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Gao Y, Xie R, Chen Y, Yang B, Wang M, Hua L, Wang X, Wang W, Wang N, Ge H, Ma J. Structural basis for substrate recognition by a S-adenosylhomocysteine hydrolase Lpg2021 from Legionella pneumophila. Int J Biol Macromol 2024; 270:132289. [PMID: 38735607 DOI: 10.1016/j.ijbiomac.2024.132289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/24/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
S-Adenosyl-l-homocysteine hydrolase (SAHH) is a crucial enzyme that governs S-adenosyl methionine (SAM)-dependent methylation reactions within cells and regulates the intracellular concentration of SAH. Legionella pneumophila, the causative pathogen of Legionnaires' disease, encodes Lpg2021, which is the first identified dimeric SAHH in bacteria and is a promising target for drug development. Here, we report the structure of Lpg2021 in its ligand-free state and in complexes with adenine (ADE), adenosine (ADO), and 3-Deazaneplanocin A (DZNep). X-ray crystallography, isothermal titration calorimetry (ITC), and molecular docking were used to elucidate the binding mechanisms of Lpg2021 to its substrates and inhibitors. Virtual screening was performed to identify potential Lpg2021 inhibitors. This study contributes a novel perspective to the understanding of SAHH evolution and establishes a structural framework for designing specific inhibitors targeting pathogenic Legionella pneumophila SAHH.
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Affiliation(s)
- Yongshan Gao
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China; School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Rao Xie
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Yanan Chen
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Beibei Yang
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Min Wang
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Lan Hua
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Xu Wang
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Weiqiang Wang
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China
| | - Na Wang
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China.
| | - Honghua Ge
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China.
| | - Jinming Ma
- Institute of Health Sciences and Technology, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China.
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2
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Malecki PH, Imiolczyk B, Barciszewski J, Czyrko-Horczak J, Sliwiak J, Gawel M, Wozniak K, Jaskolski M, Brzezinski K. Biochemical and structural insights into an unusual, alkali-metal-independent S-adenosyl- L-homocysteine hydrolase from Synechocystis sp. PCC 6803. Acta Crystallogr D Struct Biol 2022; 78:865-882. [DOI: 10.1107/s2059798322005605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 05/23/2022] [Indexed: 11/10/2022] Open
Abstract
The mesophilic cyanobacterium Synechocystis sp. PCC 6803 encodes an S-adenosyl-L-homocysteine hydrolase (SAHase) of archaeal origin in its genome. SAHases are essential enzymes involved in the regulation of cellular S-adenosyl-L-methionine (SAM)-dependent methylation reactions. They are usually active as homotetramers or, less commonly, as homodimers. A SAHase subunit is composed of two major domains: a cofactor (NAD+)-binding domain and a substrate (S-adenosyl-L-homocysteine)-binding domain. These are connected by a hinge element that is also a coordination site for an alkali-metal cation that influences domain movement during the catalytic cycle. Typically, the highest activity and strongest substrate binding of bacterial SAHases are observed in the presence of K+ ions. The SAHase from Synechocystis (SynSAHase) is an exception in this respect. Enzymatic and isothermal titration calorimetry studies demonstrated that in contrast to K+-dependent SAHases, the activity and ligand binding of SynSAHase are not affected by the presence of any particular alkali ion. Moreover, in contrast to other SAHases, the cyanobacterial enzyme is in an equilibrium of two distinct oligomeric states corresponding to its dimeric and tetrameric forms in solution. To explain these phenomena, crystal structures of SynSAHase were determined for the enzyme crystallized in the presence of adenosine (a reaction byproduct or substrate) and sodium or rubidium cations. The structural data confirm that while SynSAHase shares common structural features with other SAHases, no alkali metal is coordinated by the cyanobacterial enzyme as a result of a different organization of the macromolecular environment of the site that is normally supposed to coordinate the metal cation. This inspired the generation of SynSAHase mutants that bind alkali-metal cations analogously to K+-dependent SAHases, as confirmed by crystallographic studies. Structural comparisons of the crystal structure of SynSAHase with other experimental models of SAHases suggest a possible explanation for the occurrence of the cyanobacterial enzyme in the tetrameric state. On the other hand, the reason for the existence of SynSAHase in the dimeric state in solution remains elusive.
