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Florez-Rueda AM, Miguel CM, Figueiredo DD. Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1134-1157. [PMID: 38709819 DOI: 10.1111/tpj.16786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies.
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Affiliation(s)
- Ana Marcela Florez-Rueda
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
- University of Potsdam, Karl-Liebknechts-Str. 24-25, Haus 26, 14476, Potsdam, Germany
| | - Célia M Miguel
- Faculty of Sciences, Biosystems and Integrative Sciences Institute (BioISI), University of Lisbon, Lisboa, Portugal
| | - Duarte D Figueiredo
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
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2
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Rahaman H, Herojit K, Singh LR, Haobam R, Fisher AB. Structural and Functional Diversity of the Peroxiredoxin 6 Enzyme Family. Antioxid Redox Signal 2024; 40:759-775. [PMID: 37463006 DOI: 10.1089/ars.2023.0287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Significance: Peroxiredoxins (Prdxs) with a single peroxidative cysteine (CP) in a conserved motif PXXX(T/S)XXCP within its thioredoxin fold, have been classified as the peroxiredoxin 6 (Prdx6 ) family. All Prdxs can reduce H2O2 and short chain hydroperoxides while Prdx6 in addition, can reduce phospholipid hydroperoxides (PLOOH) due to its ability to interact with peroxidized phospholipid substrate. The single CP of Prdx6 uses various external electron donors including glutathione thioredoxin, and ascorbic acid for resolution of its peroxidized state and, therefore, its peroxidase activity. Prdx6 proteins also exhibit Ca2+-independent phospholipase A2 (PLA2), lysophosphatidylcholine acyltransferase (LPCAT), and chaperone activities that depend on cellular localization and the oxidation and oligomerisation states of the protein. Thus, Prdx6 is a "moonlighting" enzyme. Recent Advance: Physiologically, Prdx6s have been reported to play an important role in protection against oxidative stress, repair of peroxidized cell membranes, mammalian lung surfactant turnover, activation of some NADPH oxidases, the regulation of seed germination in plants, as an indicator of cellular levels of reactive O2 species through Nrf-Klf9 activation, and possibly in male fertility, regulation of cell death through ferroptosis, cancer metastasis, and oxidative stress-related signalling pathways. Critical Issues: This review outlines Prdx6 enzyme unique structural features and explores its wide range of physiological functions. Yet, existing structural data falls short of fully revealing all of human Prdx6 multifunctional roles. Further endeavour is required to bridge this gap in its understanding. Although there are wide variations in both the structure and function of Prdx6 family members in various organisms, all Prdx6 proteins show the unique a long C-terminal extension that is also seen in Prdx1, but not in other Prdxs. Future Directions: As research data continues to accumulate, the potential for detailed insights into the role of C-terminal of Prdx6 in its oligomerisation and activities. There is a need for thorough exploration of structural characteristics of the various biological functions. Additionally, uncovering the interacting partners of Prdx6 and understanding its involvement in signalling pathways will significantly contribute to a more profound comprehension of its role.
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Affiliation(s)
- Hamidur Rahaman
- Department of Biotechnology, Manipur University, Imphal, India
| | - Khundrakpam Herojit
- Department of Biotechnology, Manipur University, Imphal, India
- Department of Biotechnology, Mangolnganbi College, Ningthoukhong, India
| | | | - Reena Haobam
- Department of Biotechnology, Manipur University, Imphal, India
| | - Aron B Fisher
- Institute for Environmental Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Montez M, Majchrowska M, Krzyszton M, Bokota G, Sacharowski S, Wrona M, Yatusevich R, Massana F, Plewczynski D, Swiezewski S. Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt. EMBO J 2023; 42:e112443. [PMID: 36705062 PMCID: PMC9975946 DOI: 10.15252/embj.2022112443] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 01/28/2023] Open
Abstract
Eukaryotic genomes are pervasively transcribed by RNA polymerase II. Yet, the molecular and biological implications of such a phenomenon are still largely puzzling. Here, we describe noncoding RNA transcription upstream of the Arabidopsis thaliana DOG1 gene, which governs salt stress responses and is a key regulator of seed dormancy. We find that expression of the DOG1 gene is induced by salt stress, thereby causing a delay in seed germination. We uncover extensive transcriptional activity on the promoter of the DOG1 gene, which produces a variety of lncRNAs. These lncRNAs, named PUPPIES, are co-directionally transcribed and extend into the DOG1 coding region. We show that PUPPIES RNAs respond to salt stress and boost DOG1 expression, resulting in delayed germination. This positive role of pervasive PUPPIES transcription on DOG1 gene expression is associated with augmented pausing of RNA polymerase II, slower transcription and higher transcriptional burst size. These findings highlight the positive role of upstream co-directional transcription in controlling transcriptional dynamics of downstream genes.
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Affiliation(s)
- Miguel Montez
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Maria Majchrowska
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Grzegorz Bokota
- Laboratory of Functional and Structural Genomics, Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Sebastian Sacharowski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Magdalena Wrona
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Ruslan Yatusevich
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Ferran Massana
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Dariusz Plewczynski
- Laboratory of Functional and Structural Genomics, Centre of New TechnologiesUniversity of WarsawWarsawPoland
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information ScienceWarsaw University of TechnologyWarsawPoland
| | - Szymon Swiezewski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
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Jiang H, Gao W, Jiang BL, Liu X, Jiang YT, Zhang LT, Zhang Y, Yan SN, Cao JJ, Lu J, Ma CX, Chang C, Zhang HP. Identification and validation of coding and non-coding RNAs involved in high-temperature-mediated seed dormancy in common wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1107277. [PMID: 36818881 PMCID: PMC9929302 DOI: 10.3389/fpls.2023.1107277] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Seed dormancy (SD) significantly decreases under high temperature (HT) environment during seed maturation, resulting in pre-harvest sprouting (PHS) damage under prolonged rainfall and wet weather during wheat harvest. However, the molecular mechanism underlying HT-mediated SD remains elusiveSeed dormancy (SD) significantly decreases under high temperature (HT) environment during seed maturation, resulting in pre-harvest sprouting (PHS) damage under prolonged rainfall and wet weather during wheat harvest. However, the molecular mechanism underlying HT-mediated SD remains elusive. METHODS Here, the wheat landrace 'Waitoubai' with strong SD and PHS resistance was treated with HT from 21 to 35 days post anthesis (DPA). Then, the seeds under HT and normal temperature (NT) environments were collected at 21 DPA, 28 DPA, and 35 DPA and subjected to whole-transcriptome sequencing. RESULTS The phenotypic data showed that the seed germination percentage significantly increased, whereas SD decreased after HT treatment compared with NT, consistent with the results of previous studies. In total, 5128 mRNAs, 136 microRNAs (miRNAs), 273 long non-coding RNAs (lncRNAs), and 21 circularRNAs were found to be responsive to HT, and some of them were further verified through qRT-PCR. In particular, the known gibberellin (GA) biosynthesis gene TaGA20ox1 (TraesCS3D02G393900) was proved to be involved in HT-mediated dormancy by using the EMS-mutagenized wheat cultivar Jimai 22. Similarly, a novel gene TaCDPK21 (TraesCS7A02G267000) involved in the calcium signaling pathway was validated to be associated with HT-mediated dormancy by using the EMS mutant. Moreover, TaCDPK21 overexpression in Arabidopsis and functional complementarity tests supported the negative role of TaCDPK21 in SD. We also constructed a co-expression regulatory network based on differentially expressed mRNAs, miRNAs, and lncRNAs and found that a novel miR27319 was located at a key node of this regulatory network. Subsequently, using Arabidopsis and rice lines overexpressing miR27319 precursor or lacking miR27319 expression, we validated the positive role of miR27319 in SD and further preliminarily dissected the molecular mechanism of miR27319 underlying SD regulation through phytohormone abscisic acid and GA biosynthesis, catabolism, and signaling pathways. DISCUSSION These findings not only broaden our understanding of the complex regulatory network of HT-mediated dormancy but also provide new gene resources for improving wheat PHS resistance to minimize PHS damage by using the molecular pyramiding approach.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Cheng Chang
- *Correspondence: Cheng Chang, ; Hai-ping Zhang,
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Combined Transcriptomics and Metabolomics Analysis Reveals the Molecular Mechanism of Salt Tolerance of Huayouza 62, an Elite Cultivar in Rapeseed ( Brassica napus L.). Int J Mol Sci 2022; 23:ijms23031279. [PMID: 35163202 PMCID: PMC8836002 DOI: 10.3390/ijms23031279] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/23/2023] Open
Abstract
Soil salinity is one of the most significant abiotic stresses affecting crop yield around the world. To explore the molecular mechanism of salt tolerance in rapeseed (Brassica napus L.), the transcriptome analysis and metabolomics analysis were used to dissect the differentially expressed genes and metabolites in two rapeseed varieties with significant differences in salt tolerance; one is an elite rapeseed cultivar, Huayouza 62. A total of 103 key differentially expressed metabolites (DEMs) and 53 key differentials expressed genes (DEGs) that might be related to salt stress were identified through metabolomics and transcriptomics analysis. GO and KEGG analysis revealed that the DEGs were mainly involved in ion transport, reactive oxygen scavenging, osmotic regulation substance synthesis, and macromolecular protein synthesis. The DEMs were involved in TCA cycle, proline metabolism, inositol metabolism, carbohydrate metabolic processes, and oxidation-reduction processes. In addition, overexpression of BnLTP3, which was one of the key DEGs, could increase tolerance to salt stress in Arabidopsis plants. This study reveals that the regulation mechanism of salt tolerance in rapeseed at the transcriptome and metabolism level and provides abundant data for further in-depth identification of essential salt tolerance genes.
