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Abdullah-Zawawi MR, Govender N, Karim MB, Altaf-Ul-Amin M, Kanaya S, Mohamed-Hussein ZA. Chemoinformatics-driven classification of Angiosperms using sulfur-containing compounds and machine learning algorithm. PLANT METHODS 2022; 18:118. [PMID: 36335358 PMCID: PMC9636760 DOI: 10.1186/s13007-022-00951-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Phytochemicals or secondary metabolites are low molecular weight organic compounds with little function in plant growth and development. Nevertheless, the metabolite diversity govern not only the phenetics of an organism but may also inform the evolutionary pattern and adaptation of green plants to the changing environment. Plant chemoinformatics analyzes the chemical system of natural products using computational tools and robust mathematical algorithms. It has been a powerful approach for species-level differentiation and is widely employed for species classifications and reinforcement of previous classifications. RESULTS This study attempts to classify Angiosperms using plant sulfur-containing compound (SCC) or sulphated compound information. The SCC dataset of 692 plant species were collected from the comprehensive species-metabolite relationship family (KNApSAck) database. The structural similarity score of metabolite pairs under all possible combinations (plant species-metabolite) were determined and metabolite pairs with a Tanimoto coefficient value > 0.85 were selected for clustering using machine learning algorithm. Metabolite clustering showed association between the similar structural metabolite clusters and metabolite content among the plant species. Phylogenetic tree construction of Angiosperms displayed three major clades, of which, clade 1 and clade 2 represented the eudicots only, and clade 3, a mixture of both eudicots and monocots. The SCC-based construction of Angiosperm phylogeny is a subset of the existing monocot-dicot classification. The majority of eudicots present in clade 1 and 2 were represented by glucosinolate compounds. These clades with SCC may have been a mixture of ancestral species whilst the combinatorial presence of monocot-dicot in clade 3 suggests sulphated-chemical structure diversification in the event of adaptation during evolutionary change. CONCLUSIONS Sulphated chemoinformatics informs classification of Angiosperms via machine learning technique.
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Affiliation(s)
- Muhammad-Redha Abdullah-Zawawi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Malaysia
- UKM Medical Molecular Biology Institute (UMBI), Jalan Yaacob Latif, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Nisha Govender
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Malaysia
| | - Mohammad Bozlul Karim
- Graduate School Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Md Altaf-Ul-Amin
- Graduate School Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Shigehiko Kanaya
- Graduate School Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Malaysia.
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Malaysia.
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2
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Reactive sulfur species and their significance in health and disease. Biosci Rep 2022; 42:231692. [PMID: 36039860 PMCID: PMC9484011 DOI: 10.1042/bsr20221006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/23/2022] Open
Abstract
Reactive sulfur species (RSS) have been recognized in the last two decades as very important molecules in redox regulation. They are involved in metabolic processes and, in this way, they are responsible for maintenance of health. This review summarizes current information about the essential biological RSS, including H2S, low molecular weight persulfides, protein persulfides as well as organic and inorganic polysulfides, their synthesis, catabolism and chemical reactivity. Moreover, the role of RSS disturbances in various pathologies including vascular diseases, chronic kidney diseases, diabetes mellitus Type 2, neurological diseases, obesity, chronic obstructive pulmonary disease and in the most current problem of COVID-19 is presented. The significance of RSS in aging is also mentioned. Finally, the possibilities of using the precursors of various forms of RSS for therapeutic purposes are discussed.
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3
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Liu FL, Yuchi XX, Zhang MH, Huang J, Hu XW, Man RJ. A fluorescent probe derived from Berberrubine for detecting hydrogen polysulfide in food samples. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120491. [PMID: 34653849 DOI: 10.1016/j.saa.2021.120491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
In this work, we chose the fluorophore Berberrubine to develop a selective probe for hydrogen polysulfide (H2Sn), and applied it into the detection in both food samples and living cells. The developed probe, HER9SS, suggested practical steadiness and serviceability, especially for multi-scene detection. The detecting system was stable in relatively wide pH (7.0-11.0) and temperature (25-45 °C) ranges. Both the storage of BER9SS in solid or in solution could maintain the steadiness over 7 d. BER9SS also indicated advantages including rapid response (within 15 min), high sensitivity (LOD = 0.02 μM; LOQ = 0.01 μM), long linear range (0-15.0 equivalent) and high selectivity among competing analytes. The recovery ranging in 95.23% - 104.8% in the applications in food sources samples (including water and plants) and food samples inferred the practical potential of BER9SS. In biological imaging, BER9SS could achieve both the dose-dependent monitoring and the β-lapachone-induced generation of H2Sn. Therefore, the information in this work might be useful for the development of fluorescent probes from natural products for multi-scene applications in future, especially with the corresponding attentions on the practicability and serviceability.
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Affiliation(s)
- Fu-Ling Liu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong 276005, China
| | - Xue-Xian Yuchi
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong 276005, China
| | - Mei-Hui Zhang
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong 276005, China
| | - Jie Huang
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong 276005, China
| | - Xiao-Wei Hu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong 276005, China.
| | - Ruo-Jun Man
- Guangxi Biological Polysaccharide Separation, Purification and Modification Research Platform, Guangxi University for Nationalities, Nanning 530006, China.
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4
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Xiong R, Cheng M, Wang R, Tao L, Wang Z, Zhang M. A Carbon Shell Covered Pd Catalyst for Hydrogenation of 4-Nitrothioanisole. Catal Letters 2022. [DOI: 10.1007/s10562-022-03925-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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5
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Ren Z, Wang RY, Huang XY, Wang Y. Sulfur Compounds in Regulation of Stomatal Movement. FRONTIERS IN PLANT SCIENCE 2022; 13:846518. [PMID: 35360293 PMCID: PMC8963490 DOI: 10.3389/fpls.2022.846518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/09/2022] [Indexed: 05/06/2023]
Abstract
Sulfur, widely present in the soil and atmosphere, is one of the essential elements for plants. Sulfate is a dominant form of sulfur in soils taken up by plant roots. In addition to the assimilation into sulfur compounds essential for plant growth and development, it has been reported recently that sulfate as well as other sulfur containing compounds can also induce stomatal movement. Here, we first summarized the uptake and transport of sulfate and atmospheric sulfur, including H2O and SO2, and then, focused on the effects of inorganic and organic sulfur on stomatal movement. We concluded all the transporters for different sulfur compounds, and compared the expression level of those transporters in guard cells and mesophyll cells. The relationship between abscisic acid and sulfur compounds in regulation of stomatal movement were also discussed.
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Affiliation(s)
- Zirong Ren
- Institute of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of Ministry of Education, Peking University, Beijing, China
| | - Ru-Yuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Xin-Yuan Huang,
| | - Yin Wang
- Institute of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of Ministry of Education, Peking University, Beijing, China
- Yin Wang,
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6
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Kerdsomboon K, Techo T, Limcharoensuk T, Tatip S, Auesukaree C. Low phosphate mitigates cadmium-induced oxidative stress in Saccharomyces cerevisiae by enhancing endogenous antioxidant defence system. Environ Microbiol 2021; 24:707-720. [PMID: 34927334 DOI: 10.1111/1462-2920.15875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/30/2022]
Abstract
Cadmium is a highly toxic heavy metal that causes many harmful effects on human health and ecosystems. Metal chelation-based techniques have become a common approach for the treatment of metal poisoning and also for the remediation of metal contamination. Phosphate, an essential nutrient required for key cellular functions, has been supposed to be effective in reducing cadmium bioavailability, possibly through its chelating potential. In this study, we explored the effects of phosphate on cadmium toxicity and cellular response to cadmium stress in the eukaryotic model Saccharomyces cerevisiae. Our results reveal that cadmium toxicity is unexpectedly enhanced during phosphate repletion and optimal phosphate levels for yeast growth under cadmium stress conditions decline with increasing cadmium concentrations. The profound cadmium toxicity during phosphate repletion is unlikely to result from either elevated cadmium accumulation or dysregulated homeostasis of essential metals, but rather due to increased production of intracellular reactive oxygen species. We show that, under phosphate-depleted conditions, the activities of antioxidant enzymes, especially Mn-superoxide dismutase and catalase, are significantly promoted through transcriptional upregulation. Our findings highlight the important role of cellular response to phosphate limitation in mitigating cadmium toxicity and endogenous oxidative stress through the enhancement of antioxidant enzyme activity.
