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Xiao Y, Li J, Wang R, Fan Y, Han X, Fu Y, Alepuz P, Wang W, Liang A. eIF5A promotes +1 programmed ribosomal frameshifting in Euplotes octocarinatus. Int J Biol Macromol 2024; 254:127743. [PMID: 38287569 DOI: 10.1016/j.ijbiomac.2023.127743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 01/31/2024]
Abstract
Programmed ribosomal frameshifting (PRF) exists in all branches of life that regulate gene expression at the translational level. The single-celled eukaryote Euplotes exhibit high frequency of PRF. However, the molecular mechanism of modulating Euplotes PRF remains largely unknown. Here, we identified two novel eIF5A genes, eIF5A1 and eIF5A2, in Euplotes octocarinatus and found that the Eo-eIF5A2 gene requires a -1 PRF to produce complete protein product. Although both Eo-eIF5As showed significant structural similarity with yeast eIF5A, neither of them could functionally replace yeast eIF5A. Eo-eIF5A knockdown inhibited +1 PRF of the η-tubulin gene. Using an in vitro reconstituted translation system, we found that hypusinated Eo-eIF5A (Eo-eIF5AH) can promote +1 PRF at the canonical AAA_UAA frameshifting site of Euplotes. The results showed eIF5A is a novel trans-regulator of PRF in Euplotes and has an evolutionary conserved role in regulating +1 PRF in eukaryotes.
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Affiliation(s)
- Yu Xiao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Jia Li
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Ruanlin Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China.
| | - Yajiao Fan
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Xiaxia Han
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Yuejun Fu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Paula Alepuz
- Instituto de Biotecnología y Biomedicina (Biotecmed) and Departamento de Bioquímica y Biología Molecular, Universitat de València, Spain
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China.
| | - Aihua Liang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China.
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Chigira K, Yamasaki M, Adachi S, Nagano AJ, Ookawa T. Identification of Novel Quantitative Trait Loci for Culm Thickness of Rice Derived from Strong-Culm Landrace in Japan, Omachi. RICE (NEW YORK, N.Y.) 2023; 16:4. [PMID: 36705856 PMCID: PMC9883377 DOI: 10.1186/s12284-023-00621-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Increasing the lodging resistance of rice through genetic improvement has been an important target in breeding. To further enhance the lodging resistance of high-yielding rice varieties amidst climate change, it is necessary to not only shorten culms but strengthen them as well. A landrace rice variety, Omachi, which was established more than 100 years ago, has the largest culm diameter and bending moment at breaking in the basal internodes among 135 temperate japonica accessions. Using unused alleles in such a landrace is an effective way to strengthen the culm. In this study, we performed quantitative trait locus (QTL) analysis to identify the genetic factors of culm strength of Omachi using recombinant inbred lines (RILs) derived from a cross between Omachi and Koshihikari, a standard variety in Japan. We identified three QTLs for the culm diameter of the 5th internode on chromosomes 3 (qCD3) and 7 (qCD7-1, qCD7-2). Among them, qCD7-2 was verified by QTL analysis using the F2 population derived from a cross between one of the RILs and Koshihikari. RNA-seq analysis of shoot apex raised 10 candidate genes underlying the region of qCD7-2. The increase in culm strength by accumulating Omachi alleles of qCD3, qCD7-1 and qCD7-2 was 25.0% in 2020. These QTLs for culm diameter pleiotropically increased spikelet number per panicle but did not affect days to heading or culm length. These results suggest that the Omachi alleles of qCD3, qCD7-1 and qCD7-2 are useful for breeding to increase lodging resistance and yield.
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Affiliation(s)
- Koki Chigira
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
| | - Masanori Yamasaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-Ku, Niigata City, Niigata 950-2181 Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata 997-0017 Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
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Ku YS, Cheung MY, Cheng SS, Nadeem MA, Chung G, Lam HM. Using the Knowledge of Post-transcriptional Regulations to Guide Gene Selections for Molecular Breeding in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:867731. [PMID: 35432392 PMCID: PMC9009170 DOI: 10.3389/fpls.2022.867731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The omics approaches allow the scientific community to successfully identify genomic regions associated with traits of interest for marker-assisted breeding. Agronomic traits such as seed color, yield, growth habit, and stress tolerance have been the targets for soybean molecular breeding. Genes governing these traits often undergo post-transcriptional modifications, which should be taken into consideration when choosing elite genes for molecular breeding. Post-transcriptional regulations of genes include transcript regulations, protein modifications, and even the regulation of the translational machinery. Transcript regulations involve elements such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for the maintenance of transcript stability or regulation of translation efficiency. Protein modifications involve molecular modifications of target proteins and the alterations of their interacting partners. Regulations of the translational machinery include those on translation factors and the ribosomal protein complex. Post-transcriptional regulations usually involve a set of genes instead of a single gene. Such a property may facilitate molecular breeding. In this review, we will discuss the post-transcriptional modifications of genes related to favorable agronomic traits such as stress tolerance, growth, and nutrient uptake, using examples from soybean as well as other crops. The examples from other crops may guide the selection of genes for marker-assisted breeding in soybean.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Sau-Shan Cheng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Pálfi P, Bakacsy L, Kovács H, Szepesi Á. Hypusination, a Metabolic Posttranslational Modification of eIF5A in Plants during Development and Environmental Stress Responses. PLANTS 2021; 10:plants10071261. [PMID: 34206171 PMCID: PMC8309165 DOI: 10.3390/plants10071261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/15/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022]
Abstract
Hypusination is a unique posttranslational modification of eIF5A, a eukaryotic translation factor. Hypusine is a rare amino acid synthesized in this process and is mediated by two enzymes, deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH). Despite the essential participation of this conserved eIF5A protein in plant development and stress responses, our knowledge of its proper function is limited. In this review, we demonstrate the main findings regarding how eIF5A and hypusination could contribute to plant-specific responses in growth and stress-related processes. Our aim is to briefly discuss the plant-specific details of hypusination and decipher those signal pathways which can be effectively modified by this process. The diverse functions of eIF5A isoforms are also discussed in this review.
