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Li W, Yan J, Zhang Y, Zhang F, Guan Z, Yao Y, Chang Y, Tu H, Li X, Wang H, Xiong H, Lai X, Yin P, Xiong L. Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice. NATURE PLANTS 2023; 9:1130-1142. [PMID: 37349549 DOI: 10.1038/s41477-023-01449-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 05/24/2023] [Indexed: 06/24/2023]
Abstract
NARROW LEAF 1 (NAL1) is a breeding-valuable pleiotropic gene that affects multiple agronomic traits in rice, although the molecular mechanism is largely unclear. Here, we report that NAL1 is a serine protease and displays a novel hexameric structure consisting of two ATP-mediated doughnut-shaped trimeric complexes. Moreover, we identified TOPLESS-related corepressor OsTPR2 involved in multiple growth and development processes as the substrate of NAL1. We found that NAL1 degraded OsTPR2, thus modulating the expression of downstream genes related to hormone signalling pathways, eventually achieving its pleiotropic physiological function. An elite allele, NAL1A, which may have originated from wild rice, could increase grain yield. Furthermore, the NAL1 homologues in different crops have a similar pleiotropic function to NAL1. Our study uncovers a NAL1-OsTPR2 regulatory module and provides gene resources for the design of high-yield crops.
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Affiliation(s)
- Wenjing Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Junjie Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Fei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yilong Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Chang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Huaijun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haiyan Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuelei Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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Rojas BE, Hartman MD, Figueroa CM, Iglesias AA. Proteolytic cleavage of Arabidopsis thaliana phosphoenolpyruvate carboxykinase-1 modifies its allosteric regulation. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2514-2524. [PMID: 33315117 DOI: 10.1093/jxb/eraa583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Phosphoenolpyruvate carboxykinase (PEPCK) plays a crucial role in gluconeogenesis. In this work, we analyze the proteolysis of Arabidopsis thaliana PEPCK1 (AthPEPCK1) in germinating seedlings. We found that the amount of AthPEPCK1 protein peaks at 24-48 h post-imbibition. Concomitantly, we observed shorter versions of AthPEPCK1, putatively generated by metacaspase-9 (AthMC9). To study the impact of AthMC9 cleavage on the kinetic and regulatory properties of AthPEPCK1, we produced truncated mutants based on the reported AthMC9 cleavage sites. The Δ19 and Δ101 truncated mutants of AthPEPCK1 showed similar kinetic parameters and the same quaternary structure as the wild type. However, activation by malate and inhibition by glucose 6-phosphate were abolished in the Δ101 mutant. We propose that proteolysis of AthPEPCK1 in germinating seedlings operates as a mechanism to adapt the sensitivity to allosteric regulation during the sink-to-source transition.
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Affiliation(s)
- Bruno E Rojas
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Matías D Hartman
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
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Catellani M, Lico C, Cerasi M, Massa S, Bromuro C, Torosantucci A, Benvenuto E, Capodicasa C. Optimised production of an anti-fungal antibody in Solanaceae hairy roots to develop new formulations against Candida albicans. BMC Biotechnol 2020; 20:15. [PMID: 32164664 PMCID: PMC7069033 DOI: 10.1186/s12896-020-00607-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 02/24/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Infections caused by fungi are often refractory to conventional therapies and urgently require the development of novel options, such as immunotherapy. To produce therapeutic antibodies, a plant-based expression platform is an attractive biotechnological strategy compared to mammalian cell cultures. In addition to whole plants, hairy roots (HR) cultures can be used, representing an expression system easy to build up, with indefinite growth while handled under containment conditions. RESULTS In this study the production in HR of a recombinant antibody, proved to be a good candidate for human immunotherapy against fungal infections, is reported. Expression and secretion of this antibody, in an engineered single chain (scFvFc) format, by HR from Nicotiana benthamiana and Solanum lycopersicum have been evaluated with the aim of directly using the deriving extract or culture medium against pathogenic fungi. Although both Solanaceae HR showed good expression levels (up to 68 mg/kg), an optimization of rhizosecretion was only obtained for N. benthamiana HR. A preliminary assessment to explain this result highlighted the fact that not only the presence of proteases, but also the chemical characteristics of the growth medium, can influence antibody yield, with implications on recombinant protein production in HR. Finally, the antifungal activity of scFvFc 2G8 antibody produced in N. benthamiana HR was evaluated in Candida albicans growth inhibition assays, evidencing encouraging results. CONCLUSIONS Production of this anti-fungal antibody in HR of N. benthamiana and S. lycopersicum elucidated factors affecting pharming in this system and allowed to obtain promising ready-to-use immunotherapeutics against C. albicans.
