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Changes in the Flower and Leaf Proteome of Common Buckwheat ( Fagopyrum esculentum Moench) under High Temperature. Int J Mol Sci 2021; 22:ijms22052678. [PMID: 33800930 PMCID: PMC7961373 DOI: 10.3390/ijms22052678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/03/2023] Open
Abstract
Common buckwheat (Fagopyrum esculentum Moench), a pseudocereal crop, produces a large number of flowers, but this does not guarantee high seed yields. This species demonstrates strong abortion of flowers and embryos. High temperatures during the generative growth phase result in an increase in the degeneration of embryo sacs. The aim of this study was to investigate proteomic changes in flowers and leaves of two common buckwheat accessions with different degrees of heat tolerance, Panda and PA15. Two-dimensional gel electrophoresis and mass spectrometry techniques were used to analyze the proteome profiles. Analyses were conducted for flower buds, open flowers capable of fertilization, and wilted flowers, as well as donor leaves, i.e., those growing closest to the inflorescences. High temperature up-regulated the expression of 182 proteins. The proteomic response to heat stress differed between the accessions and among their organs. In the Panda accession, we observed a change in abundance of 17, 13, 28, and 11 proteins, in buds, open and wilted flowers, and leaves, respectively. However, in the PA15 accession there were 34, 21, 63, and 21 such proteins, respectively. Fifteen heat-affected proteins were common to both accessions. The indole-3-glycerol phosphate synthase chloroplastic-like isoform X2 accumulated in the open flowers of the heat-sensitive cultivar Panda in response to high temperature, and may be a candidate protein as a marker of heat sensitivity in buckwheat plants.
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Wei X, Lv Y, Zhao Y, Nath UK, Yuan Y, Wang Z, Yang S, Jia H, Wei F, Zhang X. Comparative transcriptome analysis in Chinese cabbage ( Brassica rapa ssp. pekinesis) for DEGs of Ogura-, Polima-CMS and their shared maintainer. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:719-731. [PMID: 32255935 PMCID: PMC7113364 DOI: 10.1007/s12298-020-00775-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/07/2020] [Accepted: 02/13/2020] [Indexed: 06/11/2023]
Abstract
Cytoplasmic male sterility (CMS) is maternally inherited trait, which hinders the ability to produce viable pollen in plants. It serves as a useful tool for hybrid seed production via exploiting heterosis in crops. The molecular mechanism of CMS and fertility restoration has been investigated in different crops. However, limited number of reports is available on comparison of Ogura- and Polima-CMS with their shared maintainer in Chinese cabbage. We performed transcript profiling of sterile Ogura CMS (Tyms), Polima CMS (22m2) and their shared maintainer line (231-330) with an aim to identify genes associated with male sterility. In this work, we identified 912, 7199 and 6381 DEGs (Differentially Expressed Genes) in 22m2 Vs Tyms, 231-330 VS 22m2 and 231-330 Vs Tyms, respectively. The GO (Gene Ontology) annotation and KEGG pathway analysis suggested that most of the DEGs were involved in pollen development, carbon metabolism, lipase activity, lipid binding, penta-tricopeptide repeat (PPR), citrate cycle and oxidative phosphorylation, which were down-regulated in both CMS lines. This result will provide an important resource for further understanding of functional pollen development, the CMS mechanism and to improve molecular breeding in Chinese cabbage.