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Wang X, Li F, Chen Z, Yang B, Komatsu S, Zhou S. Proteomic analysis reveals the effects of melatonin on soybean root tips under flooding stress. J Proteomics 2021; 232:104064. [PMID: 33276190 DOI: 10.1016/j.jprot.2020.104064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/14/2020] [Accepted: 11/22/2020] [Indexed: 11/30/2022]
Abstract
Flooding constrains soybean growth, while melatonin enhances the ability of plants to tolerate abiotic stresses. To interpret the melatonin-mediated flooding response in soybeans, proteomic analysis was performed in root tips. Retarded growth and severe cell death were observed in flooded soybeans, but these phenotypes were ameliorated by melatonin treatment. A total of 634, 1401, and 1205 proteins were identified under control, flood, and flood plus melatonin conditions, respectively; and these proteins were predominantly associated with metabolism of protein, RNA, and the cell wall. Among these melatonin-induced proteins, eukaryotic aspartyl protease family protein was increased after flood compared with melatonin treatment group, in accordance with its upregulated transcript levels during stress. Eukaryotic translation initiation factor 5A was decreased after flood compared with melatonin. When stress was prolonged, its transcript levels were upregulated by flood, while they were not changed by melatonin. Furthermore, 13-hydroxylupanine O-tigloyltransferase was decreased by flood compared with melatonin; however, its transcription was upregulated by melatonin. In addition, reduced lignification in root tips of flooded soybeans was restored by melatonin. These results suggest that factors related to protein degradation and functional states of RNA play critical roles in promoting the effects of melatonin on soybean plants under flooding. SIGNIFICANCE: Flooding stress threatens soybean growth, while melatonin treatment enhances plant tolerance to stress stimuli. To examine the effects of melatonin on flooded soybeans, morphological analysis was performed. Melatonin promoted soybean growth as judged from greater fresh weight of plant, longer seedling length, and less evident cell death in flooding-stressed soybeans treated with melatonin than those plants exposed to flood alone. Proteomic analysis was conducted to explore the promoting effects of melatonin on soybeans under flooding stress. As a result, metabolism of protein metabolism, RNA regulation, and cell wall was enriched by proteins identified under control, flood, and flood plus melatonin conditions. Among these melatonin-induced proteins, abundance of eukaryotic aspartyl protease family protein, eukaryotic translation initiation factor 5A, and 13-hydroxylupanine O-tigloyltransferase displayed similar change patterns between the control and melatonin compared with flood; and transcript levels of genes encoding these proteins responded to flooding stress and melatonin treatment. In addition, activated cell degradation, expanded intercellular spaces, and reduced lignification in root tips of flooded soybeans were ameliorated by melatonin treatment.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Fang Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhenyuan Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Bingxian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Shunli Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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Duan D, Tong J, Xu Q, Dai L, Ye J, Wu H, Xu C, Shi J. Regulation mechanisms of humic acid on Pb stress in tea plant (Camellia sinensis L.). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115546. [PMID: 32892024 DOI: 10.1016/j.envpol.2020.115546] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/19/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Though the interaction between humic acid (HA) and heavy metals has been widely reported, the effects of HA on the toxicity of heavy metals to plants are still in debate. In this study, the regulation mechanisms of HA on Pb stress in tea plant (Camellia sinensis L.) was investigated through hydroponic experiments, and the experimental results were explained by using transmission electron microscope (TEM), scanning transmission X-ray microscopes (STXM) and isobaric tags for relative and absolute quantitation (iTRAQ) differential proteomics. Significant alleviation of Pb stress was found with HA coexistence. TEM results showed that HA greatly mitigated the damage of cells caused by Pb stress. Compared with sole Pb treatment, the addition of HA increased the contents of pectin and pectic acid in the cell wall by 10.5% and 30.5%, while arabinose (Ara) and galactose (Gal) decreased by 20.5% and 15.9%, respectively, which were beneficial for increasing Pb adsorption capacity of the cell wall and promoting cell elongation. Moreover, iTRAQ differential proteomics analysis proved that HA strengthened the antioxidant system, promoted the synthesis of cell wall, and stabilized protein and sulfur-containing substance metabolism in molecular level. Notably, the concentration of calcium (Ca) in the cell wall of HA coexistence treatment was 47.4% higher than Pb treatment. STXM results also indicated that the distribution of Ca in the cell wall was restored with the presence of HA. This might promote the formation of the egg-box model, thus alleviating Pb stress in cells. Our results reveal the regulation mechanisms of HA on Pb detoxification in plants and provide useful information for improving the safety of agricultural products.
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Affiliation(s)
- Dechao Duan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Towards Environment Co., Ltd, Hangzhou, 310012, China
| | - Jianhao Tong
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiao Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Luying Dai
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; CETHIK Research Institute, Hangzhou, 310012, China
| | - Jien Ye
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hanxin Wu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chen Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Towards Environment Co., Ltd, Hangzhou, 310012, China
| | - Jiyan Shi
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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In-silico analysis of eukaryotic translation initiation factors (eIFs) in response to environmental stresses in rice (Oryza sativa). Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00467-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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8
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Changes in Proteome and Protein Phosphorylation Reveal the Protective Roles of Exogenous Nitrogen in Alleviating Cadmium Toxicity in Poplar Plants. Int J Mol Sci 2019; 21:ijms21010278. [PMID: 31906144 PMCID: PMC6982014 DOI: 10.3390/ijms21010278] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 01/18/2023] Open
Abstract
Phytoremediation soil polluted by cadmium has drawn worldwide attention. However, how to improve the efficiency of plant remediation of cadmium contaminated soil remains unknown. Previous studies showed that nitrogen (N) significantly enhances cadmium uptake and accumulation in poplar plants. In order to explore the important role of nitrogen in plants’ responses to cadmium stress, this study investigates the poplar proteome and phosphoproteome difference between Cd stress and Cd + N treatment. In total, 6573 proteins were identified, and 5838 of them were quantified. With a fold-change threshold of > 1.3, and a p-value < 0.05, 375 and 108 proteins were up- and down-regulated by Cd stress when compared to the control, respectively. Compared to the Cd stress group, 42 and 89 proteins were up- and down-regulated by Cd + N treatment, respectively. Moreover, 522 and 127 proteins were up- and down-regulated by Cd + N treatment compared to the CK group. In addition, 1471 phosphosites in 721 proteins were identified. Based on a fold-change threshold of > 1.2, and a p-value < 0.05, the Cd stress up-regulated eight proteins containing eight phosphosites, and down-regulated 58 proteins containing 69 phosphosites, whereas N + Cd treatment up-regulated 86 proteins containing 95 phosphosites, and down-regulated 17 proteins containing 17 phosphosites, when compared to Cd stress alone. N + Cd treatment up-regulated 60 proteins containing 74 phosphosites and down-regulated 37 proteins containing 42 phosphosites, when compared to the control. Several putative responses to stress proteins, as well as transcriptional and translational regulation factors, were up-regulated by the addition of exogenous nitrogen following Cd stress. Especially, heat shock protein 70 (HSP70), 14-3-3 protein, peroxidase (POD), zinc finger protein (ZFP), ABC transporter protein, eukaryotic translation initiation factor (elF) and splicing factor 3 B subunit 1-like (SF3BI) were up-regulated by Cd + N treatment at both the proteome and the phosphoproteome levels. Combing the proteomic data and phosphoproteomics data, the mechanism by which exogenous nitrogen can alleviate cadmium toxicity in poplar plants was explained at the molecular level. The results of this study will establish the solid molecular foundation of the phytoremediation method to improve cadmium-contaminated soil.
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Li LJ, Lu XC, Ma HY, Lyu DG. Comparative proteomic analysis reveals the roots response to low root-zone temperature in Malus baccata. JOURNAL OF PLANT RESEARCH 2018; 131:865-878. [PMID: 29855747 DOI: 10.1007/s10265-018-1045-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 05/10/2018] [Indexed: 05/16/2023]
Abstract
Soil temperature is known to affect plant growth and productivity. In this study we found that low root-zone temperature (LRT) inhibited the growth of apple (Malus baccata Borkh.) seedlings. To elucidate the molecular mechanism of LRT response, we performed comparative proteome analysis of the apple roots under LRT for 6 days. Total proteins of roots were extracted and separated by two-dimensional gel electrophoresis (2-DE) and 29 differentially accumulated proteins were successfully identified by MALDI-TOF/TOF mass spectrometry. They were involved in protein transport/processing/degradation (21%), glycometabolism (20%), response to stress (14%), oxidoreductase activity (14%), protein binding (7%), RNA metabolism (7%), amino acid biosynthesis (3%) and others (14%). The results revealed that LRT inhibited glycometabolism and RNA metabolism. The up-regulated proteins which were associated with oxidoreductase activity, protein metabolism and defense response, might be involved in protection mechanisms against LRT stress in the apple seedlings. Subsequently, 8 proteins were selected for the mRNA quantification analysis, and we found 6 of them were consistently regulated between protein and mRNA levels. In addition, the enzyme activities in ascorbate-glutathione (AsA-GSH) cycle were determined, and APX activity was increased and GR activity was decreased under LRT, in consistent with the protein levels. This study provides new insights into the molecular mechanisms of M. baccata in responding to LRT.
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Affiliation(s)
- Li-Jie Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiao-Chen Lu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Huai-Yu Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
- Key Lab of Fruit Quality Development and Regulation of Liaoning Province, Shenyang, 110866, China.
| | - De-Guo Lyu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
- Key Lab of Fruit Quality Development and Regulation of Liaoning Province, Shenyang, 110866, China.