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3
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Shi D, Zhang Y, Wang J, Ren W, Zhang J, Mbadianya JI, Zhu Y, Chen C, Ma H. S-adenosyl-L-homocysteine hydrolase FgSah1 is required for fungal development and virulence in Fusarium graminearum. Virulence 2021; 12:2171-2185. [PMID: 34424830 PMCID: PMC8386609 DOI: 10.1080/21505594.2021.1965821] [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] [Indexed: 10/29/2022] Open
Abstract
The S-adenosyl-L-homocysteine hydrolase (Sah1) plays a crucial role in methylation and lipid metabolism in yeast and mammals, yet its function remains elusive in filamentous fungi. In this study, we characterized Sah1 in the phytopathogenic fungus F. graminearum by generating knockout and knockout-complemented strains of FgSAH1. We found that the FgSah1-GFP fusion protein was localized to the cytoplasm, and that deletion of FgSAH1 resulted in defects in vegetative growth, asexual and sexual reproduction, stress responses, virulence, lipid metabolism, and tolerance against fungicides. Moreover, the accumulations of S-adenosyl-L-homocysteine (AdoHcy) and S-adenosyl-L-methionine (AdoMet) (the methyl group donor in most methyl transfer reactions) in ΔFgSah1 were seven- and ninefold higher than those in the wild-type strain, respectively. All of these defective phenotypes in ΔFgSah1 mutants were rescued by target gene complementation. Taken together, these results demonstrate that FgSah1 plays essential roles in methylation metabolism, fungal development, full virulence, multiple stress responses, lipid metabolism, and fungicide sensitivity in F. graminearum. To our knowledge, this is the first report on the systematic functional characterization of Sah1 in F. graminearum.
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Affiliation(s)
- Dongya Shi
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yu Zhang
- Department of Crop Protection, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Jin Wang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Weichao Ren
- Department of Plant Pathology, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jie Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jane Ifunanya Mbadianya
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yuanye Zhu
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Changjun Chen
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hongyu Ma
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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4
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Vizán P, Di Croce L, Aranda S. Functional and Pathological Roles of AHCY. Front Cell Dev Biol 2021; 9:654344. [PMID: 33869213 PMCID: PMC8044520 DOI: 10.3389/fcell.2021.654344] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/24/2021] [Indexed: 11/25/2022] Open
Abstract
Adenosylhomocysteinase (AHCY) is a unique enzyme and one of the most conserved proteins in living organisms. AHCY catalyzes the reversible break of S-adenosylhomocysteine (SAH), the by-product and a potent inhibitor of methyltransferases activity. In mammals, AHCY is the only enzyme capable of performing this reaction. Controlled subcellular localization of AHCY is believed to facilitate local transmethylation reactions, by removing excess of SAH. Accordingly, AHCY is recruited to chromatin during replication and active transcription, correlating with increasing demands for DNA, RNA, and histone methylation. AHCY deletion is embryonic lethal in many organisms (from plants to mammals). In humans, AHCY deficiency is associated with an incurable rare recessive disorder in methionine metabolism. In this review, we focus on the AHCY protein from an evolutionary, biochemical, and functional point of view, and we discuss the most recent, relevant, and controversial contributions to the study of this enzyme.
