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Martínez-Márquez A, Selles-Marchart S, Nájera H, Morante-Carriel J, Martínez-Esteso MJ, Bru-Martínez R. Biosynthesis of Piceatannol from Resveratrol in Grapevine Can Be Mediated by Cresolase-Dependent Ortho-Hydroxylation Activity of Polyphenol Oxidase. PLANTS (BASEL, SWITZERLAND) 2024; 13:2602. [PMID: 39339576 PMCID: PMC11434850 DOI: 10.3390/plants13182602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 09/07/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024]
Abstract
Piceatannol is a naturally occurring hydroxylated analogue of the stilbene phytoalexin resveratrol that can be found in grape fruit and derived products. Piceatannol has aroused great interest as it has been shown to surpass some human health-beneficial properties of resveratrol including antioxidant activity, several pharmacological activities and also bioavailability. The plant biosynthetic pathway of piceatannol is still poorly understood, which is a bottleneck for the development of both plant defence and bioproduction strategies. Cell cultures of Vitis vinifera cv. Gamay, when elicited with dimethyl-β-cyclodextrin (MBCD) and methyl jasmonate (MeJA), lead to large increases in the accumulation of resveratrol, and after 120 h of elicitation, piceatannol is also detected due to the regiospecific hydroxylation of resveratrol. Therefore, an ortho-hydroxylase must participate in the biosynthesis of piceatannol. Herein, three possible types of resveratrol hydroxylation enzymatic reactions have been tested, specifically, a reaction catalyzed by an NADPH-dependent cytochrome, P450 hydroxylase, a 2-oxoglutarate-dependent dioxygenase and ortho-hydroxylation, similar to polyphenol oxidase (PPO) cresolase activity. Compared with P450 hydoxylase and the dioxygenase activities, PPO displayed the highest specific activity detected either in the crude extract, the particulate or the soluble fraction obtained from cell cultures elicited with MBCD and MeJA for 120 h. The overall yield of PPO activity present in the crude extract (107.42 EU) was distributed mostly in the soluble fraction (66.15 EU) rather than in the particulate fraction (3.71 EU). Thus, partial purification of the soluble fraction by precipitation with ammonium sulphate, dialysis and ion exchange chromatography was carried out. The soluble fraction precipitated with 80% ammonium sulphate and the chromatographic fractions also showed high levels of PPO activity, and the presence of the PPO protein was confirmed by Western blot and LC-MS/MS. In addition, a kinetic characterization of the cresolase activity of partially purified PPO was carried out for the resveratrol substrate, including Vmax and Km parameters. The Km value was 118.35 ± 49.84 µM, and the Vmax value was 2.18 ± 0.46 µmol min-1 mg-1.
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Affiliation(s)
- Ascensión Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (S.S.-M.); (H.N.); (J.M.-C.); (M.J.M.-E.); (R.B.-M.)
- Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain
| | - Susana Selles-Marchart
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (S.S.-M.); (H.N.); (J.M.-C.); (M.J.M.-E.); (R.B.-M.)
- Research Technical Facility, Proteomics and Genomics Division, University of Alicante, San Vicente del Raspeig, 03690 Alicante, Spain
| | - Hugo Nájera
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (S.S.-M.); (H.N.); (J.M.-C.); (M.J.M.-E.); (R.B.-M.)
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana–Cuajimalpa, Av. Vasco de Quiroga 4871, Colonia Santa Fe Cuajimalpa, Alcaldía Cuajimalpa de Morelos, Mexico City 05348, Mexico
| | - Jaime Morante-Carriel
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (S.S.-M.); (H.N.); (J.M.-C.); (M.J.M.-E.); (R.B.-M.)
- Plant Biotechnology Group, Faculty of Forestry and Agricultural Sciences, Quevedo State Technical University, Av. Quito km. 1 1/2 vía a Santo Domingo de los Tsachilas, Quevedo 120501, Ecuador
| | - Maria J. Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (S.S.-M.); (H.N.); (J.M.-C.); (M.J.M.-E.); (R.B.-M.)
- Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (S.S.-M.); (H.N.); (J.M.-C.); (M.J.M.-E.); (R.B.-M.)
- Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain
- Multidisciplinary Institute for the Study of the Environment (IMEM), University of Alicante, 03690 Alicante, Spain
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S A, Das A, Kalita PJ, Patil RI, Pandey N, Bhattacharjee M, Sharma BK, Das D, Acharjee S. Improved methods for total and chloroplast protein extraction from Cajanus species for two-dimensional gel electrophoresis and mass spectrometry. PLoS One 2024; 19:e0308909. [PMID: 39146296 PMCID: PMC11326652 DOI: 10.1371/journal.pone.0308909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024] Open
Abstract
The recent advances in pigeon pea genomics, including high-quality whole genome and chloroplast genome sequence information helped develop improved varieties. However, a comprehensive Cajanus proteome, including the organelle proteome, is yet to be fully mapped. The spatial delineation of pigeon pea proteins at sub-cellular levels and inter-organelle communication could offer valuable insights into its defense mechanism against various stresses. However, the major bottleneck in the proteomic study is the lack of a suitable method of protein extraction and sample preparation compatible with two-dimensional gel electrophoresis (2D-PAGE), liquid chromatography-mass spectrometry (LCMS), or matrix-assisted laser desorption ionization-time of flight (MALDi-ToF). Our study introduces two efficient methods, one for isolating total proteins and another for organelle (chloroplast) proteins from various Cajanus spp. For total protein extraction, we have optimized a protocol using phenol in combination with a reducing agent (DTT) and protease inhibitor cocktail, also washing (6-7 times) with ice-cold acetone after overnight protein precipitation of total proteins. Our modified extraction method using phenol for total leaf protein yielded approximately 2-fold more proteins than the previously reported protocols from C. cajan (3.18 ± 0.11 mg/gm) and C. scarabaeoides (2.06 ± 0.08 mg/gm). We have also optimized a protocol for plastid protein extraction, which yielded 1.33 ± 0.25 mg/10 gm plastid proteins from C. cajan and 0.88 ± 0.19 mg/10 gm plastid proteins from C. scarabaeoides. The 2D-PAGE analysis revealed 678 ± 08 reproducible total protein spots from C. cajan and 597 ± 22 protein spots from C. scarabaeoides. Similarly, we found 566 ± 10 and 486 ± 14 reproducible chloroplast protein spots in C. cajan and C. scarabaeoides, respectively. We confirmed the plastid protein fractions through immunoblot analysis using antibodies against LHCb1/LHCⅡ type Ⅰ protein. We found both methods suitable for 2D-PAGE and mass spectrometry (MS). This is the first report on developing protocols for total and chloroplastic protein extraction of Cajanus spp. suitable for advanced proteomics research.