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Affiliation(s)
- Xiaochun Wei
- School of Agricultural Sciences, College of Life Science, Zhengzhou University, Zhengzhou, 450001 People’s Republic of China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 People’s Republic of China
| | - Yanyan Lv
- School of Agricultural Sciences, College of Life Science, Zhengzhou University, Zhengzhou, 450001 People’s Republic of China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 People’s Republic of China
| | - Yanyan Zhao
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 People’s Republic of China
| | - Ujjal Kumar Nath
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 People’s Republic of China
| | - Zhiyong Wang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 People’s Republic of China
| | - Shuangjuan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 People’s Republic of China
| | - Hao Jia
- School of Agricultural Sciences, College of Life Science, Zhengzhou University, Zhengzhou, 450001 People’s Republic of China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 People’s Republic of China
| | - Fang Wei
- School of Agricultural Sciences, College of Life Science, Zhengzhou University, Zhengzhou, 450001 People’s Republic of China
| | - Xiaowei Zhang
- School of Agricultural Sciences, College of Life Science, Zhengzhou University, Zhengzhou, 450001 People’s Republic of China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 People’s Republic of China
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Grossmann J, Fernández H, Chaubey PM, Valdés AE, Gagliardini V, Cañal MJ, Russo G, Grossniklaus U. Proteogenomic Analysis Greatly Expands the Identification of Proteins Related to Reproduction in the Apogamous Fern Dryopteris affinis ssp. affinis. FRONTIERS IN PLANT SCIENCE 2017; 8:336. [PMID: 28382042 PMCID: PMC5360702 DOI: 10.3389/fpls.2017.00336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/27/2017] [Indexed: 05/19/2023]
Abstract
Performing proteomic studies on non-model organisms with little or no genomic information is still difficult. However, many specific processes and biochemical pathways occur only in species that are poorly characterized at the genomic level. For example, many plants can reproduce both sexually and asexually, the first one allowing the generation of new genotypes and the latter their fixation. Thus, both modes of reproduction are of great agronomic value. However, the molecular basis of asexual reproduction is not well understood in any plant. In ferns, it combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells (apogamy). To set the basis to study these processes, we performed transcriptomics by next-generation sequencing (NGS) and shotgun proteomics by tandem mass spectrometry in the apogamous fern D. affinis ssp. affinis. For protein identification we used the public viridiplantae database (VPDB) to identify orthologous proteins from other plant species and new transcriptomics data to generate a "species-specific transcriptome database" (SSTDB). In total 1,397 protein clusters with 5,865 unique peptide sequences were identified (13 decoy proteins out of 1,410, protFDR 0.93% on protein cluster level). We show that using the SSTDB for protein identification increases the number of identified peptides almost four times compared to using only the publically available VPDB. We identified homologs of proteins involved in reproduction of higher plants, including proteins with a potential role in apogamy. With the increasing availability of genomic data from non-model species, similar proteogenomics approaches will improve the sensitivity in protein identification for species only distantly related to models.
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Affiliation(s)
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology (BOS), Oviedo UniversityOviedo, Spain
- *Correspondence: Helena Fernández
| | - Pururawa M. Chaubey
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of ZurichZürich, Switzerland
| | - Ana E. Valdés
- Physiological Botany, Uppsala BioCenter, Uppsala UniversityUppsala, Sweden
- Linnean Centre for Plant BiologyUppsala, Sweden
| | - Valeria Gagliardini
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of ZurichZürich, Switzerland
| | - María J. Cañal
- Area of Plant Physiology, Department of Organisms and Systems Biology (BOS), Oviedo UniversityOviedo, Spain
| | | | - Ueli Grossniklaus
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of ZurichZürich, Switzerland
- Ueli Grossniklaus
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Danchenko M, Klubicova K, Krivohizha MV, Berezhna VV, Sakada VI, Hajduch M, Rashydov NM. Systems biology is an efficient tool for investigation of low-dose chronic irradiation influence on plants in the Chernobyl zone. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716060050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Gupta R, Min CW, Kim SW, Wang Y, Agrawal GK, Rakwal R, Kim SG, Lee BW, Ko JM, Baek IY, Bae DW, Kim ST. Comparative investigation of seed coats of brown- versus yellow-colored soybean seeds using an integrated proteomics and metabolomics approach. Proteomics 2015; 15:1706-16. [PMID: 25545850 DOI: 10.1002/pmic.201400453] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/09/2014] [Accepted: 12/17/2014] [Indexed: 12/27/2022]
Abstract
Seed coat color is an important attribute determining consumption of soybean seeds. Soybean cultivar Mallikong (M) has yellow seed coat while its naturally mutated cultivar Mallikong mutant (MM), has brown colored seed coat. We used integrated proteomics and metabolomics approach to investigate the differences between seed coats of M and MM during different stages of seed development (4, 5, and 6 weeks after flowering). 2DE profiling of total seed coat proteins from three stages showed 178 differentially expressed spots between M and MM of which 172 were identified by MALDI-TOF/TOF. Of these, 62 were upregulated and 105 were downregulated in MM compared with M, while five spots were detected only in MM. Proteins involved in primary metabolism showed downregulation in MM suggesting energy in MM might be utilized for proanthocyanidin biosynthesis via secondary metabolic pathways that leads to the development of brown seed coat color. Besides, downregulation of two isoforms of isoflavone reductase indicated reduced isoflavones in seed coat of MM that was confirmed by quantitative estimation of total and individual isoflavones using HPLC. We propose that low isoflavones level in MM may offer a high substrate for proanthocyanidin production that results in the development of brown seed coat in MM.