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Affiliation(s)
- Pedro Vizán
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
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5
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Brzezinski K. S-adenosyl-l-homocysteine Hydrolase: A Structural Perspective on the Enzyme with Two Rossmann-Fold Domains. Biomolecules 2020; 10:biom10121682. [PMID: 33339190 PMCID: PMC7765604 DOI: 10.3390/biom10121682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/27/2022] Open
Abstract
S-adenosyl-l-homocysteine hydrolase (SAHase) is a major regulator of cellular methylation reactions that occur in eukaryotic and prokaryotic organisms. SAHase activity is also a significant source of l-homocysteine and adenosine, two compounds involved in numerous vital, as well as pathological processes. Therefore, apart from cellular methylation, the enzyme may also influence other processes important for the physiology of particular organisms. Herein, presented is the structural characterization and comparison of SAHases of eukaryotic and prokaryotic origin, with an emphasis on the two principal domains of SAHase subunit based on the Rossmann motif. The first domain is involved in the binding of a substrate, e.g., S-adenosyl-l-homocysteine or adenosine and the second domain binds the NAD+ cofactor. Despite their structural similarity, the molecular interactions between an adenosine-based ligand molecule and macromolecular environment are different in each domain. As a consequence, significant differences in the conformation of d-ribofuranose rings of nucleoside and nucleotide ligands, especially those attached to adenosine moiety, are observed. On the other hand, the chemical nature of adenine ring recognition, as well as an orientation of the adenine ring around the N-glycosidic bond are of high similarity for the ligands bound in the substrate- and cofactor-binding domains.
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Affiliation(s)
- Krzysztof Brzezinski
- Laboratory of Structural Microbiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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6
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Alegre S, Pascual J, Trotta A, Angeleri M, Rahikainen M, Brosche M, Moffatt B, Kangasjärvi S. Evolutionary conservation and post-translational control of S-adenosyl-L-homocysteine hydrolase in land plants. PLoS One 2020; 15:e0227466. [PMID: 32678822 PMCID: PMC7367456 DOI: 10.1371/journal.pone.0227466] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/30/2020] [Indexed: 02/01/2023] Open
Abstract
Trans-methylation reactions are intrinsic to cellular metabolism in all living organisms. In land plants, a range of substrate-specific methyltransferases catalyze the methylation of DNA, RNA, proteins, cell wall components and numerous species-specific metabolites, thereby providing means for growth and acclimation in various terrestrial habitats. Trans-methylation reactions consume vast amounts of S-adenosyl-L-methionine (SAM) as a methyl donor in several cellular compartments. The inhibitory reaction by-product, S-adenosyl-L-homocysteine (SAH), is continuously removed by SAH hydrolase (SAHH), which essentially maintains trans-methylation reactions in all living cells. Here we report on the evolutionary conservation and post-translational control of SAHH in land plants. We provide evidence suggesting that SAHH forms oligomeric protein complexes in phylogenetically divergent land plants and that the predominant protein complex is composed by a tetramer of the enzyme. Analysis of light-stress-induced adjustments of SAHH in Arabidopsis thaliana and Physcomitrella patens further suggests that regulatory actions may take place on the levels of protein complex formation and phosphorylation of this metabolically central enzyme. Collectively, these data suggest that plant adaptation to terrestrial environments involved evolution of regulatory mechanisms that adjust the trans-methylation machinery in response to environmental cues.
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Affiliation(s)
- Sara Alegre
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Jesús Pascual
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Andrea Trotta
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
- Institute of Biosciences and Bioresources, National Research Council of Italy, Sesto Fiorentino, Firenze, Italy
| | - Martina Angeleri
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Moona Rahikainen
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Mikael Brosche
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Barbara Moffatt
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Saijaliisa Kangasjärvi
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
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7
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Parkhitko AA, Jouandin P, Mohr SE, Perrimon N. Methionine metabolism and methyltransferases in the regulation of aging and lifespan extension across species. Aging Cell 2019; 18:e13034. [PMID: 31460700 PMCID: PMC6826121 DOI: 10.1111/acel.13034] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/11/2019] [Accepted: 08/08/2019] [Indexed: 12/20/2022] Open
Abstract
Methionine restriction (MetR) extends lifespan across different species and exerts beneficial effects on metabolic health and inflammatory responses. In contrast, certain cancer cells exhibit methionine auxotrophy that can be exploited for therapeutic treatment, as decreasing dietary methionine selectively suppresses tumor growth. Thus, MetR represents an intervention that can extend lifespan with a complementary effect of delaying tumor growth. Beyond its function in protein synthesis, methionine feeds into complex metabolic pathways including the methionine cycle, the transsulfuration pathway, and polyamine biosynthesis. Manipulation of each of these branches extends lifespan; however, the interplay between MetR and these branches during regulation of lifespan is not well understood. In addition, a potential mechanism linking the activity of methionine metabolism and lifespan is regulation of production of the methyl donor S-adenosylmethionine, which, after transferring its methyl group, is converted to S-adenosylhomocysteine. Methylation regulates a wide range of processes, including those thought to be responsible for lifespan extension by MetR. Although the exact mechanisms of lifespan extension by MetR or methionine metabolism reprogramming are unknown, it may act via reducing the rate of translation, modifying gene expression, inducing a hormetic response, modulating autophagy, or inducing mitochondrial function, antioxidant defense, or other metabolic processes. Here, we review the mechanisms of lifespan extension by MetR and different branches of methionine metabolism in different species and the potential for exploiting the regulation of methyltransferases to delay aging.
