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Koeksoy E, Bezuidt OM, Bayer T, Chan CS, Emerson D. Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export. Front Microbiol 2021; 12:679409. [PMID: 34220764 PMCID: PMC8250860 DOI: 10.3389/fmicb.2021.679409] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022] Open
Abstract
Twisted stalks are morphologically unique bacterial extracellular organo-metallic structures containing Fe(III) oxyhydroxides that are produced by microaerophilic Fe(II)-oxidizers belonging to the Betaproteobacteria and Zetaproteobacteria. Understanding the underlying genetic and physiological mechanisms of stalk formation is of great interest based on their potential as novel biogenic nanomaterials and their relevance as putative biomarkers for microbial Fe(II) oxidation on ancient Earth. Despite the recognition of these special biominerals for over 150 years, the genetic foundation for the stalk phenotype has remained unresolved. Here we present a candidate gene cluster for the biosynthesis and secretion of the stalk organic matrix that we identified with a trait-based analyses of a pan-genome comprising 16 Zetaproteobacteria isolate genomes. The “stalk formation in Zetaproteobacteria” (sfz) cluster comprises six genes (sfz1-sfz6), of which sfz1 and sfz2 were predicted with functions in exopolysaccharide synthesis, regulation, and export, sfz4 and sfz6 with functions in cell wall synthesis manipulation and carbohydrate hydrolysis, and sfz3 and sfz5 with unknown functions. The stalk-forming Betaproteobacteria Ferriphaselus R-1 and OYT-1, as well as dread-forming Zetaproteobacteria Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8 contain distant sfz gene homologs, whereas stalk-less Zetaproteobacteria and Betaproteobacteria lack the entire gene cluster. Our pan-genome analysis further revealed a significant enrichment of clusters of orthologous groups (COGs) across all Zetaproteobacteria isolate genomes that are associated with the regulation of a switch between sessile and motile growth controlled by the intracellular signaling molecule c-di-GMP. Potential interactions between stalk-former unique transcription factor genes, sfz genes, and c-di-GMP point toward a c-di-GMP regulated surface attachment function of stalks during sessile growth.
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Affiliation(s)
- Elif Koeksoy
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures), Braunschweig, Germany
| | - Oliver M Bezuidt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Timm Bayer
- Geomicrobiology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States.,School of Marine Sciences and Policy, University of Delaware, Newark, DE, United States
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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Bandini G, Agop-Nersesian C, van der Wel H, Mandalasi M, Kim HW, West CM, Samuelson J. The nucleocytosolic O-fucosyltransferase SPINDLY affects protein expression and virulence in Toxoplasma gondii. J Biol Chem 2021; 296:100039. [PMID: 33158988 PMCID: PMC7949088 DOI: 10.1074/jbc.ra120.015883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
Once considered unusual, nucleocytoplasmic glycosylation is now recognized as a conserved feature of eukaryotes. While in animals, O-GlcNAc transferase (OGT) modifies thousands of intracellular proteins, the human pathogen Toxoplasma gondii transfers a different sugar, fucose, to proteins involved in transcription, mRNA processing, and signaling. Knockout experiments showed that TgSPY, an ortholog of plant SPINDLY and paralog of host OGT, is required for nuclear O-fucosylation. Here we verify that TgSPY is the nucleocytoplasmic O-fucosyltransferase (OFT) by 1) complementation with TgSPY-MYC3, 2) its functional dependence on amino acids critical for OGT activity, and 3) its ability to O-fucosylate itself and a model substrate and to specifically hydrolyze GDP-Fuc. While many of the endogenous proteins modified by O-Fuc are important for tachyzoite fitness, O-fucosylation by TgSPY is not essential. Growth of Δspy tachyzoites in fibroblasts is modestly affected, despite marked reductions in the levels of ectopically expressed proteins normally modified with O-fucose. Intact TgSPY-MYC3 localizes to the nucleus and cytoplasm, whereas catalytic mutants often displayed reduced abundance. Δspy tachyzoites of a luciferase-expressing type II strain exhibited infection kinetics in mice similar to wild-type but increased persistence in the chronic brain phase, potentially due to an imbalance of regulatory protein levels. The modest changes in parasite fitness in vitro and in mice, despite profound effects on reporter protein accumulation, and the characteristic punctate localization of O-fucosylated proteins suggest that TgSPY controls the levels of proteins to be held in reserve for response to novel stresses.
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Affiliation(s)
- Giulia Bandini
- Department of Molecular and Cell Biology, Boston University Henry Goldman School of Dental Medicine, Boston, Massachusetts, USA.
| | - Carolina Agop-Nersesian
- Department of Molecular and Cell Biology, Boston University Henry Goldman School of Dental Medicine, Boston, Massachusetts, USA
| | - Hanke van der Wel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Msano Mandalasi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Hyun W Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Christopher M West
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - John Samuelson
- Department of Molecular and Cell Biology, Boston University Henry Goldman School of Dental Medicine, Boston, Massachusetts, USA
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Gene expression abundance dictated exopolysaccharide modification in Rhizobium radiobacter SZ4S7S14 as the cell's response to salt stress. Int J Biol Macromol 2020; 164:4339-4347. [PMID: 32931833 DOI: 10.1016/j.ijbiomac.2020.09.038] [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: 07/03/2020] [Revised: 08/25/2020] [Accepted: 09/07/2020] [Indexed: 12/24/2022]
Abstract
A molecular and metabolic behaviour of EPS-producing and salt-tolerant bacterium Rhizobium radiobacter SZ4S7S14 along with its practical application in salt-stress was investigated. The research target was identification and expression profiles of a large EPS biosynthesis gene cluster, possible structural modification of EPS under salt-stress effect and analysis of the gene(s) relative expression and structural modification correlation. As expected, transposons insertions were identified within or near the coding regions of exoK and exoM, previously known large gene cluster that is required for EPS I synthesis. Different expression levels of exoK and exoM in different salt-stress models resulted in structural modification of EPS, which was seen basically in monomers molar ratio. As a result of downregulation of the genes the strain produced EPS samples with monomers ratio: (1) Glu:Man:Gal:Xyl:Ara:Rha:Rib = 31.21:3.02:2.77:1:0.91:0.64:0.41 (in 0.25% NaCl); (2) Glu:Man:Gal:Xyl:Ara:Rha:Rib = 7.65:1:0.69:0.22:0.2:0.16:0.1 (in 0.5% NaCl); (3) Glu:Man:Gal:Ara:Xyl:Rha:Rib = 9.39:1.89:1:0.58:0.52:0.46:0.26 (in 1% NaCl); and (4) Glu:Man:Ara:Xyl:Rib:Gal = 7.9:2:2:1.58:1.1:1 (in 2.0% NaCl), whereas in control (without NaCl): Glc:Man:Gal:Xyl:Ara:Rha:Rib = 11.66:1:0.90:0.37:0.37:0.15:0.14. It was found that, salt-stress not only leads to downregulation of a large EPS biosynthesis gene cluster, including exoK and exoM genes, but also impacting on their relative expression degree, re-groups of the monomers within the EPS matrix and dictates molar ratio of the monosaccharides in the final metabolite.
