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An F, Li G, Li QX, Li K, Carvalho LJCB, Ou W, Chen S. The Comparatively Proteomic Analysis in Response to Cold Stress in Cassava Plantlets. PLANT MOLECULAR BIOLOGY REPORTER 2016; 34:1095-1110. [PMID: 27881899 PMCID: PMC5099363 DOI: 10.1007/s11105-016-0987-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a tropical root crop and sensitive to low temperature. However, it is poorly to know how cassava can modify its metabolism and growth to adapt to cold stress. An investigation aimed at a better understanding of cold-tolerant mechanism of cassava plantlets was carried out with the approaches of physiology and proteomics in the present study. The principal component analysis of seven physiological characteristics showed that electrolyte leakage (EL), chlorophyll content, and malondialdehyde (MDA) may be the most important physiological indexes for determining cold-resistant abilities of cassava. The genome-wide proteomic analysis showed that 20 differential proteins had the same patterns in the apical expanded leaves of cassava SC8 and Col1046. They were mainly related to photosynthesis, carbon metabolism and energy metabolism, defense, protein synthesis, amino acid metabolism, signal transduction, structure, detoxifying and antioxidant, chaperones, and DNA-binding proteins, in which 40 % were related with photosynthesis. The remarkable variation in photosynthetic activity and expression level of peroxiredoxin is closely linked with expression levels of proteomic profiles. Moreover, analysis of differentially expressed proteins under cold stress is an important step toward further elucidation of mechanisms of cold stress resistance.
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Affiliation(s)
- Feifei An
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Danzhou, 571737 China
| | - Genghu Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Danzhou, 571737 China
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Manoa, HI USA
| | - Kaimian Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Danzhou, 571737 China
| | | | - Wenjun Ou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Danzhou, 571737 China
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Danzhou, 571737 China
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Dong Y, Wang Q, Zhang L, Du C, Xiong W, Chen X, Deng F, Ma Z, Qiao D, Hu C, Ren Y, Li Y. Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn. PLoS One 2015; 10:e0143181. [PMID: 26587848 PMCID: PMC4654522 DOI: 10.1371/journal.pone.0143181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 11/02/2015] [Indexed: 12/31/2022] Open
Abstract
The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.
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Affiliation(s)
- Yongbin Dong
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Qilei Wang
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Long Zhang
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Chunguang Du
- Deptment of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, United States of America
| | - Wenwei Xiong
- Deptment of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, United States of America
| | - Xinjian Chen
- College of Life Sciences, Henan Agricultural University, 63 Nongye Rd, Zhengzhou, China
| | - Fei Deng
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Zhiyan Ma
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Dahe Qiao
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Chunhui Hu
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Yangliu Ren
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Yuling Li
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
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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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Zhao P, Liu P, Shao J, Li C, Wang B, Guo X, Yan B, Xia Y, Peng M. Analysis of different strategies adapted by two cassava cultivars in response to drought stress: ensuring survival or continuing growth. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1477-88. [PMID: 25547914 PMCID: PMC4438449 DOI: 10.1093/jxb/eru507] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cassava is one of the most drought-tolerant crops, however, the underlying mechanism for its ability to survive and produce under drought remains obscure. In this study, two cassava cultivars, SC124 and Arg7, were treated by gradually reducing the soil water content. Their responses to the drought stress were examined through their morphological and physiological traits and isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis. SC124 plants adapted a 'survival' mode under mild drought stress as evidenced by early stomatal closure and a reduction in the levels of various photosynthetic proteins and photosynthetic capacity, resulting in early growth quiescence. In contrast, Arg7 plants underwent senescence of older leaves but continued to grow, although at a reduced rate, under mild drought. SC124 plants were more capable of surviving prolonged severe drought than Arg7. The iTRAQ analysis identified over 5000 cassava proteins. Among the drought-responsive proteins identified in the study were an aquaporin, myo-inositol 1-phosphate synthases, and a number of proteins involved in the antioxidant systems and secondary metabolism. Many proteins that might play a role in signalling or gene regulation were also identified as drought-responsive proteins, which included several protein kinases, two 14-3-3 proteins, several RNA-binding proteins and transcription factors, and two histone deacetylases. Our study also supports the notion that linamarin might play a role in nitrogen reallocation in cassava under drought.
