H N van den Berg
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Hermen S Overkleeft
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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26
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Kytidou K, Beekwilder J, Artola M, van Meel E, Wilbers RHP, Moolenaar GF, Goosen N, Ferraz MJ, Katzy R, Voskamp P, Florea BI, Hokke CH, Overkleeft HS, Schots A, Bosch D, Pannu N, Aerts JMFG. Nicotiana benthamiana α-galactosidase A1.1 can functionally complement human α-galactosidase A deficiency associated with Fabry disease. J Biol Chem 2018; 293:10042-10058. [PMID: 29674318 PMCID: PMC6028973 DOI: 10.1074/jbc.ra118.001774] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/17/2018] [Indexed: 11/06/2022] Open
Abstract
α-Galactosidases (EC 3.2.1.22) are retaining glycosidases that cleave terminal α-linked galactose residues from glycoconjugate substrates. α-Galactosidases take part in the turnover of cell wall-associated galactomannans in plants and in the lysosomal degradation of glycosphingolipids in animals. Deficiency of human α-galactosidase A (α-Gal A) causes Fabry disease (FD), a heritable, X-linked lysosomal storage disorder, characterized by accumulation of globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3). Current management of FD involves enzyme-replacement therapy (ERT). An activity-based probe (ABP) covalently labeling the catalytic nucleophile of α-Gal A has been previously designed to study α-galactosidases for use in FD therapy. Here, we report that this ABP labels proteins in Nicotiana benthamiana leaf extracts, enabling the identification and biochemical characterization of an N. benthamiana α-galactosidase we name here A1.1 (gene accession ID GJZM-1660). The transiently overexpressed and purified enzyme was a monomer lacking N-glycans and was active toward 4-methylumbelliferyl-α-d-galactopyranoside substrate (Km = 0.17 mm) over a broad pH range. A1.1 structural analysis by X-ray crystallography revealed marked similarities with human α-Gal A, even including A1.1's ability to hydrolyze Gb3 and lyso-Gb3, which are not endogenous in plants. Of note, A1.1 uptake into FD fibroblasts reduced the elevated lyso-Gb3 levels in these cells, consistent with A1.1 delivery to lysosomes as revealed by confocal microscopy. The ease of production and the features of A1.1, such as stability over a broad pH range, combined with its capacity to degrade glycosphingolipid substrates, warrant further examination of its value as a potential therapeutic agent for ERT-based FD management.
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Affiliation(s)
| | - Jules Beekwilder
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | | | | | - Ruud H P Wilbers
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | - Geri F Moolenaar
- Cloning and Protein Purification Facility, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden
| | - Nora Goosen
- Cloning and Protein Purification Facility, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden
| | | | | | | | | | - Cornelis H Hokke
- the Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | | | - Arjen Schots
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | - Dirk Bosch
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
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27
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Husaini AM, Morimoto K, Chandrasekar B, Kelly S, Kaschani F, Palmero D, Jiang J, Kaiser M, Ahrazem O, Overkleeft HS, van der Hoorn RAL. Multiplex Fluorescent, Activity-Based Protein Profiling Identifies Active α-Glycosidases and Other Hydrolases in Plants. PLANT PHYSIOLOGY 2018; 177:24-37. [PMID: 29555787 PMCID: PMC5933116 DOI: 10.1104/pp.18.00250] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 05/25/2023]
Abstract
With nearly 140 α-glycosidases in 14 different families, plants are well equipped with enzymes that can break the α-glucosidic bonds in a large diversity of molecules. Here, we introduce activity-based protein profiling (ABPP) of α-glycosidases in plants using α-configured cyclophellitol aziridine probes carrying various fluorophores or biotin. In Arabidopsis (Arabidopsis thaliana), these probes label members of the GH31 family of glycosyl hydrolases, including endoplasmic reticulum-resident α-glucosidase-II Radial Swelling3/Priority for Sweet Life5 (RSW3/PSL5) and Golgi-resident α-mannosidase-II Hybrid Glycosylation1 (HGL1), both of which trim N-glycans on glycoproteins. We detected the active state of extracellular α-glycosidases such as α-xylosidase XYL1, which acts on xyloglucans in the cell wall to promote cell expansion, and α-glucosidase AGLU1, which acts in starch hydrolysis and can suppress fungal invasion. Labeling of α-glycosidases generates pH-dependent signals that can be suppressed by α-glycosidase inhibitors in a broad range of plant species. To demonstrate its use on a nonmodel plant species, we applied ABPP on saffron crocus (Crocus sativus), a cash crop for the production of saffron spice. Using a combination of biotinylated glycosidase probes, we identified and quantified 67 active glycosidases in saffron crocus stigma, of which 10 are differentially active. We also uncovered massive changes in hydrolase activities in the corms upon infection with Fusarium oxysporum using multiplex fluorescence labeling in combination with probes for serine hydrolases and cysteine proteases. These experiments demonstrate the ease with which active α-glycosidases and other hydrolases can be analyzed through ABPP in model and nonmodel plants.
