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Nasseri SA, Lazarski AC, Lemmer IL, Zhang CY, Brencher E, Chen HM, Sim L, Panwar D, Betschart L, Worrall LJ, Brumer H, Strynadka NCJ, Withers SG. An alternative broad-specificity pathway for glycan breakdown in bacteria. Nature 2024; 631:199-206. [PMID: 38898276 DOI: 10.1038/s41586-024-07574-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
The vast majority of glycosidases characterized to date follow one of the variations of the 'Koshland' mechanisms1 to hydrolyse glycosidic bonds through substitution reactions. Here we describe a large-scale screen of a human gut microbiome metagenomic library using an assay that selectively identifies non-Koshland glycosidase activities2. Using this, we identify a cluster of enzymes with extremely broad substrate specificities and thoroughly characterize these, mechanistically and structurally. These enzymes not only break glycosidic linkages of both α and β stereochemistry and multiple connectivities, but also cleave substrates that are not hydrolysed by standard glycosidases. These include thioglycosides, such as the glucosinolates from plants, and pseudoglycosidic bonds of pharmaceuticals such as acarbose. This is achieved through a distinct mechanism of hydrolysis that involves oxidation/reduction and elimination/hydration steps, each catalysed by enzyme modules that are in many cases interchangeable between organisms and substrate classes. Homologues of these enzymes occur in both Gram-positive and Gram-negative bacteria associated with the gut microbiome and other body parts, as well as other environments, such as soil and sea. Such alternative step-wise mechanisms appear to constitute largely unrecognized but abundant pathways for glycan degradation as part of the metabolism of carbohydrates in bacteria.
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Affiliation(s)
- Seyed Amirhossein Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aleksander C Lazarski
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Center for Blood Research, University of British Columbia, Vancouver, Canada
| | - Imke L Lemmer
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chloe Y Zhang
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eva Brencher
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hong-Ming Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lyann Sim
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Deepesh Panwar
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leo Betschart
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam J Worrall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Center for Blood Research, University of British Columbia, Vancouver, Canada
| | - Harry Brumer
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Center for Blood Research, University of British Columbia, Vancouver, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
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2
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Sancéau JY, Bélanger P, Maltais R, Poirier D. An Improved Synthesis of Glucuronide Metabolites of Hindered Phenolic Xenoestrogens. Curr Org Synth 2022; 19:838-845. [PMID: 35473530 DOI: 10.2174/1570179419666220426104848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/18/2022] [Accepted: 03/08/2022] [Indexed: 11/22/2022]
Abstract
AIM AND OBJECTIVE The syntheses of glucuronide metabolites of phenolic xenoestrogens triclosan and 2-phenylphenol, namely triclosan-O-glucuronide (TCS-G; 1), and 2-phenylphenol-O-glucuronide (OPP-G; 2), were achieved for use as analytical standards. METHODS Under classical conditions previously reported for glucuronide synthesis, the final basic hydrolysis of the peracylated ester intermediate leading to the free glucuronides is often a limiting step. Indeed, the presence of contaminating by-products resulting from ester elimination has often been observed during this step. This is particularly relevant when the sugar unit is close to a crowded environment as for triclosan and 2-phenylphenol. RESULTS To circumvent these problems, we proposed mild conditions for the deprotection of peracetylated glucuronate intermediates. CONCLUSION A new methodology using a key imidate following a two-step saponification protocol for acetates and methyl ester hydrolysis was successfully applied to the preparation of TCS-d3 (1) and OPP-G (2) as well as deuterated isotopomers TCS-d3-G (1-d3) and OPP-d5-G (2-d5).
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Affiliation(s)
- Jean-Yves Sancéau
- Organic Synthesis Service, Medicinal Chemistry Platform, Centre Hospitalier Universitaire (CHU) de Québec-Research Center, Québec, QC, G1V 4G2, Canada
| | - Patrick Bélanger
- Laboratoire du Centre de Toxicologie (CTQ), Institut national de santé publique du Québec (INSPQ), Québec, QC, G1V 5B3, Canada
| | - René Maltais
- Organic Synthesis Service, Medicinal Chemistry Platform, Centre Hospitalier Universitaire (CHU) de Québec-Research Center, Québec, QC, G1V 4G2, Canada
| | - Donald Poirier
- Organic Synthesis Service, Medicinal Chemistry Platform, Centre Hospitalier Universitaire (CHU) de Québec-Research Center, Québec, QC, G1V 4G2, Canada.,Laboratoire du Centre de Toxicologie (CTQ), Institut national de santé publique du Québec (INSPQ), Québec, QC, G1V 5B3, Canada
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3
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Synthesis of Human Phase I and Phase II Metabolites of Hop (Humulus lupulus) Prenylated Flavonoids. Metabolites 2022; 12:metabo12040345. [PMID: 35448532 PMCID: PMC9030851 DOI: 10.3390/metabo12040345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 12/12/2022] Open
Abstract
Hop prenylated flavonoids have been investigated for their in vivo activities due to their broad spectrum of positive health effects. Previous studies on the metabolism of xanthohumol using untargeted methods have found that it is first degraded into 8-prenylnaringenin and 6-prenylnaringenin, by spontaneous cyclisation into isoxanthohumol, and subsequently demethylated by gut bacteria. Further combinations of metabolism by hydroxylation, sulfation, and glucuronidation result in an unknown number of isomers. Most investigations involving the analysis of prenylated flavonoids used surrogate or untargeted approaches in metabolite identification, which is prone to errors in absolute identification. Here, we present a synthetic approach to obtaining reference standards for the identification of human xanthohumol metabolites. The synthesised metabolites were subsequently analysed by qTOF LC-MS/MS, and some were matched to a human blood sample obtained after the consumption of 43 mg of micellarised xanthohumol. Additionally, isomers of the reference standards were identified due to their having the same mass fragmentation pattern and different retention times. Overall, the methods unequivocally identified the metabolites of xanthohumol that are present in the blood circulatory system. Lastly, in vitro bioactive testing should be applied using metabolites and not original compounds, as free compounds are scarcely found in human blood.