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Affiliation(s)
- Arunima S
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Alakesh Das
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Prakash Jyoti Kalita
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Rahul Ishwar Patil
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Neha Pandey
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Mamta Bhattacharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Bidyut Kumar Sharma
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Debajit Das
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Sumita Acharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- DBT-North-East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
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Anoop AA, Pillai PKS, Nickerson M, Ragavan KV. Plant leaf proteins for food applications: Opportunities and challenges. Compr Rev Food Sci Food Saf 2023; 22:473-501. [PMID: 36478122 DOI: 10.1111/1541-4337.13079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/25/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022]
Abstract
Plant-based proteins are gaining a lot of attention for their health benefits and are considered as an alternative to animal proteins for developing sustainable food systems. Against the backdrop, ensuring a healthy diet supplemented with good quality protein will be a massive responsibility of governments across the globe. Increasing the yield of food crops has its limitations, including low acceptance of genetically modified crops, land availability for cultivation, and the need for large quantities of agrochemicals. It necessitates the sensible use of existing resources and farm output to derive the proteins. On average, the protein content of plant leaves is similar to that of milk, which can be efficiently tapped for food applications across the globe. There has been limited research on utilizing plant leaf proteins for food product development over the years, which has not been fruitful. However, the current global food production scenario has pushed some leading economies to reconsider the scope of plant leaf proteins with dedicated efforts. It is evident from installing pilot-scale demonstration plants for protein extraction from agro-food residues to cater to the protein demand with product formulation. The present study thoroughly reviews the opportunities and challenges linked to the production of plant leaf proteins, including its nutritional aspects, extraction and purification strategies, anti-nutritional factors, functional and sensory properties in food product development, and finally, its impact on the environment. Practical Application: Plant leaf proteins are one of the sustainable and alternative source of proteins. It can be produced in most of the agroclimatic conditions without requiring much agricultural inputs. It's functional properties are unique and finds application in novel food product formulations.
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Affiliation(s)
- A A Anoop
- Agro-Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Prasanth K S Pillai
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Michael Nickerson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Canada
| | - K V Ragavan
- Agro-Processing and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Technologies for Solubility, Dissolution and Permeation Enhancement of Natural Compounds. Pharmaceuticals (Basel) 2022; 15:ph15060653. [PMID: 35745572 PMCID: PMC9227247 DOI: 10.3390/ph15060653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 12/10/2022] Open
Abstract
The current review is based on the advancements in the field of natural therapeutic agents which could be utilized for a variety of biomedical applications and against various diseases and ailments. In addition, several obstacles have to be circumvented to achieve the desired therapeutic effectiveness, among which limited dissolution and/or solubility and permeability are included. To counteract these issues, several advancements in the field of natural therapeutic substances needed to be addressed. Therefore, in this review, the possible techniques for the dissolution/solubility and permeability improvements have been addressed which could enhance the dissolution and permeability up to several times. In addition, the conventional and modern isolation and purification techniques have been emphasized to achieve the isolation and purification of single or multiple therapeutic constituents with convenience and smarter approaches. Moreover, a brief overview of advanced natural compounds with multiple therapeutic effectiveness have also been anticipated. In brief, enough advancements have been carried out to achieve safe, effective and economic use of natural medicinal agents with improved stability, handling and storage.
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Dhar S, Bhattacharjee M, Baishya D, Acharjee S. Characterization of Seed Proteome Profile of Wild and Cultivated Chickpeas of India. Protein Pept Lett 2021; 28:323-332. [PMID: 32914710 DOI: 10.2174/0929866527666200910164118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/14/2020] [Accepted: 09/21/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Chickpea is a widely grown legume in India, Australia, Canada, and Mediterranean regions. Seeds of chickpea are good source of protein for both human and animals. Wild relatives of chickpea (Cicer arietinum) are the potential gene pool for crop improvement; however, very little information is available on the seed proteome of these wild chickpeas. OBJECTIVE We aimed to analyze the seed proteome profiles of three wild relatives of chickpea, Cicer bijugum, Cicer judaicum and Cicer microphyllum along with two cultivated varieties JG11 and DCP 92/3. METHODS Total seed proteins were extracted using various extraction buffers for 2-D gel electrophoresis. Protein separated in a 2-D gels were subjected to image analyses, differentially expressed proteins were extracted from the gels and identified by the MALDI TOF/TOF. Seed protease inhibitors were analysed biochemically. RESULTS We have standardized the 2-D gel electrophoresis method and separated seed proteins using the modified method. We identified a large number (400) of protein proteins which were differentially expressed in cultivated and wild type species of chickpea. A comparative analysis between C. bijugum and JG 11 revealed the presence of 9 over-expressed and 22 under-expressed proteins, while the comparison between C. bijugum with DCP 92/3 showed 8 over-expressed and 18 under-- expressed proteins. Similarly, comparative analysis between C. microphyllum with DCP 92/3 showed 8 over-expressed proteins along with 22 under-expressed proteins, while the comparative study of C. microphyllum with JG11 displayed 9 over-expressed and 24 under-expressed proteins. We also compared C. judaicum with DCP 92/3 which revealed 15 overexpressed and 11 under-expressed proteins. On the other hand, the comparative analysis of C. judaicum with JG11 showed 10 over-expressed proteins, while the numbers of under-expressed proteins were 14. Among the differentially expressed protein proteins, 19 proteins were analyzed by the MS/MS, and peptides were identified using the MASCOT search engine. In the wild relatives the differentially expressed proteins are phosphatidylinositol 4-phosphate 5- kinase, β-1-6 galactosyltransferase, RNA helicase, phenyl alanine ammonia lyase 2, flavone 3'-0-methyl transferase, Argonaute 2, Myb related protein, Tubulin beta-2 chain and others. The most important one was legumin having α- amylase inhibition activity which was up regulated in C. bijugum. We also studied the activity of protease inhibitor (trypsin and α- amylase inhibitors) in these seed lines which showed differential activity of protease inhibitors. The highest trypsin and α- amylase inhibition was observed in C. judaicum and C. bijugum, respectively. CONCLUSION The differentially expressed proteins of wild relatives of chickpea appeared to be involved in various metabolic pathways. The study provides us information about the differences in the seed proteome of these wild species and cultivated varieties for the first time.
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Affiliation(s)
- Santanu Dhar
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India
| | - Mamta Bhattacharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India
| | - Debabrat Baishya
- Department of Bioengineering and Technology, Gauhati University, Guwahati 781014, India
| | - Sumita Acharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India
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Yadav RK, Chatrath A, Tripathi K, Gerard M, Ahmad A, Mishra V, Abraham G. Salinity tolerance mechanism in the aquatic nitrogen fixing pteridophyte Azolla: a review. Symbiosis 2020. [DOI: 10.1007/s13199-020-00736-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Shahmirzaie M, Safarnejad MR, Rakhshandehroo F, Safarpour H, Shirazi FH, Zamanizadeh HR, Elbeaino T. Generation and molecular docking analysis of specific single-chain variable fragments selected by phage display against the recombinant nucleocapsid protein of fig mosaic virus. J Virol Methods 2020; 276:113796. [DOI: 10.1016/j.jviromet.2019.113796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022]
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Asif A, K Ansari MY, Hashem A, Tabassum B, Abd Allah EF, Ahmad A. Proteome Profiling of the Mutagen-Induced Morphological and Yield Macro-Mutant Lines of Nigella sativa L. PLANTS 2019; 8:plants8090321. [PMID: 31480701 PMCID: PMC6784210 DOI: 10.3390/plants8090321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 01/01/2023]
Abstract
In the present investigation, the leaf proteome profile of the macro-mutant lines of Nigella sativa L. was analyzed to identify the key proteins involved in the expression of traits associated with the morphology, seed yield, and content of thymoquinone. In our earlier study, the macro-mutants were generated with contrasting morphological traits and seed yields through induced mutagenesis, using ethyl methyl sulfonate, gamma rays, and combinations of both. Analysis of the leaf proteome of the control and macro-mutant lines of N. sativa showed that twenty-three proteins were differentially expressed. These differentially expressed proteins were sequenced through mass spectrometry and identified using the MASCOT software. On the basis of their function, these proteins were categorized into several groups. Most proteins were found in the categories of signal transduction (18%) and carbon metabolism (18%). A total of 13% of proteins belonged to the categories of energy and metabolism. Proteins in the categories of secondary plant metabolism, stress defense, cytoskeleton, and protein synthesis were also found. The polycomb group protein (FIE1), transcription factor (PRE1), and geranyl diphosphate synthase were notable proteins, in addition to some proteins of signal transduction and carbon metabolism. Expression patterns of the differentially expressed proteins were also studied at the transcript level by using qRT-PCR. Transcriptomics analysis was consistent with the proteomics data. This study shows the changes that take place at the proteomic level through induced mutagenesis, as well as the involvement of some proteins in the expression traits associated with plant height, seed yield, and the thymoquinone content of N. sativa. The identified proteins might help elucidate the metabolic pathways involved in the expression of traits, including seed yield, and the active compounds of medicinal plants.
