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Zang J, Yao X, Zhang T, Yang B, Wang Z, Quan S, Zhang Z, Liu J, Chen H, Zhang X, Hou Y. Excess iron accumulation affects maize endosperm development by inhibiting starch synthesis and inducing DNA damage. J Cell Physiol 2024:e31427. [PMID: 39239803 DOI: 10.1002/jcp.31427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 09/07/2024]
Abstract
Iron (Fe) storage in cereal seeds is the principal source of dietary Fe for humans. In maize (Zea mays), the accumulation of Fe in seeds is known to be negatively correlated with crop yield. Hence, it is essential to understand the underlying mechanism, which is crucial for developing and breeding maize cultivars with high yields and high Fe concentrations in the kernels. Here, through the successful application of in vitro kernel culture, we demonstrated that excess Fe supply in the medium caused the kernel to become collapsed and lighter in color, consistent with those found in yellow strip like 2 (ysl2, a small kernel mutant), implicated a crucial role of Fe concentration in kernel development. Indeed, over-accumulation of Fe in endosperm inhibited the abundance and activity of ADP-glucose pyrophosphorylase (AGPase) and the kernel development defect was alleviated by overexpression of Briittle 2 (Bt2, encoding a small subunit of AGPase) in ysl2 mutant. Imaging and quantitative analyses of reactive oxygen species (ROS) and cell death showed that Fe stress-induced ROS burst and severe DNA damage in endosperm cells. In addition, we have successfully identified candidate genes that are associated with iron homeostasis within the kernel, as well as upstream transcription factors that regulate ZmYSL2 by yeast one-hybrid screening. Collectively, our study will provide insights into the molecular mechanism of Fe accumulation-regulated seed development and promote the future efficient application of Fe element in corn improvement.
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Affiliation(s)
- Jie Zang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
| | - Xueyan Yao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
| | - Tengfei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Boming Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
| | - Shuxuan Quan
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
| | - Zhaogui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Juan Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huabang Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiansheng Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yifeng Hou
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
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Seyed Hajizadeh H, Azizi S, Aghaee A, Karakus S, Kaya O. Nano-silicone and Ascophyllum nodosum-based biostimulant down-regulates the negative effect of in vitro induced-salinity in Rosa damascena. BMC PLANT BIOLOGY 2023; 23:560. [PMID: 37957557 PMCID: PMC10644502 DOI: 10.1186/s12870-023-04584-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Rosa damascena is extensively cultivated in various regions of Iran due to its aesthetic attributes, medicinal qualities, and essential oil production. This study investigated the efficacy of Ascophyllum nodosum extract (AnE) at concentrations of 0, 2, and 3 g L- 1 and Nano-silicon (nSiO2) at concentrations of 0, 50, and 100 mg L- 1 in ameliorating the impact of salinity on two genotypes of Damask rose ('Chaharfasl' and 'Kashan') under in vitro culture conditions. Additionally, various physio-chemical characteristics of R. damascena explants were assessed. RESULTS The findings revealed that exposure to 100 mM NaCl resulted in a substantial reduction in the Relative Water Content (RWC), Membrane Stability Index (MSI), leaf pigments (Chlorophyll b, Chlorophyll a, total Chlorophyll, and carotenoids), chlorophyll fluorescence parameters, and protein content in both genotypes when compared to control conditions. Salinity induced a significant increase in the parameter F0 and a decrease in the parameter Fv/Fm compared to the control conditions in both genotypes. Nonetheless, the genotype Kashan treated with 3 g L- 1 AnE + 100 mg L- 1 nSiO2 exhibited the maximum Fm value under control conditions, with a significant difference compared to other treatments. Furthermore, salinity caused a considerable reduction in Fm in both 'Kashan' and 'Chaharfasl' by 22% and 17%, respectively, when compared to the control condition. 'Kashan' displayed the maximum Fv/Fm compared to the other genotype. The maximum levels of Malondialdehyde (MAD) and hydrogen peroxide (H2O2) were also observed in explants affected by salinity. The combination of 3 g L- 1 AnE + 100 mg L- 1 nSiO2, followed by 2 g L- 1 AnE + 100 mg L- 1 nSiO2, exhibited substantial positive effects. Salinity also led to an increase in proline content and the activity of peroxidase (POD), superoxide dismutase (SOD), guaiacol peroxidase (GPX), and catalase (CAT) in both genotypes. The activity of these enzymes was further enhanced when AnE was applied at concentrations of 2 and 3 g L- 1 in combination with 100 mg L- 1 nSiO2. CONCLUSIONS The 'Kashan' genotype displayed greater tolerance to salinity by enhancing water balance, maintaining membrane integrity, and augmenting the activity of antioxidant enzymes compared to 'Chaharfasl'. The utilization of nSiO2 and AnE biostimulants demonstrated potential benefits for R. damascena, both under salinity and control conditions. These findings hold substantial importance for researchers, policymakers, and farmers, offering valuable insights into the development of salinity-tolerant crop varieties.