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Affiliation(s)
- Kittikhun Kerdsomboon
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, 12120, Thailand.,Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.,Mahidol University-Osaka University Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Todsapol Techo
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.,Mahidol University-Osaka University Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Tossapol Limcharoensuk
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.,Mahidol University-Osaka University Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Supinda Tatip
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.,Mahidol University-Osaka University Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Choowong Auesukaree
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.,Mahidol University-Osaka University Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
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7
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Kitainda V, Jez JM. Structural Studies of Aliphatic Glucosinolate Chain-Elongation Enzymes. Antioxidants (Basel) 2021; 10:antiox10091500. [PMID: 34573132 PMCID: PMC8468904 DOI: 10.3390/antiox10091500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Plants evolved specialized metabolic pathways through gene duplication and functional divergence of enzymes involved in primary metabolism. The results of this process are varied pathways that produce an array of natural products useful to both plants and humans. In plants, glucosinolates are a diverse class of natural products. Glucosinolate function stems from their hydrolysis products, which are responsible for the strong flavors of Brassicales plants, such as mustard, and serve as plant defense molecules by repelling insects, fighting fungal infections, and discouraging herbivory. Additionally, certain hydrolysis products such as isothiocyanates can potentially serve as cancer prevention agents in humans. The breadth of glucosinolate function is a result of its great structural diversity, which comes from the use of aliphatic, aromatic and indole amino acids as precursors and elongation of some side chains by up to nine carbons, which, after the formation of the core glucosinolate structure, can undergo further chemical modifications. Aliphatic methionine-derived glucosinolates are the most abundant form of these compounds. Although both elongation and chemical modification of amino acid side chains are important for aliphatic glucosinolate diversity, its elongation process has not been well described at the molecular level. Here, we summarize new insights on the iterative chain-elongation enzymes methylthioalkylmalate synthase (MAMS) and isopropylmalate dehydrogenase (IPMDH).
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8
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Liu H, Li Y, Li S. Cu and Na contents regulate N uptake of Leymus chinensis growing in soda saline-alkali soil. PLoS One 2020; 15:e0243172. [PMID: 33259559 PMCID: PMC7707461 DOI: 10.1371/journal.pone.0243172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/16/2020] [Indexed: 12/02/2022] Open
Abstract
Leymus chinensis (L. chinensis) is the dominant plant in the eastern margins of the Eurasian temperate grasslands. It is a very robust species, exhibiting good saline-alkali resistance and stabilizing soil. In this study, 67 soil samples and L. chinensis were collected in western Jilin province, China. The contents of N, P, K, S, Mn, Fe, Zn, Cu and Na were measured, revealing that the growth of L. chinensis was mainly restricted by N based on the stoichiometric N: P ratios of plant. Furthermore, path analysis indicated that N was significantly correlated with K, S, Cu, and Zn. Imbalances in the homeostasis of these four elements may thus constrain N. The homeostasis index of Cu (HCu) in sites with 100%-70% of vegetation cover was only 0.79, it was classified as a sensitive element. However, K, S and Zn, whose concentrations in L. chinensis were significantly related to those of N, exhibited no homeostatic characteristics. These results suggest that when seeking to treat saline-alkali stress, it is important to add fertilizers containing K, S, and Zn to avoid growth limitation. Na+, an ion associated with high soil alkalinity, exhibited weak homeostasis in L. chinensis even in sites with only 40%-10% of vegetation cover. When soil Na exceeded 16000 mg/kg, the homeostasis mechanism of L. chinensis appeared to be overwhelmed, resulting in rapid and probably harmful accumulation of Na. Proper control of N content can alleviate the toxicity of Na stress in L. chinensis and enhance its Na tolerance. Together, these results suggest that combined fertilization with N, K, S, Zn and Cu should be applied to improve grasslands growth. The results of this study can provide a reference basis for sustainable grassland management.
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Affiliation(s)
- Hongshan Liu
- College of Earth Sciences, Jilin University, Changchun, Jilin, China
| | - Yuefen Li
- College of Earth Sciences, Jilin University, Changchun, Jilin, China
- Key Laboratory of Mineral Resources Evaluation in Northeast Asia, Ministry of Land and Resources, Changchun, Jilin, China
| | - Shujie Li
- College of Earth Sciences, Jilin University, Changchun, Jilin, China
- * E-mail:
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9
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Aarabi F, Naake T, Fernie AR, Hoefgen R. Coordinating Sulfur Pools under Sulfate Deprivation. TRENDS IN PLANT SCIENCE 2020; 25:1227-1239. [PMID: 32800669 DOI: 10.1016/j.tplants.2020.07.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 05/22/2023]
Abstract
Plants display manifold metabolic changes on sulfate deficiency (S deficiency) with all sulfur-containing pools of primary and secondary metabolism affected. O-Acetylserine (OAS), whose levels are rapidly altered on S deficiency, is correlated tightly with novel regulators of plant sulfur metabolism that have key roles in balancing plant sulfur pools, including the Sulfur Deficiency Induced genes (SDI1 and SDI2), More Sulfur Accumulation1 (MSA1), and GGCT2;1. Despite the importance of OAS in the coordination of S pools under stress, mechanisms of OAS perception and signaling have remained elusive. Here, we put particular focus on the general OAS-responsive genes but also elaborate on the specific roles of SDI1 and SDI2 genes, which downregulate the glucosinolate (GSL) pool size. We also highlight the key open questions in sulfur partitioning.
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Affiliation(s)
- Fayezeh Aarabi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Thomas Naake
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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10
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Abstract
Flavin-dependent monooxygenases (FMOs) are ancient enzymes present in all kingdoms of life. FMOs typically catalyze the incorporation of an oxygen atom from molecular oxygen into small molecules. To date, the majority of functional characterization studies have been performed on mammalian, fungal and bacterial FMOs, showing that they play fundamental roles in drug and xenobiotic metabolism. By contrast, our understanding of FMOs across the plant kingdom is very limited, despite plants possessing far greater FMO diversity compared to both bacteria and other multicellular organisms. Here, we review the progress of plant FMO research, with a focus on FMO diversity and functionality. Significantly, of the FMOs characterized to date, they all perform oxygenation reactions that are crucial steps within hormone metabolism, pathogen resistance, signaling and chemical defense. This demonstrates the fundamental role FMOs have within plant metabolism, and presents significant opportunities for future research pursuits and downstream applications.