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Cao XQ, Wang JY, Zhou L, Chen B, Jin Y, He YW. Biosynthesis of the yellow xanthomonadin pigments involves an ATP-dependent 3-hydroxybenzoic acid: acyl carrier protein ligase and an unusual type II polyketide synthase pathway. Mol Microbiol 2018; 110:16-32. [PMID: 29995983 DOI: 10.1111/mmi.14064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2018] [Indexed: 11/30/2022]
Abstract
Xanthomonadins are yellow pigments that are produced by the phytopathogen Xanthomonas campestris pv. campestris (Xcc). A pig cluster is responsible for xanthomonadin biosynthesis. Previously, Xcc4014 of the cluster was characterized as a bifunctional chorismatase that produces 3-hydroxybenzoic acid (3-HBA) and 4-HBA. In this study, genetic analysis identified 11 genes within the pig cluster to be essential for xanthomonadin biosynthesis. Biochemical and bioinformatics analysis suggest that xanthomonadins are synthesized via an unusual type II polyketide synthase pathway. Heterologous expression of the pig cluster in non-xanthomonadin-producing Pseudomonas aeruginosa strain resulted in the synthesis of chlorinated xanthomonadin-like pigments. Further analysis showed that xanC encodes an acyl carrier protein (ACP) while xanA2 encodes a ATP-dependent 3-HBA:ACP ligase. Both of them act together to catalyse the formation of 3-HBA-S-ACP from 3-HBA to initiate xanthomonadin biosynthesis. Finally, we showed that xanH encodes a FabG-like enzyme and xanK encodes a novel glycosyltransferase. Both xanH and xanK are not only required for xanthomonadin biosynthesis, but also required for the balanced biosynthesis of extracellular polysaccharides and DSF-family quorum sensing signals. These findings provide us with a better understanding of xanthomonadin biosynthetic mechanisms and directly demonstrate the presence of extensive cross-talk among xanthomonadin biosynthetic pathways and other metabolic pathways.
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Affiliation(s)
- Xue-Qiang Cao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jia-Yuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lian Zhou
- Zhiyuan Innovation Research Centre, Student Innovation Institute, Zhiyuan College, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu Jin
- School of Biotechnology, East China Science and Technology University, Shanghai, China
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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A comparison of genes involved in sphingan biosynthesis brought up to date. Appl Microbiol Biotechnol 2014; 98:7719-33. [DOI: 10.1007/s00253-014-5940-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 10/25/2022]
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Bullard W, Lopes da Rosa-Spiegler J, Liu S, Wang Y, Sabatini R. Identification of the glucosyltransferase that converts hydroxymethyluracil to base J in the trypanosomatid genome. J Biol Chem 2014; 289:20273-82. [PMID: 24891501 DOI: 10.1074/jbc.m114.579821] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
O-linked glucosylation of thymine in DNA (base J) is an important regulatory epigenetic mark in trypanosomatids. β-d-glucopyranosyloxymethyluracil (base J) synthesis is initiated by the JBP1/2 enzymes that hydroxylate thymine, forming 5-hydroxymethyluracil (hmU). hmU is then glucosylated by a previously unknown glucosyltransferase. A recent computational screen identified a possible candidate for the base J-associated glucosyltransferase (JGT) in trypanosomatid genomes. We demonstrate that recombinant JGT utilizes uridine diphosphoglucose to transfer glucose to hmU in the context of dsDNA. Mutation of conserved residues typically involved in glucosyltransferase catalysis impairs DNA glucosylation in vitro. The deletion of both alleles of JGT from the genome of Trypanosoma brucei generates a cell line that completely lacks base J. Reintroduction of JGT in the JGT KO restores J synthesis. Ablation of JGT mRNA levels by RNAi leads to the sequential reduction in base J and increased levels of hmU that dissipate rapidly. The analysis of JGT function confirms the two-step J synthesis model and demonstrates that JGT is the only glucosyltransferase enzyme required for the second step of the pathway. Similar to the activity of the related Ten-Eleven Translocation (TET) family of dioxygenases on 5mC, our studies also suggest the ability of the base J-binding protein enzymes to catalyze iterative oxidation of thymine in trypanosome DNA. Here we discuss the regulation of hmU and base J formation in the trypanosome genome by JGT and base J-binding protein.
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Affiliation(s)
- Whitney Bullard
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
| | | | - Shuo Liu
- the Environmental Toxicology Graduate Program and
| | - Yinsheng Wang
- the Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521
| | - Robert Sabatini
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and
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Structure-function features of a Mycoplasma glycolipid synthase derived from structural data integration, molecular simulations, and mutational analysis. PLoS One 2013; 8:e81990. [PMID: 24312618 PMCID: PMC3849446 DOI: 10.1371/journal.pone.0081990] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/18/2013] [Indexed: 11/19/2022] Open
Abstract
Glycoglycerolipids are structural components of mycoplasma membranes with a fundamental role in membrane properties and stability. Their biosynthesis is mediated by glycosyltransferases (GT) that catalyze the transfer of glycosyl units from a sugar nucleotide donor to diacylglycerol. The essential function of glycolipid synthases in mycoplasma viability, and the absence of glycoglycerolipids in animal host cells make these GT enzymes a target for drug discovery by designing specific inhibitors. However, rational drug design has been hampered by the lack of structural information for any mycoplasma GT. Most of the annotated GTs in pathogenic mycoplasmas belong to family GT2. We had previously shown that MG517 in Mycoplasma genitalium is a GT-A family GT2 membrane-associated glycolipid synthase. We present here a series of structural models of MG517 obtained by homology modeling following a multiple-template approach. The models have been validated by mutational analysis and refined by long scale molecular dynamics simulations. Based on the models, key structure-function relationships have been identified: The N-terminal GT domain has a GT-A topology that includes a non-conserved variable region involved in acceptor substrate binding. Glu193 is proposed as the catalytic base in the GT mechanism, and Asp40, Tyr126, Tyr169, Ile170 and Tyr218 define the substrates binding site. Mutation Y169F increases the enzyme activity and significantly alters the processivity (or sequential transferase activity) of the enzyme. This is the first structural model of a GT-A glycoglycerolipid synthase and provides preliminary insights into structure and function relationships in this family of enzymes.
