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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.
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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:
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Paucar-Menacho LM, Peñas E, Dueñas M, Frias J, Martínez-Villaluenga C. Optimizing germination conditions to enhance the accumulation of bioactive compounds and the antioxidant activity of kiwicha (Amaranthus caudatus) using response surface methodology. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2016.07.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Cheng J, Wang L, Zeng P, He Y, Zhou R, Zhang H, Wang Z. Identification of genes involved in rice seed priming in the early imbibition stage. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:61-69. [PMID: 26833720 DOI: 10.1111/plb.12438] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/29/2016] [Indexed: 05/23/2023]
Abstract
Phase II of seed imbibition is a critical process during seed priming. To identify genes involved in rice seed priming, the altered proteins between the dry and imbibed (24 h) seeds were compared using a two-dimensional gel electrophoresis system in this study. Ten significantly changed proteins (fold change ≥ twofold; P < 0.01) were successfully identified, which could be categorised as carbohydrate and protein biosynthesis and metabolism-related, signalling-related, storage and stress-related proteins. A meta-analysis indicated that the highest expression of the identified genes was at the milk and dough stages and in the endosperm tissue. Quantitative real-time PCR analysis showed that there was significant variation in gene expression (except FAD-dependent oxidoreductase) in embryos during seed priming (0-48 h). The expression of genes associated with stress appeared at the early imbibition stage, while those associated with carbohydrate metabolism, protein synthesis and signalling increased at the late imbibition stage. Three identified proteins (glucose-1-phosphate adenylyltransferase large subunit, aminotransferase and prolamin precursor) had similar transcript and protein expression patterns in embryos. Based on phenotype and gene expression, the optimal stop time for seed priming is 24 h, when these three genes have relatively low expression, followed by significant induction during imbibition in embryos. These three genes are ideal candidate biomarkers for rice seed priming.
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Affiliation(s)
- J Cheng
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - L Wang
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - P Zeng
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Y He
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - R Zhou
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - H Zhang
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Z Wang
- Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
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Rosental L, Perelman A, Nevo N, Toubiana D, Samani T, Batushansky A, Sikron N, Saranga Y, Fait A. Environmental and genetic effects on tomato seed metabolic balance and its association with germination vigor. BMC Genomics 2016; 17:1047. [PMID: 27993127 PMCID: PMC5168813 DOI: 10.1186/s12864-016-3376-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 12/05/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The metabolite content of a seed and its ability to germinate are determined by genetic makeup and environmental effects during development. The interaction between genetics, environment and seed metabolism and germination was studied in 72 tomato homozygous introgression lines (IL) derived from Solanum pennelli and S. esculentum M82 cultivar. Plants were grown in the field under saline and fresh water irrigation during two consecutive seasons, and collected seeds were subjected to morphological analysis, gas chromatograph-mass spectrometry (GC-MS) metabolic profiling and germination tests. RESULTS Seed weight was under tight genetic regulation, but it was not related to germination vigor. Salinity significantly reduced seed number but had little influence on seed metabolites, affecting only 1% of the statistical comparisons. The metabolites negatively correlated to germination were simple sugars and most amino acids, while positive correlations were found for several organic acids and the N metabolites urea and dopamine. Germination tests identified putative loci for improved germination as compared to M82 and in response to salinity, which were also characterized by defined metabolic changes in the seed. CONCLUSIONS An integrative analysis of the metabolite and germination data revealed metabolite levels unambiguously associated with germination percentage and rate, mostly conserved in the different tested seed development environments. Such consistent relations suggest the potential for developing a method of germination vigor prediction by metabolic profiling, as well as add to our understanding of the importance of primary metabolic processes in germination.
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Affiliation(s)
- Leah Rosental
- The French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion, 84990, Israel
| | - Adi Perelman
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Noa Nevo
- The French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion, 84990, Israel
| | - David Toubiana
- The French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion, 84990, Israel
| | - Talya Samani
- The French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion, 84990, Israel
| | - Albert Batushansky
- The French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion, 84990, Israel
| | - Noga Sikron
- The French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion, 84990, Israel
| | - Yehoshua Saranga
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Aaron Fait
- The French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion, 84990, Israel.
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Chiu RS, Pan S, Zhao R, Gazzarrini S. ABA-dependent inhibition of the ubiquitin proteasome system during germination at high temperature in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:749-761. [PMID: 27496613 DOI: 10.1111/tpj.13293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/07/2016] [Accepted: 07/29/2016] [Indexed: 05/09/2023]
Abstract
During germination, endogenous and environmental factors trigger changes in the transcriptome, translatome and proteome to break dormancy. In Arabidopsis thaliana, the ubiquitin proteasome system (UPS) degrades proteins that promote dormancy to allow germination. While research on the UPS has focused on the identification of proteasomal substrates, little information is known about the regulation of its activity. Here we characterized the activity of the UPS during dormancy release and maintenance by monitoring protein ubiquitination and degradation of two proteasomal substrates: Suc-LLVY-AMC, a well characterized synthetic substrate, and FUSCA3 (FUS3), a dormancy-promoting transcription factor degraded by the 26S proteasome. Our data indicate that proteasome activity and protein ubiquitination increase during imbibition at optimal temperature (21°C), and are required for seed germination. However, abscisic acid (ABA) and supraoptimal temperature (32°C) inhibit germination by dampening both protein ubiquitination and proteasome activity. Inhibition of UPS function by high temperature is reduced by the ABA biosynthesis inhibitor, fluridone, and in ABA biosynthetic mutants, suggesting that it is ABA dependent. Accordingly, inhibition of FUS3 degradation at 32°C is also dependent on ABA. Native gels show that inhibition of proteasome activity is caused by interference with the 26S/30S ratio as well as free 19S and 20S levels, impacting the proteasome degradation cycle. Transfer experiments show that ABA-mediated inhibition of proteasome activity at 21°C is restricted to the first 2 days of germination, a time window corresponding to seed sensitivity to environmental and ABA-mediated growth inhibition. Our data show that ABA and high temperature inhibit germination under unfavourable growth conditions by repressing the UPS.
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Affiliation(s)
- Rex Shun Chiu
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Shiyue Pan
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Rongmin Zhao
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
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Dissection of brassinosteroid-regulated proteins in rice embryos during germination by quantitative proteomics. Sci Rep 2016; 6:34583. [PMID: 27703189 PMCID: PMC5050409 DOI: 10.1038/srep34583] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/15/2016] [Indexed: 12/11/2022] Open
Abstract
Brassinosteroids (BRs), essential plant-specific steroidal hormones, function in a wide spectrum of plant growth and development events, including seed germination. Rice is not only a monocotyledonous model plant but also one of the most important staple food crops of human beings. Rice seed germination is a decisive event for the next-generation of plant growth and successful seed germination is critical for rice yield. However, little is known about the molecular mechanisms on how BR modulates seed germination in rice. In the present study, we used isobaric tags for relative and absolute quantification (iTRAQ) based proteomic approach to study BR-regulated proteome during the early stage of seed germination. The results showed that more than 800 BR-responsive proteins were identified, including 88 reliable target proteins responsive to stimuli of both BR-deficiency and BR-insensitivity. Moreover, 90% of the 88 target proteins shared a similar expression change pattern. Gene ontology and string analysis indicated that ribosomal structural proteins, as well as proteins involved in protein biosynthesis and carbohydrate metabolisms were highly clustered. These findings not only enrich BR-regulated protein database in rice seeds, but also allow us to gain novel insights into the molecular mechanism of BR regulated seed germination.
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57
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Jan R, Saxena D, Singh S. Physico-chemical, textural, sensory and antioxidant characteristics of gluten – Free cookies made from raw and germinated Chenopodium (Chenopodium album) flour. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.04.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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58
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Chen L, Huang Y, Xu M, Cheng Z, Zhang D, Zheng J. iTRAQ-Based Quantitative Proteomics Analysis of Black Rice Grain Development Reveals Metabolic Pathways Associated with Anthocyanin Biosynthesis. PLoS One 2016; 11:e0159238. [PMID: 27415428 PMCID: PMC4944901 DOI: 10.1371/journal.pone.0159238] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/29/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Black rice (Oryza sativa L.), whose pericarp is rich in anthocyanins (ACNs), is considered as a healthier alternative to white rice. Molecular species of ACNs in black rice have been well documented in previous studies; however, information about the metabolic mechanisms underlying ACN biosynthesis during black rice grain development is unclear. RESULTS The aim of the present study was to determine changes in the metabolic pathways that are involved in the dynamic grain proteome during the development of black rice indica cultivar, (Oryza sativa L. indica var. SSP). Isobaric tags for relative and absolute quantification (iTRAQ) MS/MS were employed to identify statistically significant alterations in the grain proteome. Approximately 928 proteins were detected, of which 230 were differentially expressed throughout 5 successive developmental stages, starting from 3 to 20 days after flowering (DAF). The greatest number of differentially expressed proteins was observed on 7 and 10 DAF, including 76 proteins that were upregulated and 39 that were downregulated. The biological process analysis of gene ontology revealed that the 230 differentially expressed proteins could be sorted into 14 functional groups. Proteins in the largest group were related to metabolic process, which could be integrated into multiple biochemical pathways. Specifically, proteins with a role in ACN biosynthesis, sugar synthesis, and the regulation of gene expression were upregulated, particularly from the onset of black rice grain development and during development. In contrast, the expression of proteins related to signal transduction, redox homeostasis, photosynthesis and N-metabolism decreased during grain maturation. Finally, 8 representative genes encoding different metabolic proteins were verified via quantitative real-time polymerase chain reaction (qRT-PCR) analysis, these genes had differed in transcriptional and translational expression during grain development. CONCLUSIONS Expression analyses of metabolism-related protein groups belonging to different functional categories and subcategories indicated that significantly upregulated proteins were related to flavonoid and starch synthesis. On the other hand, the downregulated proteins were determined to be related to nitrogen metabolism, as well as other functional categories and subcategories, including photosynthesis, redox homeostasis, tocopherol biosynthetic, and signal transduction. The results provide valuable new insights into the characterization and understanding of ACN pigment production in black rice.