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Bäumgen M, Dutschei T, Bartosik D, Suster C, Reisky L, Gerlach N, Stanetty C, Mihovilovic MD, Schweder T, Hehemann JH, Bornscheuer UT. A new carbohydrate-active oligosaccharide dehydratase is involved in the degradation of ulvan. J Biol Chem 2021; 297:101210. [PMID: 34547290 PMCID: PMC8511951 DOI: 10.1016/j.jbc.2021.101210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/28/2022] Open
Abstract
Marine algae catalyze half of all global photosynthetic production of carbohydrates. Owing to their fast growth rates, Ulva spp. rapidly produce substantial amounts of carbohydrate-rich biomass and represent an emerging renewable energy and carbon resource. Their major cell wall polysaccharide is the anionic carbohydrate ulvan. Here, we describe a new enzymatic degradation pathway of the marine bacterium Formosa agariphila for ulvan oligosaccharides involving unsaturated uronic acid at the nonreducing end linked to rhamnose-3-sulfate and glucuronic or iduronic acid (Δ-Rha3S-GlcA/IdoA-Rha3S). Notably, we discovered a new dehydratase (P29_PDnc) acting on the nonreducing end of ulvan oligosaccharides, i.e., GlcA/IdoA-Rha3S, forming the aforementioned unsaturated uronic acid residue. This residue represents the substrate for GH105 glycoside hydrolases, which complements the enzymatic degradation pathway including one ulvan lyase, one multimodular sulfatase, three glycoside hydrolases, and the dehydratase P29_PDnc, the latter being described for the first time. Our research thus shows that the oligosaccharide dehydratase is involved in the degradation of carboxylated polysaccharides into monosaccharides.
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Affiliation(s)
- Marcus Bäumgen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Daniel Bartosik
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - Christoph Suster
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
| | - Lukas Reisky
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Nadine Gerlach
- Max Planck-Institute for Marine Microbiology, Bremen, Germany; Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany
| | | | | | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Max Planck-Institute for Marine Microbiology, Bremen, Germany; Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany.
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5
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Quirke JCK, Crich D. GH47 and Other Glycoside Hydrolases Catalyze Glycosidic Bond Cleavage with the Assistance of Substrate Super-arming at the Transition State. ACS Catal 2021; 11:10308-10315. [PMID: 34777906 PMCID: PMC8579916 DOI: 10.1021/acscatal.1c02750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Super-armed glycosyl donors, whose substituents are predominantly held in pseudoaxial positions, exhibit strongly increased reactivity in glycosylation through significant stabilization of oxocarbenium-like transition states. Examination of X-ray crystal structures reveals that the GH47 family of glycoside hydrolases have evolved so as to distort their substrates away from the ground state conformation in such a manner as to present multiple C-O bonds in pseudoaxial positions and so benefit from conformational super-arming of their substrates, thereby enhancing catalysis. Through analysis of literature mutagenic studies, we show that a suitably placed aromatic residue in GHs 6 and 47 sterically enforces super-armed conformations on their substrates. GH families 45, 81, and 134 on the other hand impose conformational super-arming on their substrates, by maintaining the more active ring conformation through hydrogen bonding rather than steric interactions. The recognition of substrate super-arming by select GH families provides a further parallel with synthetic carbohydrate chemistry and nature and opens further avenues for the design of improved glycosidase inhibitors.
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Affiliation(s)
- Jonathan C K Quirke
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, GA 30602, USA
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, GA 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, GA 30602, USA
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, GA 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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6
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Solid state structure of sodium β-1-thiophenyl glucuronate identifies 5-coordinate sodium with three independent glucoronates. Carbohydr Res 2021; 502:108281. [PMID: 33770633 DOI: 10.1016/j.carres.2021.108281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/21/2022]
Abstract
Glucuronic acid is a key component of the glycosaminoglycans (GAGs) Chrondroitin Sulfate (CS), Heparin/Heparan sulfate (HS) and Hyaluronic Acid (HA), as well an important metabolite derivative. In biological systems the carboxylate of uronic acids in GAGs is involved in important H-binding interactions, and the role of metal coordination, such as sodiated systems, has indications associated with a number of biological effects, and physiological GAG-related processes. In synthetic approaches to GAG fragments, thioglycoside intermediates, or derivatives from these, are commonly employed. Of the reported examples of sodium coordination in carbohydrates, 6-coordinate systems are usually observed often with water ligands involved, Herein we report an unexpected 5-coordinate sodiated GlcA crystal structure of the parent GlcA, but as a thioglycoside derivative, whose crystal coordination differs from previous examples, with no involvement of water as a ligand and containing a distorted trigonal bypramidal sodium with each GlcA having five of 6 oxygens sodium-coordinated.