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Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation. Sci Rep 2016; 6:31697. [PMID: 27545962 PMCID: PMC4992866 DOI: 10.1038/srep31697] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/25/2016] [Indexed: 01/11/2023] Open
Abstract
Since years, research on SnRK1, the major cellular energy sensor in plants, has tried to define its role in energy signalling. However, these attempts were notoriously hampered by the lethality of a complete knockout of SnRK1. Therefore, we generated an inducible amiRNA::SnRK1α2 in a snrk1α1 knock out background (snrk1α1/α2) to abolish SnRK1 activity to understand major systemic functions of SnRK1 signalling under energy deprivation triggered by extended night treatment. We analysed the in vivo phosphoproteome, proteome and metabolome and found that activation of SnRK1 is essential for repression of high energy demanding cell processes such as protein synthesis. The most abundant effect was the constitutively high phosphorylation of ribosomal protein S6 (RPS6) in the snrk1α1/α2 mutant. RPS6 is a major target of TOR signalling and its phosphorylation correlates with translation. Further evidence for an antagonistic SnRK1 and TOR crosstalk comparable to the animal system was demonstrated by the in vivo interaction of SnRK1α1 and RAPTOR1B in the cytosol and by phosphorylation of RAPTOR1B by SnRK1α1 in kinase assays. Moreover, changed levels of phosphorylation states of several chloroplastic proteins in the snrk1α1/α2 mutant indicated an unexpected link to regulation of photosynthesis, the main energy source in plants.
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11
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Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis. Sci Rep 2015; 5:15407. [PMID: 26472343 PMCID: PMC4607945 DOI: 10.1038/srep15407] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/22/2015] [Indexed: 01/13/2023] Open
Abstract
Cultivation and environmental changes can induce development of novel phenotypes in plants. For example, the root morphology of cultivated purple root Eichhornia crassipes differs remarkably from normal Eichhornia crassipes and also shows an enhanced ability to absorb heavy metal from groundwater. However, the changes in gene expression associated with these processes are unknown because of the lack of information on its large and unsequenced genome and its complex plant-rhizosphere symbiotic system. To investigate these gene expression changes, we applied a new strategy, direct de novo metatranscriptome analysis. Using this approach, we assembled the metatranscriptome of the entire rhizosphere and identified species-specific differentially expressed genes (DEGs) via hyper-accurate algorithms, showing a polarized plant/fungus distribution: the plant genes were responsible for morphological changes to the root system, offering a greater volume and surface area that hosts more fungi; while genes associated with heavy metal response in the fungus Fusarium were upregulated more than 3600-fold. These results suggested a distinct and synergistic functional response by the plant and fungal transcriptomes, indicating significant plant/fungal crosstalk during environmental changes. This study demonstrates that the metatranscriptomic approach adopted here offers a cost-efficient strategy to study symbiosis systems without the need for a priori genomic knowledge.
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Xu XY, Ding ZJ, Chen L, Yan JY, Li GX, Zheng SJ. An eukaryotic translation initiation factor, AteIF5A-2, affects cadmium accumulation and sensitivity in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:848-58. [PMID: 25559189 DOI: 10.1111/jipb.12329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 12/31/2014] [Indexed: 05/22/2023]
Abstract
Cadmium (Cd) is one of the most toxic elements and can be accumulated in plants easily; meanwhile, eIF5A is a highly conserved protein in all eukaryotic organisms. The present work tried to investigate whether eIF5A is involved in Cd accumulation and sensitivity in Arabidopsis (Arabidopsis thaliana L.) by comparing the wild-type Columbia-0 (Col-0) with a knockdown mutant of AteIF5A-2, fbr12-3 under Cd stress conditions. The results showed that the mutant fbr12-3 accumulated more Cd in roots and shoots and had significantly lower chlorophyll content, shorter root length, and smaller biomass, suggesting that downregulation of AteIF5A-2 makes the mutant more Cd sensitive. Real-time polymerase chain reaction revealed that the expressions of metal transporters involved in Cd uptake and translocation including IRT1, ZIP1, AtNramp3, and AtHMA4 were significantly increased but the expressions of PCS1 and PCS2 related to Cd detoxification were decreased notably in fbr12-3 compared with Col-0. As a result, an increase in MDA and H2 O2 content but decrease in root trolox, glutathione and proline content under Cd stress was observed, indicating that a severer oxidative stress occurs in the mutant. All these results demonstrated for the first time that AteIF5A influences Cd sensitivity by affecting Cd uptake, accumulation, and detoxification in Arabidopsis.
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Affiliation(s)
- Xiao-Yan Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhong-Jie Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jin-Ying Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Gui-Xin Li
- College of Agronomy and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shao-Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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Chen C, Song Y, Zhuang K, Li L, Xia Y, Shen Z. Proteomic Analysis of Copper-Binding Proteins in Excess Copper-Stressed Roots of Two Rice (Oryza sativa L.) Varieties with Different Cu Tolerances. PLoS One 2015; 10:e0125367. [PMID: 25919452 PMCID: PMC4412397 DOI: 10.1371/journal.pone.0125367] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 03/12/2015] [Indexed: 12/30/2022] Open
Abstract
To better understand the mechanisms involved in the heavy metal stress response and tolerance in plants, a proteomic approach was used to investigate the differences in Cu-binding protein expression in Cu-tolerant and Cu-sensitive rice varieties. Cu-binding proteins from Cu-treated rice roots were separated using a new IMAC method in which an IDA-sepharose column was applied prior to the Cu-IMAC column to remove metal ions from protein samples. More than 300 protein spots were reproducibly detected in the 2D gel. Thirty-five protein spots exhibited changes greater than 1.5-fold in intensity compared to the control. Twenty-four proteins contained one or more of nine putative metal-binding motifs reported by Smith et al., and 19 proteins (spots) contained one to three of the top six motifs reported by Kung et al. The intensities of seven protein spots were increased in the Cu-tolerant variety B1139 compared to the Cu-sensitive variety B1195 (p<0.05) and six protein spots were markedly up-regulated in B1139, but not detectable in B1195. Four protein spots were significantly up-regulated in B1139, but unchanged in B1195 under Cu stress. In contrast, two protein spots were significantly down-regulated in B1195, but unchanged in B1139. These Cu-responsive proteins included those involved in antioxidant defense and detoxification (spots 5, 16, 21, 22, 28, 29 and 33), pathogenesis (spots 5, 16, 21, 22, 28, 29 and 33), regulation of gene transcription (spots 8 and 34), amino acid synthesis (spots 8 and 34), protein synthesis, modification, transport and degradation (spots 1, 2, 4, 10, 15, 19, 30, 31, 32 and 35), cell wall synthesis (spot 14), molecular signaling (spot 3), and salt stress (spots 7, 9 and 27); together with other proteins, such as a putative glyoxylate induced protein, proteins containing dimeric alpha-beta barrel domains, and adenosine kinase-like proteins. Our results suggest that these proteins, together with related physiological processes, play an important role in the detoxification of excess Cu and in maintaining cellular homeostasis.
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Affiliation(s)
- Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yufeng Song
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Kai Zhuang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Lu Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yan Xia
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People’s Republic of China
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14
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Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
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Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
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15
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Parkash J, Vaidya T, Kirti S, Dutt S. Translation initiation factor 5A in Picrorhiza is up-regulated during leaf senescence and in response to abscisic acid. Gene 2014; 542:1-7. [PMID: 24656625 DOI: 10.1016/j.gene.2014.03.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/17/2014] [Indexed: 11/25/2022]
Abstract
Translation initiation, the first step of protein synthesis process is the principal regulatory step controlling translation and involves a pool of translation initiation factors. In plants, from recent studies it is becoming evident that these translation initiation factors impact various aspects of plant growth and development in addition to their role in protein synthesis. Eukaryotic translation initiation factor eIF5A is one such factor which functions in start site selection for the eIF2-GTP-tRNAi ternary complex within the ribosomal-bound preinitiation complex and also stabilizes the binding of GDP to eIF2. In the present study we have cloned and analysed a gene (eIF5a) encoding eIF5A from Picrorhiza (Picrorhiza kurrooa Royle ex Benth.) a medicinal plant of the western Himalayan region. The full length eIF5a cDNA consisted of 838 bp with an open reading frame of 480 bp, 88 bp 5' untranslated region and 270 bp 3' untranslated region. The deduced eIF5A protein contained 159 amino acids with a molecular weight of 17.359 kDa and an isoelectric point of 5.59. Secondary structure analysis revealed eIF5A having 24.53% α-helices, 8.81% β-turns, 23.27% extended strands and 43.40% random coils. pk-eIF5a transcript was found to be expressing during the active growth phase as well as during leaf senescence stage, however, highest expression was observed during leaf senescence stage. Further, its expression was up-regulated in response to exogenous application of abscisic acid. Both high intensity as well as low intensity light decreased the expression of pk-eIF5a. The findings suggest eIF5a to be an important candidate to develop genetic engineering based strategies for delaying leaf senescence.
