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Tan YZ, Zhang L, Rodrigues J, Zheng RB, Giacometti SI, Rosário AL, Kloss B, Dandey VP, Wei H, Brunton R, Raczkowski AM, Athayde D, Catalão MJ, Pimentel M, Clarke OB, Lowary TL, Archer M, Niederweis M, Potter CS, Carragher B, Mancia F. Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria. Mol Cell 2020; 78:683-699.e11. [PMID: 32386575 PMCID: PMC7263364 DOI: 10.1016/j.molcel.2020.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/21/2020] [Accepted: 04/13/2020] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis causes tuberculosis, a disease that kills over 1 million people each year. Its cell envelope is a common antibiotic target and has a unique structure due, in part, to two lipidated polysaccharides-arabinogalactan and lipoarabinomannan. Arabinofuranosyltransferase D (AftD) is an essential enzyme involved in assembling these glycolipids. We present the 2.9-Å resolution structure of M. abscessus AftD, determined by single-particle cryo-electron microscopy. AftD has a conserved GT-C glycosyltransferase fold and three carbohydrate-binding modules. Glycan array analysis shows that AftD binds complex arabinose glycans. Additionally, AftD is non-covalently complexed with an acyl carrier protein (ACP). 3.4- and 3.5-Å structures of a mutant with impaired ACP binding reveal a conformational change, suggesting that ACP may regulate AftD function. Mutagenesis experiments using a conditional knockout constructed in M. smegmatis confirm the essentiality of the putative active site and the ACP binding for AftD function.
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Affiliation(s)
- Yong Zi Tan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - José Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | | | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ana L Rosário
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Brian Kloss
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY 10027, USA
| | - Venkata P Dandey
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Hui Wei
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Richard Brunton
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ashleigh M Raczkowski
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Diogo Athayde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; Department of Anesthesiology, Columbia University, New York, NY 10032, USA
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128 Nangang, Taipei 11529, Taiwan
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
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Kalita M, Parker MFL, Luu JM, Stewart MN, Blecha JE, VanBrocklin HF, Evans MJ, Flavell RR, Rosenberg OS, Ohliger MA, Wilson DM. Arabinofuranose-derived positron-emission tomography radiotracers for detection of pathogenic microorganisms. J Labelled Comp Radiopharm 2020; 63:231-239. [PMID: 32222086 DOI: 10.1002/jlcr.3835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/06/2020] [Accepted: 02/26/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE Detection of bacteria-specific metabolism via positron emission tomography (PET) is an emerging strategy to image human pathogens, with dramatic implications for clinical practice. In silico and in vitro screening tools have recently been applied to this problem, with several monosaccharides including l-arabinose showing rapid accumulation in Escherichia coli and other organisms. Our goal for this study was to evaluate several synthetically viable arabinofuranose-derived 18 F analogs for their incorporation into pathogenic bacteria. PROCEDURES We synthesized four radiolabeled arabinofuranose-derived sugars: 2-deoxy-2-[18 F]fluoro-arabinofuranoses (d-2-18 F-AF and l-2-18 F-AF) and 5-deoxy-5-[18 F]fluoro-arabinofuranoses (d-5-18 F-AF and l-5-18 F-AF). The arabinofuranoses were synthesized from 18 F- via triflated, peracetylated precursors analogous to the most common radiosynthesis of 2-deoxy-2-[18 F]fluoro-d-glucose ([18 F]FDG). These radiotracers were screened for their uptake into E. coli and Staphylococcus aureus. Subsequently, the sensitivity of d-2-18 F-AF and l-2-18 F-AF to key human pathogens was investigated in vitro. RESULTS All 18 F radiotracer targets were synthesized in high radiochemical purity. In the screening study, d-2-18 F-AF and l-2-18 F-AF showed greater accumulation in E. coli than in S. aureus. When evaluated in a panel of pathologic microorganisms, both d-2-18 F-AF and l-2-18 F-AF demonstrated sensitivity to most gram-positive and gram-negative bacteria. CONCLUSIONS Arabinofuranose-derived 18 F PET radiotracers can be synthesized with high radiochemical purity. Our study showed absence of bacterial accumulation for 5-substitued analogs, a finding that may have mechanistic implications for related tracers. Both d-2-18 F-AF and l-2-18 F-AF showed sensitivity to most gram-negative and gram-positive organisms. Future in vivo studies will evaluate the diagnostic accuracy of these radiotracers in animal models of infection.