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Affiliation(s)
- Amjad M Husaini
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar- 190025, Jammu and Kashmir, India
| | - Kyoko Morimoto
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | | | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Farnusch Kaschani
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, 45117 Essen, Germany
| | - Daniel Palmero
- Universidad Politécnica de Madrid, Escuela Técnica Superior de Ingenieria Agronómica, Alimentaria cv de Biosistemas, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Jianbing Jiang
- Gorlaeus Laboratories, Leiden Institute of Chemistry and Netherlands Center for Proteomics, 2333 CC Leiden, The Netherlands
| | - Markus Kaiser
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, 45117 Essen, Germany
| | - Oussama Ahrazem
- Instituto Botánico, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Hermen S Overkleeft
- Gorlaeus Laboratories, Leiden Institute of Chemistry and Netherlands Center for Proteomics, 2333 CC Leiden, The Netherlands
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28
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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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29
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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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30
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Kuo CL, van Meel E, Kytidou K, Kallemeijn WW, Witte M, Overkleeft HS, Artola ME, Aerts JM. Activity-Based Probes for Glycosidases: Profiling and Other Applications. Methods Enzymol 2017; 598:217-235. [PMID: 29306436 DOI: 10.1016/bs.mie.2017.06.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycosidases mediate the fragmentation of glycoconjugates in the body, including the vital recycling of endogenous molecules. Several inherited diseases in man concern deficiencies in lysosomal glycosidases degrading glycosphingolipids. Prominent is Gaucher disease caused by an impaired lysosomal β-glucosidase (glucocerebrosidase, GBA) and resulting in pathological lysosomal storage of glucosylceramide (glucocerebroside) in tissue macrophages. GBA is a retaining glucosidase with a characteristic glycosyl-enzyme intermediate formed during catalysis. Using the natural suicide inhibitor cyclophellitol as a lead, we developed mechanism-based irreversible inhibitors of GBA equipped with a fluorescent reporter. These reagents covalently link to the catalytic nucleophile residue of GBA and permit specific and sensitive visualization of active enzyme molecules. The amphiphilic activity-based probes (ABPs) allow in situ detection of active GBA in cells and organisms. Furthermore, they may be used to biochemically confirm the diagnosis of Gaucher disease and they might assist in screening for small compounds interacting with the catalytic pocket. While the focus of this chapter is ABPs for β-glucosidases and Gaucher disease, the described concept has meanwhile been extended to other retaining glycosidases and related disease conditions as well.
