1
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Gnanapragasam A, Kirbizakis E, Li A, White KH, Mortenson KL, Cavalcante de Moura J, Jawhar W, Yan Y, Falter R, Russett C, Giannias B, Camilleri-Broët S, Bertos N, Cools-Lartigue J, Garzia L, Sangwan V, Ferri L, Zhang X, Bailey SD. HiChIP-Based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 That Confers Genetic Susceptibility to Gastroesophageal Cancer. Cancer Res 2024; 84:2377-2389. [PMID: 38748784 PMCID: PMC11247317 DOI: 10.1158/0008-5472.can-23-2397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 02/01/2024] [Accepted: 05/08/2024] [Indexed: 07/16/2024]
Abstract
Genome-wide association studies (GWAS) have identified more than a hundred single nucleotide variants (SNV) associated with the risk of gastroesophageal cancer (GEC). The majority of the identified SNVs map to noncoding regions of the genome. Uncovering the causal SNVs and genes they modulate could help improve GEC prevention and treatment. Herein, we used HiChIP against histone 3 lysine 27 acetylation (H3K27ac) to simultaneously annotate active promoters and enhancers, identify the interactions between them, and detect nucleosome-free regions (NFR) harboring potential causal SNVs in a single assay. The application of H3K27ac HiChIP in GEC relevant models identified 61 potential functional SNVs that reside in NFRs and interact with 49 genes at 17 loci. The approach led to a 67% reduction in the number of SNVs in linkage disequilibrium at these 17 loci, and at 7 loci, a single putative causal SNV was identified. One SNV, rs147518036, located within the promoter of the UDP-glucuronate decarboxylase 1 (UXS1) gene, seemed to underlie the GEC risk association captured by the rs75460256 index SNV. The rs147518036 SNV creates a GABPA DNA recognition motif, resulting in increased promoter activity, and CRISPR-mediated inhibition of the UXS1 promoter reduced the viability of the GEC cells. These findings provide a framework that simplifies the identification of potentially functional regulatory SNVs and target genes underlying risk-associated loci. In addition, the study implicates increased expression of the enzyme UXS1 and activation of its metabolic pathway as a predisposition to gastric cancer, which highlights potential therapeutic avenues to treat this disease. Significance: Epigenomic footprinting using a histone posttranslational modification targeted 3D genomics methodology elucidates functional noncoding sequence variants and their target genes at cancer risk loci.
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Affiliation(s)
- Ansley Gnanapragasam
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Eftyhios Kirbizakis
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Anna Li
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Kyle H White
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
| | | | - Juliana Cavalcante de Moura
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Wajih Jawhar
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Surgery, McGill University, Montreal, Canada
| | - Yifei Yan
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Reilly Falter
- Department of Experimental Medicine, McGill University, Montreal, Canada
| | - Colleen Russett
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Betty Giannias
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Sophie Camilleri-Broët
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Nicholas Bertos
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Jonathan Cools-Lartigue
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
| | - Livia Garzia
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
- Department of Surgery, McGill University, Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
| | - Veena Sangwan
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
| | - Lorenzo Ferri
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
| | - Xiaoyang Zhang
- Department of Experimental Medicine, McGill University, Montreal, Canada
| | - Swneke D Bailey
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
- Department of Surgery, McGill University, Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
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Rustad CF, Backe PH, Jin C, Merckoll E, Tveten K, Maciej‐Hulme ML, Karlsson N, Prescott T, Sand ES, Woldseth B, Elgstøen KBP, Holla ØL. A monoallelic UXS1 variant associated with short-limbed short stature. Mol Genet Genomic Med 2024; 12:e2472. [PMID: 38860481 PMCID: PMC11165340 DOI: 10.1002/mgg3.2472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/15/2024] [Accepted: 05/14/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Serine residues in the protein backbone of heavily glycosylated proteoglycans are bound to glycosaminoglycans through a tetrasaccharide linker. UXS1 encodes UDP-glucuronate decarboxylase 1, which catalyzes synthesis of UDP-xylose, the donor of the first building block in the linker. Defects in other enzymes involved in formation of the tetrasaccharide linker cause so-called linkeropathies, characterized by short stature, radio-ulnar synostosis, decreased bone density, congenital contractures, dislocations, and more. METHODS Whole exome sequencing was performed in a father and son who presented with a mild skeletal dysplasia, as well as the father's unaffected parents. Wild-type and mutant UXS1 were recombinantly expressed in Escherichia coli and purified. Enzyme activity was evaluated by LC-MS/MS. In vivo effects were studied using HeparinRed assay and metabolomics. RESULTS The son had short long bones, normal epiphysis, and subtle metaphyseal changes especially in his legs. The likely pathogenic heterozygous variant NM_001253875.1(UXS1):c.557T>A p.(Ile186Asn) detected in the son was de novo in the father. Purified Ile186Asn-UXS1, in contrast to the wild-type, was not able to convert UDP-glucuronic acid to UDP-xylose. Plasma glycosaminoglycan levels were decreased in both son and father. CONCLUSION This is the first report linking UXS1 to short-limbed short stature in humans.
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Affiliation(s)
| | - Paul Hoff Backe
- Department of MicrobiologyOslo University Hospital HF, RikshospitaletOsloNorway
- Department of Medical Biochemistry, Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Chunsheng Jin
- Proteomics Core Facility at Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | | | - Kristian Tveten
- Department of Medical GeneticsTelemark Hospital TrustSkienNorway
| | | | - Niclas Karlsson
- Department of Life Sciences and HealthOslo Metropolitan UniversityOsloNorway
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Trine Prescott
- Department of Medical GeneticsTelemark Hospital TrustSkienNorway
| | - Elise Sandås Sand
- Department of Medical BiochemistryOslo University HospitalOsloNorway
| | - Berit Woldseth
- Department of Medical BiochemistryOslo University HospitalOsloNorway
| | | | - Øystein L. Holla
- Department of Medical GeneticsTelemark Hospital TrustSkienNorway
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3
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Simons ME, Narindoshvili T, Raushel FM. Biosynthesis of UDP-β-l-Arabinofuranoside for the Capsular Polysaccharides of Campylobacter jejuni. Biochemistry 2023; 62:3012-3019. [PMID: 37737649 PMCID: PMC10615251 DOI: 10.1021/acs.biochem.3c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/05/2023] [Indexed: 09/23/2023]
Abstract
Campylobacter jejuni is the leading cause of food poisoning in North America and Europe. The exterior surface of this bacterium is coated with a capsular polysaccharide (CPS) which enables adherence to the host epithelial cells and evasion of the host immune system. Many strains of C. jejuni can be differentiated from one another by changes in the sequence of the carbohydrates found within the CPS. The CPS structures of serotypes HS:15 and HS:41 of C. jejuni were chemically characterized and found to contain an l-arabinofuranoside moiety in the repeating CPS sequence. Sequence similarity and genome neighborhood networks were used to identify the putative gene cluster within the HS:15 serotype for the biosynthesis of the l-arabinofuranoside fragment. The first enzyme (HS:15.18) in the pathway was found to catalyze the NAD+-dependent oxidation of UDP-α-d-glucose to UDP-α-d-glucuronate, while the second enzyme (HS:15.19) catalyzes the NAD+-dependent decarboxylation of this product to form UDP-α-d-xylose. The UDP-α-d-xylose is then epimerized at C4 by the third enzyme (HS:15.17) to produce UDP-β-l-arabinopyranoside. In the last step, HS:15.16 catalyzes the FADH2-dependent conversion of UDP-β-l-arabinopyranoside into UDP-β-l-arabinofuranoside. The UDP-β-l-arabinopyranoside mutase catalyzed reaction was further interrogated by measurement of a positional isotope exchange reaction within [18O]-UDP-β-l-arabinopyranoside.