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7
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Alginate Degradation: Insights Obtained through Characterization of a Thermophilic Exolytic Alginate Lyase. Appl Environ Microbiol 2021; 87:AEM.02399-20. [PMID: 33397696 DOI: 10.1128/aem.02399-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/19/2020] [Indexed: 01/07/2023] Open
Abstract
Enzymatic depolymerization of seaweed polysaccharides is gaining interest for the production of functional oligosaccharides and fermentable sugars. Herein, we describe a thermostable alginate lyase that belongs to polysaccharide lyase family 17 (PL17) and was derived from an Arctic Mid-Ocean Ridge (AMOR) metagenomics data set. This enzyme, AMOR_PL17A, is a thermostable exolytic oligoalginate lyase (EC 4.2.2.26), which can degrade alginate, poly-β-d-mannuronate, and poly-α-l-guluronate within a broad range of pHs, temperatures, and salinity conditions. Site-directed mutagenesis showed that tyrosine Y251, previously suggested to act as a catalytic acid, indeed is essential for catalysis, whereas mutation of tyrosine Y446, previously proposed to act as a catalytic base, did not affect enzyme activity. The observed reaction products are protonated and deprotonated forms of the 4,5-unsaturated uronic acid monomer, Δ, two hydrates of DEH (4-deoxy-l-erythro-5-hexulosuronate), which are formed after ring opening, and, finally, two epimers of a 5-member hemiketal called 4-deoxy-d-manno-hexulofuranosidonate (DHF), formed through intramolecular cyclization of hydrated DEH. The detection and nuclear magnetic resonance (NMR) assignment of these hemiketals refine our current understanding of alginate degradation.IMPORTANCE The potential markets for seaweed-derived products and seaweed processing technologies are growing, yet commercial enzyme cocktails for complete conversion of seaweed to fermentable sugars are not available. Such an enzyme cocktail would require the catalytic properties of a variety of different enzymes, where fucoidanases, laminarinases, and cellulases together with endo- and exo-acting alginate lyases would be the key enzymes. Here, we present an exo-acting alginate lyase that efficiently produces monomeric sugars from alginate. Since it is only the second characterized exo-acting alginate lyase capable of degrading alginate at a high industrially relevant temperature (≥60°C), this enzyme may be of great biotechnological and industrial interest. In addition, in-depth NMR-based structural elucidation revealed previously undescribed rearrangement products of the unsaturated monomeric sugars generated from exo-acting lyases. The insight provided by the NMR assignment of these products facilitates future assessment of product formation by alginate lyases.
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8
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Ma ST, Lee CW, Liu WM. Synthesis of 4-thiol-furanosidic uronate via hydrothiolation reaction. RSC Adv 2021; 11:18409-18416. [PMID: 35480947 PMCID: PMC9033442 DOI: 10.1039/d1ra02110a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/05/2021] [Indexed: 11/25/2022] Open
Abstract
Uronic acids are not only important building blocks of polysaccharides and oligosaccharides but also are widely used in the food and pharmaceutical industries. Inspired by the structure of natural products, here, we disclosed base-mediated and radical-mediated hydrothiolation reactions for the preparation of thiol-contained uronates. In comparison with base-mediated reaction, radical-mediated hydrothiolation is inefficient due to the electron-withdrawing group on the ethylene group; nevertheless, the adduct had excellent stereoselectivity at both C-4 and C-5 positions. For the alkaline approach, thiols as nucleophiles can regioselectively and stereoselectively attach to the C-4 position of Δ-4,5-unsaturated uronate with moderate to good yields. However, poor stereoselectivity at the C-5 position was observed due to retro thiol-Michael addition. After removing the protecting group of the thiol, the thiol adduct was isomerized to the furanosidic form and the 4-thiol-furanosidic uronate derivative was synthesized for the first time. Uronic acids are not only important building blocks of bioactive molecules but also are widely used in the food and pharmaceutical industries. Its derivative, 4-thiol-furanosidic uronate was successfully synthesized and firstly reported here.![]()
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Affiliation(s)
- Shih-Ting Ma
- Department of Chemistry
- Fu Jen Catholic University
- New Taipei City 24205
- Republic of China
| | - Chia-Wei Lee
- Department of Chemistry
- Fu Jen Catholic University
- New Taipei City 24205
- Republic of China
| | - Wei-Min Liu
- Department of Chemistry
- Fu Jen Catholic University
- New Taipei City 24205
- Republic of China
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9
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Sugawara S, Meguro Y, Sato S, Enomoto M, Ogura Y, Kuwahara S. Total synthesis of terfestatins a and B. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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10
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Beltrame G, Trygg J, Rahkila J, Leino R, Yang B. Structural investigation of cell wall polysaccharides extracted from wild Finnish mushroom Craterellus tubaeformis (Funnel Chanterelle). Food Chem 2019; 301:125255. [DOI: 10.1016/j.foodchem.2019.125255] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 12/27/2022]
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11
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Sharipova RR, Belenok MG, Garifullin BF, Sapunova AS, Voloshina AD, Andreeva OV, Strobykina IY, Skvortsova PV, Zuev YF, Kataev VE. Synthesis and anti-cancer activities of glycosides and glycoconjugates of diterpenoid isosteviol. MEDCHEMCOMM 2019; 10:1488-1498. [PMID: 31673312 PMCID: PMC6786240 DOI: 10.1039/c9md00242a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/20/2019] [Indexed: 11/21/2022]
Abstract
A series of glycosides and glycoconjugates of diterpenoid isosteviol (16-oxo-ent-beyeran-19-oic acid) with various monosaccharide residues were synthesized and their cytotoxicity against some human cancer and normal cell lines was assayed. Most of the synthesized compounds demonstrated moderate to significant cytotoxicity against human cancer cell lines M-HeLa and MCF-7. Three lead compounds exhibited selective cytotoxic activities against M-HeLa (IC50 = 10.0-15.1 μM) that were three times better than the cytotoxicity of the anti-cancer drug Tamoxifen (IC50 = 28.0 μM). Moreover, the lead compounds were not cytotoxic with respect to the normal human cell line Chang liver (IC50 > 100 μM), whereas Tamoxifen inhibited the viability of normal human Chang liver cells with an IC50 value of 46.0 μM. It was determined that the cytotoxicity of the lead compounds was due to induction of apoptosis proceeding along the mitochondrial pathway. The cytotoxic activity of the synthesized compounds substantially depended on the nature of the monosaccharide residue and its position, that is, whether the monosaccharide residue was attached directly to the isosteviol skeleton or was moved away from it by means of a polymethylene linker.