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Affiliation(s)
- Chi-Lin Kuo
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Eline van Meel
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Kassiani Kytidou
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Martin Witte
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Marta Elena Artola
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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Proteomic Investigations of Proteases Involved in Cotyledon Senescence: A Model to Explore the Genotypic Variability of Proteolysis Machinery Associated with Nitrogen Remobilization Efficiency during the Leaf Senescence of Oilseed Rape. Proteomes 2017; 5:proteomes5040029. [PMID: 29099081 PMCID: PMC5748564 DOI: 10.3390/proteomes5040029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 12/18/2022] Open
Abstract
Oilseed rape is characterized by a low nitrogen remobilization efficiency during leaf senescence, mainly due to a lack of proteolysis. Because cotyledons are subjected to senescence, it was hypothesized that contrasting protease activities between genotypes may be distinguishable early in the senescence of cotyledons. To verify this assumption, our goals were to (i) characterize protease activities in cotyledons between two genotypes with contrasting nitrogen remobilization efficiency (Ténor and Samouraï) under limiting or ample nitrate supply; and (ii) test the role of salicylic acid (SA) and abscisic acid (ABA) in proteolysis regulation. Protease activities were measured and identified by a proteomics approach combining activity-based protein profiling with LC-MS/MS. As in senescing leaves, chlorophyll and protein contents decrease in senescing cotyledons and are correlated with an increase in serine and cysteine protease activities. Two RD21-like and SAG-12 proteases previously associated with an efficient proteolysis in senescing leaves of Ténor are also detected in senescing cotyledons. The infiltration of ABA and SA provokes the induction of senescence and several cysteine and serine protease activities. The study of protease activities during the senescence of cotyledons seems to be a promising experimental model to investigate the regulation and genotypic variability of proteolysis associated with efficient N remobilization.
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Peng T, Nagy G, Trinidad JC, Jackson JM, Pohl NLB. A High-Throughput Mass-Spectrometry-Based Assay for Identifying the Biochemical Functions of Putative Glycosidases. Chembiochem 2017; 18:2306-2311. [PMID: 28960712 DOI: 10.1002/cbic.201700292] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Indexed: 11/10/2022]
Abstract
The most commonly employed glycosidase assays rely on bulky ultraviolet or fluorescent tags at the anomeric position in potential carbohydrate substrates, thereby limiting the utility of these assays for broad substrate characterization. Here we report a qualitative mass spectrometry-based glycosidase assay amenable to high-throughput screening for the identification of the biochemical functions of putative glycosidases. The assay utilizes a library of methyl glycosides and is demonstrated on a high-throughput robotic liquid handling system for enzyme substrate screening. Identification of glycosidase biochemical function is achieved through the observation of an appropriate decrease in mass between a potential sugar substrate and its corresponding product by electrospray ionization mass spectrometry (ESI-MS). In addition to screening known glycosidases, the assay was demonstrated to characterize the biochemical function and enzyme substrate competency of the recombinantly expressed product of a putative glycosidase gene from the thermophilic bacterium Thermus thermophilus.
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Affiliation(s)
- Tianyuan Peng
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA
| | - Gabe Nagy
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA.,Laboratory for Biological Mass Spectrometry, Indiana University, Bloomington, IN, 47405-7102, USA
| | - Joy Marie Jackson
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA
| | - Nicola L B Pohl
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA
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van Smeden J, Dijkhoff IM, Helder RWJ, Al-Khakany H, Boer DEC, Schreuder A, Kallemeijn WW, Absalah S, Overkleeft HS, Aerts JMFG, Bouwstra JA. In situ visualization of glucocerebrosidase in human skin tissue: zymography versus activity-based probe labeling. J Lipid Res 2017; 58:2299-2309. [PMID: 29025868 DOI: 10.1194/jlr.m079376] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/06/2017] [Indexed: 12/15/2022] Open
Abstract
Epidermal β-glucocerebrosidase (GBA1), an acid β-glucosidase normally located in lysosomes, converts (glucosyl)ceramides into ceramides, which is crucial to generate an optimal barrier function of the outermost skin layer, the stratum corneum (SC). Here we report on two developed in situ methods to localize active GBA in human epidermis: i) an optimized zymography method that is less labor intensive and visualizes enzymatic activity with higher resolution than currently reported methods using either substrate 4-methylumbelliferyl-β-D-glucopyranoside or resorufin-β-D-glucopyranoside; and ii) a novel technique to visualize active GBA1 molecules by their specific labeling with a fluorescent activity-based probe (ABP), MDW941. The latter method pro-ved to be more robust and sensitive, provided higher resolution microscopic images, and was less prone to sample preparation effects. Moreover, in contrast to the zymography substrates that react with various β-glucosidases, MDW941 specifically labeled GBA1. We demonstrate that active GBA1 in the epidermis is primarily located in the extracellular lipid matrix at the interface of the viable epidermis and the lower layers of the SC. With ABP-labeling, we observed reduced GBA1 activity in 3D-cultured skin models when supplemented with the reversible inhibitor, isofagomine, irrespective of GBA expression. This inhibition affected the SC ceramide composition: MS analysis revealed an inhibitor-dependent increase in the glucosylceramide:ceramide ratio.
