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Im JH, Park CH, Shin JH, Oh YL, Oh M, Paek NC, Park YJ. Effects of Light on the Fruiting Body Color and Differentially Expressed Genes in Flammulina velutipes. J Fungi (Basel) 2024; 10:372. [PMID: 38921359 PMCID: PMC11204606 DOI: 10.3390/jof10060372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Light plays vital roles in fungal growth, development, reproduction, and pigmentation. In Flammulina velutipes, the color of the fruiting body exhibits distinct changes in response to light; however, the underlying molecular mechanisms remain unknown. Therefore, in this study, we aimed to analyze the F. velutipes transcriptome under red, green, and blue light-emitting diode (LED) lights to identify the key genes affecting the light response and fruiting body color in this fungus. Additionally, we conducted protein-protein interaction (PPI) network analysis of the previously reported fruiting body color-related gene, Fvpal1, to identify the hub genes. Phenotypic analysis revealed that fruiting bodies exposed to green and blue lights were darker than those untreated or exposed to red light, with the color intensifying more after 48 h of exposure to blue light compared to that after 24 h of exposure. Differentially expressed gene (DEG) analyses of all light treatments for 24 h revealed that the numbers of DEGs were 17, 74, and 257 under red, green, and blue lights, respectively. Subsequently, functional enrichment analysis was conducted of the DEGs identified under green and blue lights, which influenced the color of F. velutipes. In total, 103 of 168 downregulated DEGs under blue and green lights were included in the enrichment analysis. Among the DEGs enriched under both green and blue light treatments, four genes were related to monooxygenases, with three genes annotated as cytochrome P450s that are crucial for various metabolic processes in fungi. PPI network analysis of Fvpal1 revealed associations with 11 genes, among which the expression of one gene, pyridoxal-dependent decarboxylase, was upregulated in F. velutipes exposed to blue light. These findings contribute to our understanding of the molecular mechanisms involved in the fruiting body color changes in response to light and offer potential molecular markers for further exploration of light-mediated regulatory pathways.
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Affiliation(s)
- Ji-Hoon Im
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea;
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong-gun 27709, Republic of Korea; (Y.-L.O.); (M.O.)
| | - Che-Hwon Park
- Department of Medicinal Biosciences, Research Institute for Biomedicinal & Health Science, College of Biomedicinal and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (C.-H.P.); (J.-H.S.)
| | - Ju-Hyeon Shin
- Department of Medicinal Biosciences, Research Institute for Biomedicinal & Health Science, College of Biomedicinal and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (C.-H.P.); (J.-H.S.)
| | - Youn-Lee Oh
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong-gun 27709, Republic of Korea; (Y.-L.O.); (M.O.)
| | - Minji Oh
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong-gun 27709, Republic of Korea; (Y.-L.O.); (M.O.)
| | - Nam-Chon Paek
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea;
| | - Young-Jin Park
- Department of Medicinal Biosciences, Research Institute for Biomedicinal & Health Science, College of Biomedicinal and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (C.-H.P.); (J.-H.S.)
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Lee KH, Distefano MD, Seelig B. Facile immobilization of pyridoxal 5'-phosphate using p-diazobenzoyl-derivatized Sepharose 4B. RESULTS IN CHEMISTRY 2023; 6:101044. [PMID: 38131063 PMCID: PMC10735239 DOI: 10.1016/j.rechem.2023.101044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Pyridoxal 5'-phosphate (PLP) is a ubiquitous and versatile cofactor utilized by numerous enzymes involved in amino acid biosynthetic pathways. Immobilized PLP is a valuable tool to isolate unknown PLP-dependent enzymes in nature or to perform in vitro selection or directed evolution on existing or de novo PLP-dependent enzymes. The C-6 position is preferred for covalent immobilization of PLP because it maintains all important functional groups in their native, unmodified form. Previously reported diazonium derivatization methods for C-6 immobilization utilized an azide linker compound that is hazardous and not readily available. Here we report a safer and more accessible method to synthesize p-diazobenzoyl-derivatized Sepharose 4B using the N-hydroxysuccinimide (NHS) ester chemistry. The derivative was used to immobilize PLP, and the resulting C-6 immobilized PLP had a loading of ~2.6 μmol PLP per mL of resin, comparable to commercially available products of other immobilized cofactors.
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Affiliation(s)
- Kun-Hwa Lee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
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3
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Abstract
ConspectusOne of the fundamental goals of chemists is to develop highly efficient methods for producing optically active compounds, given their wide range of applications in chemistry, pharmaceutical industry, chemical biology, and material science. Biomimetic asymmetric catalysis, which imitates the structures and functions of enzymes, has emerged as an extremely attractive strategy for producing chiral compounds. This field has drawn tremendous research interest and has led to various protocols for constructing complex molecular scaffolds. The Vitamin B6 family, including pyridoxal, pyridoxamine, pyridoxine, and the corresponding phosphorylated derivatives, serves as the cofactors to catalyze more than 200 enzymatic functions, accounting for ∼4% of all enzyme activities. Although significant progress has been made in simulating the biological roles of vitamin B6 during the past several decades, its extraordinary catalytic power has not yet been successfully applied into asymmetric synthesis. In recent years, our group has been devoted to developing vitamin B6-based biomimetic asymmetric catalysis using chiral pyridoxals/pyridoxamines as catalysts. We are particularly interested in mimicking the processes of enzymatic transamination and biological aldol reaction of glycine, respectively, developing asymmetric biomimetic transamination and carbonyl catalysis enabled α-C-H transformation of primary amines. Using a chiral α,α-diarylprolinol-derived pyridoxal as the catalyst, we reported the first chiral pyridoxal catalyzed asymmetric transamination of α-keto acids in 2015. A significant breakthrough in biomimetic transamination was achieved by using an axially chiral biaryl pyridoxamine catalyst that bears a lateral amine side arm. The amine side arm acts as an intramolecular base, accelerating the transamination and proving highly effective for transamination of α-keto acids and α-keto amides. In addition, we discovered the catalytic power of chiral pyridoxals as carbonyl catalysts for asymmetric biomimetic Mannich/aldol reactions of glycinates. These chiral pyridoxals also enabled more α-C-H conversions of glycinates, such as asymmetric 1,4-addition toward α,β-unsaturated esters and asymmetric α-allylation with Morita-Baylis-Hillman acetates. Moreover, carbonyl catalysis can be further applied to highly challenging primary amines with inert α-C-H bonds, such as propargylamines and benzylamines, which represents a powerful strategy for direct asymmetric α-C-H functionalization of various primary amines without protection of the NH2 group. These biomimetic/bioinspired transformations provide efficient new protocols for the synthesis of chiral amines. Herein, we summarize our recent efforts on the development of the vitamin B6-based biomimetic asymmetric catalysis.
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Affiliation(s)
- Xiao Xiao
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, and Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 200234, P. R. China
| | - Baoguo Zhao
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, and Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 200234, P. R. China
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Heli Z, Hongyu C, Dapeng B, Yee Shin T, Yejun Z, Xi Z, Yingying W. Recent advances of γ-aminobutyric acid: Physiological and immunity function, enrichment, and metabolic pathway. Front Nutr 2022; 9:1076223. [PMID: 36618705 PMCID: PMC9813243 DOI: 10.3389/fnut.2022.1076223] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
γ-aminobutyric acid (GABA) is a non-protein amino acid which naturally and widely occurs in animals, plants, and microorganisms. As the chief inhibitory neurotransmitter in the central nervous system of mammals, it has become a popular dietary supplement and has promising application in food industry. The current article reviews the most recent literature regarding the physiological functions, preparation methods, enrichment methods, metabolic pathways, and applications of GABA. This review sheds light on developing GABA-enriched plant varieties and food products, and provides insights for efficient production of GABA through synthetic biology approaches.