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Affiliation(s)
- Pingjuan Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China College of Agronomy, Hainan University, Haikou, PR China
| | - Pei Liu
- Department of Biology, Hong Kong Baptist University, Hong Kong, PR China
| | - Jiaofang Shao
- Department of Biology, Hong Kong Baptist University, Hong Kong, PR China
| | - Chunqiang Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Bin Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Xin Guo
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Bin Yan
- Department of Biology, Hong Kong Baptist University, Hong Kong, PR China
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Hong Kong, PR China Partner State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, PR China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
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Fukao Y. Discordance between protein and transcript levels detected by selected reaction monitoring. PLANT SIGNALING & BEHAVIOR 2015; 10:e1017697. [PMID: 26039477 PMCID: PMC4623550 DOI: 10.1080/15592324.2015.1017697] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 05/25/2023]
Abstract
Expression levels between transcript and protein are not always correlated. In the present study, the abundance of protein PDR9/ABCG37 in 3 Arabidopsis pdr9/abcg37 mutant alleles was evaluated using selected reaction monitoring analysis. The results showed that protein and mRNA expression levels were similar in 2 mutant alleles. The mRNA expression levels in another mutant, determined by both semi-quantitative and quantitative RT-PCR, were similar to the wild-type, although the abundance of protein was about half the abundance of the wild-type. These results suggested that using only mRNA expression levels to infer protein abundance, compare mutants or responses to various stimuli may lead to incorrect interpretation and conclusions.
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Affiliation(s)
- Yoichiro Fukao
- Plant Global Education Project; Graduate School of Biological Sciences; Nara Institute of Science and Technology; Takayama, Ikoma, Japan
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56
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Chu P, Yan GX, Yang Q, Zhai LN, Zhang C, Zhang FQ, Guan RZ. iTRAQ-based quantitative proteomics analysis of Brassica napus leaves reveals pathways associated with chlorophyll deficiency. J Proteomics 2014; 113:244-59. [PMID: 25317966 DOI: 10.1016/j.jprot.2014.10.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/10/2014] [Accepted: 10/02/2014] [Indexed: 11/15/2022]
Abstract
Photosynthesis, the primary source of plant biomass, is important for plant growth and crop yield. Chlorophyll is highly abundant in plant leaves and plays essential roles in photosynthesis. We recently isolated a chlorophyll-deficient mutant (cde1) from ethyl methanesulfonate (EMS) mutagenized Brassica napus. Herein, quantitative proteomics analysis using the iTRAQ approach was conducted to investigate cde1-induced changes in the proteome. We identified 5069 proteins from B. napus leaves, of which 443 showed differential accumulations between the cde1 mutant and its corresponding wild-type. The differentially accumulated proteins were found to be involved in photosynthesis, porphyrin and chlorophyll metabolism, biosynthesis of secondary metabolites, carbon fixation, spliceosome, mRNA surveillance and RNA degradation. Our results suggest that decreased abundance of chlorophyll biosynthetic enzymes and photosynthetic proteins, impaired carbon fixation efficiency and disturbed redox homeostasis might account for the reduced chlorophyll contents, impaired photosynthetic capacity and increased lipid peroxidation in this mutant. Epigenetics was implicated in the regulation of gene expression in cde1, as proteins involved in DNA/RNA/histone methylation and methylation-dependent chromatin silencing were up-accumulated in the mutant. Biological significance Photosynthesis produces more than 90% of plant biomass and is an important factor influencing potential crop yield. The pigment chlorophyll plays essential roles in light harvesting and energy transfer during photosynthesis. Mutants deficient in chlorophyll synthesis have been used extensively to investigate the chlorophyll metabolism, development and photosynthesis. However, limited information is available with regard to the changes of protein profiles upon chlorophyll deficiency. Here, a combined physiological, histological, proteomics and molecular analysis revealed several important pathways associated with chlorophyll deficiency. This work provides new insights into the regulation of chlorophyll biosynthesis and photosynthesis in higher plants and these findings may be applied to genetic engineering for high photosynthetic efficiency in crops.