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Affiliation(s)
- Marcello Catellani
- Department of Sustainability, Laboratory Biotechnologies, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Chiara Lico
- Department of Sustainability, Laboratory Biotechnologies, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Mauro Cerasi
- Department of Sustainability, Laboratory Biotechnologies, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Silvia Massa
- Department of Sustainability, Laboratory Biotechnologies, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Carla Bromuro
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonella Torosantucci
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Eugenio Benvenuto
- Department of Sustainability, Laboratory Biotechnologies, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Cristina Capodicasa
- Department of Sustainability, Laboratory Biotechnologies, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
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Holdsworth MJ, Vicente J, Sharma G, Abbas M, Zubrycka A. The plant N-degron pathways of ubiquitin-mediated proteolysis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:70-89. [PMID: 31638740 DOI: 10.1111/jipb.12882] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/20/2019] [Indexed: 05/29/2023]
Abstract
The amino-terminal residue of a protein (or amino-terminus of a peptide following protease cleavage) can be an important determinant of its stability, through the Ubiquitin Proteasome System associated N-degron pathways. Plants contain a unique combination of N-degron pathways (previously called the N-end rule pathways) E3 ligases, PROTEOLYSIS (PRT)6 and PRT1, recognizing non-overlapping sets of amino-terminal residues, and others remain to be identified. Although only very few substrates of PRT1 or PRT6 have been identified, substrates of the oxygen and nitric oxide sensing branch of the PRT6 N-degron pathway include key nuclear-located transcription factors (ETHYLENE RESPONSE FACTOR VIIs and LITTLE ZIPPER 2) and the histone-modifying Polycomb Repressive Complex 2 component VERNALIZATION 2. In response to reduced oxygen or nitric oxide levels (and other mechanisms that reduce pathway activity) these stabilized substrates regulate diverse aspects of growth and development, including response to flooding, salinity, vernalization (cold-induced flowering) and shoot apical meristem function. The N-degron pathways show great promise for use in the improvement of crop performance and for biotechnological applications. Upstream proteases, components of the different pathways and associated substrates still remain to be identified and characterized to fully appreciate how regulation of protein stability through the amino-terminal residue impacts plant biology.
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Affiliation(s)
| | - Jorge Vicente
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Gunjan Sharma
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Mohamad Abbas
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Agata Zubrycka
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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Stührwohldt N, Schaller A. Regulation of plant peptide hormones and growth factors by post-translational modification. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21 Suppl 1:49-63. [PMID: 30047205 DOI: 10.1111/plb.12881] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/20/2018] [Indexed: 05/24/2023]
Abstract
The number, diversity and significance of peptides as regulators of cellular differentiation, growth, development and defence of plants has long been underestimated. Peptides have now emerged as an important class of signals for cell-to-cell communication over short distances, and also for long-range signalling. We refer to these signalling molecules as peptide growth factors and peptide hormones, respectively. As compared to remarkable progress with respect to the mechanisms of peptide perception and signal transduction, the biogenesis of signalling peptides is still in its infancy. This review focuses on the biogenesis and activity of small post-translationally modified peptides. These peptides are derived from inactive pre-pro-peptides of approximately 70-120 amino acids. Multiple post-translational modifications (PTMs) may be required for peptide maturation and activation, including proteolytic processing, tyrosine sulfation, proline hydroxylation and hydroxyproline glycosylation. While many of the enzymes responsible for these modifications have been identified, their impact on peptide activity and signalling is not fully understood. These PTMs may or may not be required for bioactivity, they may inactivate the peptide or modify its signalling specificity, they may affect peptide stability or targeting, or its binding affinity with the receptor. In the present review, we will first introduce the peptides that undergo PTMs and for which these PTMs were shown to be functionally relevant. We will then discuss the different types of PTMs and the impact they have on peptide activity and plant growth and development. We conclude with an outlook on the open questions that need to be addressed in future research.
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Affiliation(s)
- N Stührwohldt
- Institute of Plant Physiology and Biotechnology, University of Hohenheim, Stuttgart, Germany
| | - A Schaller
- Institute of Plant Physiology and Biotechnology, University of Hohenheim, Stuttgart, Germany
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Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL. N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. THE NEW PHYTOLOGIST 2018; 218:1106-1126. [PMID: 29168982 PMCID: PMC5947142 DOI: 10.1111/nph.14909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/23/2017] [Indexed: 05/04/2023]
Abstract
The N-end rule pathway of targeted protein degradation is an important regulator of diverse processes in plants but detailed knowledge regarding its influence on the proteome is lacking. To investigate the impact of the Arg/N-end rule pathway on the proteome of etiolated seedlings, we used terminal amine isotopic labelling of substrates with tandem mass tags (TMT-TAILS) for relative quantification of N-terminal peptides in prt6, an Arabidopsis thaliana N-end rule mutant lacking the E3 ligase PROTEOLYSIS6 (PRT6). TMT-TAILS identified over 4000 unique N-terminal peptides representing c. 2000 protein groups. Forty-five protein groups exhibited significantly increased N-terminal peptide abundance in prt6 seedlings, including cruciferins, major seed storage proteins, which were regulated by Group VII Ethylene Response Factor (ERFVII) transcription factors, known substrates of PRT6. Mobilisation of endosperm α-cruciferin was delayed in prt6 seedlings. N-termini of several proteases were downregulated in prt6, including RD21A. RD21A transcript, protein and activity levels were downregulated in a largely ERFVII-dependent manner. By contrast, cathepsin B3 protein and activity were upregulated by ERFVIIs independent of transcript. We propose that the PRT6 branch of the pathway regulates protease activities in a complex manner and optimises storage reserve mobilisation in the transition from seed to seedling via control of ERFVII action.