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Affiliation(s)
- Jeroen van Smeden
- Division of Drug Delivery Technology, Cluster Biotherapeutics, Leiden Academic Centre for Drug Research Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Irini M Dijkhoff
- Division of Drug Delivery Technology, Cluster Biotherapeutics, Leiden Academic Centre for Drug Research Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Richard W J Helder
- Division of Drug Delivery Technology, Cluster Biotherapeutics, Leiden Academic Centre for Drug Research Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Hanin Al-Khakany
- Division of Drug Delivery Technology, Cluster Biotherapeutics, Leiden Academic Centre for Drug Research Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Daphne E C Boer
- Medical Biochemistry Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Anne Schreuder
- Medical Biochemistry Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Wouter W Kallemeijn
- Medical Biochemistry Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Samira Absalah
- Division of Drug Delivery Technology, Cluster Biotherapeutics, Leiden Academic Centre for Drug Research Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Herman S Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Johannes M F G Aerts
- Medical Biochemistry Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Joke A Bouwstra
- Division of Drug Delivery Technology, Cluster Biotherapeutics, Leiden Academic Centre for Drug Research Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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34
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Comparative morphology and transcriptome analysis reveals distinct functions of the primary and secondary laticifer cells in the rubber tree. Sci Rep 2017; 7:3126. [PMID: 28600566 PMCID: PMC5466658 DOI: 10.1038/s41598-017-03083-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/24/2017] [Indexed: 12/27/2022] Open
Abstract
Laticifers are highly specialized cells that synthesize and store natural rubber. Rubber trees (Hevea brasiliensis Muell. Arg.) contain both primary and secondary laticifers. Morphological and functional differences between the two types of laticifers are largely unknown, but such information is important for breeding and cultivation practices. Morphological comparison using paraffin sections revealed only distribution differences: the primary laticifers were distributed randomly, while the secondary laticifers were distributed in concentric rings. Using isolated laticifer networks, the primary laticifers were shown to develop via intrusive "budding" and formed necklace-like morphology, while the secondary laticifers developed straight and smooth cell walls. Comparative transcriptome analysis indicated that genes involved in cell wall modification, such as pectin esterase, lignin metabolic enzymes, and expansins, were highly up-regulated in the primary laticifers and correspond to its necklace-like morphology. Genes involved in defense against biotic stresses and rubber biosynthesis were highly up-regulated in the primary laticifers, whereas genes involved in abiotic stresses and dormancy were up-regulated in the secondary laticifers, suggesting that the primary laticifers are more adequately prepared to defend against biotic stresses, while the secondary laticifers are more adequately prepared to defend against abiotic stresses. Therefore, the two types of laticifers are morphologically and functionally distinct.
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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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36
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Schalli M, Wolfsgruber A, Gonzalez Santana A, Tysoe C, Fischer R, Stütz AE, Thonhofer M, Withers SG. C-5a-substituted validamine type glycosidase inhibitors. Carbohydr Res 2017; 440-441:1-9. [PMID: 28135569 DOI: 10.1016/j.carres.2017.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 11/30/2022]
Abstract
A series of N-alkyl derivatives of the D-galactosidase inhibitor 1,4-di-epi-validamine featuring lipophilic substituents at position C-5a was prepared and screened for their glycosidase inhibitory properties. Products turned out selective for β-galactosidases as well as β-glucosidases.
