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Chaâbene Z, Rorat A, Kriaa W, Rekik I, Mejdoub H, Vandenbulcke F, Elleuch A. In-site and Ex-site Date Palm Exposure to Heavy Metals Involved Infra-Individual Biomarkers Upregulation. PLANTS 2021; 10:plants10010137. [PMID: 33445405 PMCID: PMC7826821 DOI: 10.3390/plants10010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
As a tree of considerable importance in arid regions-date palm, Phoenix dactylifera L. survival in contaminated areas of Sfax city has drawn our attention. Leaf samples of the plants grown in the study area showed high levels of cadmium (Cd), copper (Cu), and chromium (Cr). On the basis of this finding, the cellular mechanisms that explain these metal accumulations were investigated in controlled conditions. After four months of exposure to Cd, Cr, or Cu, high bioconcentration and translocation factor (TF>1) have been shown for date palm plantlets exposed to Cd and low TF values were obtained for plantlets treated with Cr and Cu. Moreover, accumulation of oxidants and antioxidant enzyme activities occurred in exposed roots to Cu and Cd. Secondary metabolites, such as polyphenols and flavonoids, were enhanced in plants exposed at low metal concentrations and declined thereafter. Accumulation of flavonoids in cells may be correlated with the expression of the gene encoding Pdmate5, responsible for the transport of secondary metabolites, especially flavonoids. Other transporter genes responded positively to metal incorporation, especially Pdhma2, but also Pdabcc and Pdnramp6. The latter would be a new candidate gene sensitive to metallic stress in plants. Expressions of gene coding metal chelators were also investigated. Pdpcs1 and Pdmt3 exhibited a strong induction in plants exposed to Cr. These modifications of the expression of some biochemical and molecular based-markers in date palm helped to better understand the ability of the plant to tolerate metals. They could be useful in assessing heavy metal contaminations in polluted soils and may improve accumulation capacity of other plants.
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Affiliation(s)
- Zayneb Chaâbene
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
- Correspondence:
| | - Agnieszka Rorat
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
| | - Walid Kriaa
- Environmental Science Center, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Imen Rekik
- High Institute of Applied Biology of Medenine, Medenine 4119, Tunisia;
| | - Hafedh Mejdoub
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
| | - Franck Vandenbulcke
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
| | - Amine Elleuch
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
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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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Electrophoresis-Based Proteomics to Study Development and Germination of Date Palm Zygotic Embryos. Methods Mol Biol 2017. [PMID: 28755235 DOI: 10.1007/978-1-4939-7159-6_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteomics has become an important and powerful tool in plant biology research. To establish a proteomic reference map of date palm zygotic embryos (ZE), we separated and identified proteins from zygotic embryos during different developmental and germination phases using one, two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. Proteins are extracted with trichloroacetic acid (TCA)/acetone-phenol and resolved by gel electrophoresis. Gel images are captured and analyzed by appropriate software and statistical packages. Quantitative or qualitative variable bands or spots are subjected to MS analysis in order to identify them and correlate differences in the protein profiles with the different stages of date palm zygotic embryo development, maturation, and germination.
