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Song J, Lu D, Niu Y, Sun H, Zhang P, Dong W, Li Y, Zhang Y, Lu L, Men Q, Zhang X, Ren P, Chen C. Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake. BMC Genomics 2022; 23:184. [PMID: 35247985 PMCID: PMC8898408 DOI: 10.1186/s12864-022-08394-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/15/2022] [Indexed: 02/07/2023] Open
Abstract
Background Maize is one of the most important food crops worldwide. Roots play important role in maize productivity through water and nutrient uptake from the soil. Improving maize root traits for efficient water uptake will help to optimize irrigation and contribute to sustainable maize production. Therefore, we investigated the protein profiles of maize cv. Anyu308 root system divided into Upper root zone (UR), Middle root (MR), and Lower root (LR), by label free quantitative shotgun proteomic approach (LFQ). The aim of our study was to identify proteins and mechanisms associated with enhanced water uptake in different maize root zones under automatic irrigation system. Results At field capacity, MR had the highest water uptake than the UR and LR. We identified a total of 489 differentially abundant proteins (DAPs) by pairwise comparison of MR, LR, and UR. Cluster analysis of DAPs revealed MR and UR had similar protein abundance patterns different from LR. More proteins were differentially abundant in MR/UR compared to LR/MR and LR/UR. Comparisons of protein profiles indicate that the DAPs in MR increased in abundance, compared to UR and LR which had more downregulated DAPs. The abundance patterns, functional category, and pathway enrichment analyses highlight chromatin structure and dynamics, ribosomal structures, polysaccharide metabolism, energy metabolism and transport, induction of water channels, inorganic ion transport, intracellular trafficking, and vesicular transport, and posttranslational modification as primary biological processes related to enhanced root water uptake in maize. Specifically, the abundance of histones, ribosomal proteins, and aquaporins, including mitochondrion electron transport proteins and the TCA cycle, underpinned MR’s enhanced water uptake. Furthermore, proteins involved in folding and vascular transport supported the radial transport of solute across cell membranes in UR and MR. Parallel reaction monitoring analysis was used to confirmed profile of the DAPs obtained by LFQ-based proteomics. Conclusion The list of differentially abundant proteins identified in MR are interesting candidates for further elucidation of their role in enhanced water uptake in maize root. Overall, the current results provided an insight into the mechanisms of maize root water uptake. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08394-y.
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Hochholdinger F, Marcon C, Baldauf JA, Yu P, Frey FP. Proteomics of Maize Root Development. FRONTIERS IN PLANT SCIENCE 2018; 9:143. [PMID: 29556242 PMCID: PMC5844967 DOI: 10.3389/fpls.2018.00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/25/2018] [Indexed: 05/19/2023]
Abstract
Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.
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Zhou Y, Li M, Zhao F, Zha H, Yang L, Lu Y, Wang G, Shi J, Chen J. Floral Nectary Morphology and Proteomic Analysis of Nectar of Liriodendron tulipifera Linn. FRONTIERS IN PLANT SCIENCE 2016; 7:826. [PMID: 27379122 PMCID: PMC4905952 DOI: 10.3389/fpls.2016.00826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/26/2016] [Indexed: 05/08/2023]
Abstract
Nectar is a primary nutrient reward for a variety of pollinators. Recent studies have demonstrated that nectar also has defensive functions against microbial invasion. In this study, the Liriodendron tulipifera nectary was first examined by scanning electron microscopy, and then the nectar was analyzed by two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry, which led to identification of 42 nectar proteins involved in various biological functions. Bioinformatic analysis was then performed on an identified novel rubber elongation factor (REF) protein in L. tulipifera nectar. The protein was particularly abundant, representing ∼60% of the major bands of 31 to 43 kDa, and showed high, stage-specific expression in nectary tissue. The REF family proteins are the major allergens in latex. We propose that REF in L. tulipifera nectar has defensive characteristics against microorganisms.