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Affiliation(s)
- Max Errickson Simons
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77842, United States
| | - Tamari Narindoshvili
- Department
of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Frank M. Raushel
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77842, United States
- Department
of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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4
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Huang CY, Loo DM, Gu W. Modeling of glycosaminoglycan biosynthesis in intervertebral disc cells. Comput Biol Med 2023; 162:107039. [PMID: 37295387 DOI: 10.1016/j.compbiomed.2023.107039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 05/05/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
Loss of proteoglycan (PG) is a potential factor responsible for degeneration of the intervertebral disc (IVD). PG consists of a core protein with covalently attached glycosaminoglycan (GAG) chains. The objective of this study was to develop a mathematical model of GAG biosynthesis to investigate the effects of glycolytic enzymes on GAG biosynthesis of IVD cells. A new mathematical model of GAG biosynthesis was developed for IVD cells by incorporating biosynthesis of uridine diphosphate-sugars into the glycolytic pathway. This new model showed good agreement between the model predictions of intracellular ATP content and GAG biosynthesis and experimental data measured at different external glucose levels. The quantitative analyses demonstrated that GAG biosynthesis may be sensitive to the activities of hexokinase (HK) and phosphofructokinase (PFK), especially at low glucose supply, with GAG biosynthesis being significantly enhanced by a slight increase in activities of HK and PFK. This suggests that metabolic reprogramming could be a potential strategy for promoting PG biosynthesis in IVD cells. Furthermore, it was shown that GAG biosynthesis may be promoted by increasing intracellular glutamine concentration or activity of glutamine:fructose-6-phosphate amidotransferase in the hexamine pathway. This study provides a better understanding of the relationship between glycolysis and PG biosynthesis in IVD cells. The theoretical framework developed in this study is useful for studying the role of glycolysis in disc degeneration and developing new preventive and treatment strategies for degeneration of the IVD.
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Affiliation(s)
- Chun-Yuh Huang
- Department of Biomedical Engineering, University of Miami, Coral Gables, FL, USA.
| | - Daniela M Loo
- Department of Biomedical Engineering, University of Miami, Coral Gables, FL, USA
| | - Weiyong Gu
- Department of Mechanical and Aerospace Engineering, University of Miami, Coral Gables, FL, USA
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5
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Dulin CC, Sharma P, Frigo L, Voehler MW, Iverson TM, Bachmann BO. EvdS6 is a bifunctional decarboxylase from the everninomicin gene cluster. J Biol Chem 2023:104893. [PMID: 37286037 PMCID: PMC10338323 DOI: 10.1016/j.jbc.2023.104893] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023] Open
Abstract
The everninomicins are bacterially produced antibiotic octasaccharides characterized by the presence of two interglycosidic spirocyclic ortho-δ-lactone (orthoester) moieties. The terminating G- and H-ring sugars, L-lyxose and C-4 branched sugar β-D-eurekanate, are proposed to be biosynthetically derived from nucleotide diphosphate pentose sugar pyranosides; however, the identity of these precursors and their biosynthetic origin remain to be determined. Herein we identify a new glucuronic acid decarboxylase from Micromonospora belonging to the superfamily of short-chain dehydrogenase/reductase enzymes, EvdS6. Biochemical characterization demonstrated that EvdS6 is an NAD+-dependent bifunctional enzyme that produces a mixture of two products, differing in the sugar C-4 oxidation state. This product distribution is atypical for glucuronic acid decarboxylating enzymes, most of which favor production of the reduced sugar and a minority of which favor release of the oxidized product. Spectroscopic and stereochemical analysis of reaction products revealed that the first product released is the oxidatively produced 4-keto-D-xylose and the second product is the reduced D-xylose. X-ray crystallographic analysis of EvdS6 at 1.51 Å resolution with bound co-factor and TDP demonstrated that the overall geometry of the EvdS6 active site is conserved with other SDR enzymes and enabled studies probing structural determinants for the reductive half of the net neutral catalytic cycle. Critical active site threonine and aspartate residues were unambiguously identified as essential in the reductive step of the reaction and resulted in enzyme variants producing almost exclusively the keto sugar. This work defines potential precursors for the G-ring L-lyxose and resolves likely origins of the H-ring β-D-eurekanate sugar precursor.
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Affiliation(s)
- Callie C Dulin
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Laura Frigo
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Markus W Voehler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
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6
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Borg AJE, Esquivias O, Coines J, Rovira C, Nidetzky B. Enzymatische C4-Epimerisierung von UDP-Glucuronsäure: präzise gesteuerte Rotation eines transienten 4-Ketointermediats für eine invertierende Reaktion ohne Decarboxylierung. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202211937. [PMID: 38515538 PMCID: PMC10952283 DOI: 10.1002/ange.202211937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Indexed: 03/23/2024]
Abstract
AbstractUDP‐Glucuronsäure(UDP‐GlcA)‐4‐Epimerase repräsentiert eine wichtige Fragestellung in der Enzymkatalyse: die Balance zwischen konformativer Flexibilität und genauer Positionierung. Das Enzym koordiniert die C4‐Oxidation des Substrats durch NAD+ mit der Rotation eines leicht decarboxylierbaren β‐Ketosäure‐Intermediats im aktiven Zentrum zur Ermöglichung der stereoinvertierenden Reduktion der Ketogruppe durch NADH. Wir zeigen hier die nur schwer erfassbare Rotationskoordinate des 4‐Ketointermediats. Distorsion des Zuckerrings in eine Boot‐Konformation erzeugt torsionale Mobilität in der Bindungstasche des Enzyms. Die Endpunkte der Rotation zeigen den 4‐Ketozucker in einer unverformten 4C1‐Sesselkonformation. Die äquatorial positionierte Carboxylatgruppe ist ungünstig für die 4‐Ketozucker‐Decarboxylierung. Varianten der Epimerase zeigen Decarboxylierung, wenn sie die Bindung mit der Carboxylatgruppe im entgegengesetzten Rotationsisomer des Substrats entfernen. R185A/D‐Substitutionen wandeln die Epimerase in UDP‐Xylose‐Synthasen um, welche UDP‐GlcA in stereospezifischen, konfigurationserhaltenden Reaktionen decarboxylieren.
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Affiliation(s)
- Annika J. E. Borg
- Institut für Biotechnologie und BioprozesstechnikTechnische Universität GrazPetersgasse 12/18010GrazÖsterreich
| | - Oriol Esquivias
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
| | - Joan Coines
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
- Derzeitige Adresse: Nostrum BiodiscoveryAv. De Josep Tarradellas, 8–1008029BarcelonaSpanien
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry)Institute of Computational and Theoretical Chemistry (IQTCUB)Martí i Franquès 108028BarcelonaSpanien
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Passeig Lluís Companys, 2308010BarcelonaSpanien
| | - Bernd Nidetzky
- Institut für Biotechnologie und BioprozesstechnikTechnische Universität GrazPetersgasse 12/18010GrazÖsterreich
- Austrian Center of Industrial Biotechnology (acib)Krenngasse 378010GrazÖsterreich
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7
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Borg AJE, Esquivias O, Coines J, Rovira C, Nidetzky B. Enzymatic C4-Epimerization of UDP-Glucuronic Acid: Precisely Steered Rotation of a Transient 4-Keto Intermediate for an Inverted Reaction without Decarboxylation. Angew Chem Int Ed Engl 2023; 62:e202211937. [PMID: 36308301 PMCID: PMC10107529 DOI: 10.1002/anie.202211937] [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: 08/12/2022] [Revised: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
UDP-glucuronic acid (UDP-GlcA) 4-epimerase illustrates an important problem regarding enzyme catalysis: balancing conformational flexibility with precise positioning. The enzyme coordinates the C4-oxidation of the substrate by NAD+ and rotation of a decarboxylation-prone β-keto acid intermediate in the active site, enabling stereoinverting reduction of the keto group by NADH. We reveal the elusive rotational landscape of the 4-keto intermediate. Distortion of the sugar ring into boat conformations induces torsional mobility in the enzyme's binding pocket. The rotational endpoints show that the 4-keto sugar has an undistorted 4 C1 chair conformation. The equatorially placed carboxylate group disfavors decarboxylation of the 4-keto sugar. Epimerase variants lead to decarboxylation upon removal of the binding interactions with the carboxylate group in the opposite rotational isomer of the substrate. Substitutions R185A/D convert the epimerase into UDP-xylose synthases that decarboxylate UDP-GlcA in stereospecific, configuration-retaining reactions.