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Affiliation(s)
- Hanifeh Seyed Hajizadeh
- Department of Horticulture, Faculty of Agriculture, University of Maragheh, Maragheh, 55136-553, Iran.
| | - Sahar Azizi
- Department of Horticulture, Faculty of Agriculture, University of Maragheh, Maragheh, 55136-553, Iran
| | - Ahmad Aghaee
- Department of Biology, Faculty of Science, University of Maragheh, Maragheh, Iran
| | - Sinem Karakus
- Çölemerik Vocational School, Hakkari University, Hakkari, 30000, Turkey
- Republic of Turkey Ministry of Agriculture and Forestry, Erzincan Horticultural Research Institute, Erzincan, 24060, Turkey
| | - Ozkan Kaya
- Republic of Turkey Ministry of Agriculture and Forestry, Erzincan Horticultural Research Institute, Erzincan, 24060, Turkey
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
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Pedroza-Garcia JA, Eekhout T, Achon I, Nisa MU, Coussens G, Vercauteren I, Van den Daele H, Pauwels L, Van Lijsebettens M, Raynaud C, De Veylder L. Maize ATR safeguards genome stability during kernel development to prevent early endosperm endocycle onset and cell death. THE PLANT CELL 2021; 33:2662-2684. [PMID: 34086963 PMCID: PMC8408457 DOI: 10.1093/plcell/koab158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/31/2021] [Indexed: 05/06/2023]
Abstract
The ataxia-telangiectasia mutated (ATM) and ATM and Rad3-related (ATR) kinases coordinate the DNA damage response. The roles described for Arabidopsis thaliana ATR and ATM are assumed to be conserved over other plant species, but molecular evidence is scarce. Here, we demonstrate that the functions of ATR and ATM are only partially conserved between Arabidopsis and maize (Zea mays). In both species, ATR and ATM play a key role in DNA repair and cell cycle checkpoint activation, but whereas Arabidopsis plants do not suffer from the absence of ATR under control growth conditions, maize mutant plants accumulate replication defects, likely due to their large genome size. Moreover, contrarily to Arabidopsis, maize ATM deficiency does not trigger meiotic defects, whereas the ATR kinase appears to be crucial for the maternal fertility. Strikingly, ATR is required to repress premature endocycle onset and cell death in the maize endosperm. Its absence results in a reduction of kernel size, protein and starch content, and a stochastic death of kernels, a process being counteracted by ATM. Additionally, while Arabidopsis atr atm double mutants are viable, no such mutants could be obtained for maize. Therefore, our data highlight that the mechanisms maintaining genome integrity may be more important for vegetative and reproductive development than previously anticipated.