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Affiliation(s)
- Michael Schalli
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010, Graz, Austria
| | - Andreas Wolfsgruber
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010, Graz, Austria
| | - Andres Gonzalez Santana
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Christina Tysoe
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Roland Fischer
- Institute of Inorganic Chemistry Graz University of Technology, Stremayrgasse 9, A-8010, Graz, Austria
| | - Arnold E Stütz
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010, Graz, Austria.
| | - Martin Thonhofer
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010, Graz, Austria
| | - Stephen G Withers
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
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37
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Cao YY, Yang JF, Liu TY, Su ZF, Zhu FY, Chen MX, Fan T, Ye NH, Feng Z, Wang LJ, Hao GF, Zhang J, Liu YG. A Phylogenetically Informed Comparison of GH1 Hydrolases between Arabidopsis and Rice Response to Stressors. FRONTIERS IN PLANT SCIENCE 2017; 8:350. [PMID: 28392792 PMCID: PMC5364172 DOI: 10.3389/fpls.2017.00350] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/28/2017] [Indexed: 05/21/2023]
Abstract
Glycoside hydrolases Family 1 (GH1) comprises enzymes that can hydrolyze β-O-glycosidic bond from a carbohydrate moiety. The plant GH1 hydrolases participate in a number of developmental processes and stress responses, including cell wall modification, plant hormone activation or deactivation and herbivore resistance. A large number of members has been observed in this family, suggesting their potential redundant functions in various biological processes. In this study, we have used 304 sequences of plant GH1 hydrolases to study the evolution of this gene family in plant lineage. Gene duplication was found to be a common phenomenon in this gene family. Although many members of GH1 hydrolases showed a high degree of similarity in Arabidopsis and rice, they showed substantial tissue specificity and differential responses to various stress treatments. This differential regulation implies each enzyme may play a distinct role in plants. Furthermore, some of salt-responsive Arabidopsis GH1 hydrolases were selected to test their genetic involvement in salt responses. The knockout mutants of AtBGLU1 and AtBGLU19 were observed to be less-sensitive during NaCl treatment in comparison to the wild type seedlings, indicating their participation in salt stress response. In summary, Arabidopsis and rice GH1 glycoside hydrolases showed distinct features in their evolutionary path, transcriptional regulation and genetic functions.
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Affiliation(s)
- Yun-Ying Cao
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural UniversityTaian, China
- College of Life Sciences, Nantong UniversityNantong, China
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, Nantong UniversityNantong, China
| | - Jing-Fang Yang
- College of Chemistry, Central China Normal UniversityWuhan, China
| | - Tie-Yuan Liu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongShatin, Hong Kong
| | - Zhen-Feng Su
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural UniversityTaian, China
| | - Fu-Yuan Zhu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongShatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong KongShenzhen, China
| | - Mo-Xian Chen
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongShatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong KongShenzhen, China
| | - Tao Fan
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural UniversityTaian, China
| | - Neng-Hui Ye
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongShatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong KongShenzhen, China
| | - Zhen Feng
- Jiangsu Entry-exit Inspection And Quarantine BureauNanjing, China
| | - Ling-Juan Wang
- College of Life Sciences, Nantong UniversityNantong, China
| | - Ge-Fei Hao
- College of Chemistry, Central China Normal UniversityWuhan, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongShatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong KongShenzhen, China
- *Correspondence: Jianhua Zhang
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural UniversityTaian, China
- Ying-Gao Liu
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38
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Abstract
Activity-based protein profiling (ABPP) has emerged as a powerful proteomic approach to study the active proteins in their native environment by using chemical probes that label active site residues in proteins. Traditionally, ABPP is classified as either comparative or competitive ABPP. In this protocol, we describe a simple method called convolution ABPP, which takes benefit from both the competitive and comparative ABPP. Convolution ABPP allows one to detect if a reduced signal observed during comparative ABPP could be due to the presence of inhibitors. In convolution ABPP, the proteomes are analyzed by comparing labeling intensities in two mixed proteomes that were labeled either before or after mixing. A reduction of labeling in the mix-and-label sample when compared to the label-and-mix sample indicates the presence of an inhibitor excess in one of the proteomes. This method is broadly applicable to detect inhibitors in proteomes against any proteome containing protein activities of interest. As a proof of concept, we applied convolution ABPP to analyze secreted proteomes from Pseudomonas syringae-infected Nicotiana benthamiana leaves to display the presence of a beta-galactosidase inhibitor.