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Affiliation(s)
- Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010, Graz, Austria
| | - Oriol Esquivias
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain
| | - Joan Coines
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain.,Present address: Nostrum Biodiscovery, Av. De Josep Tarradellas, 8-10, 08029, Barcelona, Spain
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry (Section of Organic Chemistry), Institute of Computational and Theoretical Chemistry (IQTCUB), Martí i Franquès 1, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010, Graz, Austria.,Austrian Center of Industrial Biotechnology (acib), Krenngasse 37, 8010, Graz, Austria
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8
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Comparative Transcriptome Analysis on the Regulatory Mechanism of Thoracic Ganglia in Eriocheir sinensis at Post-Molt and Inter-Molt Stages. Life (Basel) 2022; 12:life12081181. [PMID: 36013360 PMCID: PMC9409648 DOI: 10.3390/life12081181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/07/2022] [Accepted: 07/14/2022] [Indexed: 11/25/2022] Open
Abstract
Eriocheir sinensis is an aquatic species found distributed worldwide. It is found in the Yangtze River of China, where the commercial fishing of this valuable catadromous aquatic species has been banned. As an important member of the phylum Arthropoda, E. sinensis grows by molting over its whole lifespan. The central nervous system of Eriocheir sinensis plays an important regulatory role in molting growth. Nevertheless, there are no reports on the regulatory mechanisms of the nervous system in E. sinensis during the molting cycle. In this study, a comparative transcriptome analysis of E. sinensis thoracic ganglia at post-molt and inter-molt stages was carried out for the first time to reveal the key regulatory pathways and functional genes operating at the post-molt stage. The results indicate that pathways and regulatory genes related to carapace development, tissue regeneration, glycolysis and lipolysis and immune and anti-stress responses were significantly differentially expressed at the post-molt stage. The results of this study lay a theoretical foundation for research on the regulatory network of the E. sinensis nervous system during the post-molt developmental period. Detailed knowledge of the regulatory network involved in E. sinensis molting can be used as a basis for breeding improved E. sinensis species, recovery of the wild E. sinensis population and prosperous development of the E. sinensis artificial breeding industry.
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9
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Wang Y, Li X, Wei J, Zhang X, Liu Y. Mechanism of Sugar Ring Contraction and Closure Catalyzed by UDP-d-apiose/UDP-d-xylose Synthase (UAXS). J Chem Inf Model 2022; 62:632-646. [PMID: 35043627 DOI: 10.1021/acs.jcim.1c01408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Uridine diphosphate (UDP)-apiose/UDP-xylose synthase (UAXS) is a member of the short-chain dehydrogenase/reductase superfamily (SDR), which catalyzes the ring contraction and closure of UDP-d-glucuronic acid (UDP-GlcA), affording UDP-apiose and UDP-xylose. UAXS is a special enzyme that integrates ring-opening, decarboxylation, rearrangement, and ring closure/contraction in a single active site. Recently, the ternary complex structure of UAXS was crystallized from Arabidopsis thaliana. In this work, to gain insights into the detailed formation mechanism of UDP-apiose and UDP-xylose, an enzyme-substrate reactant model has been constructed and quantum mechanical/molecular mechanical (QM/MM) calculations have been performed. Our calculation results reveal that the reaction starts from the C4-OH oxidation, which is accompanied by the conformational transformation of the sugar ring from chair type to boat type. The sugar ring-opening is prior to decarboxylation, and the deprotonation of the C2-OH group is the prerequisite for sugar ring-opening. Moreover, the keto-enol tautomerization of the decarboxylated intermediate is a necessary step for ring closure/contraction. Based on our calculation results, more UDP-apiose product was expected, which is in line with the experimental observation. Three titratable residues, Tyr185, Cys100, and Cys140, steer the reaction by proton transfer from or to UDP-GlcA, and Arg182, Glu141, and D337 constitute a proton conduit for sugar C2-OH deprotonation. Although Thr139 and Tyr105 are not directly involved in the enzymatic reaction, they are responsible for promoting the catalysis by forming hydrogen-bonding interactions with GlcA. Our calculations may provide useful information for understanding the catalysis of the SDR family.
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Affiliation(s)
- Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xue Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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10
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Song H, Zhao G, Zhang M, Bi R, Meng X, Song J, Wang B, Liu J, Liu L, Lyu Y, Zhang X. Optimization of the UDP-Xyl biocatalytic synthesis from Crassostrea gigas by orthogonal design method. Protein Expr Purif 2021; 190:106002. [PMID: 34666163 DOI: 10.1016/j.pep.2021.106002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 08/25/2021] [Accepted: 10/14/2021] [Indexed: 10/20/2022]
Abstract
UDP-Xyl, a nucleotide sugar involved in the biosynthesis of various glycoconjugates, is difficult to obtain and quite expensive. Biocatalysis using a one-pot multi-enzyme cascade is one of the most valuable biotransformation processes widely used in the industry. Herein, two enzymes, UDP-glucose (UDP-Glc) dehydrogenase (CGIUGD) and UDP-Xyl synthase (CGIUXS) from the Pacific oyster Crassostrea gigas, which are coupled together for the biotransformation of UDP-Xyl, were characterized. The optimum pH was determined to be pH 9.0 for CGIUGD and pH 7.5 for CGIUXS. Both enzymes showed the highest activity at 37 °C. Neither enzyme is metal ion-dependent. On this basis, a single factor and orthogonal test were applied to optimize the condition of biotransformation of UDP-Xyl from UDP-Glc. Orthogonal design L9 (33) was conducted to optimize processing variables of enzyme amount, pH, and temperature. The conversion of UDP-Xyl was selected as an analysis indicator. Optimum variables were the ratio of CGIUGD to CGIUXS of 2:5, enzymatic pH of 8.0, and temperature of 37 °C, which is confirmed by three repeated validation experiments. The UDP-Xyl conversion was 69.921% in a 1 mL reaction mixture by optimized condition for 1 h. This is the first report for the biosynthesis of UDP-Xyl from oyster enzymes.
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Affiliation(s)
- Huibo Song
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Guihong Zhao
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Ming Zhang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Ruiming Bi
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Xinhui Meng
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Junliu Song
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Bo Wang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Jian Liu
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongmei Lyu
- School of Marine and Bioengineering, Yancheng Institute of Technology, NO 1, Xiwang Road, Yancheng, 224051, China.
| | - Xiaoyang Zhang
- School of Marine and Bioengineering, Yancheng Institute of Technology, NO 1, Xiwang Road, Yancheng, 224051, China.
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11
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Da Costa M, Gevaert O, Van Overtveldt S, Lange J, Joosten HJ, Desmet T, Beerens K. Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering. Biotechnol Adv 2021; 48:107705. [PMID: 33571638 DOI: 10.1016/j.biotechadv.2021.107705] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/18/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
Short-chain Dehydrogenase/Reductase enzymes that are active on nucleotide sugars (abbreviated as NS-SDR) are of paramount importance in the biosynthesis of rare sugars and glycosides. Some family members have already been extensively characterized due to their direct implication in metabolic disorders or in the biosynthesis of virulence factors. In this review, we combine the knowledge gathered from studies that typically focused only on one NS-SDR activity with an in-depth analysis and overview of all of the different NS-SDR families (169,076 enzyme sequences). Through this structure-based multiple sequence alignment of NS-SDRs retrieved from public databases, we could identify clear patterns in conservation and correlation of crucial residues. Supported by this analysis, we suggest updating and extending the UDP-galactose 4-epimerase "hexagonal box model" to an "heptagonal box model" for all NS-SDR enzymes. This specificity model consists of seven conserved regions surrounding the NDP-sugar substrate that serve as fingerprint for each specificity. The specificity fingerprints highlighted in this review will be beneficial for functional annotation of the large group of NS-SDR enzymes and form a guide for future enzyme engineering efforts focused on the biosynthesis of rare and specialty carbohydrates.