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Affiliation(s)
- Jose Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ignacio Achon
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Maher-Un Nisa
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, 91405, Orsay, France
| | - Griet Coussens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Hilde Van den Daele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, 91405, Orsay, France
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Nájera-Martínez M, Pedroza-García JA, Suzuri-Hernández LJ, Mazubert C, Drouin-Wahbi J, Vázquez-Ramos J, Raynaud C, Plasencia J. Maize Thymidine Kinase Activity Is Present throughout Plant Development and Its Heterologous Expression Confers Tolerance to an Organellar DNA-Damaging Agent. PLANTS 2020; 9:plants9080930. [PMID: 32717805 PMCID: PMC7463494 DOI: 10.3390/plants9080930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022]
Abstract
Thymidine kinase 1 (TK1) phosphorylates thymidine nucleosides to generate thymidine monophosphate. This reaction belongs to the pyrimidine salvage route that is phylogenetically conserved. In the model plant Arabidopsis thaliana, TK activity contributes to maintain nuclear and organellar genome integrity by providing deoxythymidine-triphosphate (dTTP) for DNA synthesis. Arabidopsis has two TK1 genes (TK1a and TK1b) and double mutants show an albino phenotype and develop poorly. In contrast, maize (Zea mays L.) has a single TK1 (ZmTK1) gene and mutant plants are albino and display reduced genome copy number in chloroplasts. We studied the role of ZmTK1 during development and genotoxic stress response by assessing its activity at different developmental stages and by complementing Arabidopsis tk1 mutants. We found that ZmTK1 transcripts and activity are present during germination and throughout maize development. We show that ZmTK1 translocation to chloroplasts depends on a 72-amino-acid N-signal and its plastid localization is consistent with its ability to complement Arabidopsis tk1b mutants which are hypersensitive to ciprofloxacin (CIP), a genotoxic agent to organellar DNA. Also, ZmTK1 partly complemented the Arabidopsis double mutant plants during development. Our results contribute to the understanding of TK1 function in monocot species as an organellar enzyme for genome replication and repair.
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Affiliation(s)
- Manuela Nájera-Martínez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.N.-M.); (J.A.P.-G.); (L.J.S.-H.); (J.V.-R.)
| | - José Antonio Pedroza-García
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.N.-M.); (J.A.P.-G.); (L.J.S.-H.); (J.V.-R.)
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France; (C.M.); (J.D.-W.); (C.R.)
| | - Luis Jiro Suzuri-Hernández
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.N.-M.); (J.A.P.-G.); (L.J.S.-H.); (J.V.-R.)
- Licenciatura en Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Christelle Mazubert
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France; (C.M.); (J.D.-W.); (C.R.)
| | - Jeannine Drouin-Wahbi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France; (C.M.); (J.D.-W.); (C.R.)
| | - Jorge Vázquez-Ramos
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.N.-M.); (J.A.P.-G.); (L.J.S.-H.); (J.V.-R.)
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France; (C.M.); (J.D.-W.); (C.R.)
| | - Javier Plasencia
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.N.-M.); (J.A.P.-G.); (L.J.S.-H.); (J.V.-R.)
- Correspondence:
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Imadi SR, Kazi AG, Ahanger MA, Gucel S, Ahmad P. Plant transcriptomics and responses to environmental stress: an overview. J Genet 2016; 94:525-37. [PMID: 26440096 DOI: 10.1007/s12041-015-0545-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Different stresses include nutrient deficiency, pathogen attack, exposure to toxic chemicals etc. Transcriptomic studies have been mainly applied to only a few plant species including the model plant, Arabidopsis thaliana. These studies have provided valuable insights into the genetic networks of plant stress responses. Transcriptomics applied to cash crops including barley, rice, sugarcane, wheat and maize have further helped in understanding physiological and molecular responses in terms of genome sequence, gene regulation, gene differentiation, posttranscriptional modifications and gene splicing. On the other hand, comparative transcriptomics has provided more information about plant's response to diverse stresses. Thus, transcriptomics, together with other biotechnological approaches helps in development of stress tolerance in crops against the climate change.
