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Madda R, Chen CM, Wang JY, Chen CF, Chao KY, Yang YM, Wu HY, Chen WM, Wu PK. Proteomic profiling and identification of significant markers from high-grade osteosarcoma after cryotherapy and irradiation. Sci Rep 2020; 10:2105. [PMID: 32034162 PMCID: PMC7005698 DOI: 10.1038/s41598-019-56024-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023] Open
Abstract
Biological reconstruction of allografts and recycled autografts have been widely implemented in high-grade osteogenic sarcoma. For treating tumor-bearing autografts, extracorporeal irradiation (ECIR) and liquid nitrogen (LN) freezing techniques are being used worldwide as a gold standard treatment procedure. Both the methods aim to eradicate the tumor cells from the local recurrence and restore the limb function. Therefore, it is essential and crucial to find, and compare the alterations at molecular and physiological levels of the treated and untreated OGS recycled autografts to obtain valuable clinical information for better clinical practice. Thus, we aimed to investigate the significantly expressed altered proteins from ECIR-and cryotherapy/freezing- treated OGS (n = 12) were compared to untreated OGS (n = 12) samples using LC-ESI-MS/MS analysis, and the selected proteins from this protein panel were verified using immunoblot analysis. From our comparative proteomic analysis identified a total of 131 differentially expressed proteins (DEPs) from OGS. Among these, 91 proteins were up-regulated (2.5 to 3.5-folds), and 40 proteins were down-regulated (0.2 to 0.5 folds) (p < 0.01 and 0.05). The functional enrichment analysis revealed that the identified DEPs have belonged to more than 10 different protein categories include cytoskeletal, extracellular matrix, immune, enzyme modulators, and cell signaling molecules. Among these, we have confirmed two potential candidates’ expressions levels such as Fibronectin and Protein S100 A4 using western blot analysis. Our proteomic study revealed that LN-freezing and ECIR treatments are effectively eradicating tumor cells, and reducing the higher expressions of DEPs at molecular levels which may help in restoring the limb functions of OGS autografts effectively. To the best of our knowledge, this is the first proteomic study that compared proteomic profiles among freezing, ECIR treated with untreated OGS in recycled autografts. Moreover, the verified proteins could be used as prognostic or diagnostic markers that reveal valuable scientific information which may open various therapeutic avenues in clinical practice to improve patient outcomes.
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Affiliation(s)
- Rashmi Madda
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Research and Development, National Yang-Ming University, Taipei, Taiwan
| | - Chao-Ming Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jir-You Wang
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Cheng-Fong Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Kuang-Yu Chao
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Min Yang
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hsin-Yi Wu
- Instrumentation center, National Taiwan University, Taipei, Taiwan
| | - Wei-Ming Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Po-Kuei Wu
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan. .,Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipei, Taiwan. .,Orthopedic Department, School of Medicine, National Yang-Ming University, Taipei, Taiwan. .,Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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2
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Al-Mohanna T, Ahsan N, Bokros NT, Dimlioglu G, Reddy KR, Shankle M, Popescu GV, Popescu SC. Proteomics and Proteogenomics Analysis of Sweetpotato (Ipomoea batatas) Leaf and Root. J Proteome Res 2019; 18:2719-2734. [DOI: 10.1021/acs.jproteome.8b00943] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Thualfeqar Al-Mohanna
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island, USA Hospital, Providence, Rhode Island 02903, United States
- Division of Biology and Medicine, Brown University, Providence, Rhode Island 02903, United States
| | - Norbert T. Bokros
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Gizem Dimlioglu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Kambham R. Reddy
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Mark Shankle
- Pontotoc Experimental Station, Mississippi State University, Pontotoc, Mississippi 38863, United States
| | - George V. Popescu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi 39759, United States
- The National Institute for Laser, Plasma and Radiation Physics, Bucharest RO-077125, Romania
| | - Sorina C. Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
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3
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Fractionation Techniques to Increase Plant Proteome Coverage: Combining Separation in Parallel at the Protein and the Peptide Level. Methods Mol Biol 2018. [PMID: 30276734 DOI: 10.1007/978-1-4939-8814-3_6] [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
Peptide spectral libraries enable targeted identification and quantitation of low-abundance proteins in a complex plant proteome. Here we describe parallel protein and peptide fractionation techniques to improve plant proteome coverage and facilitate construction of spectral libraries.
