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Zhang S, Du H, Ma Y, Li H, Kan G, Yu D. Linkage and association study discovered loci and candidate genes for glycinin and β-conglycinin in soybean (Glycine max L. Merr.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1201-1215. [PMID: 33464377 DOI: 10.1007/s00122-021-03766-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE Linkage mapping and GWAS identified 67 QTLs related to soybean glycinin, β-conglycinin and relevant traits. Polymorphisms of the candidate gene Gy1 promoter were associated with the glycinin content in soybean. The major components of storage proteins in soybean seeds are glycinin and β-conglycinin, which play important roles in determining protein nutrition and soy food processing properties. Increasing the protein content while improving the ratio of glycinin to β-conglycinin is substantially important for soybean protein improvement. To investigate the genetic mechanism of storage protein subunits, 184 recombinant inbred lines (RILs) derived from a cross of Kefeng No. 1 and Nannong 1138-2 and 211 diverse soybean cultivars were used to detect loci related to glycinin (11S), β-conglycinin (7S), the sum of glycinin and β-conglycinin (SGC), and the ratio of glycinin to β-conglycinin (RGC). Sixty-seven QTLs and 11 hot genomic regions were identified as affecting the four traits. One genetic region (q10-1) on chromosome 10 was associated with multiple traits by both linkage and association analysis. Eight genes in 11 hot genomic regions might be related to soybean protein subunit. The candidate gene analysis showed that polymorphisms in Gy1 promoters were significantly correlated with the 11S content. The QTLs and candidate genes identified in the present study allow for further understanding the genetic basis of 11S and 7S regulation and provide useful information for marker-assisted selection (MAS) in soybean quality improvement.
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Affiliation(s)
- Shanshan Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongyang Du
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yujie Ma
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haiyang Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
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2
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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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Krishnan HB, Jez JM. Review: The promise and limits for enhancing sulfur-containing amino acid content of soybean seed. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 272:14-21. [PMID: 29807584 DOI: 10.1016/j.plantsci.2018.03.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 06/08/2023]
Abstract
Soybeans are an excellent source of protein in monogastric diets and rations with ∼75% of soybeans produced worldwide used primarily for animal feed. Even though soybeans are protein-rich and have a well-balanced amino acid profile, the nutritive quality of this important crop could be further improved by elevating the concentrations of certain amino acids. The levels of the sulfur-containing amino acids cysteine and methionine in soybean seed proteins are inadequate for optimal growth and development of monogastric animals, which necessitates dietary supplementation. Subsequently, concerted efforts have been made to increase the concentrations of cysteine and methionine in soybean seeds by both classical breeding and genetic engineering; however, these efforts have met with only limited success. In this review, we discuss the strengths and weakness of different approaches in elevating the sulfur amino acid content of soybeans. Manipulation of enzymes involved in the sulfur assimilatory pathway appears to be a viable avenue for improving sulfur amino acid content. This approach requires a through biochemical characterization of sulfur assimilatory enzymes in soybean seeds. We highlight recent studies targeting key sulfur assimilatory enzymes and the manipulation of sulfur metabolism in transgenic soybeans to improve the nutritive value of soybean proteins.
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Affiliation(s)
- Hari B Krishnan
- Plant Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Missouri, Columbia, MO 65211, USA.
| | - Joseph M Jez
- Department of Biology,Washington University in St. Louis, St. Louis, MO 63130, USA
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Shi Y, Yue X, An L. Integrated regulation triggered by a cryophyte ω-3 desaturase gene confers multiple-stress tolerance in tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2131-2148. [PMID: 29432580 PMCID: PMC6019038 DOI: 10.1093/jxb/ery050] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/02/2018] [Indexed: 05/16/2023]
Abstract
ω-3 fatty acid desaturases (FADs) are thought to contribute to plant stress tolerance mainly through linolenic acid (C18:3)-induced membrane stabilization, but a comprehensive analysis of their roles in stress adaptation is lacking. Here, we isolated a microsomal ω-3 FAD gene (CbFAD3) from a cryophyte (Chorispora bungeana) and elucidated its functions in stress tolerance. CbFAD3, exhibiting a high identity to Arabidopsis AtFAD3, was up-regulated by abiotic stresses. Its functionality was verified by heterogonous expression in yeast. Overexpression of CbFAD3 in tobacco constitutively increased C18:3 in both leaves and roots, which maintained the membrane fluidity, and enhanced plant tolerance to cold, drought, and salt stresses. Notably, the constitutively increased C18:3 induced a sustained activation of plasma membrane Ca2+-ATPase, thereby, changing the stress-induced Ca2+ signaling. The reactive oxygen species (ROS) scavenging system, which was positively correlated with the level of C18:3, was also activated in the transgenic lines. Microarray analysis showed that CbFAD3-overexpressing plants increased the expression of stress-responsive genes, most of which are affected by C18:3, Ca2+, or ROS. Together, CbFAD3 confers tolerance to multiple stresses in tobacco through the C18:3-induced integrated regulation of membrane, Ca2+, ROS, and stress-responsive genes. This is in contrast with previous observations that simply attribute stress tolerance to membrane stabilization.