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Affiliation(s)
- Radmila R Sharipova
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov str., 8 , Kazan , 420088 , Russian Federation .
| | - Mayya G Belenok
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov str., 8 , Kazan , 420088 , Russian Federation .
| | - Bulat F Garifullin
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov str., 8 , Kazan , 420088 , Russian Federation .
| | - Anastasiya S Sapunova
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov str., 8 , Kazan , 420088 , Russian Federation .
| | - Alexandra D Voloshina
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov str., 8 , Kazan , 420088 , Russian Federation .
| | - Olga V Andreeva
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov str., 8 , Kazan , 420088 , Russian Federation .
| | - Irina Yu Strobykina
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov str., 8 , Kazan , 420088 , Russian Federation .
| | - Polina V Skvortsova
- Kazan Institute of Biochemistry and Biophysics , FRC Kazan Scientific Center , Russian Academy of Sciences , Lobachevsky Str., 2/31 , Kazan , 420111 , Russian Federation
| | - Yuriy F Zuev
- Kazan Institute of Biochemistry and Biophysics , FRC Kazan Scientific Center , Russian Academy of Sciences , Lobachevsky Str., 2/31 , Kazan , 420111 , Russian Federation
- Kazan State Power Engineering University , 51, Krasnoselskaya str. , Kazan , 420066 , Russian Federation
| | - Vladimir E Kataev
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center , Russian Academy of Sciences , Arbuzov str., 8 , Kazan , 420088 , Russian Federation .
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12
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Liu X, Wen GE, Liu JC, Liao JX, Sun JS. Total synthesis of scutellarin and apigenin 7-O-β-d-glucuronide. Carbohydr Res 2019; 475:69-73. [DOI: 10.1016/j.carres.2019.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/12/2022]
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13
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Biochemical Reconstruction of a Metabolic Pathway from a Marine Bacterium Reveals Its Mechanism of Pectin Depolymerization. Appl Environ Microbiol 2018; 85:AEM.02114-18. [PMID: 30341080 DOI: 10.1128/aem.02114-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022] Open
Abstract
Pectin is a complex uronic acid-containing polysaccharide typically found in plant cell walls, though forms of pectin are also found in marine diatoms and seagrasses. Genetic loci that target pectin have recently been identified in two phyla of marine bacteria. These loci appear to encode a pectin saccharification pathway that is distinct from the canonical pathway typically associated with phytopathogenic terrestrial bacteria. However, very few components of the marine pectin metabolism pathway have been experimentally validated. Here, we biochemically reconstructed the pectin saccharification pathway from a marine Pseudoalteromonas sp. in vitro and show that it results in the production of galacturonate and the key metabolic intermediate 5-keto-4-deoxyuronate (DKI). We demonstrate the sequential de-esterification and depolymerization of pectin into oligosaccharides and the synergistic action of glycoside hydrolases (GHs) to fully degrade these oligosaccharides into monosaccharides. Furthermore, we show that this pathway relies on enzymes belonging to GH family 105 to carry out the equivalent chemistry afforded by an exolytic polysaccharide lyase (PL) and KdgF in the canonical pectin pathway. Finally, we synthesize our findings into a model of marine pectin degradation and compare it with the canonical pathway. Our results underline the shifting view of pectin as a solely terrestrial polysaccharide and highlight the importance of marine pectin as a carbon source for suitably adapted marine heterotrophs. This alternate pathway has the potential to be exploited in the growing field of biofuel production from plant waste.IMPORTANCE Marine polysaccharides, found in the cell walls of seaweeds and other marine macrophytes, represent a vast sink of photosynthetically fixed carbon. As such, their breakdown by marine microbes contributes significantly to global carbon cycling. Pectin is an abundant polysaccharide found in the cell walls of terrestrial plants, but it has recently been reported that some marine bacteria possess the genetic capacity to degrade it. In this study, we biochemically characterized seven key enzymes from a marine bacterium that, together, fully degrade the backbone of pectin into its constituent monosaccharides. Our findings highlight the importance of pectin as a marine carbon source available to bacteria that possess this pathway. The characterized enzymes also have the potential to be utilized in the production of biofuels from plant waste.
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14
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Chan HCS, Pan L, Li Y, Yuan S. Rationalization of stereoselectivity in enzyme reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- H. C. Stephen Chan
- Faculty of Chemistry, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
- Faculty of Life Sciences University of Bradford Bradford UK
| | - Lu Pan
- Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai China
| | - Yi Li
- Department of Neurology University of Southern California Los Angeles California
| | - Shuguang Yuan
- Faculty of Chemistry, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne Lausanne Switzerland
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15
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Sharma B, Pickens JB, Striegler S, Barnett JD. Biomimetic Glycoside Hydrolysis by a Microgel Templated with a Competitive Glycosidase Inhibitor. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Babloo Sharma
- Department of Chemistry and Biochemistry, University of Arkansas, 345 North Campus Drive, Fayetteville, Arkansas 72701, United States
| | - Jessica B. Pickens
- Department of Chemistry and Biochemistry, University of Arkansas, 345 North Campus Drive, Fayetteville, Arkansas 72701, United States
| | - Susanne Striegler
- Department of Chemistry and Biochemistry, University of Arkansas, 345 North Campus Drive, Fayetteville, Arkansas 72701, United States
| | - James D. Barnett
- Department of Chemistry and Biochemistry, University of Arkansas, 345 North Campus Drive, Fayetteville, Arkansas 72701, United States
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16
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Nasseri SA, Betschart L, Opaleva D, Rahfeld P, Withers SG. A Mechanism-Based Approach to Screening Metagenomic Libraries for Discovery of Unconventional Glycosidases. Angew Chem Int Ed Engl 2018; 57:11359-11364. [PMID: 30001477 DOI: 10.1002/anie.201806792] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/10/2018] [Indexed: 11/11/2022]
Abstract
Functional metagenomics has opened new opportunities for enzyme discovery. To exploit the full potential of this new tool, the design of selective screens is essential, especially when searching for rare enzymes. To identify novel glycosidases that employ cleavage strategies other than the conventional Koshland mechanisms, a suitable screen was needed. Focusing on the unsaturated glucuronidases (UGLs), it was found that use of simple aryl glycoside substrates did not allow sufficient discrimination against β-glucuronidases, which are widespread in bacteria. While conventional glycosidases cannot generally hydrolyze thioglycosides efficiently, UGLs follow a distinct mechanism that allows them to do so. Thus, fluorogenic thioglycoside substrates featuring thiol-based self-immolative linkers were synthesized and assessed as selective substrates. The generality of the approach was validated with another family of unconventional glycosidases, the GH4 enzymes. Finally, the utility of these substrates was tested by screening a small metagenomic library.