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Affiliation(s)
- Ambreen Asif
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | | | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Gaza 12511, Egypt
| | - Baby Tabassum
- Toxicology Laboratory, Department of Zoology, Govt. Raza PG College, Rampur 244901, UP, India
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India.
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Li Z, Luo R, Zhang Y, Yan X, Pang Q. Effective protein extraction from mycelium and fruiting body of Auricularia auricula for proteomics studies. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2018. [DOI: 10.1080/10942912.2018.1499111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ziwei Li
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, Heilongjiang, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
| | - Rui Luo
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, Heilongjiang, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
| | - Yuexin Zhang
- Heilongjiang Forest By-product and Speciality Institute, Mudanjiang, Heilongjiang, China
| | - Xiufeng Yan
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, Heilongjiang, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
| | - Qiuying Pang
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, Heilongjiang, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
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Wang WQ, Jensen ON, Møller IM, Hebelstrup KH, Rogowska-Wrzesinska A. Evaluation of sample preparation methods for mass spectrometry-based proteomic analysis of barley leaves. PLANT METHODS 2018; 14:72. [PMID: 30159003 PMCID: PMC6109330 DOI: 10.1186/s13007-018-0341-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 08/16/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Sample preparation is a critical process for proteomic studies. Many efficient and reproducible sample preparation methods have been developed for mass spectrometry-based proteomic analysis of human and animal tissues or cells, but no attempt has been made to evaluate these protocols for plants. We here present an LC-MS/MS-based proteomics study of barley leaf aimed at optimization of methods to achieve efficient and unbiased trypsin digestion of proteins prior to LC-MS/MS based sequencing and quantification of peptides. We evaluated two spin filter-aided sample preparation protocols using either sodium dodecyl-sulphate or sodium deoxycholate (SDC), and three in-solution digestion (ISD) protocols using SDC or trichloroacetic acid/acetone precipitation. RESULTS The proteomics workflow identified and quantified up to 1800 barley proteins based on sequencing of up to 6900 peptides per sample. The two spin filter-based protocols provided a 12-38% higher efficiency than the ISD protocols, including more proteins of low abundance. Among the ISD protocols, a simple one-step reduction and S-alkylation method (OP-ISD) was the most efficient for barley leaf sample preparation; it identified and quantified 1500 proteins and displayed higher peptide-to-protein inference ratio and higher average amino acid sequence coverage of proteins. The two spin filter-aided sample preparation protocols are compatible with TMT labelling for quantitative proteomics studies. They exhibited complementary performance as about 30% of the proteins were identified by either one or the other protocol, but also demonstrated a positive bias for membrane proteins when using SDC as detergent. CONCLUSIONS We provide detailed protocols for efficient plant protein sample preparation for LC-MS/MS-based proteomics studies. Spin filter-based protocols are the most efficient for the preparation of leaf samples for MS-based proteomics. However, a simple protocol provides comparable results although with different peptide digestion profile.
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Affiliation(s)
- Wei-Qing Wang
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Ole Nørregaard Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
| | - Kim H. Hebelstrup
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Thangella PAV, Pasumarti SNBS, Pullakhandam R, Geereddy BR, Daggu MR. Differential expression of leaf proteins in four cultivars of peanut ( Arachis hypogaea L.) under water stress. 3 Biotech 2018; 8:157. [PMID: 29515963 PMCID: PMC5834407 DOI: 10.1007/s13205-018-1180-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 02/20/2018] [Indexed: 11/25/2022] Open
Abstract
Drought is a major constraint to the productivity of many crops affecting various physiological and biochemical processes. Seventy percent of the peanuts are grown in semiarid tropics that are frequently prone to drought stress. So, we analyzed its effect in 4 cultivars of peanut, with different degrees of drought tolerance, under 10 and 20 days of water stress using two-dimensional gel electrophoresis and mass spectrometry. A total of 189 differentially expressed protein spots were identified in the leaf proteome of all the 4 cultivars using PD Quest Basic software; 74 in ICGV 91114, 41 in ICGS 76, 44 in J 11 and 30 in JL 24. Of these, 30 protein spots were subjected to in-gel trypsin digestion followed by MALDI-TOF that are functionally categorized into 5 groups: molecular chaperones, signal transducers, photosynthetic proteins, defense proteins and detoxification proteins. Of these, 12 proteins were sequenced. Late embryogenesis abundant protein, calcium ion binding protein, sucrose synthase isoform-1, 17.3 kDa heat shock protein and structural maintenance of chromosome proteins were overexpressed only in the 15 and 20 days stressed plants of ICGV 91114 cultivar while cytosolic ascorbate peroxidase was expressed with varying levels in the 10 and 20 days stressed plants of all the 4 cultivars. Signaling protein like 14-3-3 and defense proteins like alpha-methyl-mannoside-specific lectin and mannose/glucose-binding lectins were differentially expressed in the 4 cultivars. Photosynthetic protein like Rubisco was down-regulated in the stressed plants of all 4 cultivars while Photosystem-I reaction center subunit-II of chloroplast precursor protein was overexpressed in only 20 days stressed plants of ICGV 91114, ICGS 76 and J11 cultivars. These differentially expressed proteins could potentially be used as protein markers for screening the peanut germplasm and further crop improvement.
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Affiliation(s)
- Padmavathi A. V. Thangella
- Department of Genetics, Osmania University, Hyderabad, India
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK USA
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Singh V, Singh B, Joshi R, Jaju P, Pati PK. Changes in the leaf proteome profile of Withania somnifera (L.) Dunal in response to Alternaria alternata infection. PLoS One 2017; 12:e0178924. [PMID: 28575108 PMCID: PMC5456394 DOI: 10.1371/journal.pone.0178924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/22/2017] [Indexed: 12/11/2022] Open
Abstract
Withania somnifera is a high value medicinal plant which is used against large number of ailments. The medicinal properties of the plant attributes to a wide array of important secondary metabolites. The plant is predominantly infected with leaf spot pathogen Alternaria alternata, which leads to substantial biodeterioration of pharmaceutically important metabolites. To develop an effective strategy to combat this disease, proteomics based approach could be useful. Hence, in the present study, three different protein extraction methods tris-buffer based, phenol based and trichloroacetic acid-acetone (TCA-acetone) based method were comparatively evaluated for two-dimensional electrophoresis (2-DE) analysis of W. somnifera. TCA-acetone method was found to be most effective and was further used to identify differentially expressed proteins in response to fungal infection. Thirty-eight differentially expressed proteins were identified by matrix assisted laser desorption/ionization time of flight-mass spectrometry (MALDI TOF/TOF MS/MS). The known proteins were categorized into eight different groups based on their function and maximum proteins belonged to energy and metabolism, cell structure, stress and defense and RNA/DNA categories. Differential expression of some key proteins were also crosschecked at transcriptomic level by using qRT-PCR and were found to be consistent with the 2-DE data. These outcomes enable us to evaluate modifications that take place at the proteomic level during a compatible host pathogen interaction. The comparative proteome analysis conducted in this paper revealed the involvement of many key proteins in the process of pathogenesis and further investigation of these identified proteins could assist in the discovery of new strategies for the development of pathogen resistance in the plant.