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El-Badri AMA, Batool M, Mohamed IAA, Khatab A, Sherif A, Wang Z, Salah A, Nishawy E, Ayaad M, Kuai J, Wang B, Zhou G. Modulation of salinity impact on early seedling stage via nano-priming application of zinc oxide on rapeseed (Brassica napus L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:376-392. [PMID: 34153882 DOI: 10.1016/j.plaphy.2021.05.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 05/07/2021] [Indexed: 06/13/2023]
Abstract
Salinity stress negatively affects the plant's developmental stages through micronutrient imbalance. As an essential micronutrient, ZnO can substitute Na+ absorption under saline conditions. Therefore, nanoparticles as technological innovation, improve the plant growth efficiency under biotic and abiotic stresses. Nano-priming has become widely applicable in agricultural research during the last decade. The current study was conducted to highlight the impact of ZnONPs priming on seedling biological processes under 150 mM of NaCl using two rapeseed cultivars during the early seedling stage. All concentrations of ZnONPs increased the germination parameters i.e., FG%, GR, VI (I), and VI (II). Meanwhile, the high concentration (ZnO 100%) showed the highest increase in shoot length (9.60% and 25.63%), root length (41.64% and 48.17%) for Yang You 9 and Zhong Shuang 11 over hydro-priming, respectively, as well as biomass. Additionally, nano-priming improved the proline, soluble sugar, and soluble protein contents as a result of osmotic protection modulation. Moreover, nano-priming alleviated ROS and biosynthesis pigments through the reduction of accumulated (H2O2) and (O2-), and chlorophyll degradation, respectively, also enhanced antioxidant adjustment via improving the plant defense system. Nano-priming substituted the Na+ by Zn2+, K+, and Ca2+, and compensated the deficit of micronutrients, thus reduced the Na+ toxicity in the cell cytosol. To track the effects of priming during seed imbibition, it noticed that ZnO 100% and ZnO 100%+S increased the Linoleic and Linolenic acids among the studied fatty acids composition by 12.02%, 7.59%, 13.27%, and 10.38% (Yang You 9), 7.42%, 2.77%, 2.93%, and 1.49% (Zhong Shuang 11) over the hydro-priming, respectively. Moreover, the gene expression patterns of BnCAM and BnPER reflected the enhancement of germination levels, notably under the influence of ZnO 100% priming, which increased the level of BnCAM by 70.42% and 111.9% in Yang You 9 and Zhong Shuang 11, respectively. Consequently, ZnO nano-priming enhanced the seedling development through the biosynthesis of pigments, osmotic protection, reduction of ROS accumulation, adjustment of antioxidant enzymes, and improvement of the nutrient absorption, thus enhancing the economic yield under saline conditions.
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Affiliation(s)
- Ali M A El-Badri
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China; Field Crops Research Institute, Agricultural Research Center, Egypt
| | - Maria Batool
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ibrahim A A Mohamed
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China; Botany Department, Faculty of Agriculture, Fayoum University, Fayoum, 63514, Egypt
| | - Ahmed Khatab
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China; Field Crops Research Institute, Agricultural Research Center, Egypt
| | - Ahmed Sherif
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China; Field Crops Research Institute, Agricultural Research Center, Egypt
| | - Zongkai Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Akram Salah
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Elsayed Nishawy
- Desert Research Center, Genetics Resource Department, Egyptian Deserts Gene Bank, Cairo, 11735, Egypt
| | - Mohammed Ayaad
- Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Abo Zaabal, 13795, Cairo, Egypt
| | - Jie Kuai
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guangsheng Zhou
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Anschau V, Ferrer-Sueta G, Aleixo-Silva RL, Bannitz Fernandes R, Tairum CA, Tonoli CCC, Murakami MT, de Oliveira MA, Netto LES. Reduction of sulfenic acids by ascorbate in proteins, connecting thiol-dependent to alternative redox pathways. Free Radic Biol Med 2020; 156:207-216. [PMID: 32615144 DOI: 10.1016/j.freeradbiomed.2020.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/25/2020] [Accepted: 06/06/2020] [Indexed: 02/06/2023]
Abstract
Sulfenic acids are the primary product of thiol oxidation by hydrogen peroxide and other oxidants. Several aspects of sulfenic acid formation through thiol oxidation were established recently. In contrast, the reduction of sulfenic acids is still scarcely investigated. Here, we characterized the kinetics of the reduction of sulfenic acids by ascorbate in several proteins. Initially, we described the crystal structure of our model protein (Tsa2-C170S). There are other Tsa2 structures in distinct redox states in public databases and all of them are decamers, with the peroxidatic cysteine very accessible to reductants, convenient features to investigate kinetics. We determined that the reaction between Tsa2-C170S-Cys-SOH and ascorbate proceeded with a rate constant of 1.40 ± 0.08 × 103 M-1 s-1 through a competition assay developed here, employing 2,6-dichlorophenol-indophenol (DCPIP). A series of peroxiredoxin enzymes (Prx6 sub family) were also analyzed by this competition assay and we observed that the reduction of sulfenic acids by ascorbate was in the 0.4-2.2 × 103 M-1 s-1 range. We also evaluated the same reaction on glyceraldehyde 3-phosphate dehydrogenase and papain, as the reduction of their sulfenic acids by ascorbate were reported previously. Once again, the rate constants are in the 0.4-2.2 × 103 M-1 s-1 range. We also analyzed the reduction of Tsa2-C170S-SOH by ascorbate by a second, independent method, following hydrogen peroxide reduction through a specific electrode (ISO-HPO-2, World Precision Instruments) and employing a bi-substrate, steady state approach. The kcat/KMAsc was 7.4 ± 0.07 × 103 M-1 s-1, which was in the same order of magnitude as the value obtained by the DCPIP competition assay. In conclusion, our data indicates that reduction of sulfenic acid in various proteins proceed at moderate rate and probably this reaction is more relevant in biological systems where ascorbate concentrations are high.
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Affiliation(s)
- Valesca Anschau
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de La República, Iguá 4225, Montevideo, 11400, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Universidad de La República, Montevideo, Uruguay
| | - Rogerio Luis Aleixo-Silva
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Renata Bannitz Fernandes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Carlos A Tairum
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biorenewables National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Mario Tyago Murakami
- Brazilian Biorenewables National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | | | - Luis Eduardo Soares Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil.
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Kijak H, Ratajczak E. What Do We Know About the Genetic Basis of Seed Desiccation Tolerance and Longevity? Int J Mol Sci 2020; 21:E3612. [PMID: 32443842 PMCID: PMC7279459 DOI: 10.3390/ijms21103612] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 01/02/2023] Open
Abstract
Long-term seed storage is important for protecting both economic interests and biodiversity. The extraordinary properties of seeds allow us to store them in the right conditions for years. However, not all types of seeds are resilient, and some do not tolerate extreme desiccation or low temperature. Seeds can be divided into three categories: (1) orthodox seeds, which tolerate water losses of up to 7% of their water content and can be stored at low temperature; (2) recalcitrant seeds, which require a humidity of 27%; and (3) intermediate seeds, which lose their viability relatively quickly compared to orthodox seeds. In this article, we discuss the genetic bases for desiccation tolerance and longevity in seeds and the differences in gene expression profiles between the mentioned types of seeds.
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Affiliation(s)
- Hanna Kijak
- Institute of Dendrology, Polish Academy of Sciences, 62-035 Kórnik, Poland;
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Chen H, Ruan J, Chu P, Fu W, Liang Z, Li Y, Tong J, Xiao L, Liu J, Li C, Huang S. AtPER1 enhances primary seed dormancy and reduces seed germination by suppressing the ABA catabolism and GA biosynthesis in Arabidopsis seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:310-323. [PMID: 31536657 DOI: 10.1111/tpj.14542] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 09/02/2019] [Accepted: 09/09/2019] [Indexed: 05/07/2023]
Abstract
Seed is vital to the conservation of germplasm and plant biodiversity. Seed dormancy is an adaptive trait in numerous seed-plant species, enabling plants to survive under stressful conditions. Seed dormancy is mainly controlled by abscisic acid (ABA) and gibberellin (GA) and can be classified as primary and secondary seed dormancy. The primary seed dormancy is induced by maternal ABA. Here we found that AtPER1, a seed-specific peroxiredoxin, is involved in enhancing primary seed dormancy. Two loss-of-function atper1 mutants, atper1-1 and atper1-2, displayed suppressed primary seed dormancy accompanied with reduced ABA and increased GA contents in seeds. Furthermore, atper1 mutant seeds were insensitive to abiotic stresses during seed germination. The expression of several ABA catabolism genes (CYP707A1, CYP707A2, and CYP707A3) and GA biosynthesis genes (GA20ox1, GA20ox3, and KAO3) in atper1 mutant seeds was increased compared to wild-type seeds. The suppressed primary seed dormancy of atper1-1 was completely reduced by deletion of CYP707A genes. Furthermore, loss-of-function of AtPER1 cannot enhance the seed germination ratio of aba2-1 or ga1-t, suggesting that AtPER1-enhanced primary seed dormancy is dependent on ABA and GA. Additionally, the level of reactive oxygen species (ROS) in atper1 mutant seeds was significantly higher than that in wild-type seeds. Taken together, our results demonstrate that AtPER1 eliminates ROS to suppress ABA catabolism and GA biosynthesis, and thus improves the primary seed dormancy and make the seeds less sensitive to adverse environmental conditions.