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Affiliation(s)
- Jai Parkash
- Academy of Scientific and Innovative Research-IHBT (AcSIR-IHBT), India; Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
| | - Tanmay Vaidya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
| | - Shruti Kirti
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
| | - Som Dutt
- Academy of Scientific and Innovative Research-IHBT (AcSIR-IHBT), India; Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India.
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16
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Chen M, Mishra S, Heckathorn SA, Frantz JM, Krause C. Proteomic analysis of Arabidopsis thaliana leaves in response to acute boron deficiency and toxicity reveals effects on photosynthesis, carbohydrate metabolism, and protein synthesis. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:235-42. [PMID: 23988561 DOI: 10.1016/j.jplph.2013.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/25/2013] [Accepted: 07/25/2013] [Indexed: 05/10/2023]
Abstract
Boron (B) stress (deficiency and toxicity) is common in plants, but as the functions of this essential micronutrient are incompletely understood, so too are the effects of B stress. To investigate mechanisms underlying B stress, we examined protein profiles in leaves of Arabidopsis thaliana plants grown under normal B (30 μM), compared to plants transferred for 60 and 84 h (i.e., before and after initial visible symptoms) in deficient (0 μM) or toxic (3 mM) levels of B. B-responsive polypeptides were sequenced by mass spectrometry, following 2D gel electrophoresis, and 1D gels and immunoblotting were used to confirm the B-responsiveness of some of these proteins. Fourteen B-responsive proteins were identified, including: 9 chloroplast proteins, 6 proteins of photosynthetic/carbohydrate metabolism (rubisco activase, OEC23, photosystem I reaction center subunit II-1, ATPase δ-subunit, glycolate oxidase, fructose bisphosphate aldolase), 6 stress proteins, and 3 proteins involved in protein synthesis (note that the 14 proteins may fall into multiple categories). Most (8) of the B-responsive proteins decreased under both B deficiency and toxicity; only 3 increased with B stress. Boron stress decreased, or had no effect on, 3 of 4 oxidative stress proteins examined, and did not affect total protein. Hence, our results indicate relatively early specific effects of B stress on chloroplasts and protein synthesis.
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Affiliation(s)
- Mei Chen
- Department of Environmental Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Sasmita Mishra
- Department of Environmental Sciences, University of Toledo, Toledo, OH 43606, USA.
| | - Scott A Heckathorn
- Department of Environmental Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Jonathan M Frantz
- United States Department of Agriculture-Agricultural Research Service, University of Toledo, Toledo, OH 43606, USA
| | - Charles Krause
- United States Department of Agriculture-Agricultural Research Service, University of Toledo, Toledo, OH 43606, USA
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17
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Griffiths CA, Gaff DF, Neale AD. Drying without senescence in resurrection plants. FRONTIERS IN PLANT SCIENCE 2014; 5:36. [PMID: 24575108 PMCID: PMC3922084 DOI: 10.3389/fpls.2014.00036] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 01/27/2014] [Indexed: 05/16/2023]
Abstract
Research into extreme drought tolerance in resurrection plants using species such as Craterostigma plantagineum, C. wilmsii, Xerophyta humilis, Tortula ruralis, and Sporobolus stapfianus has provided some insight into the desiccation tolerance mechanisms utilized by these plants to allow them to persist under extremely adverse environmental conditions. Some of the mechanisms used to ensure cellular preservation during severe dehydration appear to be peculiar to resurrection plants. Apart from the ability to preserve vital cellular components during drying and rehydration, such mechanisms include the ability to down-regulate growth-related metabolism rapidly in response to changes in water availability, and the ability to inhibit dehydration-induced senescence programs enabling reconstitution of photosynthetic capacity quickly following a rainfall event. Extensive research on the molecular mechanism of leaf senescence in non-resurrection plants has revealed a multi-layered regulatory network operates to control programed cell death pathways. However, very little is known about the molecular mechanisms that resurrection plants employ to avoid undergoing drought-related senescence during the desiccation process. To survive desiccation, dehydration in the perennial resurrection grass S. stapfianus must proceed slowly over a period of 7 days or more. Leaves detached from the plant before 60% relative water content (RWC) is attained are desiccation-sensitive indicating that desiccation tolerance is conferred in vegetative tissue of S. stapfianus when the leaf RWC has declined to 60%. Whilst some older leaves remaining attached to the plant during dehydration will senesce, suggesting dehydration-induced senescence may be influenced by leaf age or the rate of dehydration in individual leaves, the majority of leaves do not senesce. Rather these leaves dehydrate to air-dryness and revive fully following rehydration. Hence it seems likely that there are genes expressed in younger leaf tissues of resurrection plants that enable suppression of drought-related senescence pathways. As very few studies have directly addressed this phenomenon, this review aims to discuss current literature surrounding the activation and suppression of senescence pathways and how these pathways may differ in resurrection plants.
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Affiliation(s)
| | | | - Alan D. Neale
- School of Biological Sciences, Monash UniversityClayton, VIC, Australia
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18
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Zhou CP, Qi YP, You X, Yang LT, Guo P, Ye X, Zhou XX, Ke FJ, Chen LS. Leaf cDNA-AFLP analysis of two citrus species differing in manganese tolerance in response to long-term manganese-toxicity. BMC Genomics 2013; 14:621. [PMID: 24034812 PMCID: PMC3847489 DOI: 10.1186/1471-2164-14-621] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/11/2013] [Indexed: 01/17/2023] Open
Abstract
Background Very little is known about manganese (Mn)-toxicity-responsive genes in citrus plants. Seedlings of ‘Xuegan’ (Citrus sinensis) and ‘Sour pummelo’ (Citrus grandis) were irrigated for 17 weeks with nutrient solution containing 2 μM (control) or 600 μM (Mn-toxicity) MnSO4. The objectives of this study were to understand the mechanisms of citrus Mn-tolerance and to identify differentially expressed genes, which might be involved in Mn-tolerance. Results Under Mn-toxicity, the majority of Mn in seedlings was retained in the roots; C. sinensis seedlings accumulated more Mn in roots and less Mn in shoots (leaves) than C. grandis ones and Mn concentration was lower in Mn-toxicity C. sinensis leaves compared to Mn-toxicity C. grandis ones. Mn-toxicity affected C. grandis seedling growth, leaf CO2 assimilation, total soluble concentration, phosphorus (P) and magenisum (Mg) more than C. sinensis. Using cDNA-AFLP, we isolated 42 up-regulated and 80 down-regulated genes in Mn-toxicity C. grandis leaves. They were grouped into the following functional categories: biological regulation and signal transduction, carbohydrate and energy metabolism, nucleic acid metabolism, protein metabolism, lipid metabolism, cell wall metabolism, stress responses and cell transport. However, only 7 up-regulated and 8 down-regulated genes were identified in Mn-toxicity C. sinensis ones. The responses of C. grandis leaves to Mn-toxicity might include following several aspects: (1) accelerating leaf senescence; (2) activating the metabolic pathway related to ATPase synthesis and reducing power production; (3) decreasing cell transport; (4) inhibiting protein and nucleic acid metabolisms; (5) impairing the formation of cell wall; and (6) triggering multiple signal transduction pathways. We also identified many new Mn-toxicity-responsive genes involved in biological and signal transduction, carbohydrate and protein metabolisms, stress responses and cell transport. Conclusions Our results demonstrated that C. sinensis was more tolerant to Mn-toxicity than C. grandis, and that Mn-toxicity affected gene expression far less in C. sinensis leaves. This might be associated with more Mn accumulation in roots and less Mn accumulation in leaves of Mn-toxicity C. sinensis seedlings than those of C. grandis seedlings. Our findings increase our understanding of the molecular mechanisms involved in the responses of plants to Mn-toxicity.