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Affiliation(s)
- Sameen Ruqia Imadi
- Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, H-12 Campus, Islamabad 25000,
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6
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Large-scale protein analysis of European beech trees following four vegetation periods of twice ambient ozone exposure. J Proteomics 2014; 109:417-35. [DOI: 10.1016/j.jprot.2014.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/24/2014] [Accepted: 05/01/2014] [Indexed: 01/02/2023]
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El Kelish A, Zhao F, Heller W, Durner J, Winkler JB, Behrendt H, Traidl-Hoffmann C, Horres R, Pfeifer M, Frank U, Ernst D. Ragweed (Ambrosia artemisiifolia) pollen allergenicity: SuperSAGE transcriptomic analysis upon elevated CO2 and drought stress. BMC PLANT BIOLOGY 2014; 14:176. [PMID: 24972689 PMCID: PMC4084800 DOI: 10.1186/1471-2229-14-176] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 06/18/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Pollen of common ragweed (Ambrosia artemisiifolia) is a main cause of allergic diseases in Northern America. The weed has recently become spreading as a neophyte in Europe, while climate change may also affect the growth of the plant and additionally may also influence pollen allergenicity. To gain better insight in the molecular mechanisms in the development of ragweed pollen and its allergenic proteins under global change scenarios, we generated SuperSAGE libraries to identify differentially expressed transcripts. RESULTS Ragweed plants were grown in a greenhouse under 380 ppm CO2 and under elevated level of CO2 (700 ppm). In addition, drought experiments under both CO2 concentrations were performed. The pollen viability was not altered under elevated CO2, whereas drought stress decreased its viability. Increased levels of individual flavonoid metabolites were found under elevated CO2 and/or drought. Total RNA was isolated from ragweed pollen, exposed to the four mentioned scenarios and four SuperSAGE libraries were constructed. The library dataset included 236,942 unique sequences, showing overlapping as well as clear differently expressed sequence tags (ESTs). The analysis targeted ESTs known in Ambrosia, as well as in pollen of other plants. Among the identified ESTs, those encoding allergenic ragweed proteins (Amb a) increased under elevated CO2 and drought stress. In addition, ESTs encoding allergenic proteins in other plants were also identified. CONCLUSIONS The analysis of changes in the transcriptome of ragweed pollen upon CO2 and drought stress using SuperSAGE indicates that under global change scenarios the pollen transcriptome was altered, and impacts the allergenic potential of ragweed pollen.
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Affiliation(s)
- Amr El Kelish
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Botany Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Feng Zhao
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Werner Heller
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Biochemical Plant Pathology, Technische Universität München, Center of Life and Food Sciences Weihenstephan, 85350 Freising-Weihenstephan, Germany
| | - J Barbro Winkler
- Research Unit for Environmental Simulation, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Heidrun Behrendt
- Center of Allergy & Environment München (ZAUM), Technische Universität and Helmholtz Zentrum München, 85764 Neuherberg, Germany
- CK-CARE, Christine Kühne – Center for Allergy Research and Education, Davos, Switzerland
| | - Claudia Traidl-Hoffmann
- CK-CARE, Christine Kühne – Center for Allergy Research and Education, Davos, Switzerland
- Institute of Environmental Medicine, UNIKA-T, Technische Universität München, Munich, Germany
| | - Ralf Horres
- GenXPro GmbH, 60438 Frankfurt am Main, Germany
| | - Matthias Pfeifer
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Ulrike Frank
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- CK-CARE, Christine Kühne – Center for Allergy Research and Education, Davos, Switzerland
| | - Dieter Ernst
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- CK-CARE, Christine Kühne – Center for Allergy Research and Education, Davos, Switzerland
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Irar S, Brini F, Masmoudi K, Pagès M. Combination of 2DE and LC for plant proteomics analysis. Methods Mol Biol 2014; 1072:131-140. [PMID: 24136519 DOI: 10.1007/978-1-62703-631-3_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The use of analytical biochemical techniques with different separation properties allows us to better understand the proteome. To demonstrate this we have used two different methodologies to analyze embryos from a Tunisian cultivar of durum wheat (Triticum durum Desf.), variety Oum Rabiaa. We compared conventional 2D electrophoresis with liquid-phase chromatography. Our results show that a similar number of proteins were detected with both techniques. However, analysis of protein resolution at different pH ranges showed significant differences. By using a large pH gradient we observed that liquid chromatography presents higher resolution at extreme pH, either acidic or basic. Conversely, 2DE is more resolutive at intermediate pH (pH 5-6.5). Taking these results in consideration, we propose that 2DE and liquid chromatography are complementary methods to analyze complex protein extracts and can be used in parallel to acquire a wider perspective and a better understanding of the embryo proteome.