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Affiliation(s)
- Huhui Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun YAT-SEN University, 510275, Guangzhou, China
| | - Jiuxiao Ruan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun YAT-SEN University, 510275, Guangzhou, China
| | - Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Wei Fu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun YAT-SEN University, 510275, Guangzhou, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun YAT-SEN University, 510275, Guangzhou, China
| | - Yin Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun YAT-SEN University, 510275, Guangzhou, China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, 410128, Changsha, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, 410128, Changsha, China
| | - Jun Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun YAT-SEN University, 510275, Guangzhou, China
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun YAT-SEN University, 510275, Guangzhou, China
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Non-Mammalian Prdx6 Enzymes (Proteins with 1-Cys Prdx Mechanism) Display PLA₂ Activity Similar to the Human Orthologue. Antioxidants (Basel) 2019; 8:antiox8030052. [PMID: 30832204 PMCID: PMC6466579 DOI: 10.3390/antiox8030052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 12/31/2022] Open
Abstract
Mammalian peroxiredoxin class 6 (Prdx6) are bifunctional enzymes. Non-mammalian Prdx6 enzymes display Cys-based peroxidase activity, but to date their putative phospholipase A2 (PLA2 activities) has not been experimentally investigated. Initially, we observed that five non-mammalian Prdx6 enzymes (enzymes from Arabidopsis thaliana (AtPER1), Triticum aestivum (TaPER1), Pseudomonas aeruginosa (PaLsfA) and Aspergillus fumigatus (AfPrx1 and AfPrxC)) present features compatible with PLA2 activities in mammalian Prdx6 by amino acid sequences alignment and tertiary structure modeling. Employing unilamellar liposomes with tracer amounts of [3H]-1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and thin layer chromatography, all the tested non-mammalian Prdx6 enzymes displayed PLA2 activities, with values ranging from 3.4 to 6.1 nmol/min/mg protein. It was previously shown that Thr177 phosphorylation of human Prdx6 increases its PLA2 activity, especially at neutral pH. Therefore, we investigated if human Erk2 kinase could also phosphorylate homologous Thr residues in non-mammalian Prdx6 proteins. We observed phosphorylation of the conserved Thr in three out of the five non-mammalian Prdx enzymes by mass spectrometry. In the case of the mitochondrial Prdx6 from A. fumigatus (AfPrxC), we also observed phosphorylation by western blot, and as a consequence, the PLA2 activity was increased in acidic and neutral conditions by the human Erk2 kinase treatment. The possible physiological meanings of these PLA2 activities described open new fields for future research.
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Liu D, Han C, Deng X, Liu Y, Liu N, Yan Y. Integrated physiological and proteomic analysis of embryo and endosperm reveals central salt stress response proteins during seed germination of winter wheat cultivar Zhengmai 366. BMC PLANT BIOLOGY 2019; 19:29. [PMID: 30658564 PMCID: PMC6339335 DOI: 10.1186/s12870-019-1643-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/09/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Salinity is a major abiotic stressor that affects seed germination, plant growth, and crop production. Seed germination represents the beginning of plant growth and is closely linked with subsequent crop development and ultimate yield formation. This study attempted to extend findings regarding the potential proteomic dynamics during wheat seed germination under salt stress and to explore the mechanism of crop salt response. RESULTS Salt stress significantly affected seed physiological activities during the germination process, resulting in significant decreases in phytohormone and α-amylase activity and significant increases in soluble sugar, starch, and ADP glucose pyrophosphorylase activity. A comparative proteomics approach was applied to analyze the dynamic proteome changes of embryo and endosperm during seed germination in Chinese winter wheat cultivar Zhengmai 366 under salt stress. Two-dimensional electrophoresis identified 92 and 61 differentially accumulated proteins (DAPs) in response to salt stress in embryo and endosperm, respectively. Both organs contained a high proportion of DAPs involved in stress defense, energy metabolism, and protein/amino acid metabolism. The endosperm had more DAPs related to storage proteins and starch metabolism than the embryo, and 2% of DAPs participating in lipid and sterol metabolism were specifically detected in the embryo. CONCLUSIONS Seed physiological activities were significantly affected during the germination process when subjected to salt stress. The DAPs involved in stress defense and energy metabolism were upregulated whereas those related to reserve substance degradation and protein/amino acid metabolism were significantly downregulated, leading to delayed seed germination under salt stress. Our proteomic results revealed synergistic regulation of the response to salt stress during seed germination.
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Affiliation(s)
- Dongmiao Liu
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
| | - Caixia Han
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
| | - Xiong Deng
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
| | - Yue Liu
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
| | - Nannan Liu
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
| | - Yueming Yan
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, Beijing, 100048 China
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, Jingzhou, 434025 China
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Misra A, Khan K, Niranjan A, Kumar V, Sane VA. Heterologous expression of two GPATs from Jatropha curcas alters seed oil levels in transgenic Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:79-88. [PMID: 28818386 DOI: 10.1016/j.plantsci.2017.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Oils and fats are stored in endosperm during seed development in the form of triacylglycerols. Three acyltransferases: glycerol-3-phosphate acyltransferase (GPAT), lysophosphatidyl acyltransferase (LPAT) and diacylglycerol acyltransferase (DGAT) are involved in the storage lipid biosynthesis and catalyze the stepwise acylation of glycerol backbone. In this study two members of GPAT gene family (JcGPAT1 and JcGPAT2) from Jatropha seeds were identified and characterized. Sequence analysis suggested that JcGPAT1 and JcGPAT2 are homologous to Arabidopsis acyltransferase-1 (ATS1) and AtGPAT9 respectively. The sub-cellular localization studies of these two GPATs showed that JcGPAT1 localizes into plastid whereas JcGPAT2 localizes in to endoplasmic reticulum. JcGPAT1 and JcGPAT2 expressed throughout the seed development with higher expression in fully matured seed compared to immature seed. The transcript levels of JcGPAT2 were higher in comparison to JcGPAT1 in different developmental stages of seed. Over-expression of JcGPAT1 and JcGPAT2 under constitutive and seed specific promoters in Arabidopsis thaliana increased total oil content. Transgenic seeds of JcGPAT2-OE lines accumulated 43-60% more oil than control seeds whereas seeds of Arabidopsis lines over-expressing plastidial GPAT lead to only 13-20% increase in oil content. Functional characterization of GPAT homologues of Jatropha in Arabidopsis suggested that these are involved in oil biosynthesis but might have specific roles in Jatropha.
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Affiliation(s)
- Aparna Misra
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow-226001, India
| | - Kasim Khan
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow-226001, India
| | - Abhishek Niranjan
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow-226001, India
| | - Vinod Kumar
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow-226001, India
| | - Vidhu A Sane
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow-226001, India.
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Hossain MS, ElSayed AI, Moore M, Dietz KJ. Redox and Reactive Oxygen Species Network in Acclimation for Salinity Tolerance in Sugar Beet. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1283-1298. [PMID: 28338762 PMCID: PMC5441856 DOI: 10.1093/jxb/erx019] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fine-tuned and coordinated regulation of transport, metabolism and redox homeostasis allows plants to acclimate to osmotic and ionic stress caused by high salinity. Sugar beet is a highly salt tolerant crop plant and is therefore an interesting model to study sodium chloride (NaCl) acclimation in crops. Sugar beet plants were subjected to a final level of 300 mM NaCl for up to 14 d in hydroponics. Plants acclimated to NaCl stress by maintaining its growth rate and adjusting its cellular redox and reactive oxygen species (ROS) network. In order to understand the unusual suppression of ROS accumulation under severe salinity, the regulation of elements of the redox and ROS network was investigated at the transcript level. First, the gene families of superoxide dismutase (SOD), peroxiredoxins (Prx), alternative oxidase (AOX), plastid terminal oxidase (PTOX) and NADPH oxidase (RBOH) were identified in the sugar beet genome. Salinity induced the accumulation of Cu-Zn-SOD, Mn-SOD, Fe-SOD3, all AOX isoforms, 2-Cys-PrxB, PrxQ, and PrxIIF. In contrast, Fe-SOD1, 1-Cys-Prx, PrxIIB and PrxIIE levels decreased in response to salinity. Most importantly, RBOH transcripts of all isoforms decreased. This pattern offers a straightforward explanation for the low ROS levels under salinity. Promoters of stress responsive antioxidant genes were analyzed in silico for the enrichment of cis-elements, in order to gain insights into gene regulation. The results indicate that special cis-elements in the promoters of the antioxidant genes in sugar beet participate in adjusting the redox and ROS network and are fundamental to high salinity tolerance of sugar beet.
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Affiliation(s)
- M Sazzad Hossain
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, D-33501 Bielefeld, Germany
| | - Abdelaleim Ismail ElSayed
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, D-33501 Bielefeld, Germany
- Biochemistry Department, Faculty of Agriculture, Zagazig University, 44519 Zagazig, Egypt
| | - Marten Moore
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, D-33501 Bielefeld, Germany
| | - Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, D-33501 Bielefeld, Germany
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Chen HH, Chu P, Zhou YL, Ding Y, Li Y, Liu J, Jiang LW, Huang SZ. Ectopic expression of NnPER1, a Nelumbo nucifera 1-cysteine peroxiredoxin antioxidant, enhances seed longevity and stress tolerance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:608-619. [PMID: 27464651 DOI: 10.1111/tpj.13286] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 07/12/2016] [Accepted: 07/19/2016] [Indexed: 05/07/2023]
Abstract
Seed longevity, the maintenance of viability during storage, is a major factor for conservation of genetic resources and biodiversity. Seed longevity is an important trait of agriculture crop and is impaired by reactive oxygen species (ROS) during seed desiccation, storage and germination (C. R. Biol., 331, 2008 and 796). Seeds possess a wide range of systems (protection, detoxification, repair) allowing them to survive during storage and to preserve a high germination ability. In many plants, 1-cys peroxiredoxin (1-Cys Prx, also named PER1) is a seed-specific antioxidant which eliminates ROS with cysteine residues. Here we identified and characterized a seed-specific PER1 protein from seeds of sacred lotus (Nelumbo nucifera Gaertn.). Purified NnPER1 protein protects DNA against the cleavage by ROS in the mixed-function oxidation system. The transcription and protein accumulation of NnPER1 increased during seed desiccation and imbibition and under abiotic stress treatment. Ectopic expression of NnPER1 in Arabidopsis enhanced the seed germination ability after controlled deterioration treatment (CDT), indicating that NnPER1 improves seed longevity of transgenic plants. Consistent with the function of NnPER1 on detoxifying ROS, we found that the level of ROS release and lipid peroxidation was strikingly lower in transgenic seeds compared to wild-type with or without CDT. Furthermore, transgenic Arabidopsis seeds ectopic-expressing NnPER1 displayed enhanced tolerance to high temperature and abscisic acid (ABA), indicating that NnPER1 may participate in the thermotolerance and ABA signaling pathway.