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Affiliation(s)
- Zhou Heli
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Chen Hongyu
- National Engineering Research Center of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilization of Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Bao Dapeng
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China,National Engineering Research Center of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilization of Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Tan Yee Shin
- Faculty of Science and Mushroom Research Centre, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Zhong Yejun
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Zhang Xi
- BannerBio Nutraceuticals Inc., Shenzhen, China
| | - Wu Yingying
- National Engineering Research Center of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilization of Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China,*Correspondence: Wu Yingying,
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Pfanzelt M, Maher TE, Absmeier RM, Schwarz M, Sieber SA. Tailored Pyridoxal Probes Unravel Novel Cofactor-Dependent Targets and Antibiotic Hits in Critical Bacterial Pathogens. Angew Chem Int Ed Engl 2022; 61:e202117724. [PMID: 35199904 PMCID: PMC9321722 DOI: 10.1002/anie.202117724] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Indexed: 01/21/2023]
Abstract
Unprecedented bacterial targets are urgently needed to overcome the resistance crisis. Herein we systematically mine pyridoxal phosphate‐dependent enzymes (PLP‐DEs) in bacteria to focus on a target class which is involved in crucial metabolic processes. For this, we tailored eight pyridoxal (PL) probes bearing modifications at various positions. Overall, the probes exceeded the performance of a previous generation and provided a detailed map of PLP‐DEs in clinically relevant pathogens including challenging Gram‐negative strains. Putative PLP‐DEs with unknown function were exemplarily characterized via in‐depth enzymatic assays. Finally, we screened a panel of PLP binders for antibiotic activity and unravelled the targets of hit molecules. Here, an uncharacterized enzyme, essential for bacterial growth, was assigned as PLP‐dependent cysteine desulfurase and confirmed to be inhibited by the marketed drug phenelzine. Our approach provides a basis for deciphering novel PLP‐DEs as essential antibiotic targets along with corresponding ways to decipher small molecule inhibitors.
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Affiliation(s)
- Martin Pfanzelt
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Thomas E Maher
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany.,Department of Chemistry, Molecular Sciences Research Hub, White City Campus and Institute of Chemical Biology, Molecular Sciences Research Hub, White City Campus, Imperial College London, 82 Wood Lane, London, W12 0BZ, UK
| | - Ramona M Absmeier
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Markus Schwarz
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Stephan A Sieber
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
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6
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Genetic bases for the metabolism of the DMS precursor S-methylmethionine by Saccharomyces cerevisiae. Food Microbiol 2022; 106:104041. [DOI: 10.1016/j.fm.2022.104041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 01/27/2023]
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7
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Tailored Pyridoxal Probes Unravel Novel Cofactor‐Dependent Targets and Antibiotic Hits in Critical Bacterial Pathogens. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Battista VD, Hey-Hawkins E. Development of Prodrugs for Treatment of Parkinson's Disease: New Inorganic Scaffolds for Blood-Brain Barrier Permeation. J Pharm Sci 2022; 111:1262-1279. [PMID: 35182542 DOI: 10.1016/j.xphs.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 10/19/2022]
Abstract
The treatment of Parkinson's disease (PD) has not been consistently modified for more than 60 years. L-DOPA, the blood-brain barrier permeable precursor prodrug of dopamine, is to date the only effective therapy on the market. However, it is well known that prolonged treatment with L-DOPA leads to several side effects, which may affect the patient's life expectancy (i.e., the wearing-off phenomenon, on-off fluctuations, and dyskinesia). For this reason, modifications, and supplements to L-DOPA treatment have been and are being studied, which, however, have not yet resulted in a valid alternative to the cornerstone drug. This review aims to summarize the main formulations currently in use for PD treatment, explaining advantages and disadvantages for each class. The attention will be focused on the promising prodrug concept, aimed at finding a suitable L-DOPA substitute with improved pharmacokinetic behavior. In this respect, new potential candidates which show interesting properties for the intended scope, the so-called dicarba-closo-dodecaboranes(12) (carboranes), will be discussed. Carboranes are inorganic molecular icosahedral boron-carbon clusters with 12 vertices and 20 deltahedral faces. They have been extensively studied for applications in medicine as potential pharmacophores, reagents in boron neutron capture therapy (BNCT) and radiotherapy. Here, we discuss them as inorganic scaffolds for dopamine delivery at the central nervous system (CNS) level.
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Key Words
- %F, Oral Bioavailability
- 5-HTP, L-5-Hydroxy-Tryptophan
- AADC, Aromatic L-Amino Acid Decarboxylase
- AGPs, Arabinogalactan Proteins
- AUC, Area Under the Plasma Concentration Curve
- Abbreviations
- BBB, Blood–Brain Barrier
- BNCT, Boron Neutron Capture Therapy
- CNS, Central Nervous System
- COMT, Catechol-O-Methyltransferase
- DBS, Deep Brain Stimulation
- DDC, Dopamine Decarboxylase
- DMSO, Dimethylsulfoxide
- FAD, Flavin Adenine Dinucleotide
- FDA, Food and Drug Administration
- GPCRs, G-Protein-Coupled Receptors
- HIV, Human Immunodeficiency Virus
- HSA, Human Serum Albumin
- ICT, Intramolecular Charge Transfer
- IPG, Implanted Pulse Generator
- IUPAC, International Union of Pure and Applied Chemistry
- IV, Intravenous Injection
- LDEE, L-DOPA Ethyl Ester
- LNAA, Large Neutral Amino Acid transport system
- MAO-A/B, Monoamine Oxidase-A/B
- MPO, Multiparameter Optimization
- Mw, Molecular Weight
- NMDAR, N-Methyl D-Aspartate Receptor
- P, Partition Coefficient
- PAMPA, Parallel Artificial Membrane Permeability Assay
- PD, Parkinson's Disease
- PLP, Pyridoxal Phosphate
- PNS, Peripheral Nervous System
- Parkinson's disease, Dopamine, Blood–brain barrier, Permeability, Bioavailability, L-DOPA, Prodrugs, Inorganic scaffold, Icosahedral carborane
- SAM, S-Adenosyl L-Methionine
- STN, Subthalamic Nucleus
- TBP, Tetrahydrobiopterin
- UPDRS, Unified Parkinson's Disease Rating Scale
- VTA, Ventral Tegmental Are
- hBMECs, human Brain Microvascular Endothelial Cells
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Affiliation(s)
- Veronica Di Battista
- Leipzig University, Faculty of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Johannisallee 29, 04103 Leipzig, Germany
| | - Evamarie Hey-Hawkins
- Leipzig University, Faculty of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Johannisallee 29, 04103 Leipzig, Germany.
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9
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Klein A, Rovó P, Sakhrani VV, Wang Y, Holmes JB, Liu V, Skowronek P, Kukuk L, Vasa SK, Güntert P, Mueller LJ, Linser R. Atomic-resolution chemical characterization of (2x)72-kDa tryptophan synthase via four- and five-dimensional 1H-detected solid-state NMR. Proc Natl Acad Sci U S A 2022; 119:e2114690119. [PMID: 35058365 PMCID: PMC8795498 DOI: 10.1073/pnas.2114690119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/13/2021] [Indexed: 02/07/2023] Open
Abstract
NMR chemical shifts provide detailed information on the chemical properties of molecules, thereby complementing structural data from techniques like X-ray crystallography and electron microscopy. Detailed analysis of protein NMR data, however, often hinges on comprehensive, site-specific assignment of backbone resonances, which becomes a bottleneck for molecular weights beyond 40 to 45 kDa. Here, we show that assignments for the (2x)72-kDa protein tryptophan synthase (665 amino acids per asymmetric unit) can be achieved via higher-dimensional, proton-detected, solid-state NMR using a single, 1-mg, uniformly labeled, microcrystalline sample. This framework grants access to atom-specific characterization of chemical properties and relaxation for the backbone and side chains, including those residues important for the catalytic turnover. Combined with first-principles calculations, the chemical shifts in the β-subunit active site suggest a connection between active-site chemistry, the electrostatic environment, and catalytically important dynamics of the portal to the β-subunit from solution.
