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Tao M, Zhu W, Han H, Liu S, Liu A, Li S, Fu H, Tian J. Mitochondrial proteomic analysis reveals the regulation of energy metabolism and reactive oxygen species production in Clematis terniflora DC. leaves under high-level UV-B radiation followed by dark treatment. J Proteomics 2021; 254:104410. [PMID: 34923174 DOI: 10.1016/j.jprot.2021.104410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/08/2021] [Accepted: 10/19/2021] [Indexed: 11/15/2022]
Abstract
Clematis terniflora DC. is an important medicinal plant from the family Ranunculaceae. A previous study has shown that active ingredients in C. terniflora, such as flavonoids and coumarins, are increased under ultraviolet B radiation (UV-B) and dark treatment and that the numbers of genes related to the tricarboxylic acid cycle and mitochondrial electron transport chain (mETC) are changed. To uncover the mechanism of the response to UV-B radiation and dark treatment in C. terniflora, mitochondrial proteomics was performed. The results showed that proteins related to photorespiration, mitochondrial membrane permeability, the tricarboxylic acid cycle, and the mETC mainly showed differential expression profiles. Moreover, the increase in alternative oxidase indicated that another oxygen-consuming respiratory pathway in plant mitochondria was induced to minimize mitochondrial reactive oxygen species production. These results suggested that respiration and mitochondrial membrane permeability were deeply influenced to avoid energy consumption and maintain energy balance under UV-B radiation and dark treatment in C. terniflora leaf mitochondria. Furthermore, oxidative phosphorylation was able to regulate intracellular oxygen balance to resist oxidative stress. This study improves understanding of the function of mitochondria in response to UV-B radiation and dark treatment in C. terniflora. SIGNIFICANCE: C. terniflora was an important traditional Chinese medicine for anti-inflammatory. Previous study showed that the contents of coumarins which were the main active ingredient in C. terniflora were induced by UV-B radiation and dark treatment. In the present study, to uncover the regulatory mechanism of metabolic changes in C. terniflora, mitochondrial proteomics analysis of leaves was performed. The results showed that photorespiration and oxidative phosphorylation pathways were influenced under UV-B radiation and dark treatment. Mitochondria in C. terniflora leaf played a crucial role in energy mechanism and regulation of cellular oxidation-reduction to maintain cell homeostasis under UV-B radiation followed with dark treatment.
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Affiliation(s)
- Minglei Tao
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China; The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China; College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wei Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China; Changshu Qiushi Technology Co. Ltd, Suzhou 215500, PR China
| | - Haote Han
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Shengzhi Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Amin Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Shouxin Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Hongwei Fu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China; The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China.
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Assessment of the Rice Panicle Initiation by Using NDVI-Based Vegetation Indexes. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112110076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The assessment of rice panicle initiation is crucial for the management of nitrogen fertilizer application that affects yield and quality of grain. The occurrence of panicle initiation could be determined via either green ring, internode-elongation, or a 1–2 mm panicle, and was observed through manual dissection. The quadratic polynomial regression model was used to construct the model of the trend of normalized difference vegetation index-based vegetation indexes (NDVI-based VIs) between pre-tillering and panicle differentiation stages. The slope of the quadratic polynomial regression model tended to be alleviated in the period in which the panicle initiation stage should occur. The results indicated that the trend of the NDVI-based VIs was correlated with panicle initiation. NDVI-based VIs could be a useful indicator to remotely assess panicle initiation.
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Wang ZQ, Zhao QM, Zhong X, Xiao L, Ma LX, Wu CF, Zhang Z, Zhang LQ, Tian Y, Fan W. Comparative analysis of maca (Lepidium meyenii) proteome profiles reveals insights into response mechanisms of herbal plants to high-temperature stress. BMC PLANT BIOLOGY 2020; 20:431. [PMID: 32938390 PMCID: PMC7493174 DOI: 10.1186/s12870-020-02645-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/10/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND High-temperature stress (HTS) is one of the main environmental stresses that limit plant growth and crop production in agricultural systems. Maca (Lepidium meyenii) is an important high-altitude herbaceous plant adapted to a wide range of environmental stimuli such as cold, strong wind and UV-B exposure. However, it is an extremely HTS-sensitive plant species. Thus far, there is limited information about gene/protein regulation and signaling pathways related to the heat stress responses in maca. In this study, proteome profiles of maca seedlings exposed to HTS for 12 h were investigated using a tandem mass tag (TMT)-based proteomic approach. RESULTS In total, 6966 proteins were identified, of which 300 showed significant alterations in expression following HTS. Bioinformatics analyses indicated that protein processing in endoplasmic reticulum was the most significantly up-regulated metabolic pathway following HTS. Quantitative RT-PCR (qRT-PCR) analysis showed that the expression levels of 19 genes encoding proteins mapped to this pathway were significantly up-regulated under HTS. These results show that protein processing in the endoplasmic reticulum may play a crucial role in the responses of maca to HTS. CONCLUSIONS Our proteomic data can be a good resource for functional proteomics of maca and our results may provide useful insights into the molecular response mechanisms underlying herbal plants to HTS.
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Affiliation(s)
- Zhan Qi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Qi Ming Zhao
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Li Xiao
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Li Xuan Ma
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Chou Fei Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Zhongshan Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Li Qin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
- Huzhou central hospital, Huzhou University, Huzhou, 313000 China
| | - Yang Tian
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Wei Fan
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
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4
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Structural and functional properties of plant mitochondrial F-ATP synthase. Mitochondrion 2020; 53:178-193. [DOI: 10.1016/j.mito.2020.06.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/25/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022]
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Xu J, Henry A, Sreenivasulu N. Rice yield formation under high day and night temperatures-A prerequisite to ensure future food security. PLANT, CELL & ENVIRONMENT 2020; 43:1595-1608. [PMID: 32112422 DOI: 10.1111/pce.13748] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 02/18/2020] [Indexed: 05/13/2023]
Abstract
Increasing temperatures resulting from climate change dramatically impact rice crop production in Asia. Depending on the specific stage of rice development, heat stress reduces tiller/panicle number, decreases grain number per plant and lower grain weight, thus negatively impacting yield formation. Hence improving rice crop tolerance to heat stress in terms of sustaining yield stability under high day temperature (HDT), high night temperature (HNT), or combined high day and night temperature (HDNT) will bolster future food security. In this review article, we highlight the phenological alterations caused by heat and the underlying molecular-physiological and genetic mechanisms operating under different types of heat conditions (HDT, HNT, and HDNT) to understand heat tolerance. Based on our synthesis of HDT, HNT, and HDNT effects on rice yield components, we outline future breeding strategies to contribute to sustained food security under climate change.
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Affiliation(s)
- Jiemeng Xu
- International Rice Research Institute, Los Baños, Philippines
| | - Amelia Henry
- International Rice Research Institute, Los Baños, Philippines
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Benjamin JJ, Miras-Moreno B, Araniti F, Salehi H, Bernardo L, Parida A, Lucini L. Proteomics Revealed Distinct Responses to Salinity between the Halophytes Suaeda maritima (L.) Dumort and Salicornia brachiata (Roxb). PLANTS 2020; 9:plants9020227. [PMID: 32050637 PMCID: PMC7076546 DOI: 10.3390/plants9020227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 02/01/2023]
Abstract
Plant resistance to salinity stress is one of the main challenges of agriculture. The comprehension of the molecular and cellular mechanisms involved in plant tolerance to salinity can help to contrast crop losses due to high salt conditions in soil. In this study, Salicornia brachiata and Suaeda maritima, two plants with capacity to adapt to high salinity levels, were investigated at proteome level to highlight the key processes involved in their tolerance to NaCl. With this purpose, plants were treated with 200 mM NaCl as optimal concentration and 500 mM NaCl as a moderate stressing concentration for 14 days. Indeed, 200 mM NaCl did not result in an evident stress condition for both species, although photosynthesis was affected (with a general up accumulation of photosynthesis-related proteins in S. brachiata under salinity). Our findings indicate a coordinated response to salinity in both the halophytes considered, under NaCl conditions. In addition to photosynthesis, heat shock proteins and peroxidase, expansins, signaling processes, and modulation of transcription/translation were affected by salinity. Interestingly, our results suggested distinct mechanisms of tolerance to salinity between the two species considered, with S. brachiata likely having a more efficient mechanism of response to NaCl.