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Affiliation(s)
- Hu-Hui Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yu-Liang Zhou
- Guangdong Provincial Key Lab of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yu Ding
- Department of Food Science and Engineering, Jinan University, Guangzhou, 510632, China
- School of Life Sciences, Center for Cell and Developmental Biology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yin Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jun Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Li-Wen Jiang
- School of Life Sciences, Center for Cell and Developmental Biology, The Chinese University of Hong Kong, Hong Kong, China
| | - Shang-Zhi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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15
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Zhou L, Luo L, Zuo JF, Yang L, Zhang L, Guang X, Niu Y, Jian J, Geng QC, Liang L, Song Q, Dunwell JM, Wu Z, Wen J, Liu YQ, Zhang YM. Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean. THE PLANT GENOME 2016; 9. [PMID: 27898807 DOI: 10.3835/plantgenome2015.09.0090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 01/23/2016] [Indexed: 05/08/2023]
Abstract
Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 trait-associated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene (). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.
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16
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Kołodziejczyk I, Dzitko K, Szewczyk R, Posmyk MM. Exogenous melatonin improves corn (Zea mays L.) embryo proteome in seeds subjected to chilling stress. JOURNAL OF PLANT PHYSIOLOGY 2016; 193:47-56. [PMID: 26945210 DOI: 10.1016/j.jplph.2016.01.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 05/19/2023]
Abstract
Melatonin (MEL; N-acetyl-5-methoxytryptamine) plays an important role in plant stress defense. Various plant species rich in this indoleamine have shown a higher capacity for stress tolerance. Moreover, it has great potential for plant biostimulation, is biodegradable and non-toxic for the environment. All this indicates that our concept of seed enrichment with exogenous MEL is justified. This work concerns the effects of corn (Zea mays L.) seed pre-sowing treatments supplemented with MEL. Non-treated seeds (nt), and those hydroprimed with water (H) or with MEL solutions 50 and 500 μM (HMel50, HMel500) were compared. Positive effects of seed priming are particularly apparent during germination under suboptimal conditions. The impact of MEL applied by priming on seed protein profiles during imbibition/germination at low temperature has not been investigated to date. In order to identify changes in the corn seed proteome after applying hydropriming techniques, purified protein extracts of chilling stressed seed embryos (14 days, 5°C) were separated by two-dimensional electrophoresis. Then proteome maps were graphically and statistically compared and selected protein spots were qualitatively analyzed using mass spectrometry techniques and identified. This study aimed to analyze the priming-induced changes in maize embryo proteome and at identifying priming-associated and MEL-associated proteins in maize seeds subjected to chilling. We attempt to explain how MEL expands plant capacity for stress tolerance.
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Affiliation(s)
- Izabela Kołodziejczyk
- Department of Ecophysiology and Plant Development, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Str., 90-237 Lodz, Poland.
| | - Katarzyna Dzitko
- Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Str., 90-237 Lodz, Poland.
| | - Rafał Szewczyk
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Str., 90-237 Lodz, Poland.
| | - Małgorzata M Posmyk
- Department of Ecophysiology and Plant Development, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Str., 90-237 Lodz, Poland.
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17
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Ozyigit II, Filiz E, Vatansever R, Kurtoglu KY, Koc I, Öztürk MX, Anjum NA. Identification and Comparative Analysis of H2O2-Scavenging Enzymes (Ascorbate Peroxidase and Glutathione Peroxidase) in Selected Plants Employing Bioinformatics Approaches. FRONTIERS IN PLANT SCIENCE 2016; 7:301. [PMID: 27047498 PMCID: PMC4802093 DOI: 10.3389/fpls.2016.00301] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/25/2016] [Indexed: 05/08/2023]
Abstract
Among major reactive oxygen species (ROS), hydrogen peroxide (H2O2) exhibits dual roles in plant metabolism. Low levels of H2O2 modulate many biological/physiological processes in plants; whereas, its high level can cause damage to cell structures, having severe consequences. Thus, steady-state level of cellular H2O2 must be tightly regulated. Glutathione peroxidases (GPX) and ascorbate peroxidase (APX) are two major ROS-scavenging enzymes which catalyze the reduction of H2O2 in order to prevent potential H2O2-derived cellular damage. Employing bioinformatics approaches, this study presents a comparative evaluation of both GPX and APX in 18 different plant species, and provides valuable insights into the nature and complex regulation of these enzymes. Herein, (a) potential GPX and APX genes/proteins from 18 different plant species were identified, (b) their exon/intron organization were analyzed, (c) detailed information about their physicochemical properties were provided, (d) conserved motif signatures of GPX and APX were identified, (e) their phylogenetic trees and 3D models were constructed, (f) protein-protein interaction networks were generated, and finally (g) GPX and APX gene expression profiles were analyzed. Study outcomes enlightened GPX and APX as major H2O2-scavenging enzymes at their structural and functional levels, which could be used in future studies in the current direction.
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Affiliation(s)
- Ibrahim I. Ozyigit
- Department of Biology, Faculty of Science and Arts, Marmara UniversityIstanbul, Turkey
| | - Ertugrul Filiz
- Department of Crop and Animal Production, Cilimli Vocational School, Düzce UniversityDüzce, Turkey
| | - Recep Vatansever
- Department of Biology, Faculty of Science and Arts, Marmara UniversityIstanbul, Turkey
| | - Kuaybe Y. Kurtoglu
- Department of Biology, Faculty of Science and Arts, Marmara UniversityIstanbul, Turkey
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul Medeniyet UniversityIstanbul, Turkey
| | - Ibrahim Koc
- Department of Molecular Biology and Genetics, Faculty of Science, Gebze Technical UniversityKocaeli, Turkey
| | - Münir X. Öztürk
- Botany Department/Center for Environmental Studies, Ege UniversityIzmir, Turkey
- Faculty of Forestry, Universiti Putra MalaysiaSelangor, Malaysia
| | - Naser A. Anjum
- Centre for Environmental and Marine Studies and Department of Chemistry, University of AveiroAveiro, Portugal
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18
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Zhang H, He D, Yu J, Li M, Damaris RN, Gupta R, Kim ST, Yang P. Analysis of dynamic protein carbonylation in rice embryo during germination through AP-SWATH. Proteomics 2016; 16:989-1000. [DOI: 10.1002/pmic.201500248] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 12/17/2015] [Accepted: 01/20/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Hui Zhang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
| | - Jianlan Yu
- Asia Pacific Application Support Center; AB Sciex; Shanghai P. R. China
| | - Ming Li
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
| | - Rebecca Njeri Damaris
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
| | - Ravi Gupta
- Department of Plant Bioscience; College of Natural Resources & Life Science; Pusan National University; Miryang Korea
| | - Sun Tae Kim
- Department of Plant Bioscience; College of Natural Resources & Life Science; Pusan National University; Miryang Korea
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
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19
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Gu A, Hao P, Lv D, Zhen S, Bian Y, Ma C, Xu Y, Zhang W, Yan Y. Integrated Proteome Analysis of the Wheat Embryo and Endosperm Reveals Central Metabolic Changes Involved in the Water Deficit Response during Grain Development. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:8478-87. [PMID: 26332669 DOI: 10.1021/acs.jafc.5b00575] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The embryo and endosperm of wheat have different physiological functions and large differences in protein level. In this study, we performed the first integrated proteome analysis of wheat embryo and endosperm in response to the water deficit during grain development. In total, 155 and 130 differentially expressed protein (DEP) spots in the embryo and endosperm, respectively, were identified by nonlinear two-dimensional electrophoresis and tandem mass spectrometry. These DEPs in the embryo were mainly involved in stress/defense responses such as heat shock-related proteins (HSP) and peroxidase, whereas those in endosperm were mainly related to starch and storage protein synthesis such as α-amylase inhibitor and the globulin-1 S allele. In particular, some storage proteins such as avenin-like proteins and high-molecular weight glutenin subunit Dy12 displayed higher expression levels in the mature endosperm under a water deficit, which might contribute to the improvement in the quality of breadmaking.
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Affiliation(s)
- Aiqin Gu
- College of Life Sciences, Capital Normal University , Beijing 100048, China
| | - Pengchao Hao
- College of Life Sciences, Capital Normal University , Beijing 100048, China
| | - Dongwen Lv
- College of Life Sciences, Capital Normal University , Beijing 100048, China
| | - Shoumin Zhen
- College of Life Sciences, Capital Normal University , Beijing 100048, China
| | - Yanwei Bian
- College of Life Sciences, Capital Normal University , Beijing 100048, China
| | - Chaoying Ma
- College of Life Sciences, Capital Normal University , Beijing 100048, China
| | - Yanhao Xu
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University , 434025 Jingzhou, China
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University , 434025 Jingzhou, China
| | - Yueming Yan
- College of Life Sciences, Capital Normal University , Beijing 100048, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University , 434025 Jingzhou, China
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20
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Proteome evolution of wheat (Triticum aestivum L.) aleurone layer at fifteen stages of grain development. J Proteomics 2015; 123:29-41. [DOI: 10.1016/j.jprot.2015.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/11/2015] [Accepted: 03/09/2015] [Indexed: 12/19/2022]
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21
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A systematic proteomic analysis of NaCl-stressed germinating maize seeds. Mol Biol Rep 2014; 41:3431-43. [PMID: 24700167 DOI: 10.1007/s11033-014-3205-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 01/27/2014] [Indexed: 10/25/2022]
Abstract
Salt (NaCl) is a common physiological stressor of plants. To better understand how germinating seeds respond to salt stress, we examined the changes that occurred in the proteome of maize seeds during NaCl-treated germination. Phenotypically, salt concentrations less than 0.2 M appear to delay germination, while higher concentrations disrupt development completely, leading to seed death. The identities of 96 proteins with expression levels altered by NaCl-incubation were established using 2-DE-MALDI-TOF-MS and 2-DE-MALDI-TOF-MS/MS. Of these 96 proteins, 79 were altered greater than twofold when incubated with a 0.2 M salt solution, while 51 were altered when incubated with a 0.1 M salt solution. According to their functional annotations in the Swiss-Prot protein-sequence databases, these proteins are mainly involved in seed storage, energy metabolism, stress response, and protein metabolism. Notably, the expression of proteins that respond to abscisic acid signals increased in response to salt stress. The results of this study provide important clues as to how NaCl stresses the physiology of germinating maize seeds.