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Affiliation(s)
- Alexander Klein
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Petra Rovó
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
| | - Varun V Sakhrani
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Yangyang Wang
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Jacob B Holmes
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Viktoriia Liu
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Patricia Skowronek
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
| | - Laura Kukuk
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Rasmus Linser
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany;
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
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10
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Gerlach T, Nugroho DL, Rother D. The Effect of Visible Light on the Catalytic Activity of PLP-Dependent Enzymes. ChemCatChem 2021; 13:2398-2406. [PMID: 34249169 PMCID: PMC8251830 DOI: 10.1002/cctc.202100163] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/26/2021] [Indexed: 11/08/2022]
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes are a versatile class of biocatalysts and feature a variety of industrial applications. However, PLP is light sensitive and can cause inactivation of enzymes in certain light conditions. As most of the PLP-dependent enzymes are usually not handled in dark conditions, we evaluated the effect of visible light on the activity of PLP-dependent enzymes during production as well as transformation. We tested four amine transaminases, from Chromobacterium violaceum, Bacillus megaterium, Vibrio fluvialis and a variant from Arthrobacter species as well as two lysine decarboxylases, from Selenomonas ruminantium and the LDCc from Escherichia coli. It appeared that five of these six enzymes suffered from a significant decrease in activity by up to 90 % when handled in laboratory light conditions. Surprisingly, only the amine transaminase variant from Arthrobacter species appeared to be unaffected by light exposure and even showed an activation to 150 % relative activity over the course of 6 h regardless of the light conditions.
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Affiliation(s)
- Tim Gerlach
- Institute of Bio- and Geosciences: Biotechnology Forschungszentrum Jülich GmbHWilhelm-Johnen-Straße52428JülichGermany
- Department Aachen Biology and BiotechnologyRWTH Aachen UniversityWorringer Weg 152062AachenGermany
| | - David Limanhadi Nugroho
- Institute of Bio- and Geosciences: Biotechnology Forschungszentrum Jülich GmbHWilhelm-Johnen-Straße52428JülichGermany
| | - Dörte Rother
- Institute of Bio- and Geosciences: Biotechnology Forschungszentrum Jülich GmbHWilhelm-Johnen-Straße52428JülichGermany
- Department Aachen Biology and BiotechnologyRWTH Aachen UniversityWorringer Weg 152062AachenGermany
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11
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Paxhia MD, Swanson MS, Downs DM. Functional characterization of the HMP-P synthase of Legionella pneumophila (Lpg1565). Mol Microbiol 2020; 115:539-553. [PMID: 33034117 DOI: 10.1111/mmi.14622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 11/30/2022]
Abstract
The production of the pyrimidine moiety in thiamine synthesis, 2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate (HMP-P), has been described to proceed through the Thi5-dependent pathway in Saccharomyces cerevisiae and other yeast. Previous work found that ScThi5 functioned poorly in a heterologous context. Here we report a bacterial ortholog to the yeast HMP-P synthase (Thi5) was necessary for HMP synthesis in Legionella pneumophila. Unlike ScThi5, LpThi5 functioned in vivo in Salmonella enterica under multiple growth conditions. The protein LpThi5 is a dimer that binds pyridoxal-5'-phosphate (PLP), apparently without a solvent-exposed Schiff base. A small percentage of LpThi5 protein co-purifies with a bound molecule that can be converted to HMP. Analysis of variant proteins both in vivo and in vitro confirmed that residues in sequence motifs conserved across bacterial and eukaryotic orthologs modulate the function of LpThi5. IMPORTANCE: Thiamine is an essential vitamin for the vast majority of organisms. There are multiple strategies to synthesize and salvage this vitamin. The predominant pathway for synthesis of the pyrimidine moiety of thiamine involves the Fe-S cluster protein ThiC. An alternative pathway utilizes Thi5, a novel enzyme that uses PLP as a substrate. The Thi5-dependent pathway is poorly characterized in yeast and has not been characterized in Bacteria. Here we demonstrate that a Thi5-dependent pathway is necessary for thiamine biosynthesis in Legionella pneumophila and provide biochemical data to extend knowledge of the Thi5 enzyme, the corresponding biosynthetic pathway, and the role of metabolic network architecture in optimizing its function.
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Affiliation(s)
- Michael D Paxhia
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Michele S Swanson
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, USA
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12
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Zheng W, Chen K, Fang S, Cheng X, Xu G, Yang L, Wu J. Construction and Application of PLP Self-sufficient Biocatalysis System for Threonine Aldolase. Enzyme Microb Technol 2020; 141:109667. [PMID: 33051017 DOI: 10.1016/j.enzmictec.2020.109667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 01/09/2023]
Abstract
A number of organic synthesis involve threonine aldolase (TA), a pyridoxal phosphate (PLP)-dependent enzyme. Although the addition of exogenous PLP is necessary for the reactions, it increases the cost and complicates the purification of the product. This work constructed a PLP self-sufficient biocatalysis system for TA, which included an improvement of the intracellular PLP level and co-immobilization of TA with PLP. Engineered strain BL-ST was constructed by introducing PLP synthase PdxS/T to Escherichia coli BL21(ED3). The intracellular PLP concentration of the strain increased approximately fivefold to 48.5 μmol/gDCW. l-TA, from Bacillus nealsonii (BnLTA), was co-expressed in the strain BL-ST with PdxS/T, resulting in the engineered strain BL-BnLTA-ST. Compared with the control strain BL-BnLTA (254.1 U/L), the enzyme activity of the strain BL-BnLTA-ST reached 1518.4 U/L without the addition of exogenous PLP. An efficient co-immobilization system was then designed. The epoxy resin LX-1000HFA wrapped by polyethyleneimine (PEI) acted as a carrier to immobilize the crude enzyme solution of the strain BL-BnLTA-ST mixed with an extra 100 μM of exogenous PLP, resulting in the catalyst HFAPEI-BnLTA-STPLP 100. HFAPEI-BnLTA-STPLP 100 exhibited a half-life of approximately 450 h, and the application of the catalyst in the continuous biosynthesis of 3-[4-(methylsulfonyl) phenyl] serine had more than 180 batch reactions (>60%conv) without the extra addition of exogenous PLP. The excellent compatibility and stability of the system were further confirmed by other TAs. This work introduced a PLP self-sufficient biocatalysis system that can reduce the cost of PLP and contribute to the industrial application of TA. In addition, the system may also be applied in other PLP-dependent enzymes.
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Affiliation(s)
- Wenlong Zheng
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Kaitong Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Sai Fang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Xiuli Cheng
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Gang Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, China.
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13
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Gamov G, Meshkov A, Zavalishin M, Khokhlova AY, Gashnikova A, Aleksandriiskii V, Sharnin V. Protonation of hydrazones derived from pyridoxal 5′-phosphate: Thermodynamic and structural elucidation. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Zhang XJ, Fan HH, Liu N, Wang XX, Cheng F, Liu ZQ, Zheng YG. A novel self-sufficient biocatalyst based on transaminase and pyridoxal 5′-phosphate covalent co-immobilization and its application in continuous biosynthesis of sitagliptin. Enzyme Microb Technol 2019; 130:109362. [DOI: 10.1016/j.enzmictec.2019.109362] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/12/2019] [Accepted: 06/16/2019] [Indexed: 12/31/2022]
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15
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Hoegl A, Nodwell MB, Kirsch VC, Bach NC, Pfanzelt M, Stahl M, Schneider S, Sieber SA. Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics. Nat Chem 2018; 10:1234-1245. [PMID: 30297752 PMCID: PMC6252082 DOI: 10.1038/s41557-018-0144-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/03/2018] [Indexed: 02/01/2023]
Abstract
Pyridoxal phosphate (PLP) is an enzyme cofactor required for the chemical transformation of biological amines in many central cellular processes. PLP-dependent enzymes (PLP-DEs) are ubiquitous and evolutionarily diverse, making their classification based on sequence homology challenging. Here we present a chemical proteomic method for reporting on PLP-DEs using functionalized cofactor probes. We synthesized pyridoxal analogues modified at the 2'-position, which are taken up by cells and metabolized in situ. These pyridoxal analogues are phosphorylated to functional cofactor surrogates by cellular pyridoxal kinases and bind to PLP-DEs via an aldimine bond which can be rendered irreversible by NaBH4 reduction. Conjugation to a reporter tag enables the subsequent identification of PLP-DEs using quantitative, label-free mass spectrometry. Using these probes we accessed a significant portion of the Staphylococcus aureus PLP-DE proteome (73%) and annotate uncharacterized proteins as novel PLP-DEs. We also show that this approach can be used to study structural tolerance within PLP-DE active sites and to screen for off-targets of the PLP-DE inhibitor D-cycloserine.