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11
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Li S, Zhu Y, Varshney RK, Zhan J, Zheng X, Shi J, Wang X, Liu G, Wang H. A systematic dissection of the mechanisms underlying the natural variation of silique number in rapeseed (Brassica napus L.) germplasm. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:568-580. [PMID: 31368615 PMCID: PMC6953207 DOI: 10.1111/pbi.13224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 07/02/2019] [Accepted: 07/17/2019] [Indexed: 05/12/2023]
Abstract
Silique number is the most important component of yield in rapeseed (Brassica napus L.). To dissect the mechanism underlying the natural variation of silique number in rapeseed germplasm, a series of studies were performed. A panel of 331 core lines was employed to genome-wide association study (GWAS), and 27 loci (including 20 novel loci) were identified. The silique number difference between the more- and fewer-silique lines can be attributed to the accumulative differences in flower number and silique setting rate. Each of them accounted for 75.2% and 24.8%, respectively. The silique number was highly associated with the total photosynthesis and biomass. Microscopic analysis showed that the difference between extremely more- and fewer-silique lines normally occurred at the amount of flower bud but not morphology. Transcriptome analysis of shoot apical meristem (SAM) suggested that most of enriched groups were associated with the auxin biosynthesis/metabolism, vegetative growth and nutrition/energy accumulation. By integrating GWAS and RNA-seq results, six promising candidate genes were identified, and some of them were related to biomass accumulation. In conclusion, the natural variation of silique number is largely affected by the biomass and nutrition accumulation, which essentially reflects the positive regulatory relationship between the source and sink. Our study provides a comprehensive and systematic explanation for natural variation of silique number in rapeseed, which provides a foundation for its improvement.
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Affiliation(s)
- Shuyu Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
- Crop Research InstituteJiangxi Academy of Agricultural SciencesNanchangChina
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yaoyao Zhu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Jiepeng Zhan
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Xiaoxiao Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanChina
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12
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Nin DS, Idres SB, Song ZJ, Moore PK, Deng LW. Biological Effects of Morpholin-4-Ium 4 Methoxyphenyl (Morpholino) Phosphinodithioate and Other Phosphorothioate-Based Hydrogen Sulfide Donors. Antioxid Redox Signal 2020; 32:145-158. [PMID: 31642346 DOI: 10.1089/ars.2019.7896] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Significance: Hydrogen sulfide (H2S) is regarded as the third gasotransmitter along with nitric oxide and carbon monoxide. Extensive studies have demonstrated a variety of biological roles for H2S in neurophysiology, cardiovascular disease, endocrine regulation, and other physiological and pathological processes. Recent Advances: Novel H2S donors have proved useful in understanding the biological functions of H2S, with morpholin-4-ium 4 methoxyphenyl (morpholino) phosphinodithioate (GYY4137) being one of the most common pharmacological tools used. One advantage of GYY4137 over sulfide salts is its ability to release H2S in a slow and sustained manner akin to endogenous H2S production, rather than the delivery of H2S as a single concentrated burst. Critical Issues: Here, we summarize recent progress made in the characterization of the biological activities and pharmacological effects of GYY4137 in a range of in vitro and in vivo systems. Recent developments in the structural modification of GYY4137 to generate new compounds and their biological effects are also discussed. Future Directions: Slow-releasing H2S donor, GYY4137, and other phosphorothioate-based H2S donors are potent tools to study the biological functions of H2S. Despite recent progress, more work needs to be performed on these new compounds to unravel the mechanisms behind H2S release and pace of its discharge, as well as to define the effects of by-products of donors after H2S liberation. This will not only lead to better in-depth understanding of the biological effects of H2S but will also shed light on the future development of a new class of therapeutic agents with potential to treat a wide range of human diseases.
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Affiliation(s)
- Dawn Sijin Nin
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shabana Binte Idres
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhi Jian Song
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Philip K Moore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lih-Wen Deng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,National University Cancer Institute, National University Health System, Singapore, Singapore
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13
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Gotor C, García I, Aroca Á, Laureano-Marín AM, Arenas-Alfonseca L, Jurado-Flores A, Moreno I, Romero LC. Signaling by hydrogen sulfide and cyanide through post-translational modification. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4251-4265. [PMID: 31087094 DOI: 10.1093/jxb/erz225] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/03/2019] [Indexed: 05/04/2023]
Abstract
Two cysteine metabolism-related molecules, hydrogen sulfide and hydrogen cyanide, which are considered toxic, have now been considered as signaling molecules. Hydrogen sulfide is produced in chloroplasts through the activity of sulfite reductase and in the cytosol and mitochondria by the action of sulfide-generating enzymes, and regulates/affects essential plant processes such as plant adaptation, development, photosynthesis, autophagy, and stomatal movement, where interplay with other signaling molecules occurs. The mechanism of action of sulfide, which modifies protein cysteine thiols to form persulfides, is related to its chemical features. This post-translational modification, called persulfidation, could play a protective role for thiols against oxidative damage. Hydrogen cyanide is produced during the biosynthesis of ethylene and camalexin in non-cyanogenic plants, and is detoxified by the action of sulfur-related enzymes. Cyanide functions include the breaking of seed dormancy, modifying the plant responses to biotic stress, and inhibition of root hair elongation. The mode of action of cyanide is under investigation, although it has recently been demonstrated to perform post-translational modification of protein cysteine thiols to form thiocyanate, a process called S-cyanylation. Therefore, the signaling roles of sulfide and most probably of cyanide are performed through the modification of specific cysteine residues, altering protein functions.
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Affiliation(s)
- Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, Seville, Spain
| | - Irene García
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, Seville, Spain
| | - Ángeles Aroca
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, Seville, Spain
| | - Ana M Laureano-Marín
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, Seville, Spain
| | - Lucía Arenas-Alfonseca
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, Seville, Spain
| | - Ana Jurado-Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, Seville, Spain
| | - Inmaculada Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, Seville, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, Seville, Spain
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14
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Jez JM. Structural biology of plant sulfur metabolism: from sulfate to glutathione. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4089-4103. [PMID: 30825314 DOI: 10.1093/jxb/erz094] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
Sulfur is an essential element for all organisms. Plants must assimilate this nutrient from the environment and convert it into metabolically useful forms for the biosynthesis of a wide range of compounds, including cysteine and glutathione. This review summarizes structural biology studies on the enzymes involved in plant sulfur assimilation [ATP sulfurylase, adenosine-5'-phosphate (APS) reductase, and sulfite reductase], cysteine biosynthesis (serine acetyltransferase and O-acetylserine sulfhydrylase), and glutathione biosynthesis (glutamate-cysteine ligase and glutathione synthetase) pathways. Overall, X-ray crystal structures of enzymes in these core pathways provide molecular-level information on the chemical events that allow plants to incorporate sulfur into essential metabolites and revealed new biochemical regulatory mechanisms, such as structural rearrangements, protein-protein interactions, and thiol-based redox switches, for controlling different steps in these pathways.
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Affiliation(s)
- Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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15
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Li H, Lyu Y, Chen X, Wang C, Yao D, Ni S, Lin Y, Chen Y, Zhang Z, Lai Z. Exploration of the Effect of Blue Light on Functional Metabolite Accumulation in Longan Embryonic Calli via RNA Sequencing. Int J Mol Sci 2019; 20:ijms20020441. [PMID: 30669555 PMCID: PMC6359358 DOI: 10.3390/ijms20020441] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 01/07/2023] Open
Abstract
Light is an important factor that affects the synthesis of functional metabolites in longan embryogenic calli (ECs). However, analysis of the effect of light on functional metabolites in longan ECs via RNA sequencing has rarely been reported and their light regulation network is unclear. The contents of various functional metabolites as well as the enzymatic activities of superoxide dismutase and peroxidase and the level of H₂O₂ in longan ECs were significantly higher under blue light treatment than under the other treatments (dark, white). In this study, we sequenced three mRNA libraries constructed from longan ECs subjected to different treatments. A total of 4463, 1639 and 1806 genes were differentially expressed in the dark versus blue (DB), dark versus white (DW) and white versus blue (WB) combinations, respectively. According to GO and KEGG analyses, most of the differentially expressed genes (DEGs) identified were involved in transmembrane transport, taurine and hypotaurine metabolism, calcium transport and so forth. Mapman analysis revealed that more DEGs were identified in each DB combination pathway than in DW combination pathways, indicating that blue light exerts a significantly stronger regulatory effect on longan EC metabolism than the other treatments. Based on previous research and transcriptome data mining, a blue light signaling network of genes that affect longan functional metabolites was constructed and HY5, PIF4 and MYC2 were shown to be the key regulatory genes in the network. The results of this study demonstrate that the expression levels of phase-specific genes vary with changes in longan EC functional metabolites.