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22
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Misra A, Khan K, Niranjan A, Nath P, Sane VA. Over-expression of JcDGAT1 from Jatropha curcas increases seed oil levels and alters oil quality in transgenic Arabidopsis thaliana. PHYTOCHEMISTRY 2013; 96:37-45. [PMID: 24125179 DOI: 10.1016/j.phytochem.2013.09.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/30/2013] [Accepted: 09/16/2013] [Indexed: 05/18/2023]
Abstract
The increasing consumption of fossil fuels and petroleum products is leading to their rapid depletion and is a matter of concern around the globe. Substitutes of fossil fuels are required to sustain the pace of economic development. In this context, oil from the non food crops (biofuel) has shown potential to substitute fossil fuels. Jatropha curcas is an excellent shrub spread and naturalized across the globe. Its oil contains a high percentage of unsaturated fatty acids (about 78-84% of total fatty acid content) making the oil suitable for biodiesel production. Despite its high oil content, it has been poorly studied in terms of important enzymes/genes responsible for oil biosynthesis. Here, we describe the isolation of the full length cDNA clone of JcDGAT1, a key enzyme involved in oil biosynthesis, from J. curcas seeds and manipulation of oil content and composition in transgenic Arabidopsis plants by its expression. Transcript analysis of JcDGAT1 reveals a gradual increase from early seed development to its maturation. Homozygous transgenic Arabidopsis lines expressing JcDGAT1 both under CaMV35S promoter and a seed specific promoter show an enhanced level of total oil content (up by 30-41%) in seeds but do not show any phenotypic differences. In addition, our studies also show alterations in the oil composition through JcDGAT1 expression. While the levels of saturated FAs such as palmitate and stearate in the oil do not change, there is significant reproducible decrease in the levels of oleic acid and a concomitant increase in levels of linolenic acid both under the CaMV35S promoter as well as the seed specific promoter. Our studies thus confirm that DGAT is involved in flux control in oil biosynthesis and show that JcDGAT1 could be used specifically to manipulate and improve oil content and composition in plants.
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Affiliation(s)
- Aparna Misra
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow 226001, India
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Dinakar C, Bartels D. Desiccation tolerance in resurrection plants: new insights from transcriptome, proteome and metabolome analysis. FRONTIERS IN PLANT SCIENCE 2013; 4:482. [PMID: 24348488 DOI: 10.3389/fpls.201300482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/06/2013] [Indexed: 05/29/2023]
Abstract
Most higher plants are unable to survive desiccation to an air-dried state. An exception is a small group of vascular angiosperm plants, termed resurrection plants. They have evolved unique mechanisms of desiccation tolerance and thus can tolerate severe water loss, and mostly adjust their water content with the relative humidity in the environment. Desiccation tolerance is a complex phenomenon and depends on the regulated expression of numerous genes during dehydration and subsequent rehydration. Most of the resurrection plants have a large genome and are difficult to transform which makes them unsuitable for genetic approaches. However, technical advances have made it possible to analyze changes in gene expression on a large-scale. These approaches together with comparative studies with non-desiccation tolerant plants provide novel insights into the molecular processes required for desiccation tolerance and will shed light on identification of orphan genes with unknown functions. Here, we review large-scale recent transcriptomic, proteomic, and metabolomic studies that have been performed in desiccation tolerant plants and discuss how these studies contribute to understanding the molecular basis of desiccation tolerance.
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Affiliation(s)
- Challabathula Dinakar
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn Bonn, Germany ; Department of Life Sciences, School of Basic and Applied Sciences, Central University of Tamil Nadu Thiruvarur, India
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn Bonn, Germany
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Dinakar C, Bartels D. Desiccation tolerance in resurrection plants: new insights from transcriptome, proteome and metabolome analysis. FRONTIERS IN PLANT SCIENCE 2013; 4:482. [PMID: 24348488 PMCID: PMC3842845 DOI: 10.3389/fpls.2013.00482] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/06/2013] [Indexed: 05/18/2023]
Abstract
Most higher plants are unable to survive desiccation to an air-dried state. An exception is a small group of vascular angiosperm plants, termed resurrection plants. They have evolved unique mechanisms of desiccation tolerance and thus can tolerate severe water loss, and mostly adjust their water content with the relative humidity in the environment. Desiccation tolerance is a complex phenomenon and depends on the regulated expression of numerous genes during dehydration and subsequent rehydration. Most of the resurrection plants have a large genome and are difficult to transform which makes them unsuitable for genetic approaches. However, technical advances have made it possible to analyze changes in gene expression on a large-scale. These approaches together with comparative studies with non-desiccation tolerant plants provide novel insights into the molecular processes required for desiccation tolerance and will shed light on identification of orphan genes with unknown functions. Here, we review large-scale recent transcriptomic, proteomic, and metabolomic studies that have been performed in desiccation tolerant plants and discuss how these studies contribute to understanding the molecular basis of desiccation tolerance.
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Affiliation(s)
- Challabathula Dinakar
- Institute of Molecular Physiology and Biotechnology of Plants, University of BonnBonn, Germany
- Department of Life Sciences, School of Basic and Applied Sciences, Central University of Tamil NaduThiruvarur, India
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants, University of BonnBonn, Germany
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Yang J, Zhao S, Yu C, Li C. Large-scale plantlet conversion and ex vitro transplantation efficiency of Siberian ginseng by bioreactor culture. ScientificWorldJournal 2013; 2013:829067. [PMID: 24302875 PMCID: PMC3835873 DOI: 10.1155/2013/829067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/18/2013] [Indexed: 11/23/2022] Open
Abstract
To achieve large-scale low-cost ex vitro acclimatization of Siberian ginseng plants, heart- and torpedo-shaped secondary somatic embryos (SEs) induced from germinated SEs on agar medium were collected and then inoculated to 10-l bubble column bioreactor, respectively. For plantlet conversion, inoculation of torpedo-shaped secondary SEs was more effective than heart-shaped SEs. TS2 (culture of torpedo-shaped SEs in a bioreactor with a 2-week subculture interval) plantlets had a higher root number and leaf number and larger leaf area than did HS3 (culture of heart-shaped SEs in a bioreactor with a 3-week subculture interval) and HS2 (culture of heart-shaped SEs in a bioreactor with a 2-week subculture interval) plantlets. Of these converted plants, TS2 plantlets had higher survival rate (83.7%) and growth characteristics after transplantation in a simple shed covered with a 50% sunshade net only for 6 months. TS2 plantlets also showed significantly lower H2O2 content and significantly increased superoxide dismutase (SOD), glutathione peroxidase (GPX), and glutathione transferase (GST) expression levels as compared to HS2 plants when exposure to ex vitro conditions.
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Affiliation(s)
- Jingli Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shicheng Zhao
- Department of Crop Science, College of Agriculture & Life Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Changyeon Yu
- Division of Bioresource Technology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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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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Cui H, Wang Y, Wang Y, Qin S. Genome-wide analysis of putative peroxiredoxin in unicellular and filamentous cyanobacteria. BMC Evol Biol 2012; 12:220. [PMID: 23157370 PMCID: PMC3514251 DOI: 10.1186/1471-2148-12-220] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Accepted: 10/25/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Cyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats. Peroxiredoxin (PRX) is an important protein that plays essential roles in protecting own cells against reactive oxygen species (ROS). PRXs have been identified from mammals, fungi and higher plants. However, knowledge on cyanobacterial PRXs still remains obscure. With the availability of 37 sequenced cyanobacterial genomes, we performed a comprehensive comparative analysis of PRXs and explored their diversity, distribution, domain structure and evolution. RESULTS Overall 244 putative prx genes were identified, which were abundant in filamentous diazotrophic cyanobacteria, Acaryochloris marina MBIC 11017, and unicellular cyanobacteria inhabiting freshwater and hot-springs, while poor in all Prochlorococcus and marine Synechococcus strains. Among these putative genes, 25 open reading frames (ORFs) encoding hypothetical proteins were identified as prx gene family members and the others were already annotated as prx genes. All 244 putative PRXs were classified into five major subfamilies (1-Cys, 2-Cys, BCP, PRX5_like, and PRX-like) according to their domain structures. The catalytic motifs of the cyanobacterial PRXs were similar to those of eukaryotic PRXs and highly conserved in all but the PRX-like subfamily. Classical motif (CXXC) of thioredoxin was detected in protein sequences from the PRX-like subfamily. Phylogenetic tree constructed of catalytic domains coincided well with the domain structures of PRXs and the phylogenies based on 16s rRNA. CONCLUSIONS The distribution of genes encoding PRXs in different unicellular and filamentous cyanobacteria especially those sub-families like PRX-like or 1-Cys PRX correlate with the genome size, eco-physiology, and physiological properties of the organisms. Cyanobacterial and eukaryotic PRXs share similar conserved motifs, indicating that cyanobacteria adopt similar catalytic mechanisms as eukaryotes. All cyanobacterial PRX proteins share highly similar structures, implying that these genes may originate from a common ancestor. In this study, a general framework of the sequence-structure-function connections of the PRXs was revealed, which may facilitate functional investigations of PRXs in various organisms.
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Affiliation(s)
- Hongli Cui
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road, Yantai 264003, People’s Republic of China
- University of Chinese Academy of Sciences, Yuquan Road, Beijing 100049, People’s Republic of China
| | - Yipeng Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road, Yantai 264003, People’s Republic of China
| | - Yinchu Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road, Yantai 264003, People’s Republic of China
- University of Chinese Academy of Sciences, Yuquan Road, Beijing 100049, People’s Republic of China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road, Yantai 264003, People’s Republic of China
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Schokraie E, Warnken U, Hotz-Wagenblatt A, Grohme MA, Hengherr S, Förster F, Schill RO, Frohme M, Dandekar T, Schnölzer M. Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state. PLoS One 2012; 7:e45682. [PMID: 23029181 PMCID: PMC3459984 DOI: 10.1371/journal.pone.0045682] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 08/24/2012] [Indexed: 12/02/2022] Open
Abstract
Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.