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Tan HS, Jacoby RP, Ong-Abdullah M, Taylor NL, Liddell S, Chee WW, Chin CF. Proteomic profiling of mature leaves from oil palm (Elaeis guineensisJacq.). Electrophoresis 2017; 38:1147-1153. [DOI: 10.1002/elps.201600506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 01/06/2017] [Accepted: 01/27/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Hooi Sin Tan
- School of Biosciences; The University of Nottingham Malaysia Campus; Semenyih Selangor Darul Ehsan Malaysia
| | - Richard P. Jacoby
- Australia Research Council Centre of Excellence in Plant Energy Biology; Crawley Western Australia Australia
- School of Chemistry and Biochemistry; The University of Western Australia; Crawley Western Australia Australia
| | - Meilina Ong-Abdullah
- Malaysian Palm Oil Board, Bandar Baru Bangi; Kajang Selangor Darul Ehsan Malaysia
| | - Nicolas L. Taylor
- Australia Research Council Centre of Excellence in Plant Energy Biology; Crawley Western Australia Australia
- School of Chemistry and Biochemistry; The University of Western Australia; Crawley Western Australia Australia
| | - Susan Liddell
- School of Biosciences, Faculty of Science, Division of Animal Sciences; University of Nottingham; Nottingham United Kingdom
| | - Wong Wei Chee
- AAR-UNMC Biotechnology Research Centre (Advanced Agriecological Research Sdn. Bhd.); Semenyih Selangor Darul Ehsan Malaysia
| | - Chiew Foan Chin
- School of Biosciences; The University of Nottingham Malaysia Campus; Semenyih Selangor Darul Ehsan Malaysia
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Tan HS, Liddell S, Ong Abdullah M, Wong WC, Chin CF. Differential proteomic analysis of embryogenic lines in oil palm (Elaeis guineensis Jacq). J Proteomics 2016; 143:334-345. [PMID: 27130535 DOI: 10.1016/j.jprot.2016.04.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/01/2016] [Accepted: 04/24/2016] [Indexed: 10/21/2022]
Abstract
UNLABELLED Oil palm tissue culture is one way to produce superior oil palm planting materials. However, the low rate of embryogenesis is a major hindrance for the adoption of this technology in oil palm tissue culture laboratories. In this study, we use proteomic technologies to compare differential protein profiles in leaves from palms of high and low proliferation rates in tissue culture in order to understand the underlying biological mechanism for the low level of embryogenesis. Two protein extraction methods, namely trichloroacetic acid/acetone precipitation and polyethylene glycol fractionation were used to produce total proteins and fractionated protein extracts respectively, with the aim of improving the resolution of protein species using two-dimensional gel electrophoresis. A total of 40 distinct differential abundant protein spots were selected from leaf samples collected from palms with proven high and low proliferation rates. The variant proteins were subsequently identified using mass spectrometric analysis. Twelve prominent protein spots were then characterised using real-time polymerase chain reaction to compare the mRNA expression and protein abundant profiles. Three proteins, namely triosephosphate isomerase, l-ascorbate peroxidase, and superoxide dismutase were identified to be potential biomarker candidates at both the protein abundant and mRNA expression levels. BIOLOGICAL SIGNIFICANCE In this study, proteomic analysis was used to identify abundant proteins from total protein extracts. PEG fractionation was used to reveal lower abundant proteins from both high and low proliferation embryogenic lines of oil palm samples in tissue culture. A total of 40 protein spots were found to be significant in abundance and the mRNA levels of 12 of these were assessed using real time PCR. Three proteins namely, triosephosphate isomerase, l-ascorbate peroxidase and superoxide dismutase were found to be concordant in their mRNA expression and protein abundance. Triosephosphate isomerase is a key enzyme in glycolysis. Both l-ascorbate peroxidase and superoxide dismutase play a role in anti-oxidative scavenging defense systems. These proteins have potential for use as biomarkers to screen for high and low embryogenic oil palm samples.
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Affiliation(s)
- Hooi Sin Tan
- School of Biosciences, Faculty of Science, University of Nottingham, Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Susan Liddell
- School of Biosciences, Faculty of Science, University of Nottingham, United Kingdom
| | - Meilina Ong Abdullah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Wei Chee Wong
- Advanced Agriecological Research Sdn Bhd, No. 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia; AAR-UNMC Biotechnology Research Centre, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Chiew Foan Chin
- School of Biosciences, Faculty of Science, University of Nottingham, Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
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Akasha I, Campbell L, Lonchamp J, Euston SR. The major proteins of the seed of the fruit of the date palm (Phoenix dactylifera L.): Characterisation and emulsifying properties. Food Chem 2016; 197:799-806. [DOI: 10.1016/j.foodchem.2015.11.046] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/06/2015] [Accepted: 11/10/2015] [Indexed: 11/26/2022]
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Mostek A, Börner A, Weidner S. Comparative proteomic analysis of β-aminobutyric acid-mediated alleviation of salt stress in barley. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 99:150-61. [PMID: 26760953 DOI: 10.1016/j.plaphy.2015.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/14/2015] [Indexed: 05/23/2023]
Abstract
The non-protein amino acid β-aminobutyric acid (BABA) is known to induce plant resistance to a broad spectrum of biotic and abiotic stresses. This is the first study describing the effect of BABA seed priming on physiological and proteomic changes under salt stress conditions in barley (Hordeum vulgare). The aim of our study was to investigate the changes of fresh weight, dry weight and relative water content (RWC) as well as root proteome changes of two barley lines contrasting in salt tolerance (DH14, DH 187) in response to salt stress after seed priming in water or in 800 μM BABA. Seed priming with BABA significantly increased (p ≤ 0.05) RWC in both barley lines, which indicates considerably lower water loss in BABA-primed plants than in the non-primed control plants. Dry and fresh matter increased significantly in line DH 187, whereas no changes were detected in line DH14. BABA-primed plants of both lines showed different proteomic patterns than the non-primed control plants. The root proteins exhibiting significant abundance changes (1.75-fold change, p ≤ 0.05) were separated by two-dimensional polyacrylamide gel electrophoresis (2D- PAGE). Thirty-one spots, representing 24 proteins, were successfully identified by MALDI TOF/TOF mass spectrometry. The most prominent differences include the up-regulation of antioxidant enzymes (catalase, peroxidase and superoxide dismutase), PR proteins (chitinase, endo-1,3-β-glucosidase), and chaperones (cyclophilin, HSC 70). Our results indicate that BABA induces defence and detoxification processes which may enable faster and more effective responses to salt stress, increasing the chances of survival under adverse environmental conditions.