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Affiliation(s)
- Hongtao Zhang
- Plant Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
| | - Lucy Gannon
- Plant Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
| | - Kirsty L. Hassall
- Computational and Analytical Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
| | - Michael J. Deery
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
| | - Daniel J. Gibbs
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | | | | | - Kathryn S. Lilley
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
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Genome-wide identification of barley MCs (metacaspases) and their possible roles in boron-induced programmed cell death. Mol Biol Rep 2018; 45:211-225. [DOI: 10.1007/s11033-018-4154-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/30/2018] [Indexed: 11/25/2022]
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8
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Khan N, Yamaguchi S, Katsube-Tanaka T. Possible cleavage sites of glutelin partial degradation confirmed by immunological analysis in globulin-less mutants of rice (Oryza sativa L.). Electrophoresis 2017; 38:2622-2630. [PMID: 28683176 DOI: 10.1002/elps.201700195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/14/2017] [Accepted: 06/27/2017] [Indexed: 11/11/2022]
Abstract
Proteolytic cleavage or partial degradation of proteins is one of the important post-translational modifications for various biological processes, but it is difficult to analyze. Previously, we demonstrated that some subunits of the major rice (Oryza sativa L.) seed storage protein glutelin are partially degraded to produce newly identified polypeptides X1-X5 in mutants in which another major seed storage protein globulin is absent. In this study, the new polypeptides X3 and X4/X5 were immunologically confirmed to be derived from GluA3 and GluA1/GluA2 subunits, respectively. Additionally, the new polypeptides X1 and X2 were at least in part the α polypeptides of the GluB4 subunit partially degraded at the C-terminus. Simulated 2D-PAGE migration patterns of intact and partially degraded α polypeptides based on the calculation of their MWs and pIs enabled us to narrow or predict the possible locations of cleavage sites. The predicted cleavage sites were also verified by the comparison of 2D-PAGE patterns between seed-extracted and E. coli-expressed proteins of the intact and truncated α polypeptides. The results and methodologies demonstrated here would be useful for analyses of partial degradation of proteins and the structure-function relationships of rice seed protein bodies.
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Affiliation(s)
- Nadar Khan
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto, Japan.,Plant Genetic Resources Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Satoru Yamaguchi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto, Japan
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Havé M, Marmagne A, Chardon F, Masclaux-Daubresse C. Nitrogen remobilization during leaf senescence: lessons from Arabidopsis to crops. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2513-2529. [PMID: 27707774 DOI: 10.1093/jxb/erw365] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
As a result of climate changes, land use and agriculture have to adapt to new demands. Agriculture is responsible for a large part of the greenhouse gas (GHG) emissions that have to be urgently reduced in order to protect the environment. At the same time, agriculture has to cope with the challenges of sustainably feeding a growing world population. Reducing the use of the ammonia-nitrate fertilizers that are responsible for a large part of the GHGs released and that have a negative impact on carbon balance is one of the objectives of precision agriculture. One way to reduce N fertilizers without dramatically affecting grain yields is to improve the nitrogen recycling and remobilization performances of plants. Mechanisms involved in nitrogen recycling, such as autophagy, are essential for nutrient remobilization at the whole-plant level and for seed quality. Studies on leaf senescence and nutrient recycling provide new perspectives for improvement. The aim of this review is to give an overview of the mechanisms involved in nitrogen recycling and remobilization during leaf senescence and to present the different approaches undertaken to improve nitrogen remobilization efficiency using both model plants and crop species.