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Affiliation(s)
- Varinder Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Baldev Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Puneet Jaju
- Field Application Specialist - Life Science Group, Bio-rad Laboratories (India) Pvt. Ltd, Bangalore, India
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, India
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13
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Proteomic Analysis of Tung Tree (Vernicia fordii) Oilseeds during the Developmental Stages. Molecules 2016; 21:molecules21111486. [PMID: 27834836 PMCID: PMC6273751 DOI: 10.3390/molecules21111486] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 01/10/2023] Open
Abstract
The tung tree (Vernicia fordii), a non-model woody plant belonging to the Euphorbiaceae family, is a promising economic plant due to the high content of a novel high-value oil in its seeds. Many metabolic pathways are active during seed development. Oil (triacylglycerols (TAGs)) accumulates in oil bodies distributed in the endosperm cells of tung tree seeds. The relationship between oil bodies and oil content during tung tree seed development was analyzed using ultrastructural observations, which confirmed that oil accumulation was correlated with the volumes and numbers of oil bodies in the endosperm cells during three different developmental stages. For a deeper understanding of seed development, we carried out proteomic analyses. At least 144 proteins were differentially expressed during three different developmental stages. A total of 76 proteins were successfully identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry/mass spectrometry (MALDI-TOF/MS/MS). These proteins were grouped into 11 classes according to their functions. The major groups of differentially expressed proteins were associated with energy metabolism (25%), fatty acid metabolism (15.79%) and defense (14.47%). These results strongly suggested that a very high percentage of gene expression in seed development is dedicated to the synthesis and accumulation of TAGs.
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14
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Thagela P, Yadav RK, Mishra V, Tripathi K, Ahmad A, Dahuja A, Singh PK, Abraham G. Sample preparation method for tissue based proteomic analysis of Azolla microphylla. Symbiosis 2016. [DOI: 10.1007/s13199-016-0463-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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A novel immune-tolerable and permeable lectin-like protein from mushroom Agaricus bisporus. Biochem Biophys Res Commun 2016; 473:1090-1093. [PMID: 27060548 DOI: 10.1016/j.bbrc.2016.04.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/05/2016] [Indexed: 11/21/2022]
Abstract
A lectin like protein designated as LSMT is recently discovered in Agaricus bisporus. The protein adopts very similar structure to Ricin-B like lectin from Clitocybe nebularis (CNL) and HA-33 from Clostridium botulinum (HA-33), which both recognize sugar molecules that decorate the surface of the epithelial cells of the intestine. A preliminary study in silico pointed out potential capability of LSMT to perform such biological activity. Following that hypothesis, we demonstrated that LSMT is indeed capable of penetrating out from a dialysis tube of the mice intestine origin. Furthermore, the protein appeared not to evoke the immune response upon introduction into mice, unlike its structural homologs. This is the first report on the biological implication of LSMT that might lead to its application.
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16
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Mujahid H, Pendarvis K, Reddy JS, Nallamilli BRR, Reddy KR, Nanduri B, Peng Z. Comparative Proteomic Analysis of Cotton Fiber Development and Protein Extraction Method Comparison in Late Stage Fibers. Proteomes 2016; 4:proteomes4010007. [PMID: 28248216 PMCID: PMC5217364 DOI: 10.3390/proteomes4010007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/19/2016] [Accepted: 01/28/2016] [Indexed: 12/21/2022] Open
Abstract
The distinct stages of cotton fiber development and maturation serve as a single-celled model for studying the molecular mechanisms of plant cell elongation, cell wall development and cellulose biosynthesis. However, this model system of plant cell development is compromised for proteomic studies due to a lack of an efficient protein extraction method during the later stages of fiber development, because of a recalcitrant cell wall and the presence of abundant phenolic compounds. Here, we compared the quality and quantities of proteins extracted from 25 dpa (days post anthesis) fiber with multiple protein extraction methods and present a comprehensive quantitative proteomic study of fiber development from 10 dpa to 25 dpa. Comparative analysis using a label-free quantification method revealed 287 differentially-expressed proteins in the 10 dpa to 25 dpa fiber developmental period. Proteins involved in cell wall metabolism and regulation, cytoskeleton development and carbohydrate metabolism among other functional categories in four fiber developmental stages were identified. Our studies provide protocols for protein extraction from maturing fiber tissues for mass spectrometry analysis and expand knowledge of the proteomic profile of cotton fiber development.
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Affiliation(s)
- Hana Mujahid
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Ken Pendarvis
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Joseph S Reddy
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Babi Ramesh Reddy Nallamilli
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
| | - K R Reddy
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Bindu Nanduri
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
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Chen T, Xu G, Wang Z, Zhang H, Yang J, Zhang J. Expression of proteins in superior and inferior spikelets of rice during grain filling under different irrigation regimes. Proteomics 2015; 16:102-21. [PMID: 26442785 DOI: 10.1002/pmic.201500070] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 12/21/2022]
Abstract
Poor grain filling of later-flowering inferior spikelets is a serious problem in modern rice cultivars, but the reason and regulation remain unclear. This study investigated post-anthesis protein expression in relation with grain filling and the possibility to use irrigation methods to enhance grain filling through regulating protein expression. One japonica rice cultivar was field-grown under three irrigation treatments imposed during the grain filling period: alternate wetting and moderate soil-drying (WMD), alternate wetting and severe soil-drying (WSD), and conventional irrigation. High resolution 2DE, combined with MALDI/TOF, was used to compare differential protein expression between superior and inferior spikelets. Results showed that the expression of proteins that function in photosynthesis, carbohydrate and energy metabolism, amino acids metabolism and defense responses were largely down-regulated in inferior spikelets compared to those in superior spikelets. The WMD treatment enhanced grain filling rate and the expression of these proteins, whereas the WSD treatment decreased them. Similar results were observed for transcript levels of the genes encoding these proteins. These results suggest that down-regulated expression of the proteins associated with grain filling contribute to the poor grain filling of inferior spikelets, and post-anthesis WMD could improve grain filling through regulating protein expression in the spikelets.