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Affiliation(s)
- Yanwei Zhou
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry UniversityNanjing, China
| | - Meiping Li
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry UniversityNanjing, China
| | - Fangfang Zhao
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry UniversityNanjing, China
| | - Hongguang Zha
- College of Life and Environment Science, Huangshan UniversityHuangshan, China
| | - Liming Yang
- School of Life science, Huaiyin Normal UniversityHuai’an, China
| | - Ye Lu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry UniversityNanjing, China
| | - Guangping Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry UniversityNanjing, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry UniversityNanjing, China
- *Correspondence: Jinhui Chen, ; Jisen Shi,
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry UniversityNanjing, China
- *Correspondence: Jinhui Chen, ; Jisen Shi,
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Abstract
Proteomic approaches have been used to understand several regulatory aspects of plant development. Somatic embryogenesis is one of those developmental pathways that have beneficiated from the integration of proteomics data to the understanding of the molecular mechanisms that control embryogenic competence acquisition, somatic embryo development and conversion into viable plants. Nevertheless, most of the results obtained are based on the traditional model systems, very often not easily compared with the somatic embryogenesis systems of economical relevant woody species. The aim of this work is to summarize some of the applications of proteomics in the understanding of particular aspects of the somatic embryogenesis process in broad-leaf woody plants (model and non-model systems).
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Jorrín-Novo JV, Pascual J, Sánchez-Lucas R, Romero-Rodríguez MC, Rodríguez-Ortega MJ, Lenz C, Valledor L. Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms. Proteomics 2015; 15:1089-112. [PMID: 25487722 DOI: 10.1002/pmic.201400349] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/23/2014] [Accepted: 12/04/2014] [Indexed: 12/21/2022]
Abstract
In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.
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Affiliation(s)
- Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
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Fraige K, González-Fernández R, Carrilho E, Jorrín-Novo JV. Metabolite and proteome changes during the ripening of Syrah and Cabernet Sauvignon grape varieties cultured in a nontraditional wine region in Brazil. J Proteomics 2015; 113:206-25. [DOI: 10.1016/j.jprot.2014.09.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/22/2014] [Accepted: 09/26/2014] [Indexed: 01/19/2023]
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Zhang M, Shen S. Effective protein extraction protocol for proteomics studies of Jerusalem artichoke leaves. J Sep Sci 2013; 36:2203-9. [PMID: 23630184 DOI: 10.1002/jssc.201300199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/16/2013] [Accepted: 04/16/2013] [Indexed: 11/11/2022]
Abstract
Protein extraction is a crucial step for proteomics studies. To establish an effective protein extraction protocol suitable for two-dimensional electrophoresis (2DE) analysis in Jerusalem artichoke (Helianthus tuberosus L.), three different protein extraction methods-trichloroacetic acid/acetone, Mg/NP-40, and phenol/ammonium acetate-were evaluated using Jerusalem artichoke leaves as source materials. Of the three methods, trichloroacetic acid/acetone yielded the best protein separation pattern and highest number of protein spots in 2DE analysis. Proteins highly abundant in leaves, such as Rubisco, are typically problematic during leaf 2DE analysis, however, and this disadvantage was evident using trichloroacetic acid/acetone. To reduce the influence of abundant proteins on the detection of low-abundance proteins, we optimized the trichloroacetic acid/acetone method by incorporating a PEG fractionation approach. After optimization, 363 additional (36.2%) protein spots were detected on the 2DE gel. Our results suggest that trichloroacetic acid/acetone method is a better protein extraction technique than Mg/NP-40 and phenol/ammonium acetate in Jerusalem artichoke leaf 2DE analysis, and that trichloroacetic acid/acetone method combined with PEG fractionation procedure is the most effective approach for leaf 2DE analysis of Jerusalem artichoke.
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Affiliation(s)
- Meide Zhang
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi, China.