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Affiliation(s)
- Marien Havé
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Anne Marmagne
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Fabien Chardon
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Céline Masclaux-Daubresse
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
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10
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Ghorbani S, Hoogewijs K, Pečenková T, Fernandez A, Inzé A, Eeckhout D, Kawa D, De Jaeger G, Beeckman T, Madder A, Van Breusegem F, Hilson P. The SBT6.1 subtilase processes the GOLVEN1 peptide controlling cell elongation. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4877-87. [PMID: 27315833 PMCID: PMC4983112 DOI: 10.1093/jxb/erw241] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The GOLVEN (GLV) gene family encode small secreted peptides involved in important plant developmental programs. Little is known about the factors required for the production of the mature bioactive GLV peptides. Through a genetic suppressor screen in Arabidopsis thaliana, two related subtilase genes, AtSBT6.1 and AtSBT6.2, were identified that are necessary for GLV1 activity. Root and hypocotyl GLV1 overexpression phenotypes were suppressed by mutations in either of the subtilase genes. Synthetic GLV-derived peptides were cleaved in vitro by the affinity-purified SBT6.1 catalytic enzyme, confirming that the GLV1 precursor is a direct subtilase substrate, and the elimination of the in vitro subtilase recognition sites through alanine substitution suppressed the GLV1 gain-of-function phenotype in vivo Furthermore, the protease inhibitor Serpin1 bound to SBT6.1 and inhibited the cleavage of GLV1 precursors by the protease. GLV1 and its homolog GLV2 were expressed in the outer cell layers of the hypocotyl, preferentially in regions of rapid cell elongation. In agreement with the SBT6 role in GLV precursor processing, both null mutants for sbt6.1 and sbt6.2 and the Serpin1 overexpression plants had shorter hypocotyls. The biosynthesis of the GLV signaling peptides required subtilase activity and might be regulated by specific protease inhibitors. The data fit with a model in which the GLV1 signaling pathway participates in the regulation of hypocotyl cell elongation, is controlled by SBT6 subtilases, and is modulated locally by the Serpin1 protease inhibitor.
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Affiliation(s)
- Sarieh Ghorbani
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Kurt Hoogewijs
- Department of Organic Chemistry, Ghent University, B-9000 Ghent, Belgium
| | - Tamara Pečenková
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Ana Fernandez
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Annelies Inzé
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Dorota Kawa
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Annemieke Madder
- Department of Organic Chemistry, Ghent University, B-9000 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Pierre Hilson
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Saclay Plant Science, F-78026 Versailles, France
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11
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De Coninck B, De Smet I. Plant peptides - taking them to the next level. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4791-5. [PMID: 27521600 PMCID: PMC5854176 DOI: 10.1093/jxb/erw309] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Barbara De Coninck
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium; Department of Plant Systems Biology, VIB, Ghent, Belgium
- Correspondence: and
| | - Ive De Smet
- Department of Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Correspondence: and
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DEG9, a serine protease, modulates cytokinin and light signaling by regulating the level of ARABIDOPSIS RESPONSE REGULATOR 4. Proc Natl Acad Sci U S A 2016; 113:E3568-76. [PMID: 27274065 DOI: 10.1073/pnas.1601724113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytokinin is an essential phytohormone that controls various biological processes in plants. A number of response regulators are known to be important for cytokinin signal transduction. ARABIDOPSIS RESPONSE REGULATOR 4 (ARR4) mediates the cross-talk between light and cytokinin signaling through modulation of the activity of phytochrome B. However, the mechanism that regulates the activity and stability of ARR4 is unknown. Here we identify an ATP-independent serine protease, degradation of periplasmic proteins 9 (DEG9), which localizes to the nucleus and regulates the stability of ARR4. Biochemical evidence shows that DEG9 interacts with ARR4, thereby targeting ARR4 for degradation, which suggests that DEG9 regulates the stability of ARR4. Moreover, genetic evidence shows that DEG9 acts upstream of ARR4 and regulates the activity of ARR4 in cytokinin and light-signaling pathways. This study thus identifies a role for a ubiquitin-independent selective protein proteolysis in the regulation of the stability of plant signaling components.
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Canut H, Albenne C, Jamet E. Post-translational modifications of plant cell wall proteins and peptides: A survey from a proteomics point of view. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:983-90. [PMID: 26945515 DOI: 10.1016/j.bbapap.2016.02.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/12/2016] [Accepted: 02/24/2016] [Indexed: 12/21/2022]
Abstract
Plant cell wall proteins (CWPs) and peptides are important players in cell walls contributing to their assembly and their remodeling during development and in response to environmental constraints. Since the rise of proteomics technologies at the beginning of the 2000's, the knowledge of CWPs has greatly increased leading to the discovery of new CWP families and to the description of the cell wall proteomes of different organs of many plants. Conversely, cell wall peptidomics data are still lacking. In addition to the identification of CWPs and peptides by mass spectrometry (MS) and bioinformatics, proteomics has allowed to describe their post-translational modifications (PTMs). At present, the best known PTMs consist in proteolytic cleavage, N-glycosylation, hydroxylation of P residues into hydroxyproline residues (O), O-glycosylation and glypiation. In this review, the methods allowing the capture of the modified proteins based on the specific properties of their PTMs as well as the MS technologies used for their characterization are briefly described. A focus is done on proteolytic cleavage leading to protein maturation or release of signaling peptides and on O-glycosylation. Some new technologies, like top-down proteomics and terminomics, are described. They aim at a finer description of proteoforms resulting from PTMs or degradation mechanisms. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Hervé Canut
- Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Cécile Albenne
- Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Elisabeth Jamet
- Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France.