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4
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A robust and effective intact protein fractionation strategy by GO/PEI/Au/PEG nanocomposites for human plasma proteome analysis. Talanta 2018; 178:49-56. [DOI: 10.1016/j.talanta.2017.08.079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 12/22/2022]
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5
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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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6
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Wongpia A, Mahatheeranont S, Lomthaisong K, Niamsup H. Evaluation of Sample Preparation Methods from Rice Seeds and Seedlings Suitable for Two-Dimensional Gel Electrophoresis. Appl Biochem Biotechnol 2014; 175:1035-51. [DOI: 10.1007/s12010-014-1333-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 10/15/2014] [Indexed: 11/25/2022]
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7
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Zhang K, Liu H, Tao P, Chen H. Comparative proteomic analyses provide new insights into low phosphorus stress responses in maize leaves. PLoS One 2014; 9:e98215. [PMID: 24858307 PMCID: PMC4032345 DOI: 10.1371/journal.pone.0098215] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 04/30/2014] [Indexed: 12/03/2022] Open
Abstract
Phosphorus deficiency limits plant growth and development. To better understand the mechanisms behind how maize responds to phosphate stress, we compared the proteome analysis results of two groups of maize leaves that were treated separately with 1,000 µM (control, +P) and 5 µM of KH2PO4 (intervention group, -P) for 25 days. In total, 1,342 protein spots were detected on 2-DE maps and 15.43% had changed (P<0.05; ≥1.5-fold) significantly in quantity between the +P and -P groups. These proteins are involved in several major metabolic pathways, including photosynthesis, carbohydrate metabolism, energy metabolism, secondary metabolism, signal transduction, protein synthesis, cell rescue and cell defense and virulence. The results showed that the reduction in photosynthesis under low phosphorus treatment was due to the down-regulation of the proteins involved in CO2 enrichment, the Calvin cycle and the electron transport system. Electron transport and photosynthesis restrictions resulted in a large accumulation of peroxides. Maize has developed many different reactive oxygen species (ROS) scavenging mechanisms to cope with low phosphorus stress, including up-regulating its antioxidant content and antioxidase activity. After being subjected to phosphorus stress over a long period, maize may increase its internal phosphorus utilization efficiency by altering photorespiration, starch synthesis and lipid composition. These results provide important information about how maize responds to low phosphorus stress.
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Affiliation(s)
- Kewei Zhang
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
| | - Hanhan Liu
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
| | - Peilin Tao
- College of Agriculture Vocational, Xuzhou Biology Engineering Technical College, Xuzhou, China
| | - Huan Chen
- School of Life Sciences, Shandong University, Ministry of Education Key Laboratory of Plant Cell Engineering and Germplasm Enhancement, Jinan, China
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8
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Chen X, Chan WL, Zhu FY, Lo C. Phosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii. Proteome Sci 2014; 12:16. [PMID: 24628833 PMCID: PMC4022089 DOI: 10.1186/1477-5956-12-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/06/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Selaginella (Selaginella moellendorffii) is a lycophyte which diverged from other vascular plants approximately 410 million years ago. As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution. Proteomics investigations on this lycophyte model have not been extensively reported. Phosphorylation represents the most common post-translational modifications and it is a ubiquitous regulatory mechanism controlling the functional expression of proteins inside living organisms. RESULTS In this study, polyethylene glycol fractionation and immobilized metal ion affinity chromatography were employed to isolate phosphopeptides from wild-growing Selaginella. Using liquid chromatography-tandem mass spectrometry analysis, 1593 unique phosphopeptides spanning 1104 non-redundant phosphosites with confirmed localization on 716 phosphoproteins were identified. Analysis of the Selaginella dataset revealed features that are consistent with other plant phosphoproteomes, such as the relative proportions of phosphorylated Ser, Thr, and Tyr residues, the highest occurrence of phosphosites in the C-terminal regions of proteins, and the localization of phosphorylation events outside protein domains. In addition, a total of 97 highly conserved phosphosites in evolutionary conserved proteins were identified, indicating the conservation of phosphorylation-dependent regulatory mechanisms in phylogenetically distinct plant species. On the other hand, close examination of proteins involved in photosynthesis revealed phosphorylation events which may be unique to Selaginella evolution. Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants. A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class. CONCLUSIONS Our work provides the first large-scale atlas of phosphoproteins in Selaginella which occupies a unique position in the evolution of terrestrial plants. Future research into the functional roles of Selaginella-specific phosphorylation events in photosynthesis and other processes may offer insight into the molecular mechanisms leading to the distinct evolution of lycophytes.