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Affiliation(s)
- Matthieu Da Costa
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Ophelia Gevaert
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Stevie Van Overtveldt
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Joanna Lange
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511, AA, Nijmegen, the Netherlands
| | - Henk-Jan Joosten
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511, AA, Nijmegen, the Netherlands
| | - Tom Desmet
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - Koen Beerens
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
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12
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Fushinobu S. Molecular evolution and functional divergence of UDP-hexose 4-epimerases. Curr Opin Chem Biol 2020; 61:53-62. [PMID: 33171387 DOI: 10.1016/j.cbpa.2020.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 01/08/2023]
Abstract
UDP-glucose 4-epimerase (GalE) catalyzes the interconversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal) and/or the interconversion of UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-N-acetylgalactosamine (UDP-GalNAc) in sugar metabolism. GalEs belong to the short-chain dehydrogenase/reductase superfamily, use a conserved 'transient keto intermediate' mechanism and have variable substrate specificity. GalEs have been classified into three groups based on substrate specificity: group 1 prefers UDP-Glc/Gal, group 3 prefers UDP-GlcNAc/GalNAc, and group 2 has comparable activities for both types of the substrates. The phylogenetic relationship and structural basis for the specificities of GalEs revealed possible molecular evolution of UDP-hexose 4-epimerases in various organisms. Based on the recent advances in studies on GalEs and related enzymes, an updated view of their evolutional diversification is presented.
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Affiliation(s)
- Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan.
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13
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Borg AJE, Beerens K, Pfeiffer M, Desmet T, Nidetzky B. Stereo-electronic control of reaction selectivity in short-chain dehydrogenases: Decarboxylation, epimerization, and dehydration. Curr Opin Chem Biol 2020; 61:43-52. [PMID: 33166830 DOI: 10.1016/j.cbpa.2020.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/18/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022]
Abstract
Sugar nucleotide-modifying enzymes of the short-chain dehydrogenase/reductase type use transient oxidation-reduction by a tightly bound nicotinamide cofactor as a common strategy of catalysis to promote a diverse set of reactions, including decarboxylation, single- or double-site epimerization, and dehydration. Although the basic mechanistic principles have been worked out decades ago, the finely tuned control of reactivity and selectivity in several of these enzymes remains enigmatic. Recent evidence on uridine 5'-diphosphate (UDP)-glucuronic acid decarboxylases (UDP-xylose synthase, UDP-apiose/UDP-xylose synthase) and UDP-glucuronic acid-4-epimerase suggests that stereo-electronic constraints established at the enzyme's active site control the selectivity, and the timing of the catalytic reaction steps, in the conversion of the common substrate toward different products. The mechanistic idea of stereo-electronic control is extended to epimerases and dehydratases that deprotonate the Cα of the transient keto-hexose intermediate. The human guanosine 5'-diphosphate (GDP)-mannose 4,6-dehydratase was recently shown to use a minimal catalytic machinery, exactly as predicted earlier from theoretical considerations, for the β-elimination of water from the keto-hexose species.
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Affiliation(s)
- Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010, Graz, Austria
| | - Koen Beerens
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010, Graz, Austria; Austrian Centre of Industrial Biotechnology (acib), 8010, Graz, Austria
| | - Tom Desmet
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium; Austrian Centre of Industrial Biotechnology (acib), 8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010, Graz, Austria; Austrian Centre of Industrial Biotechnology (acib), 8010, Graz, Austria.
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14
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Borg AJE, Dennig A, Weber H, Nidetzky B. Mechanistic characterization of UDP-glucuronic acid 4-epimerase. FEBS J 2020; 288:1163-1178. [PMID: 32645249 PMCID: PMC7984243 DOI: 10.1111/febs.15478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/22/2020] [Accepted: 07/06/2020] [Indexed: 12/27/2022]
Abstract
UDP-glucuronic acid (UDP-GlcA) is a central precursor in sugar nucleotide biosynthesis and common substrate for C4-epimerases and decarboxylases releasing UDP-galacturonic acid (UDP-GalA) and UDP-pentose products, respectively. Despite the different reactions catalyzed, the enzymes are believed to share mechanistic analogy rooted in their joint membership to the short-chain dehydrogenase/reductase (SDR) protein superfamily: Oxidation at the substrate C4 by enzyme-bound NAD+ initiates the catalytic pathway. Here, we present mechanistic characterization of the C4-epimerization of UDP-GlcA, which in comparison with the corresponding decarboxylation has been largely unexplored. The UDP-GlcA 4-epimerase from Bacillus cereus functions as a homodimer and contains one NAD+ /subunit (kcat = 0.25 ± 0.01 s-1 ). The epimerization of UDP-GlcA proceeds via hydride transfer from and to the substrate's C4 while retaining the enzyme-bound cofactor in its oxidized form (≥ 97%) at steady state and without trace of decarboxylation. The kcat for UDP-GlcA conversion shows a kinetic isotope effect of 2.0 (±0.1) derived from substrate deuteration at C4. The proposed enzymatic mechanism involves a transient UDP-4-keto-hexose-uronic acid intermediate whose formation is rate-limiting overall, and is governed by a conformational step before hydride abstraction from UDP-GlcA. Precise positioning of the substrate in a kinetically slow binding step may be important for the epimerase to establish stereo-electronic constraints in which decarboxylation of the labile β-keto acid species is prevented effectively. Mutagenesis and pH studies implicate the conserved Tyr149 as the catalytic base for substrate oxidation and show its involvement in the substrate positioning step. Collectively, this study suggests that based on overall mechanistic analogy, stereo-electronic control may be a distinguishing feature of catalysis by SDR-type epimerases and decarboxylases active on UDP-GlcA.
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Affiliation(s)
- Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Austria
| | - Alexander Dennig
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Austria.,Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Hansjörg Weber
- Institute of Organic Chemistry, Graz University of Technology, NAWI Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Austria.,Austrian Centre of Industrial Biotechnology, Graz, Austria
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15
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Iacovino LG, Savino S, Borg AJE, Binda C, Nidetzky B, Mattevi A. Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction. J Biol Chem 2020; 295:12461-12473. [PMID: 32661196 DOI: 10.1074/jbc.ra120.014692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/10/2020] [Indexed: 11/06/2022] Open
Abstract
UDP-glucuronic acid is converted to UDP-galacturonic acid en route to a variety of sugar-containing metabolites. This reaction is performed by a NAD+-dependent epimerase belonging to the short-chain dehydrogenase/reductase family. We present several high-resolution crystal structures of the UDP-glucuronic acid epimerase from Bacillus cereus The geometry of the substrate-NAD+ interactions is finely arranged to promote hydride transfer. The exquisite complementarity between glucuronic acid and its binding site is highlighted by the observation that the unligated cavity is occupied by a cluster of ordered waters whose positions overlap the polar groups of the sugar substrate. Co-crystallization experiments led to a structure where substrate- and product-bound enzymes coexist within the same crystal. This equilibrium structure reveals the basis for a "swing and flip" rotation of the pro-chiral 4-keto-hexose-uronic acid intermediate that results from glucuronic acid oxidation, placing the C4' atom in position for receiving a hydride ion on the opposite side of the sugar ring. The product-bound active site is almost identical to that of the substrate-bound structure and satisfies all hydrogen-bonding requirements of the ligand. The structure of the apoenzyme together with the kinetic isotope effect and mutagenesis experiments further outlines a few flexible loops that exist in discrete conformations, imparting structural malleability required for ligand rotation while avoiding leakage of the catalytic intermediate and/or side reactions. These data highlight the double nature of the enzymatic mechanism: the active site features a high degree of precision in substrate recognition combined with the flexibility required for intermediate rotation.