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14
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Walton A, Tsiatsiani L, Jacques S, Stes E, Messens J, Van Breusegem F, Goormachtig S, Gevaert K. Diagonal chromatography to study plant protein modifications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:945-51. [PMID: 26772901 DOI: 10.1016/j.bbapap.2016.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/01/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022]
Abstract
An interesting asset of diagonal chromatography, which we have introduced for contemporary proteome research, is its high versatility concerning proteomic applications. Indeed, the peptide modification or sorting step that is required between consecutive peptide separations can easily be altered and thereby allows for the enrichment of specific, though different types of peptides. Here, we focus on the application of diagonal chromatography for the study of modifications of plant proteins. In particular, we show how diagonal chromatography allows for studying proteins processed by proteases, protein ubiquitination, and the oxidation of protein-bound methionines. We discuss the actual sorting steps needed for each of these applications and the obtained results. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Alan Walton
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Liana Tsiatsiani
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Silke Jacques
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Elisabeth Stes
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium.
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15
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Poncet V, Scutt C, Tournebize R, Villegente M, Cueff G, Rajjou L, Balliau T, Zivy M, Fogliani B, Job C, de Kochko A, Sarramegna-Burtet V, Job D. The Amborella vacuolar processing enzyme family. FRONTIERS IN PLANT SCIENCE 2015; 6:618. [PMID: 26347753 PMCID: PMC4544213 DOI: 10.3389/fpls.2015.00618] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/27/2015] [Indexed: 05/30/2023]
Abstract
Most vacuolar proteins are synthesized on rough endoplasmic reticulum as proprotein precursors and then transported to the vacuoles, where they are converted into their respective mature forms by vacuolar processing enzymes (VPEs). In the case of the seed storage proteins, this process is of major importance, as it conditions the establishment of vigorous seedlings. Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013). In the present study, proteomic and genomic approaches were used to characterize the VPE family in this species. Three genes were found to encode VPEs in the Amborella's genome. Phylogenetic analyses showed that the Amborella sequences grouped within two major clades of angiosperm VPEs, indicating that the duplication that generated the ancestors of these clades occurred before the most recent common ancestor of living angiosperms. A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella. An analysis of natural genetic variation for each of the three Amborella VPE genes revealed the absence of selective forces acting on intronic and exonic single-nucleotide polymorphisms among several natural Amborella populations in New Caledonia.
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Affiliation(s)
- Valérie Poncet
- Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des PlantesMontpellier, France
| | - Charlie Scutt
- Laboratoire Reproduction et Développement des Plantes, UMR 5667, Ecole Normale Supérieure de LyonLyon, France
| | - Rémi Tournebize
- Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des PlantesMontpellier, France
| | - Matthieu Villegente
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-CalédonieNouméa, New Caledonia
| | - Gwendal Cueff
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, UMR 1318 Institut National de la Recherche Agronomique/AgroParisTech, ERL Centre National de la Recherche Scientifique 3559, Laboratoire d'Excellence “Saclay Plant Sciences” (LabEx SPS), RD10Versailles, France
- AgroParisTech, Chaire de Physiologie VégétaleParis, France
| | - Loïc Rajjou
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, UMR 1318 Institut National de la Recherche Agronomique/AgroParisTech, ERL Centre National de la Recherche Scientifique 3559, Laboratoire d'Excellence “Saclay Plant Sciences” (LabEx SPS), RD10Versailles, France
- AgroParisTech, Chaire de Physiologie VégétaleParis, France
| | - Thierry Balliau
- Institut National de la Recherche Agronomique, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Institut National de la Recherche Agronomique/Université Paris-Sud/Centre National de la Recherche Scientifique/AgroParisTech, UMR 0320/UMR 8120 Génétique Quantitative et Evolution – Le MoulonGif-sur-Yvette, France
| | - Michel Zivy
- Institut National de la Recherche Agronomique, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Institut National de la Recherche Agronomique/Université Paris-Sud/Centre National de la Recherche Scientifique/AgroParisTech, UMR 0320/UMR 8120 Génétique Quantitative et Evolution – Le MoulonGif-sur-Yvette, France
| | - Bruno Fogliani
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-CalédonieNouméa, New Caledonia
- Institut Agronomique Néo-Calédonien, Diversités Biologique et Fonctionnelle des Ecosystèmes TerrestresPaïta, New Caledonia