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Affiliation(s)
- Mausam Kalita
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Matthew F L Parker
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Justin M Luu
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Megan N Stewart
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Joseph E Blecha
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Henry F VanBrocklin
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Michael J Evans
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Robert R Flavell
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Oren S Rosenberg
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Michael A Ohliger
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California.,Department of Radiology, Zuckerberg San Francisco General Hospital, San Francisco, California
| | - David M Wilson
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
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Saqib A, Scheller HV, Fredslund F, Welner DH. Molecular characteristics of plant UDP-arabinopyranose mutases. Glycobiology 2020; 29:839-846. [PMID: 31679023 PMCID: PMC6861824 DOI: 10.1093/glycob/cwz067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/22/2019] [Accepted: 08/22/2019] [Indexed: 12/13/2022] Open
Abstract
l-arabinofuranose is a ubiquitous component of the cell wall and various natural products in plants, where it is synthesized from cytosolic UDP-arabinopyranose (UDP-Arap). The biosynthetic machinery long remained enigmatic in terms of responsible enzymes and subcellular localization. With the discovery of UDP-Arap mutase in plant cytosol, the demonstration of its role in cell-wall arabinose incorporation and the identification of UDP-arabinofuranose transporters in the Golgi membrane, it is clear that the cytosolic UDP-Arap mutases are the key enzymes converting UDP-Arap to UDP-arabinofuranose for cell wall and natural product biosynthesis. This has recently been confirmed by several genotype/phenotype studies. In contrast to the solid evidence pertaining to UDP-Arap mutase function in vivo, the molecular features, including enzymatic mechanism and oligomeric state, remain unknown. However, these enzymes belong to the small family of proteins originally identified as reversibly glycosylated polypeptides (RGPs), which has been studied for >20 years. Here, we review the UDP-Arap mutase and RGP literature together, to summarize and systemize reported molecular characteristics and relations to other proteins.
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Affiliation(s)
- Anam Saqib
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Kongens Lyngby, DK-2800, Denmark.,Industrial Enzymes and Biofuels Group, National Institute for Biotechnology and Genetic Engineering, Jhang Road, 44000 Faisalabad, Pakistan
| | - Henrik Vibe Scheller
- Feedstocks Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Environmental Engineering and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Folmer Fredslund
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Kongens Lyngby, DK-2800, Denmark
| | - Ditte Hededam Welner
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Kongens Lyngby, DK-2800, Denmark
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Pathak AK, Pathak V, Seitz L, Gurcha SS, Besra GS, Riordan JM, Reynolds RC. Disaccharide analogs as probes for glycosyltransferases in Mycobacterium tuberculosis. Bioorg Med Chem 2007; 15:5629-50. [PMID: 17544276 PMCID: PMC2699567 DOI: 10.1016/j.bmc.2007.04.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 04/02/2007] [Accepted: 04/04/2007] [Indexed: 11/25/2022]
Abstract
Glycosyltransferases (GTs) play a crucial role in mycobacterial cell wall biosynthesis and are necessary for the survival of mycobacteria. Hence, these enzymes are potential new drug targets for the treatment of tuberculosis (TB), especially multiple drug-resistant TB (MDR-TB). Herein, we report the efficient syntheses of Araf(alpha 1-->5)Araf, Galf(beta 1-->5)Galf, and Galf(beta 1-->6)Galf disaccharides possessing a 5-N,N-dimethylaminonaphthalene-1-sulfonamidoethyl (dansyl) unit that were prepared as fluorescent disaccharide acceptors for arabinosyl- and galactosyl-transferases, respectively. Such analogs may offer advantages relative to radiolabeled acceptors or donors for studying the enzymes and for assay development and compound screening. Additionally, analogs possessing a 5-azidonaphthalene-1-sulfonamidoethyl unit were prepared as photoaffinity probes for their potential utility in studying active site labeling of the GTs (arabinosyl and galactosyl) in Mycobacterium tuberculosis (MTB). Beyond their preparation, initial biological testing and kinetic analysis of these disaccharides as acceptors toward glycosyltransferases are also presented.
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Affiliation(s)
- Ashish K. Pathak
- Drug Discovery Division, Southern Research Institute, P.O. Box 55305, Birmingham, AL 35255, USA
| | - Vibha Pathak
- Drug Discovery Division, Southern Research Institute, P.O. Box 55305, Birmingham, AL 35255, USA
| | - Lainne Seitz
- Drug Discovery Division, Southern Research Institute, P.O. Box 55305, Birmingham, AL 35255, USA
| | - Sudagar S. Gurcha
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James M. Riordan
- Drug Discovery Division, Southern Research Institute, P.O. Box 55305, Birmingham, AL 35255, USA
| | - Robert C. Reynolds
- Drug Discovery Division, Southern Research Institute, P.O. Box 55305, Birmingham, AL 35255, USA
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