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Affiliation(s)
- Jenifer Joseph Benjamin
- Department of Plant molecular Biology, MS Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Taramani, Chennai 600113, India;
| | - Begoña Miras-Moreno
- Council for Agricultural Research and Economics—Research Centre for Genomics and Bioinformatics (CREA-GB), via San Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy
- Correspondence: (B.M.-M.); (A.P.)
| | - Fabrizio Araniti
- Department of AGRARIA, University “Mediterranea” of Reggio Calabria, I-89124 Reggio Calabria, Italy;
| | - Hajar Salehi
- Laboratory of Plant Cell Biology, Department of Biology, Bu Ali Sina University, Hamedan 65178-38695, Iran;
| | - Letizia Bernardo
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (L.B.); (L.L.)
| | - Ajay Parida
- Department of Plant molecular Biology, MS Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Taramani, Chennai 600113, India;
- Institute of Life Sciences, Department of Biotechnology, Government of India, Bhubaneswar 10, Odisha 751023, India
- Correspondence: (B.M.-M.); (A.P.)
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (L.B.); (L.L.)
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Gázquez A, Abdelgawad H, Baggerman G, Van Raemdonck G, Asard H, Maiale SJ, Rodríguez AA, Beemster GTS. Redox homeostasis in the growth zone of the rice leaf plays a key role in cold tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1053-1066. [PMID: 31624838 DOI: 10.1093/jxb/erz455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
We analysed the cellular and molecular changes in the leaf growth zone of tolerant and sensitive rice varieties in response to suboptimal temperatures. Cold reduced the final leaf length by 35% and 51% in tolerant and sensitive varieties, respectively. Tolerant lines exhibited a smaller reduction of the leaf elongation rate and greater compensation by an increased duration of leaf growth. Kinematic analysis showed that cold reduced cell production in the meristem and the expansion rate in the elongation zone, but the latter was compensated for by a doubling of the duration of cell expansion. We performed iTRAQ proteome analysis on proliferating and expanding parts of the leaf growth zone. We identified 559 and 542 proteins, of which 163 and 210 were differentially expressed between zones, and 96 and 68 between treatments, in the tolerant and sensitive lines, respectively. The categories protein biosynthesis and redox homeostasis were significantly overrepresented in the up-regulated proteins. We therefore measured redox metabolites and enzyme activities in the leaf growth zone, demonstrating that tolerance of rice lines to suboptimal temperatures correlates with the ability to up-regulate enzymatic antioxidants in the meristem and non-enzymatic antioxidants in the elongation zone.
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Affiliation(s)
- Ayelén Gázquez
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Laboratorio de Fisiología de Estrés Abiótico en Plantas, Unidad de Biotecnología 1, IIB-INTECH - CONICET - UNSAM, Chascomús, Argentina
| | - Hamada Abdelgawad
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Department of Botany and Microbiology, Science Faculty, Beni-Suef University, Beni-Suef, Egypt
| | - Geert Baggerman
- Centre for Proteomics (CFP) Core Facility, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Systemic Physiological & Ecotoxicological Research (SPHERE), Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Geert Van Raemdonck
- Centre for Proteomics (CFP) Core Facility, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Han Asard
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Santiago Javier Maiale
- Laboratorio de Fisiología de Estrés Abiótico en Plantas, Unidad de Biotecnología 1, IIB-INTECH - CONICET - UNSAM, Chascomús, Argentina
| | - Andrés Alberto Rodríguez
- Laboratorio de Fisiología de Estrés Abiótico en Plantas, Unidad de Biotecnología 1, IIB-INTECH - CONICET - UNSAM, Chascomús, Argentina
| | - Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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Di Silvestre D, Bergamaschi A, Bellini E, Mauri P. Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World. Proteomes 2018; 6:proteomes6020027. [PMID: 29865292 PMCID: PMC6027444 DOI: 10.3390/proteomes6020027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/26/2022] Open
Abstract
The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.
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Affiliation(s)
- Dario Di Silvestre
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Andrea Bergamaschi
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Edoardo Bellini
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - PierLuigi Mauri
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
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Yu L, Wang W, Zeng S, Chen Z, Yang A, Shi J, Zhao X, Song B. Label-free quantitative proteomics analysis of Cytosinpeptidemycin responses in southern rice black-streaked dwarf virus-infected rice. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2018; 147:20-26. [PMID: 29933987 DOI: 10.1016/j.pestbp.2017.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/19/2017] [Accepted: 06/06/2017] [Indexed: 05/20/2023]
Abstract
Southern rice black-streaked dwarf virus (SRBSDV), a genus Fijivirus of the family Reoviridae, could result in the significant crop losses because being short of an effective controlling measures. Cytosinpeptidemycin, a microbial pesticides developed by China, displayed a wide antiviral activity against many plant viruses. However, its underlying mechanism remains unclear. In this study, a total of 2321 proteins were identified using label-free proteomics technology. Compared with the treatment of SRBSDV-infected rice, 84 and 207 proteins were detected to be up-regulated and only presented in treatment group of SDBSDV-infected rice pre-treated by Cytosinpeptidemycin, which were partially enriched to stress and defense response, such as pathogenesis-related protein 5 (PR-5), pathogenesis-related protein 10 (PR-10) and heat shock protein (Hsp protein). Meanwhile, the real-time quantitative PCR (RT-qPCR) showed that Cytosinpeptidemycin could also up-regulate some resistance genes, and these results indicated a similar trends with the data of the label-free proteomics. Moreover, Cytosinpeptidemycin could enhance the defense enzymatic activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT). These data offer a more comprehensive view about the response of SRBSDV-infected rice triggered by Cytosinpeptidemycin in the level of the proteome, mRNA and enzymatic activity.
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Affiliation(s)
- Lu Yu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Wenli Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Song Zeng
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Zhuo Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China.
| | - Anming Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Jing Shi
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Xiaozhen Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China.
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Rurek M, Czołpińska M, Pawłowski TA, Krzesiński W, Spiżewski T. Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes. Int J Mol Sci 2018; 19:ijms19030877. [PMID: 29547512 PMCID: PMC5877738 DOI: 10.3390/ijms19030877] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 12/11/2022] Open
Abstract
Complex proteomic and physiological approaches for studying cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower (Brassica oleracea var. botrytis) curds after cold and heat and after stress recovery were assayed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) in relation to mRNA abundance and respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold, major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed. In contrast, carbohydrate metabolism enzymes, heat-shock proteins, translation, protein import, and OXPHOS components were involved in heat response and recovery. Several transcriptomic and metabolic regulation mechanisms are also suggested. Cauliflower plants appeared less susceptible to heat; closed stomata in heat stress resulted in moderate photosynthetic, but only minor respiratory impairments, however, photosystem II performance was unaffected. Decreased photorespiration corresponded with proteomic alterations in cold. Our results show that cold and heat stress not only operate in diverse modes (exemplified by cold-specific accumulation of some heat shock proteins), but exert some associations at molecular and physiological levels. This implies a more complex model of action of investigated stresses on plant mitochondria.