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Affiliation(s)
- Yulan Shi
- Extreme Stress Resistance and Biotechnology Laboratory, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, PR China
| | - Xiule Yue
- School of Life Sciences, Lanzhou University, Lanzhou, PR China
| | - Lizhe An
- Extreme Stress Resistance and Biotechnology Laboratory, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, PR China
- School of Life Sciences, Lanzhou University, Lanzhou, PR China
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Krishnan HB, Song B, Oehrle NW, Cameron JC, Jez JM. Impact of overexpression of cytosolic isoform of O-acetylserine sulfhydrylase on soybean nodulation and nodule metabolome. Sci Rep 2018; 8:2367. [PMID: 29402985 PMCID: PMC5799319 DOI: 10.1038/s41598-018-20919-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/25/2018] [Indexed: 01/05/2023] Open
Abstract
Nitrogen-fixing nodules, which are also major sites of sulfur assimilation, contribute significantly to the sulfur needs of whole soybean plants. Nodules are the predominant sites for cysteine accumulation and the activity of O-acetylserine(thiol)lyase (OASS) is central to the sulfur assimilation process in plants. Here, we examined the impact of overexpressing OASS on soybean nodulation and nodule metabolome. Overexpression of OASS did not affect the nodule number, but negatively impacted plant growth. HPLC measurement of antioxidant metabolites demonstrated that levels of cysteine, glutathione, and homoglutathione nearly doubled in OASS overexpressing nodules when compared to control nodules. Metabolite profiling by LC-MS and GC-MS demonstrated that several metabolites related to serine, aspartate, glutamate, and branched-chain amino acid pathways were significantly elevated in OASS overexpressing nodules. Striking differences were also observed in the flavonoid levels between the OASS overexpressing and control soybean nodules. Our results suggest that OASS overexpressing plants compensate for the increase in carbon requirement for sulfur assimilation by reducing the biosynthesis of some amino acids, and by replenishing the TCA cycle through fatty acid hydrolysis. These data may indicate that in OASS overexpressing soybean nodules there is a moderate decease in the supply of energy metabolites to the nodule, which is then compensated by the degradation of cellular components to meet the needs of the nodule energy metabolism.
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Affiliation(s)
- Hari B Krishnan
- USDA-ARS, Plant Genetics Research Unit, 105 Curtis Hall, University of Missouri, Columbia, MO, 65211, USA.
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Bo Song
- USDA-ARS, Plant Genetics Research Unit, 105 Curtis Hall, University of Missouri, Columbia, MO, 65211, USA
- Key Laboratory of Soybean Biology at the Chinese Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Nathan W Oehrle
- USDA-ARS, Plant Genetics Research Unit, 105 Curtis Hall, University of Missouri, Columbia, MO, 65211, USA
| | - Jeffrey C Cameron
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
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6
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Biochemistry and Physiology of Heavy Metal Resistance and Accumulation in Euglena. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 979:91-121. [PMID: 28429319 DOI: 10.1007/978-3-319-54910-1_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Free-living microorganisms may become suitable models for removal of heavy metals from polluted water bodies, sediments, and soils by using and enhancing their metal accumulating abilities. The available research data indicate that protists of the genus Euglena are a highly promising group of microorganisms to be used in bio-remediation of heavy metal-polluted aerobic and anaerobic acidic aquatic environments. This chapter analyzes the variety of biochemical mechanisms evolved in E. gracilis to resist, accumulate and remove heavy metals from the environment, being the most relevant those involving (1) adsorption to the external cell pellicle; (2) intracellular binding by glutathione and glutathione polymers, and their further compartmentalization as heavy metal-complexes into chloroplasts and mitochondria; (3) polyphosphate biosynthesis; and (4) secretion of organic acids. The available data at the transcriptional, kinetic and metabolic levels on these metabolic/cellular processes are herein reviewed and analyzed to provide mechanistic basis for developing genetically engineered Euglena cells that may have a greater removal and accumulating capacity for bioremediation and recycling of heavy metals.
