1
|
Gamba M, Asllanaj E, Raguindin PF, Glisic M, Franco OH, Minder B, Bussler W, Metzger B, Kern H, Muka T. Nutritional and phytochemical characterization of radish (Raphanus sativus): A systematic review. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.04.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
2
|
Xia Q, Ponnaiah M, Cueff G, Rajjou L, Prodhomme D, Gibon Y, Bailly C, Corbineau F, Meimoun P, El-Maarouf-Bouteau H. Integrating proteomics and enzymatic profiling to decipher seed metabolism affected by temperature in seed dormancy and germination. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:118-125. [PMID: 29606208 DOI: 10.1016/j.plantsci.2018.01.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/24/2018] [Accepted: 01/28/2018] [Indexed: 06/08/2023]
Abstract
Temperature is an important environmental factor affecting seed dormancy and germination. The mechanism by which temperature induces germination in dormant seeds is however still unclear. Proteomic study has been performed in dormant sunflower seeds during imbibition at permissive and non-permissive temperatures for germination, 20 and 10 °C, respectively. Proteome analysis showed an increase of proteins belonging to metabolism and energy from the first hours of imbibition followed by a decrease of proteins involved in protein metabolism and seed storage in germinating compared to non-germinating seeds. Proteomic study was completed by polysome and proteasome activity assessment and enzymatic profiling on several altered proteins involved in metabolism and energy. Results showed that 20 °C treatment induced the activation of both protein synthesis and degradation processes, the latter being related to proteasome activity during the germination sensu stricto, and to other degradation processes such as proteases during the post-germination. Interestingly, enzymatic profiles showed that TCA cycle and glycolysis were more active in non-germinating seeds in the phase I of the germination sensu stricto. This result suggests the regulation of central metabolism activity in germinating seeds. The control of energy production during imbibition seems to be involved in molecular networks controlling seed dormancy and germination.
Collapse
Affiliation(s)
- Qiong Xia
- Sorbonne Université, UMR 7622, 75005 Paris, France; CNRS, UMR 7622, 75005 Paris, France
| | - Maharajah Ponnaiah
- Sorbonne Université, UMR 7622, 75005 Paris, France; CNRS, UMR 7622, 75005 Paris, France
| | - Gwendal Cueff
- Institut Jean-Pierre Bourgin (UMR1318 INRA - AgroParisTech), Institut National de la Recherche Agronomique, Saclay Plant Science, Versailles, France
| | - Loïc Rajjou
- Institut Jean-Pierre Bourgin (UMR1318 INRA - AgroParisTech), Institut National de la Recherche Agronomique, Saclay Plant Science, Versailles, France
| | - Duyen Prodhomme
- UMR1332 Biologie du Fruit et Pathologie, Université de Bordeaux, Institut National de la Recherche Agronomique, Villenave d'Ornon, France; Plateforme Métabolome, Centre Génomique Fonctionnelle Bordeaux, Villenave d'Ornon, France
| | - Yves Gibon
- UMR1332 Biologie du Fruit et Pathologie, Université de Bordeaux, Institut National de la Recherche Agronomique, Villenave d'Ornon, France; Plateforme Métabolome, Centre Génomique Fonctionnelle Bordeaux, Villenave d'Ornon, France
| | - Christophe Bailly
- Sorbonne Université, UMR 7622, 75005 Paris, France; CNRS, UMR 7622, 75005 Paris, France
| | - Françoise Corbineau
- Sorbonne Université, UMR 7622, 75005 Paris, France; CNRS, UMR 7622, 75005 Paris, France
| | - Patrice Meimoun
- Sorbonne Université, UMR 7622, 75005 Paris, France; CNRS, UMR 7622, 75005 Paris, France
| | | |
Collapse
|
3
|
Ying J, Zhao J, Hou Y, Wang Y, Qiu J, Li Z, Tong X, Shi Z, Zhu J, Zhang J. Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos. PLoS One 2017; 12:e0173853. [PMID: 28328971 PMCID: PMC5362090 DOI: 10.1371/journal.pone.0173853] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/28/2017] [Indexed: 11/19/2022] Open
Abstract
Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered. Inspection of the motifs and sequence structures involved suggested that all the glycosites were concentrated within [NxS/T] motif, while 82.3% of them were in a coil structure. N-glycosylation preferentially occurred on proteins with glycoside hydrolase activities, which were significantly enriched in the starch and sucrose metabolism pathway, suggesting that N-glycosylation is involved in embryo germination by regulating carbohydrate metabolism. Notably, protein-protein interaction analysis revealed a network with several Brassinosteroids signaling proteins, including XIAO and other BR-responsive proteins, implying that glycosylation-mediated Brassinosteroids signaling may be a key mechanism regulating rice embryo germination. In summary, this study expanded our knowledge of protein glycosylation in rice, and provided novel insight into the PTM regulation in rice seed germination.