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Affiliation(s)
- Michał Rurek
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | - Magdalena Czołpińska
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | | | - Włodzimierz Krzesiński
- Department of Vegetable Crops, Poznan University of Life Sciences, Dąbrowskiego 159, 60-594 Poznań, Poland.
| | - Tomasz Spiżewski
- Department of Vegetable Crops, Poznan University of Life Sciences, Dąbrowskiego 159, 60-594 Poznań, Poland.
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11
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Huang W, Ma HY, Huang Y, Li Y, Wang GL, Jiang Q, Wang F, Xiong AS. Comparative proteomic analysis provides novel insights into chlorophyll biosynthesis in celery under temperature stress. PHYSIOLOGIA PLANTARUM 2017; 161:468-485. [PMID: 28767140 DOI: 10.1111/ppl.12609] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/09/2017] [Accepted: 07/18/2017] [Indexed: 05/03/2023]
Abstract
Chlorophyll (Chl) is essential for light harvesting and energy transduction in photosynthesis. A proper amount of Chl within plant cells is important to celery (Apium graveolens) yield and quality. Temperature stress is an influential abiotic stress affecting Chl biosynthesis and plant growth. There are limited proteomic studies regarding Chl accumulation under temperature stress in celery leaves. Here, the proteins from celery leaves under different temperature treatments (4, 25 and 38°C) were analyzed using a proteomic approach. There were 71 proteins identified through MALDI-TOF-TOF analysis. The relative abundance of proteins involved in carbohydrate and energy metabolism, protein metabolism, amino acid metabolism, antioxidant and polyamine biosynthesis were enhanced under cold stress. These temperature stress-responsive proteins may establish a new homeostasis to enhance temperature tolerance. Magnesium chelatase (Mg-chelatase) and glutamate-1-semialdehyde aminotransferase (GSAT), related to Chl biosynthesis, showed increased abundances under cold stress. Meanwhile, the Chl contents were decreased in heat- and cold-stressed celery leaves. The inhibition of Chl biosynthesis may be due to the downregulated mRNA levels of 15 genes involved in Chl biosynthesis. The study will expand our knowledge on Chl biosynthesis and the temperature tolerance mechanisms in celery leaves.
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Affiliation(s)
- Wei Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong-Yu Ma
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guang-Long Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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Abstract
Low temperature can greatly restrict the growth and development of rice. The rice seedlings show growth retardation, lamina wrap, and part of blade even died under the condition of low temperature. In order to get more information about cold stress responses in rice, two dimensional electrophoresis and bioinformatics analysis of mass spectrometry were used to preliminary survey the cold tolerance of cold sensitive line 9311 and cold resistance variety Fujisaka 5 under cold stress. Two dimensional electrophoresis maps of 9311 and Fujisaka 5 were established under cold treatment. With analysis of bioinformation, the proteins were found involve in many aspects of rice development. The largest category of proteins is functioning on metabolism. By comparing the proteins from the two varieties, it can be found that most proteins from 9311 were down-regulated and were up-regulated in Fujisaka 5. The results showed that the membrane composition and structure were damaged, metabolism changed dramatically and rice defense system was activated under the cold stimulation. Fifty-nine proteins related to the resistance of cold stress were identified in our study, and we have investigated and classified all of their biological functions. The importance of our study are providing some conduct for the research of rice resistant to cold stress, supporting auxiliary technique for rice varieties and widening the search field of cold tolerance in plants.
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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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14
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Sang Q, Shan X, An Y, Shu S, Sun J, Guo S. Proteomic Analysis Reveals the Positive Effect of Exogenous Spermidine in Tomato Seedlings' Response to High-Temperature Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:120. [PMID: 28220137 PMCID: PMC5292424 DOI: 10.3389/fpls.2017.00120] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/20/2017] [Indexed: 05/02/2023]
Abstract
Polyamines are phytohormones that regulate plant growth and development as well as the response to environmental stresses. To evaluate their functions in high-temperature stress responses, the effects of exogenous spermidine (Spd) were determined in tomato leaves using two-dimensional electrophoresis and MALDI-TOF/TOF MS. A total of 67 differentially expressed proteins were identified in response to high-temperature stress and/or exogenous Spd, which were grouped into different categories according to biological processes. The four largest categories included proteins involved in photosynthesis (27%), cell rescue, and defense (24%), protein synthesis, folding and degradation (22%), and energy and metabolism (13%). Exogenous Spd up-regulated most identified proteins involved in photosynthesis, implying an enhancement in photosynthetic capacity. Meanwhile, physiological analysis showed that Spd could improve net photosynthetic rate and the biomass accumulation. Moreover, an increased high-temperature stress tolerance by exogenous Spd would contribute to the higher expressions of proteins involved in cell rescue and defense, and Spd regulated the antioxidant enzymes activities and related genes expression in tomato seedlings exposed to high temperature. Taken together, these findings provide a better understanding of the Spd-induced high-temperature resistance by proteomic approaches, providing valuable insight into improving the high-temperature stress tolerance in the global warming epoch.
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Affiliation(s)
- Qinqin Sang
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Xi Shan
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yahong An
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Sheng Shu
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Jin Sun
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- Nanjing Agricultural University (Suqian), Academy of Protected HorticultureSuqian, China
| | - Shirong Guo
- Key Laboratory of Southern Vegetable Crop Genetic Improvement in Ministry of Agriculture, College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- Nanjing Agricultural University (Suqian), Academy of Protected HorticultureSuqian, China
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15
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Momčilović I, Pantelić D, Zdravković-Korać S, Oljača J, Rudić J, Fu J. Heat-induced accumulation of protein synthesis elongation factor 1A implies an important role in heat tolerance in potato. PLANTA 2016; 244:671-9. [PMID: 27116429 DOI: 10.1007/s00425-016-2534-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/15/2016] [Indexed: 05/14/2023]
Abstract
Potato eukaryotic elongation factor 1A comprises multiple isoforms, some of which are heat-inducible or heat-upregulated and might be important in alleviating adverse effects of heat stress on plant productivity. Heat stress substantially reduces crop productivity worldwide, and will become more severe due to global warming. Identification of proteins involved in heat stress response may help develop varieties for heat tolerance. Eukaryotic elongation factor 1A (eEF1A) is a cytosolic, multifunctional protein that plays a central role in the elongation phase of translation. Some of the non-canonical eEF1A activities might be important in developing plant heat-stress tolerance. In this study, we investigated effects of heat stress (HS) on eEF1A expression at the protein level in potato, a highly heat vulnerable crop. Our results from both the controlled environment and the field have shown that potato eEF1A is a heat-inducible protein of 49.2-kDa with multiple isoforms (5-8). Increase in eEF1A abundance under HS can be mainly attributed to 2-3 basic polypeptides/isoforms. A significant correlation between eEF1A abundance and the potato productivity in the field was observed in two extremely hot years 2011 and 2012. Genomic Southern blot analysis indicated the existence of multiple genes encoding eEF1A in potato. Identification, isolation and utilization of heat-inducible eEF1A genes might be helpful for the development of the heat-tolerant varieties.