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Xu HH, Liu SJ, Song SH, Wang RX, Wang WQ, Song SQ. Proteomics analysis reveals distinct involvement of embryo and endosperm proteins during seed germination in dormant and non-dormant rice seeds. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 103:219-42. [PMID: 27035683 DOI: 10.1016/j.plaphy.2016.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 03/01/2016] [Accepted: 03/04/2016] [Indexed: 05/09/2023]
Abstract
Seed germination is a complex trait which is influenced by many genetic, endogenous and environmental factors, but the key event(s) associated with seed germination are still poorly understood. In present study, the non-dormant cultivated rice Yannong S and the dormant Dongxiang wild rice seeds were used as experimental materials, we comparatively investigated the water uptake, germination time course, and the differential proteome of the effect of embryo and endosperm on germination of these two types of seeds. A total of 231 and 180 protein spots in embryo and endosperm, respectively, showed a significant change in abundance during germination. We observed that the important proteins associated with seed germination included those involved in metabolism, energy production, protein synthesis and destination, storage protein, cell growth and division, signal transduction, cell defense and rescue. The contribution of embryo and endosperm to seed germination is different. In embryo, the proteins involved in amino acid activation, sucrose cleavage, glycolysis, fermentation and protein synthesis increased; in endosperm, the proteins involved in sucrose cleavage and glycolysis decreased, and those with ATP and CoQ synthesis and proteolysis increased. Our results provide some new knowledge to understand further the mechanism of seed germination.
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Affiliation(s)
- Heng-Heng Xu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shu-Jun Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shun-Hua Song
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Rui-Xia Wang
- College of Life Science, Linyi University, Linyi 276005, China
| | - Wei-Qing Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Song-Quan Song
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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8
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García-García JD, Sánchez-Thomas R, Moreno-Sánchez R. Bio-recovery of non-essential heavy metals by intra- and extracellular mechanisms in free-living microorganisms. Biotechnol Adv 2016; 34:859-873. [PMID: 27184302 DOI: 10.1016/j.biotechadv.2016.05.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 01/29/2023]
Abstract
Free-living microorganisms may become suitable models for recovery of non-essential and essential heavy metals from wastewater bodies and soils by using and enhancing their accumulating and/or leaching abilities. This review analyzes the variety of different mechanisms developed mainly in bacteria, protists and microalgae to accumulate heavy metals, being the most relevant those involving phytochelatin and metallothionein biosyntheses; phosphate/polyphosphate metabolism; compartmentalization of heavy metal-complexes into vacuoles, chloroplasts and mitochondria; and secretion of malate and other organic acids. Cyanide biosynthesis for extra-cellular heavy metal bioleaching is also examined. These metabolic/cellular processes are herein analyzed at the transcriptional, kinetic and metabolic levels to provide mechanistic basis for developing genetically engineered microorganisms with greater capacities and efficiencies for heavy metal recovery, recycling of heavy metals, biosensing of metal ions, and engineering of metalloenzymes.
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Affiliation(s)
- Jorge D García-García
- Departamento de Bioquímica, Instituto Nacional de Cardiología "Ignacio Chávez", México D.F. 14080, México.