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8
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García-Mata C, Lamattina L. Gasotransmitters are emerging as new guard cell signaling molecules and regulators of leaf gas exchange. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 201-202:52-65. [PMID: 23352403 DOI: 10.1016/j.plantsci.2012.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 11/13/2012] [Accepted: 11/15/2012] [Indexed: 05/21/2023]
Abstract
Specialized guard cells modulate plant gas exchange through the regulation of stomatal aperture. The size of the stomatal pore is a direct function of the volume of the guard cells. The transport of solutes across channels in plasma membrane is a crucial process in the maintenance of guard cell water status. The fine tuned regulation of that transport requires an integrated convergence of multiple endogenous and exogenous signals perceived at both the cellular and the whole plant level. Gasotransmitters are novel signaling molecules with key functions in guard cell physiology. Three gasotransmitters, nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H(2)S) are involved in guard cell regulatory processes. These molecules are endogenously produced by plant cells and are part of the guard cells responses to drought stress conditions through ABA-dependent pathways. In this review, we summarize the current knowledge of gasotransmitters as versatile molecules interacting with different components of guard cell signaling network and propose them as players in new paradigms to study ABA-independent guard cell responses to water deficit.
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Affiliation(s)
- Carlos García-Mata
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, UNMdP-CONICET, CC 1245, (7600) Mar del Plata, Argentina
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9
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Di G, You W, Yu J, Wang D, Ke C. Genetic changes in muscle protein following hybridization between Haliotis diversicolor
reeve Japan and Taiwan populations revealed using a proteomic approach. Proteomics 2013; 13:845-59. [DOI: 10.1002/pmic.201200351] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/28/2012] [Accepted: 11/14/2012] [Indexed: 12/23/2022]
Affiliation(s)
- Guilan Di
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen P. R. China
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen P. R. China
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Jinjin Yu
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Dexiang Wang
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen P. R. China
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
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10
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Abstract
To gain insights into the protein dynamics during seed development, a proteomic study on the developing Brassica campestri L. seeds with embryos in different embryogenesis stages was carried out. The seed proteins at 10, 16, 20, 25 and 35 DAP (days after pollination), respectively, were separated using two-dimensional gel electrophoresis and identities of 209 spots with altered abundance were determined by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS). These proteins were classified into 16 groups according to their functions. The most abundant proteins were related to primary metabolism, indicating the heavy demand of materials for rapid embryo growth. Besides, the high amount of proteins involved in protein processing and destination indicated importance of protein renewal during seed development. The remaining were those participated in oxidation/detoxification, energy, defense, transcription, protein synthesis, transporter, cell structure, signal transduction, secondary metabolism, transposition, DNA repair, storage and so on. Protein abundance profiles of each functional class were generated and hierarchical cluster analysis established 8 groups of dynamic patterns. Our results revealed novel characters of protein dynamics in seed development in Brassica campestri L. and provided valuable information about the complex process of seed development in plants.
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Affiliation(s)
- Wenlan Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Yi Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hong Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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11
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Portillo L, Olmedilla A, Santacruz-Ruvalcaba F. Cellular and molecular changes associated with somatic embryogenesis induction in Agave tequilana. PROTOPLASMA 2012; 249:1101-1107. [PMID: 22270826 DOI: 10.1007/s00709-011-0354-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/16/2011] [Indexed: 05/31/2023]
Abstract
In spite of the importance of somatic embryogenesis for basic research in plant embryology as well as for crop improvement and plant propagation, it is still unclear which mechanisms and cell signals are involved in acquiring embryogenic competence by a somatic cell. The aim of this work was to study cellular and molecular changes involved in the induction stage in calli of Agave tequilana Weber cultivar azul in order to gain more information on the initial stages of somatic embryogenesis in this species. Cytochemical and immunocytochemical techniques were used to identify differences between embryogenic and non-embryogenic cells from several genotypes. Presence of granular structures was detected after somatic embryogenesis induction in embryogenic cells; composition of these structures as well as changes in protein and polysaccharide distribution was studied using Coomassie brilliant blue and Periodic Acid-Schiff stains. Distribution of arabinogalactan proteins (AGPs) and pectins was investigated in embryogenic and non-embryogenic cells by immunolabelling using anti-AGP monoclonal antibodies (JIM4, JIM8 and JIM13) as well as an anti-methyl-esterified pectin-antibody (JIM7), in order to evaluate major modifications in cell wall composition in the initial stages of somatic embryogenesis. Our observations pointed out that induction of somatic embryogenesis produced accumulation of proteins and polysaccharides in embryogenic cells. Presence of JIM8, JIM13 and JIM7 epitopes were detected exclusively in embryogenic cells, which supports the idea that specific changes in cell wall are involved in the acquisition of embryogenic competence of A. tequilana.