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Affiliation(s)
- Linghua Chen
- FujianAgriculture and Forestry University, Fuzhou Fujian, China
- Jinshan College of Fujian Agriculture and Forestry University, Fuzhou Fujian, China
| | - Yining Huang
- FujianAgriculture and Forestry University, Fuzhou Fujian, China
- Department of Food and Biology Engineering, Zhangzhou Institute of Technology, Zhangzhou Fujian, China
| | - Ming Xu
- FujianAgriculture and Forestry University, Fuzhou Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou Fujian, China
| | - Zuxin Cheng
- FujianAgriculture and Forestry University, Fuzhou Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou Fujian, China
| | - Dasheng Zhang
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory for Plant Functional Genomics and Resources, Shanghai, China
| | - Jingui Zheng
- FujianAgriculture and Forestry University, Fuzhou Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou Fujian, China
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59
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Liu SJ, Xu HH, Wang WQ, Li N, Wang WP, Lu Z, Møller IM, Song SQ. Identification of embryo proteins associated with seed germination and seedling establishment in germinating rice seeds. JOURNAL OF PLANT PHYSIOLOGY 2016; 196-197:79-92. [PMID: 27085178 DOI: 10.1016/j.jplph.2016.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 02/06/2016] [Accepted: 02/16/2016] [Indexed: 06/05/2023]
Abstract
Seed germination is a critical phase in the plant life cycle, but the mechanism of seed germination is still poorly understood. In the present study, rice (Oryza sativa L. cv. Peiai 64S) seeds were sampled individually when they reached different germination stages, quiescent, germinated sensu stricto, germinated completely and seedling, and were used to study the changes in the embryo proteome. A total of 88 protein spots showed a significant change in abundance during germination in water, and the results showed an activation of metabolic processes. Cell division, cell wall synthesis, and secondary metabolism were activated at late seed germination and during preparation for subsequent seedling establishment. Cycloheximide (CHX) at 70μM inhibited seedling establishment without an apparent negative effect on seed germination, while CHX at 500μM completely blocked seed germination. We used this observation to identify the potentially important proteins involved in seed germination (coleoptile protrusion) and seedling establishment (coleoptile and radicle protrusion). Twenty-six protein spots, mainly associated with sugar/polysaccharide metabolism and energy production, showed a significant difference in abundance during seed germination. Forty-nine protein spots, mainly involved in cell wall biosynthesis, proteolysis as well as cell defense and rescue, were required for seedling establishment. The results help improve our understanding of the key events (proteins) involved in germination and seedling development.
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Affiliation(s)
- Shu-Jun Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Heng-Heng Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wei-Qing Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ni Li
- Hunan Hybrid Rice Research Center/State Key Laboratory of Hybrid Rice, Changsha 410125, China
| | - Wei-Ping Wang
- Hunan Hybrid Rice Research Center/State Key Laboratory of Hybrid Rice, Changsha 410125, China
| | - Zhuang Lu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, Slagelse, DK-4200, Denmark
| | - Song-Quan Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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60
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Gao J, Fu H, Zhou X, Chen Z, Luo Y, Cui B, Chen G, Liu J. Comparative proteomic analysis of seed embryo proteins associated with seed storability in rice (Oryza sativa L) during natural aging. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 103:31-44. [PMID: 26950923 DOI: 10.1016/j.plaphy.2016.02.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 02/01/2016] [Accepted: 02/17/2016] [Indexed: 05/19/2023]
Abstract
Seed storability is considered an important trait in rice breeding; however, the underlying regulating mechanisms remain largely unknown. Here, we carried out a physiological and proteomic study to identify proteins possibly related to seed storability under natural conditions. Two hybrid cultivars, IIYou998 (IIY998) and BoYou998 (BY998), were analyzed in parallel because they share the same restorer line but have significant differences in seed storability. After a 2-year storage period, the germination percentage of IIY998 was significantly lower than that of BY998, whereas the level of malondialdehyde was reversed, indicating that IIY998 seeds may suffer from more severe damage than BY998 during storage. However, we did not find correlation between activities of antioxidant enzymes of superoxide dismutase, peroxidase, and catalase and seed storability. We identified 78 embryo proteins in embryo whose abundance varied more than 3-fold different during storage or between IIY998 and BY998. More proteins changed in abundance in IIY998 embryo (67 proteins) during storage than in BY998 (10 proteins). Several redox regulation proteins, mainly glutathione-related proteins, exhibited different degree of change during storage between BY998 and IIY998 and might play an important role protecting embryo proteins from oxidation. In addition, some disease/defense proteins, including DNA-damage-repair/toleration proteins, and a putative late embryogenesis abundant protein were significantly downregulated in IIY998, whereas their levels did not change in BY998, indicating that they might be correlated with seed storability. Further studies on these candidate seed storage proteins might help improve our understanding of seed aging.
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Affiliation(s)
- Jiadong Gao
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China; Hunan Agricultural University, Changsha, 410128, China
| | - Hua Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xinqiao Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zhongjian Chen
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yi Luo
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Baiyuan Cui
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Guanghui Chen
- Hunan Agricultural University, Changsha, 410128, China.
| | - Jun Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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61
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Xu HH, Liu SJ, Song SH, Wang RX, Wang WQ, Song SQ. Proteomics analysis reveals distinct involvement of embryo and endosperm proteins during seed germination in dormant and non-dormant rice seeds. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 103:219-42. [PMID: 27035683 DOI: 10.1016/j.plaphy.2016.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 03/01/2016] [Accepted: 03/04/2016] [Indexed: 05/09/2023]
Abstract
Seed germination is a complex trait which is influenced by many genetic, endogenous and environmental factors, but the key event(s) associated with seed germination are still poorly understood. In present study, the non-dormant cultivated rice Yannong S and the dormant Dongxiang wild rice seeds were used as experimental materials, we comparatively investigated the water uptake, germination time course, and the differential proteome of the effect of embryo and endosperm on germination of these two types of seeds. A total of 231 and 180 protein spots in embryo and endosperm, respectively, showed a significant change in abundance during germination. We observed that the important proteins associated with seed germination included those involved in metabolism, energy production, protein synthesis and destination, storage protein, cell growth and division, signal transduction, cell defense and rescue. The contribution of embryo and endosperm to seed germination is different. In embryo, the proteins involved in amino acid activation, sucrose cleavage, glycolysis, fermentation and protein synthesis increased; in endosperm, the proteins involved in sucrose cleavage and glycolysis decreased, and those with ATP and CoQ synthesis and proteolysis increased. Our results provide some new knowledge to understand further the mechanism of seed germination.
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Affiliation(s)
- Heng-Heng Xu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shu-Jun Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shun-Hua Song
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Rui-Xia Wang
- College of Life Science, Linyi University, Linyi 276005, China
| | - Wei-Qing Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Song-Quan Song
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Cao H, He M, Zhu C, Yuan L, Dong L, Bian Y, Zhang W, Yan Y. Distinct metabolic changes between wheat embryo and endosperm during grain development revealed by 2D-DIGE-based integrative proteome analysis. Proteomics 2016; 16:1515-36. [PMID: 26968330 DOI: 10.1002/pmic.201500371] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 02/23/2016] [Accepted: 03/05/2016] [Indexed: 12/31/2022]
Abstract
Two Chinese bread wheat cultivars, Jinghua 9 and Zhongmai 175, distinct in grain weight and dough quality, were used to study proteome changes in the embryo and endosperm during grain development using a two-dimensional difference gel electrophoresis (2D-DIGE)-based proteomics approach. In total, 138 and 127 differentially expressed protein (DEP) spots representing 116 and 113 unique DEPs were identified in the embryo and endosperm, respectively. Among them, 54 (31%) DEPs were commonly present in both organs while 62 (35%) and 59 (34%) DEPs occurred only in the embryo and endosperm, respectively. Embryonic DEPs are primarily stress-related proteins and involved in carbohydrate and lipid metabolism, while those from the endosperm are related primarily to carbohydrate metabolism and storage. Principal component analysis (PCA) indicated that the proteome differences in the endosperm caused by different cultivars were greater than those by development stages, while the differences in the embryo showed the opposite pattern. Protein-protein interaction (PPI) analysis revealed a complex network centered primarily on enzymes involved in carbohydrate and protein metabolism. The transcriptional levels of fourteen important DEPs encoding genes showed high similarity between organs and cultivars. In particular, some key DEPs of the endosperm, such as phosphoglucomutase, ADP-glucose pyrophosphorylase (AGPase), and sucrose synthase (SUS), showed significantly upregulated expression, indicating their key roles in starch biosynthesis and grain yield. Moreover, upregulated expression of some storage proteins in the endosperm could improve wheat bread-making quality.