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Affiliation(s)
- Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Gui Xia Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Na Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Cheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Qi Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Rong Zhan Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; Nanjing Agricultural University, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, Jiangsu, China.
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Yan J, Tian H, Wang S, Shao J, Zheng Y, Zhang H, Guo L, Ding Y. Pollen developmental defects in ZD-CMS rice line explored by cytological, molecular and proteomic approaches. J Proteomics 2014; 108:110-23. [PMID: 24878425 DOI: 10.1016/j.jprot.2014.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 05/13/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Cytoplasmic male sterility (CMS) is a widely observed phenomenon, which is especially useful in hybrid seed production. Meixiang A (MxA) is a new rice CMS line derived from a pollen-free sterile line named Yunnan ZidaoA (ZD-CMS). In this study, a homologous WA352 gene with variation in two nucleotides was identified in MxA. Cytological analysis revealed that MxA was aborted in the early uninucleate stage. The protein expression profiles of MxA and its maintainer line MeixiangB (MxB) were systematically compared using iTRAQ-based quantitative proteomics technology using young florets at the early uninucleate stage. A total of 688 proteins were quantified in both rice lines, and 45 of these proteins were found to be differentially expressed. Bioinformatics analysis indicated a large number of the proteins involved in carbohydrate metabolism or the stress response were downregulated in MxA, suggesting that these metabolic processes had been hindered during pollen development in MxA. The ROS (reactive oxygen species) level was increased in the mitochondrion of MxA, and further ultrastructural analysis showed the mitochondria with disrupted cristae in the rice CMS line MxA. These findings substantially contribute to our knowledge of pollen developmental defects in ZD-CMS rice line. BIOLOGICAL SIGNIFICANCE MeixiangA (MxA) is a new type of rice CMS line, which is derived from pollen-free sterile line Yunnan ZidaoA. In this study, the cytological, molecular and proteomic approaches were used to study the characteristics of this new CMS line. Cytological study indicates the CMS line is aborted at the early uninucleate stage. A potential sterile gene ZD352 is identified in MxA, the protein product of which is mainly accumulated at the MMC/Meiotic stage. iTRAQ based proteomic analysis is performed to study the relevant proteins involved in the CMS occurance, 45 proteins are found to be significant differentially expressed and these proteins are involved in many cellular processes such as carbohydrate metabolism, stress response, protein synthesis. To our knowledge, this is the first report using the iTRAQ-labeled quantitative proteomic to study the protein expression variation during the abortion processes between a CMS line and its maintainer line. These results provide new insights on the CMS mechanisms of ZD-CMS rice line.
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Affiliation(s)
- Junjie Yan
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Han Tian
- State Key Laboratory of Virology, Department of Biochemistry, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Shuzhen Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Jinzhen Shao
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yinzhen Zheng
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Hongyuan Zhang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Lin Guo
- State Key Laboratory of Virology, Department of Biochemistry, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China.
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Martínez-Esteso MJ, Casado-Vela J, Sellés-Marchart S, Pedreño MA, Bru-Martínez R. Differential plant proteome analysis by isobaric tags for relative and absolute quantitation (iTRAQ). Methods Mol Biol 2014; 1072:155-69. [PMID: 24136521 DOI: 10.1007/978-1-62703-631-3_12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Protein relative quantitation is one of the main targets in many proteomic experiments. Among the range of techniques available for both top-down and bottom-up approaches, isobaric tags for relative and absolute quantitation (iTRAQ) have gained positions within the top-rank techniques used for this purpose in the recent years. Briefly, each iTRAQ reagent consists of three different components: a reporter group (with a variable mass in the range of 114-117 amu), a balance group, and an amino-reactive group. The isobaric nature of iTRAQ-labeled peptides adds a signal to every peptide in the sample which is detectable in both MS and MS/MS spectra, thus enhancing the sensitivity of detection. During MS/MS, the reporter groups are released as singly charged ions with m/z ratios ranking from 114 to 117 amu, visible in the low mass region of MS/MS spectra. The iTRAQ technology can be used to analyze up to four different samples using the 4-plex kit (reporter groups 114-115 amu) or can be scaled up to eight different samples using the 8-plex kit (reporter groups 113-121 amu). In this chapter, we focus on the experimental procedures typically using 4-plex labeling, including tips leading to successful application of iTRAQ technology for the analysis of plant protein mixtures.