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Affiliation(s)
- Andrey A. Parkhitko
- Department of GeneticsBlavatnik InstituteHarvard Medical SchoolBostonMassachusetts
| | - Patrick Jouandin
- Department of GeneticsBlavatnik InstituteHarvard Medical SchoolBostonMassachusetts
| | - Stephanie E. Mohr
- Department of GeneticsBlavatnik InstituteHarvard Medical SchoolBostonMassachusetts
| | - Norbert Perrimon
- Department of GeneticsBlavatnik InstituteHarvard Medical SchoolBostonMassachusetts
- Howard Hughes Medical InstituteBostonMassachusetts
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8
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Kailing LL, Bertinetti D, Paul CE, Manszewski T, Jaskolski M, Herberg FW, Pavlidis IV. S-Adenosyl-L-Homocysteine Hydrolase Inhibition by a Synthetic Nicotinamide Cofactor Biomimetic. Front Microbiol 2018; 9:505. [PMID: 29619018 PMCID: PMC5871694 DOI: 10.3389/fmicb.2018.00505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/06/2018] [Indexed: 11/13/2022] Open
Abstract
S-adenosyl-L-homocysteine (SAH) hydrolases (SAHases) are involved in the regulation of methylation reactions in many organisms and are thus crucial for numerous cellular functions. Consequently, their dysregulation is associated with severe health problems. The SAHase-catalyzed reaction is reversible and both directions depend on the redox activity of nicotinamide adenine dinucleotide (NAD+) as a cofactor. Therefore, nicotinamide cofactor biomimetics (NCB) are a promising tool to modulate SAHase activity. In the present in vitro study, we investigated 10 synthetic truncated NAD+ analogs against a SAHase from the root-nodulating bacterium Bradyrhizobium elkanii. Among this set of analogs, one was identified to inhibit the SAHase in both directions. Isothermal titration calorimetry (ITC) and crystallography experiments suggest that the inhibitory effect is not mediated by a direct interaction with the protein. Neither the apo-enzyme (i.e., deprived of the natural cofactor), nor the holo-enzyme (i.e., in the NAD+-bound state) were found to bind the inhibitor. Yet, enzyme kinetics point to a non-competitive inhibition mechanism, where the inhibitor acts on both, the enzyme and enzyme-SAH complex. Based on our experimental results, we hypothesize that the NCB inhibits the enzyme via oxidation of the enzyme-bound NADH, which may be accessible through an open molecular gate, leaving the enzyme stalled in a configuration with oxidized cofactor, where the reaction intermediate can be neither converted nor released. Since the reaction mechanism of SAHase is quite uncommon, this kind of inhibition could be a viable pharmacological route, with a low risk of off-target effects. The NCB presented in this work could be used as a template for the development of more potent SAHase inhibitors.
