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Wyllie JA, McKay MV, Barrow AS, Soares da Costa TP. Biosynthesis of uridine diphosphate N-Acetylglucosamine: An underexploited pathway in the search for novel antibiotics? IUBMB Life 2022; 74:1232-1252. [PMID: 35880704 PMCID: PMC10087520 DOI: 10.1002/iub.2664] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/04/2022] [Indexed: 11/06/2022]
Abstract
Although the prevalence of antibiotic resistance is increasing at an alarming rate, there are a dwindling number of effective antibiotics available. Thus, the development of novel antibacterial agents should be of utmost importance. Peptidoglycan biosynthesis has been and is still an attractive source for antibiotic targets; however, there are several components that remain underexploited. In this review, we examine the enzymes involved in the biosynthesis of one such component, UDP-N-acetylglucosamine, an essential building block and precursor of bacterial peptidoglycan. Furthermore, given the presence of a similar biosynthesis pathway in eukaryotes, we discuss the current knowledge on the differences and similarities between the bacterial and eukaryotic enzymes. Finally, this review also summarises the recent advances made in the development of inhibitors targeting the bacterial enzymes.
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Affiliation(s)
- Jessica A Wyllie
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Mirrin V McKay
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew S Barrow
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Tatiana P Soares da Costa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
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2
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Ruegenberg S, Mayr FAMC, Atanassov I, Baumann U, Denzel MS. Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1. Nat Commun 2021; 12:2176. [PMID: 33846315 PMCID: PMC8041777 DOI: 10.1038/s41467-021-22320-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/10/2021] [Indexed: 02/01/2023] Open
Abstract
The hexosamine pathway (HP) is a key anabolic pathway whose product uridine 5'-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc) is an essential precursor for glycosylation processes in mammals. It modulates the ER stress response and HP activation extends lifespan in Caenorhabditis elegans. The highly conserved glutamine fructose-6-phosphate amidotransferase 1 (GFAT-1) is the rate-limiting HP enzyme. GFAT-1 activity is modulated by UDP-GlcNAc feedback inhibition and via phosphorylation by protein kinase A (PKA). Molecular consequences of GFAT-1 phosphorylation, however, remain poorly understood. Here, we identify the GFAT-1 R203H substitution that elevates UDP-GlcNAc levels in C. elegans. In human GFAT-1, the R203H substitution interferes with UDP-GlcNAc inhibition and with PKA-mediated Ser205 phosphorylation. Our data indicate that phosphorylation affects the interactions of the two GFAT-1 domains to control catalytic activity. Notably, Ser205 phosphorylation has two discernible effects: it lowers baseline GFAT-1 activity and abolishes UDP-GlcNAc feedback inhibition. PKA controls the HP by uncoupling the metabolic feedback loop of GFAT-1.
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Affiliation(s)
- Sabine Ruegenberg
- grid.419502.b0000 0004 0373 6590Max Planck Institute for Biology of Ageing, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Felix A. M. C. Mayr
- grid.419502.b0000 0004 0373 6590Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ilian Atanassov
- grid.419502.b0000 0004 0373 6590Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ulrich Baumann
- grid.6190.e0000 0000 8580 3777Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Martin S. Denzel
- grid.419502.b0000 0004 0373 6590Max Planck Institute for Biology of Ageing, Cologne, Germany ,grid.6190.e0000 0000 8580 3777CECAD - Cluster of Excellence, University of Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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3
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Oliveira IA, Allonso D, Fernandes TVA, Lucena DMS, Ventura GT, Dias WB, Mohana-Borges RS, Pascutti PG, Todeschini AR. Enzymatic and structural properties of human glutamine:fructose-6-phosphate amidotransferase 2 (hGFAT2). J Biol Chem 2020; 296:100180. [PMID: 33303629 PMCID: PMC7948480 DOI: 10.1074/jbc.ra120.015189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 11/24/2022] Open
Abstract