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Affiliation(s)
- María J Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
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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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Nyaboga E, Njiru J, Nguu E, Gruissem W, Vanderschuren H, Tripathi L. Unlocking the potential of tropical root crop biotechnology in east Africa by establishing a genetic transformation platform for local farmer-preferred cassava cultivars. FRONTIERS IN PLANT SCIENCE 2013; 4:526. [PMID: 24400011 PMCID: PMC3872047 DOI: 10.3389/fpls.2013.00526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/06/2013] [Indexed: 05/12/2023]
Abstract
Cassava genetic transformation capacity is still mostly restricted to advanced laboratories in the USA, Europe and China; and its implementation and maintenance in African laboratories has remained scarce. The impact of transgenic technologies for genetic improvement of cassava will depend largely on the transfer of such capabilities to researchers in Africa, where cassava has an important socioeconomic niche. A major constraint to the development of genetic transformation technologies for cassava improvement has been the lack of an efficient and robust transformation and regeneration system. Despite the success achieved in genetic modification of few cassava cultivars, including the model cultivar 60444, transgenic cassava production remains difficult for farmer-preferred cultivars. In this study, a protocol for cultivar 60444 developed at ETH Zurich was successfully implemented and optimized to establish transformation of farmer-preferred cassava cultivars popular in east Africa. The conditions for production and proliferation of friable embryogenic calli (FEC) and Agrobacterium-mediated transformation were optimized for three east African farmer-preferred cultivars (Ebwanatereka, Kibandameno and Serere). Our results demonstrated transformation efficiencies of about 14-22 independent transgenic lines per 100 mg of FEC for farmer-preferred cultivars in comparison to 28 lines per 100 mg of the model cultivar 60444. The presence, integration and expression of the transgenes were confirmed by PCR, Southern blot analysis and histochemical GUS assay. This study reports the establishment of a cassava transformation platform at International Institute of Tropical Agriculture (IITA) hosted by Biosciences eastern and central Africa (BecA) hub in Kenya and provides the basis for transferring important traits such as virus resistance and prolonged shelf-life to farmer-preferred cultivars in east Africa. We anticipate that such platform will also be instrumental to transfer technologies to national agricultural research systems (NARS) in sub-Saharan Africa.
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Affiliation(s)
- Evans Nyaboga
- International Institute of Tropical AgricultureNairobi, Kenya
- Department of Biology, Plant Biotechnology, Eidgenössische Technische HochschuleZurich, Switzerland
- Department of Biochemistry, University of NairobiNairobi, Kenya
| | - Joshua Njiru
- International Institute of Tropical AgricultureNairobi, Kenya
| | - Edward Nguu
- Department of Biochemistry, University of NairobiNairobi, Kenya
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, Eidgenössische Technische HochschuleZurich, Switzerland
| | - Herve Vanderschuren
- Department of Biology, Plant Biotechnology, Eidgenössische Technische HochschuleZurich, Switzerland
| | - Leena Tripathi
- International Institute of Tropical AgricultureNairobi, Kenya
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Li L, Song J, Kalt W, Forney C, Tsao R, Pinto D, Chisholm K, Campbell L, Fillmore S, Li X. Quantitative proteomic investigation employing stable isotope labeling by peptide dimethylation on proteins of strawberry fruit at different ripening stages. J Proteomics 2013; 94:219-39. [DOI: 10.1016/j.jprot.2013.09.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/27/2013] [Accepted: 09/12/2013] [Indexed: 02/01/2023]
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62
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Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement. J Proteomics 2013; 93:5-19. [DOI: 10.1016/j.jprot.2013.05.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/20/2013] [Accepted: 05/29/2013] [Indexed: 12/22/2022]
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Zi J, Zhang J, Wang Q, Zhou B, Zhong J, Zhang C, Qiu X, Wen B, Zhang S, Fu X, Lin L, Liu S. Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis. PLoS One 2013; 8:e74229. [PMID: 24058531 PMCID: PMC3776822 DOI: 10.1371/journal.pone.0074229] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 07/28/2013] [Indexed: 11/19/2022] Open
Abstract
Embryogenesis is the initial step in a plant’s life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with the shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2 165 unique proteins were identified in rice embryos, and the abundances of 867 proteins were actively changed based on the statistical evaluation of the quantitative MS/MS signals. The quantitative data were then confirmed using multiple reactions monitoring (MRM) and were also supported by our previous study based on two-dimensional gel electrophoresis (2 DE). Using the proteome at 6 days after pollination (DAP) as a reference, cluster analysis of these differential proteins throughout rice embryogenesis revealed that 25% were up-regulated and 75% were down-regulated. Gene Ontology (GO) analysis implicated that most of the up-regulated proteins were functionally categorized as stress responsive, mainly including heat shock-, lipid transfer-, and reactive oxygen species-related proteins. The stress-responsive proteins were thus postulated to play an important role during seed maturation.