| | - Rosina Sánchez-Thomas
- Departamento de Bioquímica, Instituto Nacional de Cardiología "Ignacio Chávez", México D.F. 14080, México
| | - Rafael Moreno-Sánchez
- Departamento de Bioquímica, Instituto Nacional de Cardiología "Ignacio Chávez", México D.F. 14080, México
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9
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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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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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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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12
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Swigonska S, Weidner S. Proteomic analysis of response to long-term continuous stress in roots of germinating soybean seeds. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:470-9. [PMID: 23394790 DOI: 10.1016/j.jplph.2012.11.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 10/12/2012] [Accepted: 11/16/2012] [Indexed: 05/27/2023]
Abstract
Germination is a complex process, highly dependent on various environmental factors, including temperature and water availability. Germinating soybean seeds are especially vulnerable to unfavorable environmental conditions and exposure to long-term abiotic stresses may result in diminishing much of the yield and most importantly - restrained germination. In the present study, a proteomic approach was employed to analyze influence of cold and osmotic stress on roots of germinated soybean (Glycine max, L.) seeds. Seeds were germinating under continuous conditions of cold stress (+10°C/H2O), osmotic stress (+25°C/-0.2MPa) as well as cold and osmotic stress combined (+10°C/-0.2MPa). Proteome maps established for control samples and stress-treated samples displayed 1272 CBB-stained spots. A total of 59 proteins, present in both control and stress-treated samples and showing significant differences in volume, were identified with LC/nanoESI-MS. Identified proteins divided into functional categories, revealed 9 proteins involved in plant defense, 8 proteins responsible for plant destination and storage and 10 proteins involved in various tracks of carbohydrate metabolism. Furthermore, a number of proteins were assigned to electron transport, range of metabolic pathways, secondary metabolism, protein synthesis, embryogenesis and development, signal transduction, cellular transport, translocation and storage. By analyzing differences in expression patterns, it was possible to trace the soybean response to long-term abiotic stress as well as to distinguish similarities and differences between response to cold and osmotic stress.
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Affiliation(s)
- Sylwia Swigonska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Street 1a, 10-957 Olsztyn, Poland.
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Grison C, Escande V, Petit E, Garoux L, Boulanger C, Grison C. Psychotriadouarrei and Geissois pruinosa, novel resources for the plant-based catalytic chemistry. RSC Adv 2013. [DOI: 10.1039/c3ra43995j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Yi H, Jez JM. Assessing functional diversity in the soybean β-substituted alanine synthase enzyme family. PHYTOCHEMISTRY 2012; 83:15-24. [PMID: 22986002 DOI: 10.1016/j.phytochem.2012.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 06/12/2012] [Accepted: 08/10/2012] [Indexed: 05/08/2023]
Abstract
In plants, proteins of the β-substituted alanine synthase (BSAS) enzyme family perform a diverse range of reactions, including formation of cysteine from O-acetylserine and sulfide, detoxification of cyanide by its addition to cysteine, the breakdown of cysteine into pyruvate, ammonia, and sulfide, and the synthesis of S-sulfocysteine. With the completed genome sequence of soybean (Glycine max (L.) Merr. cv. Williams 82), the functional diversity of the BSAS in this highly duplicated plant species was examined to determine whether soybean BSAS enzymes catalyze the various reactions connected to cysteine metabolism. The 16 soybean BSAS can be grouped into clades that are similar to those observed in Arabidopsis. Biochemical analysis of soybean BSAS proteins demonstrate that enzymes of clades I and III function as O-acetylserine sulfhydrylases for cysteine synthesis, clade II encodes cysteine desulfhydrase activity, and that clade V proteins function as β-cyanoalanine synthase for cyanide detoxification. Although clade IV is similar to Arabidopsis S-sulfocysteine synthase, this activity was not detected in the soybean homolog. Overall, our results show that bioinformatics approach provides a useful method to assess the biochemical properties of BSAS enzymes in plant species.
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Affiliation(s)
- Hankuil Yi
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO 63130, USA
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Ravilious GE, Jez JM. Structural biology of plant sulfur metabolism: From assimilation to biosynthesis. Nat Prod Rep 2012; 29:1138-52. [DOI: 10.1039/c2np20009k] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Structural basis and evolution of redox regulation in plant adenosine-5'-phosphosulfate kinase. Proc Natl Acad Sci U S A 2011; 109:309-14. [PMID: 22184237 DOI: 10.1073/pnas.1115772108] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Adenosine-5'-phosphosulfate (APS) kinase (APSK) catalyzes the phosphorylation of APS to 3'-phospho-APS (PAPS). In Arabidopsis thaliana, APSK is essential for reproductive viability and competes with APS reductase to partition sulfate between the primary and secondary branches of the sulfur assimilatory pathway; however, the biochemical regulation of APSK is poorly understood. The 1.8-Å resolution crystal structure of APSR from A. thaliana (AtAPSK) in complex with β,γ-imidoadenosine-5'-triphosphate, Mg(2+), and APS provides a view of the Michaelis complex for this enzyme and reveals the presence of an intersubunit disulfide bond between Cys86 and Cys119. Functional analysis of AtAPSK demonstrates that reduction of Cys86-Cys119 resulted in a 17-fold higher k(cat)/K(m) and a 15-fold increase in K(i) for substrate inhibition by APS compared with the oxidized enzyme. The C86A/C119A mutant was kinetically similar to the reduced WT enzyme. Gel- and activity-based titrations indicate that the midpoint potential of the disulfide in AtAPSK is comparable to that observed in APS reductase. Both cysteines are invariant among the APSK from plants, but not other organisms, which suggests redox-control as a unique regulatory feature of the plant APSK. Based on structural, functional, and sequence analyses, we propose that the redox-sensitive APSK evolved after bifurcation of the sulfur assimilatory pathway in the green plant lineage and that changes in redox environment resulting from oxidative stresses may affect partitioning of APS into the primary and secondary thiol metabolic routes by having opposing effects on APSK and APS reductase in plants.