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Affiliation(s)
- Ivana Momčilović
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bul. Despota Stefana 142, 11060, Belgrade, Serbia.
| | - Danijel Pantelić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bul. Despota Stefana 142, 11060, Belgrade, Serbia
| | - Snežana Zdravković-Korać
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bul. Despota Stefana 142, 11060, Belgrade, Serbia
| | - Jasmina Oljača
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080, Belgrade, Serbia
| | - Jelena Rudić
- Faculty of Biology, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Jianming Fu
- USDA/ARS/Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan, KS, 66506, USA
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
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16
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Meng X, Zhao Q, Jin Y, Yu J, Yin Z, Chen S, Dai S. Chilling-responsive mechanisms in halophyte Puccinellia tenuiflora seedlings revealed from proteomics analysis. J Proteomics 2016; 143:365-381. [PMID: 27130536 DOI: 10.1016/j.jprot.2016.04.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/14/2016] [Accepted: 04/24/2016] [Indexed: 11/28/2022]
Abstract
Alkali grass (Puccinellia tenuiflora), a monocotyledonous perennial halophyte species, is a good pasture with great nutritional value for livestocks. It can thrive under low temperature in the saline-alkali soil of Songnen plain in northeastern China. In the present study, the chilling-responsive mechanism in P. tenuiflora leaves was investigated using physiological and proteomic approaches. After treatment of 10°C for 10 and 20days, photosynthesis, biomass, contents of osmolytes and antioxidants, and activities of reactive oxygen species scavenging enzymes were analyzed in leaves of 20-day-old seedlings. Besides, 89 chilling-responsive proteins were revealed from proteomic analysis. All the results highlighted that the growth of seedlings was inhibited due to chilling-decreased enzymes in photosynthesis, carbohydrate metabolism, and energy supplying. The accumulation of osmolytes (i.e., proline, soluble sugar, and glycine betaine) and enhancement of ascorbate-glutathione cycle and glutathione peroxidase/glutathione S-transferase pathway in leaves could minimize oxidative damage of membrane and other molecules under the chilling conditions. In addition, protein synthesis and turnover in cytoplasm and chloroplast were altered to cope with the chilling stress. This study provides valuable information for understanding the chilling-responsive and cross-tolerant mechanisms in monocotyledonous halophyte plant species.
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Affiliation(s)
- Xuejiao Meng
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China
| | - Qi Zhao
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China
| | - Yudan Jin
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China
| | - Juanjuan Yu
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China
| | - Zepeng Yin
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
| | - Shaojun Dai
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China.
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17
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Litholdo CG, Parker BL, Eamens AL, Larsen MR, Cordwell SJ, Waterhouse PM. Proteomic Identification of Putative MicroRNA394 Target Genes in Arabidopsis thaliana Identifies Major Latex Protein Family Members Critical for Normal Development. Mol Cell Proteomics 2016; 15:2033-47. [PMID: 27067051 DOI: 10.1074/mcp.m115.053124] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/06/2022] Open
Abstract
Expression of the F-Box protein Leaf Curling Responsiveness (LCR) is regulated by microRNA, miR394, and alterations to this interplay in Arabidopsis thaliana produce defects in leaf polarity and shoot apical meristem organization. Although the miR394-LCR node has been documented in Arabidopsis, the identification of proteins targeted by LCR F-box itself has proven problematic. Here, a proteomic analysis of shoot apices from plants with altered LCR levels identified a member of the Latex Protein (MLP) family gene as a potential LCR F-box target. Bioinformatic and molecular analyses also suggested that other MLP family members are likely to be targets for this post-translational regulation. Direct interaction between LCR F-Box and MLP423 was validated. Additional MLP members had reduction in protein accumulation, in varying degrees, mediated by LCR F-Box. Transgenic Arabidopsis lines, in which MLP28 expression was reduced through an artificial miRNA technology, displayed severe developmental defects, including changes in leaf patterning and morphology, shoot apex defects, and eventual premature death. These phenotypic characteristics resemble those of Arabidopsis plants modified to over-express LCR Taken together, the results demonstrate that MLPs are driven to degradation by LCR, and indicate that MLP gene family is target of miR394-LCR regulatory node, representing potential targets for directly post-translational regulation mediated by LCR F-Box. In addition, MLP28 family member is associated with the LCR regulation that is critical for normal Arabidopsis development.
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Affiliation(s)
- Celso G Litholdo
- From the ‡School of Biological Sciences, The University of Sydney, Camperdown NSW 2006, Australia; §Laboratório de Biologia Molecular de Plantas, Universidade Federal do Rio de Janeiro, Cidade Universitária, RJ, Brazil;
| | - Benjamin L Parker
- ¶Charles Perkins Centre, School of Molecular Bioscience, The University of Sydney, Darlington NSW 2006, Australia
| | - Andrew L Eamens
- ‖School of Environmental and Life Sciences, The University of Newcastle, Callaghan NSW 2308, Australia
| | - Martin R Larsen
- **Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark
| | - Stuart J Cordwell
- ¶Charles Perkins Centre, School of Molecular Bioscience, The University of Sydney, Darlington NSW 2006, Australia
| | - Peter M Waterhouse
- From the ‡School of Biological Sciences, The University of Sydney, Camperdown NSW 2006, Australia; ‡‡Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane QLD 4001, Australia
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18
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Sun CX, Li MQ, Gao XX, Liu LN, Wu XF, Zhou JH. Metabolic response of maize plants to multi-factorial abiotic stresses. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18 Suppl 1:120-9. [PMID: 25622534 DOI: 10.1111/plb.12305] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/08/2015] [Indexed: 05/09/2023]
Abstract
Clarification of the metabolic mechanisms underlying multi-stress responses in plants will allow further optimisation of crop breeding and cultivation to obtain high yields in an increasingly variable environment. Using NMR metabolomic techniques, we examined the metabolic responses of maize plants grown under different conditions: soil drought, soil salinity, heat and multiple concurrent stresses. A detailed time-course metabolic profile was also performed on maize plants sampled 1, 3 and 7 days after initiation of soil drought and heat stress. The metabolic profile of maize plants subjected to soil drought was more similar to plants exposed to salt stress than to heat-stressed plants. Drought-stressed maize plants subjected to salt or heat stress showed distinct integrated metabolic profiles compared with those exposed to either stressor individually. These differences show the considerable metabolic plasticity of maize in response to different growth conditions. Moreover, glucose, fructose, malate, citrate, proline, alanine, aspartate, asparagine, threonine and one unknown compound fluctuated obviously between maize plants grown in controlled growth cabinet and a natural regime. These changes were associated with the TCA cycle and core nitrogen metabolism, and could be related to their multiple functions during plant growth. The evident stress-induced trajectory of metabolic changes in maize indicated that the primary metabolic responses to soil drought, heat and combined drought and heat stresses occurred in a time-dependent manner. Plasticity at the metabolic level may allow maize plants to acclimatise their metabolic ranges in response to changing environmental conditions.