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Affiliation(s)
- Hui Cao
- College of Life Science, Capital Normal University, Beijing, P. R. China
| | - Miao He
- College of Life Science, Capital Normal University, Beijing, P. R. China
| | - Chong Zhu
- College of Life Science, Capital Normal University, Beijing, P. R. China
| | - Linlin Yuan
- College of Life Science, Capital Normal University, Beijing, P. R. China
| | - Liwei Dong
- College of Life Science, Capital Normal University, Beijing, P. R. China
| | - Yanwei Bian
- College of Life Science, Capital Normal University, Beijing, P. R. China
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, P. R. China
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing, P. R. China.,Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, P. R. China
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63
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Zhang H, He D, Yu J, Li M, Damaris RN, Gupta R, Kim ST, Yang P. Analysis of dynamic protein carbonylation in rice embryo during germination through AP-SWATH. Proteomics 2016; 16:989-1000. [DOI: 10.1002/pmic.201500248] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 12/17/2015] [Accepted: 01/20/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Hui Zhang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
| | - Jianlan Yu
- Asia Pacific Application Support Center; AB Sciex; Shanghai P. R. China
| | - Ming Li
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
| | - Rebecca Njeri Damaris
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
| | - Ravi Gupta
- Department of Plant Bioscience; College of Natural Resources & Life Science; Pusan National University; Miryang Korea
| | - Sun Tae Kim
- Department of Plant Bioscience; College of Natural Resources & Life Science; Pusan National University; Miryang Korea
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
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64
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Lu XJ, Zhang XL, Mei M, Liu GL, Ma BB. Proteomic analysis of Magnolia sieboldii K. Koch seed germination. J Proteomics 2016; 133:76-85. [DOI: 10.1016/j.jprot.2015.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 11/26/2015] [Accepted: 12/03/2015] [Indexed: 11/29/2022]
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65
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He D, Wang Q, Li M, Damaris RN, Yi X, Cheng Z, Yang P. Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed. J Proteome Res 2016; 15:879-90. [PMID: 26767346 DOI: 10.1021/acs.jproteome.5b00805] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Regulation of rice seed germination has been shown to mainly occur at post-transcriptional levels, of which the changes on proteome status is a major one. Lysine acetylation and succinylation are two prevalent protein post-translational modifications (PTMs) involved in multiple biological processes, especially for metabolism regulation. To investigate the potential mechanism controlling metabolism regulation in rice seed germination, we performed the lysine acetylation and succinylation analyses simultaneously. Using high-accuracy nano-LC-MS/MS in combination with the enrichment of lysine acetylated or succinylated peptides from digested embryonic proteins of 24 h after imbibition (HAI) rice seed, a total of 699 acetylated sites from 389 proteins and 665 succinylated sites from 261 proteins were identified. Among these modified lysine sites, 133 sites on 78 proteins were commonly modified by two PTMs. The overlapped PTM sites were more likely to be in polar acidic/basic amino acid regions and exposed on the protein surface. Both of the acetylated and succinylated proteins cover nearly all aspects of cellular functions. Ribosome complex and glycolysis/gluconeogenesis-related proteins were significantly enriched in both acetylated and succinylated protein profiles through KEGG enrichment and protein-protein interaction network analyses. The acetyl-CoA and succinyl-CoA metabolism-related enzymes were found to be extensively modified by both modifications, implying the functional interaction between the two PTMs. This study provides a rich resource to examine the modulation of the two PTMs on the metabolism pathway and other biological processes in germinating rice seed.
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Affiliation(s)
- Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
| | - Qiong Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Ming Li
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
| | - Rebecca Njeri Damaris
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xingling Yi
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd. , Hangzhou 310018, China
| | - Zhongyi Cheng
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd. , Hangzhou 310018, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
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66
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He D, Damaris RN, Fu J, Tu J, Fu T, Xi C, Yi B, Yang P. Differential Molecular Responses of Rapeseed Cotyledons to Light and Dark Reveal Metabolic Adaptations toward Autotrophy Establishment. FRONTIERS IN PLANT SCIENCE 2016; 7:988. [PMID: 27471506 PMCID: PMC4944393 DOI: 10.3389/fpls.2016.00988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/22/2016] [Indexed: 05/23/2023]
Abstract
Photosynthesis competent autotrophy is established during the postgerminative stage of plant growth. Among the multiple factors, light plays a decisive role in the switch from heterotrophic to autotrophic growth. Under dark conditions, the rapeseed hypocotyl extends quickly with an apical hook, and the cotyledon is yellow and folded, and maintains high levels of the isocitrate lyase (ICL). By contrast, in the light, the hypocotyl extends slowly, the cotyledon unfolds and turns green, the ICL content changes in parallel with cotyledon greening. To reveal metabolic adaptations during the establishment of postgerminative autotrophy in rapeseed, we conducted comparative proteomic and metabolomic analyses of the cotyledons of seedlings grown under light versus dark conditions. Under both conditions, the increase in proteases, fatty acid β-oxidation and glyoxylate-cycle related proteins was accompanied by rapid degradation of the stored proteins and lipids with an accumulation of the amino acids. While light condition partially retarded these conversions. Light significantly induced the expression of chlorophyll-binding and photorespiration related proteins, resulting in an increase in reducing-sugars. However, the levels of some chlorophyllide conversion, Calvin-cycle and photorespiration related proteins also accumulated in dark grown cotyledons, implying that the transition from heterotrophy to autotrophy is programmed in the seed rather than induced by light. Various anti-stress systems, e.g., redox related proteins, salicylic acid, proline and chaperones, were employed to decrease oxidative stress, which was mainly derived from lipid oxidation or photorespiration, under both conditions. This study provides a comprehensive understanding of the differential molecular responses of rapeseed cotyledons to light and dark conditions, which will facilitate further study on the complex mechanism underlying the transition from heterotrophy to autotrophy.
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Affiliation(s)
- Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Rebecca N. Damaris
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jinlei Fu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
| | - Chen Xi
- Wuhan Institute of BiotechnologyWuhan, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Bin Yi, Pingfang Yang,
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- Sino-African Joint Research Center, Chinese Academy of SciencesWuhan, China
- *Correspondence: Bin Yi, Pingfang Yang,
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67
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Abstract
Phosphorylation is one of the most important reversible protein modifications and is involved in regulating signal transduction, subcellular localization and enzyme activity of target proteins. Phosphorylation or dephosphorylation of proteins is directly reflected in changed ratios of phosphoprotein abundance and total protein abundance. Two-dimensional gel electrophoresis (2-DE)-based proteomics allow quantification of both total protein abundance by Coomassie Brilliant Blue (CBB) staining and phosphoprotein abundance by fluorescence-based staining. Pro-Q diamond phosphoprotein stain (Pro-Q DPS) can bind to the phosphate moiety of the phospho-amino acid directly, regardless of the nature of the phospho-amino acid. Phosphoproteins can thus be detected using proper excitation light, quantified using image analysis software and subsequently be subjected to analysis by mass spectrometry. Here, we describe a protein phosphorylation status analysis method combining both CBB and Pro-Q DPS staining based on 2-DE gel-based phosphoproteomics, which has been widely applied to plant phosphoproteomics studies.
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Affiliation(s)
- Chao Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan, 430074, China.
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68
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Xu E, Chen M, He H, Zhan C, Cheng Y, Zhang H, Wang Z. Proteomic Analysis Reveals Proteins Involved in Seed Imbibition under Salt Stress in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:2006. [PMID: 28105039 PMCID: PMC5213780 DOI: 10.3389/fpls.2016.02006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/16/2016] [Indexed: 05/20/2023]
Abstract
Enhancement of salinity tolerance during seed germination is very important for direct seeding in rice. In this study, the salt-tolerant japonica landrace Jiucaiqing was used to determine the regulators that are involved in seed imbibition under salt stress. Briefly, the comparative proteomic analysis was conducted between dry (0 h) and imbibed (24 h) seeds with 150 mM NaCl. Under salt stress, the uptake of water increased rapidly before 24 h imbibition (Phase I), followed by a plateau of seed imbibition from 24 to 96 h imbibition (Phase II). We identified 14 proteins involved in seed imbibition, in which the majority of these proteins were involved in energy supply and storage protein. The early imbibition process was mediated by protein catabolism; the most of proteins were down-regulated after 24 h imbibition. Eleven genes in salt stress treated seeds were expressed early during the seed imbibition in comparison to control seeds. By comparison, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (BPM), glutelin (GLU2.2 and GLU2.3), glucose-1-phosphate adenylyltransferase large subunit (GAS8), and cupin domain containing protein (CDP3.1 and CDP3.2) were near the regions of quantitative trait loci (QTLs) for seed dormancy, seed reserve utilization, and seed germination in Jiucaiqing. In particular, CDP3.1 was co-located in the region of qIR-3 for imbibition rate, and qGP-3 for germination percentage. The role of CDP3.1 was verified in enhancing seed germination under salt stress using T-DNA mutant. The identified proteins might be applicable for the improvement of seed germination under salt stress in rice.
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Affiliation(s)
- Enshun Xu
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Mingming Chen
- Department of Plant Science, College of Biological Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Hui He
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Chengfang Zhan
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Yanhao Cheng
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Hongsheng Zhang
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Hongsheng Zhang
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
- Zhoufei Wang
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69
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Induction and quantitative proteomic analysis of cell dedifferentiation during callus formation of lotus (Nelumbo nucifera Gaertn.spp. baijianlian). J Proteomics 2016; 131:61-70. [DOI: 10.1016/j.jprot.2015.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/29/2015] [Accepted: 10/08/2015] [Indexed: 11/23/2022]
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70
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Gu J, Chao H, Gan L, Guo L, Zhang K, Li Y, Wang H, Raboanatahiry N, Li M. Proteomic Dissection of Seed Germination and Seedling Establishment in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1482. [PMID: 27822216 PMCID: PMC5075573 DOI: 10.3389/fpls.2016.01482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/20/2016] [Indexed: 05/22/2023]
Abstract
The success of seed germination and establishment of a normal seedling are key determinants of plant species propagation. At present, only a few studies have focused on the genetic control of seed germination by using a proteomic approach in Brassica napus. In the present study, the protein expression pattern of seed germination was investigated using differential fluorescence two-dimensional gel electrophoresis in B. napus. One hundred and thirteen differentially expressed proteins (DEPs) that were mainly involved in storage (23.4%), energy metabolism (18.9%), protein metabolism (16.2%), defense/disease (12.6%), seed maturation (11.7%), carbohydrate metabolism (4.5%), lipid metabolism (4.5%), amino acids metabolism (3.6%), cell growth/division (3.6%), and some unclear functions (2.7%) were observed by proteomic analysis. Seventeen genes corresponding to 11 DEPs were identified within or near the associated linkage disequilibrium regions related to seed germination and vigor quantitative traits reported in B. napus in previous studies. The expression pattern of proteins showed that heterotrophic metabolism could be activated in the process of seed germination and that the onset of defense mechanisms might start during seed germination. These findings will help generate a more in-depth understanding of the mobilization of seed storage reserves and regulation mechanisms of the germination process in B. napus.