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Affiliation(s)
- Seyed Amirhossein Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Leo Betschart
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Daria Opaleva
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Peter Rahfeld
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
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17
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Nasseri SA, Betschart L, Opaleva D, Rahfeld P, Withers SG. A Mechanism-Based Approach to Screening Metagenomic Libraries for Discovery of Unconventional Glycosidases. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Leo Betschart
- Department of Chemistry; University of British Columbia; Vancouver British Columbia V6T 1Z1 Canada
| | - Daria Opaleva
- Department of Chemistry; University of British Columbia; Vancouver British Columbia V6T 1Z1 Canada
| | - Peter Rahfeld
- Department of Chemistry; University of British Columbia; Vancouver British Columbia V6T 1Z1 Canada
| | - Stephen G. Withers
- Department of Chemistry; University of British Columbia; Vancouver British Columbia V6T 1Z1 Canada
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18
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Moniruzzaman M, Gann ER, Wilhelm SW. Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 - A Harmful Bloom Algae. Front Microbiol 2018; 9:752. [PMID: 29725322 PMCID: PMC5917014 DOI: 10.3389/fmicb.2018.00752] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/03/2018] [Indexed: 01/05/2023] Open
Abstract
While viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, “giant” dsDNA viruses have been found to be associated with important ecological processes, including the collapse of algal blooms. However, the molecular aspects of giant virus–host interactions remain largely unknown. Aureococcus anophagefferens virus (AaV), a giant virus in the Mimiviridae clade, is known to play a critical role in regulating the fate of brown tide blooms caused by the pelagophyte Aureococcus anophagefferens. To understand the physiological response of A. anophagefferens CCMP1984 upon AaV infection, we studied the transcriptomic landscape of this host–virus pair over an entire infection cycle using a RNA-sequencing approach. A massive transcriptional response of the host was evident as early as 5 min post-infection, with modulation of specific processes likely related to both host defense mechanism(s) and viral takeover of the cell. Infected Aureococcus showed a relative suppression of host-cell transcripts associated with photosynthesis, cytoskeleton formation, fatty acid, and carbohydrate biosynthesis. In contrast, host cell processes related to protein synthesis, polyamine biosynthesis, cellular respiration, transcription, and RNA processing were overrepresented compared to the healthy cultures at different stages of the infection cycle. A large number of redox active host-selenoproteins were overexpressed, which suggested that viral replication and assembly progresses in a highly oxidative environment. The majority (99.2%) of annotated AaV genes were expressed at some point during the infection cycle and demonstrated a clear temporal–expression pattern and an increasing relative expression for the majority of the genes through the time course. We detected a putative early promoter motif for AaV, which was highly similar to the early promoter elements of two other Mimiviridae members, indicating some degree of evolutionary conservation of gene regulation within this clade. This large-scale transcriptome study provides insights into the Aureococcus cells infected by a giant virus and establishes a foundation to test hypotheses regarding metabolic and regulatory processes critical for AaV and other Mimiviridae members.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA, United States
| | - Eric R Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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19
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Belenok MG, Andreeva OV, Garifullin BF, Strobykina AS, Kravchenko MA, Voloshina AD, Kataev VE. Synthesis and Antitubercular, Antimicrobial, and Hemolytic Activity of Methyl D-Glucopyranuronate and Its Simplest Derivatives. RUSS J GEN CHEM+ 2017. [DOI: 10.1134/s1070363217120106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Sharipova RR, Andreeva OV, Strobykina IY, Voloshina AD, Strobykina AS, Kataev VE. Synthesis and Antimicrobial Activity of Glucuronosyl Derivatives of Steviolbioside from Stevia rebaudiana. Chem Nat Compd 2017. [DOI: 10.1007/s10600-017-2211-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Izmest’ev ES, Andreeva OV, Sharipova RR, Kravchenko MA, Garifullin BF, Strobykina IY, Kataev VE, Mironov VF. Synthesis and antitubercular activity of first glucuronosyl phosphates and amidophosphates containing polymethylene chains. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1070428017010092] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Xiong J, Xu D. Insights into the Catalytic Mechanism of Unsaturated Glucuronyl Hydrolase of Bacillus sp. GL1. J Phys Chem B 2017; 121:931-941. [DOI: 10.1021/acs.jpcb.6b10501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Xiong
- MOE Key Laboratory of Green Chemistry, College of Chemistry and ‡Geonome Research
Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry, College of Chemistry and ‡Geonome Research
Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
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23
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Nakamichi Y, Oiki S, Mikami B, Murata K, Hashimoto W. Conformational Change in the Active Site of Streptococcal Unsaturated Glucuronyl Hydrolase Through Site-Directed Mutagenesis at Asp-115. Protein J 2016; 35:300-9. [PMID: 27402448 DOI: 10.1007/s10930-016-9673-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Bacterial unsaturated glucuronyl hydrolase (UGL) degrades unsaturated disaccharides generated from mammalian extracellular matrices, glycosaminoglycans, by polysaccharide lyases. Two Asp residues, Asp-115 and Asp-175 of Streptococcus agalactiae UGL (SagUGL), are completely conserved in other bacterial UGLs, one of which (Asp-175 of SagUGL) acts as a general acid and base catalyst. The other Asp (Asp-115 of SagUGL) also affects the enzyme activity, although its role in the enzyme reaction has not been well understood. Here, we show substitution of Asp-115 in SagUGL with Asn caused a conformational change in the active site. Tertiary structures of SagUGL mutants D115N and D115N/K370S with negligible enzyme activity were determined at 2.00 and 1.79 Å resolution, respectively, by X-ray crystallography. The side chain of Asn-115 is drastically shifted in both mutants owing to the interaction with several residues, including Asp-175, by formation of hydrogen bonds. This interaction between Asn-115 and Asp-175 probably prevents the mutants from triggering the enzyme reaction using Asp-175 as an acid catalyst.