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Affiliation(s)
- Xi Chen
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China.,Wuhan Institute of Biotechnology, Wuhan, Hubei, China
| | - Wai Lung Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China
| | - Fu-Yuan Zhu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam Hong Kong, China
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9
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Caverzan A, Bonifacio A, Carvalho FEL, Andrade CMB, Passaia G, Schünemann M, Maraschin FDS, Martins MO, Teixeira FK, Rauber R, Margis R, Silveira JAG, Margis-Pinheiro M. The knockdown of chloroplastic ascorbate peroxidases reveals its regulatory role in the photosynthesis and protection under photo-oxidative stress in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 214:74-87. [PMID: 24268165 DOI: 10.1016/j.plantsci.2013.10.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/12/2013] [Accepted: 10/01/2013] [Indexed: 05/26/2023]
Abstract
The inactivation of the chloroplast ascorbate peroxidases (chlAPXs) has been thought to limit the efficiency of the water-water cycle and photo-oxidative protection under stress conditions. In this study, we have generated double knockdown rice (Oryza sativa L.) plants in both OsAPX7 (sAPX) and OsAPX8 (tAPX) genes, which encode chloroplastic APXs (chlAPXs). By employing an integrated approach involving gene expression, proteomics, biochemical and physiological analyses of photosynthesis, we have assessed the role of chlAPXs in the regulation of the protection of the photosystem II (PSII) activity and CO2 assimilation in rice plants exposed to high light (HL) and methyl violagen (MV). The chlAPX knockdown plants were affected more severely than the non-transformed (NT) plants in the activity and structure of PSII and CO2 assimilation in the presence of MV. Although MV induced significant increases in pigment content in the knockdown plants, the increases were apparently not sufficient for protection. Treatment with HL also caused generalized damage in PSII in both types of plants. The knockdown and NT plants exhibited differences in photosynthetic parameters related to efficiency of utilization of light and CO2. The knockdown plants overexpressed other antioxidant enzymes in response to the stresses and increased the GPX activity in the chloroplast-enriched fraction. Our data suggest that a partial deficiency of chlAPX expression modulate the PSII activity and integrity, reflecting the overall photosynthesis when rice plants are subjected to acute oxidative stress. However, under normal growth conditions, the knockdown plants exhibit normal phenotype, biochemical and physiological performance.