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Affiliation(s)
- Jin Zi
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jiyuan Zhang
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Quanhui Wang
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Baojin Zhou
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Junyan Zhong
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | | | - Xuemei Qiu
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Bo Wen
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Shenyan Zhang
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiqin Fu
- Hunan Hybrid Rice Research Center, Changsha, China
| | - Liang Lin
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- * E-mail: (LL); (SL)
| | - Siqi Liu
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (LL); (SL)
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64
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Ge P, Hao P, Cao M, Guo G, Lv D, Subburaj S, Li X, Yan X, Xiao J, Ma W, Yan Y. iTRAQ-based quantitative proteomic analysis reveals new metabolic pathways of wheat seedling growth under hydrogen peroxide stress. Proteomics 2013; 13:3046-58. [DOI: 10.1002/pmic.201300042] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 05/16/2013] [Accepted: 06/26/2013] [Indexed: 01/03/2023]
Affiliation(s)
- Pei Ge
- College of Life Sciences; Capital Normal University; Beijing China
| | - Pengchao Hao
- College of Life Sciences; Capital Normal University; Beijing China
| | - Min Cao
- College of Life Sciences; Capital Normal University; Beijing China
| | - Guangfang Guo
- College of Life Sciences; Capital Normal University; Beijing China
| | - Dongwen Lv
- College of Life Sciences; Capital Normal University; Beijing China
| | | | - Xiaohui Li
- College of Life Sciences; Capital Normal University; Beijing China
| | - Xing Yan
- College of Life Sciences; Capital Normal University; Beijing China
| | - Jitian Xiao
- School of Computer and Security Science; Edith Cowan University; Perth WA Australia
| | - Wujun Ma
- State Agriculture Biotechnology Centre; Murdoch University; Perth WA Australia
- Western Australian Department of Agriculture and Food; Perth WA Australia
| | - Yueming Yan
- College of Life Sciences; Capital Normal University; Beijing China
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Pedreschi R, Lurie S, Hertog M, Nicolaï B, Mes J, Woltering E. Post-harvest proteomics and food security. Proteomics 2013; 13:1772-83. [PMID: 23483703 DOI: 10.1002/pmic.201200387] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/27/2012] [Accepted: 11/11/2012] [Indexed: 12/12/2022]
Abstract
To guarantee sufficient food supply for a growing world population, efforts towards improving crop yield and plant resistance should be complemented with efforts to reduce post-harvest losses. Post-harvest losses are substantial and occur at different stages of the food chain in developed and developing countries. In recent years, a substantially increasing interest can be seen in the application of proteomics to understand post-harvest events. In the near future post-harvest proteomics will be poised to move from fundamental research to aiding the reduction of food losses. Proteomics research can help in reducing food losses through (i) identification and validation of gene products associated to specific quality traits supporting marker-assisted crop improvement programmes, (ii) delivering markers of initial quality that allow optimisation of distribution conditions and prediction of remaining shelf-life for decision support systems and (iii) delivering early detection tools of physiological or pathogen-related post-harvest problems. In this manuscript, recent proteomics studies on post-harvest and stress physiology are reviewed and discussed. Perspectives on future directions of post-harvest proteomics studies aiming to reduce food losses are presented.