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Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, College of Natural Resources and Life Sciences, Pusan National University, Miryang, South Korea
| | - Chul Woo Min
- Department of Plant Bioscience, College of Natural Resources and Life Sciences, Pusan National University, Miryang, South Korea
| | - So Wun Kim
- Department of Plant Bioscience, College of Natural Resources and Life Sciences, Pusan National University, Miryang, South Korea
| | - Yiming Wang
- Department of Plant Microbe Interaction, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
- GRADE Academy Private Limited, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal
- GRADE Academy Private Limited, Birgunj, Nepal
- Organization for Educational Initiatives, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Anatomy I, Showa University School of Medicine, Shinagawa, Tokyo, Japan
| | - Sang Gon Kim
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Byong Won Lee
- Department of Functional Crops, NICS, RDA, Miryang, South Korea
| | - Jong Min Ko
- Department of Functional Crops, NICS, RDA, Miryang, South Korea
| | - In Yeol Baek
- Department of Functional Crops, NICS, RDA, Miryang, South Korea
| | - Dong Won Bae
- Central Laboratory, Gyeongsang National University, Jinju, South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, College of Natural Resources and Life Sciences, Pusan National University, Miryang, South Korea
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Shemesh-Mayer E, Ben-Michael T, Rotem N, Rabinowitch HD, Doron-Faigenboim A, Kosmala A, Perlikowski D, Sherman A, Kamenetsky R. Garlic (Allium sativum L.) fertility: transcriptome and proteome analyses provide insight into flower and pollen development. FRONTIERS IN PLANT SCIENCE 2015; 6:271. [PMID: 25972879 PMCID: PMC4411974 DOI: 10.3389/fpls.2015.00271] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/05/2015] [Indexed: 05/18/2023]
Abstract
Commercial cultivars of garlic, a popular condiment, are sterile, making genetic studies and breeding of this plant challenging. However, recent fertility restoration has enabled advanced physiological and genetic research and hybridization in this important crop. Morphophysiological studies, combined with transcriptome and proteome analyses and quantitative PCR validation, enabled the identification of genes and specific processes involved in gametogenesis in fertile and male-sterile garlic genotypes. Both genotypes exhibit normal meiosis at early stages of anther development, but in the male-sterile plants, tapetal hypertrophy after microspore release leads to pollen degeneration. Transcriptome analysis and global gene-expression profiling showed that >16,000 genes are differentially expressed in the fertile vs. male-sterile developing flowers. Proteome analysis and quantitative comparison of 2D-gel protein maps revealed 36 significantly different protein spots, 9 of which were present only in the male-sterile genotype. Bioinformatic and quantitative PCR validation of 10 candidate genes exhibited significant expression differences between male-sterile and fertile flowers. A comparison of morphophysiological and molecular traits of fertile and male-sterile garlic flowers suggests that respiratory restrictions and/or non-regulated programmed cell death of the tapetum can lead to energy deficiency and consequent pollen abortion. Potential molecular markers for male fertility and sterility in garlic are proposed.