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Identification of biotic and abiotic stress up-regulated ESTs in Gossypium arboreum. Mol Biol Rep 2011; 39:1011-8. [PMID: 21556756 DOI: 10.1007/s11033-011-0826-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 05/03/2011] [Indexed: 12/25/2022]
Abstract
Asiatic desi cotton (Gossypium arboreum) shows great potential against biotic and abiotic stresses. The stress resistant nature makes it a best source for the identification of biotic and abiotic stress resistant genes. As in many plants same set of genes show responding behavior against the various abiotic and biotic stresses. Thus in the present study the ESTs from the G. arboreum drought stressed leaves were subjected to find the up-regulated ESTs in abiotic and biotic stresses through homology and in-silico analysis. A cDNA library has been constructed from the drought stressed G. arboreum plant. 778 clones were randomly picked and sequenced. All these sequences were subjected to in-silico identification of biotic and abiotic up-regulated ESTs. Total 39 abiotic and biotic up-regulated ESTs were identified. The results were further validated by real-time PCR; by randomly selection of ten ESTs. These findings will help to develop stress resistant crop varieties for better yield and growth performance under stresses.
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Yi H, Ravilious GE, Galant A, Krishnan HB, Jez JM. From sulfur to homoglutathione: thiol metabolism in soybean. Amino Acids 2010; 39:963-78. [PMID: 20364282 DOI: 10.1007/s00726-010-0572-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Accepted: 03/16/2010] [Indexed: 12/11/2022]
Abstract
Sulfur is an essential plant nutrient and is metabolized into the sulfur-containing amino acids (cysteine and methionine) and into molecules that protect plants against oxidative and environmental stresses. Although studies of thiol metabolism in the model plant Arabidopsis thaliana (thale cress) have expanded our understanding of these dynamic processes, our knowledge of how sulfur is assimilated and metabolized in crop plants, such as soybean (Glycine max), remains limited in comparison. Soybean is a major crop used worldwide for food and animal feed. Although soybeans are protein-rich, they do not contain high levels of the sulfur-containing amino acids, cysteine and methionine. Ultimately, unraveling the fundamental steps and regulation of thiol metabolism in soybean is important for optimizing crop yield and quality. Here we review the pathways from sulfur uptake to glutathione and homoglutathione synthesis in soybean, the potential biotechnology benefits of understanding and modifying these pathways, and how information from the soybean genome may guide the next steps in exploring this biochemical system.
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Affiliation(s)
- Hankuil Yi
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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Yi H, Galant A, Ravilious GE, Preuss ML, Jez JM. Sensing sulfur conditions: simple to complex protein regulatory mechanisms in plant thiol metabolism. MOLECULAR PLANT 2010; 3:269-79. [PMID: 20080815 DOI: 10.1093/mp/ssp112] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Sulfur is essential for plant growth and development, and the molecular systems for maintaining sulfur and thiol metabolism are tightly controlled. From a biochemical perspective, the regulation of plant thiol metabolism highlights nature's ability to engineer pathways that respond to multiple inputs and cellular demands under a range of conditions. In this review, we focus on the regulatory mechanisms that form the molecular basis of biochemical sulfur sensing in plants by translating the intracellular concentration of sulfur-containing compounds into control of key metabolic steps. These mechanisms range from the simple (substrate availability, thermodynamic properties of reactions, feedback inhibition, and organelle localization) to the elaborate (formation of multienzyme complexes and thiol-based redox switches). Ultimately, the dynamic interplay of these regulatory systems is critical for sensing and maintaining sulfur assimilation and thiol metabolism in plants.