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May JF, Levengood MR, Splain RA, Brown CD, Kiessling LL. A processive carbohydrate polymerase that mediates bifunctional catalysis using a single active site. Biochemistry 2012; 51:1148-59. [PMID: 22217153 DOI: 10.1021/bi201820p] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Even in the absence of a template, glycosyltransferases can catalyze the synthesis of carbohydrate polymers of specific sequence. The paradigm has been that one enzyme catalyzes the formation of one type of glycosidic linkage, yet certain glycosyltransferases generate polysaccharide sequences composed of two distinct linkage types. In principle, bifunctional glycosyltransferases can possess separate active sites for each catalytic activity or one active site with dual activities. We encountered the fundamental question of one or two distinct active sites in our investigation of the galactosyltransferase GlfT2. GlfT2 catalyzes the formation of mycobacterial galactan, a critical cell-wall polymer composed of galactofuranose residues connected with alternating, regioisomeric linkages. We found that GlfT2 mediates galactan polymerization using only one active site that manifests dual regioselectivity. Structural modeling of the bifunctional glycosyltransferases hyaluronan synthase and cellulose synthase suggests that these enzymes also generate multiple glycosidic linkages using a single active site. These results highlight the versatility of glycosyltransferases for generating polysaccharides of specific sequence. We postulate that a hallmark of processive elongation of a carbohydrate polymer by a bifunctional enzyme is that one active site can give rise to two separate types of glycosidic bonds.
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Affiliation(s)
- John F May
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, United States
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Pak JE, Satkunarajah M, Seetharaman J, Rini JM. Structural and Mechanistic Characterization of Leukocyte-Type Core 2 β1,6-N-Acetylglucosaminyltransferase: A Metal-Ion-Independent GT-A Glycosyltransferase. J Mol Biol 2011; 414:798-811. [DOI: 10.1016/j.jmb.2011.10.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 10/14/2011] [Accepted: 10/21/2011] [Indexed: 10/15/2022]
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Cheng PW, Radhakrishnan P. Mucin O-glycan branching enzymes: structure, function, and gene regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 705:465-92. [PMID: 21618125 DOI: 10.1007/978-1-4419-7877-6_25] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pi-Wan Cheng
- Department of Biochemistry and Molecular Biology, College of Medicine and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA.
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Guttenplan SB, Blair KM, Kearns DB. The EpsE flagellar clutch is bifunctional and synergizes with EPS biosynthesis to promote Bacillus subtilis biofilm formation. PLoS Genet 2010; 6:e1001243. [PMID: 21170308 PMCID: PMC3000366 DOI: 10.1371/journal.pgen.1001243] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 11/08/2010] [Indexed: 11/24/2022] Open
Abstract
Many bacteria inhibit motility concomitant with the synthesis of an extracellular polysaccharide matrix and the formation of biofilm aggregates. In Bacillus subtilis biofilms, motility is inhibited by EpsE, which acts as a clutch on the flagella rotor to inhibit motility, and which is encoded within the 15 gene eps operon required for EPS production. EpsE shows sequence similarity to the glycosyltransferase family of enzymes, and we demonstrate that the conserved active site motif is required for EPS biosynthesis. We also screen for residues specifically required for either clutch or enzymatic activity and demonstrate that the two functions are genetically separable. Finally, we show that, whereas EPS synthesis activity is dominant for biofilm formation, both functions of EpsE synergize to stabilize cell aggregates and relieve selective pressure to abolish motility by genetic mutation. Thus, the transition from motility to biofilm formation may be governed by a single bifunctional enzyme. Bacteria form persistent and antibiotic-resistant cell aggregates known as biofilms. Biofilms can form in environmental settings on plant and animal tissues, in industrial settings on pipes and the hulls of ships, and in clinical settings on catheters and medical devices. Biofilms are characterized by two features: the cells within the aggregates are non-motile, and they produce an extracellular polysaccharide (EPS) matrix. We have found a bifunctional enzyme EpsE that contributes to both features of biofilm formation in Bacillus subtilis. EpsE interacts with the flagella rotor to inhibit motility and also cooperates with other enzymes to synthesize the EPS matrix. Thus, the transition from motility to biofilm formation may be governed by a single bifunctional protein. In the past decade, research on biofilms has been focused on biofilm eradication. Understanding how cells transition into the biofilm state may provide additional approaches of preventing the formation of a biofilm in the first place.
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Affiliation(s)
- Sarah B. Guttenplan
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Kris M. Blair
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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Identification of residues important for the activity of Haloferax volcanii AglD, a component of the archaeal N-glycosylation pathway. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2010; 2010:315108. [PMID: 20585355 PMCID: PMC2877612 DOI: 10.1155/2010/315108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 02/10/2010] [Indexed: 12/02/2022]
Abstract
In Haloferax volcanii, AglD adds the final hexose to the N-linked pentasaccharide decorating the S-layer glycoprotein. Not knowing the natural substrate of the glycosyltransferase, together with the challenge of designing assays compatible with hypersalinity, has frustrated efforts at biochemical characterization of AglD activity. To circumvent these obstacles, an in vivo assay designed to identify amino acid residues important for AglD activity is described. In the assay, restoration of AglD function in an Hfx. volcanii aglD deletion strain transformed to express plasmid-encoded versions of AglD, generated through site-directed mutagenesis at positions encoding residues conserved in archaeal homologues of AglD, is reflected in the behavior of a readily detectable reporter of N-glycosylation. As such Asp110 and Asp112 were designated as elements of the DXD motif of AglD, a motif that interacts with metal cations associated with nucleotide-activated sugar donors, while Asp201 was predicted to be the catalytic base of the enzyme.