Glycoconjugates play a central role in several cellular processes, and alteration in their composition is associated with numerous human pathologies. Substrates for cellular glycosylation are synthesized in the hexosamine biosynthetic pathway, which is controlled by the glutamine:fructose-6-phosphate amidotransfera-se (GFAT). Human isoform 2 GFAT (hGFAT2) has been implicated in diabetes and cancer; however, there is no information about structural and enzymatic properties of this enzyme. Here, we report a successful expression and purification of a catalytically active recombinant hGFAT2 (rhGFAT2) in Escherichia coli cells fused or not to a HisTag at the C-terminal end. Our enzyme kinetics data suggest that hGFAT2 does not follow the expected ordered bi–bi mechanism, and performs the glucosamine-6-phosphate synthesis much more slowly than previously reported for other GFATs. In addition, hGFAT2 is able to isomerize fructose-6-phosphate into glucose-6-phosphate even in the presence of equimolar amounts of glutamine, which results in unproductive glutamine hydrolysis. Structural analysis of a three-dimensional model of rhGFAT2, corroborated by circular dichroism data, indicated the presence of a partially structured loop in the glutaminase domain, whose sequence is present in eukaryotic enzymes but absent in the E. coli homolog. Molecular dynamics simulations suggest that this loop is the most flexible portion of the protein and plays a key role on conformational states of hGFAT2. Thus, our study provides the first comprehensive set of data on the structure, kinetics, and mechanics of hGFAT2, which will certainly contribute to further studies on the (patho)physiology of hGFAT2.
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Affiliation(s)
- Isadora A Oliveira
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
| | - Diego Allonso
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, UFRJ, Rio de Janeiro, RJ, Brazil
| | - Tácio V A Fernandes
- Laboratório de Modelagem e Dinâmica Molecular, IBCCF, UFRJ, Rio de Janeiro, RJ, Brazil; Laboratório de Macromoléculas, Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Duque de Caxias, RJ, Brazil
| | - Daniela M S Lucena
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gustavo T Ventura
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Wagner Barbosa Dias
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Pedro G Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, IBCCF, UFRJ, Rio de Janeiro, RJ, Brazil
| | - Adriane R Todeschini
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
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4
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Coussement P, Bauwens D, Peters G, Maertens J, De Mey M. Mapping and refactoring pathway control through metabolic and protein engineering: The hexosamine biosynthesis pathway. Biotechnol Adv 2020; 40:107512. [DOI: 10.1016/j.biotechadv.2020.107512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/07/2019] [Accepted: 09/30/2019] [Indexed: 01/14/2023]
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5
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Khan MA, Durica-Mitic S, Göpel Y, Heermann R, Görke B. Small RNA-binding protein RapZ mediates cell envelope precursor sensing and signaling in Escherichia coli. EMBO J 2020; 39:e103848. [PMID: 32065419 PMCID: PMC7073468 DOI: 10.15252/embj.2019103848] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 11/24/2022] Open
Abstract
The RNA‐binding protein RapZ cooperates with small RNAs (sRNAs) GlmY and GlmZ to regulate the glmS mRNA in Escherichia coli. Enzyme GlmS synthesizes glucosamine‐6‐phosphate (GlcN6P), initiating cell envelope biosynthesis. GlmZ activates glmS expression by base‐pairing. When GlcN6P is ample, GlmZ is bound by RapZ and degraded through ribonuclease recruitment. Upon GlcN6P depletion, the decoy sRNA GlmY accumulates through a previously unknown mechanism and sequesters RapZ, suppressing GlmZ decay. This circuit ensures GlcN6P homeostasis and thereby envelope integrity. In this work, we identify RapZ as GlcN6P receptor. GlcN6P‐free RapZ stimulates phosphorylation of the two‐component system QseE/QseF by interaction, which in turn activates glmY expression. Elevated GlmY levels sequester RapZ into stable complexes, which prevents GlmZ decay, promoting glmS expression. Binding of GlmY also prevents RapZ from activating QseE/QseF, generating a negative feedback loop limiting the response. When GlcN6P is replenished, GlmY is released from RapZ and rapidly degraded. We reveal a multifunctional sRNA‐binding protein that dynamically engages into higher‐order complexes for metabolite signaling.