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Affiliation(s)
- C X Sun
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - M Q Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - X X Gao
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - L N Liu
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - X F Wu
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - J H Zhou
- College of Life and Health Sciences, Northeastern University, Shenyang, China
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19
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Song L, Liu Z, Tong J, Xiao L, Ma H, Zhang H. Comparative proteomics analysis reveals the mechanism of fertility alternation of thermosensitive genic male sterile rice lines under low temperature inducement. Proteomics 2015; 15:1884-905. [PMID: 25641954 DOI: 10.1002/pmic.201400103] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 12/18/2014] [Accepted: 01/28/2015] [Indexed: 11/10/2022]
Abstract
Thermosensitive genic male sterile (TGMS) rice line has made great economical contributions in rice production. However, the fertility of TGMS rice line during hybrid seed production is frequently influenced by low temperature, thus leading to its fertility/sterility alteration and hybrid seed production failure. To understand the mechanism of fertility alternation under low temperature inducement, the extracted proteins from young panicles of two TGMS rice lines at the fertility alternation sensitivity stage were analyzed by 2DE. Eighty-three protein spots were found to be significantly changed in abundance, and identified by MALDI-TOF-TOF MS. The identified proteins were involved in 16 metabolic pathways and cellular processes. The young panicles of TGMS rice line Zhu 1S possessed the lower ROS-scavenging, indole-3-acetic acid level, soluble protein, and sugar contents as well as the faster anther wall disintegration than those of TGMS rice line Zhun S. All these major differences might result in that the former is more stable in fertility than the latter. Based on the majority of the 83 identified proteins, together with microstructural, physiological, and biochemical results, a possible fertile alteration mechanism in the young panicles of TGMS rice line under low temperature inducement was proposed. Such a result will help us in breeding TGMS rice lines and production of hybrid seed.
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Affiliation(s)
- Liru Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, P. R. China
| | - Zhongqi Liu
- College of Agronomy, Hunan Agricultural University, Collaborative Innovation Center of Grain and Oil crops in South China, Changsha, P. R. China.,State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, P. R. China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Agricultural University, Changsha, P. R. China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Agricultural University, Changsha, P. R. China
| | - Hao Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, P. R. China
| | - Haiqing Zhang
- College of Agronomy, Hunan Agricultural University, Collaborative Innovation Center of Grain and Oil crops in South China, Changsha, P. R. China.,State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, P. R. China
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20
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Rurek M, Woyda-Ploszczyca AM, Jarmuszkiewicz W. Biogenesis of mitochondria in cauliflower (Brassica oleracea var. botrytis) curds subjected to temperature stress and recovery involves regulation of the complexome, respiratory chain activity, organellar translation and ultrastructure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:399-417. [PMID: 25617518 DOI: 10.1016/j.bbabio.2015.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 12/05/2014] [Accepted: 01/16/2015] [Indexed: 12/30/2022]
Abstract
The biogenesis of the cauliflower curd mitochondrial proteome was investigated under cold, heat and the recovery. For the first time, two dimensional fluorescence difference gel electrophoresis was used to study the plant mitochondrial complexome in heat and heat recovery. Particularly, changes in the complex I and complex III subunits and import proteins, and the partial disintegration of matrix complexes were observed. The presence of unassembled subunits of ATP synthase was accompanied by impairment in mitochondrial translation of its subunit. In cold and heat, the transcription profiles of mitochondrial genes were uncorrelated. The in-gel activities of respiratory complexes were particularly affected after stress recovery. Despite a general stability of respiratory chain complexes in heat, functional studies showed that their activity and the ATP synthesis yield were affected. Contrary to cold stress, heat stress resulted in a reduced efficiency of oxidative phosphorylation likely due to changes in alternative oxidase (AOX) activity. Stress and stress recovery differently modulated the protein level and activity of AOX. Heat stress induced an increase in AOX activity and protein level, and AOX1a and AOX1d transcript level, while heat recovery reversed the AOX protein and activity changes. Conversely, cold stress led to a decrease in AOX activity (and protein level), which was reversed after cold recovery. Thus, cauliflower AOX is only induced by heat stress. In heat, contrary to the AOX activity, the activity of rotenone-insensitive internal NADH dehydrogenase was diminished. The relevance of various steps of plant mitochondrial biogenesis to temperature stress response and recovery is discussed.
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Affiliation(s)
- Michal Rurek
- Department of Cellular and Molecular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | - Andrzej M Woyda-Ploszczyca
- Department of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Wieslawa Jarmuszkiewicz
- Department of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
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21
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Obrępalska-Stęplowska A, Renaut J, Planchon S, Przybylska A, Wieczorek P, Barylski J, Palukaitis P. Effect of temperature on the pathogenesis, accumulation of viral and satellite RNAs and on plant proteome in peanut stunt virus and satellite RNA-infected plants. FRONTIERS IN PLANT SCIENCE 2015; 6:903. [PMID: 26579153 PMCID: PMC4625170 DOI: 10.3389/fpls.2015.00903] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/09/2015] [Indexed: 05/08/2023]
Abstract
Temperature is an important environmental factor influencing plant development in natural and diseased conditions. The growth rate of plants grown at C27°C is more rapid than for plants grown at 21°C. Thus, temperature affects the rate of pathogenesis progression in individual plants. We have analyzed the effect of temperature conditions (either 21°C or 27°C during the day) on the accumulation rate of the virus and satellite RNA (satRNA) in Nicotiana benthamiana plants infected by peanut stunt virus (PSV) with and without its satRNA, at four time points. In addition, we extracted proteins from PSV and PSV plus satRNA-infected plants harvested at 21 dpi, when disease symptoms began to appear on plants grown at 21°C and were well developed on those grown at 27°C, to assess the proteome profile in infected plants compared to mock-inoculated plants grown at these two temperatures, using 2D-gel electrophoresis and mass spectrometry approaches. The accumulation rate of the viral RNAs and satRNA was more rapid at 27°C at the beginning of the infection and then rapidly decreased in PSV-infected plants. At 21 dpi, PSV and satRNA accumulation was higher at 21°C and had a tendency to increase further. In all studied plants grown at 27°C, we observed a significant drop in the identified proteins participating in photosynthesis and carbohydrate metabolism at the proteome level, in comparison to plants maintained at 21°C. On the other hand, the proteins involved in protein metabolic processes were all more abundant in plants grown at 27°C. This was especially evident when PSV-infected plants were analyzed, where increase in abundance of proteins involved in protein synthesis, degradation, and folding was revealed. In mock-inoculated and PSV-infected plants we found an increase in abundance of the majority of stress-related differently-regulated proteins and those associated with protein metabolism. In contrast, in PSV plus satRNA-infected plants the shift in the temperature barely increased the level of stress-related proteins.
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Affiliation(s)
- Aleksandra Obrępalska-Stęplowska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection – National Research InstitutePoznań, Poland
- *Correspondence: Aleksandra Obrępalska-Stęplowska
| | - Jenny Renaut
- Department Environmental Research and Innovation, Integrative Biology Facility, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Sebastien Planchon
- Department Environmental Research and Innovation, Integrative Biology Facility, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Arnika Przybylska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection – National Research InstitutePoznań, Poland
| | - Przemysław Wieczorek
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection – National Research InstitutePoznań, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz UniversityPoznań, Poland
| | - Peter Palukaitis
- Department of Horticultural Sciences, Seoul Women UniversitySeoul, South Korea
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22
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Yuan XY, Liang F, Jiang SH, Wan MF, Ma J, Zhang XY, Cui B. Differential protein expression in Phalaenopsis under low temperature. Appl Biochem Biotechnol 2014; 175:909-24. [PMID: 25349090 DOI: 10.1007/s12010-014-1345-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/20/2014] [Indexed: 11/25/2022]
Abstract
A comparative proteomic analysis was carried out to explore the molecular mechanisms of responses to cold stress in Phalaenopsis after treated by low temperature (13/8 °C day/night) for 15 days. Differentially expressed proteins were examined using two-dimensional electrophoresis (2-DE) and matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-TOF/MS). Among 85 differentially expressed proteins, 73 distinct proteins were identified. Comparative analysis revealed that the identified proteins mainly participate in photosynthesis, protein synthesis, folding and degradation, respiration, defense response, amino acid metabolism, energy pathway, cytoskeleton, transcription regulation, signal transduction, and seed storage protein, while the functional classification of the remaining four proteins was not determined. These data suggested that the proteins might work cooperatively to establish a new homeostasis under cold stress; 37 % of the identified cold-responsive proteins were associated with various aspects of chloroplast physiology, and 56 % of them were predicted to be located in the chloroplasts, implying that the cold stress tolerance of Phalaenopsis was achieved, at least partly, by regulation of chloroplast function. Moreover, the protein destination control, which was mediated by chaperones and proteases, plays an important role in tolerance to cold stress.