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Affiliation(s)
- Yusuke Nakamichi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan.,Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Sayoko Oiki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Bunzo Mikami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Kousaku Murata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan.,Department of Life Science, Faculty of Science and Engineering, Setsunan University, Neyagawa, Osaka, 572-8508, Japan
| | - Wataru Hashimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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24
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KdgF, the missing link in the microbial metabolism of uronate sugars from pectin and alginate. Proc Natl Acad Sci U S A 2016; 113:6188-93. [PMID: 27185956 DOI: 10.1073/pnas.1524214113] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Uronates are charged sugars that form the basis of two abundant sources of biomass-pectin and alginate-found in the cell walls of terrestrial plants and marine algae, respectively. These polysaccharides represent an important source of carbon to those organisms with the machinery to degrade them. The microbial pathways of pectin and alginate metabolism are well studied and essentially parallel; in both cases, unsaturated monouronates are produced and processed into the key metabolite 2-keto-3-deoxygluconate (KDG). The enzymes required to catalyze each step have been identified within pectinolytic and alginolytic microbes; yet the function of a small ORF, kdgF, which cooccurs with the genes for these enzymes, is unknown. Here we show that KdgF catalyzes the conversion of pectin- and alginate-derived 4,5-unsaturated monouronates to linear ketonized forms, a step in uronate metabolism that was previously thought to occur spontaneously. Using enzyme assays, NMR, mutagenesis, and deletion of kdgF, we show that KdgF proteins from both pectinolytic and alginolytic bacteria catalyze the ketonization of unsaturated monouronates and contribute to efficient production of KDG. We also report the X-ray crystal structures of two KdgF proteins and propose a mechanism for catalysis. The discovery of the function of KdgF fills a 50-y-old gap in the knowledge of uronate metabolism. Our findings have implications not only for the understanding of an important metabolic pathway, but also the role of pectinolysis in plant-pathogen virulence and the growing interest in the use of pectin and alginate as feedstocks for biofuel production.
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25
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Andreeva OV, Sharipova RR, Strobykina IY, Kravchenko MA, Strobykina AS, Voloshina AD, Musin RZ, Kataeva VE. Development of synthetic approaches to macrocyclic glycoterpenoids on the basis of glucuronic acid and diterpenoid isosteviol. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2015. [DOI: 10.1134/s1070428015090201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Germane KL, Servinsky MD, Gerlach ES, Sund CJ, Hurley MM. Structural analysis of Clostridium acetobutylicum ATCC 824 glycoside hydrolase from CAZy family GH105. Acta Crystallogr F Struct Biol Commun 2015; 71:1100-8. [PMID: 26249707 PMCID: PMC4528949 DOI: 10.1107/s2053230x15012121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/24/2015] [Indexed: 11/10/2022] Open
Abstract
Clostridium acetobutylicum ATCC 824 gene CA_C0359 encodes a putative unsaturated rhamnogalacturonyl hydrolase (URH) with distant amino-acid sequence homology to YteR of Bacillus subtilis strain 168. YteR, like other URHs, has core structural homology to unsaturated glucuronyl hydrolases, but hydrolyzes the unsaturated disaccharide derivative of rhamnogalacturonan I. The crystal structure of the recombinant CA_C0359 protein was solved to 1.6 Å resolution by molecular replacement using the phase information of the previously reported structure of YteR (PDB entry 1nc5) from Bacillus subtilis strain 168. The YteR-like protein is a six-α-hairpin barrel with two β-sheet strands and a small helix overlaying the end of the hairpins next to the active site. The protein has low primary protein sequence identity to YteR but is structurally similar. The two tertiary structures align with a root-mean-square deviation of 1.4 Å and contain a highly conserved active pocket. There is a conserved aspartic acid residue in both structures, which has been shown to be important for hydration of the C=C bond during the release of unsaturated galacturonic acid by YteR. A surface electrostatic potential comparison of CA_C0359 and proteins from CAZy families GH88 and GH105 reveals the make-up of the active site to be a combination of the unsaturated rhamnogalacturonyl hydrolase and the unsaturated glucuronyl hydrolase from Bacillus subtilis strain 168. Structural and electrostatic comparisons suggests that the protein may have a slightly different substrate specificity from that of YteR.
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Affiliation(s)
- Katherine L. Germane
- Oak Ridge Associated Universities, 4692 Millennium Drive, Suite 101, Belcamp, MD 21017, USA
| | - Matthew D. Servinsky
- RDRL-SEE-B, US Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Elliot S. Gerlach
- Federal Staffing Resources, 2200 Somerville Road, Annapolis, MD 21401, USA
| | - Christian J. Sund
- RDRL-SEE-B, US Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Margaret M. Hurley
- RDRL-SEE-B, US Army Research Laboratory, 4600 Deer Creek Loop, Aberdeen Proving Ground, MD 21005, USA
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27
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28
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Synthesis and binding affinity analysis of positional thiol analogs of mannopyranose for the elucidation of sulfur in different position. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.04.060] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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29
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Zhou Y, Zhang X, Ren B, Wu B, Pei Z, Dong H. S-Acetyl migration in synthesis of sulfur-containing glycosides. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.07.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Jongkees SAK, Yoo H, Withers SG. Mechanistic investigations of unsaturated glucuronyl hydrolase from Clostridium perfringens. J Biol Chem 2014; 289:11385-11395. [PMID: 24573682 DOI: 10.1074/jbc.m113.545293] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Experiments were carried out to probe the details of the hydration-initiated hydrolysis catalyzed by the Clostridium perfringens unsaturated glucuronyl hydrolase of glycoside hydrolase family 88 in the CAZy classification system. Direct (1)H NMR monitoring of the enzymatic reaction detected no accumulated reaction intermediates in solution, suggesting that rearrangement of the initial hydration product occurs on-enzyme. An attempt at mechanism-based trapping of on-enzyme intermediates using a 1,1-difluoro-substrate was unsuccessful because the probe was too deactivated to be turned over by the enzyme. Kinetic isotope effects arising from deuterium-for-hydrogen substitution at carbons 1 and 4 provide evidence for separate first-irreversible and overall rate-determining steps in the hydration reaction, with two potential mechanisms proposed to explain these results. Based on the positioning of catalytic residues in the enzyme active site, the lack of efficient turnover of a 2-deoxy-2-fluoro-substrate, and several unsuccessful attempts at confirmation of a simpler mechanism involving a covalent glycosyl-enzyme intermediate, the most plausible mechanism is one involving an intermediate bearing an epoxide on carbons 1 and 2.