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Affiliation(s)
- Jianwei Gu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Lu Gan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Yonghong Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic ImprovementYangling, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- *Correspondence: Maoteng Li
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71
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He D, Wang Q, Wang K, Yang P. Genome-Wide Dissection of the MicroRNA Expression Profile in Rice Embryo during Early Stages of Seed Germination. PLoS One 2015; 10:e0145424. [PMID: 26681181 PMCID: PMC4683037 DOI: 10.1371/journal.pone.0145424] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
The first 24 hours after imbibition (HAI) is pivotal for rice seed germination, during which embryo cells switch from a quiescent state to a metabolically active state rapidly. MicroRNAs (miRNAs) have increasingly been shown to play important roles in rice development. Nevertheless, limited knowledge about miRNA regulation has been obtained in the early stages of rice seed germination. In this study, the small RNAs (sRNAs) from embryos of 0, 12, and 24 HAI rice seeds were sequenced to investigate the composition and expression patterns of miRNAs. The bioinformatics analysis identified 289 miRNA loci, including 59 known and 230 novel miRNAs, and 35 selected miRNAs were confirmed by stem-loop real-time RT-PCR. Expression analysis revealed that the dry and imbibed seeds have unique miRNA expression patterns compared with other tissues, particularly for the dry seeds. Using three methods, Mireap, psRNATarget and degradome analyses, 1197 potential target genes of identified miRNAs involved in various molecular functions were predicted. Among these target genes, 39 had significantly negative correlations with their corresponding miRNAs as inferred from published transcriptome data, and 6 inversely expressed miRNA-target pairs were confirmed by 5'-RACE assay. Our work provides an inventory of miRNA expression profiles and miRNA-target interactions in rice embryos, and lays a foundation for further studies of miRNA-mediated regulation in initial seed germination.
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Affiliation(s)
- Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qiong Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Wang
- College of life science, Wuhan University, Wuhan 430072, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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72
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Li M, Wang K, Li S, Yang P. Exploration of rice pistil responses during early post-pollination through a combined proteomic and transcriptomic analysis. J Proteomics 2015; 131:214-226. [PMID: 26546731 DOI: 10.1016/j.jprot.2015.11.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 11/27/2022]
Abstract
UNLABELLED Pollen-stigma interaction is a multi-step and complex physiological process which contains different signaling and biochemical pathways. However, little is known about the molecular mechanism underlying this process in rice (Oryza sativa). In this study, the changes of gene expression were investigated through a combination study of transcriptome and proteome profiles in rice pistil during pollination. Totally, 1117 differentially expressed genes were identified, among which 962 and 167 were detected at transcriptional and protein level respectively. Functional categorization analysis showed that the genes involved in central metabolism were up-regulated, which can lead to the enhancement of these metabolisms. The reactive oxygen species (ROS) were over-accumulated in the stigma. In response to this, the proteins or transcripts involved in redox homeostasis regulation were differentially expressed. Furthermore, significant changes of protein ubiquitination and its related genes or proteins, especially some E3 ligases encoding genes, indicate that protein ubiquitination might play important roles in cell signal transduction during the pollination process. Our study sheds some lights on gene and protein expression profiles of rice pistil pollination process, and gives us a comprehensive understanding of the basic molecular mechanisms controlling pollination in rice. BIOLOGICAL SIGNIFICANCE Using RNA-seq, 2-DE and iTRAQ assays, we have generated the large-scale transcriptomic and proteomic data containing abundant information on genes involved in pollen and pistil interaction. Our results showed that ROS were significantly accumulated in stigma after pollination, and the abundance of genes involve in redox homeostasis system were changed variously. We also show that, changes of some E3 ligases encoding genes might indicate that protein ubiquitination play important roles in cell signal transduction during the pollination process. Data in this study might be helpful to deeply understand the pollination in rice.
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Affiliation(s)
- Ming Li
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Kun Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
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73
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Chinma CE, Anuonye JC, Simon OC, Ohiare RO, Danbaba N. Effect of germination on the physicochemical and antioxidant characteristics of rice flour from three rice varieties from Nigeria. Food Chem 2015; 185:454-8. [DOI: 10.1016/j.foodchem.2015.04.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/03/2015] [Accepted: 04/04/2015] [Indexed: 01/01/2023]
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74
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Takano S, Matsuda S, Funabiki A, Furukawa JI, Yamauchi T, Tokuji Y, Nakazono M, Shinohara Y, Takamure I, Kato K. The rice RCN11 gene encodes β1,2-xylosyltransferase and is required for plant responses to abiotic stresses and phytohormones. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:75-88. [PMID: 26025522 DOI: 10.1016/j.plantsci.2015.03.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/17/2015] [Accepted: 03/30/2015] [Indexed: 05/23/2023]
Abstract
Seed germination rates and plant development and growth under abiotic stress are important aspects of crop productivity. Here, our characterization of the rice (Oryza sativa L.) mutant reduced culm number11 (rcn11) showed that RCN11 controls growth of plants exposed to abnormal temperature, salinity and drought conditions. RCN11 also mediates root aerenchyma formation under oxygen-deficient conditions and ABA sensitivity during seed germination. Molecular studies showed that the rcn11 mutation resulted from a 966-bp deletion that caused loss of function of β1,2-xylosyltransferase (OsXylT). This enzyme is located in the Golgi apparatus where it catalyzes the transfer of xylose from UDP-xylose to the core β-linked mannose of N-glycans. RCN11/OsXylT promoter activity was observed in the basal part of the shoot containing the shoot and axillary meristems and in the base of crown roots. The level of RCN11/OsXylT expression was regulated by multiple phytohormones and various abiotic stresses suggesting that plant specific N-glycosylation is regulated by multiple signals in rice plants. The present study is the first to demonstrate that rice β1,2-linked xylose residues on N-glycans are critical for seed germination and plant development and growth under conditions of abiotic stress.
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Affiliation(s)
- Sho Takano
- Department of Agro-environmental Science, Obihiro University of Agricultural and Veterinary Medicine, 2-11 Nishi, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Shuichi Matsuda
- Department of Agro-environmental Science, Obihiro University of Agricultural and Veterinary Medicine, 2-11 Nishi, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Atsushi Funabiki
- Department of Agro-environmental Science, Obihiro University of Agricultural and Veterinary Medicine, 2-11 Nishi, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Jun-ichi Furukawa
- Graduate School of Advanced Life Science, Laboratory of Advanced Chemical Biology, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Takaki Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Yoshihiko Tokuji
- Department of Food Science, Obihiro University of Agricultural and Veterinary Medicine, 2-11 Nishi, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Mikio Nakazono
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Yasuro Shinohara
- Graduate School of Advanced Life Science, Laboratory of Advanced Chemical Biology, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Itsuro Takamure
- Graduate School of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Kiyoaki Kato
- Department of Agro-environmental Science, Obihiro University of Agricultural and Veterinary Medicine, 2-11 Nishi, Inada, Obihiro, Hokkaido 080-8555, Japan.
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75
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Li M, Yin X, Sakata K, Yang P, Komatsu S. Proteomic Analysis of Phosphoproteins in the Rice Nucleus During the Early Stage of Seed Germination. J Proteome Res 2015; 14:2884-96. [DOI: 10.1021/acs.jproteome.5b00215] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ming Li
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Xiaojian Yin
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Katsumi Sakata
- Department
of Life Science and Informatics, Maebashi Institute of Technology, Maebashi 371-0816, Japan
| | - Pingfang Yang
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Setsuko Komatsu
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
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76
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Xu H, Wei Y, Zhu Y, Lian L, Xie H, Cai Q, Chen Q, Lin Z, Wang Z, Xie H, Zhang J. Antisense suppression of LOX3 gene expression in rice endosperm enhances seed longevity. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:526-39. [PMID: 25545811 DOI: 10.1111/pbi.12277] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/04/2014] [Accepted: 09/10/2014] [Indexed: 05/20/2023]
Abstract
Lipid peroxidation plays a major role in seed longevity and viability. In rice grains, lipid peroxidation is catalyzed by the enzyme lipoxygenase 3 (LOX3). Previous reports showed that grain from the rice variety DawDam in which the LOX3 gene was deleted had less stale flavour after grain storage than normal rice. The molecular mechanism by which LOX3 expression is regulated during endosperm development remains unclear. In this study, we expressed a LOX3 antisense construct in transgenic rice (Oryza sativa L.) plants to down-regulate LOX3 expression in rice endosperm. The transgenic plants exhibited a marked decrease in LOX mRNA levels, normal phenotypes and a normal life cycle. We showed that LOX3 activity and its ability to produce 9-hydroperoxyoctadecadienoic acid (9-HPOD) from linoleic acid were significantly lower in transgenic seeds than in wild-type seeds by measuring the ultraviolet absorption of 9-HPOD at 234 nm and by high-performance liquid chromatography. The suppression of LOX3 expression in rice endosperm increased grain storability. The germination rate of TS-91 (antisense LOX3 transgenic line) was much higher than the WT (29% higher after artificial ageing for 21 days, and 40% higher after natural ageing for 12 months). To our knowledge, this is the first report to demonstrate that decreased LOX3 expression can preserve rice grain quality during storage with no impact on grain yield, suggesting potential applications in agricultural production.