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Affiliation(s)
- Chen-Ping Zhou
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.
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19
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Zhao L, Zhang N, Ma PF, Liu Q, Li DZ, Guo ZH. Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae. PLoS One 2013; 8:e64642. [PMID: 23734211 PMCID: PMC3667173 DOI: 10.1371/journal.pone.0064642] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/16/2013] [Indexed: 11/23/2022] Open
Abstract
BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.
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Affiliation(s)
- Lei Zhao
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ning Zhang
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Peng-Fei Ma
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qi Liu
- Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - De-Zhu Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhen-Hua Guo
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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20
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Gu X, Gao Z, Zhuang W, Qiao Y, Wang X, Mi L, Zhang Z, Lin Z. Comparative proteomic analysis of rd29A:RdreB1BI transgenic and non-transgenic strawberries exposed to low temperature. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:696-706. [PMID: 23394786 DOI: 10.1016/j.jplph.2012.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 12/05/2012] [Accepted: 12/11/2012] [Indexed: 05/25/2023]
Abstract
Low-temperature stress is one of the major abiotic stresses in plants worldwide, and the dehydration responsive element binding protein (DREB) transcription factor induces expression of genes involved in environmental stress tolerance in plants. A proteomic approach based on two-dimensional gel electrophoresis (2-DE) and subsequent mass spectrometric identification was used to study the changes in the leaf proteome profiles of rd29A:RdreB1BI transgenic and non-transgenic strawberries exposed to low-temperature conditions. By comparing the proteomic profiles, we located 21 protein spots that were reproducibly up- or down-regulated by more than twofold between transgenic and non-transgenic strawberries. Eight identified proteins function in energy and metabolism, four in biosynthetic processes, four were stress and defense related, three spots were identified as cold-stress related expressed sequence tags (ESTs), and two were unknown proteins. The change patterns of low-temperature tolerance proteins, including photosynthetic proteins (RuBisCO large subunit and RuBisCO activase), cytoplasmic Cu/Zn-superoxide dismutase (Cu/Zn-SOD), late embryogenesis abundant protein 14-A (Lea14-A), eukaryotic translation initiation factor 5A (eIF5A), and cold-stress related ESTs, were differentially regulated between non-transgenic and rd29A:RdreB1BI transgenic strawberries. They are likely important gene products in the regulatory network of the RdreB1BI gene. Consequently, this study provides the first characterization of the transgenic strawberry proteome and the predicted target proteins of the RdreB1BI gene by using proteomic approaches.
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Affiliation(s)
- Xianbin Gu
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, PR China.
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21
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Chung J, Rocha AA, Tonelli RR, Castilho BA, Schenkman S. Eukaryotic initiation factor 5A dephosphorylation is required for translational arrest in stationary phase cells. Biochem J 2013; 451:257-67. [PMID: 23368777 DOI: 10.1042/bj20121553] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The protein known as eIF5A (eukaryotic initiation factor 5A) has an elusive role in translation. It has a unique and essential hypusine modification at a conserved lysine residue in most eukaryotes. In addition, this protein is modified by phosphorylation with unknown functions. In the present study we show that a phosphorylated state of eIF5A predominates in exponentially growing Trypanosoma cruzi cells, and extensive dephosphorylation occurs in cells in stationary phase. Phosphorylation occurs mainly at Ser(2), as shown in yeast eIF5A. In addition, a novel phosphorylation site was identified at Tyr(21). In exponential cells, T. cruzi eIF5A is partially associated with polysomes, compatible with a proposed function as an elongation factor, and becomes relatively enriched in polysomal fractions in stationary phase. Overexpression of the wild-type eIF5A, or eIF5A with Ser(2) replaced by an aspartate residue, but not by alanine, increases the rate of cell proliferation and protein synthesis. However, the presence of an aspartate residue instead of Ser(2) is toxic for cells reaching the stationary phase, which show a less-pronounced protein synthesis arrest and a decreased amount of eIF5A in dense fractions of sucrose gradients. We conclude that eIF5A phosphorylation and dephosphorylation cycles regulate translation according to the growth conditions.
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Affiliation(s)
- Janete Chung
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Rua Pedro de Toledo 669 L6A, São Paulo, S.P. 04039-032, Brazil
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22
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Wang L, Xu C, Wang C, Wang Y. Characterization of a eukaryotic translation initiation factor 5A homolog from Tamarix androssowii involved in plant abiotic stress tolerance. BMC PLANT BIOLOGY 2012; 12:118. [PMID: 22834699 PMCID: PMC3479025 DOI: 10.1186/1471-2229-12-118] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 07/09/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND The eukaryotic translation initiation factor 5A (eIF5A) promotes formation of the first peptide bond at the onset of protein synthesis. However, the function of eIF5A in plants is not well understood. RESULTS In this study, we characterized the function of eIF5A (TaeIF5A1) from Tamarix androssowii. The promoter of TaeIF5A1 with 1,486 bp in length was isolated, and the cis-elements in the promoter were identified. A WRKY (TaWRKY) and RAV (TaRAV) protein can specifically bind to a W-box motif in the promoter of TaeIF5A1 and activate the expression of TaeIF5A1. Furthermore, TaeIF5A1, TaWRKY and TaRAV share very similar expression pattern and are all stress-responsive gene that functions in the abscisic acid (ABA) signaling pathway, indicating that they are components of a single regulatory pathway. Transgenic yeast and poplar expressing TaeIF5A1 showed elevated protein levels combined with improved abiotic stresses tolerance. Furthermore, TaeIF5A1-transformed plants exhibited enhanced superoxide dismutase (SOD) and peroxidase (POD) activities, lower electrolyte leakage and higher chlorophyll content under salt stress. CONCLUSIONS These results suggested that TaeIF5A1 is involved in abiotic stress tolerance, and is likely regulated by transcription factors TaWRKY and TaRAV both of which can bind to the W-box motif. In addition, TaeIF5A1 may mediate stress tolerance by increasing protein synthesis, enhancing ROS scavenging by improving SOD and POD activities, and preventing chlorophyll loss and membrane damage. Therefore, eIF5A may play an important role in plant adaptation to changing environmental conditions.