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Affiliation(s)
- Luca Giacinto Iacovino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Simone Savino
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Claudia Binda
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria .,Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Andrea Mattevi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
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16
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Savino S, Borg AJE, Dennig A, Pfeiffer M, de Giorgi F, Weber H, Dubey KD, Rovira C, Mattevi A, Nidetzky B. Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis. Nat Catal 2019; 2:1115-1123. [PMID: 31844840 PMCID: PMC6914363 DOI: 10.1038/s41929-019-0382-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
D-Apiose is a C-branched pentose sugar important for plant cell wall development. Its biosynthesis as UDP-D-apiose involves decarboxylation of the UDP-D-glucuronic acid precursor coupled to pyranosyl-to-furanosyl sugar ring contraction. This unusual multistep reaction is catalyzed within a single active site by UDP-D-apiose/UDP-D-xylose synthase (UAXS). Here, we decipher the UAXS catalytic mechanism based on crystal structures of the enzyme from Arabidopsis thaliana, molecular dynamics simulations expanded by QM/MM calculations, and mutational-mechanistic analyses. Our studies show how UAXS uniquely integrates a classical catalytic cycle of oxidation and reduction by a tightly bound nicotinamide coenzyme with retro-aldol/aldol chemistry for the sugar ring contraction. They further demonstrate that decarboxylation occurs only after the sugar ring opening and identify the thiol group of Cys100 in steering the sugar skeleton rearrangement by proton transfer to and from the C3’. The mechanistic features of UAXS highlight the evolutionary expansion of the basic catalytic apparatus of short-chain dehydrogenases/reductases for functional versatility in sugar biosynthesis.
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Affiliation(s)
- Simone Savino
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Alexander Dennig
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.,Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Francesca de Giorgi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy.,Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Hansjörg Weber
- Institute of Organic Chemistry, Graz University of Technology, NAWI Graz, Stremayrgasse 9, 8010 Graz, Austria
| | - Kshatresh Dutta Dubey
- Department of Inorganic and Organic Chemistry (Organic Chemistry Section) & Institute of Computational and Theoretical Chemistry (IQTCUB), University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry (Organic Chemistry Section) & Institute of Computational and Theoretical Chemistry (IQTCUB), University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Catalan Institution for Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy
| | - Bernd Nidetzky
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.,Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
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17
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Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum. Sci Rep 2019; 9:11081. [PMID: 31366978 PMCID: PMC6668579 DOI: 10.1038/s41598-019-47591-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 07/19/2019] [Indexed: 12/17/2022] Open
Abstract
Infant gut-associated bifidobacteria has a metabolic pathway that specifically utilizes lacto-N-biose I (Gal-β1,3-GlcNAc) and galacto-N-biose (Gal-β1,3-GalNAc) from human milk and mucin glycans. UDP-glucose 4-epimerase (GalE) from Bifidobacterium longum (bGalE) catalyzes epimerization reactions of UDP-Gal into UDP-Glc and UDP-GalNAc into UDP-GlcNAc with the same level of activity that is required to send galacto-hexoses into glycolysis. Here, we determined the crystal structures of bGalE in three ternary complex forms: NAD+/UDP, NAD+/UDP-GlcNAc, and NAD+/UDP-Glc. The broad specificity of bGalE was explained by structural features of the binding pocket for the N-acetyl or C2 hydroxy group of the substrate. Asn200 is located in a pocket of the C2 group, and its side chain adopts different conformations in the complex structures with UDP-Glc and UDP-GlcNAc. On the other side, Cys299 forms a large pocket for the C5 sugar ring atom. The flexible C2 pocket and the large C5 pocket of bGalE are suitable for accommodating both the hydroxy and N-acetyl groups of the substrate during sugar ring rotation in the catalytic cycle. The substrate specificity and active site structure of bGalE were distinct from those of Esherichia coli GalE but similar to those of human GalE.
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18
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Fischer B, Ly TD, Hendig D, Kuhn J, Pécheur EI, Reungoat E, Knabbe C, Faust I. First description of a compensatory xylosyltransferase I induction observed after an antifibrotic UDP-treatment of normal human dermal fibroblasts. Biochem Biophys Res Commun 2019; 512:7-13. [PMID: 30853184 DOI: 10.1016/j.bbrc.2019.02.150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 02/27/2019] [Indexed: 02/06/2023]
Abstract
Fibrosis is a serious health problem often leading to accompanying organ failure. During the manifestation of the disease, an accumulation of different extracellular matrix (ECM) molecules, such as proteoglycans, takes place. There is no appropriate therapeutic option available to heal fibrosis to date. Current research focuses primarily on targets such as the cytokine transforming growth factor-β1 (TGF-β1), which is assumed to be one of the key mediators of fibrosis. Both xylosyltransferase isoforms, XT-I and XT-II, catalyze the rate-limiting step of the proteoglycan biosynthesis. Consequently, inhibiting XT activity could be a promising approach to treat fibrosis. It was shown in earlier studies that nucleotides and nucleosides have anti-fibrotic properties and decrease XT activity in cell-free systems. In contrast, we evaluated the mechanisms beyond an UDP-mediated induction of intracellular XT-activity in normal human dermal fibroblasts (NHDF). The observed pseudo-fibrotic XT increasement could be attributed to a compensation of decreased UDP-glucuronate decarboxylase 1 (UXS1) mRNA expression as well as a diminished intracellular UDP-xylose concentration. In summary, our results describe a so far unknown XT-inductive pathway and show that UDP could be a promising molecule for the development of an anti-fibrotic therapy. Nevertheless, XT activity has to be inhibited in parallel intracellularly.
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Affiliation(s)
- Bastian Fischer
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen, Universitätsklinik der Ruhr-Universität Bochum, Georgstrasse 11, 32545, Bad Oeynhausen, Germany.
| | - Thanh-Diep Ly
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen, Universitätsklinik der Ruhr-Universität Bochum, Georgstrasse 11, 32545, Bad Oeynhausen, Germany
| | - Doris Hendig
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen, Universitätsklinik der Ruhr-Universität Bochum, Georgstrasse 11, 32545, Bad Oeynhausen, Germany
| | - Joachim Kuhn
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen, Universitätsklinik der Ruhr-Universität Bochum, Georgstrasse 11, 32545, Bad Oeynhausen, Germany
| | - Eve-Isabelle Pécheur
- UMR INSERM 1052 / CNRS 5286, CRCL, Centre de Recherche en Cancerologie de Lyon, France
| | - Emma Reungoat
- UMR INSERM 1052 / CNRS 5286, CRCL, Centre de Recherche en Cancerologie de Lyon, France
| | - Cornelius Knabbe
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen, Universitätsklinik der Ruhr-Universität Bochum, Georgstrasse 11, 32545, Bad Oeynhausen, Germany
| | - Isabel Faust
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen, Universitätsklinik der Ruhr-Universität Bochum, Georgstrasse 11, 32545, Bad Oeynhausen, Germany
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19
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Eixelsberger T, Horvat D, Gutmann A, Weber H, Nidetzky B. Reaktion von UDP-Apiose/UDP-Xylose-Synthase mit isotopenmarkierten Substraten: Hinweise auf einen Mechanismus mit gekoppelter Oxidation und Aldolspaltung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Thomas Eixelsberger
- Institut für Biotechnologie und Bioprozesstechnik; Technische Universität Graz; NAWI Graz; Petersgasse 12 8010 Graz Österreich
| | - Doroteja Horvat
- Institut für Biotechnologie und Bioprozesstechnik; Technische Universität Graz; NAWI Graz; Petersgasse 12 8010 Graz Österreich
| | - Alexander Gutmann
- Institut für Biotechnologie und Bioprozesstechnik; Technische Universität Graz; NAWI Graz; Petersgasse 12 8010 Graz Österreich
| | - Hansjörg Weber
- Institut für Organische Chemie; Technische Universität Graz; NAWI Graz; Stremayrgasse 16 8010 Graz Österreich
| | - Bernd Nidetzky
- Institut für Biotechnologie und Bioprozesstechnik; Technische Universität Graz; NAWI Graz; Petersgasse 12 8010 Graz Österreich
- Austrian Centre of Industrial Biotechnology (acib); Petersgasse 14 8010 Graz Österreich
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20
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Eixelsberger T, Horvat D, Gutmann A, Weber H, Nidetzky B. Isotope Probing of the UDP-Apiose/UDP-Xylose Synthase Reaction: Evidence of a Mechanism via a Coupled Oxidation and Aldol Cleavage. Angew Chem Int Ed Engl 2017; 56:2503-2507. [PMID: 28102965 PMCID: PMC5324594 DOI: 10.1002/anie.201609288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/09/2016] [Indexed: 12/05/2022]
Abstract
The C-branched sugar d-apiose (Api) is essential for plant cell-wall development. An enzyme-catalyzed decarboxylation/pyranoside ring-contraction reaction leads from UDP-α-d-glucuronic acid (UDP-GlcA) to the Api precursor UDP-α-d-apiose (UDP-Api). We examined the mechanism of UDP-Api/UDP-α-d-xylose synthase (UAXS) with site-selectively 2 H-labeled and deoxygenated substrates. The analogue UDP-2-deoxy-GlcA, which prevents C-2/C-3 aldol cleavage as the plausible initiating step of pyranoside-to-furanoside conversion, did not give the corresponding Api product. Kinetic isotope effects (KIEs) support an UAXS mechanism in which substrate oxidation by enzyme-NAD+ and retro-aldol sugar ring-opening occur coupled in a single rate-limiting step leading to decarboxylation. Rearrangement and ring-contracting aldol addition in an open-chain intermediate then give the UDP-Api aldehyde, which is intercepted via reduction by enzyme-NADH.