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Affiliation(s)
- Sami Irar
- Centre de Recerca en Agrigenomica (CRAG), Campus UAB, Edificio CRAG, Bellaterra, Cerdanyola del Vallès, Barcelona, Spain
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Sánchez-Pons N, Vicient CM. Identification of a type I Ca2+/Mg2+-dependent endonuclease induced in maize cells exposed to camptothecin. BMC PLANT BIOLOGY 2013; 13:186. [PMID: 24256432 PMCID: PMC4225560 DOI: 10.1186/1471-2229-13-186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/16/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND Camptothecin is a plant alkaloid that specifically binds topoisomerase I, inhibiting its activity and inducing double stranded breaks in DNA and activating the cell responses to DNA damage. RESULTS Maize cultured cells were incubated in the presence of different concentrations of camptothecin. Camptothecin inhibits cultured cell growth, induces genomic DNA degradation, and induces a 32 kDa Ca2+/Mg2+-dependent nuclease activity. This nuclease, we called CaMNUC32, is inhibited by Zn2+ and by acid pH, it is mainly localized in the nucleus and it cleaves single- and double-stranded DNA, with a higher activity against single-stranded DNA. Two-dimensional electrophoresis combined with mass spectrometry suggests that CaMNUC32 is a member of the type I S1/P1 nuclease family. This type of nucleases are usually Zn2+-dependent but our results support previous indications that S1-type nucleases have a wide variety of enzyme activities, including Ca2+/Mg2+-dependent. CONCLUSIONS We have identified and characterized CaMNUC32, a 32 kDa Ca2+/Mg2+-dependent nuclease of the S1/P1 family induced by the topoisomerase I inhibitor camptothecin in maize cultured cells.
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Affiliation(s)
- Núria Sánchez-Pons
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Carlos M Vicient
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
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Gomez-Garay A, Lopez JA, Camafeita E, Bueno MA, Pintos B. Proteomic perspective of Quercus suber somatic embryogenesis. J Proteomics 2013; 93:314-25. [PMID: 23770300 DOI: 10.1016/j.jprot.2013.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 05/28/2013] [Accepted: 06/03/2013] [Indexed: 01/22/2023]
Abstract
UNLABELLED Quercus suber L. is a forest tree with remarkable ecological, social and economic value in the southern Europe ecosystems. To circumvent the difficulties of breeding such long-lived species like Q. suber in a conventional fashion, clonal propagation of Q. suber elite trees can be carried out, although this process is sometimes unsuccessful. To help decipher the complex program underlying the development of Q. suber somatic embryos from the first early stage until maturity, a proteomic approach based on DIGE and MALDI-MS has been envisaged. Results highlighted several key processes involved in the three developmental stages (proliferative, cotyledonary and mature) of Q. suber somatic embryogenesis studied. Results show that the proliferation stage is characterized by fermentation as an alternative energy source at the first steps of somatic embryo development, as well as by up-regulation of proteins involved in cell division. In this stage reactive oxygen species play a role in proliferation, while other proteins like CAD and PR5 seem to be implied in embryonic competence. In the transition to the cotyledonary stage diverse ROS detoxification enzymes are activated and reserve products (mainly carbohydrates and proteins) are accumulated, whereas energy production is increased probably to participate in the synthesis of primary metabolites such as amino acids and fatty acids. Finally, in the mature stage ethylene accumulation regulates embryo development. BIOLOGICAL SIGNIFICANCE Quercus suber L. is a forest tree with remarkable ecological, social and economic value in the southern Europe ecosystems. To circumvent the difficulties of breeding such long-lived species like Q. suber in a conventional fashion, clonal propagation of Q. suber elite trees can be carried out, although this process is sometimes unsuccessful. To help decipher the complex program underlying the development of Q. suber somatic embryos from the first early stage until maturity, in deep studies become necessary. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Aranzazu Gomez-Garay
- Departamento de Biologia Vegetal I. Facultad de CC Biologicas, UCM, Madrid, Spain.