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MESH Headings
- Abscisic Acid/metabolism
- Abscisic Acid/pharmacology
- Adaptation, Physiological
- Cell Membrane/genetics
- Cell Membrane/metabolism
- Chlorophyll/genetics
- Chlorophyll/metabolism
- Cloning, Molecular
- Gene Expression Regulation, Plant
- Genetic Vectors
- Peptide Initiation Factors/genetics
- Peptide Initiation Factors/metabolism
- Peroxidase/genetics
- Peroxidase/metabolism
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Plants, Genetically Modified/physiology
- Promoter Regions, Genetic
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Regulatory Sequences, Nucleic Acid
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Salt-Tolerant Plants/genetics
- Salt-Tolerant Plants/metabolism
- Salt-Tolerant Plants/physiology
- Signal Transduction
- Sodium Chloride/pharmacology
- Solubility
- Stress, Physiological
- Superoxide Dismutase/genetics
- Superoxide Dismutase/metabolism
- Tamaricaceae/genetics
- Tamaricaceae/metabolism
- Tamaricaceae/physiology
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transformation, Genetic
- Eukaryotic Translation Initiation Factor 5A
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Affiliation(s)
- Liuqiang Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, China
| | - Chenxi Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, China
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, China
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23
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Le Provost G, Sulmon C, Frigerio JM, Bodénès C, Kremer A, Plomion C. Role of waterlogging-responsive genes in shaping interspecific differentiation between two sympatric oak species. TREE PHYSIOLOGY 2012; 32:119-34. [PMID: 22170438 DOI: 10.1093/treephys/tpr123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Pedunculate (Quercus robur L.) and sessile oak (Quercus petreae Matt. Liebl.) are closely related species with a widely sympatric distribution in Europe. These two oak species are also known to display different ecological features, particularly related to their adaptation to soil waterlogging. Pedunculate oak grows in humid areas and can withstand high moisture content of the soil, whereas sessile oak requires drier soil with better drainage. The main goal of this study was to explore the role of gene expression contributing to differences in terms of waterlogging tolerance between these two species. We implemented a series of experiments aimed at evaluating whether differentially expressed genes between species are associated with their ecological preferences and underlie adaptive genetic divergence. Rooted cuttings of both species were grown in hydroponic conditions and subjected to gradual root hypoxia. White roots were sampled after 6, 12, 24 and 48 h. Real-time polymerase chain reaction (qPCR) was first used to monitor the expression of 10 known waterlogging-responsive genes, to identify discriminating sampling time points along the kinetics of hypoxia. Secondly, four subtractive suppressive hybridization libraries (sessile vs. pedunculate, pedunculate vs. sessile for early and late responses) were generated to isolate differentially expressed genes between species. A total of 2160 high-quality expressed sequence tags were obtained and annotated, and a subset of 45 genes were selected for qPCR analysis in a second independent factorial experimental design applying two stress durations per two species. Significant differences of gene expression between pedunculate and sessile oaks were detected, suggesting species-specific molecular strategies to respond to hypoxia. This study revealed that the ability of pedunculate oak to maintain glycolysis and fermentation under hypoxic conditions may help explain its tolerance to waterlogging.
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Lewandowska-Gnatowska E, Szymona L, Łebska M, Szczegielniak J, Muszyńska G. Phosphorylation of maize eukaryotic translation initiation factor on Ser2 by catalytic subunit CK2. Mol Cell Biochem 2011; 356:241-4. [PMID: 21750984 DOI: 10.1007/s11010-011-0952-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
Abstract
Alignment of eukaryotic translation initiation factor 5A (eIF5A) sequences has shown, for plants, in contrast to most other eukaryotes, the presence of N-terminal serine residue (Ser2) which could be phosphorylated by CK2. Using point directed mutagenesis, we demonstrate here that in recombinant maize ZmeIF5Awt Ser2 is exclusively phosphorylated by catalytic subunit of CK2 (CK2α), whereas its mutated variant Ser2Ala is not phosphorylated. To shed light on the physiological significance of this Ser2 phosphorylation, transient expression of fluorescence-labeled proteins was performed in maize protoplast. Wild-type ZmeIF5A was distributed evenly between nucleus and cytoplasm, but the replacement of Ser2 by aspartic acid, which mimics the phosphorylated serine, influences its intracellular localization. We postulate that phosphorylation of Ser2 in maize eIF5A, and most probably in other plant cells, plays a role in specific regulation of nuclear export of eIF5A-bound mRNAs.
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Xu J, Zhang B, Jiang C, Ming F. RceIF5A, encoding an eukaryotic translation initiation factor 5A in Rosa chinensis, can enhance thermotolerance, oxidative and osmotic stress resistance of Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2011; 75:167-78. [PMID: 21107886 DOI: 10.1007/s11103-010-9716-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Accepted: 11/15/2010] [Indexed: 05/04/2023]
Abstract
Eukaryotic translation initiation factor 5A (eIF5A) is the only cellular protein known to contain the unusual amino acid hypusine. It is a highly conserved protein found in all eukaryotic organisms. Although originally identified as a translation initiation factor, recent studies suggest that eIF5A is mainly involved in translation elongation, mRNA turnover and decay, cell proliferation, and programmed cell death. However, the precise cellular function of eIF5A remains largely unknown, especially in plants. Here, we report the identification and characterization of RceIF5A from Rosa chinensis. RceIF5A expression is up-regulated in Rosa chinensis under high temperature, and oxidative and osmotic stress conditions. We produced transgenic Arabidopsis that constitutively enhanced or suppressed expression of RceIF5A. The RceIF5A over-expression plants exhibited increased resistance to heat, and oxidative and osmotic stresses, while the suppressed expression plants (three AteIF5A isoforms in Arabidopsis were down-regulated) showed more susceptibility to these stresses. These results reveal a new physiological role for eIF5A in plants and contribute to the elucidation of the molecular mechanisms involved in the stress response pathway.
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Affiliation(s)
- Jianyao Xu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Fudan University, 220 Handan Road, Shanghai, 200433, People's Republic of China
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Zhou Y, Gao F, Li X, Zhang J, Zhang G. Alterations in phosphoproteome under salt stress in Thellungiella roots. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11434-010-4116-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ma Y, Miura E, Ham BK, Cheng HW, Lee YJ, Lucas WJ. Pumpkin eIF5A isoforms interact with components of the translational machinery in the cucurbit sieve tube system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:536-50. [PMID: 20807213 DOI: 10.1111/j.1365-313x.2010.04347.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In yeast, eIF5A, in combination with eEF2, functions at the translation step, during the protein elongation cycle. This result is of significance with respect to functioning of the enucleate sieve tube system, as eIF5A was recently detected in Cucurbita maxima (pumpkin) phloem sap. In the present study, we further characterized four CmeIF5A isoforms, encoding three proteins, all of which were present in the phloem sap. Although hypusination of CmeIF5A was not necessary for entry into the sieve elements, this unique post-translational modification was necessary for RNA binding. The two enzymes required for hypusination were detected in pumpkin phloem sap, where presumably this modification takes place. A combination of gel-filtration chromatography and protein overlay assays demonstrated that, as in yeast, CmeIF5A interacts with phloem proteins, like eEF2, known to be involved in protein synthesis. These findings are discussed in terms of a potential role for eIF5A in regulating protein synthesis within the enucleate sieve tube system of the angiosperms.
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Affiliation(s)
- Yi Ma
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
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Ma F, Liu Z, Wang TW, Hopkins MT, Peterson CA, Thompson JE. Arabidopsis eIF5A3 influences growth and the response to osmotic and nutrient stress. PLANT, CELL & ENVIRONMENT 2010; 33:1682-96. [PMID: 20492553 DOI: 10.1111/j.1365-3040.2010.02173.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
AteIF5A3, one of three genes encoding eukaryotic translation initiation factor 5A (eIF5A) in Arabidopsis thaliana, and corresponding genes PdeIF5A3 from Populus deltoides (eastern cottonwood) and SleIF5A4 from Solanum lycopersicum (tomato) were constitutively over-expressed in A. thaliana. The resultant transgenic plants exhibited enhanced vegetative and reproductive growth. Indeed, the increase in seed yield relative to empty vector controls for the PdeIF5A3 over-expressing plants ranged from 50% to 300% depending on the line. The PdeIF5A3 over-expressing plants also exhibited enhanced fitness when exposed to osmotic and nutrient (N, P and K) stress. The spatial localization of AteIF5A3 was visualized by confocal microscopy using transgenic plants expressing P(AteIF5A3) :GFP-AteIF5A3. GFP fluorescence reflecting expression of AteIF5A3 was detectable in the phloem, particularly companion cells, of roots, stems and leaves, in the epidermal cells of the root tip, in the columella cells of the root cap and in the chalazal tissue of fertilized ovules, which all play a pivotal role in nutrient or hormone translocation. Thus, AteIF5A3 appears to be involved in supporting growth and to play a regulatory role in the response of plants to sub-lethal osmotic and nutrient stress.