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Affiliation(s)
- Hansheng Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Resources and Chemical Engineering, Sanming University, Sanming 365004, China.
| | - Yumeng Lyu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Congqiao Wang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Deheng Yao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shanshan Ni
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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16
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The Complete Pathway for Thiosulfate Utilization in Saccharomyces cerevisiae. Appl Environ Microbiol 2018; 84:AEM.01241-18. [PMID: 30217845 DOI: 10.1128/aem.01241-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/02/2018] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae is known to grow with thiosulfate as a sulfur source, and it produces more ethanol when using thiosulfate than using sulfate. Here, we report how it assimilates thiosulfate. S. cerevisiae absorbed thiosulfate into the cell through two sulfate permeases, Sul1 and Sul2. Two rhodaneses, Rdl1 and Rdl2, converted thiosulfate to a persulfide and sulfite. The persulfide was reduced by cellular thiols to H2S, and sulfite was reduced by sulfite reductase to H2S. Cysteine synthase incorporated H2S into O-acetyl-l-homoserine to produce l-homocysteine, which is the precursor for cysteine and methionine in S. cerevisiae Several other rhodaneses replaced Rdl1 and Rdl2 for thiosulfate utilization in the yeast. Thus, any organisms with the sulfate assimilation system potentially could use thiosulfate as a sulfur source, since rhodaneses are common in most organisms.IMPORTANCE The complete pathway of thiosulfate assimilation in baker's yeast is determined. The finding reveals the extensive overlap between sulfate and thiosulfate assimilation. Rhodanese is the only additional enzyme for thiosulfate utilization. The common presence of rhodanese in most organisms, including Bacteria, Archaea, and Eukarya, suggests that most organisms with the sulfate assimilation system also use thiosulfate. Since it takes less energy to reduce thiosulfate than sulfate for assimilation, thiosulfate has the potential to become a choice of sulfur in optimized media for industrial fermentation.
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17
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Theoretical investigations on the conversions of cyclic polysulfides to acyclic polysulfide diradicals and subsequent reactions of biological interest. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Zhou LH, Liu SB, Wang PF, Lu TJ, Xu F, Genin GM, Pickard BG. The Arabidopsis trichome is an active mechanosensory switch. PLANT, CELL & ENVIRONMENT 2017; 40:611-621. [PMID: 26920667 DOI: 10.1111/pce.12728] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 05/18/2023]
Abstract
Trichomes ('hair cells') on Arabidopsis thaliana stem and leaf surfaces provide a range of benefits arising from their shape and disposition. These include tempting herbivores to sample constitutive toxins before they reach the bulk of the tissue. We asked whether, in addition, small mechanical disturbances such as an insect can make elicit signals that might help the plant respond to herbivory. We imaged, pressed and brushed trichomes in several ways, most notably with confocal microscopy of trichomes transgenically provided with apoplastic pH reporter apo-pHusion and cytosolic Ca2+ reporter cameleon. In parallel, we modelled trichome wall mechanics with finite element analysis. The stimulated trichome focuses force on a pliant zone and the adjoining podium of the stalk. A buckling instability can further focus force on a skirt of cells surrounding the podium, eliciting oscillations of cytosolic Ca2+ and shifts in apoplastic pH. These observations represent active physiological response. Modelling establishes that the effectiveness of force focusing and buckling is due to the peculiar tapering wall structure of the trichome. Hypothetically, these active mechanosensing functions enhance toxin synthesis above constitutive levels, probably via a priming process, thus minimizing the costly accumulation of toxins in the absence of herbivore attack but assuring rapid build-up when needed.
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Affiliation(s)
- Li Hong Zhou
- Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Bioinspired Engineering & Biomechanics Center, Xi'an Jiaotong University, Xi'an, 710049, China
- Gladys Levis Allen Laboratory of Plant Sensory Physiology, Biology Department, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Shao Bao Liu
- Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Bioinspired Engineering & Biomechanics Center, Xi'an Jiaotong University, Xi'an, 710049, China
- Gladys Levis Allen Laboratory of Plant Sensory Physiology, Biology Department, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Peng Fei Wang
- Bioinspired Engineering & Biomechanics Center, Xi'an Jiaotong University, Xi'an, 710049, China
- Qian Xuesen Laboratory of Space Technology, China Academy of Space Technology, Beijing, 100094, China
| | - Tian Jian Lu
- Bioinspired Engineering & Biomechanics Center, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Feng Xu
- Bioinspired Engineering & Biomechanics Center, Xi'an Jiaotong University, Xi'an, 710049, China
- Ministry of Education Key Laboratory of Biomedical Information Engineering, School of Life Science & Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Guy M Genin
- Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Bioinspired Engineering & Biomechanics Center, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Barbara G Pickard
- Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Gladys Levis Allen Laboratory of Plant Sensory Physiology, Biology Department, Washington University in St. Louis, St. Louis, MO, 63130, USA
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19
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Jez JM, Ravilious GE, Herrmann J. Structural biology and regulation of the plant sulfation pathway. Chem Biol Interact 2016; 259:31-38. [DOI: 10.1016/j.cbi.2016.02.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/16/2016] [Accepted: 02/22/2016] [Indexed: 11/26/2022]
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20
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Liu H, Zhou LH, Jiao J, Liu S, Zhang Z, Lu TJ, Xu F. Gradient Mechanical Properties Facilitate Arabidopsis Trichome as Mechanosensor. ACS APPLIED MATERIALS & INTERFACES 2016; 8:9755-61. [PMID: 27010517 DOI: 10.1021/acsami.6b02253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
It has been reported that Arabidopsis thaliana leaf trichome can act as a mechanosensory switch, transducing mechanical stimuli into physiological signals, mainly through a buckling instability to focus external force (e.g., exerted by insects) on the base of trichome. The material and structural properties of trichomes remain largely unknown in this buckling instability. In this report, we mainly focused on material standpoint to explore the possible mechanism facilitating the buckling instability. We observed that the Young's modulus of trichome cell wall decreased gradually from branch to the base region of trichome. Interestingly, we also found a corresponding decline of calcium concentration on the trichome cell wall. Results of finite element method (FEM) simulation suggested that such a gradient distribution of Young's modulus significantly promotes force focusing and buckling instability on the base of trichome. It is indicated that Arabidopsis trichome has developed into an active mechanosensor benefiting from gradient cell wall mechanical properties.