Collapse
Affiliation(s)
- Jiezheng Ying
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Juan Zhao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Yuxuan Hou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | | | - Jun Zhu
- Jingjie PTM-Biolabs, Hangzhou, P.R. China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
- * E-mail:
| |
Collapse
|
4
|
Xia Q, El-Maarouf-Bouteau H, Bailly C, Meimoun P. Determination of Protein Carbonylation and Proteasome Activity in Seeds. Methods Mol Biol 2016; 1450:205-212. [PMID: 27424756 DOI: 10.1007/978-1-4939-3759-2_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Reactive oxygen species (ROS) have been shown to be toxic but also function as signaling molecules in a process called redox signaling. In seeds, ROS are produced at different developmental stages including dormancy release and germination. Main targets of oxidation events by ROS in cell are lipids, nucleic acids, and proteins. Protein oxidation has various effects on their function, stability, location, and degradation. Carbonylation represents an irreversible and unrepairable modification that can lead to protein degradation through the action of the 20S proteasome. Here, we present techniques which allow the quantification of protein carbonyls in complex protein samples after derivatization by 2,4-dinitrophenylhydrazine (DNPH) and the determination proteasome activity by an activity-based protein profiling (ABPP) using the probe MV151. These techniques, routinely easy to handle, allow the rapid assessment of protein carbonyls and proteasome activity in seeds in various physiological conditions where ROS may act as signaling or toxic elements.
Collapse
Affiliation(s)
- Qiong Xia
- Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Sorbonne Universités, 75005, Paris, France
- Biologie du Développement, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Centre National de la Recherche Scientifique, 75005, Paris, France
| | - Hayat El-Maarouf-Bouteau
- Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Sorbonne Universités, 75005, Paris, France
- Biologie du Développement, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Centre National de la Recherche Scientifique, 75005, Paris, France
| | - Christophe Bailly
- Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Sorbonne Universités, 75005, Paris, France
- Biologie du Développement, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Centre National de la Recherche Scientifique, 75005, Paris, France
| | - Patrice Meimoun
- Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Sorbonne Universités, 75005, Paris, France.
- Biologie du Développement, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Centre National de la Recherche Scientifique, 75005, Paris, France.
| |
Collapse
|
5
|
Harada Y, Hirayama H, Suzuki T. Generation and degradation of free asparagine-linked glycans. Cell Mol Life Sci 2015; 72:2509-33. [PMID: 25772500 PMCID: PMC11113800 DOI: 10.1007/s00018-015-1881-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/19/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
Abstract
Asparagine (N)-linked protein glycosylation, which takes place in the eukaryotic endoplasmic reticulum (ER), is important for protein folding, quality control and the intracellular trafficking of secretory and membrane proteins. It is known that, during N-glycosylation, considerable amounts of lipid-linked oligosaccharides (LLOs), the glycan donor substrates for N-glycosylation, are hydrolyzed to form free N-glycans (FNGs) by unidentified mechanisms. FNGs are also generated in the cytosol by the enzymatic deglycosylation of misfolded glycoproteins during ER-associated degradation. FNGs derived from LLOs and misfolded glycoproteins are eventually merged into one pool in the cytosol and the various glycan structures are processed to a near homogenous glycoform. This article summarizes the current state of our knowledge concerning the formation and catabolism of FNGs.
Collapse
Affiliation(s)
- Yoichiro Harada
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Hiroto Hirayama
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Tadashi Suzuki
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| |
Collapse
|
6
|
Han C, Wang K, Yang P. Gel-based comparative phosphoproteomic analysis on rice embryo during germination. PLANT & CELL PHYSIOLOGY 2014; 55:1376-94. [PMID: 24793751 DOI: 10.1093/pcp/pcu060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Seed germination is a well regulated process, which incorporates many events including signal transduction, mobilization of reserves, reactive oxygen species scavenging and cell division. Although many transcriptomic and proteomic studies have been conducted on this process, regulation of protein modification has not been studied. To better understand the mechanism, a gel-based comparative phosphoproteomic study was performed on rice embryo during the germination process. In total, 168 protein spots exhibited significantly changed Pro-Q staining intensity during germination. Using matrix-assisted laser deionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) analysis, 193 proteins were identified. By combining Pro-Q and Coomassie brilliant blue stain intensity analyses, 109 proteins were verified to be phosphorylation regulation proteins. Functional analyses indicated that phosphorylation of proteins involved in stress response and storage was gradually enhanced. Phosphorylation of signal transduction proteins was mainly activated during the early stage of germination, while stress response and storage protein phosphorylation were enhanced at the late stage. Enzyme assays proved that the phosphorylation of fructokinase, pyruvate kinase, malate dehydrogenase, GDP-mannose 3,5-epimerase1, ascorbate peroxidase and glutathione S-transferase could consistently enhance their activity. This study showed the dynamic changes of protein phosphorylation status in rice embryo during germination and provided new insight into understanding the mechanism underlying this process.