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Affiliation(s)
- Annabelle Hoegl
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Matthew B Nodwell
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Volker C Kirsch
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Nina C Bach
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Martin Pfanzelt
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Matthias Stahl
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany
| | - Stephan A Sieber
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching, Germany.
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16
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Korasick DA, White TA, Chakravarthy S, Tanner JJ. NAD + promotes assembly of the active tetramer of aldehyde dehydrogenase 7A1. FEBS Lett 2018; 592:3229-3238. [PMID: 30184263 PMCID: PMC6188814 DOI: 10.1002/1873-3468.13238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/24/2018] [Accepted: 08/28/2018] [Indexed: 02/04/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) is the redox cofactor of many enzymes, including the vast aldehyde dehydrogenase (ALDH) superfamily. Although the function of NAD(H) in hydride transfer is established, its influence on protein structure is less understood. Herein, we show that NAD+ -binding promotes assembly of the ALDH7A1 tetramer. Multiangle light scattering, small-angle X-ray scattering, and sedimentation velocity all show a pronounced shift of the dimer-tetramer equilibrium toward the tetramer when NAD+ is present. Furthermore, electron microscopy shows that cofactor binding enhances tetramer formation even at the low enzyme concentration used in activity assays, suggesting the tetramer is the active species. Altogether, our results suggest that the catalytically active oligomer of ALDH7A1 is assembled on demand in response to cofactor availability.
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Affiliation(s)
- David A. Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Tommi A. White
- Department of Biochemistry, University of Missouri, Columbia, Missouri
- Electron Microscopy Core Facility, University of Missouri, Columbia, Missouri
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri
- Department of Chemistry, University of Missouri, Columbia, Missouri
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17
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Orrego AH, López-Gallego F, Espaillat A, Cava F, Guisan JM, Rocha-Martin J. One-step Synthesis of α-Keto Acids from Racemic Amino Acids by A Versatile Immobilized Multienzyme Cell-free System. ChemCatChem 2018. [DOI: 10.1002/cctc.201800359] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alejandro H. Orrego
- Department of Biocatalysis; Institute of Catalysis and Petrochemistry (ICP) CSIC; Campus UAM. Cantoblanco. 28049 Madrid Spain
| | - Fernando López-Gallego
- Departamento de Química Orgánica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); CSIC-Universidad de Zaragoza; 50009 Zaragoza Spain
- ARAID Foundation; Zaragoza Spain
| | - Akbar Espaillat
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden; Umea Centre for Microbial Research; Umea University; Umea Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden; Umea Centre for Microbial Research; Umea University; Umea Sweden
| | - José M. Guisan
- Department of Biocatalysis; Institute of Catalysis and Petrochemistry (ICP) CSIC; Campus UAM. Cantoblanco. 28049 Madrid Spain
| | - Javier Rocha-Martin
- Department of Biocatalysis; Institute of Catalysis and Petrochemistry (ICP) CSIC; Campus UAM. Cantoblanco. 28049 Madrid Spain
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18
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Tissue specific expression and in-silico characterization of a putative cysteine synthase gene from Lathyrus sativus L. Gene Expr Patterns 2017; 27:128-134. [PMID: 29247850 DOI: 10.1016/j.gep.2017.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 11/22/2022]
Abstract
Grass pea (Lathyrus sativus L.) is a worldwide popular pulse crop especially for its protein rich seeds with least production cost. However, the use of the crop became controversial due to the presence of non-protein amino acid, β-N-oxalyl-L-α, β-diaminopropionic acid (β-ODAP) in its seed and leaf, which is known as the principle neurotoxin to cause neurolathyrism (a motor neurodegenerative disease of humans and animals) during prolonged consumption as regular diet. Till date, the knowledge on β-ODAP biosynthesis in Lathyrus sp. is limited only to a small part of the complex bio-chemical steps involved including a few known sulfur-containing enzymes (viz. cysteine synthase, ODAP synthase etc.). In Lathyrus sativus, biosynthesis of β-ODAP varies differentially in a tissue-specific manner as well as in response to several environmental stresses viz. zinc deficiency, iron over-exposure, moisture stress etc. In the present study, a novel cysteine synthase gene (LsCSase) from Lathyrus sativus L was identified and characterized through bioinformatics approaches. The bioinformatic analysis revealed that LsCSase showed maximum similarity with the O-acetyl serine (thiol) lyase of Medicago truncatula with respect to several significant sequence-specific conserved motifs (cysK, CBS like, ADH_zinc_N, PALP), sub-cellular localization (chloroplast or cytoplasm) etc., similar to other members of cysteine synthase protein family. Moreover, the tissue-specific regulation of the LsCSase as well as its transcriptional activation under certain previously reported stressed conditions (low Zn+2-high Fe+2, PEG induced osmotic stress) were also documented through quantitative real-time PCR analyses, suggesting a possible link between the LsCSase gene activation and β-ODAP biosynthesis to manage external stresses in grass pea. This preliminary study offers a probable way towards the development of less toxic consumer-safe grass pea by down-regulation or deactivation of such gene/s (cysteine synthase) through genetic manipulations.
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19
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Pyridoxine 5'-phosphate oxidase is a novel therapeutic target and regulated by the TGF-β signalling pathway in epithelial ovarian cancer. Cell Death Dis 2017; 8:3214. [PMID: 29238081 PMCID: PMC5870590 DOI: 10.1038/s41419-017-0050-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 12/12/2022]
Abstract
Pyridoxine 5'-phosphate oxidase (PNPO) is an enzyme that converts pyridoxine 5'-phosphate into pyridoxal 5'-phosphate (PLP), an active form of vitamin B6 implicated in several types of cancer. However, the role of PNPO and its regulatory mechanism in epithelial ovarian cancer (EOC) are unknown. In the present study, PNPO expression in human ovarian tumour tissue and its association with the clinicopathological features of patients with EOC were examined. Further, the biological function of PNPO in EOC cells and in xenograft was evaluated. We demonstrated for the first time that PNPO was overexpressed in human EOC. Knockdown of PNPO induced EOC cell apoptosis, arrested cell cycle at G2/M phase, decreased cell proliferation, migration and invasion. Xenografts of PNPO-shRNA-expressing cells into the nude mouse attenuated tumour growth. PNPO at mRNA and protein levels in EOC cells was decreased after transforming growth factor-β1 (TGF-β1) treatment. The inhibitory effect of TGF-β1 on PNPO expression was abolished in the presence of SB-431542, a TGF-β type I receptor kinase inhibitor. Moreover, we found that TGF-β1-mediated PNPO expression was at least in part through the upregulation of miR-143-3p. These data indicate a mechanism underlying PNPO regulation by the TGF-β signalling pathway. Furthermore, PLP administration reduced PNPO expression and decreased EOC cell proliferation, suggesting a feedback loop between PLP and PNPO. Thus, our findings reveal that PNPO can serve as a novel tissue biomarker of EOC and may be a potential target for therapeutic intervention.