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Affiliation(s)
- Han Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an 710049, P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University , Xi'an 710049, P. R. China
| | - Li Hong Zhou
- College of Life Sciences, Agricultural University of Hebei , Baoding 071001, P. R. China
| | - Jiaojiao Jiao
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University , Xi'an 710049, P. R. China
- State Key Laboratory for Mechanical Structure Strength and Vibration, Xi'an Jiaotong University , Xi'an 710049, P. R. China
| | - Shaobao Liu
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University , Xi'an 710049, P. R. China
- State Key Laboratory for Mechanical Structure Strength and Vibration, Xi'an Jiaotong University , Xi'an 710049, P. R. China
| | - Zhanming Zhang
- State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University , Xi'an 710049, P. R. China
| | - Tian Jian Lu
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University , Xi'an 710049, P. R. China
- State Key Laboratory for Mechanical Structure Strength and Vibration, Xi'an Jiaotong University , Xi'an 710049, P. R. China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an 710049, P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University , Xi'an 710049, P. R. China
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21
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Herrmann J, Nathin D, Lee SG, Sun T, Jez JM. Recapitulating the Structural Evolution of Redox Regulation in Adenosine 5'-Phosphosulfate Kinase from Cyanobacteria to Plants. J Biol Chem 2015; 290:24705-14. [PMID: 26294763 DOI: 10.1074/jbc.m115.679514] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Indexed: 11/06/2022] Open
Abstract
In plants, adenosine 5'-phosphosulfate (APS) kinase (APSK) is required for reproductive viability and the production of 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfur donor in specialized metabolism. Previous studies of the APSK from Arabidopsis thaliana (AtAPSK) identified a regulatory disulfide bond formed between the N-terminal domain (NTD) and a cysteine on the core scaffold. This thiol switch is unique to mosses, gymnosperms, and angiosperms. To understand the structural evolution of redox control of APSK, we investigated the redox-insensitive APSK from the cyanobacterium Synechocystis sp. PCC 6803 (SynAPSK). Crystallographic analysis of SynAPSK in complex with either APS and a non-hydrolyzable ATP analog or APS and sulfate revealed the overall structure of the enzyme, which lacks the NTD found in homologs from mosses and plants. A series of engineered SynAPSK variants reconstructed the structural evolution of the plant APSK. Biochemical analyses of SynAPSK, SynAPSK H23C mutant, SynAPSK fused to the AtAPSK NTD, and the fusion protein with the H23C mutation showed that the addition of the NTD and cysteines recapitulated thiol-based regulation. These results reveal the molecular basis for structural changes leading to the evolution of redox control of APSK in the green lineage from cyanobacteria to plants.
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Affiliation(s)
- Jonathan Herrmann
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - David Nathin
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Soon Goo Lee
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Tony Sun
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Joseph M Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
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22
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Funahashi E, Saiki K, Honda K, Sugiura Y, Kawano Y, Ohtsu I, Watanabe D, Wakabayashi Y, Abe T, Nakanishi T, Suematsu M, Takagi H. Finding of thiosulfate pathway for synthesis of organic sulfur compounds in Saccharomyces cerevisiae and improvement of ethanol production. J Biosci Bioeng 2015; 120:666-9. [PMID: 26188417 DOI: 10.1016/j.jbiosc.2015.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/23/2015] [Accepted: 04/16/2015] [Indexed: 11/16/2022]
Abstract
We found that Saccharomyces cerevisiae utilizes thiosulfate as a sole sulfur source. The energetically-favored thiosulfate rather than sulfate as sulfur sources is also more effective for improving growth and ethanol-production rate in S. cerevisiae due to high levels of intracellular NADPH during thiosulfate utilization.
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Affiliation(s)
- Eri Funahashi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Kyohei Saiki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Kurara Honda
- Department of Biochemistry, Keio University School of Medicine, 35 Shinanomachi, Shinjyuku-ku, Tokyo 160-8582, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, 35 Shinanomachi, Shinjyuku-ku, Tokyo 160-8582, Japan
| | - Yusuke Kawano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Iwao Ohtsu
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.
| | - Daisuke Watanabe
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Yukari Wakabayashi
- Technical Research Laboratories, Kyowa Hakko Bio Co. Ltd., 1-1 Kyowa-cho, Hofu, Yamaguchi 747-8522, Japan
| | - Tetsuya Abe
- Technical Research Laboratories, Kyowa Hakko Bio Co. Ltd., 1-1 Kyowa-cho, Hofu, Yamaguchi 747-8522, Japan
| | - Tsuyoshi Nakanishi
- MS Business Unit, Shimadzu Co., 1 Nishinokyo, Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, 35 Shinanomachi, Shinjyuku-ku, Tokyo 160-8582, Japan
| | - Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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23
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Cahoon RE, Lutke WK, Cameron JC, Chen S, Lee SG, Rivard RS, Rea PA, Jez JM. Adaptive Engineering of Phytochelatin-based Heavy Metal Tolerance. J Biol Chem 2015; 290:17321-30. [PMID: 26018077 DOI: 10.1074/jbc.m115.652123] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 11/06/2022] Open
Abstract
Metabolic engineering approaches are increasingly employed for environmental applications. Because phytochelatins (PC) protect plants from heavy metal toxicity, strategies directed at manipulating the biosynthesis of these peptides hold promise for the remediation of soils and groundwaters contaminated with heavy metals. Directed evolution of Arabidopsis thaliana phytochelatin synthase (AtPCS1) yields mutants that confer levels of cadmium tolerance and accumulation greater than expression of the wild-type enzyme in Saccharomyces cerevisiae, Arabidopsis, or Brassica juncea. Surprisingly, the AtPCS1 mutants that enhance cadmium tolerance and accumulation are catalytically less efficient than wild-type enzyme. Metabolite analyses indicate that transformation with AtPCS1, but not with the mutant variants, decreases the levels of the PC precursors, glutathione and γ-glutamylcysteine, upon exposure to cadmium. Selection of AtPCS1 variants with diminished catalytic activity alleviates depletion of these metabolites, which maintains redox homeostasis while supporting PC synthesis during cadmium exposure. These results emphasize the importance of metabolic context for pathway engineering and broaden the range of tools available for environmental remediation.
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Affiliation(s)
- Rebecca E Cahoon
- From the Department of Biology, Washington University, St. Louis, Missouri 63130, the Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - W Kevin Lutke
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Jeffrey C Cameron
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Sixue Chen
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, the Department of Biology, Genetics Institute, University of Florida, Gainesville, Florida 32610, and
| | - Soon Goo Lee
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Rebecca S Rivard
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Philip A Rea
- the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Joseph M Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130, the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, the Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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24
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Kawano Y, Ohtsu I, Tamakoshi A, Shiroyama M, Tsuruoka A, Saiki K, Takumi K, Nonaka G, Nakanishi T, Hishiki T, Suematsu M, Takagi H. Involvement of the yciW gene in l-cysteine and l-methionine metabolism in Escherichia coli. J Biosci Bioeng 2015; 119:310-3. [DOI: 10.1016/j.jbiosc.2014.08.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/12/2014] [Accepted: 08/21/2014] [Indexed: 01/19/2023]
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25
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Abstract
Hydrogen sulfide (H2S) is now recognized as the so called "third gasotransmitter" taking its place alongside nitric oxide and carbon monoxide. In recent years, H2S has been reported to exhibit a diverse range of pharmacological effects in biological systems. Much of this evidence is derived from a combination of conventional pharmacological and genetic approaches coupled with the use of chemical compounds such as sodium hydrosulfide, a rapid H2S releasing donor. Developments in the design of new drug entities which attempt to take into account physicochemical properties, targeting to specific cellular organelles, triggering of H2S release upon specific chemical reactions in the cell, and controlling the release of H2S over extended periods of time have been described. For most of these molecules, little or no work has been conducted to determine their biological activity or possible therapeutic effects. It is therefore not clear whether such molecules have therapeutic potential which highlights the need for further in vivo studies. One exception to the general rule is GYY4137 (morpholin-4-ium 4-methoxyphenyl(morpholino) phosphinodithioate), a slow releasing H2S donor, which has been evaluated for activity in a range of pharmacological models both in vitro and in vivo. GYY4137 was first reported to release H2S and exhibit vasodilator activity over 5 years ago and, to date, GYY4137 is becoming increasingly employed as a pharmacological "tool" to explore the biological functions of H2S.