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Magdalou J, Fournel-Gigleux S, Ouzzine M. Insights on membrane topology and structure/function of UDP-glucuronosyltransferases. Drug Metab Rev 2010; 42:159-66. [PMID: 19807219 DOI: 10.3109/03602530903209270] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The main characteristic of uridine diphosphate (UDP)-glucuronosyltransferases is their potency to glucuronidate a large array of structurally unrelated substances with various nucleophilic groups. The activity of these enzymes strongly depends on their tight association to the membrane of the endoplasmic reticulum. In light of recent data, this review is focused on the membrane-assembly process, which is a prerequisite for activity, and on the amino acids that govern substrate recognition and catalysis at the active site. The major implication of the highly variable N-terminal domain of UDP-glucuronosyltransferases in the substrate specificity of these enzymes is highlighted. In the absence of crystal data of the N-terminal domain, multidisciplinary approaches of genetic-/protein-engineering techniques, homology modeling with glycosyltransferases, and quantitative structure-activity relationships allowed us to point out crucial amino acids. On the basis of these results, possible reaction mechanisms for the glucuronidation of xenobiotics, involving histidine and aspartic acid residues, have been built and are discussed.
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Affiliation(s)
- Jacques Magdalou
- UMR 7561 CNRS-Université Henri Poincaré-Nancy-1, Faculté de Médecine, Vandoeuvre-lès-Nancy, France.
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15
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Moscoso JA, Korres H, George DT, Verma NK. Identification of active site residues in the Shigella flexneri glucosyltransferase GtrV. Mol Membr Biol 2010; 27:104-13. [PMID: 20334579 DOI: 10.3109/09687680903581267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The serotype-specific glucosyltransferase, GtrV, is responsible for glucosylation of the O-antigen repeating unit of Shigella flexneri serotype 5a strains. GtrV is an integral inner membrane protein with two essential periplasmic loops: the large Loop 2 and the C-terminal Loop 10. In this study, the full length of the Loop 2 was shown to be necessary for GtrV function. Site-directed mutagenesis within this loop revealed that conserved aromatic and charged amino acids have a critical role in the formation of the active site. Sequential deletions of the C-terminal end indicated that this region may be essential for assembly of the protein in the cytoplasmic membrane. The highly conserved FWAED motif is thought to form the substrate-binding site and was found to be critical in GtrV and GtrX, a serotype-specific glucosyltransferase with homology to GtrV. The data presented constitutes a targeted analysis of the formation of the GtrV active site and highlights the essential role of the large periplasmic Loop 2 in its function.
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Affiliation(s)
- Joana A Moscoso
- Division of Biomedical Science and Biochemistry, Research School of Biology, College of Medicine, Biology & Environment, Australian National University, Canberra, Australia
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16
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Lairson LL, Henrissat B, Davies GJ, Withers SG. Glycosyltransferases: structures, functions, and mechanisms. Annu Rev Biochem 2008; 77:521-55. [PMID: 18518825 DOI: 10.1146/annurev.biochem.76.061005.092322] [Citation(s) in RCA: 1374] [Impact Index Per Article: 85.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glycosyltransferases catalyze glycosidic bond formation using sugar donors containing a nucleoside phosphate or a lipid phosphate leaving group. Only two structural folds, GT-A and GT-B, have been identified for the nucleotide sugar-dependent enzymes, but other folds are now appearing for the soluble domains of lipid phosphosugar-dependent glycosyl transferases. Structural and kinetic studies have provided new insights. Inverting glycosyltransferases utilize a direct displacement S(N)2-like mechanism involving an enzymatic base catalyst. Leaving group departure in GT-A fold enzymes is typically facilitated via a coordinated divalent cation, whereas GT-B fold enzymes instead use positively charged side chains and/or hydroxyls and helix dipoles. The mechanism of retaining glycosyltransferases is less clear. The expected two-step double-displacement mechanism is rendered less likely by the lack of conserved architecture in the region where a catalytic nucleophile would be expected. A mechanism involving a short-lived oxocarbenium ion intermediate now seems the most likely, with the leaving phosphate serving as the base.
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Affiliation(s)
- L L Lairson
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada.
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17
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Qu Y, Egelund J, Gilson PR, Houghton F, Gleeson PA, Schultz CJ, Bacic A. Identification of a novel group of putative Arabidopsis thaliana beta-(1,3)-galactosyltransferases. PLANT MOLECULAR BIOLOGY 2008; 68:43-59. [PMID: 18548197 DOI: 10.1007/s11103-008-9351-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 05/16/2008] [Indexed: 05/18/2023]
Abstract
To begin biochemical and molecular studies on the biosynthesis of the type II arabinogalactan chains on arabinogalactan-proteins (AGPs), we adopted a bioinformatic approach to identify and systematically characterise the putative galactosyltransferases (GalTs) responsible for synthesizing the beta-(1,3)-Gal linkage from CAZy GT-family-31 from Arabidopsis thaliana. These analyses confirmed that 20 members of the GT-31 family contained domains/motifs typical of biochemically characterised beta-(1,3)-GTs from mammalian systems. Microarray data confirm that members of this family are expressed throughout all tissues making them likely candidates for the assembly of the ubiquitously found AGPs. One member, At1g77810, was selected for further analysis including location studies that confirmed its presence in the Golgi and preliminary enzyme substrate specificity studies that demonstrated beta-(1,3)-GalT activity. This bioinformatic/molecular study of CAZy GT-family-31 was validated by the recent report of Strasser et al. (Plant Cell 19:2278-2292, 2007) that another member of this family (At1g26810; GALT1) encodes a beta-(1,3)-GalT involved in the biosynthesis of the Lewis a epitope of N-glycans in Arabidopsis thaliana.