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Affiliation(s)
- Xiu-Yun Yuan
- Institute of Bioengineering, Zhengzhou Normal University, Zhengzhou, 450044, China,
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23
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Wearne TA, Mirzaei M, Franklin JL, Goodchild AK, Haynes PA, Cornish JL. Methamphetamine-induced sensitization is associated with alterations to the proteome of the prefrontal cortex: implications for the maintenance of psychotic disorders. J Proteome Res 2014; 14:397-410. [PMID: 25245100 DOI: 10.1021/pr500719f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Repeat administration of psychostimulants, such as methamphetamine, produces a progressive increase in locomotor activity (behavioral sensitization) in rodents that is believed to represent the underlying neurochemical changes driving psychoses. Alterations to the prefrontal cortex (PFC) are suggested to mediate the etiology and maintenance of these behavioral changes. As such, the aim of the current study was to investigate changes to protein expression in the PFC in male rats sensitized to methamphetamine using quantitative label-free shotgun proteomics. A methamphetamine challenge resulted in a significant sensitized locomotor response in methamphetamine pretreated animals compared to saline controls. Proteomic analysis revealed 96 proteins that were differentially expressed in the PFC of methamphetamine treated rats, with 20% of these being previously implicated in the neurobiology of schizophrenia in the PFC. We identified multiple biological functions in the PFC that appear to be commonly altered across methamphetamine-induced sensitization and schizophrenia, and these include synaptic regulation, protein phosphatase signaling, mitochondrial function, and alterations to the inhibitory GABAergic network. These changes could inform how alterations to the PFC could underlie the cognitive and behavioral dysfunction commonly seen across psychoses and places such biological changes as potential mediators in the maintenance of psychosis vulnerability.
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Affiliation(s)
- Travis A Wearne
- Department of Psychology, ‡Department of Chemistry and Biomolecular Sciences, §Australian School of Advanced Medicine, Macquarie University , Sydney, New South Wales 2109, Australia
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Ng ZX, Chua KH, Kuppusamy UR. Proteomic analysis of heat treated bitter gourd (Momordica charantia L. var. Hong Kong Green) using 2D-DIGE. Food Chem 2014; 148:155-61. [DOI: 10.1016/j.foodchem.2013.10.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 09/07/2013] [Accepted: 10/06/2013] [Indexed: 10/26/2022]
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25
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Mora L, Bramley PM, Fraser PD. Development and optimisation of a label-free quantitative proteomic procedure and its application in the assessment of genetically modified tomato fruit. Proteomics 2014; 13:2016-30. [PMID: 23616442 DOI: 10.1002/pmic.201200480] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 04/01/2013] [Accepted: 04/10/2013] [Indexed: 01/01/2023]
Abstract
A key global challenge for plant biotechnology is addressing food security, whereby provision must be made to feed 9 billion people with nutritional feedstuffs by 2050. To achieve this step change in agricultural production new crop varieties are required that are tolerant to environmental stresses imposed by climate change, have better yields, are more nutritious and require less resource input. Genetic modification (GM) and marker-assisted screening will need to be fully utilised to deliver these new crop varieties. To evaluate these varieties both in terms of environmental and food safety and the rational design of traits a systems level characterisation is necessary. To link the transcriptome to the metabolome, quantitative proteomics is required. Routine quantitative proteomics is an important challenge. Gel-based densitometry and MS analysis after stable isotope labeling have been employed. In the present article, we describe the application of a label-free approach that can be used in combination with SDS-PAGE and reverse-phase chromatography to evaluate the changes in the proteome of new crop varieties. The workflow has been optimised for protein coverage, accuracy and robustness, then its application demonstrated using a GM tomato variety engineered to deliver nutrient dense fruit.
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Affiliation(s)
- Leticia Mora
- Centre for Systems and Synthetic Biology, School of Biological Sciences, Royal Holloway, University of London, Egham, UK
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26
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Barkla BJ, Vera-Estrella R, Pantoja O. Progress and challenges for abiotic stress proteomics of crop plants. Proteomics 2014; 13:1801-15. [PMID: 23512887 DOI: 10.1002/pmic.201200401] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 12/12/2022]
Abstract
Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS-based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome.
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Affiliation(s)
- Bronwyn J Barkla
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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27
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Liu HM, Fang L, Che YS, Wu FZ, Yang CP. Protein expression patterns in two Spiraea species in response to cold treatment. Mol Biol Rep 2014; 41:4533-47. [DOI: 10.1007/s11033-014-3324-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 02/26/2014] [Indexed: 10/25/2022]
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28
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Liao JL, Zhou HW, Zhang HY, Zhong PA, Huang YJ. Comparative proteomic analysis of differentially expressed proteins in the early milky stage of rice grains during high temperature stress. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:655-71. [PMID: 24376254 PMCID: PMC3904723 DOI: 10.1093/jxb/ert435] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rice yield and quality are adversely affected by high temperatures, and these effects are more pronounced at the 'milky stage' of the rice grain ripening phase. Identifying the functional proteins involved in the response of rice to high temperature stress may provide the basis for improving heat tolerance in rice. In the present study, a comparative proteomic analysis of paired, genetically similar heat-tolerant and heat-sensitive rice lines was conducted. Two-dimensional electrophoresis (2-DE) revealed a total of 27 differentially expressed proteins in rice grains, predominantly from the heat-tolerant lines. The protein profiles clearly indicated variations in protein expression between the heat-tolerant and heat-sensitive rice lines. Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS) analysis revealed that 25 of the 27 differentially displayed proteins were homologous to known functional proteins. These homologous proteins were involved in biosynthesis, energy metabolism, oxidation, heat shock metabolism, and the regulation of transcription. Seventeen of the 25 genes encoding the differentially displayed proteins were mapped to rice chromosomes according to the co-segregating conditions between the simple sequence repeat (SSR) markers and the target genes in recombinant inbred lines (RILs). The proteins identified in the present study provide a basis to elucidate further the molecular mechanisms underlying the adaptation of rice to high temperature stress.