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Affiliation(s)
- L Portillo
- Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, A. P. 1-139, Zapopan, Jal. 45101, Mexico.
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12
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Jiang J, Jiang L, Zhang L, Luo H, Opiyo AM, Yu Z. Changes of protein profile in fresh-cut lotus tuber before and after browning. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:3955-3965. [PMID: 22455495 DOI: 10.1021/jf205303y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Browning is a critical problem, which often limits the shelf life and marketability in fresh-cut lotus tuber. Proteome level changes in response to the browning metabolism were investigated using two-dimensional electrophoresis (2-DE) and MALDI-TOF-TOF. A total of 34 functional protein spots were identified by comparing 2-DE protein patterns of fresh-cut lotus tuber before and after browning. These 34 identified proteins could be classified into 7 functional groups based on the NCBI database, that is, material and energy metabolism (35%), stress response (20%), respiration metabolism (12%), cell structure (12%), signal transduction (6%), gene expression regulation (6%), and unclassified proteins (9%). The group with the greatest difference in protein expression was related to material metabolism and regulation, reactive oxygen species metabolism, and respiratory control. The distinct proteins included universal stress protein (USP), superoxide dismutase (SOD), peroxidase (POD), ferritin, and ATPase.
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Affiliation(s)
- Juan Jiang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
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13
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Correia S, Vinhas R, Manadas B, Lourenço AS, Veríssimo P, Canhoto JM. Comparative Proteomic Analysis of Auxin-Induced Embryogenic and Nonembryogenic Tissues of the Solanaceous Tree Cyphomandra betacea (Tamarillo). J Proteome Res 2012; 11:1666-75. [DOI: 10.1021/pr200856w] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandra Correia
- Center of Functional Ecology,
Department of Life Sciences, University of Coimbra, Ap. 3046, 3001-401 Coimbra, Portugal
| | - Raquel Vinhas
- Center for Neuroscience and
Cell Biology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- Proteomics Unit, Center for Neuroscience
and Cell Biology, University of Coimbra, Coimbra, Portugal
- Cell
Biology Unit, Biocant, Cantanhede, Portugal
| | | | - Paula Veríssimo
- Center for Neuroscience and
Cell Biology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Jorge M. Canhoto
- Center of Functional Ecology,
Department of Life Sciences, University of Coimbra, Ap. 3046, 3001-401 Coimbra, Portugal
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14
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Uváčková L, Takáč T, Boehm N, Obert B, Samaj J. Proteomic and biochemical analysis of maize anthers after cold pretreatment and induction of androgenesis reveals an important role of anti-oxidative enzymes. J Proteomics 2012; 75:1886-94. [PMID: 22252011 DOI: 10.1016/j.jprot.2011.12.033] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 12/22/2011] [Accepted: 12/23/2011] [Indexed: 11/25/2022]
Abstract
In stress conditions, microspores and young pollen grains can be switched from their normal pollen development toward an embryogenic pathway via a process called androgenesis. Androgenic embryos can produce completely homozygous, haploid or double-haploid plants. This study aimed to investigate changes in the abundance of protein species during cold pretreatment and subsequent cultivation of maize anthers on induction media using gel-based proteomics. Proteins upregulated on the third day of anther induction were identified and discussed here. Simultaneous microscopic observations revealed that the first division occurred in microspores within this period. Using 2-D electrophoresis combined with MALDI TOF/TOF MS/MS analysis 19 unique proteins were identified and classified into 8 functional groups. Proteins closely associated with metabolism, protein synthesis and cell structure were the most abundant ones. Importantly, ascorbate peroxidase, an enzyme decomposing hydrogen peroxide, was also upregulated. Isozyme analysis of peroxidases validated the proteomic data and showed increased peroxidase activities during androgenic induction. Further, the isozyme pattern of SOD revealed increased activity of the MnSOD, which could provide hydrogen peroxide as a substrate for in vivo peroxidase reactions (including ascorbate peroxidase). Together, these data reveal the role of enzymes controlling oxidative stress during induction of maize androgenesis.