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Affiliation(s)
- Peter Rose
- University of Lincoln, Lincoln, Lincolnshire, United Kingdom
| | - Brian W Dymock
- Department of Pharmacy, National University of Singapore, Singapore
| | - Philip K Moore
- Neurobiology Program, Life Science Institute and Department of Pharmacology, National University of Singapore, Singapore.
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26
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Kumar S, Kumar N, Alam N, Gourinath S. Crystal structure of serine acetyl transferase from Brucella abortus and its complex with coenzyme A. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1741-8. [PMID: 25058332 DOI: 10.1016/j.bbapap.2014.07.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/09/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
Abstract
Brucella abortus is the major cause of premature foetal abortion in cattle, can be transmitted from cattle to humans, and is considered a powerful biological weapon. De novo cysteine biosynthesis is one of the essential pathways reported in bacteria, protozoa, and plants. Serine acetyltransferase (SAT) initiates this reaction by catalyzing the formation of O-acetylserine (OAS) using l-serine and acetyl coenzyme A as substrates. Here we report kinetic and crystallographic studies of this enzyme from B. abortus. The kinetic studies indicate that cysteine competitively inhibits the binding of serine to B. abortus SAT (BaSAT) and noncompetitively inhibits the binding of acetyl coenzyme A. The crystal structures of BaSAT in its apo state and in complex with coenzyme A (CoA) were determined to 1.96Å and 1.87Å resolution, respectively. BaSAT was observed as a trimer in a size exclusion column; however, it was seen as a hexamer in dynamic light scattering (DLS) studies and in the crystal structure, indicating it may exist in both states. The complex structure shows coenzyme A bound to the C-terminal region, making mostly hydrophobic contacts from the center of the active site extending up to the surface of the protein. There is no conformational difference in the enzyme between the apo and the complexed states, indicating lock and key binding and the absence of an induced fit mechanism.
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Affiliation(s)
- Sudhir Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Nitesh Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Neelima Alam
- Technology Bhavan, Ministry of Science and Technology, New Mehrauli Road, New Delhi 110016, India
| | - Samudrala Gourinath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India.
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27
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Herrmann J, Ravilious GE, McKinney SE, Westfall CS, Lee SG, Baraniecka P, Giovannetti M, Kopriva S, Krishnan HB, Jez JM. Structure and mechanism of soybean ATP sulfurylase and the committed step in plant sulfur assimilation. J Biol Chem 2014; 289:10919-10929. [PMID: 24584934 PMCID: PMC4036203 DOI: 10.1074/jbc.m113.540401] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/27/2014] [Indexed: 11/06/2022] Open
Abstract
Enzymes of the sulfur assimilation pathway are potential targets for improving nutrient content and environmental stress responses in plants. The committed step in this pathway is catalyzed by ATP sulfurylase, which synthesizes adenosine 5'-phosphosulfate (APS) from sulfate and ATP. To better understand the molecular basis of this energetically unfavorable reaction, the x-ray crystal structure of ATP sulfurylase isoform 1 from soybean (Glycine max ATP sulfurylase) in complex with APS was determined. This structure revealed several highly conserved substrate-binding motifs in the active site and a distinct dimerization interface compared with other ATP sulfurylases but was similar to mammalian 3'-phosphoadenosine 5'-phosphosulfate synthetase. Steady-state kinetic analysis of 20 G. max ATP sulfurylase point mutants suggests a reaction mechanism in which nucleophilic attack by sulfate on the α-phosphate of ATP involves transition state stabilization by Arg-248, Asn-249, His-255, and Arg-349. The structure and kinetic analysis suggest that ATP sulfurylase overcomes the energetic barrier of APS synthesis by distorting nucleotide structure and identifies critical residues for catalysis. Mutations that alter sulfate assimilation in Arabidopsis were mapped to the structure, which provides a molecular basis for understanding their effects on the sulfur assimilation pathway.
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Affiliation(s)
- Jonathan Herrmann
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | | | - Samuel E McKinney
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Corey S Westfall
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Soon Goo Lee
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | | | - Marco Giovannetti
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom; Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, I-10125 Torino, Italy
| | - Stanislav Kopriva
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Hari B Krishnan
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, Missouri 65211
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130.
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28
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Preuss ML, Cameron JC, Berg RH, Jez JM. Immunolocalization of glutathione biosynthesis enzymes in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 75:9-13. [PMID: 24361505 DOI: 10.1016/j.plaphy.2013.11.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 11/28/2013] [Indexed: 05/12/2023]
Abstract
In plants, glutathione serves as a versatile redox buffer and cellular protective compound against a range of biotic and abiotic stresses. Glutathione production involves glutamate-cysteine ligase (GCL), the redox-regulated limiting enzyme of the pathway, and glutathione synthetase (GS). Because the sub-cellular and sub-organellar localization of these enzymes will have an impact on metabolism, here we examine the localization of GCL and GS in the leaves of Arabidopsis thaliana. Immuno-electron microscopy of leaf cells indicates localization of GCL primarily to the chloroplast with GS found in both the chloroplast and cytosol. Detailed examination of the localization of both enzymes within chloroplasts was performed using fractionation followed by immunoblot analysis and indicates that GCL and GS are found in the stroma. The localization of these enzymes to the stroma of chloroplasts has implications for the redox-regulation of GCL and plant glutathione biosynthesis.
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Affiliation(s)
- Mary L Preuss
- Department of Biological Sciences, Webster University, 470 East Lockwood Ave., WEBH 9A, Webster Groves, MO 63119, USA
| | - Jeffrey C Cameron
- Department of Biology, Washington University, One Brookings Drive, Campus Box 1137, St. Louis, MO 63130, USA
| | - R Howard Berg
- Donald Danforth Plant Science Center, 975 North Warson Rd., St. Louis, MO 63132, USA
| | - Joseph M Jez
- Department of Biology, Washington University, One Brookings Drive, Campus Box 1137, St. Louis, MO 63130, USA.
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29
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Gigolashvili T, Kopriva S. Transporters in plant sulfur metabolism. FRONTIERS IN PLANT SCIENCE 2014; 5:442. [PMID: 25250037 PMCID: PMC4158793 DOI: 10.3389/fpls.2014.00442] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/18/2014] [Indexed: 05/02/2023]
Abstract
Sulfur is an essential nutrient, necessary for synthesis of many metabolites. The uptake of sulfate, primary and secondary assimilation, the biosynthesis, storage, and final utilization of sulfur (S) containing compounds requires a lot of movement between organs, cells, and organelles. Efficient transport systems of S-containing compounds across the internal barriers or the plasma membrane and organellar membranes are therefore required. Here, we review a current state of knowledge of the transport of a range of S-containing metabolites within and between the cells as well as of their long distance transport. An improved understanding of mechanisms and regulation of transport will facilitate successful engineering of the respective pathways, to improve the plant yield, biotic interaction and nutritional properties of crops.