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Affiliation(s)
- Andréia Caverzan
- Department of Genetics, Federal University of Rio Grande do Sul, Brazil; Biotechnology Center, Federal University of Rio Grande do Sul, Brazil
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10
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Making Progress in Plant Proteomics for Improved Food Safety. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62650-9.00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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11
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Yiou P, Shaoli A, Kebin L, Tao W, Kui F, Hua Z, Yu S, Xun Y, Jinghui X. Evaluation of extraction procedures for 2-DE analysis of aphid proteins. J Sep Sci 2013; 36:532-9. [DOI: 10.1002/jssc.201200642] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 09/21/2012] [Accepted: 10/09/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Pan Yiou
- College of Plant Science; Jilin University; Changchun P. R. China
| | - An Shaoli
- College of Plant Science; Jilin University; Changchun P. R. China
| | - Li Kebin
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection; Chinese Academy of Agricultural Science; Beijing P. R. China
| | - Wang Tao
- College of Plant Science; Jilin University; Changchun P. R. China
| | - Fang Kui
- College of Plant Science; Jilin University; Changchun P. R. China
| | - Zhang Hua
- College of Plant Science; Jilin University; Changchun P. R. China
| | - Sun Yu
- College of Plant Science; Jilin University; Changchun P. R. China
| | - Yang Xun
- College of Plant Science; Jilin University; Changchun P. R. China
| | - Xi Jinghui
- College of Plant Science; Jilin University; Changchun P. R. China
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12
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Artichoke and Cynar liqueur: Two (not quite) entangled proteomes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:119-26. [DOI: 10.1016/j.bbapap.2012.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 01/13/2023]
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13
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Arenhart RA, Lima JCD, Pedron M, Carvalho FEL, Silveira JAGD, Rosa SB, Caverzan A, Andrade CMB, Schünemann M, Margis R, Margis-Pinheiro M. Involvement of ASR genes in aluminium tolerance mechanisms in rice. PLANT, CELL & ENVIRONMENT 2013; 36:52-67. [PMID: 22676236 DOI: 10.1111/j.1365-3040.2012.02553.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Among cereal crops, rice is considered the most tolerant to aluminium (Al). However, variability among rice genotypes leads to remarkable differences in the degree of Al tolerance for distinct cultivars. A number of studies have demonstrated that rice plants achieve Al tolerance through an unknown mechanism that is independent of root tip Al exclusion. We have analysed expression changes of the rice ASR gene family as a function of Al treatment. The gene ASR5 was differentially regulated in the Al-tolerant rice ssp. Japonica cv. Nipponbare. However, ASR5 expression did not respond to Al exposure in Indica cv. Taim rice roots, which are highly Al sensitive. Transgenic plants carrying RNAi constructs that targeted the ASR genes were obtained, and increased Al susceptibility was observed in T1 plants. Embryogenic calli of transgenic rice carrying an ASR5-green fluorescent protein fusion revealed that ASR5 was localized in both the nucleus and cytoplasm. Using a proteomic approach to compare non-transformed and ASR-RNAi plants, a total of 41 proteins with contrasting expression patterns were identified. We suggest that the ASR5 protein acts as a transcription factor to regulate the expression of different genes that collectively protect rice cells from Al-induced stress responses.
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Affiliation(s)
- Rafael Augusto Arenhart
- Programa de Pós-Graduação em Genética e Biologia Molecular Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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14
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Ribeiro CW, Carvalho FEL, Rosa SB, Alves-Ferreira M, Andrade CMB, Ribeiro-Alves M, Silveira JAG, Margis R, Margis-Pinheiro M. Modulation of genes related to specific metabolic pathways in response to cytosolic ascorbate peroxidase knockdown in rice plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:944-955. [PMID: 22686276 DOI: 10.1111/j.1438-8677.2012.00587.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
As a central component of the hydrogen peroxide detoxifying system in plant cells, ascorbate peroxidases (APX) play an essential role in the control of intracellular reactive oxygen species (ROS) levels. To characterise the function of cytosolic APX isoforms (OsAPX1 and OsAPX2) in the mechanisms of plant defence, OsAPX1/2 knockdown rice plants were previously obtained. OsAPX1/2 knockdown plants (APx1/2s) exhibited a normal phenotype and development, even though they showed a global reduction of APX activity and increased hydrogen peroxide accumulation. To understand how rice plants compensate for the deficiency of cytosolic APX, expression and proteomic analyses were performed to characterise the global expression pattern of the APx1/2s mutant line compared with non-transformed plants. Our results strongly suggest that deficiencies in cytosolic APX isoforms markedly alter expression of genes associated with several key metabolic pathways, especially of genes involved in photosynthesis and antioxidant defence. These metabolic changes are compensatory because central physiological processes such as photosynthesis and growth were similar to non-transformed rice plants. Our analyses showed modulation of groups of genes and proteins related to specific metabolic pathways. Among the differentially expressed genes, the largest number corresponded to those with catalytic activity. Genes related to oxidative stress, carbohydrate metabolism, photosynthesis and transcription factor-encoding genes were also modulated. These results represent an important step toward understanding of the role played by cytosolic APX isoforms and hydrogen peroxide in the regulation of metabolism by redox modulation in monocots.