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20
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Guerriero RM, Patel AA, Walsh B, Baumer FM, Shah AS, Peters JM, Rodan LH, Agrawal PB, Pearl PL, Takeoka M. Systemic Manifestations in Pyridox(am)ine 5'-Phosphate Oxidase Deficiency. Pediatr Neurol 2017; 76:47-53. [PMID: 28985901 PMCID: PMC6008785 DOI: 10.1016/j.pediatrneurol.2017.05.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 05/24/2017] [Accepted: 05/28/2017] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Pyridoxine is converted to its biologically active form pyridoxal-5-phosphate (P5P) by the enzyme pyridox(am)ine 5'-phosphate oxidase and serves as a cofactor in nearly 200 reactions in the central nervous system. Pyridox(am)ine 5'-phosphate oxidase deficiency leads to P5P dependent epilepsy, typically a neonatal- or infantile-onset epileptic encephalopathy treatable with P5P or in some cases, pyridoxine. Following identification of retinopathy in a patient with pyridox(am)ine 5'-phosphate oxidase deficiency that was reversible with P5P therapy, we describe the systemic manifestations of pyridox(am)ine 5'-phosphate oxidase deficiency. METHODS A series of six patients with homozygous mutations of PNPO, the gene coding pyridox(am)ine 5'-phosphate oxidase, were evaluated in our center over the course of two years for phenotyping of neurological and systemic manifestations. RESULTS Five of six were born prematurely, three had anemia and failure to thrive, and two had elevated alkaline phosphatase. A movement disorder was observed in two children, and a reversible retinopathy was observed in the most severely affected infant. All patients had neonatal-onset epilepsy and were on a continuum of developmental delay to profound encephalopathy. Electroencephalographic features included background slowing and disorganization, absent sleep features, and multifocal and generalized epileptiform discharges. All the affected probands carried a homozygous PNPO mutation (c.674 G>T, c.686 G>A and c.352G>A). CONCLUSION In addition to the well-described epileptic encephalopathy, pyridox(am)ine 5'-phosphate oxidase deficiency causes a range of neurological and systemic manifestations. A movement disorder, developmental delay, and encephalopathy, as well as retinopathy, anemia, and failure to thrive add to the broadening clinical spectrum of P5P dependent epilepsy.
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Affiliation(s)
- Réjean M. Guerriero
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts,Division of Pediatric and Developmental Neurology, Department of Neurology, Washington University School of Medicine, St. Louis, Missouri,Communications should be addressed to: Dr. Guerriero; Division of Pediatric and Developmental Neurology; Department of Neurology; Washington University School of Medicine; Campus Box 8111; 660 South Euclid Ave; St. Louis, MO 63110.
| | - Archana A. Patel
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Brian Walsh
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Fiona M. Baumer
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ankoor S. Shah
- Department of Ophthalmology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jurriaan M. Peters
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lance H. Rodan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Pankaj B. Agrawal
- Division of Newborn Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts,Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts,Manton Center for Orphan Disease Research, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Phillip L. Pearl
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Masanori Takeoka
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
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21
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Kulikova VV, Morozova EA, Revtovich SV, Kotlov MI, Anufrieva NV, Bazhulina NP, Raboni S, Faggiano S, Gabellieri E, Cioni P, Belyi YF, Mozzarelli A, Demidkina TV. Gene cloning, characterization, and cytotoxic activity of methionine γ-lyase fromClostridium novyi. IUBMB Life 2017; 69:668-676. [DOI: 10.1002/iub.1649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Vitalia V. Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Elena A. Morozova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Svetlana V. Revtovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Mikhail I. Kotlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Natalya V. Anufrieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Natalya P. Bazhulina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
| | - Samanta Raboni
- Department of Food and Drug; University of Parma; Parma Italy
- Institute of Biophysics, National Research Council; Pisa Italy
| | - Serena Faggiano
- Department of Food and Drug; University of Parma; Parma Italy
- Institute of Biophysics, National Research Council; Pisa Italy
| | - Edi Gabellieri
- Institute of Biophysics, National Research Council; Pisa Italy
| | - Patrizia Cioni
- Institute of Biophysics, National Research Council; Pisa Italy
| | - Yury F. Belyi
- Gamaleya Research Institute of Epidemiology and Microbiology, Ministry of Public Health; Moscow Russia
| | - Andrea Mozzarelli
- Department of Food and Drug; University of Parma; Parma Italy
- Institute of Biophysics, National Research Council; Pisa Italy
- National Institute of Biostructures and Biosystems; Rome Italy
| | - Tatyana V. Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Moscow Russia
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22
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Uddin R, Rafi S. Structural and functional characterization of a unique hypothetical protein (WP_003901628.1) of Mycobacterium tuberculosis: a computational approach. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1822-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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23
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Engskog MKR, Ersson L, Haglöf J, Arvidsson T, Pettersson C, Brittebo E. β-N-Methylamino-L-alanine (BMAA) perturbs alanine, aspartate and glutamate metabolism pathways in human neuroblastoma cells as determined by metabolic profiling. Amino Acids 2017; 49:905-919. [PMID: 28161796 PMCID: PMC5383692 DOI: 10.1007/s00726-017-2391-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/28/2017] [Indexed: 12/15/2022]
Abstract
β-Methylamino-L-alanine (BMAA) is a non-proteinogenic amino acid that induces long-term cognitive deficits, as well as an increased neurodegeneration and intracellular fibril formation in the hippocampus of adult rodents following short-time neonatal exposure and in vervet monkey brain following long-term exposure. It has also been proposed to be involved in the etiology of neurodegenerative disease in humans. The aim of this study was to identify metabolic effects not related to excitotoxicity or oxidative stress in human neuroblastoma SH-SY5Y cells. The effects of BMAA (50, 250, 1000 µM) for 24 h on cells differentiated with retinoic acid were studied. Samples were analyzed using LC-MS and NMR spectroscopy to detect altered intracellular polar metabolites. The analysis performed, followed by multivariate pattern recognition techniques, revealed significant perturbations in protein biosynthesis, amino acid metabolism pathways and citrate cycle. Of specific interest were the BMAA-induced alterations in alanine, aspartate and glutamate metabolism and as well as alterations in various neurotransmitters/neuromodulators such as GABA and taurine. The results indicate that BMAA can interfere with metabolic pathways involved in neurotransmission in human neuroblastoma cells.
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Affiliation(s)
- Mikael K R Engskog
- Division of Analytical Pharmaceutical Chemistry, Uppsala University, Box 574, 751 23, Uppsala, Sweden.
| | - Lisa Ersson
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 23, Uppsala, Sweden
| | - Jakob Haglöf
- Division of Analytical Pharmaceutical Chemistry, Uppsala University, Box 574, 751 23, Uppsala, Sweden
| | - Torbjörn Arvidsson
- Division of Analytical Pharmaceutical Chemistry, Uppsala University, Box 574, 751 23, Uppsala, Sweden.,Medical Product Agency, Box 26, Dag Hammarskjölds väg 42, 751 03, Uppsala, Sweden
| | - Curt Pettersson
- Division of Analytical Pharmaceutical Chemistry, Uppsala University, Box 574, 751 23, Uppsala, Sweden
| | - Eva Brittebo
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 23, Uppsala, Sweden
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24
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Korasick DA, Tanner JJ, Henzl MT. Impact of disease-Linked mutations targeting the oligomerization interfaces of aldehyde dehydrogenase 7A1. Chem Biol Interact 2017; 276:31-39. [PMID: 28087462 DOI: 10.1016/j.cbi.2017.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/05/2016] [Accepted: 01/09/2017] [Indexed: 11/24/2022]
Abstract
Aldehyde dehydrogenase 7A1 (ALDH7A1) is involved in lysine catabolism, catalyzing the oxidation of α-aminoadipate semialdehyde to α-aminoadipate. Certain mutations in the ALDH7A1 gene, which are presumed to reduce catalytic activity, cause an autosomal recessive seizure disorder known as pyridoxine-dependent epilepsy (PDE). Although the genetic association between ALDH7A1 and PDE is well established, little is known about the impact of PDE-mutations on the structure and catalytic function of the enzyme. Herein we report the first study of the molecular consequences of PDE mutations using purified ALDH7A1 variants. Eight variants, with mutations in the oligomer interfaces, were expressed in Escherichia coli: P78L, G83E, A129P, G137V, G138V, A149E, G255D, and G263E. All but P78L and G83E were soluble and could be purified. All six soluble mutants were catalytically inactive. The impact of the mutations on oligomerization was assessed by analytical ultracentrifugation. Wild-type ALDH7A1 is shown to exist in a dimer-tetramer equilibrium with a dissociation constant of 16 μM. In contrast to the wild-type enzyme, the variants reside in monomer-dimer equilibria and are apparently incapable of forming a tetrameric species, even at high enzyme concentration. The available evidence suggests that they are misfolded assemblies lacking the three-dimensional structure required for catalysis.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA; Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.
| | - Michael T Henzl
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.
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25
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Caulkins BG, Young RP, Kudla RA, Yang C, Bittbauer T, Bastin B, Hilario E, Fan L, Marsella MJ, Dunn MF, Mueller LJ. NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity. J Am Chem Soc 2016; 138:15214-15226. [PMID: 27779384 PMCID: PMC5129030 DOI: 10.1021/jacs.6b08937] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Indexed: 12/22/2022]
Abstract
Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography-the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry-to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate Cα and positive charge at C4' of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites.