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Affiliation(s)
- Lyn L Kailing
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | | | - Caroline E Paul
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Tomasz Manszewski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.,Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University in Poznań, Poznań, Poland
| | | | - Ioannis V Pavlidis
- Department of Biochemistry, University of Kassel, Kassel, Germany.,Department of Chemistry, University of Crete, Heraklion, Greece
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9
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Brzezinski K, Czyrko J, Sliwiak J, Nalewajko-Sieliwoniuk E, Jaskolski M, Nocek B, Dauter Z. S-adenosyl-L-homocysteine hydrolase from a hyperthermophile (Thermotoga maritima) is expressed in Escherichia coli in inactive form - Biochemical and structural studies. Int J Biol Macromol 2017; 104:584-596. [PMID: 28629859 PMCID: PMC7888557 DOI: 10.1016/j.ijbiomac.2017.06.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 11/26/2022]
Abstract
Thermotoga maritima is a hyperthermophilic bacterium but its genome encodes a number of archaeal proteins including S-adenosyl-L-homocysteine hydrolase (SAHase), which regulates cellular methylation reactions. The question of proper folding and activity of proteins of extremophilic origin is an intriguing problem. When expressed in E.coli and purified (as a homotetramer) at room temperature, the hyperthermophilic SAHase from T.maritima was inactive. ITC study indicated that the protein undergoes heat-induced conformational changes, and enzymatic activity assays demonstrated that these changes are required to attain enzymatic activity. To explain the mechanism of thermal activation, two crystal structures of the inactive form of T. maritima SAHase (iTmSAHase) were determined for an incomplete binary complex with the reduced cofactor (NADH), and in a mixture of binary complexes with NADH and with adenosine. In contrast to active SAHases, in iTmSAHase only two of the four subunits contain a bound cofactor, predominantly in its non-reactive, reduced state. Moreover, the closed-like conformation of the cofactor-containing subunits precludes substrate delivery to the active site. The two other subunits cannot be involved in the enzymatic reaction either; although they have an open-like conformation, they do not contain the cofactor, whose binding site may be occupied by an adenosine molecule. The results suggest that this enzyme, when expressed in mesophilic cells, is arrested in the activity-incompatible conformation revealed by its crystal structures.
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Affiliation(s)
- Krzysztof Brzezinski
- Institute of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland.
| | - Justyna Czyrko
- Institute of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Joanna Sliwiak
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | | | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
| | - Boguslaw Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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10
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Manszewski T, Szpotkowski K, Jaskolski M. Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii. IUCRJ 2017; 4:271-282. [PMID: 28512574 PMCID: PMC5414401 DOI: 10.1107/s2052252517002433] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/13/2017] [Indexed: 05/14/2023]
Abstract
S-Adenosyl-l-homocysteine hydrolase (SAHase) from the symbiotic bacterium Bradyrhizobium elkanii (BeSAHase) was crystallized in four ligand complexes with (i) mixed adenosine (Ado) and cordycepin (Cord; 3'-deoxyadenosine), (ii) adenine (Ade), (iii) Ado and (iv) mixed 2'-deoxyadenosine (2'-dAdo) and Ade. The crystal structures were solved at resolutions of 1.84, 1.95, 1.95 and 1.54 Å, respectively. Only the Ade complex crystallized with a dimer in the asymmetric unit, while all of the other complexes formed a crystallographically independent tetrameric assembly. In the Ado/Cord complex, adenosine is found in three subunits while the fourth subunit has cordycepin bound in the active site. In the Ade and Ado complexes only these ligand molecules are present in the active sites. The 2'-dAdo/Ade complex has Ade bound in two subunits and 2'-dAdo bound in the other two subunits. The BeSAHase fold adopted a closed conformation in the complexes with Ado, Ade and 2'-dAdo, and a semi-open conformation when cordycepin occupied the active site. An SAHase-specific molecular gate, consisting of residues His342 and Phe343, behaves differently in the different complexes, but there is no simple correlation with the ligand type. Additional small-angle X-ray scattering (SAXS) experiments confirm the tetrameric state of the protein in solution. The main conclusions from this work are (i) that the SAHase subunit does not simply oscillate between two discrete conformational open/closed states in correlation with the absence/presence of a ligand in the active site, but can also assume an intermediate form for some ligands; (ii) that the shut/open state of the molecular gate in the access channel to the active site is not correlated in a simple way with the open/closed subunit conformation or empty/occupied status of the active site, but that a variety of states are possible even for the same ligand; (iii) that a cation (typically sodium) coordinated in an intersubunit loop rigidifies a molecular hinge and thus stabilizes the closed conformation; (iv) that BeSAHase in solution is a tetramer, consistent with the model derived from crystallography.