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Affiliation(s)
- Thomas Eixelsberger
- Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyNAWI GrazPetersgasse 128010GrazAustria
| | - Doroteja Horvat
- Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyNAWI GrazPetersgasse 128010GrazAustria
| | - Alexander Gutmann
- Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyNAWI GrazPetersgasse 128010GrazAustria
| | - Hansjörg Weber
- Institute of Organic ChemistryGraz University of TechnologyNAWI GrazStremayrgasse 98010GrazAustria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyNAWI GrazPetersgasse 128010GrazAustria
- Austrian Centre of Industrial Biotechnology (acib)Petersgasse 148010GrazAustria
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21
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Binding pattern of intermediate UDP-4-keto-xylose to human UDP-xylose synthase: Synthesis and STD NMR of model keto-saccharides. Carbohydr Res 2017; 437:50-58. [DOI: 10.1016/j.carres.2016.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/30/2016] [Accepted: 11/01/2016] [Indexed: 11/30/2022]
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22
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Yin S, Kong JQ. Transcriptome-guided gene isolation and functional characterization of UDP-xylose synthase and UDP-D-apiose/UDP-D-xylose synthase families from Ornithogalum caudatum Ait. PLANT CELL REPORTS 2016; 35:2403-2421. [PMID: 27591771 DOI: 10.1007/s00299-016-2044-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
The present study first identified the involvement of OcUAXS2 and OcUXS1-3 in anticancer polysaccharides biosynthesis in O. caudatum. UDP-xylose synthase (UXS) and UDP-D-apiose/UDP-D-xylose synthase (UAXS), both capable of converting UDP-D-glucuronic acid to UDP-D-xylose, are believed to transfer xylosyl residue to anticancer polysaccharides biosynthesis in Ornithogalum caudatum Ait. However, the cDNA isolation and functional characterization of genes encoding the two enzymes from O. caudatum has never been documented. Previously, the transcriptome sequencing of O. caudatum was performed in our laboratory. In this study, a total of six and two unigenes encoding UXS and UAXS were first retrieved based on RNA-Seq data. The eight putative genes were then successfully isolated from transcriptome of O. caudatum by reverse transcription polymerase chain reaction (RT-PCR). Phylogenetic analysis revealed the six putative UXS isoforms can be classified into three types, one soluble and two distinct putative membrane-bound. Moreover, the two UAXS isoenzymes were predicted to be soluble forms. Subsequently, these candidate cDNAs were characterized to be bona fide genes by functional expression in Escherichia coli individually. Although UXS and UAXS catalyzed the same reaction, their biochemical properties varied significantly. It is worth noting that a ratio switch of UDP-D-xylose/UDP-D-apiose for UAXS was established, which is assumed to be helpful for its biotechnological application. Furthermore, a series of mutants were generated to test the function of NAD+ binding motif GxxGxxG. Most importantly, the present study determined the involvement of OcUAXS2 and OcUXS1-3 in xylose-containing polysaccharides biosynthesis in O. caudatum. These data provide a comprehensive knowledge for UXS and UAXS families in plants.
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Affiliation(s)
- Sen Yin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian-Qiang Kong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines and Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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23
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Matsumoto K, Ayukawa T, Ishio A, Sasamura T, Yamakawa T, Matsuno K. Dual Roles of O-Glucose Glycans Redundant with Monosaccharide O-Fucose on Notch in Notch Trafficking. J Biol Chem 2016; 291:13743-52. [PMID: 27129198 DOI: 10.1074/jbc.m115.710483] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 12/25/2022] Open
Abstract
Notch is a transmembrane receptor that mediates cell-cell interactions and controls various cell-fate specifications in metazoans. The extracellular domain of Notch contains multiple epidermal growth factor (EGF)-like repeats. At least five different glycans are found in distinct sites within these EGF-like repeats. The function of these individual glycans in Notch signaling has been investigated, primarily by disrupting their individual glycosyltransferases. However, we are just beginning to understand the potential functional interactions between these glycans. Monosaccharide O-fucose and O-glucose trisaccharide (O-glucose-xylose-xylose) are added to many of the Notch EGF-like repeats. In Drosophila, Shams adds a xylose specifically to the monosaccharide O-glucose. We found that loss of the terminal dixylose of O-glucose-linked saccharides had little effect on Notch signaling. However, our analyses of double mutants of shams and other genes required for glycan modifications revealed that both the monosaccharide O-glucose and the terminal dixylose of O-glucose-linked saccharides function redundantly with the monosaccharide O-fucose in Notch activation and trafficking. The terminal dixylose of O-glucose-linked saccharides and the monosaccharide O-glucose were required in distinct Notch trafficking processes: Notch transport from the apical plasma membrane to adherens junctions, and Notch export from the endoplasmic reticulum, respectively. Therefore, the monosaccharide O-glucose and terminal dixylose of O-glucose-linked saccharides have distinct activities in Notch trafficking, although a loss of these activities is compensated for by the presence of monosaccharide O-fucose. Given that various glycans attached to a protein motif may have redundant functions, our results suggest that these potential redundancies may lead to a serious underestimation of glycan functions.
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Affiliation(s)
- Kenjiroo Matsumoto
- From the Department of Biological Sciences, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043 and
| | - Tomonori Ayukawa
- the Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-1500, Japan
| | - Akira Ishio
- the Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-1500, Japan
| | - Takeshi Sasamura
- From the Department of Biological Sciences, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043 and
| | - Tomoko Yamakawa
- From the Department of Biological Sciences, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043 and
| | - Kenji Matsuno
- From the Department of Biological Sciences, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043 and
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24
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Eixelsberger T, Weber H, Nidetzky B. Probing of the reaction pathway of human UDP-xylose synthase with site-directed mutagenesis. Carbohydr Res 2015; 416:1-6. [PMID: 26342152 DOI: 10.1016/j.carres.2015.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 11/28/2022]
Abstract
Uridine 5'-diphosphate (UDP)-xylose (UDP-Xyl) synthase (UXS) catalyzes the oxidative decarboxylation of UDP-glucuronic acid (UDP-GlcUA) to UDP-Xyl. The closely related UDP-glucuronic acid 4-epimerase (UGAE) interconverts UDP-GlcUA and UDP-galacturonic acid (UDP-GalUA) in a highly similar manner via the intermediate UDP-xylo-hexopyranos-4-uluronic acid (UDP-4-keto-GlcUA). Unlike UXS, however, UGAE prevents the decarboxylation. Human UXS (hUXS) and UGAE from Arabidopsis thaliana exhibit high structural similarity in the active site, but two catalytically important residues in hUXS (Glu(120) and Arg(277)) are replaced by Ser and Thr in the UGAE group. Additionally, Asn(176), which participates in substrate binding, is changed to Thr. We therefore analyzed single, double and triple mutants of hUXS carrying these substitutions to evaluate their significance for product specificity. All mutants showed considerably lower activities than wild-type hUXS (>1000-fold reduction). NMR spectroscopic analysis of the reaction products showed that UDP-β-L-threo-pentopyranos-4-ulose (UDP-4-keto-Xyl), UDP-Xyl or both, but no UDP-GalUA or UDP-4-keto-GlcUA were formed. Correlation of product characteristics, such as deuterium incorporation, with the amino acid replacements gave insights into structure-function relationships in UXS, suggesting that interaction between active site and overall enzyme structure rather than distinct conserved residues are decisive for product formation.