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Affiliation(s)
- Bethany G. Caulkins
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Robert P. Young
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Ryan A. Kudla
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Chen Yang
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Thomas
J. Bittbauer
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Baback Bastin
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Eduardo Hilario
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Li Fan
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Michael J. Marsella
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Michael F. Dunn
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Leonard J. Mueller
- Department of Chemistry, and Department of Biochemistry, University of California, Riverside, California 92521, United States
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26
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Ronda L, Bruno S, Bettati S, Storici P, Mozzarelli A. From protein structure to function via single crystal optical spectroscopy. Front Mol Biosci 2015; 2:12. [PMID: 25988179 PMCID: PMC4428442 DOI: 10.3389/fmolb.2015.00012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 11/23/2022] Open
Abstract
The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.
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Affiliation(s)
- Luca Ronda
- Department of Neurosciences, University of Parma Parma, Italy
| | - Stefano Bruno
- Department of Pharmacy, University of Parma Parma, Italy
| | - Stefano Bettati
- Department of Neurosciences, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy ; Institute of Biophysics, Consiglio Nazionale delle Ricerche Pisa, Italy
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Marchetti M, Bruno S, Campanini B, Bettati S, Peracchi A, Mozzarelli A. Regulation of human serine racemase activity and dynamics by halides, ATP and malonate. Amino Acids 2014; 47:163-73. [PMID: 25331425 DOI: 10.1007/s00726-014-1856-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/09/2014] [Indexed: 02/03/2023]
Abstract
D-Serine is a non-proteinogenic amino acid that acts as a co-agonist of the NMDA receptors in the central nervous system. D-Serine is produced by human serine racemase (hSR), a homodimeric pyridoxal 5'-phosphate (PLP)-dependent enzyme that also catalyzes the physiologically relevant β-elimination of both L- and D-serine to pyruvate and ammonia. After improving the protein purification yield and stability, which had so far limited the biochemical characterization of hSR, we found that the catalytic activity is affected by halides, in the order fluoride > chloride > bromide. On the contrary, iodide elicited a complete inhibition, accompanied by a modulation of the tautomeric equilibrium of the internal aldimine. We also investigated the reciprocal effects of ATP and malonate, an inhibitor that reversibly binds at the active site, 20 Å away from the ATP-binding site. ATP increased ninefold the affinity of hSR for malonate and malonate increased 100-fold that of ATP, confirming an allosteric interaction between the two binding sites. To further investigate this allosteric communication, we probed the active site accessibility by quenching of the coenzyme fluorescence in the absence and presence of ATP. We found that ATP stabilizes a closed conformation of the external aldimine Schiff base, suggesting a possible mechanism for ATP-induced hSR activation.
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Fleischman NM, Das D, Kumar A, Xu Q, Chiu HJ, Jaroszewski L, Knuth MW, Klock HE, Miller MD, Elsliger MA, Godzik A, Lesley SA, Deacon AM, Wilson IA, Toney MD. Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome. Protein Sci 2014; 23:1060-76. [PMID: 24888348 DOI: 10.1002/pro.2493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/27/2014] [Accepted: 05/27/2014] [Indexed: 11/10/2022]
Abstract
Pyridoxal-5'-phosphate or PLP, the active form of vitamin B6, is a highly versatile cofactor that participates in a large number of mechanistically diverse enzymatic reactions in basic metabolism. PLP-dependent enzymes account for ∼1.5% of most prokaryotic genomes and are estimated to be involved in ∼4% of all catalytic reactions, making this an important class of enzymes. Here, we structurally and functionally characterize three novel PLP-dependent enzymes from bacteria in the human microbiome: two are from Eubacterium rectale, a dominant, nonpathogenic, fecal, Gram-positive bacteria, and the third is from Porphyromonas gingivalis, which plays a major role in human periodontal disease. All adopt the Type I PLP-dependent enzyme fold and structure-guided biochemical analysis enabled functional assignments as tryptophan, aromatic, and probable phosphoserine aminotransferases.
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Chitnumsub P, Ittarat W, Jaruwat A, Noytanom K, Amornwatcharapong W, Pornthanakasem W, Chaiyen P, Yuthavong Y, Leartsakulpanich U. The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1517-27. [PMID: 24914963 PMCID: PMC4051499 DOI: 10.1107/s1399004714005598] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/11/2014] [Indexed: 11/10/2022]
Abstract
Plasmodium falciparum serine hydroxymethyltransferase (PfSHMT), an enzyme in the dTMP synthesis cycle, is an antimalarial target because inhibition of its expression or function has been shown to be lethal to the parasite. As the wild-type enzyme could not be crystallized, protein engineering of residues on the surface was carried out. The surface-engineered mutant PfSHMT-F292E was successfully crystallized and its structure was determined at 3 Å resolution. The PfSHMT-F292E structure is a good representation of PfSHMT as this variant revealed biochemical properties similar to those of the wild type. Although the overall structure of PfSHMT is similar to those of other SHMTs, unique features including the presence of two loops and a distinctive cysteine pair formed by Cys125 and Cys364 in the tetrahydrofolate (THF) substrate binding pocket were identified. These structural characteristics have never been reported in other SHMTs. Biochemical characterization and mutation analysis of these two residues confirm that they act as a disulfide/sulfhydryl switch to regulate the THF-dependent catalytic function of the enzyme. This redox switch is not present in the human enzyme, in which the cysteine pair is absent. The data reported here can be further exploited as a new strategy to specifically disrupt the activity of the parasite enzyme without interfering with the function of the human enzyme.
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Affiliation(s)
- Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Wanwipa Ittarat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Krittikar Noytanom
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Watcharee Amornwatcharapong
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Wichai Pornthanakasem
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
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Asakura H, Hashii N, Uema M, Kawasaki N, Sugita-Konishi Y, Igimi S, Yamamoto S. Campylobacter jejuni pdxA affects flagellum-mediated motility to alter host colonization. PLoS One 2013; 8:e70418. [PMID: 23936426 PMCID: PMC3735588 DOI: 10.1371/journal.pone.0070418] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 06/24/2013] [Indexed: 11/18/2022] Open
Abstract
Vitamin B6 (pyridoxal-5'-phosphate, PLP) is linked to a variety of biological functions in prokaryotes. Here, we report that the pdxA (putative 4-hydroxy-L-threonine phosphate dehydrogenase) gene plays a pivotal role in the PLP-dependent regulation of flagellar motility, thereby altering host colonization in a leading foodborne pathogen, Campylobacter jejuni. A C. jejuni pdxA mutant failed to produce PLP and exhibited a coincident loss of flagellar motility. Mass spectrometric analyses showed a 3-fold reduction in the main flagellar glycan pseudaminic acid (Pse) associated with the disruption of pdxA. The pdxA mutant also exhibited reduced growth rates compared with the WT strain. Comparative metabolomic analyses revealed differences in respiratory/energy metabolism between WT C. jejuni and the pdxA mutant, providing a possible explanation for the differential growth fitness between the two strains. Consistent with the lack of flagellar motility, the pdxA mutant showed impaired motility-mediated responses (bacterial adhesion, ERK1/2 activation, and IL-8 production) in INT407 cells and reduced colonization of chickens compared with the WT strain. Overall, this study demonstrated that the pdxA gene affects the PLP-mediated flagellar motility function, mainly through alteration of Pse modification, and the disruption of this gene also alters the respiratory/energy metabolisms to potentially affect host colonization. Our data therefore present novel implications regarding the utility of PLP and its dependent enzymes as potent target(s) for the control of this pathogen in the poultry host.
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Affiliation(s)
- Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, Setagaya-ku, Tokyo, Japan.