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Affiliation(s)
- Einat Shemesh-Mayer
- Agricultural Research Organization, The Volcani Center, Institute of Plant ScienceBet Dagan, Israel
- The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Robert H. Smith Institute of Plant Science and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Tomer Ben-Michael
- Agricultural Research Organization, The Volcani Center, Institute of Plant ScienceBet Dagan, Israel
- The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Robert H. Smith Institute of Plant Science and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Neta Rotem
- The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Robert H. Smith Institute of Plant Science and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Haim D. Rabinowitch
- The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Robert H. Smith Institute of Plant Science and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Adi Doron-Faigenboim
- Agricultural Research Organization, The Volcani Center, Institute of Plant ScienceBet Dagan, Israel
| | - Arkadiusz Kosmala
- Department of Environmental Stress Biology, Institute of Plant Genetics of the Polish Academy of SciencesPoznan, Poland
| | - Dawid Perlikowski
- Department of Environmental Stress Biology, Institute of Plant Genetics of the Polish Academy of SciencesPoznan, Poland
| | - Amir Sherman
- Agricultural Research Organization, The Volcani Center, Institute of Plant ScienceBet Dagan, Israel
| | - Rina Kamenetsky
- Agricultural Research Organization, The Volcani Center, Institute of Plant ScienceBet Dagan, Israel
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Smith-Hammond CL, Hoyos E, Miernyk JA. The pea seedling mitochondrial Nε-lysine acetylome. Mitochondrion 2014; 19 Pt B:154-65. [PMID: 24780491 DOI: 10.1016/j.mito.2014.04.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/12/2014] [Accepted: 04/16/2014] [Indexed: 12/17/2022]
Abstract
Posttranslational lysine acetylation is believed to occur in all taxa and to affect thousands of proteins. In contrast to the hundreds of mitochondrial proteins reported to be lysine-acetylated in non-plant species, only a handful have been reported from the plant taxa previously examined. To investigate whether this reflects a biologically significant difference or merely a peculiarity of the samples thus far examined, we immunoenriched and analyzed acetylated peptides from highly purified pea seedling mitochondria using mass spectrometry. Our results indicate that a multitude of mitochondrial proteins, involved in a variety of processes, are acetylated in pea seedlings.
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Affiliation(s)
- Colin L Smith-Hammond
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
| | - Elizabeth Hoyos
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
| | - Ján A Miernyk
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA; Plant Genetics Research Unit, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211, USA.
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8
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Valledor L, Menéndez V, Canal MJ, Revilla A, Fernández H. Proteomic approaches to sexual development mediated by antheridiogen in the fern Blechnum spicant
L. Proteomics 2014; 14:2061-71. [DOI: 10.1002/pmic.201300166] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/11/2014] [Accepted: 07/07/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Luis Valledor
- Area de Fisiología Vegetal, Dpto. Biología de Organismos y Sistemas, Universidad de Oviedo; Oviedo Spain
| | - Virginia Menéndez
- Area de Fisiología Vegetal, Dpto. Biología de Organismos y Sistemas, Universidad de Oviedo; Oviedo Spain
| | - María Jesús Canal
- Area de Fisiología Vegetal, Dpto. Biología de Organismos y Sistemas, Universidad de Oviedo; Oviedo Spain
| | - Angeles Revilla
- Area de Fisiología Vegetal, Dpto. Biología de Organismos y Sistemas, Universidad de Oviedo; Oviedo Spain
| | - Helena Fernández
- Area de Fisiología Vegetal, Dpto. Biología de Organismos y Sistemas, Universidad de Oviedo; Oviedo Spain
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9
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Smith-Hammond CL, Swatek KN, Johnston ML, Thelen JJ, Miernyk JA. Initial description of the developing soybean seed protein Lys-N(ε)-acetylome. J Proteomics 2014; 96:56-66. [PMID: 24211405 DOI: 10.1016/j.jprot.2013.10.038] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/28/2013] [Accepted: 10/29/2013] [Indexed: 12/29/2022]