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Affiliation(s)
- Tomasz Manszewski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Kamil Szpotkowski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
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11
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Manszewski T, Singh K, Imiolczyk B, Jaskolski M. An enzyme captured in two conformational states: crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii. ACTA ACUST UNITED AC 2015; 71:2422-32. [PMID: 26627650 DOI: 10.1107/s1399004715018659] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/05/2015] [Indexed: 11/10/2022]
Abstract
S-Adenosyl-L-homocysteine hydrolase (SAHase) is involved in the enzymatic regulation of S-adenosyl-L-methionine (SAM)-dependent methylation reactions. After methyl-group transfer from SAM, S-adenosyl-L-homocysteine (SAH) is formed as a byproduct, which in turn is hydrolyzed to adenosine (Ado) and homocysteine (Hcy) by SAHase. The crystal structure of BeSAHase, an SAHase from Bradyrhizobium elkanii, which is a nitrogen-fixing bacterial symbiont of legume plants, was determined at 1.7 Å resolution, showing the domain organization (substrate-binding domain, NAD(+) cofactor-binding domain and dimerization domain) of the subunits. The protein crystallized in its biologically relevant tetrameric form, with three subunits in a closed conformation enforced by complex formation with the Ado product of the enzymatic reaction. The fourth subunit is ligand-free and has an open conformation. The BeSAHase structure therefore provides a unique snapshot of the domain movement of the enzyme induced by the binding of its natural ligands.
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Affiliation(s)
- Tomasz Manszewski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Kriti Singh
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Barbara Imiolczyk
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Li X, Huang L, Hong Y, Zhang Y, Liu S, Li D, Zhang H, Song F. Co-silencing of tomato S-adenosylhomocysteine hydrolase genes confers increased immunity against Pseudomonas syringae pv. tomato DC3000 and enhanced tolerance to drought stress. FRONTIERS IN PLANT SCIENCE 2015; 6:717. [PMID: 26442031 PMCID: PMC4561804 DOI: 10.3389/fpls.2015.00717] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/27/2015] [Indexed: 05/08/2023]
Abstract
S-adenosylhomocysteine hydrolase (SAHH), catalyzing the reversible hydrolysis of S-adenosylhomocysteine (SAH) to adenosine and homocysteine, is a key enzyme that maintain the cellular methylation potential in all organisms. We report here the biological functions of tomato SlSAHHs in stress response. The tomato genome contains three SlSAHH genes that encode SlSAHH proteins with high level of sequence identity. qRT-PCR analysis revealed that SlSAHHs responded with distinct expression induction patterns to Pseudomonas syringae pv. tomato (Pst) DC3000 and Botrytis cinerea as well as to defense signaling hormones such as salicylic acid, jasmonic acid and a precursor of ethylene. Virus-induced gene silencing-based knockdown of individual SlSAHH gene did not affect the growth performance and the response to Pst DC3000. However, co-silencing of three SlSAHH genes using a conserved sequence led to significant inhibition of vegetable growth. The SlSAHH-co-silenced plants displayed increased resistance to Pst DC3000 but did not alter the resistance to B. cinerea. Co-silencing of SlSAHHs resulted in constitutively activated defense responses including elevated SA level, upregulated expression of defense-related and PAMP-triggered immunity marker genes and increased callose deposition and H2O2 accumulation. Furthermore, the SlSAHH-co-silenced plants also exhibited enhanced drought stress tolerance although they had relatively small roots. These data demonstrate that, in addition to the functions in growth and development, SAHHs also play important roles in regulating biotic and abiotic stress responses in plants.