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Affiliation(s)
- Muna A Khan
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Svetlana Durica-Mitic
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Yvonne Göpel
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Ralf Heermann
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
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6
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Peacock RB, Hicks CW, Walker AM, Dewing SM, Lewis KM, Abboud JC, Stewart SWA, Kang C, Watson JM. Structural and Functional Characterization of Dynamic Oligomerization in Burkholderia cenocepacia HMG-CoA Reductase. Biochemistry 2019; 58:3960-3970. [PMID: 31469273 DOI: 10.1021/acs.biochem.9b00494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR), in most organisms, catalyzes the four-electron reduction of the thioester (S)-HMG-CoA to the primary alcohol (R)-mevalonate, utilizing NADPH as the hydride donor. In some organisms, including the opportunistic lung pathogen Burkholderia cenocepacia, it catalyzes the reverse reaction, utilizing NAD+ as a hydride acceptor in the oxidation of mevalonate. B. cenocepacia HMGR has been previously shown to exist as an ensemble of multiple non-additive oligomeric states, each with different levels of enzymatic activity, suggesting that the enzyme exhibits characteristics of the morpheein model of allostery. We have characterized a number of factors, including pH, substrate concentration, and enzyme concentration, that modulate the structural transitions that influence the interconversion among the multiple oligomers. We have also determined the crystal structure of B. cenocepacia HMGR in the hexameric state bound to coenzyme A and ADP. This hexameric assembly provides important clues about how the transition among oligomers might occur, and why B. cenocepacia HMGR, unique among characterized HMGRs, exhibits morpheein-like behavior.
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Affiliation(s)
- Riley B Peacock
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Chad W Hicks
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Alexander M Walker
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Sophia M Dewing
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Kevin M Lewis
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Jean-Claude Abboud
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Samuel W A Stewart
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - ChulHee Kang
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - Jeffrey M Watson
- Department of Chemistry and Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
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7
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Kwiatkowska-Semrau K, Wojciechowski M, Gabriel I, Crucho S, Milewski S. Modification of quaternary structure of Candida albicans GlcN-6-P synthase and its desensitization to inhibition by UDP-GlcNAc by site-directed mutagenesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1181-1189. [DOI: 10.1016/j.bbapap.2018.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/15/2018] [Indexed: 02/02/2023]
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8
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Hardouin P, Velours C, Bou-Nader C, Assrir N, Laalami S, Putzer H, Durand D, Golinelli-Pimpaneau B. Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding. Biophys J 2018; 115:2102-2113. [PMID: 30447990 DOI: 10.1016/j.bpj.2018.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 09/17/2018] [Accepted: 10/17/2018] [Indexed: 12/12/2022] Open
Abstract
Although RNase Y acts as the key enzyme initiating messenger RNA decay in Bacillus subtilis and likely in many other Gram-positive bacteria, its three-dimensional structure remains unknown. An antibody belonging to the rare immunoglobulin G (IgG) 2b λx isotype was raised against a 12-residue conserved peptide from the N-terminal noncatalytic domain of B. subtilis RNase Y (BsRNaseY) that is predicted to be intrinsically disordered. Here, we show that this domain can be produced as a stand-alone protein called Nter-BsRNaseY that undergoes conformational changes between monomeric and dimeric forms. Circular dichroism and size exclusion chromatography coupled with multiangle light scattering or with small angle x-ray scattering indicate that the Nter-BsRNaseY dimer displays an elongated form and a high content of α-helices, in agreement with the existence of a central coiled-coil structure appended with flexible ends, and that the monomeric state of Nter-BsRNaseY is favored upon binding the fragment antigen binding (Fab) of the antibody. The dissociation constants of the IgG/BsRNaseY, IgG/Nter-BsRNaseY, and IgG/peptide complexes indicate that the affinity of the IgG for Nter-BsRNaseY is in the nM range and suggest that the peptide is less accessible in BsRNaseY than in Nter-BsRNaseY. The crystal structure of the Fab in complex with the peptide antigen shows that the peptide adopts an elongated U-shaped conformation in which the unique hydrophobic residue of the peptide, Leu6, is completely buried. The peptide/Fab complex may mimic the interaction of a microdomain of the N-terminal domain of BsRNaseY with one of its cellular partners within the degradosome complex. Altogether, our results suggest that BsRNaseY may become accessible for protein interaction upon dissociation of its N-terminal domain into the monomeric form.
