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Schaff H, Dey P, Heiss C, Keiser G, Moro TR, Azadi P, Patel P, Free SJ. Characterization of the need for galactofuranose during the Neurospora crassa life cycle. Fungal Genet Biol 2023; 168:103826. [PMID: 37541569 DOI: 10.1016/j.fgb.2023.103826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
Galactofuranose is a constituent of the cell walls of filamentous fungi. The galactofuranose can be found as a component of N-linked oligosaccharides, in O-linked oligosaccharides, in GPI-anchored galactomannan, and in free galactomannan. The Neurospora genome contains a single UDP-galactose mutase gene (ugm-1/NCU01824) and two UDP-galactofuranose translocases used to import UDP-galactofuranose into the lumen of the Golgi apparatus (ugt-1/NCU01826 and ugt-2/NCU01456). Our results demonstrate that loss of galactofuranose synthesis or its translocation into the lumen of the secretory pathway affects the morphology and growth rate of the vegetative hyphae, the production of conidia (asexual spores), and dramatically affects the sexual stages of the life cycle. In mutants that are unable to make galactofuranose or transport it into the lumen of the Golgi apparatus, ascospore development is aborted soon after fertilization and perithecium maturation is aborted prior to the formation of the neck and ostiole. The Neurospora genome contains three genes encoding possible galactofuranosyltransferases from the GT31 family of glycosyltransferases (gfs-1/NCU05878, gfs-2/NCU07762, and gfs-3/NCU02213) which might be involved in generating galactofuranose-containing oligosaccharide structures. Analysis of triple KO mutants in GT31 glycosyltransferases shows that these mutants have normal morphology, suggesting that these genes do not encode vital galactofuranosyltransferases.
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Affiliation(s)
- Hayden Schaff
- Dept. of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, United States
| | - Protyusha Dey
- Dept. of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, United States
| | - Christian Heiss
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Griffin Keiser
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Tatiana Rojo Moro
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Pavan Patel
- Dept. of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, United States
| | - Stephen J Free
- Dept. of Biological Sciences, SUNY University at Buffalo, Buffalo, NY 14260, United States.
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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Cossio-Pérez R, Pierdominici-Sottile G, Sobrado P, Palma J. Molecular Dynamics Simulations of Substrate Release from Trypanosoma cruzi UDP-Galactopyranose Mutase. J Chem Inf Model 2019; 59:809-817. [PMID: 30608160 DOI: 10.1021/acs.jcim.8b00675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The enzyme UDP-galactopyranose mutase (UGM) represents a promising drug target for the treatment of infections with Trypanosoma cruzi. We have computed the Potential of Mean Force for the release of UDP-galactopyranose from UGM, using Umbrella Sampling simulations. The simulations revealed the conformational changes that both substrate and enzyme undergo during the process. It was determined that the galactopyranose portion of the substrate is highly mobile and that the opening/closing of the active site occurs in stages. Previously uncharacterized interactions with highly conserved residues were also identified. These findings provide new pieces of information that contribute to the rational design of drugs against T. cruzi.
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Affiliation(s)
- Rodrigo Cossio-Pérez
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
| | - Pablo Sobrado
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - Juliana Palma
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
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Gadda G, Sobrado P. Kinetic Solvent Viscosity Effects as Probes for Studying the Mechanisms of Enzyme Action. Biochemistry 2018; 57:3445-3453. [DOI: 10.1021/acs.biochem.8b00232] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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Pierdominici-Sottile G, Cossio-Pérez R, Da Fonseca I, Kizjakina K, Tanner JJ, Sobrado P. Steric Control of the Rate-Limiting Step of UDP-Galactopyranose Mutase. Biochemistry 2018; 57:3713-3721. [PMID: 29757624 DOI: 10.1021/acs.biochem.8b00323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Galactose is an abundant monosaccharide found exclusively in mammals as galactopyranose (Gal p), the six-membered ring form of this sugar. In contrast, galactose appears in many pathogenic microorganisms as the five-membered ring form, galactofuranose (Gal f). Gal f biosynthesis begins with the conversion of UDP-Gal p to UDP-Gal f catalyzed by the flavoenzyme UDP-galactopyranose mutase (UGM). Because UGM is essential for the survival and proliferation of several pathogens, there is interest in understanding the catalytic mechanism to aid inhibitor development. Herein, we have used kinetic measurements and molecular dynamics simulations to explore the features of UGM that control the rate-limiting step (RLS). We show that UGM from the pathogenic fungus Aspergillus fumigatus also catalyzes the isomerization of UDP-arabinopyranose (UDP-Ara p), which differs from UDP-Gal p by lacking a -CH2-OH substituent at the C5 position of the hexose ring. Unexpectedly, the RLS changed from a chemical step for the natural substrate to product release with UDP-Ara p. This result implicated residues that contact the -CH2-OH of UDP-Gal p in controlling the mechanistic path. The mutation of one of these residues, Trp315, to Ala changed the RLS of the natural substrate to product release, similar to the wild-type enzyme with UDP-Ara p. Molecular dynamics simulations suggest that steric complementarity in the Michaelis complex is responsible for this distinct behavior. These results provide new insight into the UGM mechanism and, more generally, how steric factors in the enzyme active site control the free energy barriers along the reaction path.