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Affiliation(s)
- Xiaohui Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Lei Huang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Yongbo Hong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Yafen Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Shixia Liu
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Huijuan Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University Hangzhou, China
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13
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Pivato M, Fabrega-Prats M, Masi A. Low-molecular-weight thiols in plants: Functional and analytical implications. Arch Biochem Biophys 2014; 560:83-99. [DOI: 10.1016/j.abb.2014.07.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 07/11/2014] [Accepted: 07/14/2014] [Indexed: 01/15/2023]
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14
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Qin Y, Song W, Xiao S, Yin G, Zhu Y, Yan Y, Hu Y. Stress-related genes distinctly expressed in unfertilized wheat ovaries under both normal and water deficit conditions whereas differed in fertilized ovaries. J Proteomics 2014; 102:11-27. [PMID: 24607492 DOI: 10.1016/j.jprot.2014.02.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/16/2014] [Accepted: 02/21/2014] [Indexed: 12/17/2022]
Abstract
UNLABELLED In this study, a proteomic approach was utilized to identify differentially accumulated proteins in developing wheat ovaries before and after fertilization and in response to water deficit. Proteins were extracted, quantified, and resolved by 2-DE at pH4-7. Statistical analysis of spot intensity was performed by using principal component analysis and samples were clustered by using Euclidean distance. In total, 136 differentially accumulated protein spots representing 88 unique proteins were successfully identified by MALDI-TOF/TOF MS. Under normal conditions, stress-related proteins were abundant in unfertilized ovaries while proteins involved in the metabolism of energy and matter were enriched in fertilized ovaries just 48h after fertilization. Similar trends were observed in unfertilized and fertilized wheat ovaries under water deficit conditions, except for increased accumulation of stress-related proteins in fertilized ovaries. Some proteins required for normal development were not present in ovaries subjected to water deficit. Our comprehensive results provide new insights into the biochemical mechanisms involved in ovary development before and after fertilization and in tolerance to water deficit. BIOLOGICAL SIGNIFICANCE Fertilization initiates the most dramatic changes that occur in the life cycle of higher plants; research into differences in gene expression before and after ovary pollination can make a substantial contribution to understanding the physiological and biochemical processes associated with fertilization. To date, a small number of studies have examined changes in transcriptional activity of the developing plant embryo sac before and after fertilization. However, comparative proteomic analysis of wheat ovary development before and after fertilization, and in response to water deficit, has not yet been reported. Our comprehensive results provide new insights into the biochemical mechanisms involved in ovary development before and after fertilization and in tolerance to water deficit.
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Affiliation(s)
- Yajuan Qin
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Wanlu Song
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Shuyang Xiao
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Guangjun Yin
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yan Zhu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yueming Yan
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
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15
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Tehlivets O, Malanovic N, Visram M, Pavkov-Keller T, Keller W. S-adenosyl-L-homocysteine hydrolase and methylation disorders: yeast as a model system. Biochim Biophys Acta Mol Basis Dis 2012; 1832:204-15. [PMID: 23017368 PMCID: PMC3787734 DOI: 10.1016/j.bbadis.2012.09.007] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/14/2012] [Accepted: 09/18/2012] [Indexed: 12/14/2022]
Abstract
S-adenosyl-L-methionine (AdoMet)-dependent methylation is central to the regulation of many biological processes: more than 50 AdoMet-dependent methyltransferases methylate a broad spectrum of cellular compounds including nucleic acids, proteins and lipids. Common to all AdoMet-dependent methyltransferase reactions is the release of the strong product inhibitor S-adenosyl-L-homocysteine (AdoHcy), as a by-product of the reaction. S-adenosyl-L-homocysteine hydrolase is the only eukaryotic enzyme capable of reversible AdoHcy hydrolysis to adenosine and homocysteine and, thus, relief from AdoHcy inhibition. Impaired S-adenosyl-L-homocysteine hydrolase activity in humans results in AdoHcy accumulation and severe pathological consequences. Hyperhomocysteinemia, which is characterized by elevated levels of homocysteine in blood, also exhibits a similar phenotype of AdoHcy accumulation due to the reversal of the direction of the S-adenosyl-L-homocysteine hydrolase reaction. Inhibition of S-adenosyl-L-homocysteine hydrolase is also linked to antiviral effects. In this review the advantages of yeast as an experimental system to understand pathologies associated with AdoHcy accumulation will be discussed.