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Affiliation(s)
- Pierre Hardouin
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Pierre et Marie Curie, Paris CEDEX 05, France
| | - Christophe Velours
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France
| | - Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Pierre et Marie Curie, Paris CEDEX 05, France
| | - Nadine Assrir
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Soumaya Laalami
- CNRS UMR8261-Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Harald Putzer
- CNRS UMR8261-Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Pierre et Marie Curie, Paris CEDEX 05, France.
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Identification of a Direct Biosynthetic Pathway for UDP- N-Acetylgalactosamine from Glucosamine-6-Phosphate in Thermophilic Crenarchaeon Sulfolobus tokodaii. J Bacteriol 2018; 200:JB.00048-18. [PMID: 29507091 DOI: 10.1128/jb.00048-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/23/2018] [Indexed: 11/20/2022] Open
Abstract
Most organisms, from Bacteria to Eukarya, synthesize UDP-N-acetylglucosamine (UDP-GlcNAc) from fructose-6-phosphate via a four-step reaction, and UDP-N-acetylgalactosamine (UDP-GalNAc) can only be synthesized from UDP-GlcNAc by UDP-GlcNAc 4-epimerase. In Archaea, the bacterial-type UDP-GlcNAc biosynthetic pathway was reported for Methanococcales. However, the complete biosynthetic pathways for UDP-GlcNAc and UDP-GalNAc present in one archaeal species are unidentified. Previous experimental analyses on enzymatic activities of the ST0452 protein, identified from the thermophilic crenarchaeon Sulfolobus tokodaii, predicted the presence of both a bacterial-type UDP-GlcNAc and an independent UDP-GalNAc biosynthetic pathway in this archaeon. In the present work, functional analyses revealed that the recombinant ST2186 protein possessed an glutamine:fructose-6-phosphate amidotransferase activity and that the recombinant ST0242 protein possessed a phosphoglucosamine-mutase activity. Along with the acetyltransferase and uridyltransferase activities of the ST0452 protein, the activities of the ST2186 and ST0242 proteins confirmed the presence of a bacterial-type UDP-GlcNAc biosynthetic pathway in S. tokodaii In contrast, the UDP-GlcNAc 4-epimerase homologue gene was not detected within the genomic data. Thus, it was expected that galactosamine-1-phosphate or galactosamine-6-phosphate (GalN-6-P) was provided by conversion of glucosamine-1-phosphate or glucosamine-6-phosphate (GlcN-6-P). A novel epimerase converting GlcN-6-P to GalN-6-P was detected in a cell extract of S. tokodaii, and the N-terminal sequence of the purified protein indicated that the novel epimerase was encoded by the ST2245 gene. Along with the ST0242 phosphogalactosamine-mutase activity, this observation confirmed the presence of a novel UDP-GalNAc biosynthetic pathway from GlcN-6-P in S. tokodaii Discovery of the novel pathway provides a new insight into the evolution of nucleotide sugar metabolic pathways.IMPORTANCE In this work, a novel protein capable of directly converting glucosamine-6-phosphate to galactosamine-6-phosphate was successfully purified from a cell extract of the thermophilic crenarchaeon Sulfolobus tokodaii Confirmation of this novel activity using the recombinant protein indicates that S. tokodaii possesses a novel UDP-GalNAc biosynthetic pathway derived from glucosamine-6-phosphate. The distributions of this and related genes indicate the presence of three different types of UDP-GalNAc biosynthetic pathways: a direct pathway using a novel enzyme and two conversion pathways from UDP-GlcNAc using known enzymes. Additionally, Crenarchaeota species lacking all three pathways were found, predicting the presence of one more unknown pathway. Identification of these novel proteins and pathways provides important insights into the evolution of nucleotide sugar biosynthesis, as well as being potentially important industrially.