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Donà M, Confalonieri M, Minio A, Biggiogera M, Buttafava A, Raimondi E, Delledonne M, Ventura L, Sabatini ME, Macovei A, Giraffa G, Carbonera D, Balestrazzi A. RNA-Seq analysis discloses early senescence and nucleolar dysfunction triggered by Tdp1α depletion in Medicago truncatula. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1941-51. [PMID: 23467834 DOI: 10.1093/jxb/ert063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
An intron-spliced hairpin RNA approach was used for the targeted silencing of the MtTdp1α gene encoding the αisoform of tyrosyl-DNA phosphodiesterase 1 in Medicago truncatula Gaertn. Tyrosyl-DNA phosphodiesterase 1, involved in the repair of DNA topoisomerase I-mediated DNA damage, has been poorly investigated in plants. RNA-Seq analysis, carried out in the MtTdp1α-depleted plants, revealed different levels of transcriptional modulation (up- and down-regulation, alternative splicing, activation of alternative promoter) in genes involved in DNA damage sensing, DNA repair, and chromatin remodelling. It is suggested that the MtTdp1α gene has new, previously undetected roles in maintaining genome integrity. Up-regulation of senescence-associated genes and telomere shortening were observed. Moreover, impaired ribosome biogenesis indicated that the MtTdp1α gene is required for the nucleolar function. In agreement with the RNA-Seq data, transmission electron microscopy detected an altered nucleolar architecture in the MtTdp1α-depleted cells. Based on the reported data, a working hypothesis related to the occurrence of a nucleolar checkpoint in plant cells is proposed.
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Affiliation(s)
- Mattia Donà
- Department of Biology and Biotechnology L Spallanzani, via Ferrata 1, 27100 Pavia, Italy
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Ernst D. Integrated Studies on Abiotic Stress Defence in Trees. DEVELOPMENTS IN ENVIRONMENTAL SCIENCE 2013. [DOI: 10.1016/b978-0-08-098349-3.00014-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Bernardo L, Prinsi B, Negri AS, Cattivelli L, Espen L, Valè G. Proteomic characterization of the Rph15 barley resistance gene-mediated defence responses to leaf rust. BMC Genomics 2012; 13:642. [PMID: 23167439 PMCID: PMC3541957 DOI: 10.1186/1471-2164-13-642] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 11/09/2012] [Indexed: 11/28/2022] Open
Abstract
Background Leaf rust, caused by the biotrophic fungal pathogen Puccinia hordei, is one of the most important foliar disease of barley (Hordeum vulgare) and represents a serious threat in many production regions of the world. The leaf rust resistance gene Rph15 is of outstanding interest for resistance breeding because it confers resistance to over 350 Puccinia hordei isolates collected from around the world. Molecular and biochemical mechanisms responsible for the Rph15 effectiveness are currently not investigated. The aim of the present work was to study the Rph15-based defence responses using a proteomic approach. Results Protein pattern changes in response to the leaf rust pathogen infection were investigated in two barley near isogenic lines (NILs), Bowman (leaf rust susceptible) and Bowman-Rph15 (leaf rust resistant), differing for the introgression of the leaf rust resistance gene Rph15. Two infection time points, 24 hours and four days post inoculation (dpi), were analysed. No statistically significant differences were identified at the early time point, while at 4 dpi eighteen protein spots were significantly up or down regulated with a fold-change equal or higher than two in response to pathogen infection. Almost all the pathogen-responsive proteins were identified in the Bowman-Rph15 resistant NIL. Protein spots were characterized by LC-MS/MS analysis and found to be involved in photosynthesis and energy metabolism, carbohydrate metabolism, protein degradation and defence. Proteomic data were complemented by transcriptional analysis of the respective genes. The