Abstract
Characterization of the myriad protein posttranslational modifications (PTM) is a key aspect of proteome profiling. While there have been previous studies of the developing soybean seed phospho-proteome, herein we present the first analysis of non-histone lysine-N(Ɛ)-acetylation in this system. In recent years there have been reports that lysine acetylation is widespread, affecting thousands of proteins in diverse species from bacteria to mammals. Recently preliminary descriptions of the protein lysine acetylome from the plants Arabidopsis thaliana and Vitis vinifera have been reported. Using a combination of immunoenrichment and mass spectrometry-based techniques, we have identified over 400 sites of lysine acetylation in 245 proteins from developing soybean (Glycine max (L.) Merr., cv. Jack) seeds, which substantially increases the number of known plant N(Ɛ)-lysine-acetylation sites. Results of functional annotation indicate acetyl-proteins are involved with a host of cellular activities. In addition to histones, and other proteins involved in RNA synthesis and processing, acetyl-proteins participate in signaling, protein folding, and a plethora of metabolic processes. Results from in silico localization indicate that lysine-acetylated proteins are present in all major subcellular compartments. In toto, our results establish developing soybean seeds as a physiologically distinct addendum to Arabidopsis thaliana seedlings for functional analysis of protein Lys-N(Ɛ)-acetylation. BIOLOGICAL SIGNIFICANCE Several modes of peptide fragmentation and database search algorithms are incorporated to identify, for the first time, sites of lysine acetylation on a plethora of proteins from developing soybean seeds. The contributions of distinct techniques to achieve increased coverage of the lysine acetylome are compared, providing insight to their respective benefits. Acetyl-proteins and specific acetylation sites are characterized, revealing intriguing similarities as well as differences with those previously identified in other plant and non-plant species.
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Affiliation(s)
- Colin L Smith-Hammond
- Division of Biochemistry, University of Missouri, Columbia, MO, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA.
| | - Kirby N Swatek
- Division of Biochemistry, University of Missouri, Columbia, MO, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA.
| | - Mark L Johnston
- Plant Genetics Research Unit, USDA, Agricultural Research Service, University of Missouri, Columbia, MO, USA.
| | - Jay J Thelen
- Division of Biochemistry, University of Missouri, Columbia, MO, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA.
| | - Ján A Miernyk
- Division of Biochemistry, University of Missouri, Columbia, MO, USA; Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA; Plant Genetics Research Unit, USDA, Agricultural Research Service, University of Missouri, Columbia, MO, USA.
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Abstract
Rather than providing a single specific protocol, the inclusive area of seed proteomics is reviewed; methods are described and compared and primary literature citations are provided. The limitations and challenges of proteomics as an approach to study seed biology are emphasized. The proteomic analysis of seeds encounters some specific problems that do not impinge on analyses of other plant cells, tissues, or organs. There are anatomic considerations. Seeds comprise the seed coat, the storage organ(s), and the embryonic axis. Are these to be studied individually or as a composite? The physiological status of the seeds must be considered; developing, mature, or germinating? If mature, are they quiescent or dormant? If mature and quiescent, then orthodox or recalcitrant? The genetic uniformity of the population of seeds being compared must be considered. Finally, seeds are protein-rich and the extreme abundance of the storage proteins results in a study-subject with a dynamic range that spans several orders of magnitude. This represents a problem that must be dealt with if the study involves analysis of proteins that are of "normal" to low abundance. Several different methods of prefractionation are described and the results compared.