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Affiliation(s)
- Huibin Xu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China; Incubator of National Key Laboratory of Fujian Crop Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture, Fuzhou, China; South-China Base of National Key Laboratory of Hybrid Rice of China, Fuzhou, China; National Engineering Laboratory of Rice, Fuzhou, Fujian, China
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77
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Liu SJ, Xu HH, Wang WQ, Li N, Wang WP, Møller IM, Song SQ. A proteomic analysis of rice seed germination as affected by high temperature and ABA treatment. PHYSIOLOGIA PLANTARUM 2015; 154:142-161. [PMID: 25270993 DOI: 10.1111/ppl.12292] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 09/07/2014] [Accepted: 09/09/2014] [Indexed: 06/03/2023]
Abstract
Seed germination is a critical phase in the plant life cycle, but the specific events associated with seed germination are still not fully understood. In this study, we used two-dimensional gel electrophoresis followed by mass spectrometry to investigate the changes in the proteome during imbibition of Oryza sativa seeds at optimal temperature with or without abscisic acid (ABA) and high temperature (germination thermoinhibition) to further identify and quantify key proteins required for seed germination. A total of 121 protein spots showed a significant change in abundance (1.5-fold increase/decrease) during germination under all conditions. Among these proteins, we found seven proteins specifically associated with seed germination including glycosyl hydrolases family 38 protein, granule-bound starch synthase 1, Os03g0842900 (putative steroleosin-B), N-carbamoylputrescine amidase, spermidine synthase 1, tubulin α-1 chain and glutelin type-A; and a total of 20 imbibition response proteins involved in energy metabolism, cell growth, cell defense and storage proteins. High temperature inhibited seed germination by decreasing the abundance of proteins involved in methionine metabolism, amino acid biosynthesis, energy metabolism, reserve degradation, protein folding and stress responses. ABA treatment inhibited germination and decreased the abundance of proteins associated with methionine metabolism, energy production and cell division. Our results show that changes in many biological processes including energy metabolism, protein synthesis and cell defense and rescue occurred as a result of all treatments, while enzymes involved in methionine metabolism and weakening of cell wall specifically accumulated when the seeds germinated at the optimal temperature.
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Affiliation(s)
- Shu-Jun Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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78
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He M, Zhu C, Dong K, Zhang T, Cheng Z, Li J, Yan Y. Comparative proteome analysis of embryo and endosperm reveals central differential expression proteins involved in wheat seed germination. BMC PLANT BIOLOGY 2015; 15:97. [PMID: 25888100 PMCID: PMC4407426 DOI: 10.1186/s12870-015-0471-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 03/16/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Wheat seeds provide a staple food and an important protein source for the world's population. Seed germination is vital to wheat growth and development and directly affects grain yield and quality. In this study, we performed the first comparative proteomic analysis of wheat embryo and endosperm during seed germination. RESULTS The proteomic changes in embryo and endosperm during the four different seed germination stages of elite Chinese bread wheat cultivar Zhengmai 9023 were first investigated. In total, 74 and 34 differentially expressed protein (DEP) spots representing 63 and 26 unique proteins were identified in embryo and endosperm, respectively. Eight common DEP were present in both tissues, and 55 and 18 DEP were specific to embryo and endosperm, respectively. These identified DEP spots could be sorted into 13 functional groups, in which the main group was involved in different metabolism pathways, particularly in the reserves necessary for mobilization in preparation for seed germination. The DEPs from the embryo were mainly related to carbohydrate metabolism, proteometabolism, amino acid metabolism, nucleic acid metabolism, and stress-related proteins, whereas those from the endosperm were mainly involved in protein storage, carbohydrate metabolism, inhibitors, stress response, and protein synthesis. During seed germination, both embryo and endosperm had a basic pattern of oxygen consumption, so the proteins related to respiration and energy metabolism were up-regulated or down-regulated along with respiration of wheat seeds. When germination was complete, most storage proteins from the endosperm began to be mobilized, but only a small amount was degraded during germination. Transcription expression of six representative DEP genes at the mRNA level was consistent with their protein expression changes. CONCLUSION Wheat seed germination is a complex process with imbibition, stirring, and germination stages, which involve a series of physiological, morphological, and proteomic changes. The first process is a rapid water uptake, in which the seed coat becomes softer and the physical state of storage materials change gradually. Then the germinated seed enters the second process (a plateau phase) and the third process (the embryonic axes elongation). Seed embryo and endosperm display distinct differentially expressed proteins, and their synergistic expression mechanisms provide a basis for the normal germination of wheat seeds.
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Affiliation(s)
- Miao He
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Chong Zhu
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Kun Dong
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Ting Zhang
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Zhiwei Cheng
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Jiarui Li
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing, 100048, China.
- Hubei Collaborative Innovation Center for Grain Industry, 434025, Jingzhou, China.
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79
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Cornejo F, Caceres PJ, Martínez-Villaluenga C, Rosell CM, Frias J. Effects of germination on the nutritive value and bioactive compounds of brown rice breads. Food Chem 2015; 173:298-304. [DOI: 10.1016/j.foodchem.2014.10.037] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/28/2014] [Accepted: 10/07/2014] [Indexed: 10/24/2022]
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80
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Han C, Yang P. Studies on the molecular mechanisms of seed germination. Proteomics 2015; 15:1671-9. [PMID: 25597791 DOI: 10.1002/pmic.201400375] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 12/03/2014] [Accepted: 01/14/2015] [Indexed: 11/07/2022]
Abstract
Seed germination that begins with imbibition and ends with radicle emergence is the first step for plant growth. Successful germination is not only crucial for seedling establishment but also important for crop yield. After being dispersed from mother plant, seed undergoes continuous desiccation in ecosystem and selects proper environment to trigger germination. Owing to the contribution of transcriptomic, proteomic, and molecular biological studies, molecular aspect of seed germination is elucidated well in Arabidopsis. Recently, more and more proteomic and genetic studies concerning cereal seed germination were performed on rice (Oryza sativa) and barley (Hordeum vulgare), which possess completely different seed structure and domestication background with Arabidopsis. In this review, both the common features and the distinct mechanisms of seed germination are compared among different plant species including Arabidopsis, rice, and maize. These features include morphological changes, cell and its related structure recovery, metabolic activation, hormone behavior, and transcription and translation activation. This review will provide more comprehensive insights into the molecular mechanisms of seed germination.
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Affiliation(s)
- Chao Han
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
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81
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Transcriptomic changes during tuber dormancy release process revealed by RNA sequencing in potato. J Biotechnol 2015; 198:17-30. [PMID: 25661840 DOI: 10.1016/j.jbiotec.2015.01.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 01/16/2015] [Accepted: 01/26/2015] [Indexed: 12/15/2022]
Abstract
Potato tuber dormancy release is a critical development process that allows potato to produce new plant. The first Illumina RNA sequencing to generate the expressed mRNAs at dormancy tuber (DT), dormancy release tuber (DRT) and sprouting tuber (ST) was performed. We identified 26,639 genes including 5,912 (3,450 up-regulated while 2,462 down-regulated) and 3,885 (2,141 up-regulated while 1,744 down-regulated) genes were differentially expressed from DT vs DRT and DRT vs ST. The RNA-Seq results were further verified using qRT-PCR. We found reserve mobilization events were activated before the bud emergence (DT vs DRT) and highlighted after dormancy release (DRT vs ST). Overexpressed genes related to metabolism of auxin, gibberellic acid, cytokinin and barssinosteriod were dominated in DT vs DRT, whereas overexpressed genes involved in metabolism of ethylene, jasmonate and salicylate were prominent in DRT vs ST. Various histone and cyclin isoforms associated genes involved in cell division/cycle were mainly up-regulated in DT vs DRT. Dormancy release process was also companied by stress response and redox regulation, those genes related to biotic stress, cell wall and second metabolism was preferentially overexpressed in DRT vs ST, which might accelerate dormancy breaking and sprout outgrowth. The metabolic processes activated during tuber dormancy release were also supported by plant seed models. These results represented the first comprehensive picture of a large number of genes involved in tuber dormancy release process.
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82
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Dogra V, Bagler G, Sreenivasulu Y. Re-analysis of protein data reveals the germination pathway and up accumulation mechanism of cell wall hydrolases during the radicle protrusion step of seed germination in Podophyllum hexandrum- a high altitude plant. FRONTIERS IN PLANT SCIENCE 2015; 6:874. [PMID: 26579141 PMCID: PMC4620410 DOI: 10.3389/fpls.2015.00874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 10/02/2015] [Indexed: 05/06/2023]
Abstract
Podophyllum hexandrum Royle is an important high-altitude plant of Himalayas with immense medicinal value. Earlier, it was reported that the cell wall hydrolases were up accumulated during radicle protrusion step of Podophyllum seed germination. In the present study, Podophyllum seed Germination protein interaction Network (PGN) was constructed by using the differentially accumulated protein (DAP) data set of Podophyllum during the radicle protrusion step of seed germination, with reference to Arabidopsis protein-protein interaction network (AtPIN). The developed PGN is comprised of a giant cluster with 1028 proteins having 10,519 interactions and a few small clusters with relevant gene ontological signatures. In this analysis, a germination pathway related cluster which is also central to the topology and information dynamics of PGN was obtained with a set of 60 key proteins. Among these, eight proteins which are known to be involved in signaling, metabolism, protein modification, cell wall modification, and cell cycle regulation processes were found commonly highlighted in both the proteomic and interactome analysis. The systems-level analysis of PGN identified the key proteins involved in radicle protrusion step of seed germination in Podophyllum.