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Affiliation(s)
- Elham Schokraie
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Markus A. Grohme
- Department of Molecular Biology and Functional Genomics, University of Applied Sciences Wildau, Wildau, Germany
| | - Steffen Hengherr
- Department of Zoology, University of Stuttgart, Stuttgart, Germany
| | - Frank Förster
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Ralph O. Schill
- Department of Zoology, University of Stuttgart, Stuttgart, Germany
| | - Marcus Frohme
- Department of Molecular Biology and Functional Genomics, University of Applied Sciences Wildau, Wildau, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- * E-mail:
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Abdalla KO, Rafudeen MS. Analysis of the nuclear proteome of the resurrection plant Xerophyta viscosa in response to dehydration stress using iTRAQ with 2DLC and tandem mass spectrometry. J Proteomics 2012; 75:2361-74. [DOI: 10.1016/j.jprot.2012.02.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/31/2012] [Accepted: 02/04/2012] [Indexed: 10/28/2022]
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Zheng J, Chen F, Wang Z, Cao H, Li X, Deng X, Soppe WJJ, Li Y, Liu Y. A novel role for histone methyltransferase KYP/SUVH4 in the control of Arabidopsis primary seed dormancy. THE NEW PHYTOLOGIST 2012; 193:605-616. [PMID: 22122546 DOI: 10.1111/j.1469-8137.2011.03969.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
• Seed dormancy controls germination and plays a crucial role in the life cycle of plants. Chromatin modifications are involved in the regulation of seed dormancy; however, little is known about the underlying mechanism. • KYP/SUVH4 is required for histone H3 lysine 9 dimethylation. Mutations in this gene cause increased seed dormancy. KYP/SUVH4-overexpressing Arabidopsis plants show decreased dormancy. KYP/SUVH4 expression is regulated by abscisic acid (ABA) and gibberellins (GA). The sensitivity of seed germination to ABA and paclobutrazol (PAC) is enhanced slightly in kryptonite-2 (kyp-2) and suvh4-2/suvh5 mutants, but weakened in KYP/SUVH4-overexpressing plants. • In the kyp-2 mutant, several dormancy-related genes, including DOG1 and ABI3, show increased expression levels, in agreement with a negative role for KYP/SUVH4 in gene transcription. • Genetic analysis showed that DOG1 and HUB1 are epistatic to KYP/SUVH4, suggesting that these genes regulate seed dormancy in the same genetic pathway.
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Affiliation(s)
- Jian Zheng
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Fengying Chen
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhi Wang
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100089, China
| | - Hong Cao
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaoying Li
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xin Deng
- Key Laboratory of Photosynthesis and Molecular Physiology, Research Center of Plant Molecular and Developmental Biology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wim J J Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Yong Li
- Center for Biological Systems Analysis, University of Freiburg, D-79104 Freiburg, Germany
| | - Yongxiu Liu
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Dinakar C, Djilianov D, Bartels D. Photosynthesis in desiccation tolerant plants: energy metabolism and antioxidative stress defense. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 182:29-41. [PMID: 22118613 DOI: 10.1016/j.plantsci.2011.01.018] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 01/10/2011] [Accepted: 01/27/2011] [Indexed: 05/07/2023]
Abstract
Resurrection plants are regarded as excellent models to study the mechanisms associated with desiccation tolerance. During the past years tremendous progress has been made in understanding the phenomenon of desiccation tolerance in resurrection plants, but many questions are open concerning the mechanisms enabling these plants to survive desiccation. The photosynthetic apparatus is very sensitive to reactive oxygen species mediated injury during desiccation and must be maintained or quickly repaired upon rehydration. The photosynthetic apparatus is a primary source of generating reactive oxygen species. The unique ability of plants to withstand the oxidative stress imposed by reactive oxygen species during desiccation depends on the production of antioxidants. The present review considers the overall strategies and the mechanisms involved in the desiccation tolerance in the first part and will focus on the effects on photosynthesis, energy metabolism and antioxidative stress defenses in the second part.
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Affiliation(s)
- Challabathula Dinakar
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
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Hancock JT, Neill SJ, Wilson ID. Nitric oxide and ABA in the control of plant function. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:119-24. [PMID: 21893252 DOI: 10.1016/j.plantsci.2011.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 03/31/2011] [Accepted: 04/20/2011] [Indexed: 05/04/2023]
Abstract
Abscisic acid (ABA) and nitric oxide (NO) are both extremely important signalling molecules employed by plants to control many aspects of physiology. ABA has been extensively studied in the mechanisms which control stomatal movement as well as in seed dormancy and germination and plant development. The addition of either ABA or NO to plant cells is known to instigate the actions of many signal transduction components. Both may have an influence on the phosphorylation of proteins in cells mediated by effects on protein kinases and phosphatases, as well as recruiting a wide range of other signal transduction molecules to mediate the final effects. Both ABA and NO may also lead to the regulation of gene expression. However, it is becoming more apparent that NO may be acting downstream of ABA, with such action being mediated by reactive oxygen species such as hydrogen peroxide in some cases. However not all ABA responses require the action of NO. Here, examples of where ABA and NO have been put together into the same signal transduction pathways are discussed.
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Affiliation(s)
- J T Hancock
- Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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33
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Bhatt I, Tripathi B. Plant peroxiredoxins: Catalytic mechanisms, functional significance and future perspectives. Biotechnol Adv 2011; 29:850-9. [DOI: 10.1016/j.biotechadv.2011.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 06/24/2011] [Accepted: 07/02/2011] [Indexed: 01/01/2023]
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Abstract
Peroxiredoxins (Prx) are central elements of the antioxidant defense system and the dithiol-disulfide redox regulatory network of the plant and cyanobacterial cell. They employ a thiol-based catalytic mechanism to reduce H2O2, alkylhydroperoxide, and peroxinitrite. In plants and cyanobacteria, there exist 2-CysPrx, 1-CysPrx, PrxQ, and type II Prx. Higher plants typically contain at least one plastid 2-CysPrx, one nucleo-cytoplasmic 1-CysPrx, one chloroplast PrxQ, and one each of cytosolic, mitochondrial, and plastidic type II Prx. Cyanobacteria express variable sets of three or more Prxs. The catalytic cycle consists of three steps: (i) peroxidative reduction, (ii) resolving step, and (iii) regeneration using diverse electron donors such as thioredoxins, glutaredoxins, cyclophilins, glutathione, and ascorbic acid. Prx proteins undergo major conformational changes in dependence of their redox state. Thus, they not only modulate cellular reactive oxygen species- and reactive nitrogen species-dependent signaling, but depending on the Prx type they sense the redox state, transmit redox information to binding partners, and function as chaperone. They serve in context of photosynthesis and respiration, but also in metabolism and development of all tissues, for example, in nodules as well as during seed and fruit development. The article surveys the current literature and attempts a mostly comprehensive coverage of present day knowledge and concepts on Prx mechanism, regulation, and function and thus on the whole Prx systems in plants.
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Affiliation(s)
- Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Bielefeld University, Bielefeld, Germany.
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35
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Yacoubi R, Job C, Belghazi M, Chaibi W, Job D. Toward Characterizing Seed Vigor in Alfalfa Through Proteomic Analysis of Germination and Priming. J Proteome Res 2011; 10:3891-903. [DOI: 10.1021/pr101274f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Rafika Yacoubi
- Laboratoire de Biologie et Physiologie Cellulaire Végétales, Département de Biologie, Université de Tunis, Tunisie
| | - Claudette Job
- Centre National de la Recherche Scientifique-Université Claude Bernard Lyon 1-Institut National des Sciences Appliquées-Bayer CropScience Joint Laboratory, UMR 5240 Lyon cedex 9, France
| | - Maya Belghazi
- Centre d’Analyses Protéomiques de Marseille (CAPM), IFR Jean Roche, Faculté de médecine, Marseille cedex 20, France
| | - Wided Chaibi
- Laboratoire de Biologie et Physiologie Cellulaire Végétales, Département de Biologie, Université de Tunis, Tunisie
| | - Dominique Job
- Centre National de la Recherche Scientifique-Université Claude Bernard Lyon 1-Institut National des Sciences Appliquées-Bayer CropScience Joint Laboratory, UMR 5240 Lyon cedex 9, France
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36
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Abstract
Peroxiredoxins (Prx) are central elements of the antioxidant defense system and the dithiol-disulfide redox regulatory network of the plant and cyanobacterial cell. They employ a thiol-based catalytic mechanism to reduce H2O2, alkylhydroperoxide, and peroxinitrite. In plants and cyanobacteria, there exist 2-CysPrx, 1-CysPrx, PrxQ, and type II Prx. Higher plants typically contain at least one plastid 2-CysPrx, one nucleo-cytoplasmic 1-CysPrx, one chloroplast PrxQ, and one each of cytosolic, mitochondrial, and plastidic type II Prx. Cyanobacteria express variable sets of three or more Prxs. The catalytic cycle consists of three steps: (i) peroxidative reduction, (ii) resolving step, and (iii) regeneration using diverse electron donors such as thioredoxins, glutaredoxins, cyclophilins, glutathione, and ascorbic acid. Prx proteins undergo major conformational changes in dependence of their redox state. Thus, they not only modulate cellular reactive oxygen species- and reactive nitrogen species-dependent signaling, but depending on the Prx type they sense the redox state, transmit redox information to binding partners, and function as chaperone. They serve in context of photosynthesis and respiration, but also in metabolism and development of all tissues, for example, in nodules as well as during seed and fruit development. The article surveys the current literature and attempts a mostly comprehensive coverage of present day knowledge and concepts on Prx mechanism, regulation, and function and thus on the whole Prx systems in plants.
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Affiliation(s)
- Karl-Josef Dietz
- Department of Biochemistry and Physiology of Plants, Bielefeld University, Bielefeld, Germany.