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Affiliation(s)
- C W Ribeiro
- Biotechnology Center, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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15
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Falvo S, Di Carli M, Desiderio A, Benvenuto E, Moglia A, America T, Lanteri S, Acquadro A. 2-D DIGE analysis of UV-C radiation-responsive proteins in globe artichoke leaves. Proteomics 2012; 12:448-60. [PMID: 22162389 DOI: 10.1002/pmic.201100337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 11/22/2011] [Accepted: 11/24/2011] [Indexed: 01/08/2023]
Abstract
Plants respond to ultraviolet stress inducing a self-defence through the regulation of specific gene family members. The UV acclimation is the result of biochemical and physiological processes, such as enhancement of the antioxidant enzymatic system and accumulation of UV-absorbing phenolic compounds (e.g. flavonoids). Globe artichoke is an attractive species for studying the protein network involved in UV stress response, being characterized by remarkable levels of inducible antioxidants. Proteomic tools can assist the evaluation of the expression patterns of UV-responsive proteins and we applied the difference in-gel electrophoresis (DIGE) technology for monitoring the globe artichoke proteome variation at four time points following an acute UV-C exposure. A total of 145 UV-C-modulated proteins were observed and 119 were identified by LC-MS/MS using a ∼144,000 customized Compositae protein database, which included about 19,000 globe artichoke unigenes. Proteins were Gene Ontology (GO) categorized, visualized on their pathways and their behaviour was discussed. A predicted protein interaction network was produced and highly connected hub-like proteins were highlighted. Most of the proteins differentially modulated were chloroplast located, involved in photosynthesis, sugar metabolisms, protein folding and abiotic stress. The identification of UV-C-responsive proteins may contribute to shed light on the molecular mechanisms underlying plant responses to UV stress.
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Affiliation(s)
- Sara Falvo
- DIVAPRA, University of Turin, Grugliasco, Torino, Italy
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16
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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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17
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Zhang A, Lu Q, Yin Y, Ding S, Wen X, Lu C. Comparative proteomic analysis provides new insights into the regulation of carbon metabolism during leaf senescence of rice grown under field conditions. JOURNAL OF PLANT PHYSIOLOGY 2010; 167:1380-9. [PMID: 20663584 DOI: 10.1016/j.jplph.2010.05.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 05/13/2010] [Accepted: 05/14/2010] [Indexed: 05/22/2023]
Abstract
In rice (Oryza sativa), approximately 60-100% of the carbon in mature grains originates from CO(2) assimilation during the grain-filling period, with the flag leaf as the most important contributor to the dry weight accumulation in grains. It is therefore important to understand molecular mechanisms of flag leaf senescence. To investigate the regulation of the metabolic network during leaf senescence, changes in protein expression were analyzed using a comparative proteomic approach during senescence of flag leaves in rice grown under field conditions. A total of 170 differentially expressed proteins during senescence of flag leaves were identified by mass spectrometry. Of these, there were 48 down-regulated proteins and 122 up-regulated proteins, corresponding to total 124 unique proteins. These identified proteins are involved in different cellular responses and metabolic processes, including photosynthesis, photorespiration, glycolysis, cell defense, redox homeostasis, signal transduction, protein synthesis, folding and assembly. Based on the abundance changes of these proteins, together with their putative functions and participation in physiological processes, we propose protein networks of carbon metabolism at the protein level during leaf senescence. These networks illustrate, for the first time, an overview of the regulations of carbon metabolic reactions occurring during leaf senescence.
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Affiliation(s)
- Aihong Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20# Nanxincun, Xiangshan, Haidian District, Beijing 100093, PR China
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18
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Comparison of Two Protein Extraction Methods for Proteomic Analysis of Chlorophyll-deficient Mutants in Brassica Juncea L.*. PROG BIOCHEM BIOPHYS 2010. [DOI: 10.3724/sp.j.1206.2010.00176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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