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Affiliation(s)
- Romina Pedreschi
- Food & Biobased Research Centre, Wageningen University, Wageningen, The Netherlands.
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66
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Kang G, Li G, Ma H, Wang C, Guo T. Proteomic analysis on the leaves of TaBTF3 gene virus-induced silenced wheat plants may reveal its regulatory mechanism. J Proteomics 2013; 83:130-43. [PMID: 23563083 DOI: 10.1016/j.jprot.2013.03.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 02/26/2013] [Accepted: 03/19/2013] [Indexed: 01/01/2023]
Abstract
UNLABELLED Basic transcription factor 3 (BTF3) is involved in the transcriptional initiation of RNA polymerase II and is also associated with apoptosis. In this study, virus-induced gene silencing of TaBTF3 caused severe viral symptoms in wheat seedlings, which then displayed stunted growth, reduced height, and decreased total fresh and dry weights. A proteomic approach was further used to identify the protein species showing differential abundance between the TaBTF3 virus-induced gene silenced wheat plants and the barley stripe mosaic virus-induced gene silencing green fluorescent protein transgenic wheat plants (control) with the objective of exploring its regulatory mechanism in higher plants. Using two-dimensional electrophoresis technologies, 59 protein spots showed significant changes, of which 54 were successfully identified by tandem mass spectrometry with matrix-assisted laser desorption/ionization-time of flight spectrometry. Analysis of protein abundance revealed that the differential protein species were associated with signal transduction, stress defense, photosynthesis, carbohydrate metabolism, and protein metabolism, and were mostly localized in both chloroplasts and mitochondria. Furthermore, the BTF3-responsive protein interaction network revealed 20 key protein species, most of which are regulated by abscisic acid, ethane, or oxidative stress. This suggested that changes of these protein species could be critical in the BTF3 pathway. BIOLOGICAL SIGNIFICANCE Basic transcription factor 3 (BTF3), the β-subunit of NAC, has originally been identified as a basic transcription factor that is both involved in the transcriptional initiation of RNA polymerase II and associated with diverse biological functions. Reports on BTF3 mainly focus in animals, however, there has been limited molecular information about BTF3 in higher plants so far. In previous studies, we first isolated the TaBTF3 gene from common wheat (Triticum aestivum L.) and obtained silenced transgenic wheat seedlings using the VIGS method. In TaBTF3-silenced transgenic wheat plants, the structure of the wheat mesophyll cell was seriously damaged and transcripts of the chloroplast- and mitochondrial-encoded genes were significantly reduced. These results suggested that the TaBTF3 gene may be involved in regulating the growth and development of wheat seedlings. However, the induced or related genes by TaBTF3 have not been identified. The significance of this study is to first identify many protein species with the altered abundance between the TaBTF3 virus-induced silencing wheat plants and the BSMV-VIGS GFP transgenic wheat plants (control) using the proteomic approach. In addition, 20 of these identified protein species which might play critical roles in the BTF3 interaction network are identified using protein interaction network. These results help to further explore the molecular mechanism of BTF3 in higher plants.
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Affiliation(s)
- Guozhang Kang
- The National Engineering Research Centre for Wheat, The Key Laboratory of Physiology, Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China.