| | - Claudette Job
- UMR 5240 Laboratoire Mixte Centre National de la Recherche Scientifique/Institut National des Sciences Appliquées/Université Claude Bernard Lyon 1/Bayer CropScienceLyon, France
| | - Alexandre de Kochko
- Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des PlantesMontpellier, France
| | - Valérie Sarramegna-Burtet
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-CalédonieNouméa, New Caledonia
| | - Dominique Job
- AgroParisTech, Chaire de Physiologie VégétaleParis, France
- UMR 5240 Laboratoire Mixte Centre National de la Recherche Scientifique/Institut National des Sciences Appliquées/Université Claude Bernard Lyon 1/Bayer CropScienceLyon, France
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16
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Lallemand J, Bouché F, Desiron C, Stautemas J, de Lemos Esteves F, Périlleux C, Tocquin P. Extracellular peptidase hunting for improvement of protein production in plant cells and roots. FRONTIERS IN PLANT SCIENCE 2015; 6:37. [PMID: 25705212 PMCID: PMC4319384 DOI: 10.3389/fpls.2015.00037] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/14/2015] [Indexed: 05/23/2023]
Abstract
Plant-based recombinant protein production systems have gained an extensive interest over the past few years, because of their reduced cost and relative safety. Although the first products are now reaching the market, progress are still needed to improve plant hosts and strategies for biopharming. Targeting recombinant proteins toward the extracellular space offers several advantages in terms of protein folding and purification, but degradation events are observed, due to endogenous peptidases. This paper focuses on the analysis of extracellular proteolytic activities in two production systems: cell cultures and root-secretion (rhizosecretion), in Arabidopsis thaliana and Nicotiana tabacum. Proteolytic activities of extracellular proteomes (secretomes) were evaluated in vitro against two substrate proteins: bovine serum albumin (BSA) and human serum immunoglobulins G (hIgGs). Both targets were found to be degraded by the secretomes, BSA being more prone to proteolysis than hIgGs. The analysis of the proteolysis pH-dependence showed that target degradation was mainly dependent upon the production system: rhizosecretomes contained more peptidase activity than extracellular medium of cell suspensions, whereas variations due to plant species were smaller. Using class-specific peptidase inhibitors, serine, and metallopeptidases were found to be responsible for degradation of both substrates. An in-depth in silico analysis of genomic and transcriptomic data from Arabidopsis was then performed and led to the identification of a limited number of serine and metallo-peptidases that are consistently expressed in both production systems. These peptidases should be prime candidates for further improvement of plant hosts by targeted silencing.
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Affiliation(s)
- Jérôme Lallemand
- Laboratory of Plant Physiology, Department of Life Sciences, University of LiègeLiège, Belgium
- PhytoSYSTEMS, University of LiègeLiège, Belgium
| | - Frédéric Bouché
- Laboratory of Plant Physiology, Department of Life Sciences, University of LiègeLiège, Belgium
- PhytoSYSTEMS, University of LiègeLiège, Belgium
| | - Carole Desiron
- Laboratory of Plant Physiology, Department of Life Sciences, University of LiègeLiège, Belgium
| | - Jennifer Stautemas
- Laboratory of Plant Physiology, Department of Life Sciences, University of LiègeLiège, Belgium
| | | | - Claire Périlleux
- Laboratory of Plant Physiology, Department of Life Sciences, University of LiègeLiège, Belgium
- PhytoSYSTEMS, University of LiègeLiège, Belgium
| | - Pierre Tocquin
- Laboratory of Plant Physiology, Department of Life Sciences, University of LiègeLiège, Belgium
- PhytoSYSTEMS, University of LiègeLiège, Belgium
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17
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Wrzaczek M, Vainonen JP, Stael S, Tsiatsiani L, Help-Rinta-Rahko H, Gauthier A, Kaufholdt D, Bollhöner B, Lamminmäki A, Staes A, Gevaert K, Tuominen H, Van Breusegem F, Helariutta Y, Kangasjärvi J. GRIM REAPER peptide binds to receptor kinase PRK5 to trigger cell death in Arabidopsis. EMBO J 2014; 34:55-66. [PMID: 25398910 DOI: 10.15252/embj.201488582] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recognition of extracellular peptides by plasma membrane-localized receptor proteins is commonly used in signal transduction. In plants, very little is known about how extracellular peptides are processed and activated in order to allow recognition by receptors. Here, we show that induction of cell death in planta by a secreted plant protein GRIM REAPER (GRI) is dependent on the activity of the type II metacaspase METACASPASE-9. GRI is cleaved by METACASPASE-9 in vitro resulting in the release of an 11 amino acid peptide. This peptide bound in vivo to the extracellular domain of the plasma membrane-localized, atypical leucine-rich repeat receptor-like kinase POLLEN-SPECIFIC RECEPTOR-LIKE KINASE 5 (PRK5) and was sufficient to induce oxidative stress/ROS-dependent cell death. This shows a signaling pathway in plants from processing and activation of an extracellular protein to recognition by its receptor.