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Beneito-Cambra M, Gareil P, Badet B, Badet-Denisot MA, Delaunay N. First investigations for the characterization of glucosamine-6-phosphate synthase by capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1072:130-135. [DOI: 10.1016/j.jchromb.2017.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 12/13/2022]
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11
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Tanner JJ. Empirical power laws for the radii of gyration of protein oligomers. Acta Crystallogr D Struct Biol 2016; 72:1119-1129. [PMID: 27710933 PMCID: PMC5053138 DOI: 10.1107/s2059798316013218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 08/16/2016] [Indexed: 11/10/2022] Open
Abstract
The radius of gyration is a fundamental structural parameter that is particularly useful for describing polymers. It has been known since Flory's seminal work in the mid-20th century that polymers show a power-law dependence, where the radius of gyration is proportional to the number of residues raised to a power. The power-law exponent has been measured experimentally for denatured proteins and derived empirically for folded monomeric proteins using crystal structures. Here, the biological assemblies in the Protein Data Bank are surveyed to derive the power-law parameters for protein oligomers having degrees of oligomerization of 2-6 and 8. The power-law exponents for oligomers span a narrow range of 0.38-0.41, which is close to the value of 0.40 obtained for monomers. This result shows that protein oligomers exhibit essentially the same power-law behavior as monomers. A simple power-law formula is provided for estimating the oligomeric state from an experimental measurement of the radius of gyration. Several proteins in the Protein Data Bank are found to deviate substantially from power-law behavior by having an atypically large radius of gyration. Some of the outliers have highly elongated structures, such as coiled coils. For coiled coils, the radius of gyration does not follow a power law and instead scales linearly with the number of residues in the oligomer. Other outliers are proteins whose oligomeric state or quaternary structure is incorrectly annotated in the Protein Data Bank. The power laws could be used to identify such errors and help prevent them in future depositions.
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Affiliation(s)
- John J. Tanner
- Departments of Biochemistry and Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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12
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Yoo W, Yoon H, Seok YJ, Lee CR, Lee HH, Ryu S. Fine-tuning of amino sugar homeostasis by EIIA(Ntr) in Salmonella Typhimurium. Sci Rep 2016; 6:33055. [PMID: 27628932 PMCID: PMC5024086 DOI: 10.1038/srep33055] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/17/2016] [Indexed: 11/08/2022] Open
Abstract
The nitrogen-metabolic phosphotransferase system, PTS(Ntr), consists of the enzymes I(Ntr), NPr and IIA(Ntr) that are encoded by ptsP, ptsO, and ptsN, respectively. Due to the proximity of ptsO and ptsN to rpoN, the PTS(Ntr) system has been postulated to be closely related with nitrogen metabolism. To define the correlation between PTS(Ntr) and nitrogen metabolism, we performed ligand fishing with EIIA(Ntr) as a bait and revealed that D-glucosamine-6-phosphate synthase (GlmS) directly interacted with EIIA(Ntr). GlmS, which converts D-fructose-6-phosphate (Fru6P) into D-glucosamine-6-phosphate (GlcN6P), is a key enzyme producing amino sugars through glutamine hydrolysis. Amino sugar is an essential structural building block for bacterial peptidoglycan and LPS. We further verified that EIIA(Ntr) inhibited GlmS activity by direct interaction in a phosphorylation-state-dependent manner. EIIA(Ntr) was dephosphorylated in response to excessive nitrogen sources and was rapidly degraded by Lon protease upon amino sugar depletion. The regulation of GlmS activity by EIIA(Ntr) and the modulation of glmS translation by RapZ suggest that the genes comprising the rpoN operon play a key role in maintaining amino sugar homeostasis in response to nitrogen availability and the amino sugar concentration in the bacterial cytoplasm.