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Affiliation(s)
- Seino A K Jongkees
- Departments of Chemistry and Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Hayoung Yoo
- Departments of Chemistry and Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Stephen G Withers
- Departments of Chemistry and Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
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31
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Abstract
Over the sixty years since Koshland initially formulated the classical mechanisms for retaining and inverting glycosidases, researchers have assembled a large body of supporting evidence and have documented variations of these mechanisms. Recently, however, researchers have uncovered a number of completely distinct mechanisms for enzymatic cleavage of glycosides involving elimination and/or hydration steps. In family GH4 and GH109 glycosidases, the reaction proceeds via transient NAD(+)-mediated oxidation at C3, thereby acidifying the proton at C2 and allowing for elimination across the C1-C2 bond. Subsequent Michael-type addition of water followed by reduction at C3 generates the hydrolyzed product. Enzymes employing this mechanism can hydrolyze thioglycosides as well as both anomers of activated substrates. Sialidases employ a conventional retaining mechanism in which a tyrosine functions as the nucleophile, but in some cases researchers have observed off-path elimination end products. These reactions occur via the normal covalent intermediate, but instead of an attack by water on the anomeric center, the catalytic acid/base residue abstracts an adjacent proton. These enzymes can also catalyze hydration of the enol ether via the reverse pathway. Reactions of α-(1,4)-glucan lyases also proceed through a covalent intermediate with subsequent abstraction of an adjacent proton to give elimination. However, in this case, the departing carboxylate "nucleophile" serves as the base in a concerted but asynchronous syn-elimination process. These enzymes perform only elimination reactions. Polysaccharide lyases, which act on uronic acid-containing substrates, also catalyze only elimination reactions. Substrate binding neutralizes the charge on the carboxylate, which allows for abstraction of the proton on C5 and leads to an elimination reaction via an E1cb mechanism. These enzymes can also cleave thioglycosides, albeit slowly. The unsaturated product of polysaccharide lyases can then serve as a substrate for a hydration reaction carried out by unsaturated glucuronyl hydrolases. This hydration is initiated by protonation at C4 and proceeds in a Markovnikov fashion rather than undergoing a Michael-type addition, giving a hemiketal at C5. This hemiketal then undergoes a rearrangement that results in cleavage of the anomeric bond. These enzymes can also hydrolyze thioglycosides efficiently and slowly turn over substrates with inverted anomeric configuration. The mechanisms discussed in this Account proceed through transition states that involve either positive or negative charges, unlike the exclusively cationic transition states of the classical Koshland retaining and inverting glycosidases. In addition, the distribution of this charge throughout the substrate can vary substantially. The nature of these mechanisms and their transition states means that any inhibitors or inactivators of these unusual enzymes probably differ from those presently used for Koshland retaining or inverting glycosidases.
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Affiliation(s)
- Seino A. K. Jongkees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
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32
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Collén PN, Jeudy A, Sassi JF, Groisillier A, Czjzek M, Coutinho PM, Helbert W. A novel unsaturated β-glucuronyl hydrolase involved in ulvan degradation unveils the versatility of stereochemistry requirements in family GH105. J Biol Chem 2014; 289:6199-211. [PMID: 24407291 DOI: 10.1074/jbc.m113.537480] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ulvans are cell wall matrix polysaccharides in green algae belonging to the genus Ulva. Enzymatic degradation of the polysaccharide by ulvan lyases leads to the production of oligosaccharides with an unsaturated β-glucuronyl residue located at the non-reducing end. Exploration of the genomic environment around the Nonlabens ulvanivorans (previously Percicivirga ulvanivorans) ulvan lyase revealed a gene highly similar to known unsaturated uronyl hydrolases classified in the CAZy glycoside hydrolase family 105. The gene was cloned, the protein was overexpressed in Escherichia coli, and enzymology experiments demonstrated its unsaturated β-glucuronyl activity. Kinetic analysis of purified oligo-ulvans incubated with the new enzyme showed that the full substrate specificity is attained by three subsites that preferentially bind anionic residues (sulfated rhamnose, glucuronic/iduronic acid). The three-dimensional crystal structure of the native enzyme reveals that a trimeric organization is required for substrate binding and recognition at the +2 binding subsite. This novel unsaturated β-glucuronyl hydrolase is part of a previously uncharacterized subgroup of GH105 members and exhibits only a very limited sequence similarity to known unsaturated β-glucuronyl sequences previously found only in family GH88. Clan-O formed by families GH88 and GH105 was singular in the fact that it covered families acting on both axial and equatorial glycosidic linkages, respectively. The overall comparison of active site structures between enzymes from these two families highlights how that within family GH105, and unlike for classical glycoside hydrolysis, the hydrolysis of vinyl ether groups from unsaturated saccharides occurs independently of the α or β configuration of the cleaved linkage.