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Affiliation(s)
- Balakumaran Chandrasekar
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Tram Ngoc Hong
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany.
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Strmiskova M, Desrochers GF, Shaw TA, Powdrill MH, Lafreniere MA, Pezacki JP. Chemical Methods for Probing Virus-Host Proteomic Interactions. ACS Infect Dis 2016; 2:773-786. [PMID: 27933785 DOI: 10.1021/acsinfecdis.6b00084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interactions between host and pathogen proteins constitute an important aspect of both infectivity and the host immune response. Different viruses have evolved complex mechanisms to hijack host-cell machinery and metabolic pathways to redirect resources and energy flow toward viral propagation. These interactions are often critical to the virus, and thus understanding these interactions at a molecular level gives rise to opportunities to develop novel antiviral strategies for therapeutic intervention. This review summarizes current advances in chemoproteomic methods for studying these molecular altercations between different viruses and their hosts.
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Affiliation(s)
- Miroslava Strmiskova
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Matthew A. Lafreniere
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
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40
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Abstract
Beta galactosidases (BGALs) are glycosyl hydrolases that remove terminal β-D-galactosyl residues from β-D-galactosides. There are 17 predicted BGAL genes in the genomes of both Arabidopsis (BGAL1-17) and tomato (TBG1-17). All tested BGALs have BGAL activity but their distinct expression profiles and ancient phylogenetic separation indicates that these enzymes fulfil diverse, non-redundant roles in plant biology. The majority of these BGALs are predicted to have signal peptide and thought to act during cell wall-related biological processes. Interestingly, deletion of BGAL6 and BGAL10 in Arabidopsis causes reduced mucilage release during seed imbibition and shorter siliques respectively, whereas TBG4 depletion by RNAi decreases in fruit softening in tomato. The majority of plant BGALs remain to be characterized.
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41
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Shindo T, Kaschani F, Yang F, Kovács J, Tian F, Kourelis J, Hong TN, Colby T, Shabab M, Chawla R, Kumari S, Ilyas M, Hörger AC, Alfano JR, van der Hoorn RAL. Screen of Non-annotated Small Secreted Proteins of Pseudomonas syringae Reveals a Virulence Factor That Inhibits Tomato Immune Proteases. PLoS Pathog 2016; 12:e1005874. [PMID: 27603016 PMCID: PMC5014320 DOI: 10.1371/journal.ppat.1005874] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/15/2016] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas syringae pv. tomato DC3000 (PtoDC3000) is an extracellular model plant pathogen, yet its potential to produce secreted effectors that manipulate the apoplast has been under investigated. Here we identified 131 candidate small, secreted, non-annotated proteins from the PtoDC3000 genome, most of which are common to Pseudomonas species and potentially expressed during apoplastic colonization. We produced 43 of these proteins through a custom-made gateway-compatible expression system for extracellular bacterial proteins, and screened them for their ability to inhibit the secreted immune protease C14 of tomato using competitive activity-based protein profiling. This screen revealed C14-inhibiting protein-1 (Cip1), which contains motifs of the chagasin-like protease inhibitors. Cip1 mutants are less virulent on tomato, demonstrating the importance of this effector in apoplastic immunity. Cip1 also inhibits immune protease Pip1, which is known to suppress PtoDC3000 infection, but has a lower affinity for its close homolog Rcr3, explaining why this protein is not recognized in tomato plants carrying the Cf-2 resistance gene, which uses Rcr3 as a co-receptor to detect pathogen-derived protease inhibitors. Thus, this approach uncovered a protease inhibitor of P. syringae, indicating that also P. syringae secretes effectors that selectively target apoplastic host proteases of tomato, similar to tomato pathogenic fungi, oomycetes and nematodes.