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Affiliation(s)
- Tamara Gigolashvili
- Department of Plant Molecular Physiology, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of CologneCologne Germany
- *Correspondence: Tamara Gigolashvili, Department of Plant Molecular Physiology, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of Cologne, Zülpicher Street 47 B, 50674 Cologne, Germany e-mail:
| | - Stanislav Kopriva
- Plant Biochemistry Department, Botanical Institute and Cluster of Excellence on Plant Sciences, Cologne Biocenter, University of CologneCologne Germany
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30
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Anjum NA, Aref IM, Duarte AC, Pereira E, Ahmad I, Iqbal M. Glutathione and proline can coordinately make plants withstand the joint attack of metal(loid) and salinity stresses. FRONTIERS IN PLANT SCIENCE 2014; 5:662. [PMID: 25484889 PMCID: PMC4240066 DOI: 10.3389/fpls.2014.00662] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/06/2014] [Indexed: 05/18/2023]
Affiliation(s)
- Naser A. Anjum
- Department of Botany, Faculty of Science, Hamdard UniversityNew Delhi, India
- CESAM-Centre for Environmental and Marine Studies and Department of Chemistry, University of AveiroAveiro, Portugal
| | - Ibrahim M. Aref
- Plant Production Department, College of Food and Agricultural Sciences, King Saud UniversityRiyadh, Saudi Arabia
| | - Armando C. Duarte
- CESAM-Centre for Environmental and Marine Studies and Department of Chemistry, University of AveiroAveiro, Portugal
| | - Eduarda Pereira
- CESAM-Centre for Environmental and Marine Studies and Department of Chemistry, University of AveiroAveiro, Portugal
| | - Iqbal Ahmad
- CESAM-Centre for Environmental and Marine Studies and Department of Chemistry, University of AveiroAveiro, Portugal
| | - Muhammad Iqbal
- Department of Botany, Faculty of Science, Hamdard UniversityNew Delhi, India
- *Correspondence:
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31
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Gläser K, Kanawati B, Kubo T, Schmitt-Kopplin P, Grill E. Exploring the Arabidopsis sulfur metabolome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:31-45. [PMID: 24147819 DOI: 10.1111/tpj.12359] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 05/18/2023]
Abstract
Sulfur plays a crucial role in protein structure and function, redox status and plant biotic stress responses. However, our understanding of sulfur metabolism is limited to identified pathways. In this study, we used a high-resolution Fourier transform mass spectrometric approach in combination with stable isotope labeling to describe the sulfur metabolome of Arabidopsis thaliana. Databases contain roughly 300 sulfur compounds assigned to Arabidopsis. In comparative analyses, we showed that the overlap of the expected sulfur metabolome and the mass spectrometric data was surprisingly low, and we were able to assign only 37 of the 300 predicted compounds. By contrast, we identified approximately 140 sulfur metabolites that have not been assigned to the databases to date. We used our method to characterize the γ-glutamyl transferase mutant ggt4-1, which is involved in the vacuolar breakdown of glutathione conjugates in detoxification reactions. Although xenobiotic substrates are well known, only a few endogenous substrates have been described. Among the specifically altered sulfur-containing masses in the ggt4-1 mutant, we characterized one endogenous glutathione conjugate and a number of further candidates for endogenous substrates. The small percentage of predicted compounds and the high proportion of unassigned sulfur compounds identified in this study emphasize the need to re-evaluate our understanding of the sulfur metabolome.
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Affiliation(s)
- Katharina Gläser
- Lehrstuhl für Botanik, Technische Universität München, Emil-Ramann Straße 4, D-85354, Freising, Germany
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32
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Yi H, Dey S, Kumaran S, Lee SG, Krishnan HB, Jez JM. Structure of soybean serine acetyltransferase and formation of the cysteine regulatory complex as a molecular chaperone. J Biol Chem 2013; 288:36463-72. [PMID: 24225955 PMCID: PMC3868759 DOI: 10.1074/jbc.m113.527143] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/04/2013] [Indexed: 01/03/2023] Open
Abstract
Serine acetyltransferase (SAT) catalyzes the limiting reaction in plant and microbial biosynthesis of cysteine. In addition to its enzymatic function, SAT forms a macromolecular complex with O-acetylserine sulfhydrylase. Formation of the cysteine regulatory complex (CRC) is a critical biochemical control feature in plant sulfur metabolism. Here we present the 1.75-3.0 Å resolution x-ray crystal structures of soybean (Glycine max) SAT (GmSAT) in apoenzyme, serine-bound, and CoA-bound forms. The GmSAT-serine and GmSAT-CoA structures provide new details on substrate interactions in the active site. The crystal structures and analysis of site-directed mutants suggest that His(169) and Asp(154) form a catalytic dyad for general base catalysis and that His(189) may stabilize the oxyanion reaction intermediate. Glu(177) helps to position Arg(203) and His(204) and the β1c-β2c loop for serine binding. A similar role for ionic interactions formed by Lys(230) is required for CoA binding. The GmSAT structures also identify Arg(253) as important for the enhanced catalytic efficiency of SAT in the CRC and suggest that movement of the residue may stabilize CoA binding in the macromolecular complex. Differences in the effect of cold on GmSAT activity in the isolated enzyme versus the enzyme in the CRC were also observed. A role for CRC formation as a molecular chaperone to maintain SAT activity in response to an environmental stress is proposed for this multienzyme complex in plants.
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Affiliation(s)
- Hankuil Yi
- From the Department of Biological Sciences, Chungnam National University, 220 Gung-Dong, Yuseong-Gu, Daejeon 305-764, Korea
| | - Sanghamitra Dey
- the Department of Biological Sciences, Presidency University, Kolkata, West Bengal 700073, India
| | - Sangaralingam Kumaran
- the Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Soon Goo Lee
- the Department of Biology, Washington University, St. Louis, Missouri 63130, and
| | - Hari B. Krishnan
- the Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Department of Agronomy, University of Missouri, Columbia, Missouri 65211
| | - Joseph M. Jez
- the Department of Biology, Washington University, St. Louis, Missouri 63130, and
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33
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Chang YL, Hsieh CL, Huang YM, Chiou WL, Kuo YH, Tseng MH. Modified method for determination of sulfur metabolites in plant tissues by stable isotope dilution-based liquid chromatography-electrospray ionization-tandem mass spectrometry. Anal Biochem 2013; 442:24-33. [PMID: 23911527 DOI: 10.1016/j.ab.2013.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 07/18/2013] [Accepted: 07/19/2013] [Indexed: 12/25/2022]
Abstract
A wide variety of sulfur metabolites play important roles in plant functions. We have developed a precise and sensitive method for the simultaneous measurement of several sulfur metabolites based on liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and (34)S metabolic labeling of sulfur-containing metabolites in Arabidopsis thaliana seedlings. However, some sulfur metabolites were unstable during the extraction procedure. Our proposed method does not allow for the detection of the important sulfur metabolite homocysteine because of its instability during sample extraction. Stable isotope-labeled sulfur metabolites of A. thaliana shoot were extracted and utilized as internal standards for quantification of sulfur metabolites with LC-MS/MS using S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), methionine (Met), glutathione (GSH), and glutathione disulfide (GSSG) as example metabolites. These metabolites were detected using electrospray ionization in positive mode. Standard curves were linear (r(2)>0.99) over a range of concentrations (SAM 0.01-2.0μM, SAH 0.002-0.10μM, Met 0.05-4.0μM, GSH 0.17-20.0μM, GSSG 0.07-20.0μM), with limits of detection for SAM, SAH, Met, GSH, and GSSG of 0.83, 0.67, 10, 0.56, and 1.1nM, respectively; and the within-run and between-run coefficients of variation based on quality control samples were less than 8%.