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Affiliation(s)
- Yongmei Qu
- Plant Cell Biology Research Centre, School of Botany, The University of Melbourne, Melbourne, VIC, Australia
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18
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Oglesby LL, Jain S, Ohman DE. Membrane topology and roles of Pseudomonas aeruginosa Alg8 and Alg44 in alginate polymerization. MICROBIOLOGY-SGM 2008; 154:1605-1615. [PMID: 18524915 DOI: 10.1099/mic.0.2007/015305-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mucoid strains of Pseudomonas aeruginosa that overproduce alginate are associated with chronic pulmonary disease (e.g. cystic fibrosis). Mutants defective in one of several periplasmic proteins (AlgKGX) for alginate secretion release alginate fragments due to the activity of an alginate lyase (AlgL) in the periplasm, which cleaves the newly formed polymers. However, mutants defective in Alg8 or Alg44 did not secrete polymer or alginate fragments, suggesting that both these membrane proteins have a role in the polymerization reaction. A model for the membrane topology of Alg8, a glycosyltransferase (GT), was constructed using PhoA fusions. This provided evidence for a large cytoplasmic loop containing the active domains predicted for beta-GTs such as Alg8 and five transmembrane (TM) domains, one of which resembles a cleavable signal peptide. The C-terminal TM domain of Alg8 was critical for the polymerization reaction in vivo. Alanine substitution mutagenesis showed that all of the predicted active site residues in the widely spaced D, DxD, D, LxxRW motif were required for polymerization activity in vivo, and two of these substitutions also affected Alg8 protein stability. A membrane topology model for Alg44 was also constructed using PhoA fusions, and this showed a central TM domain and predicted an N-terminal TM domain that may be a membrane anchor. An N-terminal PilZ domain in Alg44 for c-di-GMP [bis-(3',5')-cyclic dimeric GMP] binding, which is required for alginate synthesis, was localized to the cytoplasmic loop. The long periplasmic C terminus of Alg44 contains a region similar to membrane fusion proteins (MFPs) of multi-drug efflux systems, which predicts the possibility of its interaction with another protein in this compartment. A Western blot analysis of the outer-membrane porin AlgE showed reduced AlgE levels in the alg44 mutant, whereas expression of Alg44 in trans restored AlgE within the cell. C-terminal truncations of Alg44 as small as 24 amino acids blocked alginate polymerization in vivo, indicating a critical role for the MFP domain. These studies suggest that Alg44 may act as a co-polymerase in concert with Alg8, the major GT, and that both inner-membrane proteins are required in vivo for the polymerization reaction leading to alginate production.
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Affiliation(s)
- Lashanda L Oglesby
- McGuire Veterans Affairs Medical Center, Richmond, VA 23249, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA 23298-0678, USA
| | - Sumita Jain
- McGuire Veterans Affairs Medical Center, Richmond, VA 23249, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA 23298-0678, USA
| | - Dennis E Ohman
- McGuire Veterans Affairs Medical Center, Richmond, VA 23249, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA 23298-0678, USA
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19
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Blair KM, Turner L, Winkelman JT, Berg HC, Kearns DB. A molecular clutch disables flagella in the Bacillus subtilis biofilm. Science 2008; 320:1636-8. [PMID: 18566286 DOI: 10.1126/science.1157877] [Citation(s) in RCA: 222] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Biofilms are multicellular aggregates of sessile bacteria encased by an extracellular matrix and are important medically as a source of drug-resistant microbes. In Bacillus subtilis, we found that an operon required for biofilm matrix biosynthesis also encoded an inhibitor of motility, EpsE. EpsE arrested flagellar rotation in a manner similar to that of a clutch, by disengaging motor force-generating elements in cells embedded in the biofilm matrix. The clutch is a simple, rapid, and potentially reversible form of motility control.
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Affiliation(s)
- Kris M Blair
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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20
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Coleman RJ, Patel YN, Harding NE. Identification and organization of genes for diutan polysaccharide synthesis from Sphingomonas sp. ATCC 53159. J Ind Microbiol Biotechnol 2008; 35:263-74. [DOI: 10.1007/s10295-008-0303-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Accepted: 12/20/2007] [Indexed: 12/01/2022]
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21
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Pak JE, Arnoux P, Zhou S, Sivarajah P, Satkunarajah M, Xing X, Rini JM. X-ray crystal structure of leukocyte type core 2 beta1,6-N-acetylglucosaminyltransferase. Evidence for a convergence of metal ion-independent glycosyltransferase mechanism. J Biol Chem 2006; 281:26693-701. [PMID: 16829524 DOI: 10.1074/jbc.m603534200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Leukocyte type core 2 beta1,6-N-acetylglucosaminyltransferase (C2GnT-L) is a key enzyme in the biosynthesis of branched O-glycans. It is an inverting, metal ion-independent family 14 glycosyltransferase that catalyzes the formation of the core 2 O-glycan (Galbeta1-3[GlcNAcbeta1-6]GalNAc-O-Ser/Thr) from its donor and acceptor substrates, UDP-GlcNAc and the core 1 O-glycan (Galbeta1-3GalNAc-O-Ser/Thr), respectively. Reported here are the x-ray crystal structures of murine C2GnT-L in the absence and presence of the acceptor substrate Galbeta1-3GalNAc at 2.0 and 2.7A resolution, respectively. C2GnT-L was found to possess the GT-A fold; however, it lacks the characteristic metal ion binding DXD motif. The Galbeta1-3GalNAc complex defines the determinants of acceptor substrate binding and shows that Glu-320 corresponds to the structurally conserved catalytic base found in other inverting GT-A fold glycosyltransferases. Comparison of the C2GnT-L structure with that of other GT-A fold glycosyltransferases further suggests that Arg-378 and Lys-401 serve to electrostatically stabilize the nucleoside diphosphate leaving group, a role normally played by metal ion in GT-A structures. The use of basic amino acid side chains in this way is strikingly similar to that seen in a number of metal ion-independent GT-B fold glycosyltransferases and suggests a convergence of catalytic mechanism shared by both GT-A and GT-B fold glycosyltransferases.