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Affiliation(s)
- Michael Wrzaczek
- Plant Biology, Department of Biosciences University of Helsinki, Helsinki, Finland
| | - Julia P Vainonen
- Plant Biology, Department of Biosciences University of Helsinki, Helsinki, Finland
| | - Simon Stael
- Department of Plant Systems Biology, VIB, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Liana Tsiatsiani
- Department of Plant Systems Biology, VIB, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Hanna Help-Rinta-Rahko
- Plant Biology, Department of Biosciences University of Helsinki, Helsinki, Finland Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Adrien Gauthier
- Plant Biology, Department of Biosciences University of Helsinki, Helsinki, Finland
| | - David Kaufholdt
- Plant Biology, Department of Biosciences University of Helsinki, Helsinki, Finland
| | - Benjamin Bollhöner
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Airi Lamminmäki
- Plant Biology, Department of Biosciences University of Helsinki, Helsinki, Finland
| | - An Staes
- Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Ykä Helariutta
- Plant Biology, Department of Biosciences University of Helsinki, Helsinki, Finland Institute of Biotechnology, University of Helsinki, Helsinki, Finland The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Jaakko Kangasjärvi
- Plant Biology, Department of Biosciences University of Helsinki, Helsinki, Finland Distinguished Scientist Fellowship Program, College of Science, King Saud University, Riyadh, Saudi Arabia
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18
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Radchuk V, Borisjuk L. Physical, metabolic and developmental functions of the seed coat. FRONTIERS IN PLANT SCIENCE 2014; 5:510. [PMID: 25346737 PMCID: PMC4193196 DOI: 10.3389/fpls.2014.00510] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/11/2014] [Indexed: 05/04/2023]
Abstract
The conventional understanding of the role of the seed coat is that it provides a protective layer for the developing zygote. Recent data show that the picture is more nuanced. The seed coat certainly represents a first line of defense against adverse external factors, but it also acts as channel for transmitting environmental cues to the interior of the seed. The latter function primes the seed to adjust its metabolism in response to changes in its external environment. The purpose of this review is to provide the reader with a comprehensive view of the structure and functionality of the seed coat, and to expose its hidden interaction with both the endosperm and embryo. Any breeding and/or biotechnology intervention seeking to increase seed size or modify seed features will have to consider the implications on this tripartite interaction.
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Affiliation(s)
| | - Ljudmilla Borisjuk
- Heterosis, Molecular Genetics, Leibniz-Institut für Pflanzengenetik und KulturpflanzenforschungGatersleben, Germany
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19
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Siritapetawee J, Limphirat W, Kantachot C, Kongmark C. The effects of metal ions in Euphorbia cf. lactea latex on the fibrinogenolytic activity of a plant protease. Appl Biochem Biotechnol 2014; 175:232-42. [PMID: 25253267 DOI: 10.1007/s12010-014-1255-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/10/2014] [Indexed: 11/30/2022]
Abstract
Two synchrotron-based techniques, synchrotron X-ray fluorescence (SXRF) and X-ray absorption spectroscopy (XAS), have demonstrated that Ca(2+) and Zn(2+) were the major metal ions distributed in the natural latex of Euphorbia cf. lactea. Both metal ions were found to affect the fibrinogenolytic activity of a homodimeric protease purified from the latex of this plant. The dimeric protein had an estimated molecular mass of about 82 kDa analyzed by SDS-PAGE. Therefore this protein was called as EuP-82. Based on the results of circular dichroism (CD) spectroscopy and the fibrinolytic activity measurement, it was found that Ca(2+) could activate the proteolytic activity of the enzyme by stabilizing its backbone structure. The intact conformation of EuP-82 was predicted from CD spectrum, which consisted of 51 % α-helix and 9 % β-sheet. Zn(2+) (10 mM) could decrease the fibrinolytic activity of EuP-82 to 30 ± 1 %. CD spectrum also supported that the inhibitory effect of Zn(2+) on the enzyme activity occurred by the drastic change of the enzyme structure with increasing the random coil conformation and by switching between α-helix and β-sheet structure. These results could be of first importance for further application to use EuP-82, the natural source protease as a potential drug for the thrombosis treatment. The fibrinolytic activity of EuP-82 may be enhanced by plasma Ca(2+) which generally involves in human hemostasis system.