Collapse
Affiliation(s)
- Chao Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan 430074, ChinaUniversity of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan 430074, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan 430074, China
| |
Collapse
|
7
|
Arc E, Galland M, Cueff G, Godin B, Lounifi I, Job D, Rajjou L. Reboot the system thanks to protein post-translational modifications and proteome diversity: How quiescent seeds restart their metabolism to prepare seedling establishment. Proteomics 2011; 11:1606-18. [DOI: 10.1002/pmic.201000641] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 12/05/2010] [Accepted: 01/07/2011] [Indexed: 11/12/2022]
|
8
|
Vuylsteker C, Cuvellier G, Berger S, Faugeron C, Karamanos Y. Evidence of two enzymes performing the de-N-glycosylation of proteins in barley: expression during germination, localization within the grain and set-up during grain formation. JOURNAL OF EXPERIMENTAL BOTANY 2000. [PMID: 10948209 DOI: 10.1093/jexbot/51.346.839] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The occurrence of two enzymes performing de-N-glycosylation of glycoproteins, namely, endo-N-acetyl-beta-D-glucosaminidase (ENGase, EC 3.2.1.96) and peptide-N(4)-(N-acetyl-beta-D-glucosaminyl) asparagine amidase (PNGase, EC 3.5.1.52) was investigated in barley, cv. Plaisant (a winter six rowed variety). The dry grain showed both activities according to the HPLC detection of the hydrolysis of fluorescent resorufin-labelled substrates. However, PNGase activity was 16-fold higher than ENGase activity. During germination, both activities increased, PNGase by only 1.5-fold compared to nearly 4.8-fold for ENGase over the 4 d following imbibition. The localization of these activities within the grain showed that the major contribution of PNGase was due to the endosperm, typically representing over 90% of the whole grain activity. In contrast, ENGase activity was especially high in the embryo and, later, in the developing plantlet (10-fold higher than in the endosperm), particularly in the rootlets and scutellum. In developing spikes, PNGase activity was 5.6-fold higher than in the leaves, but similar ENGase activity was measured in both organs. During grain formation, PNGase activity followed dry matter increase together with endosperm development. In contrast, ENGase activity dropped by 66% at the beginning of grain filling before stabilizing until harvest. The occurrence of de-N-glycosylation-performing enzymes throughout the development of barley raises the question of the nature of their natural substrates. Moreover, the prevalence of one of these enzymes over the other depending on the organ and the developmental stage, could represent the first evidence of specific functions for each enzyme.
Collapse
Affiliation(s)
- C Vuylsteker
- Laboratoire de Biochimie Moléculaire et Cellulaire, Université d'Artois, Faculté J Perrin, rue J Souvraz, SP18, 62307 Lens, France
| | | | | | | | | |
Collapse
|
9
|
Karamanos Y. Endo-N-acetyl-beta-D-glucosaminidases and their potential substrates: structure/function relationships. Res Microbiol 1997; 148:661-71. [PMID: 9765851 DOI: 10.1016/s0923-2508(99)80065-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Endo-N-acetyl-beta-D-glucosaminidases (ENGases) have been defined as the enzymes that hydrolyse the glycosidic bond between an N-acetyl-beta-D-glucosamine residue and the adjacent (partner) monosaccharide within an oligosaccharide chain. Three types of enzymes have been distinguished according to this definition: ENGases acting on murein (type I), those acting on chitin (type II) and, finally, those acting on N-glycans (type III). Considering that N-acetylmuramic acid is a derivative of N-acetylglucosamine (3-O-substituted by a lactyl group), only ENGases acting between two N-acetylglucosamine residues are actually known despite the fact that other possibilities of partner monosaccharides for N-acetyl-beta-D-glucosamine are reported. Similarities in the amino acid sequences were found to occur only between chitin-ENGases and N-glycan-ENGases, but the substrate specificities of these two types of enzymes are different. However, it is possible that certain enzymes are able to cleave more than one type of substrate, and this could in particular explain why the N-glycan-ENGases are largely produced by bacteria in which no potential substrate for this type of enzymes was identified. Further study in this area is expected.
Collapse
Affiliation(s)
- Y Karamanos
- Laboratoire de Biochimie, Université d'Artois, Faculté Jean Perrin, Lens, France
| |
Collapse
|