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Affiliation(s)
- Woongjae Yoo
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Korea
| | - Yeong-Jae Seok
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido 17058, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
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13
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Göpel Y, Khan MA, Görke B. Ménage à trois: post-transcriptional control of the key enzyme for cell envelope synthesis by a base-pairing small RNA, an RNase adaptor protein, and a small RNA mimic. RNA Biol 2014; 11:433-42. [PMID: 24667238 PMCID: PMC4152352 DOI: 10.4161/rna.28301] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In Escherichia coli, small RNAs GlmY and GlmZ feedback control synthesis of glucosamine-6-phosphate (GlcN6P) synthase GlmS, a key enzyme required for synthesis of the cell envelope. Both small RNAs are highly similar, but only GlmZ is able to activate the glmS mRNA by base-pairing. Abundance of GlmZ is controlled at the level of decay by RNase adaptor protein RapZ. RapZ binds and targets GlmZ to degradation by RNase E via protein–protein interaction. GlmY activates glmS indirectly by protecting GlmZ from degradation. Upon GlcN6P depletion, GlmY accumulates and sequesters RapZ in an RNA mimicry mechanism, thus acting as an anti-adaptor. As a result, this regulatory circuit adjusts synthesis of GlmS to the level of its enzymatic product, thereby mediating GlcN6P homeostasis. The interplay of RNase adaptor proteins and anti-adaptors provides an elegant means how globally acting RNases can be re-programmed to cleave a specific transcript in response to a cognate stimulus.
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Affiliation(s)
- Yvonne Göpel
- Max F. Perutz Laboratories; Department of Microbiology; Immunobiology and Genetics; Center of Molecular Biology; University of Vienna; Vienna, Austria
| | - Muna A Khan
- Max F. Perutz Laboratories; Department of Microbiology; Immunobiology and Genetics; Center of Molecular Biology; University of Vienna; Vienna, Austria
| | - Boris Görke
- Max F. Perutz Laboratories; Department of Microbiology; Immunobiology and Genetics; Center of Molecular Biology; University of Vienna; Vienna, Austria
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Jaffe EK. Impact of quaternary structure dynamics on allosteric drug discovery. Curr Top Med Chem 2013; 13:55-63. [PMID: 23409765 DOI: 10.2174/1568026611313010006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 11/22/2022]
Abstract
The morpheein model of allosteric regulation draws attention to proteins that can exist as an equilibrium of functionally distinct assemblies where: one subunit conformation assembles into one multimer; a different subunit conformation assembles into a different multimer; and the various multimers are in a dynamic equilibrium whose position can be modulated by ligands that bind to a multimer-specific ligand binding site. The case study of porphobilinogen synthase (PBGS) illustrates how such an equilibrium holds lessons for disease mechanisms, drug discovery, understanding drug side effects, and identifying proteins wherein drug discovery efforts might focus on quaternary structure dynamics. The morpheein model of allostery has been proposed as applicable for a wide assortment of disease-associated proteins (Selwood, T., Jaffe, E., (2012) Arch. Bioch. Biophys, 519:131-143). Herein we discuss quaternary structure dynamics aspects to drug discovery for the disease-associated putative morpheeins phenylalanine hydroxylase, HIV integrase, pyruvate kinase, and tumor necrosis factor α. Also highlighted is the quaternary structure equilibrium of transthyretin and successful drug discovery efforts focused on controlling its quaternary structure dynamics.
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Affiliation(s)
- Eileen K Jaffe
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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15
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Wilson MZ, Gitai Z. Beyond the cytoskeleton: mesoscale assemblies and their function in spatial organization. Curr Opin Microbiol 2013; 16:177-83. [PMID: 23601587 DOI: 10.1016/j.mib.2013.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 03/06/2013] [Accepted: 03/06/2013] [Indexed: 10/27/2022]
Abstract
Recent studies have identified a growing number of mesoscale protein assemblies in both bacterial and eukaryotic cells. Traditionally, these polymeric assemblies are thought to provide structural support for the cell and thus have been classified as the cytoskeleton. However a new class of macromolecular structure is emerging as an organizer of cellular processes that occur on scales hundreds of times larger than a single protein. We propose two types of self-assembling structures, dynamic globules and crystalline scaffolds, and suggest they provide a means to achieve cell-scale order. We discuss general mechanisms for assembly and regulation. Finally, we discuss assemblies that are found to organize metabolism and what possible mechanisms may serve these metabolic enzyme complexes.
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Affiliation(s)
- Maxwell Z Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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