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Affiliation(s)
- Fengshan Ma
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Carvajal-Gamez B, Arroyo R, Lira R, López-Camarillo C, Alvarez-Sánchez ME. Identification of two novel Trichomonas vaginalis eif-5a genes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2010; 10:284-91. [PMID: 20060503 DOI: 10.1016/j.meegid.2009.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 12/17/2009] [Accepted: 12/25/2009] [Indexed: 11/19/2022]
Abstract
The eukaryotic translation initiation factor 5A (eIF-5A) is highly conserved and is the only protein that is known to contain the unique and essential amino acid residue hypusine. Synthesis of hypusine is essential for the function of eIF5A in eukaryotic cell proliferation and survival. In this study, we identified two novel eukaryotic translation initiation factor 5A (eIF-5A) genes in Trichomonas vaginalis. The tveif-5a1 and tveif-5a2 putative genes were localized in different contigs, both containing ORFs encoding proteins of 168 amino acids that share high sequence identity with eIF-5A sequences from other eukaryotic organisms. A phylogenetic tree constructed with TveIF-5A1 and TveIF-5A2 from T. vaginalis and 13 other eIF-5A sequences of eukaryotic and archaebacterial origin revealed that both trichomonal TveIF-5As show the highest degree of similarity to bacteria. Using an anti-TveIF-5A antibody, we detected two protein bands and spots of 19 and 20kDa with isoelectric points (pI) of 5.2 and 5.5, respectively, by one and two-dimensional Western blot assays. In addition, we used reverse transcription polymerase chain reaction (RT-PCR) to demonstrate that both of these tveif-5a genes are expressed in T. vaginalis. Immunofluorescence assays showed that the TveIF-5A protein was dispersed throughout the parasite cytoplasm. In conclusion, T. vaginalis has two eif-5a genes, and both genes are expressed as highly conserved proteins of 19kDa, which are localized in the cytoplasm of this parasite.
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Affiliation(s)
- B Carvajal-Gamez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM). San Lorenzo # 290, Col. Del Valle, CP 03100 Mexico City, Mexico
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Łebska M, Ciesielski A, Szymona L, Godecka L, Lewandowska-Gnatowska E, Szczegielniak J, Muszyńska G. Phosphorylation of maize eukaryotic translation initiation factor 5A (eIF5A) by casein kinase 2: identification of phosphorylated residue and influence on intracellular localization of eIF5A. J Biol Chem 2010; 285:6217-26. [PMID: 20018887 PMCID: PMC2825417 DOI: 10.1074/jbc.m109.018770] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 12/15/2009] [Indexed: 11/06/2022] Open
Abstract
Maize eukaryotic translation initiation factor 5A (ZmeIF5A) co-purifies with the catalytic alpha subunit of protein kinase CK2 and is phosphorylated by this enzyme. Phosphorylated ZmeIF5A was also identified after separation of maize leaf proteins by two-dimensional electrophoresis. Multiple sequence alignment of eIF5A proteins showed that in monocots, in contrast to other eukaryotes, there are two serine/threonine residues that could potentially be phosphorylated by CK2. To identify the phosphorylation site(s) of ZmeIF5A, the serine residues potentially phosphorylated by CK2 were mutated. ZmeIF5A and its mutated variants S2A and S4A were expressed in Escherichia coli and purified. Of these recombinant proteins, only ZmeIF5A-S2A was not phosphorylated by maize CK2. Also, Arabidopsis thaliana and Saccharomyces cerevisiae eIF5A-S2A mutants were not phosphorylated despite effective phosphorylation of wild-type variants. A newly developed method exploiting the specificity of thrombin cleavage was used to confirm that Ser(2) in ZmeIF5A is indeed phosphorylated. To find a role of the Ser(2) phosphorylation, ZmeIF5A and its variants mutated at Ser(2) (S2A and S2D) were transiently expressed in maize protoplasts. The expressed fluorescence labeled proteins were visualized by confocal microscopy. Although wild-type ZmeIF5A and its S2A variant were distributed evenly between the nucleus and cytoplasm, the variant with Ser(2) replaced by aspartic acid, which mimics a phosphorylated serine, was sequestered in the nucleus. These results suggests that phosphorylation of Ser(2) plays a role in regulation of nucleocytoplasmic shuttling of eIF5A in plant cells.
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Affiliation(s)
- Maja Łebska
- From the Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Arkadiusz Ciesielski
- From the Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Lidia Szymona
- From the Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Luiza Godecka
- From the Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5a, 02-106 Warsaw, Poland
| | | | - Jadwiga Szczegielniak
- From the Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Grażyna Muszyńska
- From the Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawińskiego 5a, 02-106 Warsaw, Poland
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31
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Mattoo AK, Minocha SC, Minocha R, Handa AK. Polyamines and cellular metabolism in plants: transgenic approaches reveal different responses to diamine putrescine versus higher polyamines spermidine and spermine. Amino Acids 2009; 38:405-13. [DOI: 10.1007/s00726-009-0399-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 10/20/2009] [Indexed: 01/06/2023]
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Valcu CM, Lalanne C, Plomion C, Schlink K. Heat induced changes in protein expression profiles of Norway spruce (Picea abies) ecotypes from different elevations. Proteomics 2009; 8:4287-302. [PMID: 18814337 DOI: 10.1002/pmic.200700992] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Although tree species typically exhibit low genetic differentiation between populations, ecotypes adapted to different environmental conditions can vary in their capacity to withstand and recover from environmental stresses like heat stress. Two month old seedlings of a Picea abies ecotype adapted to high elevation showed lower level of thermotolerance and higher level of tolerance to oxidative stress relative to a low elevation ecotype. Protein expression patterns following exposure to severe heat stress of the two ecotypes were compared by means of 2-DE. Several proteins exhibiting ecotype and tissue specific expression were identified by MS/MS. Among them, small heat shock proteins of the HSP 20 family and proteins involved in protection from oxidative stress displayed qualitative and quantitative differences in expression between the ecotypes correlated with the observed phenotypic differences. On the basis of these results, it can be speculated that the observed interpopulation polymorphism of protein regulation in response to heat stress could underlie their different capacities to withstand and recover from heat stress. These local adaptations are potentially relevant for the species adaptation to the conditions predicted by the current models for climate change.
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Affiliation(s)
- Cristina-Maria Valcu
- Section of Forest Genetics, Technische Universität München, Freising-Weihenstephan, Germany.
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33
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Li H, Wang Y, Jiang J, Liu G, Gao C, Yang C. Identification of genes responsive to salt stress on Tamarix hispida roots. Gene 2008; 433:65-71. [PMID: 19146931 DOI: 10.1016/j.gene.2008.12.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 11/27/2008] [Accepted: 12/03/2008] [Indexed: 10/21/2022]
Abstract
Plant roots are the primary site of perception and injury for salinity stress. In order to characterize the complexity of adaptation to salty environments in roots of Tamarix hispida, a woody halophyte, expressed sequence tag (EST) analysis was performed. Three cDNA libraries were generated from root tissues of T. hispida that were exposed to 0.4 M NaCl for 0 (control), 24 and 48 h. A total of 7726 ESTs were generated from the three libraries, and were assembled into 1142 contigs and 3026 singletons. EST analysis was performed to compare gene expression in the three cDNA libraries. Ninety redundant unique transcripts responsive to NaCl treatment were identified. Of them, 21 genes were novel or of unknown function while others were involved in the functional activities, such as ROS scavenging, lipid metabolism, osmolyte biosynthesis, signal transduction, transport, lignin synthesis and homeostasis. The genes, including those for metallothionein-like protein, polyubiquitin, hypothetical protein, and glycine-rich cell wall structural protein, were abundant in the libraries and showed obvious up-regulation after NaCl treatments, suggesting important roles in NaCl tolerance. The results of this study may contribute to our understanding of the molecular mechanism of salt tolerance in the roots of plants.