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Affiliation(s)
- Ya-Lan Chang
- Department of Applied Physics and Chemistry, University of Taipei, Taipei 10048, Taiwan
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34
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Ravilious G, Herrmann J, Goo Lee S, Westfall C, Jez J. Kinetic mechanism of the dimeric ATP sulfurylase from plants. Biosci Rep 2013; 33:e00053. [PMID: 23789618 PMCID: PMC3728988 DOI: 10.1042/bsr20130073] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 06/18/2013] [Accepted: 06/19/2013] [Indexed: 12/12/2022] Open
Abstract
In plants, sulfur must be obtained from the environment and assimilated into usable forms for metabolism. ATP sulfurylase catalyses the thermodynamically unfavourable formation of a mixed phosphosulfate anhydride in APS (adenosine 5'-phosphosulfate) from ATP and sulfate as the first committed step of sulfur assimilation in plants. In contrast to the multi-functional, allosterically regulated ATP sulfurylases from bacteria, fungi and mammals, the plant enzyme functions as a mono-functional, non-allosteric homodimer. Owing to these differences, here we examine the kinetic mechanism of soybean ATP sulfurylase [GmATPS1 (Glycine max (soybean) ATP sulfurylase isoform 1)]. For the forward reaction (APS synthesis), initial velocity methods indicate a single-displacement mechanism. Dead-end inhibition studies with chlorate showed competitive inhibition versus sulfate and non-competitive inhibition versus APS. Initial velocity studies of the reverse reaction (ATP synthesis) demonstrate a sequential mechanism with global fitting analysis suggesting an ordered binding of substrates. ITC (isothermal titration calorimetry) showed tight binding of APS to GmATPS1. In contrast, binding of PPi (pyrophosphate) to GmATPS1 was not detected, although titration of the E•APS complex with PPi in the absence of magnesium displayed ternary complex formation. These results suggest a kinetic mechanism in which ATP and APS are the first substrates bound in the forward and reverse reactions, respectively.
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Affiliation(s)
- Geoffrey E. Ravilious
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, U.S.A
| | - Jonathan Herrmann
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, U.S.A
| | - Soon Goo Lee
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, U.S.A
| | - Corey S. Westfall
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, U.S.A
| | - Joseph M. Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, U.S.A
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35
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Yarmolinsky D, Brychkova G, Fluhr R, Sagi M. Sulfite reductase protects plants against sulfite toxicity. PLANT PHYSIOLOGY 2013; 161:725-43. [PMID: 23221833 PMCID: PMC3561015 DOI: 10.1104/pp.112.207712] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/06/2012] [Indexed: 05/03/2023]
Abstract
Plant sulfite reductase (SiR; Enzyme Commission 1.8.7.1) catalyzes the reduction of sulfite to sulfide in the reductive sulfate assimilation pathway. Comparison of SiR expression in tomato (Solanum lycopersicum 'Rheinlands Ruhm') and Arabidopsis (Arabidopsis thaliana) plants revealed that SiR is expressed in a different tissue-dependent manner that likely reflects dissimilarity in sulfur metabolism between the plant species. Using Arabidopsis and tomato SiR mutants with modified SiR expression, we show here that resistance to ectopically applied sulfur dioxide/sulfite is a function of SiR expression levels and that plants with reduced SiR expression exhibit higher sensitivity than the wild type, as manifested in pronounced leaf necrosis and chlorophyll bleaching. The sulfite-sensitive mutants accumulate applied sulfite and show a decline in glutathione levels. In contrast, mutants that overexpress SiR are more tolerant to sulfite toxicity, exhibiting little or no damage. Resistance to high sulfite application is manifested by fast sulfite disappearance and an increase in glutathione levels. The notion that SiR plays a role in the protection of plants against sulfite is supported by the rapid up-regulation of SiR transcript and activity within 30 min of sulfite injection into Arabidopsis and tomato leaves. Peroxisomal sulfite oxidase transcripts and activity levels are likewise promoted by sulfite application as compared with water injection controls. These results indicate that, in addition to participating in the sulfate assimilation reductive pathway, SiR also plays a role in protecting leaves against the toxicity of sulfite accumulation.
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Affiliation(s)
- Dmitry Yarmolinsky
- Jacob Blaustein Institute for Desert Research, Albert Katz Department of Dryland Biotechnologies, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel (D.Y., G.B., M.S.); and Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel (R.F.)
| | - Galina Brychkova
- Jacob Blaustein Institute for Desert Research, Albert Katz Department of Dryland Biotechnologies, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel (D.Y., G.B., M.S.); and Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel (R.F.)
| | - Robert Fluhr
- Jacob Blaustein Institute for Desert Research, Albert Katz Department of Dryland Biotechnologies, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel (D.Y., G.B., M.S.); and Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel (R.F.)
| | - Moshe Sagi
- Jacob Blaustein Institute for Desert Research, Albert Katz Department of Dryland Biotechnologies, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel (D.Y., G.B., M.S.); and Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel (R.F.)
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36
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Ravilious GE, Westfall CS, Jez JM. Redox-linked gating of nucleotide binding by the N-terminal domain of adenosine 5'-phosphosulfate kinase. J Biol Chem 2013; 288:6107-15. [PMID: 23322773 DOI: 10.1074/jbc.m112.439414] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate (APS) to 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Crystallographic studies of APSK from Arabidopsis thaliana revealed the presence of a regulatory intersubunit disulfide bond (Cys(86)-Cys(119)). The reduced enzyme displayed improved catalytic efficiency and decreased effectiveness of substrate inhibition by APS compared with the oxidized form. Here we examine the effect of disulfide formation and the role of the N-terminal domain on nucleotide binding using isothermal titration calorimetry (ITC) and steady-state kinetics. Formation of the disulfide bond in A. thaliana APSK (AtAPSK) inverts the binding affinities at the ATP/ADP and APS/PAPS sites from those observed in the reduced enzyme, consistent with initial binding of APS as inhibitory, and suggests a role for the N-terminal domain in guiding nucleotide binding order. To test this, an N-terminal truncation variant (AtAPSKΔ96) was generated. The resulting protein was completely insensitive to substrate inhibition by APS. ITC analysis of AtAPSKΔ96 showed decreased affinity for APS binding, although the N-terminal domain does not directly interact with this ligand. Moreover, AtAPSKΔ96 displayed reduced affinity for ADP, which corresponds to a loss of substrate inhibition by formation of an E·ADP·APS dead end complex. Examination of the AtAPSK crystal structure suggested Arg(93) as important for positioning of the N-terminal domain. ITC and kinetic analysis of the R93A mutant also showed a complete loss of substrate inhibition and altered nucleotide binding affinities, which mimics the effect of the N-terminal deletion. These results show how thiol-linked changes in AtAPSK alter the energetics of binding equilibria to control its activity.
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37
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Wu B, Andersch F, Weschke W, Weber H, Becker JS. Diverse accumulation and distribution of nutrient elements in developing wheat grain studied by laser ablation inductively coupled plasma mass spectrometry imaging. Metallomics 2013; 5:1276-84. [DOI: 10.1039/c3mt00071k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Ravilious GE, Jez JM. Nucleotide binding site communication in Arabidopsis thaliana adenosine 5'-phosphosulfate kinase. J Biol Chem 2012; 287:30385-94. [PMID: 22810229 DOI: 10.1074/jbc.m112.387001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the ATP-dependent synthesis of adenosine 3'-phosphate 5'-phosphosulfate (PAPS), which is an essential metabolite for sulfur assimilation in prokaryotes and eukaryotes. Using APSK from Arabidopsis thaliana, we examine the energetics of nucleotide binary and ternary complex formation and probe active site features that coordinate the order of ligand addition. Calorimetric analysis shows that binding can occur first at either nucleotide site, but that initial interaction at the ATP/ADP site was favored and enhanced affinity for APS in the second site by 50-fold. The thermodynamics of the two possible binding models (i.e. ATP first versus APS first) differs and implies that active site structural changes guide the order of nucleotide addition. The ligand binding analysis also supports an earlier suggestion of intermolecular interactions in the dimeric APSK structure. Crystallographic, site-directed mutagenesis, and energetic analyses of oxyanion recognition by the P-loop in the ATP/ADP binding site and the role of Asp(136), which bridges the ATP/ADP and APS/PAPS binding sites, suggest how the ordered nucleotide binding sequence and structural changes are dynamically coordinated for catalysis.
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