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Affiliation(s)
- Agnieszka Mostek
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Street 1a, 10-957 Olsztyn, Poland.
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Stanisław Weidner
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Street 1a, 10-957 Olsztyn, Poland
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Rasool KG, Khan MA, Aldawood AS, Tufail M, Mukhtar M, Takeda M. Identification of Proteins Modulated in the Date Palm Stem Infested with Red Palm Weevil (Rhynchophorus ferrugineus Oliv.) Using Two Dimensional Differential Gel Electrophoresis and Mass Spectrometry. Int J Mol Sci 2015; 16:19326-46. [PMID: 26287180 PMCID: PMC4581299 DOI: 10.3390/ijms160819326] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/30/2015] [Accepted: 08/03/2015] [Indexed: 12/31/2022] Open
Abstract
A state of the art proteomic methodology using Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI TOF) has been employed to characterize peptides modulated in the date palm stem subsequent to infestation with red palm weevil (RPW). Our analyses revealed 32 differentially expressed peptides associated with RPW infestation in date palm stem. To identify RPW infestation associated peptides (I), artificially wounded plants (W) were used as additional control beside uninfested plants, a conventional control (C). A constant unique pattern of differential expression in infested (I), wounded (W) stem samples compared to control (C) was observed. The upregulated proteins showed relative fold intensity in order of I > W and downregulated spots trend as W > I, a quite interesting pattern. This study also reveals that artificially wounding of date palm stem affects almost the same proteins as infestation; however, relative intensity is quite lower than in infested samples both in up and downregulated spots. All 32 differentially expressed spots were subjected to MALDI-TOF analysis for their identification and we were able to match 21 proteins in the already existing databases. Relatively significant modulated expression pattern of a number of peptides in infested plants predicts the possibility of developing a quick and reliable molecular methodology for detecting plants infested with date palm.
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Affiliation(s)
- Khawaja Ghulam Rasool
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan.
| | - Muhammad Altaf Khan
- Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Abdulrahman Saad Aldawood
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Muhammad Tufail
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan.
| | - Muhammad Mukhtar
- Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah 10021, United Arab Emirates.
| | - Makio Takeda
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan.
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Optimization of Protein Extraction and Two-Dimensional Electrophoresis Protocols for Oil Palm Leaf. Protein J 2015; 34:304-12. [DOI: 10.1007/s10930-015-9626-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Mostek A, Börner A, Badowiec A, Weidner S. Alterations in root proteome of salt-sensitive and tolerant barley lines under salt stress conditions. JOURNAL OF PLANT PHYSIOLOGY 2015; 174:166-76. [PMID: 25462980 DOI: 10.1016/j.jplph.2014.08.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/08/2014] [Accepted: 08/17/2014] [Indexed: 05/21/2023]
Abstract
Salinity is one of the most important abiotic stresses causing a significant reduction of crop plants yield. To gain a better understanding of salinity tolerance mechanisms in barley (Hordeum vulgare), we investigated the changes in root proteome of salt-sensitive (DH14) and tolerant (DH187) lines in response to salt-stress. The seeds of both barley lines were germinating in water or in 100mM NaCl for 6 days. The root proteins were separated by two-dimensional gel electrophoresis. To identify proteins regulated in response to salt stress, MALDI-TOF/TOF mass spectrometry was applied. It was demonstrated that the sensitive and tolerant barley lines respond differently to salt stress. Some of the identified proteins are well-documented as markers of salinity resistance, but several proteins have not been detected in response to salt stress earlier, although they are known to be associated with other abiotic stresses. The most significant differences concerned the proteins that are involved in signal transduction (annexin, translationally-controlled tumor protein homolog, lipoxygenases), detoxification (osmotin, vacuolar ATP-ase), protein folding processes (protein disulfide isomerase) and cell wall metabolism (UDP-glucuronic acid decarboxylase, β-d-glucan exohydrolase, UDP-glucose pyrophosphorylase). The results suggest that the enhanced salinity tolerance of DH187 line results mainly from an increased activity of signal transduction mechanisms eventually leading to the accumulation of stress protective proteins and cell wall structure changes.
