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Kryvokhyzha M, Litvinov S, Danchenko M, Khudolieieva L, Kutsokon N, Baráth P, Rashydov N. How does ionizing radiation affect amyloidogenesis in plants? Int J Radiat Biol 2024; 100:922-933. [PMID: 38530837 DOI: 10.1080/09553002.2024.2331126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
PURPOSE Ionizing radiation is a harsh environmental factor that could induce plant senescence. We hypothesized that radiation-related senescence remodels proteome, particularly by triggering the accumulation of prion-like proteins in plant tissues. The object of this study, pea (Pisum sativum L.), is an agriculturally important legume. Research on the functional importance of amyloidogenic proteins was never performed on this species. MATERIALS AND METHODS Pea seeds were irradiated in the dose range 5-50 Gy of X-rays. Afterward, Fourier-transform infrared spectroscopy (FTIR) was used to investigate changes in the secondary structure of proteins in germinated 3-day-old seedlings. Specifically, we evaluated the ratio between the amide I and II peaks. Next, we performed protein staining with Congo red to compare the presence of amyloids in the samples. In parallel, we profiled the detergent-resistant proteome fraction by ultrahigh-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS). Differentially accumulated proteins were functionally analyzed in MapMan software, and the PLAAC tool was used to predict putative prion-like proteins. RESULTS We showed a reduced germination rate but higher plant height and faster appearance of reproductive organs in the irradiated at dose of 50 Gy group compared with the control; furthermore, we demonstrated more β-sheets and amyloid aggregates in the roots of stressed plants. We detected 531 proteins in detergent-resistant fraction extracted from roots, and 45 were annotated as putative prion-like proteins. Notably, 29 proteins were significantly differentially abundant between the irradiated and the control groups. These proteins belong to several functional categories: amino acid metabolism, carbohydrate metabolism, cytoskeleton organization, regulatory processes, protein biosynthesis, and RNA processing. Thus, the discovery proteomics provided deep data on novel aspects of plant stress biology. CONCLUSION Our data hinted that protein accumulation stimulated seedlings' growth as well as accelerated ontogenesis and, eventually, senescence, primarily through translation and RNA processing. The increased abundance of primary metabolism-related proteins indicates more intensive metabolic processes triggered in germinating pea seeds upon X-ray exposure. The functional role of detected putative amyloidogenic proteins should be validated in overexpression or knockout follow-up studies.
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Affiliation(s)
- Maryna Kryvokhyzha
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Nitra, Slovakia
| | - Sergii Litvinov
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Maksym Danchenko
- Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Nitra, Slovakia
| | - Lidiia Khudolieieva
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Nataliia Kutsokon
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Peter Baráth
- Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Namik Rashydov
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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Moradi A, Dai S, Wong EOY, Zhu G, Yu F, Lam HM, Wang Z, Burlingame A, Lin C, Afsharifar A, Yu W, Wang T, Li N. Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars. Biomolecules 2021; 11:1218. [PMID: 34439883 PMCID: PMC8393417 DOI: 10.3390/biom11081218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/29/2022] Open
Abstract
Isotopically dimethyl labeling was applied in a quantitative post-translational modification (PTM) proteomic study of phosphoproteomic changes in the drought responses of two contrasting soybean cultivars. A total of 9457 phosphopeptides were identified subsequently, corresponding to 4571 phosphoprotein groups and 3889 leading phosphoproteins, which contained nine kinase families consisting of 279 kinases. These phosphoproteins contained a total of 8087 phosphosites, 6106 of which were newly identified and constituted 54% of the current soybean phosphosite repository. These phosphosites were converted into the highly conserved kinase docking sites by bioinformatics analysis, which predicted six kinase families that matched with those newly found nine kinase families. The overly post-translationally modified proteins (OPP) occupies 2.1% of these leading phosphoproteins. Most of these OPPs are photoreceptors, mRNA-, histone-, and phospholipid-binding proteins, as well as protein kinase/phosphatases. The subgroup population distribution of phosphoproteins over the number of phosphosites of phosphoproteins follows the exponential decay law, Y = 4.13e-0.098X - 0.04. Out of 218 significantly regulated unique phosphopeptide groups, 188 phosphoproteins were regulated by the drought-tolerant cultivar under the water loss condition. These significantly regulated phosphoproteins (SRP) are mainly enriched in the biological functions of water transport and deprivation, methionine metabolic processes, photosynthesis/light reaction, and response to cadmium ion, osmotic stress, and ABA response. Seventeen and 15 SRPs are protein kinases/phosphatases and transcription factors, respectively. Bioinformatics analysis again revealed that three members of the calcium dependent protein kinase family (CAMK family), GmSRK2I, GmCIPK25, and GmAKINβ1 kinases, constitute a phosphor-relay-mediated signal transduction network, regulating ion channel activities and many nuclear events in this drought-tolerant cultivar, which presumably contributes to the development of the soybean drought tolerance under water deprivation process.