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Affiliation(s)
- Tingting Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China.,State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, P. R. China
| | - Genwen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Zhiqin Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Hao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Jianchang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, P. R. China
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18
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Vergara-Barberán M, Lerma-García M, Herrero-Martínez J, Simó-Alfonso E. Use of an enzyme-assisted method to improve protein extraction from olive leaves. Food Chem 2015; 169:28-33. [DOI: 10.1016/j.foodchem.2014.07.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 02/10/2014] [Accepted: 07/24/2014] [Indexed: 10/24/2022]
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19
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Guo H, Li F, Wang S, Li S, Xiao W, Liu W. Enhanced Protein Extraction from Tobacco Roots for Proteomic Analysis. ANAL LETT 2014. [DOI: 10.1080/00032719.2014.930871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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Hunte C, Schnabl H, Traub O, Willecke K, Schulz M. Immunological Evidence of Connexin-like Proteins in the Plasma Membrane ofVicia fabaL. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1992.tb00273.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Li Q, Wang D, Lv S, Zhang Y. Comparative proteomics and expression analysis of five genes in Epicauta chinensis larvae from the first to fifth instar. PLoS One 2014; 9:e89607. [PMID: 24586908 PMCID: PMC3931803 DOI: 10.1371/journal.pone.0089607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 01/21/2014] [Indexed: 11/18/2022] Open
Abstract
Blister beetle is an important insect model for both medicinal and pure research. Previous research has mainly focused on its biology and biochemistry, but very little data is yet available in the molecular biology. This study uses differential proteomics technology to analyze the soluble proteins extracted from each of the 5 instars larvae of Epicauta chinensis. 42 of the differentially-expressed proteins were identified successfully by MALDI-TOF/TOF-MS. Some of these proteins' function and their expression profiles are analyzed. Our analysis revealed dynamics regulation of the following proteins: Axin-like protein pry-1 (APR-1), dihydrolipoyl dehydrogenase (DLD), vitellogenin (Vg) and lysozyme C (Lmz-S). APR-1 negatively regulates the Wnt signaling pathway. Its overexpression could result in embryo, leg, eye and ovary ectopica or malformation. DLD catalyzes the pyruvate into acetyl-CoA, the latter is the starting material of juvenile hormone (JH) and ipsdienol biosynthesis through the MVA pathway in insects. While Vg synthesis can be regulated by JH and stimulated by food factors. So DLD may affect the synthesis of JH, ipsdienol and Vg indirectly. The activity of lysozyme is an indicator of the immunity. Nutrition/food should be taken into account for its potential role during the development of larva in the future. Among the five genes and their corresponding proteins' expression, only hsc70 gene showed a good correspondence with the protein level. This reflects the fluctuating relationship between mRNA and protein levels.
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Affiliation(s)
- Qiurong Li
- Key Laboratory of Plant Protection Resources & Pest Management of Ministry of Education, Northwest A & F University, Yangling, Shaanxi, P. R. China
| | - Dun Wang
- Institute of Entomology, Northwest A & F University, Yangling, Shaanxi, P. R. China
| | - Shumin Lv
- Key Laboratory of Plant Protection Resources & Pest Management of Ministry of Education, Northwest A & F University, Yangling, Shaanxi, P. R. China
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources & Pest Management of Ministry of Education, Northwest A & F University, Yangling, Shaanxi, P. R. China
- * E-mail:
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22
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Wu X, Gong F, Wang W. Protein extraction from plant tissues for 2DE and its application in proteomic analysis. Proteomics 2014; 14:645-58. [PMID: 24395710 DOI: 10.1002/pmic.201300239] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 12/03/2013] [Accepted: 12/10/2013] [Indexed: 11/09/2022]
Abstract
Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE-based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).
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Affiliation(s)
- Xiaolin Wu
- State Key Laboratory of Wheat & Maize Crop Science in Henan Province, Synergetic Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University, Zhengzhou, China
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23
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Marzban G, Herndl A, Maghuly F, Katinger H, Laimer M. Mapping of fruit allergens by 2D electrophoresis and immunodetection. Expert Rev Proteomics 2014; 5:61-75. [DOI: 10.1586/14789450.5.1.61] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Li HH, Huang ZY, Ye SP, Lu CY, Cheng PC, Chen SH, Chen CS. Membrane labeling of coral gastrodermal cells by biotinylation: the proteomic identification of surface proteins involving cnidaria-dinoflagellate endosymbiosis. PLoS One 2014; 9:e85119. [PMID: 24409319 PMCID: PMC3883709 DOI: 10.1371/journal.pone.0085119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 11/22/2013] [Indexed: 11/18/2022] Open
Abstract
The cellular and molecular-scale processes underlying the stability of coral-Symbiodinium endosymbioses remain unclear despite decades of investigation. As the coral gastroderm is the only tissue layer characterized by this unique symbiotic association, the membranes of these symbiotic gastrodermal cells (SGCs) may play important roles in the initiation and maintenance of the endosymbiosis. In order to elucidate the interactions between the endosymbiotic dinoflagellates and their coral hosts, a thorough characterization of SGC membranes is therefore required. Cell surface proteins of isolated SGCs were biotinylated herein by a cell impermeant agent, biotin-XX sulfosuccinimidyl ester. The in situ distribution of these biotinylated proteins was uncovered by both fluorescence and transmission electron microscopic imaging of proteins bound to Alexa Fluor® 488-conjugated streptavidin. The identity of these proteins was then determined by two-dimensional gel electrophoresis followed by liquid chromatography-tandem mass spectrometry. Nineteen (19) proteins were identified, and they are known to be involved in the molecular chaperone/stress response, cytoskeletal remodeling, and energy metabolism. These results not only reveal the molecular characters of the host SGC membrane, but also provide critical insight into understanding the possible role of host membranes in this ecologically important endosymbiotic association.
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Affiliation(s)
- Hsing-Hui Li
- Graduate Institute of Marine Biotechnology, National Dong Hwa University, Pingtung, Taiwan
- Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - Zi-Yu Huang
- Graduate Institute of Marine Biotechnology, National Dong Hwa University, Pingtung, Taiwan
| | - Shih-Png Ye
- Graduate Institute of Marine Biotechnology, National Dong Hwa University, Pingtung, Taiwan
| | - Chi-Yu Lu
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Pai-Chiao Cheng
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shu-Hwa Chen
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Chii-Shiarng Chen
- Graduate Institute of Marine Biotechnology, National Dong Hwa University, Pingtung, Taiwan
- Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, Taiwan
- * E-mail:
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25
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Sebastiana M, Figueiredo A, Monteiro F, Martins J, Franco C, Coelho AV, Vaz F, Simões T, Penque D, Pais MS, Ferreira S. A possible approach for gel-based proteomic studies in recalcitrant woody plants. SPRINGERPLUS 2013; 2:210. [PMID: 23724367 PMCID: PMC3663981 DOI: 10.1186/2193-1801-2-210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/04/2013] [Indexed: 12/26/2022]
Abstract
Woody plants are particularly difficult to investigate due to high phenolic, resin, and tannin contents and laborious sample preparation. In particular, protein isolation from woody plants for two-dimensional gel electrophoresis (2-DE) is challenging as secondary metabolites negatively interfere with protein extraction and separation. In this study, three protein extraction protocols, using TCA, phenol and ethanol as precipitation or extraction agents, were tested in order to select the more efficient for woody recalcitrant plant gel-based proteomics. Grapevine leaves, pine needles and cork oak ectomycorrhizal roots were used to represent woody plant species and tissues. The phenol protocol produced higher quality 2-DE gels, with increased number of resolved spots, better spot focusing and representation of all molecular mass and isoelectric point ranges tested. In order to test the compatibility of the phenol extracted proteomes with protein identification several spots were excised from the phenol gels and analyzed by mass spectrometry (MALDI-TOF/TOF). Regardless the incomplete genome/protein databases for the plant species under analysis, 49 proteins were identified by Peptide Mass Fingerprint (PMF). Proteomic data have been deposited to the ProteomeXchange with identifier PXD000224. Our results demonstrate the complexity of protein extraction from woody plant tissues and the suitability of the phenol protocol for obtaining high quality protein extracts for efficient 2-DE separation and downstream applications such as protein identification by mass spectrometry.