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Affiliation(s)
- Agnieszka Mostek
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Street 1a, 10-957 Olsztyn, Poland.
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Anna Badowiec
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Street 1a, 10-957 Olsztyn, Poland
| | - Stanisław Weidner
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Street 1a, 10-957 Olsztyn, Poland
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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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12
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Universal sample preparation method integrating trichloroacetic acid/acetone precipitation with phenol extraction for crop proteomic analysis. Nat Protoc 2014; 9:362-74. [PMID: 24434803 DOI: 10.1038/nprot.2014.022] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Crop plants contain large amounts of secondary compounds that interfere with protein extraction and gel-based proteomic analysis. Thus, a protein extraction protocol that can be easily applied to various crop materials with minimal optimization is essential. Here we describe a universal protocol for total protein extraction involving trichloroacetic acid (TCA)/acetone precipitation followed by SDS and phenol extraction. Through SDS extraction, the proteins precipitated by the TCA/acetone treatment can be fully resolubilized and then further purified by phenol extraction. This protocol combines TCA/acetone precipitation, which aggressively removes nonprotein compounds, and phenol extraction, which selectively dissolves proteins, resulting in effective purification of proteins from crop tissues. This protocol can also produce high-quality protein preparations from various recalcitrant tissues, and therefore it has a wide range of applications in crop proteomic analysis. Designed to run on a small scale, this protocol can be completed within 5 h.
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Szuba A, Wojakowska A, Lorenc-Plucińska G. An optimized method to extract poplar leaf proteins for two-dimensional gel electrophoresis guided by analysis of polysaccharides and phenolic compounds. Electrophoresis 2013; 34:3234-43. [DOI: 10.1002/elps.201300223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Agnieszka Szuba
- Laboratory of Proteomics; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
| | - Anna Wojakowska
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznan Poland
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Ma R, Sun L, Chen X, Jiang R, Sun H, Zhao D. Proteomic changes in different growth periods of ginseng roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 67:20-32. [PMID: 23537955 DOI: 10.1016/j.plaphy.2013.02.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 02/27/2013] [Indexed: 06/02/2023]
Abstract
For the first time, proteomics and biochemical variables have been employed to unravel the growth strategies for the different root growth periods of ginseng (Panax ginseng CA May., Araliaceae). Enzymatic activities and cellular contents, except for starch, related to defence and metabolism were significantly increased in the slow-growth period but decreased in the fast-growth period. Proteomic characterisation by two-dimensional gel electrophoresis (2DE) showed 83 differentially expressed spots; 62 spots were up-regulated and 21 spots were down-regulated in the slow-growth period when compared to the fast-growth period. The identification of these spots indicated that the major groups of differential proteins were associated with energy metabolism (37%) and defence (17%), which was consistent with the changes observed in the biochemical measurements. These results clearly demonstrate that ginseng stores energy during its fast-growth period to promote root elongation, whereas it expends energy to improve the synthesis of secondary metabolites and stress resistance during its slow-growth period. The levels of many proteins were changed during the conversion period from fast to slow growth, providing new insights into ginseng proteome evolution. The proposed hypothetical model explains the interaction of metabolic proteins associated with the growth strategies of ginseng.