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Affiliation(s)
- Jiang-Lin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province 330045, China
- Key Laboratory of Agriculture responding to Climate Change (Jiangxi Agricultural University), Nanchang City, Jiangxi Province 330045, China
- * These authors contributed equally to this work
| | - Hui-Wen Zhou
- Key Laboratory of Agriculture responding to Climate Change (Jiangxi Agricultural University), Nanchang City, Jiangxi Province 330045, China
- * These authors contributed equally to this work
| | - Hong-Yu Zhang
- Key Laboratory of Agriculture responding to Climate Change (Jiangxi Agricultural University), Nanchang City, Jiangxi Province 330045, China
| | - Ping-An Zhong
- Key Laboratory of Agriculture responding to Climate Change (Jiangxi Agricultural University), Nanchang City, Jiangxi Province 330045, China
| | - Ying-Jin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education, Jiangxi Province 330045, China
- Key Laboratory of Agriculture responding to Climate Change (Jiangxi Agricultural University), Nanchang City, Jiangxi Province 330045, China
- To whom correspondence should be addressed. E-mail:
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29
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Kim ST, Kim SG, Agrawal GK, Kikuchi S, Rakwal R. Rice proteomics: a model system for crop improvement and food security. Proteomics 2014; 14:593-610. [PMID: 24323464 DOI: 10.1002/pmic.201300388] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/24/2013] [Accepted: 11/07/2013] [Indexed: 12/14/2022]
Abstract
Rice proteomics has progressed at a tremendous pace since the year 2000, and that has resulted in establishing and understanding the proteomes of tissues, organs, and organelles under both normal and abnormal (adverse) environmental conditions. Established proteomes have also helped in re-annotating the rice genome and revealing the new role of previously known proteins. The progress of rice proteomics had recognized it as the corner/stepping stone for at least cereal crops. Rice proteomics remains a model system for crops as per its exemplary proteomics research. Proteomics-based discoveries in rice are likely to be translated in improving crop plants and vice versa against ever-changing environmental factors. This review comprehensively covers rice proteomics studies from August 2010 to July 2013, with major focus on rice responses to diverse abiotic (drought, salt, oxidative, temperature, nutrient, hormone, metal ions, UV radiation, and ozone) as well as various biotic stresses, especially rice-pathogen interactions. The differentially regulated proteins in response to various abiotic stresses in different tissues have also been summarized, indicating key metabolic and regulatory pathways. We envision a significant role of rice proteomics in addressing the global ground level problem of food security, to meet the demands of the human population which is expected to reach six to nine billion by 2040.
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Affiliation(s)
- Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
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30
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Neilson KA, George IS, Emery SJ, Muralidharan S, Mirzaei M, Haynes PA. Analysis of rice proteins using SDS-PAGE shotgun proteomics. Methods Mol Biol 2014; 1072:289-302. [PMID: 24136530 DOI: 10.1007/978-1-62703-631-3_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this chapter we describe the workflow used in our laboratory to analyze rice leaf samples using label-free shotgun proteomics based on SDS-PAGE fractionation of proteins. Rice proteomics has benefitted substantially from successful execution of shotgun proteomics techniques. We describe steps on how to proceed starting from rice protein extraction, SDS-PAGE, in-gel protein digestion with trypsin, nanoLC-MS/MS, and database searching using the GPM. Data from these experiments can be used for spectral counting, where simultaneous quantitation of several thousand proteins can be obtained.
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Affiliation(s)
- Karlie A Neilson
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
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31
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Capriotti AL, Borrelli GM, Colapicchioni V, Papa R, Piovesana S, Samperi R, Stampachiacchiere S, Laganà A. Proteomic study of a tolerant genotype of durum wheat under salt-stress conditions. Anal Bioanal Chem 2013; 406:1423-35. [PMID: 24337188 DOI: 10.1007/s00216-013-7549-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/21/2013] [Accepted: 12/02/2013] [Indexed: 11/24/2022]
Abstract
Salinity is one of the major abiotic stress conditions limiting crop growth and productivity. Duilio is a wheat genotype that shows tolerant behavior in both salt-stress and drought-stress conditions. Toward better understanding of the biochemical response to salinity in this genotype of durum wheat, a comparative label-free shotgun proteomic analysis based on normalized spectral abundance factors was conducted on wheat leaf samples subjected to increasing salt-stress levels (100 and 200 mmol L(-1) NaCl) with respect to untreated samples. We found significant changes in 71 proteins for the first stress level, in 83 proteins at the higher salinity level, and in 88 proteins when comparing salt-stress levels with each other. The major changes concerned the proteins involved in primary metabolism and production of energy, followed by those involved in protein metabolism and cellular defense mechanisms. Some indications of different specific physiological and defense mechanisms implicated in increasing tolerance were obtained. The enhanced salinity tolerance in Duilio appeared to be governed by a higher capacity for osmotic homeostasis, a more efficient defense, and an improvement of protection from mechanical stress by increased cell wall lignifications, allowing a better potential for growth recovery.
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Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy,
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32
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Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement. J Proteomics 2013; 93:5-19. [DOI: 10.1016/j.jprot.2013.05.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/20/2013] [Accepted: 05/29/2013] [Indexed: 12/22/2022]
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33
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Zhang Y, Gao P, Xing Z, Jin S, Chen Z, Liu L, Constantino N, Wang X, Shi W, Yuan JS, Dai SY. Application of an improved proteomics method for abundant protein cleanup: molecular and genomic mechanisms study in plant defense. Mol Cell Proteomics 2013; 12:3431-42. [PMID: 23943779 DOI: 10.1074/mcp.m112.025213] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
High abundance proteins like ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) impose a consistent challenge for the whole proteome characterization using shot-gun proteomics. To address this challenge, we developed and evaluated Polyethyleneimine Assisted Rubisco Cleanup (PARC) as a new method by combining both abundant protein removal and fractionation. The new approach was applied to a plant insect interaction study to validate the platform and investigate mechanisms for plant defense against herbivorous insects. Our results indicated that PARC can effectively remove Rubisco, improve the protein identification, and discover almost three times more differentially regulated proteins. The significantly enhanced shot-gun proteomics performance was translated into in-depth proteomic and molecular mechanisms for plant insect interaction, where carbon re-distribution was used to play an essential role. Moreover, the transcriptomic validation also confirmed the reliability of PARC analysis. Finally, functional studies were carried out for two differentially regulated genes as revealed by PARC analysis. Insect resistance was induced by over-expressing either jacalin-like or cupin-like genes in rice. The results further highlighted that PARC can serve as an effective strategy for proteomics analysis and gene discovery.
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Affiliation(s)
- Yixiang Zhang
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub (SSBiH), Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843
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34
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Neilson KA, Scafaro AP, Chick JM, George IS, Van Sluyter SC, Gygi SP, Atwell BJ, Haynes PA. The influence of signals from chilled roots on the proteome of shoot tissues in rice seedlings. Proteomics 2013; 13:1922-33. [DOI: 10.1002/pmic.201200475] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/06/2012] [Accepted: 02/07/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Karlie A. Neilson
- Department of Chemistry and Biomolecular Sciences; Macquarie University; New South Wales; Australia
| | - Andrew P. Scafaro
- Department of Biological Sciences, Macquarie University; New South Wales Australia
| | - Joel M. Chick
- Department of Cell Biology, Harvard Medical School; MA USA
| | - Iniga S. George
- Department of Chemistry and Biomolecular Sciences; Macquarie University; New South Wales; Australia
| | - Steven C. Van Sluyter
- Department of Chemistry and Biomolecular Sciences; Macquarie University; New South Wales; Australia
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School; MA USA
| | - Brian J. Atwell
- Department of Biological Sciences, Macquarie University; New South Wales Australia
| | - Paul A. Haynes
- Department of Chemistry and Biomolecular Sciences; Macquarie University; New South Wales; Australia
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35
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Lee LY, Hincapie M, Packer N, Baker MS, Hancock WS, Fanayan S. An optimized approach for enrichment of glycoproteins from cell culture lysates using native multi-lectin affinity chromatography. J Sep Sci 2013; 35:2445-52. [PMID: 22997032 DOI: 10.1002/jssc.201200049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Lectins are capable of recognizing specific glycan structures and serve as invaluable tools for the separation of glycosylated proteins from nonglycosylated proteins in biological samples. We report on the optimization of native multi-lectin affinity chromatography, combining three lectins, namely, concanavalin A, jacalin, and wheat germ agglutinin for fractionation of cellular glycoproteins from MCF-7 breast cancer lysate. We evaluated several conditions for optimum recovery of total proteins and glycoproteins such as low pH and saccharide elution buffers, and the inclusion of detergents in binding and elution buffers. Optimum recovery was observed with overnight incubation of cell lysate with lectins at 4°C, and inclusion of detergent in binding and saccharide elution buffers. Total protein and bound recoveries were 80 and 9%, respectively. Importantly, we found that high saccharide strength elution buffers were not necessary to release bound glycoproteins. This study demonstrates that multi-lectin affinity chromatography can be extended to total cell lysate to investigate the cellular glycoproteome.