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Affiliation(s)
- Ján A Miernyk
- USDA, Agricultural Research Service, Plant Genetics Research Unit, Department of Biochemistry, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
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11
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Klubicová K, Danchenko M, Skultety L, Berezhna VV, Rashydov NM, Hajduch M. Radioactive Chernobyl environment has produced high-oil flax seeds that show proteome alterations related to carbon metabolism during seed development. J Proteome Res 2013; 12:4799-806. [PMID: 24111740 DOI: 10.1021/pr400528m] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Starting in 2007, we have grown soybean (Glycine max [L.] Merr. variety Soniachna) and flax (Linum usitatissimum, L. variety Kyivskyi) in the radio-contaminated Chernobyl area and analyzed the seed proteomes. In the second-generation flax seeds, we detected a 12% increase in oil content. To characterize the bases for this increase, seed development has been studied. Flax seeds were harvested in biological triplicate at 2, 4, and 6 weeks after flowering and at maturity from plants grown in nonradioactive and radio-contaminated plots in the Chernobyl area for two generations. Quantitative proteomic analyses based on 2-D gel electrophoresis (2-DE) allowed us to establish developmental profiles for 199 2-DE spots in both plots, out of which 79 were reliably identified by tandem mass spectrometry. The data suggest a statistically significant increased abundance of proteins associated with pyruvate biosynthesis via cytoplasmic glycolysis, L-malate decarboxylation, isocitrate dehydrogenation, and ethanol oxidation to acetaldehyde in early stages of seed development. This was followed by statistically significant increased abundance of ketoacyl-[acylcarrier protein] synthase I related to condensation of malonyl-ACP with elongating fatty acid chains. On the basis of these and previous data, we propose a preliminary model for plant adaptation to growth in a radio-contaminated environment. One aspect of the model suggests that changes in carbon assimilation and fatty acid biosynthesis are an integral part of plant adaptation.
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Affiliation(s)
- Katarína Klubicová
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences , Akademicka 2, P.O. Box 39A, Nitra 95007, Slovakia
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Miernyk JA, Johnston ML. Proteomic analysis of the testa from developing soybean seeds. J Proteomics 2013; 89:265-72. [PMID: 23707235 DOI: 10.1016/j.jprot.2013.05.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/09/2013] [Accepted: 05/13/2013] [Indexed: 01/20/2023]
Abstract
Soybean (Glycine max (L.) Merr. cv Jack) seed development was separated into nine defined stages (S1 to S9). Testa (seed coats) were removed from developing seeds at stages S2, 4, 6, 8, and 9, and subjected to shotgun proteomic profiling. For each stage "total proteins" were isolated from 150 mg dry weight of seed coat using a phenol-based method, then reduced, alkylated, and digested with trypsin. The tryptic peptides were separated using a C18-reversed phase matrix, then analyzed using an LTQ Orbitrap Mass Spectrometer. Spectra were searched against the Phytozome G. max DB using the Sorcerer 2 IDA Sequest-based search algorithm. Identities were verified using Scaffold 3. A total of 306 (S2), 328 (S4), 273 (S6), 193 (S8), and 272 (S9) proteins were identified in three out of three biological replicates, and sorted into 11 functional groups: Primary Metabolism, Secondary Metabolism, Cellular Structure, Stress Responses, Nucleic Acid metabolism, Protein Synthesis, Protein Folding, Protein Targeting, Hormones and Signaling, Seed Storage Proteins, and Proteins of Unknown Function. In selected instances, individual seed coat proteins were quantified by spectral counting. The number of proteins involved in intermediary metabolism, flavonoid biosynthesis, protein folding and degradation are discussed as they relate to seed coat function. BIOLOGICAL SIGNIFICANCE Most previous analyses of seed coats have either targeted individual enzymes or used the results from high-throughput transcript profiling to infer biological function. Because there is seldom a linear correlation between transcript and protein levels, we have undertaken a shotgun proteomics-based description of soybean (G. max (L.) Merr. cv Jack) seed coats, as a function of development, in order to bridge this gap and to establish the baseline for a more comprehensive understanding of seed biology.
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Affiliation(s)
- Ján A Miernyk
- USDA, Agricultural Research Service, Plant Genetics Research Unit, USA.