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Asymmetry of the active site loop conformation between subunits of glutamate-1-semialdehyde aminomutase in solution. BIOMED RESEARCH INTERNATIONAL 2013; 2013:353270. [PMID: 23984351 PMCID: PMC3747428 DOI: 10.1155/2013/353270] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 06/27/2013] [Indexed: 02/02/2023]
Abstract
Glutamate-1-semialdehyde aminomutase (GSAM) is a dimeric, pyridoxal 5′-phosphate (PLP)- dependent enzyme catalysing in plants and some bacteria the isomerization of L-glutamate-1-semialdehyde to 5-aminolevulinate, a common precursor of chlorophyll, haem, coenzyme B12, and other tetrapyrrolic compounds. During the catalytic cycle, the coenzyme undergoes conversion from pyridoxamine 5′-phosphate (PMP) to PLP. The entrance of the catalytic site is protected by a loop that is believed to switch from an open to a closed conformation during catalysis. Crystallographic studies indicated that the structure of the mobile loop is related to the form of the cofactor bound to the active site, allowing for asymmetry within the dimer. Since no information on structural and functional asymmetry of the enzyme in solution is available in the literature, we investigated the active site accessibility by determining the cofactor fluorescence quenching of PMP- and PLP-GSAM forms. PLP-GSAM is partially quenched by potassium iodide, suggesting that at least one catalytic site is accessible to the anionic quencher and therefore confirming the asymmetry observed in the crystal structure. Iodide induces release of the cofactor from PMP-GSAM, apparently from only one catalytic site, therefore suggesting an asymmetry also in this form of the enzyme in solution, in contrast with the crystallographic data.
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Coquille S, Roux C, Fitzpatrick TB, Thore S. The last piece in the vitamin B1 biosynthesis puzzle: structural and functional insight into yeast 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase. J Biol Chem 2012; 287:42333-43. [PMID: 23048037 DOI: 10.1074/jbc.m112.397240] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vitamin B(1) is essential for all organisms being well recognized as a necessary cofactor for key metabolic pathways such as glycolysis, and was more recently implicated in DNA damage responses. Little is known about the enzyme responsible for the formation of the pyrimidine moiety (4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase). We report a structure-function study of the HMP-P synthase from yeast, THI5p. Our crystallographic structure shows that THI5p is a mix between periplasmic binding proteins and pyridoxal 5'-phosphate-dependent enzymes. Mutational and yeast complementation studies identify the key residues for HMP-P biosynthesis as well as the use of pyridoxal 5'-phosphate as a substrate rather than as a cofactor. Furthermore, we could show that iron binding to HMP-P synthase is essential for the reaction.
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Affiliation(s)
- Sandrine Coquille
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
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Bisht S, Rajaram V, Bharath SR, Kalyani JN, Khan F, Rao AN, Savithri HS, Murthy MRN. Crystal structure of Escherichia coli diaminopropionate ammonia-lyase reveals mechanism of enzyme activation and catalysis. J Biol Chem 2012; 287:20369-81. [PMID: 22505717 PMCID: PMC3370218 DOI: 10.1074/jbc.m112.351809] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/12/2012] [Indexed: 11/06/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize the unique chemistry of a pyridine ring to carry out diverse reactions involving amino acids. Diaminopropionate (DAP) ammonia-lyase (DAPAL) is a prokaryotic PLP-dependent enzyme that catalyzes the degradation of d- and l-forms of DAP to pyruvate and ammonia. Here, we report the first crystal structure of DAPAL from Escherichia coli (EcDAPAL) in tetragonal and monoclinic forms at 2.0 and 2.2 Å resolutions, respectively. Structures of EcDAPAL soaked with substrates were also determined. EcDAPAL has a typical fold type II PLP-dependent enzyme topology consisting of a large and a small domain with the active site at the interface of the two domains. The enzyme is a homodimer with a unique biological interface not observed earlier. Structure of the enzyme in the tetragonal form had PLP bound at the active site, whereas the monoclinic structure was in the apo-form. Analysis of the apo and holo structures revealed that the region around the active site undergoes transition from a disordered to ordered state and assumes a conformation suitable for catalysis only upon PLP binding. A novel disulfide was found to occur near a channel that is likely to regulate entry of ligands to the active site. EcDAPAL soaked with dl-DAP revealed density at the active site appropriate for the reaction intermediate aminoacrylate, which is consistent with the observation that EcDAPAL has low activity under crystallization conditions. Based on the analysis of the structure and results of site-directed mutagenesis, a two-base mechanism of catalysis involving Asp(120) and Lys(77) is suggested.
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Affiliation(s)
| | | | | | | | - Farida Khan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Appaji N. Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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Saenko SV, Jerónimo MA, Beldade P. Genetic basis of stage-specific melanism: a putative role for a cysteine sulfinic acid decarboxylase in insect pigmentation. Heredity (Edinb) 2012; 108:594-601. [PMID: 22234245 DOI: 10.1038/hdy.2011.127] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Melanism, the overall darkening of the body, is a widespread form of animal adaptation to particular environments, and includes bookcase examples of evolution by natural selection, such as industrial melanism in the peppered moth. The major components of the melanin biosynthesis pathway have been characterized in model insects, but little is known about the genetic basis of life-stage specific melanism such as cases described in some lepidopteran species. Here, we investigate two melanic mutations of Bicyclus anynana butterflies, called Chocolate and melanine, that exclusively affect pigmentation of the larval and adult stages, respectively. Our analysis of Mendelian segregation patterns reveals that the larval and adult melanic phenotypes are due to alleles at different, independently segregating loci. Our linkage mapping analysis excludes the pigmentation candidate gene black as the melanine locus, and implicates a gene encoding a putative pyridoxal phosphate-dependant cysteine sulfinic acid decarboxylase as the Chocolate locus. We show variation in coding sequence and in expression levels for this candidate larval melanism locus. This is the first study that suggests a biological function for this gene in insects. Our findings open up exciting opportunities to study the role of this locus in the evolution of adaptive variation in pigmentation, and the uncoupling of regulation of pigment biosynthesis across developmental stages with different ecologies and pressures on body coloration.
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Affiliation(s)
- S V Saenko
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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Moccand C, Kaufmann M, Fitzpatrick TB. It takes two to tango: defining an essential second active site in pyridoxal 5'-phosphate synthase. PLoS One 2011; 6:e16042. [PMID: 21283685 PMCID: PMC3024981 DOI: 10.1371/journal.pone.0016042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 12/09/2010] [Indexed: 11/24/2022] Open
Abstract
The prevalent de novo biosynthetic pathway of vitamin B6 involves only two enzymes (Pdx1 and Pdx2) that form an ornate multisubunit complex functioning as a glutamine amidotransferase. The synthase subunit, Pdx1, utilizes ribose 5-phosphate and glyceraldehyde 3-phosphate, as well as ammonia derived from the glutaminase activity of Pdx2 to directly form the cofactor vitamer, pyridoxal 5′-phosphate. Given the fact that a single enzyme performs the majority of the chemistry behind this reaction, a complicated mechanism is anticipated. Recently, the individual steps along the reaction co-ordinate are beginning to be unraveled. In particular, the binding of the pentose substrate and the first steps of the reaction have been elucidated but it is not known if the latter part of the chemistry, involving the triose sugar, takes place in the same or a disparate site. Here, we demonstrate through the use of enzyme assays, enzyme kinetics, and mutagenesis studies that indeed a second site is involved in binding the triose sugar and moreover, is the location of the final vitamin product, pyridoxal 5′-phosphate. Furthermore, we show that product release is triggered by the presence of a PLP-dependent enzyme. Finally, we provide evidence that a single arginine residue of the C terminus of Pdx1 is responsible for coordinating co-operativity in this elaborate protein machinery.