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Affiliation(s)
- Mónica Sebastiana
- />Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon, 1749-016 Portugal
| | - Andreia Figueiredo
- />Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon, 1749-016 Portugal
| | - Filipa Monteiro
- />Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon, 1749-016 Portugal
| | - Joana Martins
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da Republica, Oeiras, 2780-157 Portugal
| | - Catarina Franco
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da Republica, Oeiras, 2780-157 Portugal
| | - Ana Varela Coelho
- />Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da Republica, Oeiras, 2780-157 Portugal
| | - Fátima Vaz
- />Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr. Ricardo Jorge INSA I.P, Lisbon, Portugal
| | - Tânia Simões
- />Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr. Ricardo Jorge INSA I.P, Lisbon, Portugal
| | - Deborah Penque
- />Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr. Ricardo Jorge INSA I.P, Lisbon, Portugal
| | - Maria Salomé Pais
- />Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon, 1749-016 Portugal
| | - Sílvia Ferreira
- />Plant Systems Biology Lab, Center of Biodiversity, Functional & Integrative Genomics (BioFIG), Science Faculty of Lisbon University, Lisbon, 1749-016 Portugal
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Kröber T, Wolff M, Hundt B, Seidel-Morgenstern A, Reichl U. Continuous purification of influenza virus using simulated moving bed chromatography. J Chromatogr A 2013; 1307:99-110. [DOI: 10.1016/j.chroma.2013.07.081] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 11/16/2022]
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27
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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CHEN TT, TAN GL, CHU G, LIU LJ, YANG JC. Differential Expressions of the Proteins Related to Grain Filling between Superior and Inferior Spikelets of Super Rice after Anthesis. ACTA AGRONOMICA SINICA 2013. [DOI: 10.3724/sp.j.1006.2012.01471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Chan Z. Proteomic responses of fruits to environmental stresses. FRONTIERS IN PLANT SCIENCE 2013; 3:311. [PMID: 23335934 PMCID: PMC3541545 DOI: 10.3389/fpls.2012.00311] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/24/2012] [Indexed: 05/18/2023]
Abstract
Fruits and vegetables are extremely susceptible to decay and easily lose commercial value after harvest. Different strategies have been developed to control postharvest decay and prevent quality deterioration during postharvest storage, including cold storage, controlled atmosphere (CA), and application of biotic and abiotic stimulus. In this review, mechanisms related to protein level responses of host side and pathogen side were characterized. Protein extraction protocols have been successfully developed for recalcitrant, low protein content fruit tissues. Comparative proteome profiling and functional analysis revealed that defense related proteins, energy metabolism, and antioxidant pathway played important roles in fruits in response to storage conditions and exogenous elicitor treatments. Secretome of pathogenic fungi has been well-investigated and the results indicated that hydrolytic enzymes were the key virulent factors for the pathogen infection. These protein level changes shed new light on interaction among fruits, pathogens, and environmental conditions. Potential postharvest strategies to reduce risk of fruit decay were further proposed based on currently available proteomic data.
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Affiliation(s)
- Zhulong Chan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
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Gonçalves L, Rodrigues R, Diz M, Robaina R, do Amaral Júnior A, Carvalho A, Gomes V. Peroxidase is involved in Pepper yellow mosaic virus resistance in Capsicum baccatum var. pendulum. GENETICS AND MOLECULAR RESEARCH 2013; 12:1411-20. [DOI: 10.4238/2013.april.26.3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Optimization of an Efficient Protein Extraction Protocol Compatible with Two-Dimensional Electrophoresis and Mass Spectrometry from Recalcitrant Phenolic Rich Roots of Chickpea (Cicer arietinum L.). INTERNATIONAL JOURNAL OF PROTEOMICS 2012. [PMID: 23193474 PMCID: PMC3502011 DOI: 10.1155/2012/536963] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two-dimensional electrophoresis and mass spectrometry are undoubtedly two essential tools popularly used in proteomic analyses. Utilization of these techniques however largely depends on efficient and optimized sample preparation, regarded as one of the most crucial steps for recovering maximum amount of reliable information. The present study highlights the optimization of an effective and efficient protocol, capable of extraction of root proteins from recalcitrant phenolic rich tissues of chickpea. The widely applicable TCA-acetone and phenol-based methods have been comparatively evaluated, amongst which the latter appeared to be better suited for the sample. The phenol extraction-based method further complemented with sodium dodecyl sulphate (SDS) and pulsatory treatments proved to be the most suitable method represented by greatest spot number, good resolution, and spot intensities. All the randomly selected spots showed successful identification when subjected to further downstream MALDI-TOF and MS/MS analyses. Hence, the information obtained collectively proposes the present protein extraction protocol to be an effective one that could be applicable for recalcitrant leguminous root samples.
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Sagar S, Gehring C, Minneman KP. Methods to Isolate and Identify New Plant Signaling Peptides. SIGNALING AND COMMUNICATION IN PLANTS 2012. [DOI: 10.1007/978-3-642-27603-3_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Aryal UK, Krochko JE, Ross ARS. Identification of phosphoproteins in Arabidopsis thaliana leaves using polyethylene glycol fractionation, immobilized metal-ion affinity chromatography, two-dimensional gel electrophoresis and mass spectrometry. J Proteome Res 2011; 11:425-37. [PMID: 22092075 DOI: 10.1021/pr200917t] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reversible protein phosphorylation is a key regulatory mechanism in cells. Identification and characterization of phosphoproteins requires specialized enrichment methods, due to the relatively low abundance of these proteins, and is further complicated in plants by the high abundance of Rubisco in green tissues. We present a novel method for plant phosphoproteome analysis that depletes Rubisco using polyethylene glycol fractionation and utilizes immobilized metal-ion affinity chromatography to enrich phosphoproteins. Subsequent protein separation by one- and two-dimensional gel electrophoresis is further improved by extracting the PEG-fractionated protein samples with SDS/phenol and methanol/chloroform to remove interfering compounds. Using this approach, we identified 132 phosphorylated proteins in a partial Arabidopsis leaf extract. These proteins are involved in a range of biological processes, including CO(2) fixation, protein assembly and folding, stress response, redox regulation, and cellular metabolism. Both large and small subunits of Rubisco were phosphorylated at multiple sites, and depletion of Rubisco enhanced detection of less abundant phosphoproteins, including those associated with state transitions between photosystems I and II. The discovery of a phosphorylated form of AtGRP7, a self-regulating RNA-binding protein that affects floral transition, as well as several previously uncharacterized ribosomal proteins confirm the utility of this approach for phosphoproteome analysis and its potential to increase our understanding of growth and development in plants.
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Affiliation(s)
- Uma K Aryal
- Plant Biotechnology Institute, National Research Council, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9.
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Clark KF, Greenwood SJ. Aerococcus viridans expression of Cpn60 is associated with virulence during infection of the American lobster, Homarus americanus Milne Edwards. JOURNAL OF FISH DISEASES 2011; 34:831-843. [PMID: 21988355 DOI: 10.1111/j.1365-2761.2011.01300.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The Gram-positive bacterium Aerococcus viridans var. homari is a well-documented causative agent of the lethal systemic disease gaffkemia in both the American lobster, Homarus americanus, and the European lobster, Homarus gammarus. Previous phenotypic characterization has been unsuccessful at differentiating avirulent from virulent strains without performing lethal animal infection trials. Recent genetic characterization of A. viridans strains through 16S rRNA sequencing and random amplification of polymorphic DNA fingerprinting has revealed the presence of two subtypes. However, subtype 1 contains both virulent and avirulent strains which are genetically identical. The purpose of this study was to determine the proteomic mediators of virulence in A. viridans. Quantitative proteomic mapping of these two strains has revealed 29 differentially expressed protein spots, seven of which are only expressed in the virulent strain and could act as virulence factors. One protein, chaperonin 60 (Cpn60), is uniquely expressed in the virulent strain and has been shown to act as a virulence factor in many other bacteria. The proteomic mapping strategy employed in this study is the first to show phenotypic differences between virulent and avirulent strains. Cpn60 expression represents a potentially useful tool for identifying the virulent strains of A. viridans in epidemiological studies.