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13
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Klubicová K, Danchenko M, Skultety L, Berezhna VV, Uvackova L, Rashydov NM, Hajduch M. Soybeans grown in the Chernobyl area produce fertile seeds that have increased heavy metal resistance and modified carbon metabolism. PLoS One 2012; 7:e48169. [PMID: 23110204 PMCID: PMC3482187 DOI: 10.1371/journal.pone.0048169] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 09/21/2012] [Indexed: 11/19/2022] Open
Abstract
Plants grow and reproduce in the radioactive Chernobyl area, however there has been no comprehensive characterization of these activities. Herein we report that life in this radioactive environment has led to alteration of the developing soybean seed proteome in a specific way that resulted in the production of fertile seeds with low levels of oil and β-conglycinin seed storage proteins. Soybean seeds were harvested at four, five, and six weeks after flowering, and at maturity from plants grown in either non-radioactive or radioactive plots in the Chernobyl area. The abundance of 211 proteins was determined. The results confirmed previous data indicating that alterations in the proteome include adaptation to heavy metal stress and mobilization of seed storage proteins. The results also suggest that there have been adjustments to carbon metabolism in the cytoplasm and plastids, increased activity of the tricarboxylic acid cycle, and decreased condensation of malonyl-acyl carrier protein during fatty acid biosynthesis.
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Affiliation(s)
- Katarína Klubicová
- Department of Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Maksym Danchenko
- Department of Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, Kyiv, Ukraine
| | - Ludovit Skultety
- Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
- Center for Molecular Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Valentyna V. Berezhna
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, Kyiv, Ukraine
| | - Lubica Uvackova
- Department of Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Namik M. Rashydov
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, Kyiv, Ukraine
| | - Martin Hajduch
- Department of Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
- Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Nitra, Slovak Republic
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Abstract
A newcomer to the -omics era, proteomics, is a broad instrument-intensive research area that has advanced rapidly since its inception less than 20 years ago. Although the 'wet-bench' aspects of proteomics have undergone a renaissance with the improvement in protein and peptide separation techniques, including various improvements in two-dimensional gel electrophoresis and gel-free or off-gel protein focusing, it has been the seminal advances in MS that have led to the ascension of this field. Recent improvements in sensitivity, mass accuracy and fragmentation have led to achievements previously only dreamed of, including whole-proteome identification, and quantification and extensive mapping of specific PTMs (post-translational modifications). With such capabilities at present, one might conclude that proteomics has already reached its zenith; however, 'capability' indicates that the envisioned goals have not yet been achieved. In the present review we focus on what we perceive as the areas requiring more attention to achieve the improvements in workflow and instrumentation that will bridge the gap between capability and achievement for at least most proteomes and PTMs. Additionally, it is essential that we extend our ability to understand protein structures, interactions and localizations. Towards these ends, we briefly focus on selected methods and research areas where we anticipate the next wave of proteomic advances.
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15
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Seed proteomics. J Proteomics 2011; 74:389-400. [DOI: 10.1016/j.jprot.2010.12.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/08/2010] [Accepted: 12/10/2010] [Indexed: 12/29/2022]
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16
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Klubicová K, Danchenko M, Skultety L, Berezhna VV, Hricová A, Rashydov NM, Hajduch M. Agricultural recovery of a formerly radioactive area: II. Systematic proteomic characterization of flax seed development in the remediated Chernobyl area. J Proteomics 2011; 74:1378-84. [PMID: 21385628 DOI: 10.1016/j.jprot.2011.02.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/21/2011] [Accepted: 02/24/2011] [Indexed: 01/12/2023]
Abstract
Molecular characterization of crop plants grown in remediated, formerly radioactive, areas could establish a framework for future agricultural use of these areas. Recently, we have established a quantitative reference map for mature flax seed proteins (Linum usitatissimum L.) harvested from a remediated plot in Chernobyl town. Herein we describe results from our ongoing studies of this subject, and provide a proteomics-based characterization of developing flax seeds harvested from same field. A quantitative approach, based on 2-dimensional electrophoresis (2-DE) and tandem mass spectrometry, yielded expression profiles for 379 2-DE spots through seed development. Despite the paucity of genomic resources for flax, the identity for 102 proteins was reliably determined. These proteins were sorted into 11 metabolic functional classes. Proteins of unknown function comprise the largest group, and displayed a pattern of decreased abundance throughout seed development. Analysis of the composite expression profiles for metabolic protein classes revealed specific expression patterns during seed development. For example, there was an overall decrease in abundance of the glycolytic enzymes during seed development.
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Affiliation(s)
- Katarína Klubicová
- Department of Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
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17
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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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