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Affiliation(s)
- Cyril Moccand
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Markus Kaufmann
- Bio-Molecular Analysis Platform, University of Geneva, Geneva, Switzerland
| | - Teresa B. Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- * E-mail:
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Dick T, Manjunatha U, Kappes B, Gengenbacher M. Vitamin B6 biosynthesis is essential for survival and virulence of Mycobacterium tuberculosis. Mol Microbiol 2010; 78:980-8. [PMID: 20815826 DOI: 10.1111/j.1365-2958.2010.07381.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
With 500000 cases of multidrug-resistant tuberculosis there is an urgent need for attractive targets to enable the discovery of novel antimycobacterials. The biosynthesis of essential cofactors is of particular interest as these pathways are absent in man and their inhibition is expected to affect the metabolism of Mycobacterium tuberculosis at multiple sites. Our data demonstrate that the pathogen synthesizes pyridoxal 5-phosphate (PLP), the bioactive form of vitamin B6, by a heteromeric PLP synthase composed of Pdx1 (Rv2606c) and Pdx2 (Rv2604c). Disruption of the pdx1 gene generated a strictly B6 auxotrophic M. tuberculosis mutant, Δpdx1. Removal of the cofactor during exponential growth or stationary phase demonstrated the essentiality of vitamin B6 biosynthesis for growth and survival of the pathogen in culture. In a tuberculosis dormancy model based on gradual oxygen depletion, de novo biosynthesis of PLP was required for regrowth of the bacillus after direct oxygen exposure. The Δpdx1 mutant showed a severe growth defect in immunocompetent mice: bacilli applied intranasally failed to persist in host tissues and were quickly cleared. We conclude that vitamin B6 biosynthesis is required for survival of M. tuberculosis in vivo and thus might represent a candidate pathway for the development of new antitubercular agents.
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Affiliation(s)
- Thomas Dick
- Novartis Institute for Tropical Diseases Pte. Ltd., 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore
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Derrer B, Windeisen V, Guédez Rodríguez G, Seidler J, Gengenbacher M, Lehmann WD, Rippe K, Sinning I, Tews I, Kappes B. Defining the structural requirements for ribose 5-phosphate-binding and intersubunit cross-talk of the malarial pyridoxal 5-phosphate synthase. FEBS Lett 2010; 584:4169-74. [PMID: 20837012 DOI: 10.1016/j.febslet.2010.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 07/23/2010] [Accepted: 09/02/2010] [Indexed: 11/28/2022]
Abstract
Most organisms synthesise the B(6) vitamer pyridoxal 5-phosphate (PLP) via the glutamine amidotransferase PLP synthase, a large enzyme complex of 12 Pdx1 synthase subunits with up to 12 Pdx2 glutaminase subunits attached. Deletion analysis revealed that the C-terminus has four distinct functionalities: assembly of the Pdx1 monomers, binding of the pentose substrate (ribose 5-phosphate), formation of the reaction intermediate I(320), and finally PLP synthesis. Deletions of distinct C-terminal regions distinguish between these individual functions. PLP formation is the only function that is conferred to the enzyme by the C-terminus acting in trans, explaining the cooperative nature of the complex.
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Affiliation(s)
- Bianca Derrer
- University Hospital Heidelberg, Department of Infectious Diseases, Parasitology, Heidelberg, Germany
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López C, Ríos SD, López-Santín J, Caminal G, Álvaro G. Immobilization of PLP-dependent enzymes with cofactor retention and enhanced stability. Biochem Eng J 2010. [DOI: 10.1016/j.bej.2010.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Ozaki S, Nakahara A, Sakaguchi C. Mutagenesis of Gln-142 and Phe-143 of O-Acetylserine Sulfhydrylase. ACTA ACUST UNITED AC 2009. [DOI: 10.3923/ajb.2009.117.124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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40
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Maenpuen S, Sopitthummakhun K, Yuthavong Y, Chaiyen P, Leartsakulpanich U. Characterization of Plasmodium falciparum serine hydroxymethyltransferase-A potential antimalarial target. Mol Biochem Parasitol 2009; 168:63-73. [PMID: 19591881 DOI: 10.1016/j.molbiopara.2009.06.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Revised: 06/02/2009] [Accepted: 06/25/2009] [Indexed: 10/20/2022]
Abstract
Serine hydroxymethyltransferase (SHMT) is a ubiquitous enzyme required for folate recycling and dTMP synthesis. A cDNA encoding Plasmodium falciparum (Pf) SHMT was expressed as a hexa-histidine tagged protein in Escherichia coli BL21-CodonPlus (DE3)-RIL. The protein was purified and the process yielded 3.6 mg protein/l cell culture. Recombinant His(6)-tagged PfSHMT exhibits a visible spectrum characteristic of pyridoxal-5'-phosphate enzyme and catalyzes the reversible conversion of l-serine and tetrahydrofolate (H(4)folate) to glycine and 5,10-methylenetetrahydrofolate (CH(2)-H(4)folate). Steady-state kinetics study indicates that His(6)-tagged PfSHMT catalyzes the reaction by a ternary-complex mechanism. The sequence of substrate binding to the enzyme was also examined by glycine product inhibition. A striking property that is unique for His(6)-tagged PfSHMT is the ability to use D-serine as a substrate in the folate-dependent serine-glycine conversion. Kinetic data in combination with expression result support the proposal of SHMT reaction being a regulatory step for dTMP cycle. This finding suggests that PfSHMT can be a potential target for antimalarial chemotherapy.
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Affiliation(s)
- Somchart Maenpuen
- Department of Biochemistry and Center for Excellence in Protein Structure & Function, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
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Murakami T, Maeda T, Yokota A, Wada M. Gene cloning and expression of pyridoxal 5'-phosphate-dependent L-threo-3-hydroxyaspartate dehydratase from Pseudomonas sp. T62, and characterization of the recombinant enzyme. J Biochem 2009; 145:661-8. [PMID: 19193709 DOI: 10.1093/jb/mvp023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
L-threo-3-Hydroxyaspartate dehydratase (L-THA DH, EC 4.3.1.16), which catalyses the cleavage of L-threo-3-hydroxyaspartate (L-THA) to oxalacetate and ammonia, has been purified from the soil bacterium Pseudomonas sp. T62. In this report, the gene encoding L-THA DH was cloned and expressed in Escherichia coli, and the gene product was purified and characterized in detail. A 957-bp nucleotide fragment was confirmed to be the gene encoding L-THA DH, based on the agreement of internal amino acid sequences. The deduced amino acid sequence, which belongs to the serine/threonine dehydratase family, shows similarity to YKL218c from Saccharomyces cerevisiae (64%), serine racemase from Schizosaccharomyces pombe (64%) and Mus musculus (36%), and biodegradative threonine dehydratase from E. coli (38%). Site-directed mutagenesis experiments revealed that lysine at position 53 is an important residue for enzymatic activity. This enzyme exhibited dehydratase activity specific only to L-THA [K(m) = 0.54 mM, V(max) = 39.0 micromol min(-1) (mg protein)(-1)], but not to other 3-hydroxyaspartate isomers, and exhibited no detectable serine/aspartate racemase activity. This is the first report of an amino acid sequence of the bacterial enzyme that acts on L-THA.
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Affiliation(s)
- Tomoko Murakami
- Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Yamauchi T, Goto M, Wu HY, Uo T, Yoshimura T, Mihara H, Kurihara T, Miyahara I, Hirotsu K, Esaki N. Serine Racemase with Catalytically Active Lysinoalanyl Residue*. ACTA ACUST UNITED AC 2009; 145:421-4. [DOI: 10.1093/jb/mvp010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Ruiz A, García-Villoria J, Ormazabal A, Zschocke J, Fiol M, Navarro-Sastre A, Artuch R, Vilaseca MA, Ribes A. A new fatal case of pyridox(am)ine 5'-phosphate oxidase (PNPO) deficiency. Mol Genet Metab 2008; 93:216-8. [PMID: 18024216 DOI: 10.1016/j.ymgme.2007.10.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 10/02/2007] [Accepted: 10/02/2007] [Indexed: 11/20/2022]
Abstract
We present a patient with severe pyridox(am)ine 5'-phosphate oxidase deficiency and homozygosity for a novel nonsense-mutation, p.A174X, in the PNPO gene who died with pyridoxal phosphate (PLP) treatment despite initial clinical recovery. He presented neonatally, with the classical clinical symptoms of the disease. Increase of urinary vanillactate was the first biochemical factor of alert. Amino acid and neurotransmitter analysis in CSF indicated reduced activity of several PLP-dependent enzymes. The diagnosis was confirmed by mutational studies. From this and the other reported patients it may be concluded that the administration of PLP should not be delayed until the complete biochemical evidence is obtained.
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Affiliation(s)
- Angeles Ruiz
- Department of Pediatrics, Hospital Son Dureta, Palma de Mallorca, Spain
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