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Affiliation(s)
- Ling Y Lee
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
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36
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Monavarfeshani A, Mirzaei M, Sarhadi E, Amirkhani A, Khayam Nekouei M, Haynes PA, Mardi M, Salekdeh GH. Shotgun proteomic analysis of the Mexican lime tree infected with "CandidatusPhytoplasma aurantifolia". J Proteome Res 2013; 12:785-95. [PMID: 23244174 DOI: 10.1021/pr300865t] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infection of Mexican lime trees (Citrus aurantifolia L.) with the specialized bacterium "CandidatusPhytoplasma aurantifolia" causes witches' broom disease. Witches' broom disease has the potential to cause significant economic losses throughout western Asia and North Africa. We used label-free quantitative shotgun proteomics to study changes in the proteome of Mexican lime trees in response to infection by "Ca. Phytoplasma aurantifolia". Of 990 proteins present in five replicates of healthy and infected plants, the abundances of 448 proteins changed significantly in response to phytoplasma infection. Of these, 274 proteins were less abundant in infected plants than in healthy plants, and 174 proteins were more abundant in infected plants than in healthy plants. These 448 proteins were involved in stress response, metabolism, growth and development, signal transduction, photosynthesis, cell cycle, and cell wall organization. Our results suggest that proteomic changes in response to infection by phytoplasmas might support phytoplasma nutrition by promoting alterations in the host's sugar metabolism, cell wall biosynthesis, and expression of defense-related proteins. Regulation of defense-related pathways suggests that defense compounds are induced in interactions with susceptible as well as resistant hosts, with the main differences between the two interactions being the speed and intensity of the response.
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Affiliation(s)
- Aboozar Monavarfeshani
- Department of Genomics, Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran
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37
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Neilson KA, Keighley T, Pascovici D, Cooke B, Haynes PA. Label-free quantitative shotgun proteomics using normalized spectral abundance factors. Methods Mol Biol 2013; 1002:205-222. [PMID: 23625406 DOI: 10.1007/978-1-62703-360-2_17] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this chapter we describe the workflow used in our laboratory for label-free quantitative shotgun proteomics based on spectral counting. The main tools used are a series of R modules known collectively as the Scrappy program. We describe how to go from peptide to spectrum matching in a shotgun proteomics experiment using the XTandem algorithm, to simultaneous quantification of up to thousands of proteins, using normalized spectral abundance factors. The outputs of the software are described in detail, with illustrative examples provided for some of the graphical images generated. While it is not strictly within the scope of this chapter, some consideration is given to how best to extract meaningful biological information from quantitative shotgun proteomics data outputs.
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38
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Zhang S, Feng L, Jiang H, Ma W, Korpelainen H, Li C. Biochemical and proteomic analyses reveal that Populus cathayana males and females have different metabolic activities under chilling stress. J Proteome Res 2012; 11:5815-26. [PMID: 23072643 DOI: 10.1021/pr3005953] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Male and female poplars (Populus cathayana Rehd.) respond differently to environmental stresses. However, little is known about sex-dependent responses to chilling at the proteome level. To better understand these differences, a comparative proteomics investigation combined with a biochemical approach was used in the current study. Three-month-old poplar cuttings were treated at 25 or 4 °C for 14 days. Results revealed significant sexual differences in nitrogen metabolic enzymes and free amino acid components in response to chilling. The chilling-treated males showed higher activities of nitrate reductase and glutamine synthetase and higher contents of reduced glutathione, serine, arginine, leucine, glycine, proline and methionine than chilling-treated females. A total of 65 chilling-responsive spots were found, of which 48 showed significant sexual differences. These proteins are involved in photosynthesis, carbon and energy metabolism, metabolic processes of proteins, lipid metabolism, vitamin metabolism, stress defense, and gene expression regulation. The study shows that males have more effective metabolic processes and protective systems to chilling than females.
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Affiliation(s)
- Sheng Zhang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China
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39
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Mirzaei M, Pascovici D, Atwell BJ, Haynes PA. Differential regulation of aquaporins, small GTPases and V-ATPases proteins in rice leaves subjected to drought stress and recovery. Proteomics 2012; 12:864-77. [PMID: 22539437 DOI: 10.1002/pmic.201100389] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mechanisms of drought tolerance are complex, interacting, and polygenic. This paper describes patterns of gene expression at precise physiological stages of drought in 35-day-old seedlings of Oryza sativa cv. Nipponbare. Drought was imposed gradually for up to 15 days, causing abscisic acid levels to rise and growth to cease, and plants were then re-watered. Proteins were identified from leaf samples after moderate drought, extreme drought, and 3 and 6 days of re-watering. Label-free quantitative shotgun proteomics resulted in identification of 1548 non-redundant proteins. More proteins were down-regulated in early stages of drought but more were up-regulated as severe drought developed. After re-watering, there was notable down regulation, suggesting that stress-related proteins were being degraded. Proteins involved in signalling and transport became dominant as severe drought took hold but decreased again on re-watering. Most of the nine aquaporins identified were responsive to drought, with six decreasing rapidly in abundance as plants were re-watered. Nine G-proteins appeared in large amounts during severe drought and dramatically degraded once plants were re-watered. We speculate that water transport and drought signalling are critical elements of the overall response to drought in rice and might be the key to biotechnological approaches to drought tolerance.
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Affiliation(s)
- Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
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40
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Abdallah C, Dumas-Gaudot E, Renaut J, Sergeant K. Gel-based and gel-free quantitative proteomics approaches at a glance. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2012:494572. [PMID: 23213324 PMCID: PMC3508552 DOI: 10.1155/2012/494572] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/12/2012] [Indexed: 05/06/2023]
Abstract
Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed.
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Affiliation(s)
- Cosette Abdallah
- Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
- UMR Agroécologie INRA 1347/Agrosup/Université de Bourgogne, Pôle Interactions Plantes Microorganismes ERL 6300 CNRS, Boite Postal 86510, 21065 Dijon Cedex, France
| | - Eliane Dumas-Gaudot
- UMR Agroécologie INRA 1347/Agrosup/Université de Bourgogne, Pôle Interactions Plantes Microorganismes ERL 6300 CNRS, Boite Postal 86510, 21065 Dijon Cedex, France
| | - Jenny Renaut
- Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Kjell Sergeant
- Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
- *Kjell Sergeant:
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41
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Mirzaei M, Soltani N, Sarhadi E, Pascovici D, Keighley T, Salekdeh GH, Haynes PA, Atwell BJ. Shotgun Proteomic Analysis of Long-distance Drought Signaling in Rice Roots. J Proteome Res 2011; 11:348-58. [DOI: 10.1021/pr2008779] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Neda Soltani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | - Elham Sarhadi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | - Dana Pascovici
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW, Australia
| | - Tim Keighley
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | - Paul A. Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Brian J. Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
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