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Affiliation(s)
- Huiyu Li
- Key Laboratory of Forest Tree Genetics Improvement and Biotechnology, Northeast Forestry University, Ministry of Education, Harbin, China
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Röhrig H, Colby T, Schmidt J, Harzen A, Facchinelli F, Bartels D. Analysis of desiccation-induced candidate phosphoproteins from Craterostigma plantagineum isolated with a modified metal oxide affinity chromatography procedure. Proteomics 2008; 8:3548-60. [PMID: 18752203 DOI: 10.1002/pmic.200700548] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Reversible protein phosphorylation/dephosphorylation is crucial for regulation of many cellular events, and increasing evidence indicates that this post-translational modification is also involved in the complex process of acquisition of desiccation tolerance. To analyze the phosphoproteome of the desiccation tolerant resurrection plant Craterostigma plantagineum, MOAC-enriched proteins from leaves at different stages of a de-/rehydration cycle were separated by 2-D PAGE and detected by phosphoprotein-specific staining. Using this strategy 20 putative phosphoproteins were identified by MALDI-TOF MS and MS/MS, which were not detected when total proteins were analyzed. The characterized desiccation-related phosphoproteins CDeT11-24 and CDeT6-19 were used as internal markers to validate the specificity of the analyses. For 16 of the identified proteins published evidence suggests that they are phosphoproteins. Comparative analysis of the 2-D gels showed that spot intensities of most identified putative phosphoproteins change during the de-/rehydration cycle. This suggests an involvement of these proteins in desiccation tolerance. Nearly all changes in the phosphoproteome of C. plantagineum, which are triggered by dehydration, are reversed within 4 days of rehydration, which is in agreement with physiological observations. Possible functions of selected proteins are discussed in the context of the de-/rehydration cycle.
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Affiliation(s)
- Horst Röhrig
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Bonn, Germany.
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35
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Song X, Ni Z, Yao Y, Xie C, Li Z, Wu H, Zhang Y, Sun Q. Wheat (Triticum aestivumL.) root proteome and differentially expressed root proteins between hybrid and parents. Proteomics 2007; 7:3538-57. [PMID: 17722204 DOI: 10.1002/pmic.200700147] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To better understand the development of wheat roots, a reference map of the major soluble proteins of wheat roots was established using a combination of 2-DE and MALDI TOF MS and MS/MS, and a total of 450 protein spots were detected with silver staining in a pH ranges of 4-7, of which 282 spots corresponding to 240 proteins were identified. These identified proteins were grouped into diverse functional categories. In comparison with a wheat leave proteome, in root, proteins involved in metabolism and transport were over-represented, whereas proteins involved in energy, disease and defense, transcription, and signal transduction were under-represented. To further get an insight into the molecular basis of wheat heterosis, differential proteome analysis between hybrid and parents were performed. A total of 45 differentially expressed protein spots were detected, and both quantitative and qualitative differences could be observed. Moreover, 25 of the 45 differentially expressed protein spots were identified, which were involved in metabolism, signal transduction, energy, cell growth and division, disease and defense, secondary metabolism. These results indicated that hybridization between two parental lines can cause expression differences between wheat hybrid and its parents not only at mRNA levels but also at protein abundances.
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Affiliation(s)
- Xiao Song
- Key Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
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36
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Hopkins M, Taylor C, Liu Z, Ma F, McNamara L, Wang TW, Thompson JE. Regulation and execution of molecular disassembly and catabolism during senescence. THE NEW PHYTOLOGIST 2007; 175:201-214. [PMID: 17587370 DOI: 10.1111/j.1469-8137.2007.02118.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Senescence is a highly orchestrated developmental stage in the life cycle of plants. The onset of senescence is tightly controlled by signaling cascades that initiate changes in gene expression and the synthesis of new proteins. This complement of new proteins includes hydrolytic enzymes capable of executing catabolism of macromolecules, which in turn sets in motion disassembly of membrane molecular matrices, leading to loss of cell function and, ultimately, complete breakdown of cellular ultrastructure. A distinguishing feature of senescence that sets it apart from other types of programmed cell death is the recovery of carbon and nitrogen from the dying tissue and their translocation to growing parts of the plant such as developing seeds. For this to be accomplished, the initiation of senescence and its execution have to be meticulously regulated. For example, the initiation of membrane disassembly has to be intricately linked with the recruitment of nutrients because their ensuing translocation out of the senescing tissue requires functional membranes. Molecular mechanisms underlying this linkage and its integration with the catabolism of macromolecules in senescing tissues are addressed.
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Affiliation(s)
- Marianne Hopkins
- Department of Biology, University of Waterloo, Waterloo, ONT Canada N2L 3G1
| | - Catherine Taylor
- Department of Biology, University of Waterloo, Waterloo, ONT Canada N2L 3G1
| | - Zhongda Liu
- Department of Biology, University of Waterloo, Waterloo, ONT Canada N2L 3G1
| | - Fengshan Ma
- Department of Biology, University of Waterloo, Waterloo, ONT Canada N2L 3G1
| | - Linda McNamara
- Department of Biology, University of Waterloo, Waterloo, ONT Canada N2L 3G1
| | - Tzann-Wei Wang
- Department of Biology, University of Waterloo, Waterloo, ONT Canada N2L 3G1
| | - John E Thompson
- Department of Biology, University of Waterloo, Waterloo, ONT Canada N2L 3G1
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Requejo R, Tena M. Maize response to acute arsenic toxicity as revealed by proteome analysis of plant shoots. Proteomics 2006; 6 Suppl 1:S156-62. [PMID: 16534746 DOI: 10.1002/pmic.200500381] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Aerial parts (shoots) of maize seedlings fed hydroponically with 300 muM sodium arsenate [As(V)] or 250 muM sodium arsenite [As(III)] for 24 h were analyzed for differentially expressed proteins by 2-DE and digital image analysis. About 15% of total detected proteins (74 out of 500) were up- or, mainly, down-regulated by arsenic, among which 14 were selected as being those most affected by the metalloid. These proteins were analyzed by MALDI-TOF MS and 7 of them were identified: translation initiation factor eIF-5A, ATP synthase, cysteine synthase, malate dehydrogenase, protein kinase C inhibitor, Tn10 transposase-like protein, and guanine nucleotide binding protein. Each of these proteins was completely repressed by As(V) and/or As(III), except protein kinase C inhibitor, which was newly detected after exposure to As(V).
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Affiliation(s)
- Raquel Requejo
- Department of Biochemistry and Molecular Biology, ETSIAM, University of Córdoba, Córdoba, Spain
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38
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Anke S, Niemüller D, Moll S, Hänsch R, Ober D. Polyphyletic origin of pyrrolizidine alkaloids within the Asteraceae. Evidence from differential tissue expression of homospermidine synthase. PLANT PHYSIOLOGY 2004; 136:4037-47. [PMID: 15557091 PMCID: PMC535835 DOI: 10.1104/pp.104.052357] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The evolution of pathways within plant secondary metabolism has been studied by using the pyrrolizidine alkaloids (PAs) as a model system. PAs are constitutively produced by plants as a defense against herbivores. The occurrence of PAs is restricted to certain unrelated families within the angiosperms. Homospermidine synthase (HSS), the first specific enzyme in the biosynthesis of the necine base moiety of PAs, was originally recruited from deoxyhypusine synthase, an enzyme involved in the posttranslational activation of the eukaryotic initiation factor 5A. Recently, this gene recruitment has been shown to have occurred several times independently within the angiosperms and even twice within the Asteraceae. Here, we demonstrate that, within these two PA-producing tribes of the Asteraceae, namely Senecioneae and Eupatorieae, HSS is expressed differently despite catalyzing the same step in PA biosynthesis. Within Eupatorium cannabinum, HSS is expressed uniformly in all cells of the root cortex parenchyma, but not within the endodermis and exodermis. Within Senecio vernalis, HSS expression has been previously identified in groups of specialized cells of the endodermis and the adjacent root cortex parenchyma. This expression pattern was confirmed for Senecio jacobaea as well. Furthermore, the expression of HSS in E. cannabinum is dependent on the development of the plant, suggesting a close linkage to plant growth.
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Affiliation(s)
- Sven Anke
- Institut für Pharmazeutische Biologie der Technischen Universität, D-38106 Braunschweig, Germany
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