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Affiliation(s)
- Atieh Moradi
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz 71946-84471, Iran
| | - Shuaijian Dai
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Emily Oi Ying Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
| | - Fengchao Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China;
| | - Zhiyong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA;
| | - Al Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA;
| | - Chengtao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA;
| | - Alireza Afsharifar
- Plant Virology Research Centre, School of Agriculture, Shiraz University, Shiraz 71946-84471, Iran;
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Tingliang Wang
- Tsinghua-Peking Joint Centre for Life Sciences, Centre for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
- The HKUST Shenzhen Research Institut, Shenzhen 518057, China
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Bai LWD, Liu J, Dai LF, Deng QW, Chen YL, Xie JK, Luo XD. Identification and characterisation of cold stress-related proteins in Oryza rufipogon at the seedling stage using label-free quantitative proteomic analysis. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:542-555. [PMID: 33487217 DOI: 10.1071/fp20046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
In this study, label-free quantitative proteomics were used to study cold stress-related proteins in Dongxiang wild rice (Oryza rufipogon Griff., DWR) and cold sensitive cultivated rice 'Xieqingzao B'(Oryza sativa L. ssp. indica cv., XB). The results demonstrated the presence of 101 and 216 differentially expressed proteins (DEPs) were detected in DWR and XB, respectively, after cold stress. Bioinformatics analysis showed that DWR and XB differed significantly in their ability to scavenge reactive oxygen species (ROS) and regulate energy metabolism. Of the 101 DEPs of DWR, 46 DEPs related to differential expressed genes were also detected by transcriptome analysis. And 13 out of 101 DEPs were located in previous cold related quantitative trait loci (QTL). Quantitative real-time PCR analysis indicated that protein expression and transcription patterns were not similar in XB and DWR. Protein-protein interaction (PPI) network was constituted using the DEPs of DWR and XB, and the following three centre proteins were identified: Q8H3I3, Q9LDN2, and Q2QXR8. Next, we selected a centre protein and two of the 37 DEPs with high levels of differential expression (fold change ≥ 2) were used for cloning and prokaryotic expression. We found that Q5Z9Q8 could significantly improve the cold tolerance of Escherichia coli.
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Affiliation(s)
- Li-Wei-Dan Bai
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Jian Liu
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Liang-Fang Dai
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Qian-Wen Deng
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Ya-Ling Chen
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Jian-Kun Xie
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China; and Corresponding authors. ;
| | - Xiang-Dong Luo
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China; and Corresponding authors. ;
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Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for Quercus ilex. Int J Mol Sci 2021; 22:ijms22063191. [PMID: 33800973 PMCID: PMC8003919 DOI: 10.3390/ijms22063191] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 01/18/2023] Open
Abstract
Drought is one of the main causes of mortality in holm oak (Quercus ilex) seedlings used in reforestation programs. Although this species shows high adaptability to the extreme climate conditions prevailing in Southern Spain, its intrinsic genetic variability may play a role in the differential response of some populations and individuals. The aim of this work was to identify proteins and derived proteotypic peptides potentially useful as putative markers for drought tolerance in holm oak by using a targeted post-acquisition proteomics approach. For this purpose, we used a set of proteins identified by shotgun (LC-MSMS) analysis in a drought experiment on Q. ilex seedlings from four different provenances (viz. the Andalusian provinces Granada, Huelva, Cadiz and Seville). A double strategy involving the quantification of proteins and target peptides by shotgun analysis and post-acquisition data analysis based on proteotypic peptides was used. To this end, an initial list of proteotypic peptides from proteins highly represented under drought conditions was compiled that was used in combination with the raw files from the shotgun experiment to quantify the relative abundance of the fragment’s ion peaks with the software Skyline. The most abundant peptides under drought conditions in at least two populations were selected as putative markers of drought tolerance. A total of 30 proteins and 46 derived peptides belonging to the redox, stress-related, synthesis,-folding and degradation, and primary and secondary metabolism functional groups were thus identified. Two proteins (viz., subtilisin and chaperone GrpE protein) were found at increased levels in three populations, which make them especially interesting for validation drought tolerance markers in subsequent experiments.
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Castillejo MÁ, Fondevilla-Aparicio S, Fuentes-Almagro C, Rubiales D. Quantitative Analysis of Target Peptides Related to Resistance Against Ascochyta Blight ( Peyronellaea pinodes) in Pea. J Proteome Res 2020; 19:1000-1012. [PMID: 32040328 DOI: 10.1021/acs.jproteome.9b00365] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Peyronellaea pinodes causes Ascochyta blight, one of the major diseases in pea worldwide. Cultivated pea plants have a low resistance to this disease. Although quantitative trait loci (QTLs) involved in the resistance to Ascochyta blight have been identified, the specific genes associated with these QTLs remain unknown, which makes marker-assisted selection difficult. Complex traits alter proteins and their abundance. Quantitative estimation of proteins in pea might therefore be useful in selecting potential markers for breeding. In this work, we developed a strategy using a combination of shotgun proteomics (viz., high performance liquid chromatography-mass spectrometry data-dependent acquisition) and data-independent acquisition (DIA) analysis, to identify putative protein markers associated with resistance to Ascochyta blight and explored its use for breeding selection. For this purpose, an initial list of target peptides based on proteins closely related to resistance to P. pinodes was compiled by using two genotypes with contrasting responses to the disease. Then, targeted data analysis (viz., shotgun proteomics-DIA) was used for constitutive quantification of the target peptides in a representative number of the recombinant inbred line population segregated for resistance as derived from a cross between the two genotypes. Finally, a peptide panel of potential markers for resistance to P. pinodes was built. The results thus obtained are discussed and compared with those of previous gene expression studies using the same parental pea genotypes responding to the pathogen. Also, a molecular defense mechanism against Ascochyta blight in pea is proposed. To the authors' knowledge, this is the first time a targeted proteomics approach based on data analysis has been used to identify peptides associated with resistance to this disease.