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Affiliation(s)
- Vivek Dogra
- Biotechnology Division, Council of Scientific and Industrial Research-Institute of Himalayan Bioresource TechnologyPalampur, India
| | - Ganesh Bagler
- Centre for Biologically Inspired System Science, Indian Institute of Technology JodhpurJodhpur, India
- Ganesh Bagler
| | - Yelam Sreenivasulu
- Biotechnology Division, Council of Scientific and Industrial Research-Institute of Himalayan Bioresource TechnologyPalampur, India
- *Correspondence: Yelam Sreenivasulu ;
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83
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Liu B, Zhang N, Zhao S, Chang J, Wang Z, Zhang G, Si H, Wang D. Proteomic changes during tuber dormancy release process revealed by iTRAQ quantitative proteomics in potato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 86:181-190. [PMID: 25514565 DOI: 10.1016/j.plaphy.2014.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/03/2014] [Indexed: 05/28/2023]
Abstract
Given that limited information is available with regard to tuber dormancy release related proteome, we conducted proteome analysis of tuber dormancy release process at dormant tuber (DT), dormancy release tuber (DRT) and sprouting tuber (ST) using the iTRAQ technology. A total of 1,752 proteins were identified. Among them, a subset of 316 proteins was screened as significant up- (137) and down regulated (179) between DT vs DRT. A subset of 120 proteins experienced significant up- (40) or down-regulation (80) between DRT vs ST. The differentially expressed proteins were grouped into 11 functional categories. Proteins enriched in functional categories of major carbohydrate (CHO) metabolism, glycolysis, fermentation, amino acid metabolism, protein and transport were highly up-regulated, while functional categories of photosynthesis and RNA were down-regulated between DT vs DRT. Proteins enriched in functional groups of protein, cell wall, lipid metabolism, miscellaneous, and signaling were strongly up-regulated, while functional categories of photosynthesis, hormone metabolism and protein were down-regulated between DRT vs ST. Consistent with previous documented differentially expressed genes, most of differentially expressed proteins were also identified between DT and DRT, indicating the metabolism shift from growth suspension to growth activation as tubers dormancy breaking. The changes in protein profiles showed lower concordance with corresponding alterations in transcript levels, indicating possible transcriptional and posttranscriptional regulation. Furthermore, the possible mechanism of tuber dormancy release was discussed in relation to what was known in transcripts change and other plant models from carbohydrate metabolism, protein metabolism, stress response, redox regulation, transcription regulation, DNA metabolism, amino acid metabolism, development, signaling as well as hormone metabolism.
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Affiliation(s)
- Bailin Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, People's Republic of China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, People's Republic of China
| | - Ning Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, People's Republic of China
| | - Shuo Zhao
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 6C2, Canada
| | - Jing Chang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, People's Republic of China
| | - Zemin Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, People's Republic of China
| | - Guodong Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, People's Republic of China
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, People's Republic of China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, People's Republic of China.
| | - Di Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou 730070, People's Republic of China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, People's Republic of China.
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84
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Yang Y, Zhu K, Xia H, Chen L, Chen K. Comparative proteomic analysis of indica and japonica rice varieties. Genet Mol Biol 2014; 37:652-61. [PMID: 25505840 PMCID: PMC4261965 DOI: 10.1590/s1415-47572014005000015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 06/10/2014] [Indexed: 11/24/2022] Open
Abstract
Indica and japonica are two main subspecies of Asian cultivated rice (Oryza sativa L.) that differ clearly in morphological and agronomic traits, in physiological and biochemical characteristics and in their genomic structure. However, the proteins and genes responsible for these differences remain poorly characterized. In this study, proteomic tools, including two-dimensional electrophoresis and mass spectrometry, were used to globally identify proteins that differed between two sequenced rice varieties (93–11 and Nipponbare). In all, 47 proteins that differed significantly between 93–11 and Nipponbare were identified using mass spectrometry and database searches. Interestingly, seven proteins were expressed only in Nipponbare and one protein was expressed specifically in 93–11; these differences were confirmed by quantitative real-time PCR and proteomic analysis of other indica and japonica rice varieties. This is the first report to successfully demonstrate differences in the protein composition of indica and japonica rice varieties and to identify candidate proteins and genes for future investigation of their roles in the differentiation of indica and japonica rice.
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Affiliation(s)
- Yanhua Yang
- Institute of Life Sciences , Jiangsu University , Zhenjiang , PR China
| | - Keming Zhu
- Institute of Life Sciences , Jiangsu University , Zhenjiang , PR China
| | - Hengchuan Xia
- Institute of Life Sciences , Jiangsu University , Zhenjiang , PR China
| | - Liang Chen
- Institute of Life Sciences , Jiangsu University , Zhenjiang , PR China
| | - Keping Chen
- Institute of Life Sciences , Jiangsu University , Zhenjiang , PR China
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85
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Han C, He D, Li M, Yang P. In-Depth Proteomic Analysis of Rice Embryo Reveals its Important Roles in Seed Germination. ACTA ACUST UNITED AC 2014; 55:1826-47. [DOI: 10.1093/pcp/pcu114] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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86
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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.
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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
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87
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The mitochondrion-located protein OsB12D1 enhances flooding tolerance during seed germination and early seedling growth in rice. Int J Mol Sci 2014; 15:13461-81. [PMID: 25089878 PMCID: PMC4159805 DOI: 10.3390/ijms150813461] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 06/22/2014] [Accepted: 07/21/2014] [Indexed: 11/17/2022] Open
Abstract
B12D belongs to a function unknown subgroup of the Balem (Barley aleurone and embryo) proteins. In our previous work on rice seed germination, we identified a B12D-like protein encoded by LOC_Os7g41350 (named OsB12D1). OsB12D1 pertains to an ancient protein family with an amino acid sequence highly conserved from moss to angiosperms. Among the six OsB12Ds, OsB12D1 is one of the major transcripts and is primarily expressed in germinating seed and root. Bioinformatics analyses indicated that OsB12D1 is an anoxic or submergence resistance-related gene. RT-PCR results showed OsB12D1 is induced remarkably in the coleoptiles or roots by flooding during seed germination and early seedling growth. The OsB12D1-overexpressed rice seeds could protrude radicles in 8 cm deep water, further exhibiting significant flooding tolerance compared to the wild type. Moreover, this tolerance was not affected by the gibberellin biosynthesis inhibitor paclobutrazol. OsB12D1 was identified in the mitochondrion by subcellular localization analysis and possibly enhances electron transport through mediating Fe and oxygen availability under flooded conditions. This work indicated that OsB12D1 is a promising gene that can help to enhance rice seedling establishment in farming practices, especially for direct seeding.
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88
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OsRACK1 is involved in abscisic acid- and H2O2-mediated signaling to regulate seed germination in rice (Oryza sativa, L.). PLoS One 2014; 9:e97120. [PMID: 24865690 PMCID: PMC4035261 DOI: 10.1371/journal.pone.0097120] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 04/07/2014] [Indexed: 12/23/2022] Open
Abstract
The receptor for activated C kinase 1 (RACK1) is one member of the most important WD repeat–containing family of proteins found in all eukaryotes and is involved in multiple signaling pathways. However, compared with the progress in the area of mammalian RACK1, our understanding of the functions and molecular mechanisms of RACK1 in the regulation of plant growth and development is still in its infancy. In the present study, we investigated the roles of rice RACK1A gene (OsRACK1A) in controlling seed germination and its molecular mechanisms by generating a series of transgenic rice lines, of which OsRACK1A was either over-expressed or under-expressed. Our results showed that OsRACK1A positively regulated seed germination and negatively regulated the responses of seed germination to both exogenous ABA and H2O2. Inhibition of ABA biosynthesis had no enhancing effect on germination, whereas inhibition of ABA catabolism significantly suppressed germination. ABA inhibition on seed germination was almost fully recovered by exogenous H2O2 treatment. Quantitative analyses showed that endogenous ABA levels were significantly higher and H2O2 levels significantly lower in OsRACK1A-down regulated transgenic lines as compared with those in wildtype or OsRACK1A-up regulated lines. Quantitative real-time PCR analyses showed that the transcript levels of OsRbohs and amylase genes, RAmy1A and RAmy3D, were significantly lower in OsRACK1A-down regulated transgenic lines. It is concluded that OsRACK1A positively regulates seed germination by controlling endogenous levels of ABA and H2O2 and their interaction.