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67
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Uversky VN. The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e24684. [PMID: 28516010 PMCID: PMC5424795 DOI: 10.4161/idp.24684] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 03/27/2013] [Accepted: 04/12/2013] [Indexed: 11/19/2022]
Abstract
The ability of a protein to fold into unique functional state or to stay intrinsically disordered is encoded in its amino acid sequence. Both ordered and intrinsically disordered proteins (IDPs) are natural polypeptides that use the same arsenal of 20 proteinogenic amino acid residues as their major building blocks. The exceptional structural plasticity of IDPs, their capability to exist as heterogeneous structural ensembles and their wide array of important disorder-based biological functions that complements functional repertoire of ordered proteins are all rooted within the peculiar differential usage of these building blocks by ordered proteins and IDPs. In fact, some residues (so-called disorder-promoting residues) are noticeably more common in IDPs than in sequences of ordered proteins, which, in their turn, are enriched in several order-promoting residues. Furthermore, residues can be arranged according to their “disorder promoting potencies,” which are evaluated based on the relative abundances of various amino acids in ordered and disordered proteins. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and concerns glutamic acid, which is the second most disorder-promoting residue.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow, Russia
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68
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Xu J, Duan X, Yang J, Beeching JR, Zhang P. Enhanced reactive oxygen species scavenging by overproduction of superoxide dismutase and catalase delays postharvest physiological deterioration of cassava storage roots. PLANT PHYSIOLOGY 2013; 161:1517-28. [PMID: 23344905 PMCID: PMC3585613 DOI: 10.1104/pp.112.212803] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/22/2013] [Indexed: 05/18/2023]
Abstract
Postharvest physiological deterioration (PPD) of cassava (Manihot esculenta) storage roots is the result of a rapid oxidative burst, which leads to discoloration of the vascular tissues due to the oxidation of phenolic compounds. In this study, coexpression of the reactive oxygen species (ROS)-scavenging enzymes copper/zinc superoxide dismutase (MeCu/ZnSOD) and catalase (MeCAT1) in transgenic cassava was used to explore the intrinsic relationship between ROS scavenging and PPD occurrence. Transgenic cassava plants integrated with the expression cassette p54::MeCu/ZnSOD-35S::MeCAT1 were confirmed by Southern-blot analysis. The expression of MeCu/ZnSOD and MeCAT1 was verified by quantitative reverse transcription-polymerase chain reaction and enzymatic activity analysis both in the leaves and storage roots. Under exposure to the ROS-generating reagent methyl viologen or to hydrogen peroxide (H2O2), the transgenic plants showed higher enzymatic activities of SOD and CAT than the wild-type plants. Levels of malondialdehyde, chlorophyll degradation, lipid peroxidation, and H2O2 accumulation were dramatically reduced in the transgenic lines compared with the wild type. After harvest, the storage roots of transgenic cassava lines show a delay in their PPD response of at least 10 d, accompanied by less mitochondrial oxidation and H2O2 accumulation, compared with those of the wild type. We hypothesize that this is due to the combined ectopic expression of Cu/ZnSOD and CAT leading to an improved synergistic ROS-scavenging capacity of the roots. Our study not only sheds light on the mechanism of the PPD process but also develops an effective approach for delaying the occurrence of PPD in cassava.
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Affiliation(s)
| | | | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.X., X.D., P.Z.); Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China (J.Y., P.Z.); and Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom (J.R.B.)
| | - John R. Beeching
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.X., X.D., P.Z.); Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China (J.Y., P.Z.); and Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom (J.R.B.)
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.X., X.D., P.Z.); Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China (J.Y., P.Z.); and Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom (J.R.B.)
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Silva-Sanchez C, Chen S, Zhu N, Li QB, Chourey PS. Proteomic comparison of basal endosperm in maize miniature1 mutant and its wild-type Mn1. FRONTIERS IN PLANT SCIENCE 2013; 4:211. [PMID: 23805148 PMCID: PMC3691554 DOI: 10.3389/fpls.2013.00211] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 06/03/2013] [Indexed: 05/08/2023]
Abstract
Developing endosperm in maize seed is a major site for biosynthesis and storage of starch and proteins, and of immense economic importance for its role in food, feed and biofuel production. The basal part of endosperm performs a major role in solute, water and nutrition acquisition from mother plant to sustain these functions. The miniature1 (mn1) mutation is a loss-of-function mutation of the Mn1-encoded cell wall invertase that is entirely expressed in the basal endosperm and is essential for many of the metabolic and signaling functions associated with metabolically released hexose sugars in developing endosperm. Here we report a comparative proteomic study between Mn1 and mn1 basal endosperm to better understand basis of pleiotropic effects on many diverse traits in the mutant. Specifically, we used iTRAQ based quantitative proteomics combined with Gene Ontology (GO) and bioinformatics to understand functional basis of the proteomic information. A total of 2518 proteins were identified from soluble and cell wall associated protein (CWAP) fractions; of these 131 proteins were observed to be differentially expressed in the two genotypes. The main functional groups of proteins that were significantly different were those involved in the carbohydrate metabolic and catabolic process, and cell homeostasis. The study constitutes the first proteomic analysis of basal endosperm cell layers in relation to endosperm growth and development in maize.