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Affiliation(s)
- Rui Ma
- Changchun University of Chinese Medicine, Jilin 130117, PR China; College of Biology and Chemistry, Beihua University, 15 Jilin Street, Jilin, Jilin Province 132013, PR China
| | - Liwei Sun
- College of Biology and Chemistry, Beihua University, 15 Jilin Street, Jilin, Jilin Province 132013, PR China.
| | - Xuenan Chen
- College of Biology and Chemistry, Beihua University, 15 Jilin Street, Jilin, Jilin Province 132013, PR China
| | - Rui Jiang
- Changchun University of Chinese Medicine, Jilin 130117, PR China; College of Biology and Chemistry, Beihua University, 15 Jilin Street, Jilin, Jilin Province 132013, PR China
| | - Hang Sun
- College of Biology and Chemistry, Beihua University, 15 Jilin Street, Jilin, Jilin Province 132013, PR China
| | - Daqing Zhao
- Changchun University of Chinese Medicine, Jilin 130117, PR China.
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15
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Slattery M, Ankisetty S, Corrales J, Marsh-Hunkin KE, Gochfeld DJ, Willett KL, Rimoldi JM. Marine proteomics: a critical assessment of an emerging technology. JOURNAL OF NATURAL PRODUCTS 2012; 75:1833-1877. [PMID: 23009278 DOI: 10.1021/np300366a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.
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Affiliation(s)
- Marc Slattery
- Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA.
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16
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Di Carli M, Benvenuto E, Donini M. Recent insights into plant-virus interactions through proteomic analysis. J Proteome Res 2012; 11:4765-80. [PMID: 22954327 DOI: 10.1021/pr300494e] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plant viruses represent a major threat for a wide range of host species causing severe losses in agricultural practices. The full comprehension of mechanisms underlying events of virus-host plant interaction is crucial to devise novel plant resistance strategies. Until now, functional genomics studies in plant-virus interaction have been limited mainly on transcriptomic analysis. Only recently are proteomic approaches starting to provide important contributions to this area of research. Classical two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MS) is still the most widely used platform in plant proteome analysis, although in the last years the application of quantitative "second generation" proteomic techniques (such as differential in gel electrophoresis, DIGE, and gel-free protein separation methods) are emerging as more powerful analytical approaches. Apparently simple, plant-virus interactions reveal a really complex pathophysiological context, in which resistance, defense and susceptibility, and direct virus-induced reactions interplay to trigger expression responses of hundreds of genes. Given that, this review is specifically focused on comparative proteome-based studies on pathogenesis of several viral genera, including some of the most important and widespread plant viruses of the genus Tobamovirus, Sobemovirus, Cucumovirus and Potyvirus. In all, this overview reveals a widespread repression of proteins associated with the photosynthetic apparatus, while energy metabolism/protein synthesis and turnover are typically up-regulated, indicating a major redirection of cell metabolism. Other common features include the modulation of metabolisms concerning sugars, cell wall, and reactive oxigen species as well as pathogenesis-related (PR) proteins. The fine-tuning between plant development and antiviral defense mechanisms determines new patterns of regulation of common metabolic pathways. By offering a 360-degree view of protein modulation, all proteomic tools reveal the extraordinary intricacy of mechanisms with which a simple viral genome perturbs the plant cell molecular networks. This "omic" approach, while providing a global perspective and useful information to the understanding of the plant host-virus interactome, may possibly reveal protein targets/markers useful in the design of future diagnosis and/or plant protection strategies.