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37
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Kim JH, Jung IJ, Kim DY, Fanata WI, Son BH, Yoo JY, Harmoko R, Ko KS, Moon JC, Jang HH, Kim WY, Kim JY, Lim CO, Lee SY, Lee KO. Proteomic identification of an embryo-specific 1Cys-Prx promoter and analysis of its activity in transgenic rice. Biochem Biophys Res Commun 2011; 408:78-83. [PMID: 21458419 DOI: 10.1016/j.bbrc.2011.03.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 03/28/2011] [Indexed: 11/25/2022]
Abstract
Proteomic analysis of a rice callus led to the identification of 10 abscisic acid (ABA)-induced proteins as putative products of the embryo-specific promoter candidates. 5'-flanking sequence of 1 Cys-Prx, a highly-induced protein gene, was cloned and analyzed. The transcription initiation site of 1 Cys-Prx maps 96 nucleotides upstream of the translation initiation codon and a TATA-box and putative seed-specific cis-acting elements, RYE and ABRE, are located 26, 115 and 124 bp upstream of the transcription site, respectively. β-glucuronidase (GUS) expression driven by the 1 Cys-Prx promoters was strong in the embryo and aleurone layer and the activity reached up to 24.9 ± 3.3 and 40.5 ± 2.1 pmol (4 MU/min/μg protein) in transgenic rice seeds and calluses, respectively. The activity of the 1 Cys-Prx promoters is much higher than that of the previously-identified embryo-specific promoters, and comparable to that of strong endosperm-specific promoters in rice. GUS expression driven by the 1 Cys-Prx promoters has been increased by ABA treatment and rapidly induced by wounding in callus and at the leaf of the transgenic plants, respectively. Furthermore, ectopic expression of the GUS construct in Arabidopsis suggested that the 1 Cys-Prx promoter also has strong activity in seeds of dicot plants.
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Affiliation(s)
- Je Hein Kim
- Division of Applied Life Science (BK21 Program) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 900 Gajwa-dong, Jinju 660-701, Republic of Korea
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Yamamoto A, Kagaya Y, Usui H, Hobo T, Takeda S, Hattori T. Diverse roles and mechanisms of gene regulation by the Arabidopsis seed maturation master regulator FUS3 revealed by microarray analysis. PLANT & CELL PHYSIOLOGY 2010; 51:2031-46. [PMID: 21045071 DOI: 10.1093/pcp/pcq162] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The FUSCA3 (FUS3) transcription factor is considered a master regulator of seed maturation because a wide range of seed maturation events are impaired in its defective mutant. To identify comprehensively genes under the control of FUS3, two types of microarray experiments were performed. First, transgenic plants in which FUS3 expression could be induced by the application of estrogen (ESTR) were used to identify any genes up-regulated in young seedlings of Arabidopsis in response to the ectopic expression of FUS3. Secondly, the transcriptomes of the fus3 mutant and wild-type developing seeds were compared. The combined results of these experiments identified genes under the relatively immediate and robust control of FUS3 during seed development. The analysis has extended the range of identified gene types under the control of FUS3. The genes positively controlled by FUS3 are not confined to previously known seed maturation-related genes and include those involved in the production of secondary metabolites, such as glucosinolates, phenylpropanoids and flavonoids, and those involved in primary metabolism, such as photosynthesis and fatty acid biosynthesis. Furthermore, several different patterns were identified in the manner of ectopic activation by FUS3 with respect to the induction kinetics and ABA requirement of downstream gene induction depending on the nature of developmental regulation, suggesting mechanistic diversity of gene regulation by FUS3.
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Affiliation(s)
- Akiko Yamamoto
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
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Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms. PLoS One 2010; 5:e9502. [PMID: 20224743 PMCID: PMC2835947 DOI: 10.1371/journal.pone.0009502] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 02/04/2010] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. PRINCIPAL FINDINGS Here we present to the best of our knowledge the first comprehensive study of Milnesium tardigradum on the protein level. To establish a proteome reference map we developed optimized protocols for protein extraction from tardigrades in the active state and for separation of proteins by high resolution two-dimensional gel electrophoresis. Since only limited sequence information of M. tardigradum on the genome and gene expression level is available to date in public databases we initiated in parallel a tardigrade EST sequencing project to allow for protein identification by electrospray ionization tandem mass spectrometry. 271 out of 606 analyzed protein spots could be identified by searching against the publicly available NCBInr database as well as our newly established tardigrade protein database corresponding to 144 unique proteins. Another 150 spots could be identified in the tardigrade clustered EST database corresponding to 36 unique contigs and ESTs. Proteins with annotated function were further categorized in more detail by their molecular function, biological process and cellular component. For the proteins of unknown function more information could be obtained by performing a protein domain annotation analysis. Our results include proteins like protein member of different heat shock protein families and LEA group 3, which might play important roles in surviving extreme conditions. CONCLUSIONS The proteome reference map of Milnesium tardigradum provides the basis for further studies in order to identify and characterize the biochemical mechanisms of tolerance to extreme desiccation. The optimized proteomics workflow will enable application of sensitive quantification techniques to detect differences in protein expression, which are characteristic of the active and anhydrobiotic states of tardigrades.
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Ikegami A, Akagi T, Potter D, Yamada M, Sato A, Yonemori K, Kitajima A, Inoue K. Molecular identification of 1-Cys peroxiredoxin and anthocyanidin/flavonol 3-O-galactosyltransferase from proanthocyanidin-rich young fruits of persimmon (Diospyros kaki Thunb.). PLANTA 2009; 230:841-55. [PMID: 19641937 PMCID: PMC2729980 DOI: 10.1007/s00425-009-0989-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 07/10/2009] [Indexed: 05/19/2023]
Abstract
Fruits of persimmon (Diospyros kaki Thunb.) accumulate large amounts of proanthocyanidins (PAs) in the early stages of development. Astringent (A)-type fruits remain rich in soluble PAs even after they reach full-mature stage, whereas non-astringent (NA)-type fruits lose these compounds before full maturation. As a first step to elucidate the mechanism of PA accumulation in this non-model species, we used suppression subtractive hybridization to identify transcripts accumulating differently in young fruits of A- and NA-type. Interestingly, only a few clones involved in PA biosynthesis were identified in A-NA libraries. Represented by multiple clones were those encoding a novel 1-Cys peroxiredoxin and a new member of family 1 glycosyltransferases. Quantitative RT-PCR analyses confirmed correlation of the amount of PAs and accumulation of transcripts encoding these proteins in young persimmon fruits. Furthermore, the new family 1 glycosyltransferase was produced in Escherichia coli and shown to efficiently catalyze galactosylation at 3-hydroxyl groups of several anthocyanidins and flavonols. These findings suggest a complex mechanism of PA accumulation in persimmon fruits.
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Affiliation(s)
- Ayako Ikegami
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
- Laboratory of Pomology, Department of Bioproduction Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836 Japan
| | - Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Daniel Potter
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Masahiko Yamada
- Department of Citrus Research, National Institute of Fruit Tree Science, Kuchinotsu, Nagasaki 859-2501 Japan
| | - Akihiko Sato
- Grape and Persimmon Research Station, National Institute of Fruit Tree Science, Akitsu, Hiroshima 739-2494 Japan
| | - Keizo Yonemori
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Akira Kitajima
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Takatsuki, Osaka 569-0096 Japan
| | - Kentaro Inoue
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616 USA
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Tripathi BN, Bhatt I, Dietz KJ. Peroxiredoxins: a less studied component of hydrogen peroxide detoxification in photosynthetic organisms. PROTOPLASMA 2009; 235:3-15. [PMID: 19219525 DOI: 10.1007/s00709-009-0032-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 01/08/2009] [Indexed: 05/21/2023]
Abstract
Peroxiredoxins (Prx) are ubiquitous thiol-dependent peroxidases capable of reducing a broad range of toxic peroxides and peroxinitrites. A cysteinyl residue of peroxiredoxins reacts with the peroxides as primary catalytic center and oxidizes to sulfenic acid. The regeneration of the reduced form of Prx is required as a next step to allow its entry into next catalytic cycle. Several proteins, such as thioredoxin, glutaredoxin, cyclophilin, among others, are known to facilitate the regeneration of the reduced (catalytically active) form of Prx in plants. Based on the cysteine residues conserved in the deduced amino acid sequence and their catalytic mechanisms, four groups of peroxiredoxins have been distinguished in plants, namely, 1-Cys Prx, 2-Cys Prx, Type II Prx and Prx Q. Peroxiredoxins are known to play an important role in combating the reactive oxygen species generated at the level of electron transport activities in the plant exposed to different types of biotic and abiotic stresses. In addition to their role in antioxidant defense mechanisms in plants, they also modulate redox signaling during development and adaptation. Besides these general properties, peroxiredoxins have been shown to protect DNA from damage in vitro and in vivo. They also regulate metabolism in thylakoids and mitochondria. The present review summarizes the most updated information on the structure and catalysis of Prx and their functional importance in plant metabolism.
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Affiliation(s)
- Bhumi Nath Tripathi
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali, 304022, Rajasthan, India.
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Pulido P, Cazalis R, Cejudo FJ. An antioxidant redox system in the nucleus of wheat seed cells suffering oxidative stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 57:132-45. [PMID: 18786001 DOI: 10.1111/j.1365-313x.2008.03675.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Cereal seed cells contain different mechanisms for protection against the oxidative stress that occurs during maturation and germination. One such mechanism is based on the antioxidant activity of a 1-Cys peroxiredoxin (1-Cys Prx) localized in the nuclei of aleurone and scutellum cells. However, nothing is known about the mechanism of activation of this enzyme. Here, we describe the pattern of localization of NADPH thioredoxin reductase (NTR) in developing and germinating wheat seeds using an immunocytochemical analysis. The presence of NTR in transfer cells, vascular tissue, developing embryo and root meristematic cells, agrees with the localization of thioredoxin h (Trx h), and supports the important function of the NTR/Trx system in cell proliferation and communication. Interestingly, NTR is found in the nuclei of seed cells suffering oxidative stress, thus showing co-localization with Trx h and 1-Cys Prx. To test whether the NTR/Trx system serves as a reductant of the 1-Cys Prx, we cloned a full-length cDNA encoding 1-Cys Prx from wheat, and expressed the recombinant protein in Escherichia coli. Using the purified components, we show NTR-dependent activity of the 1-Cys Prx. Mutants of the 1-Cys Prx allowed us to demonstrate that the peroxidatic residue of the wheat enzyme is Cys46, which is overoxidized in vitro under oxidant conditions. Analysis of extracts from developing and germinating seeds confirmed 1-Cys Prx overoxidation in vivo. Based on these results, we propose that NADPH is the source of the reducing power to regenerate 1-Cys Prx in the nuclei of seed cells suffering oxidative stress, in a process that is catalyzed by NTR.