identified proteins can be related to modulation of the photosynthetic apparatus components, re-direction of the metabolism to sustain defence responses and deployment of defence proteins. Conclusions The identification of leaf rust infection-modulated defence responses restricted to the resistant NIL support the hypothesis that basal defence responses of Bowman, but not the Rph15 resistance gene-based ones, are suppressed or delayed by pathogen effectors to levels below the detection power of the adopted proteomic approach. Additionally, Rph15-mediated resistance processes identified mainly resides on a modulation of primary metabolism, affecting photosyntesis and carbohydrate pool.
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Affiliation(s)
- Letizia Bernardo
- CRA-Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda, PC I-29017, Italy
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Tnani H, García-Muniz N, Vicient CM, López-Ribera I. Expression profile of maize (Zea mays) scutellar epithelium during imbibition. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:1430-1433. [PMID: 22784472 DOI: 10.1016/j.jplph.2012.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 05/10/2012] [Accepted: 05/11/2012] [Indexed: 06/01/2023]
Abstract
The scutellum is a shield-shaped structure surrounding the embryo axis in grass species. The scutellar epithelium (Sep) is a monolayer of cells in contact with the endosperm. The Sep plays an important role during seed germination in the secretion of gibberellins and hydrolytic enzymes and in the transport of the hydrolized products to the growing embryo. We identified 30 genes predominantly expressed after imbibition in the Sep as compared to other parts of the scutellum. A high proportion of these genes is involved in metabolic processes. Some other identified genes are involved in the synthesis or modification of cell walls, which may be reflected in the changes of cell shape and cell wall composition that can be observed during imbibition. One of the genes encodes a proteinase that belongs to a proteinase family typical of carnivorous plants. Almost nothing is known about their role in other plants or organs, but the scutellar presence may point to a "digestive" function during germination. Genes involved in the production of energy and the transport of peptides were also identified.
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Affiliation(s)
- Hedia Tnani
- Department of Molecular Genetics, Centre for Research in Agrigenomics CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès, Barcelona), Spain
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Mannuss A, Trapp O, Puchta H. Gene regulation in response to DNA damage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:154-65. [PMID: 21867786 DOI: 10.1016/j.bbagrm.2011.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/25/2011] [Accepted: 08/04/2011] [Indexed: 11/17/2022]
Abstract
To deal with different kinds of DNA damages, there are a number of repair pathways that must be carefully orchestrated to guarantee genomic stability. Many proteins that play a role in DNA repair are involved in multiple pathways and need to be tightly regulated to conduct the functions required for efficient repair of different DNA damage types, such as double strand breaks or DNA crosslinks caused by radiation or genotoxins. While most of the factors involved in DNA repair are conserved throughout the different kingdoms, recent results have shown that the regulation of their expression is variable between different organisms. In the following paper, we give an overview of what is currently known about regulating factors and gene expression in response to DNA damage and put this knowledge in context with the different DNA repair pathways in plants. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.
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Affiliation(s)
- Anja Mannuss
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
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