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Affiliation(s)
- Takayuki Shindo
- Plant Chemetics lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Farnusch Kaschani
- Plant Chemetics lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Fan Yang
- Center for Plant Science Innovation and the Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Judit Kovács
- Department of Plant Biology, University of Szeged, Szeged, Hungary
| | - Fang Tian
- Center for Plant Science Innovation and the Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jiorgos Kourelis
- Plant Chemetics lab, Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Tram Ngoc Hong
- Plant Chemetics lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Plant Chemetics lab, Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Tom Colby
- Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mohammed Shabab
- Plant Chemetics lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rohini Chawla
- Plant Chemetics lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Selva Kumari
- Plant Chemetics lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Muhammad Ilyas
- Plant Chemetics lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anja C. Hörger
- Plant Chemetics lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - James R. Alfano
- Center for Plant Science Innovation and the Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Renier A. L. van der Hoorn
- Plant Chemetics lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Plant Chemetics lab, Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- * E-mail:
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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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43
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Twelve ways to confirm targets of activity-based probes in plants. Bioorg Med Chem 2016; 24:3304-11. [DOI: 10.1016/j.bmc.2016.05.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 05/14/2016] [Accepted: 05/19/2016] [Indexed: 11/19/2022]
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Rosnow JJ, Anderson LN, Nair RN, Baker ES, Wright AT. Profiling microbial lignocellulose degradation and utilization by emergent omics technologies. Crit Rev Biotechnol 2016; 37:626-640. [PMID: 27439855 DOI: 10.1080/07388551.2016.1209158] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The use of plant materials to generate renewable biofuels and other high-value chemicals is the sustainable and preferable option, but will require considerable improvements to increase the rate and efficiency of lignocellulose depolymerization. This review highlights novel and emerging technologies that are being developed and deployed to characterize the process of lignocellulose degradation. The review will also illustrate how microbial communities deconstruct and metabolize lignocellulose by identifying the necessary genes and enzyme activities along with the reaction products. These technologies include multi-omic measurements, cell sorting and isolation, nuclear magnetic resonance spectroscopy (NMR), activity-based protein profiling, and direct measurement of enzyme activity. The recalcitrant nature of lignocellulose necessitates the need to characterize the methods microbes employ to deconstruct lignocellulose to inform new strategies on how to greatly improve biofuel conversion processes. New technologies are yielding important insights into microbial functions and strategies employed to degrade lignocellulose, providing a mechanistic blueprint in order to advance biofuel production.
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Affiliation(s)
- Joshua J Rosnow
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Lindsey N Anderson
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Reji N Nair
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Erin S Baker
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Aaron T Wright
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
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45
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Daneri-Castro SN, Svensson B, Roberts TH. Barley germination: Spatio-temporal considerations for designing and interpreting ‘omics’ experiments. J Cereal Sci 2016. [DOI: 10.1016/j.jcs.2016.05.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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46
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Poret M, Chandrasekar B, van der Hoorn RAL, Avice JC. Characterization of senescence-associated protease activities involved in the efficient protein remobilization during leaf senescence of winter oilseed rape. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 246:139-153. [PMID: 26993244 DOI: 10.1016/j.plantsci.2016.02.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/08/2016] [Accepted: 02/11/2016] [Indexed: 06/05/2023]
Abstract
Oilseed rape (Brassica napus L.) is a crop plant characterized by a poor nitrogen (N) use efficiency that is mainly due to low N remobilization efficiency during the sequential leaf senescence of the vegetative stage. As a high leaf N remobilization efficiency was strongly linked to a high remobilization of proteins during leaf senescence of rapeseed, our objective was to identify senescence-associated protease activities implicated in the protein degradation. To reach this goal, leaf senescence processes and protease activities were investigated in a mature leaf becoming senescent in plants subjected to ample or low nitrate supply. The characterization of protease activities was performed by using in vitro analysis of RuBisCO degradation with or without inhibitors of specific protease classes followed by a protease activity profiling using activity-dependent probes. As expected, the mature leaf became senescent regardless of the nitrate treatment, and nitrate limitation enhanced the senescence processes associated with an enhanced degradation of soluble proteins. The characterization of protease activities revealed that: (i) aspartic proteases and the proteasome were active during senescence regardless of nitrate supply, and (ii) the activities of serine proteases and particularly cysteine proteases (Papain-like Cys proteases and vacuolar processing enzymes) increased when protein remobilization associated with senescence was accelerated by nitrate limitation. Short statement: Serine and particularly cysteine proteases (both PLCPs and VPEs) seem to play a crucial role in the efficient protein remobilization when leaf senescence of oilseed rape was accelerated by nitrate limitation.