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Affiliation(s)
- John E Pak
- Department of Molecular, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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22
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Ciocchini AE, Roset MS, Briones G, Iñón de Iannino N, Ugalde RA. Identification of active site residues of the inverting glycosyltransferase Cgs required for the synthesis of cyclic beta-1,2-glucan, a Brucella abortus virulence factor. Glycobiology 2006; 16:679-91. [PMID: 16603625 DOI: 10.1093/glycob/cwj113] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Brucella abortus cyclic glucan synthase (Cgs) is a 320-kDa (2868-amino acid) polytopic integral inner membrane protein responsible for the synthesis of the virulence factor cyclic beta-1,2-glucan by a novel mechanism in which the enzyme itself acts as a protein intermediate. Cgs functions as an inverting processive beta-1,2-autoglucosyltransferase and has the three enzymatic activities required for the synthesis of the cyclic glucan: initiation, elongation, and cyclization. To gain further insight into the protein domains that are essential for the enzymatic activity, we have compared the Cgs sequence with other glycosyltransferases (GTs). This procedure allowed us to identify in the Cgs region (475-818) the widely spaced D, DxD, E/D, (Q/R)xxRW motif that is highly conserved in the active site of numerous GTs. By site-directed mutagenesis and in vitro and in vivo activity assays, we have demonstrated that most of the amino acid residues of this motif are essential for Cgs activity. These sequence and site-directed mutagenesis analyses also indicate that Cgs should be considered a bi-functional modular GT, with an N-terminal GT domain belonging to a new GT family related to GT-2 (GT-84) followed by a GH-94 glycoside hydrolase C-terminal domain. Furthermore, over-expression of inactive mutants results in wild-type (WT) production of cyclic glucan when bacteria co-express the mutant and the WT form, indicating that Cgs may function in the membrane as a monomeric enzyme. Together, these results are compatible with a single addition model by which Cgs acts in the membrane as a monomer and uses the identified motif to form a single center for substrate binding and glycosyl-transfer reaction.
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Affiliation(s)
- Andrés E Ciocchini
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, CONICET-Universidad Nacional de General San Martín, Buenos Aires, Argentina
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23
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Power PM, Roddam LF, Rutter K, Fitzpatrick SZ, Srikhanta YN, Jennings MP. Genetic characterization of pilin glycosylation and phase variation in Neisseria meningitidis. Mol Microbiol 2003; 49:833-47. [PMID: 12864863 DOI: 10.1046/j.1365-2958.2003.03602.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pili of Neisseria meningitidis are a key virulence factor, being the major adhesin of this capsulate organism and contributing to specificity for the human host. Pili are post-translationally modified by addition of either an O-linked trisaccharide, Gal (beta1-4) Gal (alpha1-3) 2,4-diacetamido-2,4,6-trideoxyhexose or an O-linked disaccharide Gal (alpha1,3) GlcNAc. The role of these structures in meningococcal pathogenesis has not been resolved. In previous studies we identified two separate genetic loci, pglA and pglBCD, involved in pilin glycosylation. Putative functions have been allocated to these genes; however, there are not enough genes to account for the complete biosynthesis of the described structures, suggesting additional genes remain to be identified. In addition, it is not known why some strains express the trisaccharide structure and some the disaccharide structure. In order to find additional genes involved in the biosynthesis of these structures, we used the recently published group A strain Z2491 and group B strain MC58 Neisseria meningitidis genomes and the unfinished Neisseria meningitidis group C strain FAM18 and Neisseria gonorrhoeae strain FA1090 genomes to identify novel genes involved in pilin glycosylation, based on homology to known oligosaccharide biosynthetic genes. We identified a new gene involved in pilin glycosylation designated pglE and examined four additional genes pglB/B2, pglF, pglG and pglH. A strain survey revealed that pglE and pglF were present in each strain examined. The pglG, pglH and pglB2 polymorphisms were not found in strain C311 musical sharp 3 but were present in a large number of clinical isolates. Insertional mutations were constructed in pglE and pglF in N. meningitidis strain C311 musical sharp 3, a strain with well-defined lipopolysaccharide (LPS) and pilin-linked glycan structures. Increased gel migration of the pilin subunit molecules of pglE and pglF mutants was observed by Western analysis, indicating truncation of the trisaccharide structure. Antisera specific for the C311 musical sharp 3 trisaccharide failed to react with pilin from these pglE and pglF mutants. GC-MS analysis of the sugar composition of the pglE mutant showed a reduction in galactose compared with C311 musical sharp 3 wild type. Analysis of amino acid sequence homologies has suggested specific roles for pglE and pglF in the biosynthesis of the trisaccharide structure. Further, we present evidence that pglE, which contains heptanucleotide repeats, is responsible for the phase variation between trisaccharide and disaccharide structures in strain C311 musical sharp 3 and other strains. We also present evidence that pglG, pglH and pglB2 are potentially phase variable.
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Affiliation(s)
- P M Power
- Department of Microbiology and Parasitology, The University of Queensland, Brisbane, Queensland, Australia
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24
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Van Der Wel H, Fisher SZ, West CM. A Bifunctional Diglycosyltransferase Forms the Fucα1,2Galβ1,3-Disaccharide on Skp1 in the Cytoplasm ofDictyostelium. J Biol Chem 2002; 277:46527-34. [PMID: 12244067 DOI: 10.1074/jbc.m208824200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Skp1 is a subunit of the Skp1 cullin-1 F-box protein (SCF) family of E3 ubiquitin ligases and of other regulatory complexes in the cytoplasm and nucleus. In Dictyostelium, Skp1 is modified by a pentasaccharide with the type I blood group H antigen (Fucalpha1,2Galbeta1,3GlcNAc-) at its core. Addition of the Fuc is catalyzed by FT85, a 768-amino acid protein whose fucosyltransferase activity maps to the C-terminal half of the protein. A strain whose FT85 gene is interrupted by a genetic insertion produces a truncated, GlcNAc-terminated glycan on Skp1, suggesting that FT85 may also have beta-galactosyltransferase activity. In support of this model, highly purified native and recombinant FT85 are each able to galactosylate Skp1 from FT85 mutant cells. Site-directed mutagenesis of predicted key amino acids in the N-terminal region of FT85 abolishes Skp1 beta-galactosyltransferase activity with minimal effects on the fucosyltransferase. In addition, a recombinant form of the N-terminal region exhibits beta-galactosyltransferase but not fucosyltransferase activity. Kinetic analysis of FT85 suggests that its two glycosyltransferase activities normally modify Skp1 processively but can have partial function individually. In conclusion, FT85 is a bifunctional diglycosyltransferase that appears to be designed to efficiently extend the Skp1 glycan in vivo.