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Affiliation(s)
- L'ubica Uváčková
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademická 2, P. O. Box 39A, 95007 Nitra, Slovak Republic
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15
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Fu Z, Jin X, Ding D, Li Y, Fu Z, Tang J. Proteomic analysis of heterosis during maize seed germination. Proteomics 2011; 11:1462-72. [DOI: 10.1002/pmic.201000481] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 12/21/2010] [Accepted: 01/18/2011] [Indexed: 12/29/2022]
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16
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Takáč T, Pechan T, Samaj J. Differential proteomics of plant development. J Proteomics 2011; 74:577-88. [PMID: 21315196 DOI: 10.1016/j.jprot.2011.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/28/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
In this mini-review, recent advances in plant developmental proteomics are summarized. The growing interest in plant proteomics continually produces large numbers of developmental studies on plant cell division, elongation, differentiation, and formation of various organs. The brief overview of changes in proteome profiles emphasizes the participation of stress-related proteins in all developmental processes, which substantially changes the view on functional classification of these proteins. Next, it is noteworthy that proteomics helped to recognize some metabolic and housekeeping proteins as important signaling inducers of developmental pathways. Further, cell division and elongation are dependent on proteins involved in membrane trafficking and cytoskeleton dynamics. These protein groups are less prevalently represented in studies concerning cell differentiation and organ formation, which do not target primarily cell division. The synthesis of new proteins, generally observed during developmental processes, is followed by active protein folding. In this respect, disulfide isomerase was found to be commonly up-regulated during several developmental processes. The future progress in plant proteomics requires new and/or complementary approaches including cell fractionation, specific chemical treatments, molecular cloning and subcellular localization of proteins combined with more sensitive methods for protein detection and identification.
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Affiliation(s)
- Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
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17
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Kaufmann K, Smaczniak C, de Vries S, Angenent GC, Karlova R. Proteomics insights into plant signaling and development. Proteomics 2011; 11:744-55. [DOI: 10.1002/pmic.201000418] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/29/2010] [Accepted: 11/02/2010] [Indexed: 12/11/2022]
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18
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Chang IF, Chen PJ, Shen CH, Hsieh TJ, Hsu YW, Huang BL, Kuo CI, Chen YT, Chu HA, Yeh KW, Huang LC. Proteomic profiling of proteins associated with the rejuvenation of Sequoia sempervirens (D. Don) Endl. Proteome Sci 2010; 8:64. [PMID: 21143964 PMCID: PMC3022872 DOI: 10.1186/1477-5956-8-64] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Accepted: 12/10/2010] [Indexed: 11/10/2022] Open
Abstract
Background Restoration of rooting competence is important for rejuvenation in Sequoia sempervirens (D. Don) Endl and is achieved by repeatedly grafting Sequoia shoots after 16 and 30 years of cultivation in vitro. Results Mass spectrometry-based proteomic analysis revealed three proteins that differentially accumulated in different rejuvenation stages, including oxygen-evolving enhancer protein 2 (OEE2), glycine-rich RNA-binding protein (RNP), and a thaumatin-like protein. OEE2 was found to be phosphorylated and a phosphopeptide (YEDNFDGNSNVSVMVpTPpTDK) was identified. Specifically, the protein levels of OEE2 increased as a result of grafting and displayed a higher abundance in plants during the juvenile and rejuvenated stages. Additionally, SsOEE2 displayed the highest expression levels in Sequoia shoots during the juvenile stage and less expression during the adult stage. The expression levels also steadily increased during grafting. Conclusion Our results indicate a positive correlation between the gene and protein expression patterns of SsOEE2 and the rejuvenation process, suggesting that this gene is involved in the rejuvenation of Sequoia sempervirens.