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Affiliation(s)
- Oksana Tehlivets
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
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16
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Brzezinski K, Dauter Z, Jaskolski M. High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:218-31. [PMID: 22349223 PMCID: PMC3282620 DOI: 10.1107/s0907444911055090] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 12/21/2011] [Indexed: 11/11/2022]
Abstract
S-Adenosyl-L-homocysteine hydrolase (SAHase) catalyzes the reversible breakdown of S-adenosyl-L-homocysteine (SAH) to adenosine and homocysteine. SAH is formed in methylation reactions that utilize S-adenosyl-L-methionine (SAM) as a methyl donor. By removing the SAH byproduct, SAHase serves as a major regulator of SAM-dependent biological methylation reactions. Here, the first crystal structure of SAHase of plant origin, that from the legume yellow lupin (LlSAHase), is presented. Structures have been determined at high resolution for three complexes of the enzyme: those with a reaction byproduct/substrate (adenosine), with its nonoxidizable analog (cordycepin) and with a product of inhibitor cleavage (adenine). In all three cases the enzyme has a closed conformation. A sodium cation is found near the active site, coordinated by residues from a conserved loop that hinges domain movement upon reactant binding. An insertion segment that is present in all plant SAHases is located near a substrate-pocket access channel and participates in its formation. In contrast to mammalian and bacterial SAHases, the channel is open when adenosine or cordycepin is bound and is closed in the adenine complex. In contrast to SAHases from other organisms, which are active as tetramers, the plant enzyme functions as a homodimer in solution.
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Affiliation(s)
- Krzysztof Brzezinski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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17
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Fulneček J, Matyášek R, Votruba I, Holý A, Křížová K, Kovařík A. Inhibition of SAH-hydrolase activity during seed germination leads to deregulation of flowering genes and altered flower morphology in tobacco. Mol Genet Genomics 2011; 285:225-36. [PMID: 21274566 DOI: 10.1007/s00438-011-0601-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 01/06/2011] [Indexed: 02/06/2023]
Abstract
Developmental processes are closely connected to certain states of epigenetic information which, among others, rely on methylation of chromatin. S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) are key cofactors of enzymes catalyzing DNA and histone methylation. To study the consequences of altered SAH/SAM levels on plant development we applied 9-(S)-(2,3-dihydroxypropyl)-adenine (DHPA), an inhibitor of SAH-hydrolase, on tobacco seeds during a short phase of germination period (6 days). The transient drug treatment induced: (1) dosage-dependent global DNA hypomethylation mitotically transmitted to adult plants; (2) pleiotropic developmental defects including decreased apical dominance, altered leaf and flower symmetry, flower whorl malformations and reduced fertility; (3) dramatic upregulation of floral organ identity genes NTDEF, NTGLO and NAG1 in leaves. We conclude that temporal SAH-hydrolase inhibition deregulated floral genes expression probably via chromatin methylation changes. The data further show that plants might be particularly sensitive to accurate setting of SAH/SAM levels during critical developmental periods.
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Affiliation(s)
- Jaroslav Fulneček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, vvi, Kralovopolska 135, 612 65 Brno, Czech Republic.
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Ishihara M, Kusakabe Y, Ohsumichi T, Tanaka N, Nakanishi M, Kitade Y, Nakamura KT. Crystallization of mouse S-adenosyl-L-homocysteine hydrolase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:313-5. [PMID: 20208169 PMCID: PMC2833045 DOI: 10.1107/s1744309110000771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Accepted: 01/07/2010] [Indexed: 11/10/2022]
Abstract
S-adenosyl-L-homocysteine hydrolase (SAHH; EC 3.3.1.1) catalyzes the reversible hydrolysis of S-adenosyl-L-homocysteine to adenosine and L-homocysteine. For crystallographic investigations, mouse SAHH (MmSAHH) was overexpressed in bacterial cells and crystallized using the hanging-drop vapour-diffusion method in the presence of the reaction product adenosine. X-ray diffraction data to 1.55 A resolution were collected from an orthorhombic crystal form belonging to space group I222 with unit-cell parameters a = 100.64, b = 104.44, c = 177.31 A. Structural analysis by molecular replacement is in progress.
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Affiliation(s)
| | | | | | | | - Masayuki Nakanishi
- College of Pharmaceutical Sciences, Matsuyama University, Ehime 790-8578, Japan
| | - Yukio Kitade
- Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
- Center for Emerging Infectious Diseases, Gifu University, Gifu 501-1193, Japan
- Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
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