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89
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Fercha A, Capriotti AL, Caruso G, Cavaliere C, Samperi R, Stampachiacchiere S, Laganà A. Comparative analysis of metabolic proteome variation in ascorbate-primed and unprimed wheat seeds during germination under salt stress. J Proteomics 2014; 108:238-57. [PMID: 24859728 DOI: 10.1016/j.jprot.2014.04.040] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/11/2014] [Accepted: 04/26/2014] [Indexed: 12/01/2022]
Abstract
UNLABELLED Seed priming with ascorbic acid improves salt tolerance in durum wheat. For understanding the potential mechanisms underlying this priming effect a gel-free shotgun proteomic analysis was performed comparing unprimed to ascorbate-primed wheat seed during germination under saline and non-saline conditions. Since seed germination is the result of interplay or cross-talk between embryo and embryo-surrounding tissues, we studied the variation of metabolic proteome in both tissues separately. 167 of 697 identified and 69 of 471 identified proteins increase or decrease in abundance significantly in response to priming and/or salinity compared to untreated, unstressed control in embryo and embryo-surrounding tissues, respectively. In untreated wheat embryo salt stress was accompanied by change in 129 proteins, most of which are belonging to metabolism, energy, disease/defense, protein destination and storage categories. Ascorbate pretreatment prevents and counteracts the effects of salinity upon most of these proteins and changes specifically the abundance of 35 others proteins, most of which are involved in metabolism, protein destination and storage categories. Hierarchical clustering analysis revealed three and two major clusters of protein expression in embryo and embryo-surrounding tissues, respectively. This study opens promising new avenues to understand priming-induced salt tolerance in plants. BIOLOGICAL SIGNIFICANCE To clearly understand how ascorbate-priming enhance the salt tolerance of durum wheat during germination, we performed for the first time a comparative shotgun proteomic analysis between unprimed and ascorbate-primed wheat seeds during germination under saline and non-saline conditions. Furthermore, since seed germination is the result of interplay or cross-talk between embryo and embryo-surrounding tissues we analyzed the variation of metabolic proteome in both tissues separately. 1168 proteins exhibiting greater molecular weight diversity (ranging from 5 to 258kDa) were identified. Among them, 167 and 69 proteins were increased or decreased in abundance significantly by priming and/or salinity as compared to control, in embryo and embryo-surrounding tissues respectively. Ascorbate pretreatment alleviates the effects of salinity upon most of these proteins, particularly those involved in metabolism, energy, disease/defense, protein destination and storage functions. Hierarchical clustering analysis revealed three and two major clusters of protein accumulation in embryo and embryo-surrounding tissues, respectively. These results may provide new avenues for understanding and advancing priming-induced salt tolerance in crop plants.
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Affiliation(s)
- Azzedine Fercha
- Department of Biology, University of Abbès Laghrour Khenchela, 40000 Khenchela, Algeria; Department of Biology, University of Mentouri Constantine, 25000 Constantine, Algeria
| | - Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Giuseppe Caruso
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Roberto Samperi
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | | | - Aldo Laganà
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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90
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Han C, Yang P, Sakata K, Komatsu S. Quantitative proteomics reveals the role of protein phosphorylation in rice embryos during early stages of germination. J Proteome Res 2014; 13:1766-82. [PMID: 24460219 DOI: 10.1021/pr401295c] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Seed germination begins with water uptake and ends with radicle emergence. A gel-free phosphoproteomic technique was used to investigate the role of protein phosphorylation events in the early stages of rice seed germination. Both seed weight and ATP content increased gradually during the first 24 h following imbibition. Proteomic analysis indicated that carbohydrate metabolism- and protein synthesis/degradation-related proteins were predominantly increased and displayed temporal patterns of expression. Analyses of cluster and protein-protein interactions indicated that the regulation of sucrose synthases and alpha-amylases was the central event controlling germination. Phosphoproteomic analysis identified several proteins involved in protein modification and transcriptional regulation that exhibited significantly temporal changes in phosphorylation levels during germination. Cluster analysis indicated that 12 protein modification-related proteins had a peak abundance of phosphoproteins at 12 h after imbibition. These results suggest that the first 12 h following imbibition is a potentially important signal transduction phase for the initiation of rice seed germination. Three core components involved in brassinosteroid signal transduction displayed significant increases in phosphoprotein abundance during the early stages of germination. Brassinolide treatment increased the rice seed germination rate but not the rate of embryonic axis elongation. These findings suggest that brassinosteroid signal transduction likely triggers seed germination.
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Affiliation(s)
- Chao Han
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences , Moshan, Wuchang, Wuhan 430074, China
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91
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Kim ST, Kim SG, Agrawal GK, Kikuchi S, Rakwal R. Rice proteomics: a model system for crop improvement and food security. Proteomics 2014; 14:593-610. [PMID: 24323464 DOI: 10.1002/pmic.201300388] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/24/2013] [Accepted: 11/07/2013] [Indexed: 12/14/2022]
Abstract
Rice proteomics has progressed at a tremendous pace since the year 2000, and that has resulted in establishing and understanding the proteomes of tissues, organs, and organelles under both normal and abnormal (adverse) environmental conditions. Established proteomes have also helped in re-annotating the rice genome and revealing the new role of previously known proteins. The progress of rice proteomics had recognized it as the corner/stepping stone for at least cereal crops. Rice proteomics remains a model system for crops as per its exemplary proteomics research. Proteomics-based discoveries in rice are likely to be translated in improving crop plants and vice versa against ever-changing environmental factors. This review comprehensively covers rice proteomics studies from August 2010 to July 2013, with major focus on rice responses to diverse abiotic (drought, salt, oxidative, temperature, nutrient, hormone, metal ions, UV radiation, and ozone) as well as various biotic stresses, especially rice-pathogen interactions. The differentially regulated proteins in response to various abiotic stresses in different tissues have also been summarized, indicating key metabolic and regulatory pathways. We envision a significant role of rice proteomics in addressing the global ground level problem of food security, to meet the demands of the human population which is expected to reach six to nine billion by 2040.
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Affiliation(s)
- Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
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92
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Neilson KA, George IS, Emery SJ, Muralidharan S, Mirzaei M, Haynes PA. Analysis of rice proteins using SDS-PAGE shotgun proteomics. Methods Mol Biol 2014; 1072:289-302. [PMID: 24136530 DOI: 10.1007/978-1-62703-631-3_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this chapter we describe the workflow used in our laboratory to analyze rice leaf samples using label-free shotgun proteomics based on SDS-PAGE fractionation of proteins. Rice proteomics has benefitted substantially from successful execution of shotgun proteomics techniques. We describe steps on how to proceed starting from rice protein extraction, SDS-PAGE, in-gel protein digestion with trypsin, nanoLC-MS/MS, and database searching using the GPM. Data from these experiments can be used for spectral counting, where simultaneous quantitation of several thousand proteins can be obtained.
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Affiliation(s)
- Karlie A Neilson
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
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93
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Arcalis E, Ibl V, Peters J, Melnik S, Stoger E. The dynamic behavior of storage organelles in developing cereal seeds and its impact on the production of recombinant proteins. FRONTIERS IN PLANT SCIENCE 2014; 5:439. [PMID: 25232360 PMCID: PMC4153030 DOI: 10.3389/fpls.2014.00439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 08/15/2014] [Indexed: 05/22/2023]
Abstract
Cereal endosperm is a highly differentiated tissue containing specialized organelles for the accumulation of storage proteins, which are ultimately deposited either within protein bodies derived from the endoplasmic reticulum, or in protein storage vacuoles (PSVs). During seed maturation endosperm cells undergo a rapid sequence of developmental changes, including extensive reorganization and rearrangement of the endomembrane system and protein transport via several developmentally regulated trafficking routes. Storage organelles have been characterized in great detail by the histochemical analysis of fixed immature tissue samples. More recently, in vivo imaging and the use of tonoplast markers and fluorescent organelle tracers have provided further insight into the dynamic morphology of PSVs in different cell layers of the developing endosperm. This is relevant for biotechnological applications in the area of molecular farming because seed storage organelles in different cereal crops offer alternative subcellular destinations for the deposition of recombinant proteins that can reduce proteolytic degradation, allow control over glycan structures and increase the efficacy of oral delivery. We discuss how the specialized architecture and developmental changes of the endomembrane system in endosperm cells may influence the subcellular fate and post-translational modification of recombinant glycoproteins in different cereal species.
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Affiliation(s)
| | | | | | | | - Eva Stoger
- *Correspondence: Eva Stoger, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria e-mail:
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94
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Cáceres PJ, Martínez-Villaluenga C, Amigo L, Frias J. Maximising the phytochemical content and antioxidant activity of Ecuadorian brown rice sprouts through optimal germination conditions. Food Chem 2013; 152:407-14. [PMID: 24444955 DOI: 10.1016/j.foodchem.2013.11.156] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/21/2013] [Accepted: 11/26/2013] [Indexed: 11/18/2022]
Abstract
Germinated brown rice (GBR) is considered a healthy alternative to white rice in the fight against chronic diseases. As the functional quality of GBR depends on genotype and germination conditions, the objectives were to identify suitable Ecuadorian brown rice cultivars and optimal germination time and temperature to maximise γ-aminobutyric acid (GABA), total phenolics compounds (TPC) and antioxidant activity of GBR. Regression models for the prediction of phytochemical composition and antioxidant activity in GBR were also obtained. Germination improved GABA, TPC and antioxidant activity in all cultivars. Maximum GABA and antioxidant activity were attained at 34 °C for 96 h, while the highest TPC was found at 28 °C for 96 h in all cultivars. GBR cv. GO displayed the highest antioxidant activity and cv. 15 was the most effective at accumulating GABA and TPC in the optimal germination conditions. Therefore, Ecuadorian GBR could be used for the preparation of functional foods serving as preventative strategies in combating chronic diseases.
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Affiliation(s)
- Patricio J Cáceres
- Technical High School of the Litoral (ESPOL), Campus Gustavo Galindo Velasco, km 30, 5 Vía Perimetral, 09-01-5863 Guayaquil, Ecuador; Institute of Food Science, Technology and Nutrition (ICTAN-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Lourdes Amigo
- Institute of Food Science Research, CIAL (CSIC-UAM), Nicolás Cabrera 9, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Juana Frias
- Institute of Food Science, Technology and Nutrition (ICTAN-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain.