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Affiliation(s)
- Ing-Feng Chang
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Peng-Jen Chen
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Chin-Hui Shen
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Tsung-Ju Hsieh
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Ya-Wen Hsu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Bau-Lian Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ching-I Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Ting Chen
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Hsiu-An Chu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Kai-Wun Yeh
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Li-Chun Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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19
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Miernyk JA, Preťová A, Olmedilla A, Klubicová K, Obert B, Hajduch M. Using proteomics to study sexual reproduction in angiosperms. ACTA ACUST UNITED AC 2010; 24:9-22. [PMID: 20830489 DOI: 10.1007/s00497-010-0149-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 08/21/2010] [Indexed: 12/18/2022]
Abstract
While a relative latecomer to the postgenomics era of functional biology, the application of mass spectrometry-based proteomic analysis has increased exponentially over the past 10 years. Some of this increase is the result of transition of chemists, physicists, and mathematicians to the study of biology, and some is due to improved methods, increased instrument sensitivity, and better techniques of bioinformatics-based data analysis. Proteomic Biological processes are typically studied in isolation, and seldom are efforts made to coordinate results obtained using structural, biochemical, and molecular-genetic strategies. Mass spectrometry-based proteomic analysis can serve as a platform to bridge these disparate results and to additionally incorporate both temporal and anatomical considerations. Recently, proteomic analyses have transcended their initial purely descriptive applications and are being employed extensively in studies of posttranslational protein modifications, protein interactions, and control of metabolic networks. Herein, we provide a brief introduction to sample preparation, comparison of gel-based versus gel-free methods, and explanation of data analysis emphasizing plant reproductive applications. We critically review the results from the relatively small number of extant proteomics-based analyses of angiosperm reproduction, from flowers to seedlings, and speculate on the utility of this strategy for future developments and directions.
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Affiliation(s)
- Ján A Miernyk
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovak Republic
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20
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Yang X, Zhang X. Regulation of Somatic Embryogenesis in Higher Plants. CRITICAL REVIEWS IN PLANT SCIENCES 2010; 29:36-57. [PMID: 0 DOI: 10.1080/07352680903436291] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Xiyan Yang
- a National Key Laboratory of Crop Genetic Improvement , Huazhong Agricultural University , Wuhan, Hubei, 430070, P. R. China
| | - Xianlong Zhang
- a National Key Laboratory of Crop Genetic Improvement , Huazhong Agricultural University , Wuhan, Hubei, 430070, P. R. China
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21
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Saleem M, Lamkemeyer T, Schützenmeister A, Madlung J, Sakai H, Piepho HP, Nordheim A, Hochholdinger F. Specification of cortical parenchyma and stele of maize primary roots by asymmetric levels of auxin, cytokinin, and cytokinin-regulated proteins. PLANT PHYSIOLOGY 2010; 152:4-18. [PMID: 19933382 PMCID: PMC2799342 DOI: 10.1104/pp.109.150425] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 11/18/2009] [Indexed: 05/19/2023]
Abstract
In transverse orientation, maize (Zea mays) roots are composed of a central stele that is embedded in multiple layers of cortical parenchyma. The stele functions in the transport of water, nutrients, and photosynthates, while the cortical parenchyma fulfills metabolic functions that are not very well characterized. To better understand the molecular functions of these root tissues, protein- and phytohormone-profiling experiments were conducted. Two-dimensional gel electrophoresis combined with electrospray ionization tandem mass spectrometry identified 59 proteins that were preferentially accumulated in the cortical parenchyma and 11 stele-specific proteins. Hormone profiling revealed preferential accumulation of indole acetic acid and its conjugate indole acetic acid-aspartate in the stele and predominant localization of the cytokinin cis-zeatin, its precursor cis-zeatin riboside, and its conjugate cis-zeatin O-glucoside in the cortical parenchyma. A root-specific beta-glucosidase that functions in the hydrolysis of cis-zeatin O-glucoside was preferentially accumulated in the cortical parenchyma. Similarly, four enzymes involved in ammonium assimilation that are regulated by cytokinin were preferentially accumulated in the cortical parenchyma. The antagonistic distribution of auxin and cytokinin in the stele and cortical parenchyma, together with the cortical parenchyma-specific accumulation of cytokinin-regulated proteins, suggest a molecular framework that specifies the function of these root tissues that also play a role in the formation of lateral roots from pericycle and endodermis cells.