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Affiliation(s)
- Hankuil Yi
- Department of Biology, Washington University, St Louis, MO 63130, USA
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Schroeder AC, Zhu C, Yanamadala SR, Cahoon RE, Arkus KAJ, Wachsstock L, Bleeke J, Krishnan HB, Jez JM. Threonine-insensitive homoserine dehydrogenase from soybean: genomic organization, kinetic mechanism, and in vivo activity. J Biol Chem 2010; 285:827-34. [PMID: 19897476 PMCID: PMC2801284 DOI: 10.1074/jbc.m109.068882] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 11/05/2009] [Indexed: 11/06/2022] Open
Abstract
Aspartate kinase (AK) and homoserine dehydrogenase (HSD) function as key regulatory enzymes at branch points in the aspartate amino acid pathway and are feedback-inhibited by threonine. In plants the biochemical features of AK and bifunctional AK-HSD enzymes have been characterized, but the molecular properties of the monofunctional HSD remain unexamined. To investigate the role of HSD, we have cloned the cDNA and gene encoding the monofunctional HSD (GmHSD) from soybean. Using heterologously expressed and purified GmHSD, initial velocity and product inhibition studies support an ordered bi bi kinetic mechanism in which nicotinamide cofactor binds first and leaves last in the reaction sequence. Threonine inhibition of GmHSD occurs at concentrations (K(i) = 160-240 mM) more than 1000-fold above physiological levels. This is in contrast to the two AK-HSD isoforms in soybean that are sensitive to threonine inhibition (K(i) approximately 150 microM). In addition, GmHSD is not inhibited by other aspartate-derived amino acids. The ratio of threonine-resistant to threonine-sensitive HSD activity in soybean tissues varies and likely reflects different demands for amino acid biosynthesis. This is the first cloning and detailed biochemical characterization of a monofunctional feedback-insensitive HSD from any plant. Threonine-resistant HSD offers a useful biotechnology tool for manipulating the aspartate amino acid pathway to increase threonine and methionine production in plants for improved nutritional content.
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Affiliation(s)
- Amy C. Schroeder
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
| | - Chuanmei Zhu
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Srinivasa Rao Yanamadala
- the Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Department of Agronomy, University of Missouri, Columbia, Missouri 65211
| | - Rebecca E. Cahoon
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
| | - Kiani A. J. Arkus
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
| | - Leia Wachsstock
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
| | - Jeremy Bleeke
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, 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
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
- the Donald Danforth Plant Science Center, St. Louis, Missouri 63132, and
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Kumaran S, Yi H, Krishnan HB, Jez JM. Assembly of the cysteine synthase complex and the regulatory role of protein-protein interactions. J Biol Chem 2009; 284:10268-75. [PMID: 19213732 PMCID: PMC2665080 DOI: 10.1074/jbc.m900154200] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 02/06/2009] [Indexed: 11/06/2022] Open
Abstract
Macromolecular assemblies play critical roles in regulating cellular functions. The cysteine synthase complex (CSC), which is formed by association of serine O-acetyltransferase (SAT) and O-acetylserine sulfhydrylase (OASS), acts as a sensor and modulator of thiol metabolism by responding to changes in nutrient conditions. Here we examine the oligomerization and energetics of formation of the soybean CSC. Biophysical examination of the CSC by size exclusion chromatography and sedimentation ultracentrifugation indicates that this assembly (complex M(r) approximately 330,000) consists of a single SAT trimer (trimer M(r) approximately 110,000) and three OASS dimers (dimer M(r) approximately 70,000). Analysis of the SAT-OASS interaction by isothermal titration calorimetry reveals negative cooperativity with three distinct binding events during CSC formation with K(d) values of 0.3, 7.5, and 78 nm. The three binding events are also observed using surface plasmon resonance with comparable affinities. The stability of the CSC derives from rapid association and extremely slow dissociation of OASS with SAT and requires the C terminus of SAT for the interaction. Steady-state kinetic analysis shows that CSC formation enhances SAT activity and releases SAT from substrate inhibition and feedback inhibition by cysteine, the final product of the biosynthesis pathway. Cysteine inhibits SAT and the CSC with K(i) values of 2 and 70 microm, respectively. These results suggest a new model for the architecture of this regulatory complex and additional control mechanisms for biochemically controlling plant cysteine biosynthesis. Based on previous work and our results, we suggest that OASS acts as an enzyme chaperone of SAT in the CSC.
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