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Affiliation(s)
- K F Clark
- AVC Lobster Science Centre, University of Prince Edward Island, Charlottetown, PE, Canada.
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Comparative proteomics of human male and female tears by two-dimensional electrophoresis. Exp Eye Res 2011; 92:454-63. [DOI: 10.1016/j.exer.2011.03.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 02/26/2011] [Accepted: 03/02/2011] [Indexed: 11/18/2022]
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Agrawal GK, Rakwal R. Rice proteomics: A move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology. Proteomics 2011; 11:1630-49. [DOI: 10.1002/pmic.201000696] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 01/05/2011] [Accepted: 01/24/2011] [Indexed: 12/13/2022]
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Chen M, Zhao L, Sun YL, Cui SX, Zhang LF, Yang B, Wang J, Kuang TY, Huang F. Proteomic analysis of hydrogen photoproduction in sulfur-deprived Chlamydomonas cells. J Proteome Res 2010; 9:3854-66. [PMID: 20509623 DOI: 10.1021/pr100076c] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The green alga Chlamydomonas reinhardtii is a model organism to study H(2) metabolism in photosynthetic eukaryotes. To understand the molecular mechanism of H(2) metabolism, we used 2-DE coupled with MALDI-TOF and MALDI-TOF/TOF-MS to investigate proteomic changes of Chlamydomonas cells that undergo sulfur-depleted H(2) photoproduction process. In this report, we obtained 2-D PAGE soluble protein profiles of Chlamydomonas at three time points representing different phases leading to H(2) production. We found over 105 Coomassie-stained protein spots, corresponding to 82 unique gene products, changed in abundance throughout the process. Major changes included photosynthetic machinery, protein biosynthetic apparatus, molecular chaperones, and 20S proteasomal components. A number of proteins related to sulfate, nitrogen and acetate assimilation, and antioxidative reactions were also changed significantly. Other proteins showing alteration during the sulfur-depleted H(2) photoproduction process were proteins involved in cell wall and flagella metabolisms. In addition, among these differentially expressed proteins, 11 were found to be predicted proteins without functional annotation in the Chlamydomonas genome database. The results of this proteomic analysis provide new insight into molecular basis of H(2) photoproduction in Chlamydomonas under sulfur depletion.
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Affiliation(s)
- Mei Chen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Wilkes MA, Seung D, Levavasseur G, Trethowan RM, Copeland L. Effects of Soil Type and Tillage on Protein and Starch Quality in Three Related Wheat Genotypes. Cereal Chem 2010. [DOI: 10.1094/cchem-87-2-0095] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Meredith A. Wilkes
- Faculty of Agriculture, Food and Natural Resources, The University of Sydney, NSW, 2006. Australia
- Corresponding author. Phone: +61 2 8627 1018. Fax: +61 2 8627 1099. E-mail:
| | - David Seung
- Faculty of Agriculture, Food and Natural Resources, The University of Sydney, NSW, 2006. Australia
| | - Gilles Levavasseur
- Visiting student from Institut Polytechnique LaSalle Beauvais, Beauvais Cedex, France
| | - Richard M. Trethowan
- Faculty of Agriculture, Food and Natural Resources, The University of Sydney, NSW, 2006. Australia
| | - Les Copeland
- Faculty of Agriculture, Food and Natural Resources, The University of Sydney, NSW, 2006. Australia
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Peng SE, Wang YB, Wang LH, Chen WNU, Lu CY, Fang LS, Chen CS. Proteomic analysis of symbiosome membranes in Cnidaria-dinoflagellate endosymbiosis. Proteomics 2010; 10:1002-16. [DOI: 10.1002/pmic.200900595] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Szulc M, Maquet A. Extraction Protocol for Winter Wheat Whole Grain Proteins Compatible with Two-Dimensional Fluorescence Difference Gel Electrophoresis (2D DIGE). Cereal Chem 2009. [DOI: 10.1094/cchem-86-6-0692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Małgorzata Szulc
- European Commission, DG Joint Research Centre, Inst. for Reference Materials and Measurements, IRMM, 111 Retieseweg, B-2440 Geel, Belgium
| | - Alain Maquet
- European Commission, DG Joint Research Centre, Inst. for Reference Materials and Measurements, IRMM, 111 Retieseweg, B-2440 Geel, Belgium
- Corresponding author. Phone: +32 14 571817. Fax: +32 14 571787. E-mail:
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Two-dimensional electrophoresis: an overview. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2009; 519:1-16. [PMID: 19381573 DOI: 10.1007/978-1-59745-281-6_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Two-dimensional gel electrophoresis (2DE) separates proteins by molecular charge and molecular size. Proteins are first solubilised in a denaturing buffer containing a neutral chaotrope, a zwitterionic or neutral detergent, and a reducing agent. First-dimension isoelectric keywords, focusing, then subjects proteins to a high voltage within a pH gradient. The amphoteric nature of proteins means each migrates to the pH where the net molecular charge is zero. After equilibration, to ensure complete protein unfolding, the second dimension separates by molecular size. Each protein is therefore resolved at a unique isoelectric point/molecular size coordinate. After visualisation by staining proteome changes are revealed by gel image analysis, and protein spots of interest excised and identified by mass spectrometry sequence analysis combined with database comparison. Variations to this procedure include staining or radio-labelling prior to electrophoresis. Although 2DE does have limitations, the most significant being the resolution of membrane and/or hydrophobic proteins, the potential solutions offered by pre-fractionation or adjustments to the electrophoresis regimen mean this technique is likely to remain central to proteomic research.
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Krishnan HB, Oehrle NW, Natarajan SS. A rapid and simple procedure for the depletion of abundant storage proteins from legume seeds to advance proteome analysis: a case study using Glycine max. Proteomics 2009; 9:3174-88. [PMID: 19526550 DOI: 10.1002/pmic.200800875] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 03/01/2009] [Indexed: 11/06/2022]
Abstract
2-D analysis of plant proteomes containing thousands of proteins has limited dynamic resolution because only abundant proteins can be detected. Proteomic assessment of the non-abundant proteins within seeds is difficult when 60-80% is storage proteins. Resolution can be improved through sample fractionation using separation techniques based upon different physiological or biochemical principles. We have developed a fast and simple fractionation technique using 10 mM Ca(2+) to precipitate soybean (Glycine max) seed storage globulins, glycinin and beta-conglycinin. This method removes 87+/-4% of the highly abundant seed proteins from the extract, allowing for 541 previously inconspicuous proteins present in soybean seed to be more detectable (volume increase of >or=50%) using fluorescent detection. Of those 541 enhanced spots, 197 increased more than 2.5-fold when visualized with Coomassie. The majority of those spots were isolated and identified using peptide mass fingerprinting. Fractionation also provided detection of 63 new phosphorylated protein spots and enhanced the visibility of 15 phosphorylated protein spots, using 2-D electrophoretic separation and an in-gel phosphoprotein stain. Application of this methodology toward other legumes, such as peanut, bean, pea, alfalfa and others, also containing high amounts of storage proteins, was examined, and is reported here.
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Affiliation(s)
- Hari B Krishnan
- Plant Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Columbia, MO 65211, USA.