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Affiliation(s)
- Mariasole Di Carli
- ENEA, Laboratorio Biotecnologie, UT BIORAD-FARM, Casaccia Research Center, Via Anguillarese 301, I-00123 Rome, Italy
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Zhang E, Chen X, Liang X. Resolubilization of TCA precipitated plant proteins for 2-D electrophoresis. Electrophoresis 2011; 32:696-8. [DOI: 10.1002/elps.201000557] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 11/09/2022]
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Wang T, Zhang E, Chen X, Li L, Liang X. Identification of seed proteins associated with resistance to pre-harvested aflatoxin contamination in peanut (Arachis hypogaea L). BMC PLANT BIOLOGY 2010; 10:267. [PMID: 21118527 PMCID: PMC3095339 DOI: 10.1186/1471-2229-10-267] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 11/30/2010] [Indexed: 05/22/2023]
Abstract
BACKGROUND Pre-harvest infection of peanuts by Aspergillus flavus and subsequent aflatoxin contamination is one of the food safety factors that most severely impair peanut productivity and human and animal health, especially in arid and semi-arid tropical areas. Some peanut cultivars with natural pre-harvest resistance to aflatoxin contamination have been identified through field screening. However, little is known about the resistance mechanism, which has slowed the incorporation of resistance into cultivars with commercially acceptable genetic background. Therefore, it is necessary to identify resistance-associated proteins, and then to recognize candidate resistance genes potentially underlying the resistance mechanism. RESULTS The objective of this study was to identify resistance-associated proteins in response to A. flavus infection under drought stress using two-dimensional electrophoresis with mass spectrometry. To identify proteins involved in the resistance to pre-harvest aflatoxin contamination, we compared the differential expression profiles of seed proteins between a resistant cultivar (YJ-1) and a susceptible cultivar (Yueyou 7) under well-watered condition, drought stress, and A. flavus infection with drought stress. A total of 29 spots showed differential expression between resistant and susceptible cultivars in response to A. flavus attack under drought stress. Among these spots, 12 protein spots that consistently exhibited an altered expression were screened by Image Master 5.0 software and successfully identified by MALDI-TOF MS. Five protein spots, including Oso7g0179400, PII protein, CDK1, Oxalate oxidase, SAP domain-containing protein, were uniquely expressed in the resistant cultivar. Six protein spots including low molecular weight heat shock protein precursor, RIO kinase, L-ascorbate peroxidase, iso-Ara h3, 50 S ribosomal protein L22 and putative 30 S ribosomal S9 were significantly up-regulated in the resistant cultivar challenged by A. flavus under drought stress. A significant decrease or down regulation of trypsin inhibitor caused by A. flavus in the resistant cultivar was also observed. In addition, variations in protein expression patterns for resistant and susceptible cultivars were further validated by real time RT-PCR analysis. CONCLUSION In summary, this study provides new insights into understanding of the molecular mechanism of resistance to pre-harvest aflatoxin contamination in peanut, and will help to develop peanut varieties with resistance to pre-harvested aflatoxin contamination.
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Affiliation(s)
- Tong Wang
- Gguangdong Key Lab of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou 510631, China
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Erhua Zhang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Ling Li
- Gguangdong Key Lab of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou 510631, China
| | - Xuanqiang Liang
- Gguangdong Key Lab of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou 510631, China
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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Karppinen K, Taulavuori E, Hohtola A. Optimization of Protein Extraction from Hypericum perforatum Tissues and Immunoblotting Detection of Hyp-1 at Different Stages of Leaf Development. Mol Biotechnol 2010; 46:219-26. [DOI: 10.1007/s12033-010-9299-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Wang X, Chang L, Wang G, Sun Z, Ma H, Sun Q, Li J. Protein extraction from the earthworm Eisenia fetida
for 2-DE. Proteomics 2010; 10:1095-9. [DOI: 10.1002/pmic.200900488] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gómez-Vidal S, Salinas J, Tena M, Lopez-Llorca LV. Proteomic analysis of date palm (Phoenix dactylifera L.) responses to endophytic colonization by entomopathogenic fungi. Electrophoresis 2009; 30:2996-3005. [PMID: 19676091 DOI: 10.1002/elps.200900192] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The entomopathogenic fungi Beauveria bassiana, Lecanicillium dimorphum and L. cf. psalliotae can survive and colonize living palm tissue as endophytes. The molecular interaction between these biocontrol agent fungi and the date palm Phoenix dactylifera L. was investigated using proteomic techniques. Field date palms inoculated with these fungi were analyzed 15 and 30 days after inoculation in two independent bioassays. In vitro date palms were also inoculated with B. bassiana or L. cf. psalliotae. Qualitative and quantitative differences in protein accumulation between controls (not inoculated) and inoculated palms were found using 2-DE analysis, and some of these responsive proteins could be identified using MALDI/TOF-TOF. Proteins involved in plant defence or stress response were induced in P. dactylifera leaves as a response to endophytic colonization by entomopathogenic fungi in field date palms. Proteins related with photosynthesis and energy metabolism were also affected by entomopathogenic fungi colonization. A myosin heavy chain-like protein was accumulated in in vitro palms inoculated with these fungi. This suggests that endophytic colonization by these entomopathogenic fungi modulates plant defence responses and energy metabolism in field date palms and possibly modulates the expression of cell division-related proteins in in vitro palms at proteomic level.