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Affiliation(s)
- Pablo Pulido
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla y CSIC, Avda Américo Vespucio 49, Seville, Spain
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Finkelstein R, Reeves W, Ariizumi T, Steber C. Molecular aspects of seed dormancy. ANNUAL REVIEW OF PLANT BIOLOGY 2008; 59:387-415. [PMID: 18257711 DOI: 10.1146/annurev.arplant.59.032607.092740] [Citation(s) in RCA: 699] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Seed dormancy provides a mechanism for plants to delay germination until conditions are optimal for survival of the next generation. Dormancy release is regulated by a combination of environmental and endogenous signals with both synergistic and competing effects. Molecular studies of dormancy have correlated changes in transcriptomes, proteomes, and hormone levels with dormancy states ranging from deep primary or secondary dormancy to varying degrees of release. The balance of abscisic acid (ABA):gibberellin (GA) levels and sensitivity is a major, but not the sole, regulator of dormancy status. ABA promotes dormancy induction and maintenance, whereas GA promotes progression from release through germination; environmental signals regulate this balance by modifying the expression of biosynthetic and catabolic enzymes. Mediators of environmental and hormonal response include both positive and negative regulators, many of which are feedback-regulated to enhance or attenuate the response. The net result is a slightly heterogeneous response, thereby providing more temporal options for successful germination.
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Affiliation(s)
- Ruth Finkelstein
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106-9610, USA.
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Chen ZY, Brown RL, Damann KE, Cleveland TE. Identification of Maize Kernel Endosperm Proteins Associated with Resistance to Aflatoxin Contamination by Aspergillus flavus. PHYTOPATHOLOGY 2007; 97:1094-103. [PMID: 18944174 DOI: 10.1094/phyto-97-9-1094] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
ABSTRACT Aflatoxins are carcinogens produced mainly by Aspergillus flavus during infection of susceptible crops such as maize (Zea mays). Previously, embryo proteins from maize genotypes resistant or susceptible to A. flavus infection were compared using proteomics, and resistance-associated proteins were identified. Here, we report the comparison of maize endosperm proteins from five resistant and five susceptible genotypes, and the identification of additional resistance-associated proteins using the same approach. Ten protein spots were upregulated twofold or higher in resistant lines compared with susceptible ones. Peptide sequencing of these proteins identified them as a globulin-2 protein, late embryogenesis abundant proteins (LEA3 and LEA14), a stress-related peroxiredoxin antioxidant (PER1), heat-shock proteins (HSP17.2), a cold-regulated protein (COR), and an antifungal trypsin-inhibitor protein (TI). The gene encoding one such upregulated protein, PER1, was cloned and overexpressed in Escherichia coli. The overexpressed PER1 protein demonstrated peroxidase activity in vitro. In addition, per1 expression was significantly higher in the resistant genotype Mp420 than in the susceptible genotype B73 during the late stage of kernel development, and was significantly induced upon A. flavus infection, suggesting that it may play an important role in enhancing kernel stress tolerance and aflatoxin resistance. The significance of other identified proteins to host resistance and stress tolerance also is discussed.
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Abstract
AbstractPeroxiredoxins are thiol–requiring antioxidants found in organisms ranging from bacteria to humans. They can be divided into two subgroups with either one or two conserved cysteine residues. In plants, 1–Cys peroxiredoxins have been identified in a number of grasses and cereals, and in the dicotyledonous speciesArabidopsis thaliana. In contrast to other antioxidants, the 1–Cys peroxiredoxin genes are expressed solely in seeds, and only in the parts of the seeds surviving desiccation, i.e. the embryo and the aleurone layer. The expression pattern is characteristic of late embryogenesis–abundant genes. The PER1 protein of barley is present in high concentrations in the nucleus at the onset of desiccation. 1–Cys genes are expressed in a dormancy–related manner in mature seeds, in that transcript levels are high in imbibed dormant seeds, but disappear upon germination of their non–dormant counterparts. 1–Cys transcript levels can be up–regulated by ABA and osmotic stresses and suppressed by gibberellic acid. Two hypotheses have been put forward on the function of 1–Cys peroxiredoxins in seed physiology. First, these proteins might protect macromolecules of embryo and aleurone cells against damaging reactive oxygen species during seed desiccation and early imbibition. And second, seed peroxiredoxins might play a role in the maintenance of dormancy. These hypotheses are discussed, taking into account present knowledge of the biochemistry and molecular biology of peroxiredoxins.
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Liu Y, Koornneef M, Soppe WJJ. The absence of histone H2B monoubiquitination in the Arabidopsis hub1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. THE PLANT CELL 2007; 19:433-44. [PMID: 17329563 PMCID: PMC1867323 DOI: 10.1105/tpc.106.049221] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Seed dormancy is defined as the failure of a viable seed to germinate under favorable conditions. Besides playing an adaptive role in nature by optimizing germination to the most suitable time, a tight control of dormancy is important in crop plants. Extensive genetic and physiological studies have identified the involvement of several factors, but the molecular mechanisms underlying this process are still largely unknown. We cloned the HISTONE MONOUBIQUITINATION1 (HUB1) gene, of which the mutant (previously identified as reduced dormancy4) has reduced seed dormancy and several pleiotropic phenotypes. HUB1 encodes a C3HC4 RING finger protein. The Arabidopsis thaliana genome contains one HUB1 homolog, which we named HUB2. The hub2 mutant also has reduced seed dormancy and is not redundant with hub1. Homologs of HUB1 and HUB2 in other species are required for histone H2B monoubiquitination. In agreement with this, the ubiquitinated form of histone H2B could not be detected in the hub1 and hub2 mutants. In yeast and human cells, histone H2B monoubiquitination is associated with actively transcribed genes. The hub1 mutant showed altered expression levels for several dormancy-related genes. We propose a role for chromatin remodeling in seed dormancy by H2B monoubiquitination through HUB1 and HUB2.
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Affiliation(s)
- Yongxiu Liu
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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Abstract
With 8 to 10 members, the peroxiredoxin gene family of each higher plant with known genome sequence is larger than in other eukaryotes. Likewise, the complexity of reductive regenerants is very high, e.g. the chloroplast 2-Cys Prx is reduced by various thioredoxins, cyclophilin Cyp20-3, the drought induced CDSP32 and the NADPH-dependent reductant NTRC. In the light of the apparent versatility of the peroxiredoxin system in plants, its specific and important functions in antioxidant defence, photosynthesis and stress adaptation, the review attempts a survey of present day knowledge on plant peroxiredoxins, their biochemical features and transcript regulation, as well as their function in photosynthesis, development, stress response and pathogenesis. The emerging evidence for plant Prx function in cell signaling is summarized.
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Affiliation(s)
- Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology W5-134, University of Bielefeld, Germany
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Cadman CSC, Toorop PE, Hilhorst HWM, Finch-Savage WE. Gene expression profiles of Arabidopsis Cvi seeds during dormancy cycling indicate a common underlying dormancy control mechanism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 46:805-22. [PMID: 16709196 DOI: 10.1111/j.1365-313x.2006.02738.x] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Physiologically dormant seeds, like those of Arabidopsis, will cycle through dormant states as seasons change until the environment is favourable for seedling establishment. This phenomenon is widespread in the plant kingdom, but has not been studied at the molecular level. Full-genome microarrays were used for a global transcript analysis of Arabidopsis thaliana (accession Cvi) seeds in a range of dormant and dry after-ripened states during cycling. Principal component analysis of the expression patterns observed showed that they differed in newly imbibed primary dormant seeds, as commonly used in experimental studies, compared with those in the maintained primary and secondary dormant states that exist during cycling. Dormant and after-ripened seeds appear to have equally active although distinct gene expression programmes, dormant seeds having greatly reduced gene expression associated with protein synthesis, potentially controlling the completion of germination. A core set of 442 genes were identified that had higher expression in all dormant states compared with after-ripened states. Abscisic acid (ABA) responsive elements were significantly over-represented in this set of genes the expression of which was enhanced when multiple copies of the elements were present. ABA regulation of dormancy was further supported by expression patterns of key genes in ABA synthesis/catabolism, and dormancy loss in the presence of fluridone. The data support an ABA-gibberelic acid hormone balance mechanism controlling cycling through dormant states that depends on synthetic and catabolic pathways of both hormones. Many of the most highly expressed genes in dormant states were stress-related even in the absence of abiotic stress, indicating that ABA, stress and dormancy responses overlap significantly at the transcriptome level.
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Becerra C, Puigdomenech P, Vicient CM. Computational and experimental analysis identifies Arabidopsis genes specifically expressed during early seed development. BMC Genomics 2006; 7:38. [PMID: 16504176 PMCID: PMC1420293 DOI: 10.1186/1471-2164-7-38] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Accepted: 02/28/2006] [Indexed: 12/01/2022] Open
Abstract
Background Plant seeds are complex organs in which maternal tissues, embryo and endosperm, follow distinct but coordinated developmental programs. Some morphogenetic and metabolic processes are exclusively associated with seed development. The goal of this study was to explore the feasibility of incorporating the available online bioinformatics databases to discover Arabidopsis genes specifically expressed in certain organs, in our case immature seeds. Results A total of 11,032 EST sequences obtained from isolated immature seeds were used as the initial dataset (178 of them newly described here). A pilot study was performed using EST virtual subtraction followed by microarray data analysis, using the Genevestigator tool. These techniques led to the identification of 49 immature seed-specific genes. The findings were validated by RT-PCR analysis and in situ hybridization. Conclusion We conclude that the combined in silico data analysis is an effective data mining strategy for the identification of tissue-specific gene expression.
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Affiliation(s)
- Cristian Becerra
- Laboratori de Genetica Molecular i Vegetal, CSIC-IRTA, Jordi Girona 18–36, 08034, Barcelona, Spain
| | - Pere Puigdomenech
- Laboratori de Genetica Molecular i Vegetal, CSIC-IRTA, Jordi Girona 18–36, 08034, Barcelona, Spain
| | - Carlos M Vicient
- Laboratori de Genetica Molecular i Vegetal, CSIC-IRTA, Jordi Girona 18–36, 08034, Barcelona, Spain
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