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Ngoka LCM. Sample prep for proteomics of breast cancer: proteomics and gene ontology reveal dramatic differences in protein solubilization preferences of radioimmunoprecipitation assay and urea lysis buffers. Proteome Sci 2008; 6:30. [PMID: 18950484 PMCID: PMC2600628 DOI: 10.1186/1477-5956-6-30] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 10/24/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An important step in the proteomics of solid tumors, including breast cancer, consists of efficiently extracting most of proteins in the tumor specimen. For this purpose, Radio-Immunoprecipitation Assay (RIPA) buffer is widely employed. RIPA buffer's rapid and highly efficient cell lysis and good solubilization of a wide range of proteins is further augmented by its compatibility with protease and phosphatase inhibitors, ability to minimize non-specific protein binding leading to a lower background in immunoprecipitation, and its suitability for protein quantitation. RESULTS In this work, the insoluble matter left after RIPA buffer extraction of proteins from breast tumors are subjected to another extraction step, using a urea-based buffer. It is shown that RIPA and urea lysis buffers fractionate breast tissue proteins primarily on the basis of molecular weights. The average molecular weight of proteins that dissolve exclusively in urea buffer is up to 60% higher than in RIPA.Gene Ontology (GO) and Directed Acyclic Graphs (DAG) are used to map the collective biological and biophysical attributes of the RIPA and urea proteomes. The Cellular Component and Molecular Function annotations reveal protein solubilization preferences of the buffers, especially the compartmentalization and functional distributions.It is shown that nearly all extracellular matrix proteins (ECM) in the breast tumors and matched normal tissues are found, nearly exclusively, in the urea fraction, while they are mostly insoluble in RIPA buffer. Additionally, it is demonstrated that cytoskeletal and extracellular region proteins are more soluble in urea than in RIPA, whereas for nuclear, cytoplasmic and mitochondrial proteins, RIPA buffer is preferred.Extracellular matrix proteins are highly implicated in cancer, including their proteinase-mediated degradation and remodelling, tumor development, progression, adhesion and metastasis. Thus, if they are not efficiently extracted by RIPA buffer, important information may be missed in cancer research. CONCLUSION For proteomics of solid tumors, a two-step extraction process is recommended. First, proteins in the tumor specimen should be extracted with RIPA buffer. Second, the RIPA-insoluble material should be extracted with the urea-based buffer employed in this work.
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Affiliation(s)
- Lambert C M Ngoka
- Department of Chemistry, Virginia Commonwealth University, Richmond, 23284-2006, USA.
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Wang W, Tai F, Chen S. Optimizing protein extraction from plant tissues for enhanced proteomics analysis. J Sep Sci 2008; 31:2032-9. [PMID: 18615819 DOI: 10.1002/jssc.200800087] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Plant tissues usually contain high levels of proteases and secondary metabolites that severely interfere with protein extraction, separation, and identification. Preparation of high-quality protein samples from plant tissues for proteomic analysis represents a great challenge. This article briefly describes the critical points in protein separation, especially secondary metabolites in plant tissues, and removal strategy. It provides an updated overview of three total protein extraction methods and their applications in proteomic analysis of various recalcitrant tissues.
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Affiliation(s)
- Wei Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, China.
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Carpentier SC, Panis B, Vertommen A, Swennen R, Sergeant K, Renaut J, Laukens K, Witters E, Samyn B, Devreese B. Proteome analysis of non-model plants: a challenging but powerful approach. MASS SPECTROMETRY REVIEWS 2008; 27:354-77. [PMID: 18381744 DOI: 10.1002/mas.20170] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Biological research has focused in the past on model organisms and most of the functional genomics studies in the field of plant sciences are still performed on model species or species that are characterized to a great extent. However, numerous non-model plants are essential as food, feed, or energy resource. Some features and processes are unique to these plant species or families and cannot be approached via a model plant. The power of all proteomic and transcriptomic methods, that is, high-throughput identification of candidate gene products, tends to be lost in non-model species due to the lack of genomic information or due to the sequence divergence to a related model organism. Nevertheless, a proteomics approach has a great potential to study non-model species. This work reviews non-model plants from a proteomic angle and provides an outline of the problems encountered when initiating the proteome analysis of a non-model organism. The review tackles problems associated with (i) sample preparation, (ii) the analysis and interpretation of a complex data set, (iii) the protein identification via MS, and (iv) data management and integration. We will illustrate the power of 2DE for non-model plants in combination with multivariate data analysis and MS/MS identification and will evaluate possible alternatives.
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Darewicz M, Dziuba J, Minkiewicz P. Celiac Disease—Background, Molecular, Bioinformatics and Analytical Aspects. FOOD REVIEWS INTERNATIONAL 2008. [DOI: 10.1080/87559120802089258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Wilkes M, Copeland L. Storage of Wheat Grains at Elevated Temperatures Increases Solubilization of Glutenin Subunits. Cereal Chem 2008. [DOI: 10.1094/cchem-85-3-0335] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Meredith Wilkes
- Faculty of Agriculture, Food and Natural Resources, The University of Sydney, NSW, 2006 Australia
- Corresponding author. Phone: +61 2 9351 2439. Fax: +61 2 9351 5108. E-mail:
| | - Les Copeland
- Faculty of Agriculture, Food and Natural Resources, The University of Sydney, NSW, 2006 Australia
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Cotado-Sampayo M, Ramos PO, Perez RO, Ojha M, Barja F. Specificity of commercial anti-spectrin antibody in the study of fungal and Oomycete spectrin: cross-reaction with proteins other than spectrin. Fungal Genet Biol 2008; 45:1008-15. [PMID: 18378170 DOI: 10.1016/j.fgb.2008.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 02/12/2008] [Accepted: 02/13/2008] [Indexed: 10/22/2022]
Abstract
Spectrin was first described in erythrocytes where it forms a filamentous network in the cytoplasmic face of the plasma membrane and participates in the membrane's structural integrity in addition to controlling the lateral mobility of integral membrane proteins. In fungi, spectrin-like proteins have been described in the plasma membrane, concentrated mainly in the region of maximum apical expansion. This localization led to the idea of a spectrin based membrane skeleton in fungi participating in mechanical integrity of the plasma membrane, generating and maintaining cell polarity. The occurrence of spectrin-like proteins in filamentous fungi, yeasts and Oomycetes, however, is questionable since the presence of such proteins has only been demonstrated with immunochemical methods using antibodies whose specificity is unclear. There is no evidence of a gene coding for the high molecular weight alphabeta-spectrin in the genome of these organisms. Mass spectrometric analysis of the anti alphabeta-spectrin immunoreacting peptides from Neurospora crassa and Phytophthora infestans identified them as elongation factor 2 (NCU07700.4) and Hsp70 (PITG_13237.1), respectively. An attempt was made to correlate the reactivity of anti-spectrin antibody to a common feature of these three proteins i.e., spectrin, elongation factor 2 and heat shock protein 70, in that they all have a hydrophobic region implicated in chaperon activity.
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Affiliation(s)
- Marta Cotado-Sampayo
- Laboratory of Bioenergetics and Microbiology, University of Geneva, ch. des Embrouchis 10, CH 1254 Jussy-Geneva, Switzerland
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Borén M, Glaring MA, Ghebremedhin H, Olsson H, Blennow A, Jansson C. Molecular and physicochemical characterization of the high-amylose barley mutant Amo1. J Cereal Sci 2008. [DOI: 10.1016/j.jcs.2007.01.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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