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Affiliation(s)
- Hanke Van Der Wel
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0235, USA
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25
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West CM, van der Wel H, Gaucher EA. Complex glycosylation of Skp1 in Dictyostelium: implications for the modification of other eukaryotic cytoplasmic and nuclear proteins. Glycobiology 2002; 12:17R-27R. [PMID: 11886837 DOI: 10.1093/glycob/12.2.17r] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Recently, complex O-glycosylation of the cytoplasmic/nuclear protein Skp1 has been characterized in the eukaryotic microorganism Dictyostelium. Skp1's glycosylation is mediated by the sequential action of a prolyl hydroxylase and five conventional sugar nucleotide-dependent glycosyltransferase activities that reside in the cytoplasm rather than the secretory compartment. The Skp1-HyPro GlcNAcTransferase, which adds the first sugar, appears to be related to a lineage of enzymes that originated in the prokaryotic cytoplasm and initiates mucin-type O-linked glycosylation in the lumen of the eukaryotic Golgi apparatus. GlcNAc is extended by a bifunctional glycosyltransferase that mediates the ordered addition of beta1,3-linked Gal and alpha1,2-linked Fuc. The architecture of this enzyme resembles that of certain two-domain prokaryotic glycosyltransferases. The catalytic domains are related to those of a large family of prokaryotic and eukaryotic, cytoplasmic, membrane-bound, inverting glycosyltransferases that modify glycolipids and polysaccharides prior to their translocation across membranes toward the secretory pathway or the cell exterior. The existence of these enzymes in the eukaryotic cytoplasm away from membranes and their ability to modify protein acceptors expose a new set of cytoplasmic and nuclear proteins to potential prolyl hydroxylation and complex O-linked glycosylation.
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Affiliation(s)
- Christopher M West
- Department of Anatomy and Cell Biology, 1600 SW Archer Road, University of Florida College of Medicine, Gainesville, FL 32610-0235, USA
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26
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Tarbouriech N, Charnock SJ, Davies GJ. Three-dimensional structures of the Mn and Mg dTDP complexes of the family GT-2 glycosyltransferase SpsA: a comparison with related NDP-sugar glycosyltransferases. J Mol Biol 2001; 314:655-61. [PMID: 11733986 DOI: 10.1006/jmbi.2001.5159] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The vast majority of glycosidic-bond synthesis in nature is performed by glycosyltransferases, which use activated glycosides as the sugar donor. Typically, the activated leaving group is a nucleoside phosphate, lipid phosphate or phosphate. The nucleotide-sugar-dependent glycosyltransferases fall into over 50 sequence-based families, with the largest and most widespread family of inverting transferases named family GT-2. Here, we present the three-dimensional crystal structure of SpsA, the first and currently the only structural representative from family GT-2, in complex with both Mn-dTDP and Mg-dTDP at a resolution of 2 A. These structures reveal how SpsA and related enzymes may display nucleotide plasticity and permit a comparison of the catalytic centre of this enzyme with those from related sequence families whose three-dimensional structures have recently been determined. Family GT-2 enzymes, together with enzymes from families 7, 13 and 43, appear to form a clan of related structures with identical catalytic apparatus and reaction mechanism.
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Affiliation(s)
- N Tarbouriech
- Department of Chemistry, Structural Biology Laboratory, Heslington, Y010 5DD, UK
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27
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van Der Wel H, Morris HR, Panico M, Paxton T, North SJ, Dell A, Thomson JM, West CM. A non-Golgi alpha 1,2-fucosyltransferase that modifies Skp1 in the cytoplasm of Dictyostelium. J Biol Chem 2001; 276:33952-63. [PMID: 11423539 DOI: 10.1074/jbc.m102555200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Skp1 is a subunit of the SCF-E3 ubiquitin ligase that targets cell cycle and other regulatory factors for degradation. In Dictyostelium, Skp1 is modified by a pentasaccharide containing the type 1 blood group H trisaccharide at its core. To address how the third sugar, fucose alpha1,2-linked to galactose, is attached, a proteomics strategy was applied to determine the primary structure of FT85, previously shown to copurify with the GDP-Fuc:Skp1 alpha 1,2-fucosyltransferase. Tryptic-generated peptides of FT85 were sequenced de novo using Q-TOF tandem mass spectrometry. Degenerate primers were used to amplify FT85 genomic DNA, which was further extended by a novel linker polymerase chain reaction method to yield an intronless open reading frame of 768 amino acids. Disruption of the FT85 gene by homologous recombination resulted in viable cells, which had altered light scattering properties as revealed by flow cytometry. FT85 was necessary and sufficient for Skp1 fucosylation, based on biochemical analysis of FT85 mutant cells and Escherichia coli that express FT85 recombinantly. FT85 lacks sequence motifs that characterize all other known alpha 1,2-fucosyltransferases and lacks the signal-anchor sequence that targets them to the secretory pathway. The C-terminal region of FT85 harbors motifs found in inverting Family 2 glycosyltransferase domains, and its expression in FT85 mutant cells restores fucosyltransferase activity toward a simple disaccharide substrate. Whereas most prokaryote and eukaryote Family 2 glycosyltransferases are membrane-bound and oriented toward the cytoplasm where they glycosylate lipid-linked or polysaccharide precursors prior to membrane translocation, the soluble, eukaryotic Skp1-fucosyltransferase modifies a protein that resides in the cytoplasm and nucleus.