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Affiliation(s)
- Jaruwan Siritapetawee
- School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand,
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20
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Kooiker M, Drenth J, Glassop D, McIntyre CL, Xue GP. TaMYB13-1, a R2R3 MYB transcription factor, regulates the fructan synthetic pathway and contributes to enhanced fructan accumulation in bread wheat. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3681-96. [PMID: 23873993 PMCID: PMC3745729 DOI: 10.1093/jxb/ert205] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Fructans are the major component of temporary carbon reserve in the stem of temperate cereals, which is used for grain filling. Three families of fructosyltransferases are directly involved in fructan synthesis in the vacuole of Triticum aestivum. The regulatory network of the fructan synthetic pathway is largely unknown. Recently, a sucrose-upregulated wheat MYB transcription factor (TaMYB13-1) was shown to be capable of activating the promoter activities of sucrose:sucrose 1-fructosyltransferase (1-SST) and sucrose:fructan 6-fructosyltransferase (6-SFT) in transient transactivation assays. This work investigated TaMYB13-1 target genes and their influence on fructan synthesis in transgenic wheat. TaMYB13-1 overexpression resulted in upregulation of all three families of fructosyltransferases including fructan:fructan 1-fructosyltransferase (1-FFT). A γ-vacuolar processing enzyme (γ-VPE1), potentially involved in processing the maturation of fructosyltransferases in the vacuole, was also upregulated by TaMYB13-1 overexpression. Multiple TaMYB13 DNA-binding motifs were identified in the Ta1-FFT1 and Taγ-VPE1 promoters and were bound strongly by TaMYB13-1. The expression profiles of these target genes and TaMYB13-1 were highly correlated in recombinant inbred lines and during stem development as well as the transgenic and non-transgenic wheat dataset, further supporting a direct regulation of these genes by TaMYB13-1. TaMYB13-1 overexpression in wheat led to enhanced fructan accumulation in the leaves and stems and also increased spike weight and grain weight per spike in transgenic plants under water-limited conditions. These data suggest that TaMYB13-1 plays an important role in coordinated upregulation of genes necessary for fructan synthesis and can be used as a molecular tool to improve the high fructan trait.
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Affiliation(s)
- Maarten Kooiker
- CSIRO Plant Industry, 306 Carmody Rd., St Lucia, Brisbane, Qld 4067, Australia
| | - Janneke Drenth
- CSIRO Plant Industry, 306 Carmody Rd., St Lucia, Brisbane, Qld 4067, Australia
| | - Donna Glassop
- CSIRO Plant Industry, 306 Carmody Rd., St Lucia, Brisbane, Qld 4067, Australia
| | - C. Lynne McIntyre
- CSIRO Plant Industry, 306 Carmody Rd., St Lucia, Brisbane, Qld 4067, Australia
| | - Gang-Ping Xue
- CSIRO Plant Industry, 306 Carmody Rd., St Lucia, Brisbane, Qld 4067, Australia
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21
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Tsiatsiani L, Timmerman E, De Bock PJ, Vercammen D, Stael S, van de Cotte B, Staes A, Goethals M, Beunens T, Van Damme P, Gevaert K, Van Breusegem F. The Arabidopsis metacaspase9 degradome. THE PLANT CELL 2013; 25:2831-47. [PMID: 23964026 PMCID: PMC3784583 DOI: 10.1105/tpc.113.115287] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Metacaspases are distant relatives of the metazoan caspases, found in plants, fungi, and protists. However, in contrast with caspases, information about the physiological substrates of metacaspases is still scarce. By means of N-terminal combined fractional diagonal chromatography, the physiological substrates of metacaspase9 (MC9; AT5G04200) were identified in young seedlings of Arabidopsis thaliana on the proteome-wide level, providing additional insight into MC9 cleavage specificity and revealing a previously unknown preference for acidic residues at the substrate prime site position P1'. The functionalities of the identified MC9 substrates hinted at metacaspase functions other than those related to cell death. These results allowed us to resolve the substrate specificity of MC9 in more detail and indicated that the activity of phosphoenolpyruvate carboxykinase 1 (AT4G37870), a key enzyme in gluconeogenesis, is enhanced upon MC9-dependent proteolysis.
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Affiliation(s)
- Liana Tsiatsiani
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Evy Timmerman
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Pieter-Jan De Bock
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Dominique Vercammen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Simon Stael
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Brigitte van de Cotte
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - An Staes
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Marc Goethals
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Tine Beunens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Petra Van Damme
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Address correspondence to
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22
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Zymography methods for visualizing hydrolytic enzymes. Nat Methods 2013; 10:211-20. [PMID: 23443633 DOI: 10.1038/nmeth.2371] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 01/11/2013] [Indexed: 12/12/2022]
Abstract
Zymography is a technique for studying hydrolytic enzymes on the basis of substrate degradation. It is a powerful, but often misinterpreted, tool yielding information on potential hydrolytic activities, enzyme forms and the locations of active enzymes. In this Review, zymography techniques are compared in terms of advantages, limitations and interpretations. With in gel zymography, enzyme forms are visualized according to their molecular weights. Proteolytic activities are localized in tissue sections with in situ zymography. In vivo zymography can pinpoint proteolytic activity to sites in an intact organism. Future development of novel substrate probes and improvement in detection and imaging methods will increase the applicability of zymography for (reverse) degradomics studies.
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