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Affiliation(s)
| | - Rodrigo Cossio-Pérez
- Sci-prot. Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , Bernal B1876BXD , Argentina
| | - Isabel Da Fonseca
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Karina Kizjakina
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - John J Tanner
- Departments of Biochemistry and Chemistry , University of Missouri-Columbia , Columbia , Missouri 65211 , United States
| | - Pablo Sobrado
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
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Martín Del Campo JS, Eckshtain-Levi M, Sobrado P. Identification of eukaryotic UDP-galactopyranose mutase inhibitors using the ThermoFAD assay. Biochem Biophys Res Commun 2017; 493:58-63. [PMID: 28919416 DOI: 10.1016/j.bbrc.2017.09.074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 09/14/2017] [Indexed: 11/26/2022]
Abstract
Aspergillus fumigatus is a human pathogen responsible for deadly infections in immune-compromised patients. A potential strategy for treating A. fumigatus infections is by targeting the biosynthesis of cell wall components, such as galactofuranase, which is absent in humans. Galactofuranose biosynthesis is initiated by the flavoenzyme UDP-galactopyranose mutase (UGM), which converts UDP-galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf). UGM requires the reduced form of the flavin for activity, which is obtained by reacting with NADPH. We aimed to identify inhibitors of UGM by screening a kinase inhibitor library using ThermoFAD, a flavin fluorescence thermal shift assay. The screening assay identified flavopiridol as a compound that increased the melting temperature of A. fumigatus UGM. Further characterization showed that flavopiridol is a non-competitive inhibitor of UGM and docking studies suggest that it binds in the active site. This compound does not inhibit the prokaryotic UGM from Mycobacteria tuberculosis.
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Affiliation(s)
| | | | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA; Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, USA.
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Kincaid VA, London N, Wangkanont K, Wesener DA, Marcus SA, Héroux A, Nedyalkova L, Talaat AM, Forest KT, Shoichet BK, Kiessling LL. Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents. ACS Chem Biol 2015. [PMID: 26214585 DOI: 10.1021/acschembio.5b00370] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Galactofuranose (Galf) is present in glycans critical for the virulence and viability of several pathogenic microbes, including Mycobacterium tuberculosis, yet the monosaccharide is absent from mammalian glycans. Uridine 5'-diphosphate-galactopyranose mutase (UGM) catalyzes the formation of UDP-Galf, which is required to produce Galf-containing glycoconjugates. Inhibitors of UGM have therefore been sought, both as antimicrobial leads and as tools to delineate the roles of Galf in cells. Obtaining cell permeable UGM probes by either design or high throughput screens has been difficult, as has elucidating how UGM binds small molecule, noncarbohydrate inhibitors. To address these issues, we employed structure-based virtual screening to uncover new inhibitor chemotypes, including a triazolothiadiazine series. These compounds are among the most potent antimycobacterial UGM inhibitors described. They also facilitated determination of a UGM-small molecule inhibitor structure, which can guide optimization. A comparison of results from the computational screen and a high-throughput fluorescence polarization (FP) screen indicated that the scaffold hits from the former had been evaluated in the FP screen but missed. By focusing on promising compounds, the virtual screen rescued false negatives, providing a blueprint for generating new UGM probes and therapeutic leads.
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Affiliation(s)
- Virginia A. Kincaid
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Nir London
- Department
of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, California 94158, United States
| | - Kittikhun Wangkanont
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Darryl A. Wesener
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Sarah A. Marcus
- Department
of Pathobiological Sciences, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Annie Héroux
- Photon
Sciences Directorate, Brookhaven National Laboratories, Upton, New York 11973, United States
| | - Lyudmila Nedyalkova
- Ontario Institute
of Cancer Research and Faculty of Pharmacy, University of Toronto, Toronto, Canada
| | - Adel M. Talaat
- Department
of Pathobiological Sciences, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Katrina T. Forest
- Department
of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, California 94158, United States
- Ontario Institute
of Cancer Research and Faculty of Pharmacy, University of Toronto, Toronto, Canada
| | - Laura L. Kiessling
- Department
of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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