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Affiliation(s)
- H van Der Wel
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0235 and the Department of Biochemistry, Imperial College, London SW7 2AY United Kingdom
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28
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Hoffmeister D, Ichinose K, Bechthold A. Two sequence elements of glycosyltransferases involved in urdamycin biosynthesis are responsible for substrate specificity and enzymatic activity. CHEMISTRY & BIOLOGY 2001; 8:557-67. [PMID: 11410375 DOI: 10.1016/s1074-5521(01)00039-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Two deoxysugar glycosyltransferases (GTs), UrdGT1b and UrdGT1c, involved in urdamycin biosynthesis share 91% identical amino acids. However, the two GTs show different specificities for both nucleotide sugar and acceptor substrate. Generally, it is proposed that GTs are two-domain proteins with a nucleotide binding domain and an acceptor substrate site with the catalytic center in an interface cleft between these domains. Our work aimed at finding out the region responsible for determination of substrate specificities of these two urdamycin GTs. RESULTS A series of 10 chimeric GT genes were constructed consisting of differently sized and positioned portions of urdGT1b and urdGT1c. Gene expression experiments in host strains Streptomyces fradiae Ax and XTC show that nine of 10 chimeric GTs are still functional, with either UrdGT1b- or UrdGT1c-like activity. A 31 amino acid region (aa 52-82) located close to the N-terminus of these enzymes, which differs in 18 residues, was identified to control both sugar donor and acceptor substrate specificity. Only one chimeric gene product of the 10 was not functional. Targeted stepwise alterations of glycine 226 (G226R, G226S, G226SR) were made to reintroduce residues conserved among streptomycete GTs. Alterations G226S and G226R restored a weak activity, whereas G226SR showed an activity comparable with other functional chimeras. CONCLUSIONS A nucleotide sugar binding motif is present in the C-terminal moiety of UrdGT1b and UrdGT1c from S. fradiae. We could demonstrate that it is an N-terminal section that determines specificity for the nucleotide sugar and also the acceptor substrate. This finding directs the way towards engineering this class of streptomycete enzymes for antibiotic derivatization applications. Amino acids 226 and 227, located outside the putative substrate binding site, might be part of a larger protein structure, perhaps a solvent channel to the catalytic center. Therefore, they could play a role in substrate accessibility to it.
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Affiliation(s)
- D Hoffmeister
- Albert-Ludwigs-Universität Freiburg, Pharmazeutische Biologie, Stefan-Meier-Strasse, Germany
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29
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Charnock SJ, Henrissat B, Davies GJ. Three-dimensional structures of UDP-sugar glycosyltransferases illuminate the biosynthesis of plant polysaccharides. PLANT PHYSIOLOGY 2001; 125:527-31. [PMID: 11161010 PMCID: PMC1539363 DOI: 10.1104/pp.125.2.527] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- S J Charnock
- Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
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30
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Keenleyside WJ, Clarke AJ, Whitfield C. Identification of residues involved in catalytic activity of the inverting glycosyl transferase WbbE from Salmonella enterica serovar borreze. J Bacteriol 2001; 183:77-85. [PMID: 11114903 PMCID: PMC94852 DOI: 10.1128/jb.183.1.77-85.2001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synthesis of the O:54 O antigen of Salmonella enterica is initiated by the nonprocessive glycosyl transferase WbbE, assigned to family 2 of the glycosyl transferase enzymes (GT2). GT2 enzymes possess a characteristic N-terminal domain, domain A. Based on structural data from the GT2 representative SpsA (S. J. Charnock and G. J. Davies, Biochemistry 38:6380-6385, 1999), this domain is responsible for nucleotide binding. It possesses two invariant Asp residues, the first forming a hydrogen bond to uracil and the second coordinating a Mn(2+) ion. Site-directed replacement of Asp41 (D41A) of WbbE, the analogue of the first Asp residue of SpsA, revealed that this is not required for activity. WbbE possesses three Asp residues near the position analogous to the second conserved residue. Whereas D95A reduced WbbE activity, activity in D93A and D96A mutants was abrogated, suggesting that either D93 or D96 may coordinate the Mn(2+) ion. Our studies also identified a C-terminal region of sequence conservation in 22 GT2 members, including WbbE. SpsA was not among these. This region is characterized by an ED(Y) motif. The Glu and Asp residues of this motif were individually replaced in WbbE. E180D in WbbE had greatly reduced activity, and an E180Q replacement completely abrogated activity; however, D181E had no effect. E180 is predicted to reside on a turn. Combined with the alignment of the motif with potential catalytic residues in the GT2 enzymes ExoM and SpsA, we speculate that E180 is the catalytic residue of WbbE. Sequence and predicted structural divergence in the catalytic region of GT2 members suggests that this is not a homogeneous family.
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Affiliation(s)
- W J Keenleyside
- Department of Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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31
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Jolly L, Stingele F. Molecular organization and functionality of exopolysaccharide gene clusters in lactic acid bacteria. Int Dairy J 2001. [DOI: 10.1016/s0958-6946(01)00117-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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Abdian PL, Lellouch AC, Gautier C, Ielpi L, Geremia RA. Identification of essential amino acids in the bacterial alpha -mannosyltransferase aceA. J Biol Chem 2000; 275:40568-75. [PMID: 11001941 DOI: 10.1074/jbc.m007496200] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The alpha-mannosyltransferase AceA from Acetobacter xylinum belongs to the CaZY family 4 of retaining glycosyltransferases. We have identified a series of either highly conserved or invariant residues that are found in all family 4 enzymes as well as other retaining glycosyltransferases. These residues included Glu-287 and Glu-295, which comprise an EX(7)E motif and have been proposed to be involved in catalysis. Alanine replacements of each conserved residue were constructed by site-directed mutagenesis. The mannosyltransferase activity of each mutant was examined by both an in vitro transferase assay using recombinant mutant AceA expressed in Escherichia coli and by an in vivo rescue assay by expressing the mutant AceA in a Xanthomonas campestris gumH(-) strain. We found that only mutants K211A and E287A lost all detectable activity both in vitro and in vivo, whereas E295A retained residual activity in the more sensitive in vivo assay. H127A and S162A each retained reduced but significant activities both in vitro and in vivo. Secondary structure predictions of AceA and subsequent comparison with the crystal structures of the T4 beta-glucosyltransferase and MurG suggest that AceA Lys-211 and Glu-295 are involved in nucleotide sugar donor binding, leaving Glu-287 of the EX(7)E as a potential catalytic residue.
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Affiliation(s)
- P L Abdian
- Instituto de Investigaciones Bioquimicas Fundación Campomar, Facultad de Ciencias Exactas y Naturales, y Consejo Nacional de Investigaciones Cientificas y Técnicas, Avenida Patricias Argentinas 435, 1045 Buenos Aires, Argentina
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Abstract
The high-resolution X-ray crystal structures of a new form of bacteriophage T4 beta-glucosyltransferase, Escherichia coli MurG, Bacillus subtilis SpsA, bovine beta-1,4-galactosyltransferase 1 and rabbit N-acetylglucosaminyltransferase I have now been solved. These glycosyltransferase structures have provided the first detailed view of the structural basis of catalysis, as well as new insight into glycosyltransferase classification.
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Affiliation(s)
- U M Unligil
- Departments of Molecular and Medical Genetics and Biochemistry, University of Toronto, Ontario, M5S 1A8, Toronto, Canada
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