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Affiliation(s)
- Sonia Gómez-Vidal
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef," Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, Spain
| | - Jesús Salinas
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef," Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, Spain
| | - Manuel Tena
- Department of Biochemistry and Molecular Biology, ETSIAM, University of Córdoba, Córdoba, Spain
| | - Luis Vicente Lopez-Llorca
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef," Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, Spain
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Fan P, Wang X, Kuang T, Li Y. An efficient method for the extraction of chloroplast proteins compatible for 2-DE and MS analysis. Electrophoresis 2009; 30:3024-3033. [PMID: 19676087 DOI: 10.1002/elps.200900172] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Comparative proteomic analysis of chloroplast by 2-DE has received significant attention in recent years. However, the complication of membrane systems in chloroplast made it challenging to elucidate entire chloroplast proteome by 2-DE. Here, we developed an efficient method for extracting chloroplast proteins, and produced excellent 2-DE profiles from both Arabidopsis thaliana and Salicornia europaea. Comparison of this method with another two protocols for the extraction of A. thaliana chloroplast proteins showed that our method obtained higher protein yields and produced more protein spots on both pH 3-10 and 4-7 2-DE gels. Moreover, this method recovered more proteins in the basic and high M(r) regions, thereby offering the best extraction of chloroplast proteins. Identification of 15 specific chloroplast-targeted proteins on our gels by MALDI-TOF MS revealed that this method was compatible with MS, and recovered more chloroplast membrane proteins than the commonly used methods. This protocol is expected to have a wide application in future chloroplast proteomic analysis.
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Affiliation(s)
- Pengxiang Fan
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Xuchu Wang
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Tingyun Kuang
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Yinxin Li
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
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Proteomic analysis of the development and germination of date palm (Phoenix dactylifera L.) zygotic embryos. Proteomics 2009; 9:2543-54. [DOI: 10.1002/pmic.200800523] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Acquadro A, Falvo S, Mila S, Giuliano Albo A, Comino C, Moglia A, Lanteri S. Proteomics in globe artichoke: Protein extraction and sample complexity reduction by PEG fractionation. Electrophoresis 2009; 30:1594-602. [DOI: 10.1002/elps.200800549] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Di Carli M, Villani ME, Renzone G, Nardi L, Pasquo A, Franconi R, Scaloni A, Benvenuto E, Desiderio A. Leaf proteome analysis of transgenic plants expressing antiviral antibodies. J Proteome Res 2009; 8:838-48. [PMID: 19099506 DOI: 10.1021/pr800359d] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The expression of exogenous antibodies in plant is an effective strategy to confer protection against viral infection or to produce molecules with pharmaceutical interest. However, the acceptance of the transgenic technology to obtain self-protecting plants depends on the assessment of their substantial equivalence compared to non-modified crops with an established history of safe use. In fact, the possibility exists that the introduction of transgenes in plants may alter expression of endogenous genes and/or normal production of metabolites. In this study, we investigated whether the expression in plant of recombinant antibodies directed against viral proteins may influence the host leaf proteome. Two transgenic plant models, generated by Agrobacterium tumefaciens-mediated transformation, were analyzed for this purpose, namely, Lycopersicon esculentum cv. MicroTom and Nicotiana benthamiana, expressing recombinant antibodies against cucumber mosaic virus and tomato spotted wilt virus, respectively. To obtain a significant representation of plant proteomes, optimized extraction procedures have been devised for each plant species. The proteome repertoire of antibody-expressing and control plants was compared by 2-DE associated to DIGE technology. Among the 2000 spots detected within the gels, about 10 resulted differentially expressed in each transgenic model and were identified by MALDI-TOF PMF and muLC-ESI-IT-MS/MS procedures. Protein variations were restricted to a limited number of defined differences with an average ratio below 2.4. Most of the differentially expressed proteins were related to photosynthesis or defense function. The overall results suggest that the expression of recombinant antibodies in both systems does not significantly alter the leaf proteomic profile, contributing to assess the biosafety of resistant plants expressing antiviral antibodies.
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Affiliation(s)
- Mariasole Di Carli
- Sezione Genetica e Genomica Vegetale, Dipartimento BAS-BIOTEC, ENEA Casaccia, Rome, Italy
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