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Affiliation(s)
- Thomas Eixelsberger
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Petersgasse 12/I, A-8010 Graz, Austria
| | - Hansjörg Weber
- Institute of Organic Chemistry, NAWI Graz, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Petersgasse 12/I, A-8010 Graz, Austria; Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria.
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25
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Thorsheim K, Siegbahn A, Johnsson RE, Stålbrand H, Manner S, Widmalm G, Ellervik U. Chemistry of xylopyranosides. Carbohydr Res 2015; 418:65-88. [PMID: 26580709 DOI: 10.1016/j.carres.2015.10.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 12/22/2022]
Abstract
Xylose is one of the few monosaccharidic building blocks that are used by mammalian cells. In comparison with other monosaccharides, xylose is rather unusual and, so far, only found in two different mammalian structures, i.e. in the Notch receptor and as the linker between protein and glycosaminoglycan (GAG) chains in proteoglycans. Interestingly, simple soluble xylopyranosides can not only initiate the biosynthesis of soluble GAG chains but also function as inhibitors of important enzymes in the biosynthesis of proteoglycans. Furthermore, xylose is a major constituent of hemicellulosic xylans and thus one of the most abundant carbohydrates on Earth. Altogether, this has spurred a strong interest in xylose chemistry. The scope of this review is to describe synthesis of xylopyranosyl donors, as well as protective group chemistry, modifications, and conformational analysis of xylose.
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Affiliation(s)
- Karin Thorsheim
- Centre for Analysis and Synthesis, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Anna Siegbahn
- Centre for Analysis and Synthesis, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Richard E Johnsson
- Centre for Analysis and Synthesis, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Henrik Stålbrand
- Centre for Molecular Protein Science, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Sophie Manner
- Centre for Analysis and Synthesis, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ulf Ellervik
- Centre for Analysis and Synthesis, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
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26
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Duan XC, Lu AM, Gu B, Cai ZP, Ma HY, Wei S, Laborda P, Liu L, Voglmeir J. Functional characterization of the UDP-xylose biosynthesis pathway in Rhodothermus marinus. Appl Microbiol Biotechnol 2015; 99:9463-72. [PMID: 26033773 DOI: 10.1007/s00253-015-6683-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/20/2015] [Accepted: 05/07/2015] [Indexed: 10/23/2022]
Abstract
UDP-glucuronic acid dehydrogenase (UGD) and UDP-xylose synthase (UXS) are the two enzymes responsible for the biosynthesis of UDP-xylose from UDP-glucose. Several UGDs from bacterial sources, which oxidize UDP-glucose to glucuronic acid, have been found and functionally characterized whereas only few reports on bacterial UXS isoforms exist. Rhodothermus marinus, a halothermophilic bacterium commonly found in hot springs, proved to be a valuable source of carbohydrate active enzymes of biotechnological interest, such as xylanases, mannanases, and epimerases. However, no enzymes of R. marinus involved in the biosynthesis or modification of nucleotide sugars have been reported yet. Herein, we describe the cloning and characterization of two putative UGD (RmUGD1 and RmUGD2) and one UXS (RmUXS) isoform from this organism. All three enzymes could be expressed in recombinant form and purified to near homogeneity. UPLC- and NMR-based activity tests showed that RmUGD1 and RmUXS are indeed active enzymes, whereas no enzymatic activity could be detected by RmUGD2. Both RmUGD1 and RmUXS showed a temperature optimum of 60 °C, with almost no loss of activity after 1 h exposure at 70 °C. No metal ions were required for enzymatic activities. Zn(2+) ions strongly inhibited both enzymes. RmUGD1 showed higher salt tolerance and had a higher pH optimum than RmUXS. Furthermore, RmUGD1 was inhibited by UDP-xylose at higher concentrations. By coupling recombinant RmUXS and RmUGD1, UDP-xylose could be successfully synthesized directly from UDP-glucose. The high activity of the herein described enzymes make RmUGD1 and RmUXS the first thermo-tolerant biocatalysts for the synthesis of UDP-glucuronic acid and UDP-xylose.
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Affiliation(s)
- Xu C Duan
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Ai M Lu
- College of Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Bin Gu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Zhi P Cai
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Hong Y Ma
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Shuang Wei
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Pedro Laborda
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China.
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27
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Fischer U, Hertlein S, Grimm C. The structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic cooperativity. ACTA ACUST UNITED AC 2015; 71:687-96. [PMID: 25760615 DOI: 10.1107/s1399004714026686] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/04/2014] [Indexed: 11/10/2022]
Abstract
The bacterial protein ArnA is an essential enzyme in the pathway leading to the modification of lipid A with the pentose sugar 4-amino-4-deoxy-L-arabinose. This modification confers resistance to polymyxins, which are antibiotics that are used as a last resort to treat infections with multiple drug-resistant Gram-negative bacteria. ArnA contains two domains with distinct catalytic functions: a dehydrogenase domain and a transformylase domain. The protein forms homohexamers organized as a dimer of trimers. Here, the crystal structure of apo ArnA is presented and compared with its ATP- and UDP-glucuronic acid-bound counterparts. The comparison reveals major structural rearrangements in the dehydrogenase domain that lead to the formation of a previously unobserved binding pocket at the centre of each ArnA trimer in its apo state. In the crystal structure, this pocket is occupied by a DTT molecule. It is shown that formation of the pocket is linked to a cascade of structural rearrangements that emerge from the NAD(+)-binding site. Based on these findings, a small effector molecule is postulated that binds to the central pocket and modulates the catalytic properties of ArnA. Furthermore, the discovered conformational changes provide a mechanistic explanation for the strong cooperative effect recently reported for the ArnA dehydrogenase function.
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Affiliation(s)
- Utz Fischer
- Department of Biochemistry, Biocenter of the University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Simon Hertlein
- Department of Biochemistry, Biocenter of the University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Clemens Grimm
- Department of Biochemistry, Biocenter of the University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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28
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Walsh RM, Polizzi SJ, Kadirvelraj R, Howard WW, Wood ZA. Man o' war mutation in UDP-α-D-xylose synthase favors the abortive catalytic cycle and uncovers a latent potential for hexamer formation. Biochemistry 2015; 54:807-19. [PMID: 25521717 DOI: 10.1021/bi501357c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The man o' war (mow) phenotype in zebrafish is characterized by severe craniofacial defects due to a missense mutation in UDP-α-d-xylose synthase (UXS), an essential enzyme in proteoglycan biosynthesis. The mow mutation is located in the UXS dimer interface ∼16 Å away from the active site, suggesting an indirect effect on the enzyme mechanism. We have examined the structural and catalytic consequences of the mow mutation (R236H) in the soluble fragment of human UXS (hUXS), which shares 93% sequence identity with the zebrafish enzyme. In solution, hUXS dimers undergo a concentration-dependent association to form a tetramer. Sedimentation velocity studies show that the R236H substitution induces the formation of a new hexameric species. Using two new crystal structures of the hexamer, we show that R236H and R236A substitutions cause a local unfolding of the active site that allows for a rotation of the dimer interface necessary to form the hexamer. The disordered active sites in the R236H and R236A mutant constructs displace Y231, the essential acid/base catalyst in the UXS reaction mechanism. The loss of Y231 favors an abortive catalytic cycle in which the reaction intermediate, UDP-α-d-4-keto-xylose, is not reduced to the final product, UDP-α-d-xylose. Surprisingly, the mow-induced hexamer is almost identical to the hexamers formed by the deeply divergent UXS homologues from Staphylococcus aureus and Helicobacter pylori (21% and 16% sequence identity, respectively). The persistence of a latent hexamer-building interface in the human enzyme suggests that the ancestral UXS may have been a hexamer.