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95
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Gao F, Rampitsch C, Chitnis VR, Humphreys GD, Jordan MC, Ayele BT. Integrated analysis of seed proteome and mRNA oxidation reveals distinct post-transcriptional features regulating dormancy in wheat (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2013; 11:921-32. [PMID: 23745731 DOI: 10.1111/pbi.12083] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/08/2013] [Accepted: 04/15/2013] [Indexed: 05/20/2023]
Abstract
Wheat seeds can be released from a dormant state by after-ripening; however, the underlying molecular mechanisms are still mostly unknown. We previously identified transcriptional programmes involved in the regulation of after-ripening-mediated seed dormancy decay in wheat (Triticum aestivum L.). Here, we show that seed dormancy maintenance and its release by dry after-ripening in wheat is associated with oxidative modification of distinct seed-stored mRNAs that mainly correspond to oxidative phosphorylation, ribosome biogenesis, nutrient reservoir and α-amylase inhibitor activities, suggesting the significance of post-transcriptional repression of these biological processes in regulating seed dormancy. We further show that after-ripening induced seed dormancy release in wheat is mediated by differential expression of specific proteins in both dry and hydrated states, including those involved in proteolysis, cellular signalling, translation and energy metabolism. Among the genes corresponding to these proteins, the expression of those encoding α-amylase/trypsin inhibitor and starch synthase appears to be regulated by mRNA oxidation. Co-expression analysis of the probesets differentially expressed and oxidized during dry after-ripening along with those corresponding to proteins differentially regulated between dormant and after-ripened seeds produced three co-expressed gene clusters containing more candidate genes potentially involved in the regulation of seed dormancy in wheat. Two of the three clusters are enriched with elements that are either abscisic acid (ABA) responsive or recognized by ABA-regulated transcription factors, indicating the association between wheat seed dormancy and ABA sensitivity.
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Affiliation(s)
- Feng Gao
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
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96
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Miro B, Ismail AM. Tolerance of anaerobic conditions caused by flooding during germination and early growth in rice (Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2013; 4:269. [PMID: 23888162 PMCID: PMC3719019 DOI: 10.3389/fpls.2013.00269] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 07/02/2013] [Indexed: 05/20/2023]
Abstract
Rice is semi-aquatic, adapted to a wide range of hydrologies, from aerobic soils in uplands to anaerobic and flooded fields in waterlogged lowlands, to even deeply submerged soils in flood-prone areas. Considerable diversity is present in native rice landraces selected by farmers over centuries. Our understanding of the adaptive features of these landraces to native ecosystems has improved considerably over the recent past. In some cases, major genes associated with tolerance have been cloned, such as SUB1A that confers tolerance of complete submergence and SNORKEL genes that control plant elongation to escape deepwater. Modern rice varieties are sensitive to flooding during germination and early growth, a problem commonly encountered in rainfed areas, but few landraces capable of germination under these conditions have recently been identified, enabling research into tolerance mechanisms. Major QTLs were also identified, and are being targeted for molecular breeding and for cloning. Nevertheless, limited progress has been made in identifying regulatory processes for traits that are unique to tolerant genotypes, including faster germination and coleoptile elongation, formation of roots and leaves under hypoxia, ability to catabolize starch into simple sugars for subsequent use in glycolysis and fermentative pathways to generate energy. Here we discuss the state of knowledge on the role of the PDC-ALDH-ACS bypass and the ALDH enzyme as the likely candidates effective in tolerant rice genotypes. Potential involvement of factors such as cytoplasmic pH regulation, phytohormones, reactive oxygen species scavenging and other metabolites is also discussed. Further characterization of contrasting genotypes would help in elucidating the genetic and biochemical regulatory and signaling mechanisms associated with tolerance. This could facilitate breeding rice varieties suitable for direct seeding systems and guide efforts for improving waterlogging tolerance in other crops.
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Affiliation(s)
| | - Abdelbagi M. Ismail
- Crop and Environmental Sciences Division, International Rice Research InstituteManila, Philippines
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97
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Kazłowski B, Chen MR, Chao PM, Lai CC, Ko YT. Identification and roles of proteins for seed development in mungbean (Vigna radiata L.) seed proteomes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:6650-6659. [PMID: 23758297 DOI: 10.1021/jf401170g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Proteomic analysis of developing mungbean (Vigna radiata L.) seeds has not yet been investigated in detail. Fifty-seven proteins were separated by 2-DE, identified by nanoelectrospray mass spectrometry from the present protein databases, and categorized according to their functions. Many of the identified enzymes were involved in central carbon metabolism; thus, a pathway illustrating starch synthesis/breakdown, sugar conversion for glycolysis, and tricarboxylic acid (TCA) cycle was proposed. Quantitative comparison of the protein expression revealed that during developmental process (11-21 days after flowering, DAF), proteins involved in glycolysis, TCA cycle, and alcoholic fermentation showed a trend to be down-regulated, whereas storage proteins were generally up-regulated. The downward tendency of central carbon metabolic proteins suggests a reduction in ATP and oxygen consumption associated with accumulation of storage compounds. UDP-glucose-1-pyrophosphorylase, an upstream enzyme in the starch ADP-Glc pathway, was found as a stably expressed protein throughout the growth stage, demonstrating its importance in mungbean starch biosynthesis. The temporal expression of metabolic enzymes suggests the coordination of an acclimation mechanism and cellular processes associated with accumulation of storage compounds in seed development.
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Affiliation(s)
- Bartosz Kazłowski
- Department of Food Science, Biotechnology Division, College of Life Sciences, National Taiwan Ocean University , 2 Pei-Ning Road, Keelung 20224, Taiwan, Republic of China (ROC)
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98
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Yang Y, Dai L, Xia H, Zhu K, Liu H, Chen K. Protein profile of rice (Oryza sativa) seeds. Genet Mol Biol 2013; 36:87-92. [PMID: 23569412 PMCID: PMC3615530 DOI: 10.1590/s1415-47572013000100012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/23/2012] [Indexed: 11/21/2022] Open
Abstract
Seeds are the most important plant storage organ and play a central role in the life cycle of plants. Since little is known about the protein composition of rice (Oryza sativa) seeds, in this work we used proteomic methods to obtain a reference map of rice seed proteins and identify important molecules. Overall, 480 reproducible protein spots were detected by two-dimensional electrophoresis on pH 4-7 gels and 302 proteins were identified by MALDI-TOF MS and database searches. Together, these proteins represented 252 gene products and were classified into 12 functional categories, most of which were involved in metabolic pathways. Database searches combined with hydropathy plots and gene ontology analysis showed that most rice seed proteins were hydrophilic and were related to binding, catalytic, cellular or metabolic processes. These results expand our knowledge of the rice proteome and improve our understanding of the cellular biology of rice seeds.
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Affiliation(s)
- Yanhua Yang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, PR China
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99
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Han C, Yin X, He D, Yang P. Analysis of proteome profile in germinating soybean seed, and its comparison with rice showing the styles of reserves mobilization in different crops. PLoS One 2013; 8:e56947. [PMID: 23460823 PMCID: PMC3584108 DOI: 10.1371/journal.pone.0056947] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/16/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Seed germination is a complex physiological process during which mobilization of nutrient reserves happens. In different crops, this event might be mediated by different regulatory and metabolic pathways. Proteome profiling has been proved to be an efficient way that can help us to construct these pathways. However, no such studies have been performed in soybean germinating seeds up to date. RESULTS Proteome profiling was conducted through one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry strategy in the germinating seeds of soybean (glycine max). Comprehensive comparisons were also carried out between rice and soybean germinating seeds. 764 proteins belonging to 14 functional groups were identified and metabolism related proteins were the largest group. Deep analyses of the proteins and pathways showed that lipids were degraded through lipoxygenase dependent pathway and proteins were degraded through both protease and 26S proteosome system, and the lipoxygenase could also help to remove the reactive oxygen species during the rapid mobilization of reserves of soybean germinating seeds. The differences between rice and soybean germinating seeds proteome profiles indicate that each crop species has distinct mechanism for reserves mobilization during germination. Different reserves could be converted into starches before they are totally utilized during the germination in different crops seeds. CONCLUSIONS This study is the first comprehensive analysis of proteome profile in germinating soybean seeds to date. The data presented in this paper will improve our understanding of the physiological and biochemical status in the imbibed soybean seeds just prior to germination. Comparison of the protein profile with that of germinating rice seeds gives us new insights on mobilization of nutrient reserves during the germination of crops seeds.
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Affiliation(s)
- Chao Han
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojian Yin
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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100
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He D, Yang P. Proteomics of rice seed germination. FRONTIERS IN PLANT SCIENCE 2013; 4:246. [PMID: 23847647 PMCID: PMC3705172 DOI: 10.3389/fpls.2013.00246] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 06/19/2013] [Indexed: 05/18/2023]
Abstract
Seed is a condensed form of plant. Under suitable environmental conditions, it can resume the metabolic activity from physiological quiescent status, and mobilize the reserves, biosynthesize new proteins, regenerate organelles, and cell membrane, eventually protrude the radicle and enter into seedling establishment. So far, how these activities are regulated in a coordinated and sequential manner is largely unknown. With the availability of more and more genome sequence information and the development of mass spectrometry (MS) technology, proteomics has been widely applied in analyzing the mechanisms of different biological processes, and proved to be very powerful. Regulation of rice seed germination is critical for rice cultivation. In recent years, a lot of proteomic studies have been conducted in exploring the gene expression regulation, reserves mobilization and metabolisms reactivation, which brings us new insights on the mechanisms of metabolism regulation during this process. Nevertheless, it also invokes a lot of questions. In this mini-review, we summarized the progress in the proteomic studies of rice seed germination. The current challenges and future perspectives were also discussed, which might be helpful for the following studies.
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Affiliation(s)
| | - Pingfang Yang
- *Correspondence: Pingfang Yang, Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan, 430074, P. R. China e-mail:
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