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Affiliation(s)
| | | | | | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
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Li Z, Kuang W, Liu Y, Peng D, Bai L. Proteomic Analysis of Horseweed (Conyza canadensis) Subjected to Caprylic Acid Stress. Proteomics 2019; 19:e1800294. [PMID: 30865362 DOI: 10.1002/pmic.201800294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 02/02/2019] [Indexed: 11/08/2022]
Abstract
Caprylic acid (CAP) is anticipated to be a potential biocontrol herbicide in the control of weeds, however the molecular mechanism of how CAP affects weeds is poorly understood. Here, the physiological and biochemical (protein-level) changes in horseweed (Conyza canadensis L.) are studied under CAP treatment, with infrared gas analyzer and label-free quantitative proteomics methods. In total, 112 differentially-accumulated proteins (DAPs) (>1.5 fold change, p < 0.05) are present between treated horseweed and control samples, with 46 up-regulated and 66 down-regulated proteins. These DAPs are involved in 28 biochemical pathways, including photosynthesis pathways. In particular, six photosynthesis proteins show significant abundance changes in the CAP-treated horseweed. The qRT-PCR results confirm three of the six genes involved in photosynthesis. Moreover, by measuring photosynthesis characteristics, CAP was shown to decrease photosynthetic rate, stomatal conductance, intercellular CO2 concentration, and the transpiration rate of horseweed. These results suggest that photosystem I is one of the main biological processes involved in the response of horseweed to CAP.
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Affiliation(s)
- Zuren Li
- Hunan Academy of Agricultural Sciences, Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China.,College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Wei Kuang
- Hunan Academy of Agricultural Sciences, Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China
| | - Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Di Peng
- Hunan Academy of Agricultural Sciences, Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China
| | - Lianyang Bai
- Hunan Academy of Agricultural Sciences, Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China.,College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China
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Tan BC, Lim YS, Lau SE. Proteomics in commercial crops: An overview. J Proteomics 2017; 169:176-188. [PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement. SIGNIFICANCE Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.
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Affiliation(s)
- Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Yin Sze Lim
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
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Meisrimler CN, Wienkoop S, Lüthje S. Proteomic Profiling of the Microsomal Root Fraction: Discrimination of Pisum sativum L. Cultivars and Identification of Putative Root Growth Markers. Proteomes 2017; 5:proteomes5010008. [PMID: 28257117 PMCID: PMC5372229 DOI: 10.3390/proteomes5010008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 12/04/2022] Open
Abstract
Legumes are a large and economically important family, containing a variety of crop plants. Alongside different cereals, some fruits, and tropical roots, a number of leguminosae evolved for millennia as crops with human society. One of these legumes is Pisum sativum L., the common garden pea. In the past, breeding has been largely selective on improved above-ground organs. However, parameters, such as root-growth, which determines acquisition of nutrients and water, have largely been underestimated. Although the genome of P. sativum is still not fully sequenced, multiple proteomic studies have been published on a variety of physiological aspects in the last years. The presented work focused on the connection between root length and the influence of the microsomal root proteome of four different pea cultivars after five days of germination (cultivar Vroege, Girl from the Rhineland, Kelvedon Wonder, and Blauwschokker). In total, 60 proteins were identified to have significantly differential abundances in the four cultivars. Root growth of five-days old seedlings and their microsomal proteome revealed a similar separation pattern, suggesting that cultivar-specific root growth performance is explained by differential membrane and ribosomal protein levels. Hence, we reveal and discuss several putative root growth protein markers possibly playing a key role for improved primary root growth breeding strategies.
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Affiliation(s)
- Claudia-Nicole Meisrimler
- Oxidative Stress and Plant Proteomics Group, Biocenter Klein Flottbek and Botanical Garden, University of Hamburg, Ohnhorststraße 18, D-22609 Hamburg, Germany.
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Stefanie Wienkoop
- Deptartment of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.
| | - Sabine Lüthje
- Oxidative Stress and Plant Proteomics Group, Biocenter Klein Flottbek and Botanical Garden, University of Hamburg, Ohnhorststraße 18, D-22609 Hamburg, Germany.
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