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Affiliation(s)
- Richard M Walsh
- Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States
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29
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Puchner C, Eixelsberger T, Nidetzky B, Brecker L. Saturation transfer difference NMR to study substrate and product binding to human UDP-xylose synthase (hUXS1A) during catalytic event. RSC Adv 2015. [DOI: 10.1039/c5ra18284k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The human form of UDP-xylose synthase (hUXS1A) is studied with respect to its substrate and co-enzyme binding in binary and ternary complexes using saturation transfer difference (STD) NMR and in situ NMR.
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Affiliation(s)
- Claudia Puchner
- University of Vienna
- Institute of Organic Chemistry
- A-1090 Vienna
- Austria
| | - Thomas Eixelsberger
- Graz University of Technology
- Institute of Biotechnology and Biochemical Engineering
- A-8010 Graz
- Austria
| | - Bernd Nidetzky
- Graz University of Technology
- Institute of Biotechnology and Biochemical Engineering
- A-8010 Graz
- Austria
| | - Lothar Brecker
- University of Vienna
- Institute of Organic Chemistry
- A-1090 Vienna
- Austria
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30
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Eixelsberger T, Nidetzky B. Enzymatic Redox Cascade for One-Pot Synthesis of Uridine 5'-Diphosphate Xylose from Uridine 5'-Diphosphate Glucose. Adv Synth Catal 2014; 356:3575-3584. [PMID: 26190959 PMCID: PMC4498474 DOI: 10.1002/adsc.201400766] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Indexed: 11/22/2022]
Abstract
Synthetic ways towards uridine 5′-diphosphate (UDP)-xylose are scarce and not well established, although this compound plays an important role in the glycobiology of various organisms and cell types. We show here how UDP-glucose 6-dehydrogenase (hUGDH) and UDP-xylose synthase 1 (hUXS) from Homo sapiens can be used for the efficient production of pure UDP-α-xylose from UDP-glucose. In a mimic of the natural biosynthetic route, UDP-glucose is converted to UDP-glucuronic acid by hUGDH, followed by subsequent formation of UDP-xylose by hUXS. The nicotinamide adenine dinucleotide (NAD+) required in the hUGDH reaction is continuously regenerated in a three-step chemo-enzymatic cascade. In the first step, reduced NAD+ (NADH) is recycled by xylose reductase from Candida tenuis via reduction of 9,10-phenanthrenequinone (PQ). Radical chemical re-oxidation of this mediator in the second step reduces molecular oxygen to hydrogen peroxide (H2O2) that is cleaved by bovine liver catalase in the last step. A comprehensive analysis of the coupled chemo-enzymatic reactions revealed pronounced inhibition of hUGDH by NADH and UDP-xylose as well as an adequate oxygen supply for PQ re-oxidation as major bottlenecks of effective performance of the overall multi-step reaction system. Net oxidation of UDP-glucose to UDP-xylose by hydrogen peroxide (H2O2) could thus be achieved when using an in situ oxygen supply through periodic external feed of H2O2 during the reaction. Engineering of the interrelated reaction parameters finally enabled production of 19.5 mM (10.5 g l−1) UDP-α-xylose. After two-step chromatographic purification the compound was obtained in high purity (>98%) and good overall yield (46%). The results provide a strong case for application of multi-step redox cascades in the synthesis of nucleotide sugar products.
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Affiliation(s)
- Thomas Eixelsberger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology NAWI Graz, Petersgasse 12/I, A-8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology NAWI Graz, Petersgasse 12/I, A-8010 Graz, Austria ; Austrian Centre of Industrial Biotechnology Petersgasse 14, A-8010 Graz, Austria, ; phone: (+43)-316-873-8400 ; e-mail:
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31
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Tiwari P, Singh N, Dixit A, Choudhury D. Multivariate sequence analysis reveals additional function impacting residues in the SDR superfamily. Proteins 2014; 82:2842-56. [DOI: 10.1002/prot.24647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 06/19/2014] [Accepted: 07/15/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Pratibha Tiwari
- School of Biotechnology, Jawaharlal Nehru University; New Delhi 110 067 India
| | - Noopur Singh
- School of Biotechnology, Jawaharlal Nehru University; New Delhi 110 067 India
| | - Aparna Dixit
- School of Biotechnology, Jawaharlal Nehru University; New Delhi 110 067 India
| | - Devapriya Choudhury
- School of Biotechnology, Jawaharlal Nehru University; New Delhi 110 067 India
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32
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Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM. The evolution of enzyme function in the isomerases. Curr Opin Struct Biol 2014; 26:121-30. [PMID: 25000289 PMCID: PMC4139412 DOI: 10.1016/j.sbi.2014.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 06/02/2014] [Accepted: 06/10/2014] [Indexed: 01/14/2023]
Abstract
The advent of computational approaches to measure functional similarity between enzymes adds a new dimension to existing evolutionary studies based on sequence and structure. This paper reviews research efforts aiming to understand the evolution of enzyme function in superfamilies, presenting a novel strategy to provide an overview of the evolution of enzymes belonging to an individual EC class, using the isomerases as an exemplar.
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Affiliation(s)
- Sergio Martinez Cuesta
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Syed Asad Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
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33
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Polizzi SJ, Walsh RM, Le Magueres P, Criswell AR, Wood ZA. Human UDP-α-d-xylose Synthase Forms a Catalytically Important Tetramer That Has Not Been Observed in Crystal Structures. Biochemistry 2013; 52:3888-98. [DOI: 10.1021/bi400294e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Samuel J. Polizzi
- Department
of Biochemistry and
Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Richard M. Walsh
- Department
of Biochemistry and
Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | | | | | - Zachary A. Wood
- Department
of Biochemistry and
Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
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34
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Polizzi SJ, Walsh RM, Peeples WB, Lim JM, Wells L, Wood ZA. Human UDP-α-D-xylose synthase and Escherichia coli ArnA conserve a conformational shunt that controls whether xylose or 4-keto-xylose is produced. Biochemistry 2012; 51:8844-55. [PMID: 23072385 DOI: 10.1021/bi301135b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Human UDP-α-D-xylose synthase (hUXS) is a member of the short-chain dehydrogenase/reductase family of nucleotide-sugar modifying enzymes. hUXS contains a bound NAD(+) cofactor that it recycles by first oxidizing UDP-α-D-glucuronic acid (UGA), and then reducing the UDP-α-D-4-keto-xylose (UX4O) to produce UDP-α-D-xylose (UDX). Despite the observation that purified hUXS contains a bound cofactor, it has been reported that exogenous NAD(+) will stimulate enzyme activity. Here we show that a small fraction of hUXS releases the NADH and UX4O intermediates as products during turnover. The resulting apoenzyme can be rescued by exogenous NAD(+), explaining the apparent stimulatory effect of added cofactor. The slow release of NADH and UX4O as side products by hUXS is reminiscent of the Escherichia coli UGA decarboxylase (ArnA), a related enzyme that produces NADH and UX4O as products. We report that ArnA can rebind NADH and UX4O to slowly make UDX. This means that both enzymes share the same catalytic machinery, but differ in the preferred final product. We present a bifurcated rate equation that explains how the substrate is shunted to the distinct final products. Using a new crystal structure of hUXS, we identify the structural elements of the shunt and propose that the local unfolding of the active site directs reactants toward the preferred products. Finally, we present evidence that the release of NADH and UX4O involves a cooperative conformational change that is conserved in both enzymes.
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Affiliation(s)
- Samuel J Polizzi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
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