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22
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Saleem M, Lamkemeyer T, Schützenmeister A, Fladerer C, Piepho HP, Nordheim A, Hochholdinger F. Tissue Specific Control of the Maize (Zea mays L.) Embryo, Cortical Parenchyma, and Stele Proteomes by RUM1 Which Regulates Seminal and Lateral Root Initiation. J Proteome Res 2009; 8:2285-97. [DOI: 10.1021/pr8009287] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Muhammad Saleem
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Tobias Lamkemeyer
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - André Schützenmeister
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Claudia Fladerer
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Hans-Peter Piepho
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Alfred Nordheim
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
| | - Frank Hochholdinger
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, 72076 Tuebingen, Germany, Proteome Centre Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany, and Institute for Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
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23
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Hochholdinger F, Tuberosa R. Genetic and genomic dissection of maize root development and architecture. CURRENT OPINION IN PLANT BIOLOGY 2009; 12:172-7. [PMID: 19157956 DOI: 10.1016/j.pbi.2008.12.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 11/26/2008] [Accepted: 12/06/2008] [Indexed: 05/21/2023]
Abstract
The complex architecture and plasticity of the maize root system is controlled by a plethora of genes. Mutant analyses have identified genes regulating shoot-borne root initiation (RTCS) and root hair elongation (RTH1 and RTH3). Quantitative trait locus (QTL) studies have highlighted the importance of seminal roots, lateral roots, and root hairs in phosphorus acquisition. Additionally, QTLs that influence root features were shown to affect yield under different water regimes and under flooding conditions. Finally, proteome and transcriptome analyses provided insights into maize root development and identified candidate genes associated with cell specification, and lateral root initiation in pericycle cells. The targeted application of forward-genetics and reverse-genetics approaches will accelerate the unraveling of the functional basis of root development and architecture.
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Affiliation(s)
- Frank Hochholdinger
- University of Tuebingen, Center for Plant Molecular Biology (ZMBP), Department of General Genetics, Auf der Morgenstelle 28, 72076 Tuebingen, Germany.
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24
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Albertin W, Langella O, Joets J, Négroni L, Zivy M, Damerval C, Thiellement H. Comparative proteomics of leaf, stem, and root tissues of synthetic Brassica napus. Proteomics 2009; 9:793-9. [PMID: 19132686 DOI: 10.1002/pmic.200800479] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Warren Albertin
- Team Evolutionary Genetics: Adaptation and Redundancy, UMR 0320/UMR 8120 Génétique Végétale, INRA, Univ Paris-Sud, CNRS, AgroParisTech, Ferme du Moulon, Gif-sur-Yvette, France.