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Affiliation(s)
- Marine Poret
- Université de Caen Normandie, F-14032 Caen, France; UCBN, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France; INRA, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France.
| | - Balakumaran Chandrasekar
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom; The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany.
| | - 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.
| | - Jean-Christophe Avice
- Université de Caen Normandie, F-14032 Caen, France; UCBN, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France; INRA, UMR INRA-UCBN 950 Ecophysiologie Végétale, Agronomie & Nutritions N.C.S., F-14032 Caen, France.
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Morimoto K, van der Hoorn RAL. The Increasing Impact of Activity-Based Protein Profiling in Plant Science. PLANT & CELL PHYSIOLOGY 2016; 57:446-61. [PMID: 26872839 DOI: 10.1093/pcp/pcw003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/28/2015] [Indexed: 05/08/2023]
Abstract
The active proteome dictates plant physiology. Yet, active proteins are difficult to predict based on transcript or protein levels, because protein activities are regulated post-translationally in their microenvironments. Over the past 10 years, activity-based protein profiling (ABPP) is increasingly used in plant science. ABPP monitors the activities of hundreds of plant proteins using tagged chemical probes that react with the active site of proteins in a mechanism-dependent manner. Since labeling is covalent and irreversible, labeled proteins can be detected and identified on protein gels and by mass spectrometry using tagged fluorophores and/or biotin. Here, we discuss general concepts, approaches and practical considerations of ABPP, before we summarize the discoveries made using 40 validated probes representing 14 chemotypes that can monitor the active state of >4,500 plant proteins. These discoveries and new opportunities indicate that this emerging functional proteomic technology is a powerful discovery tool that will have an increasing impact on plant science.
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Affiliation(s)
- Kyoko Morimoto
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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Iminosugar inhibitors of carbohydrate-active enzymes that underpin cereal grain germination and endosperm metabolism. Biochem Soc Trans 2016; 44:159-65. [PMID: 26862201 PMCID: PMC4747157 DOI: 10.1042/bst20150222] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Starch is a major energy store in plants. It provides most of the calories in the human diet and, as a bulk commodity, it is used across broad industry sectors. Starch synthesis and degradation are not fully understood, owing to challenging biochemistry at the liquid/solid interface and relatively limited knowledge about the nature and control of starch degradation in plants. Increased societal and commercial demand for enhanced yield and quality in starch crops requires a better understanding of starch metabolism as a whole. Here we review recent advances in understanding the roles of carbohydrate-active enzymes in starch degradation in cereal grains through complementary chemical and molecular genetics. These approaches have allowed us to start dissecting aspects of starch degradation and the interplay with cell-wall polysaccharide hydrolysis during germination. With a view to improving and diversifying the properties and uses of cereal grains, it is possible that starch degradation may be amenable to manipulation through genetic or chemical intervention at the level of cell wall metabolism, rather than simply in the starch degradation pathway per se.
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Jiang J, Beenakker TJM, Kallemeijn WW, van der Marel GA, van den Elst H, Codée JDC, Aerts JMFG, Overkleeft HS. Comparing CyclophellitolN-Alkyl andN-Acyl Cyclophellitol Aziridines as Activity-Based Glycosidase Probes. Chemistry 2015; 21:10861-9. [DOI: 10.1002/chem.201501313] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Indexed: 11/12/2022]
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