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Affiliation(s)
- Cecilia Silva-Sanchez
- Proteomics, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
| | - Sixue Chen
- Proteomics, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
- Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
- *Correspondence: Sixue Chen, Interdisciplinary Center for Biotechnology Research and Department of Biology, UF Genetics Institute, University of Florida, 2033 Mowry Rd., CGRC Rm. 438, Gainesville, FL 32610, USA e-mail: ;
| | - Ning Zhu
- Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
| | - Qin-Bao Li
- USDA-Agricultural Research Service, Center for Medical, Agricultural and Veterinary EntomologyGainesville, FL, USA
| | - Prem S. Chourey
- USDA-Agricultural Research Service, Center for Medical, Agricultural and Veterinary EntomologyGainesville, FL, USA
- Departments of Agronomy and Plant Pathology, University of FloridaGainesville, FL, USA
- Prem S. Chourey, USDA-Agricultural Research Service, Center for Medical, Agricultural and Veterinary Entomology, 1600/1700 SW 23rd Drive, Gainesville, FL 32608, USA e-mail:
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70
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Chen YZ, Pang QY, He Y, Zhu N, Branstrom I, Yan XF, Chen S. Proteomics and metabolomics of Arabidopsis responses to perturbation of glucosinolate biosynthesis. MOLECULAR PLANT 2012; 5:1138-50. [PMID: 22498773 DOI: 10.1093/mp/sss034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To understand plant molecular networks of glucosinolate metabolism, perturbation of aliphatic glucosinolate biosynthesis was established using inducible RNA interference (RNAi) in Arabidopsis. Two RNAi lines were chosen for examining global protein and metabolite changes using complementary proteomics and metabolomics approaches. Proteins involved in metabolism including photosynthesis and hormone metabolism, protein binding, energy, stress, and defense showed marked responses to glucosinolate perturbation. In parallel, metabolomics revealed major changes in the levels of amino acids, carbohydrates, peptides, and hormones. The metabolomics data were correlated with the proteomics results and revealed intimate molecular connections between cellular pathways/processes and glucosinolate metabolism. This study has provided an unprecedented view of the molecular networks of glucosinolate metabolism and laid a foundation towards rationale glucosinolate engineering for enhanced defense and quality.
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Affiliation(s)
- Ya-zhou Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
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Pottiez G, Wiederin J, Fox HS, Ciborowski P. Comparison of 4-plex to 8-plex iTRAQ quantitative measurements of proteins in human plasma samples. J Proteome Res 2012; 11:3774-81. [PMID: 22594965 PMCID: PMC3390908 DOI: 10.1021/pr300414z] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Methods for isobaric tagging of peptides, iTRAQ or TMT,
are commonly used platforms in mass spectrometry based quantitative
proteomics. These two methods are very often used to quantitate proteins
in complex samples, e.g., serum/plasma or CSF supporting biomarker
discovery studies. The success of these studies depends on multiple
factors, including the accuracy of ratios of reporter ions reflecting
quantitative changes of proteins. Because reporter ions are generated
during peptide fragmentation, the differences of chemical structure
of iTRAQ balance groups may have an effect on how efficiently these
groups are fragmented and thus how differences in protein expression
will be measured. Because 4-plex and 8-plex iTRAQ reagents do have
different structures of balanced groups, it has been postulated that
indeed differences in protein identification and quantitation exist
between these two reagents. In this study we controlled the ratios
of tagged samples and compared quantitation of proteins using 4-plex
versus 8-plex reagents in the context of a highly complex sample of
human plasma using ABSciex 4800 MALDI-TOF/TOF mass spectrometer and
ProteinPilot 4.0 software. We observed that 8-plex tagging provides
more consistent ratios than 4-plex without compromising protein identification,
thus allowing investigation of eight experimental conditions in one
analytical experiment.
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Affiliation(s)
- Gwenael Pottiez
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68198-5800, USA
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