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25
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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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26
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Hoecker N, Lamkemeyer T, Sarholz B, Paschold A, Fladerer C, Madlung J, Wurster K, Stahl M, Piepho HP, Nordheim A, Hochholdinger F. Analysis of nonadditive protein accumulation in young primary roots of a maize (Zea mays L.) F1-hybrid compared to its parental inbred lines. Proteomics 2008; 8:3882-94. [DOI: 10.1002/pmic.200800023] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Abstract
This 2006 'Plant Proteomics Update' is a continuation of the two previously published in 'Proteomics' by 2004 (Canovas et al., Proteomics 2004, 4, 285-298) and 2006 (Rossignol et al., Proteomics 2006, 6, 5529-5548) and it aims to bring up-to-date the contribution of proteomics to plant biology on the basis of the original research papers published throughout 2006, with references to those appearing last year. According to the published papers and topics addressed, we can conclude that, as observed for the three previous years, there has been a quantitative, but not qualitative leap in plant proteomics. The full potential of proteomics is far from being exploited in plant biology research, especially if compared to other organisms, mainly yeast and humans, and a number of challenges, mainly technological, remain to be tackled. The original papers published last year numbered nearly 100 and deal with the proteome of at least 26 plant species, with a high percentage for Arabidopsis thaliana (28) and rice (11). Scientific objectives ranged from proteomic analysis of organs/tissues/cell suspensions (57) or subcellular fractions (29), to the study of plant development (12), the effect of hormones and signalling molecules (8) and response to symbionts (4) and stresses (27). A small number of contributions have covered PTMs (8) and protein interactions (4). 2-DE (specifically IEF-SDS-PAGE) coupled to MS still constitutes the almost unique platform utilized in plant proteome analysis. The application of gel-free protein separation methods and 'second generation' proteomic techniques such as multidimensional protein identification technology (MudPIT), and those for quantitative proteomics including DIGE, isotope-coded affinity tags (ICAT), iTRAQ and stable isotope labelling by amino acids in cell culture (SILAC) still remains anecdotal. This review is divided into seven sections: Introduction, Methodology, Subcellular proteomes, Development, Responses to biotic and abiotic stresses, PTMs and Protein interactions. Section 8 summarizes the major pitfalls and challenges of plant proteomics.
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Affiliation(s)
- Jesús V Jorrín
- Agricultural and Plant Biochemistry Research Group-Plant Proteomics, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain.
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28
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Hennig L. Patterns of beauty--omics meets plant development. TRENDS IN PLANT SCIENCE 2007; 12:287-93. [PMID: 17580122 DOI: 10.1016/j.tplants.2007.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Revised: 04/17/2007] [Accepted: 05/31/2007] [Indexed: 05/15/2023]
Abstract
Developmental biology aims to identify mechanisms that govern cell proliferation and differentiation in the body plan formation of multicellular organisms. In the past, developmental biologists described how anatomy and morphology are established during ontogenesis, and developmental geneticists identified many developmental regulators. In contrast to the traditional approaches that mostly focus on one or a few genes at a time, highly parallel profiling technologies have been developed for use in biological research over the past decade. Such parallel profiling technologies probe many genes, transcripts, proteins or metabolites at once. In this review, I discuss the growing impact of transcriptomics, proteomics, metabolomics and modelling on plant developmental biology. Novel profiling technologies will not make traditional gene-centred approaches obsolete but should instead complement forward developmental genetics.
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Affiliation(s)
- Lars Hennig
- Institute of Plant Sciences & Zurich-Basel Plant Science Center, ETH Zurich, LFW E17, CH-8092 Zurich, Switzerland.
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29
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Cañas B, Piñeiro C, Calvo E, López-Ferrer D, Gallardo JM. Trends in sample preparation for classical and second generation proteomics. J Chromatogr A 2007; 1153:235-58. [PMID: 17276441 DOI: 10.1016/j.chroma.2007.01.045] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 12/18/2006] [Accepted: 01/12/2007] [Indexed: 11/16/2022]
Abstract
Sample preparation is a fundamental step in the proteomics workflow. However, it is not easy to find compiled information updating this subject. In this paper, the strategies and protocols for protein extraction and identification, following either classical or second generation proteomics methodologies, are reviewed. Procedures for: tissue disruption, cell lysis, sample pre-fractionation, protein separation by 2-DE, protein digestion, mass spectrometry analysis, multidimensional peptide separations and quantification of protein expression level are described.
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Affiliation(s)
- Benito Cañas
- Dept. Química Analítica, Facultad de CC, Químicas, UCM, Av.Complutense s/n, Madrid 28040, Spain.
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