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Affiliation(s)
- Pi Nyvall Collén
- From the CNRS, Université Pierre et Marie Curie-Paris 6, Unité Mixte de Recherche 7139 "Marine Plants and Biomolecules," Station Biologique, F-29682 Roscoff Cedex, France
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33
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Enquist-Newman M, Faust AME, Bravo DD, Santos CNS, Raisner RM, Hanel A, Sarvabhowman P, Le C, Regitsky DD, Cooper SR, Peereboom L, Clark A, Martinez Y, Goldsmith J, Cho MY, Donohoue PD, Luo L, Lamberson B, Tamrakar P, Kim EJ, Villari JL, Gill A, Tripathi SA, Karamchedu P, Paredes CJ, Rajgarhia V, Kotlar HK, Bailey RB, Miller DJ, Ohler NL, Swimmer C, Yoshikuni Y. Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform. Nature 2014; 505:239-43. [PMID: 24291791 DOI: 10.1038/nature12771] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/08/2013] [Indexed: 12/21/2022]
Abstract
The increasing demands placed on natural resources for fuel and food production require that we explore the use of efficient, sustainable feedstocks such as brown macroalgae. The full potential of brown macroalgae as feedstocks for commercial-scale fuel ethanol production, however, requires extensive re-engineering of the alginate and mannitol catabolic pathways in the standard industrial microbe Saccharomyces cerevisiae. Here we present the discovery of an alginate monomer (4-deoxy-L-erythro-5-hexoseulose uronate, or DEHU) transporter from the alginolytic eukaryote Asteromyces cruciatus. The genomic integration and overexpression of the gene encoding this transporter, together with the necessary bacterial alginate and deregulated native mannitol catabolism genes, conferred the ability of an S. cerevisiae strain to efficiently metabolize DEHU and mannitol. When this platform was further adapted to grow on mannitol and DEHU under anaerobic conditions, it was capable of ethanol fermentation from mannitol and DEHU, achieving titres of 4.6% (v/v) (36.2 g l(-1)) and yields up to 83% of the maximum theoretical yield from consumed sugars. These results show that all major sugars in brown macroalgae can be used as feedstocks for biofuels and value-added renewable chemicals in a manner that is comparable to traditional arable-land-based feedstocks.
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Affiliation(s)
- Maria Enquist-Newman
- 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2]
| | - Ann Marie E Faust
- 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2]
| | - Daniel D Bravo
- 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2]
| | - Christine Nicole S Santos
- 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2] Manus Biosynthesis Inc., 790 Memorial Drive, Suite 102, Cambridge, Massachusetts 02139 (C.N.S.S.); Calysta Energy, 1140 O'Brien Drive, Menlo Park, California 94025 (D.D.R.); Sutro Biopharma lnc., 310 Utah Avenue, Suite 150, South San Francisco, California 94080, USA (A.G.); Total New Energies USA, 5858 Horton Street, Emeryville, California 94560 (S.A.T.; V.R.)
| | - Ryan M Raisner
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Arthur Hanel
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Preethi Sarvabhowman
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Chi Le
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Drew D Regitsky
- 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2] Manus Biosynthesis Inc., 790 Memorial Drive, Suite 102, Cambridge, Massachusetts 02139 (C.N.S.S.); Calysta Energy, 1140 O'Brien Drive, Menlo Park, California 94025 (D.D.R.); Sutro Biopharma lnc., 310 Utah Avenue, Suite 150, South San Francisco, California 94080, USA (A.G.); Total New Energies USA, 5858 Horton Street, Emeryville, California 94560 (S.A.T.; V.R.)
| | - Susan R Cooper
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Lars Peereboom
- Department of Chemical Engineering and Materials Science, Michigan State University, 2527 Engineering Building, East Lansing, Michigan 48824-1226, USA
| | - Alana Clark
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Yessica Martinez
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Joshua Goldsmith
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Min Y Cho
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Paul D Donohoue
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Lily Luo
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Brigit Lamberson
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Pramila Tamrakar
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Edward J Kim
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Jeffrey L Villari
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Avinash Gill
- 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2] Manus Biosynthesis Inc., 790 Memorial Drive, Suite 102, Cambridge, Massachusetts 02139 (C.N.S.S.); Calysta Energy, 1140 O'Brien Drive, Menlo Park, California 94025 (D.D.R.); Sutro Biopharma lnc., 310 Utah Avenue, Suite 150, South San Francisco, California 94080, USA (A.G.); Total New Energies USA, 5858 Horton Street, Emeryville, California 94560 (S.A.T.; V.R.)
| | - Shital A Tripathi
- 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2] Manus Biosynthesis Inc., 790 Memorial Drive, Suite 102, Cambridge, Massachusetts 02139 (C.N.S.S.); Calysta Energy, 1140 O'Brien Drive, Menlo Park, California 94025 (D.D.R.); Sutro Biopharma lnc., 310 Utah Avenue, Suite 150, South San Francisco, California 94080, USA (A.G.); Total New Energies USA, 5858 Horton Street, Emeryville, California 94560 (S.A.T.; V.R.)
| | - Padma Karamchedu
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Carlos J Paredes
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Vineet Rajgarhia
- 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2] Manus Biosynthesis Inc., 790 Memorial Drive, Suite 102, Cambridge, Massachusetts 02139 (C.N.S.S.); Calysta Energy, 1140 O'Brien Drive, Menlo Park, California 94025 (D.D.R.); Sutro Biopharma lnc., 310 Utah Avenue, Suite 150, South San Francisco, California 94080, USA (A.G.); Total New Energies USA, 5858 Horton Street, Emeryville, California 94560 (S.A.T.; V.R.)
| | - Hans Kristian Kotlar
- Statoil ASA, Statoil Research Centre, Arkitekt Ebbells vei 10, Rotvoll, 7005 Trondheim, Norway
| | - Richard B Bailey
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Dennis J Miller
- Department of Chemical Engineering and Materials Science, Michigan State University, 2527 Engineering Building, East Lansing, Michigan 48824-1226, USA
| | - Nicholas L Ohler
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Candace Swimmer
- Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA
| | - Yasuo Yoshikuni
- 1] Bio Architecture Lab Inc., 604 Bancroft Way, Suite A, Berkeley, California 94710, USA [2] BALChile S.A., Badajoz 100, Oficina 1404, Las Condes, Santiago 7550000, Chile [3] BAL Biofuels S.A., Badajoz 100, Oficina 1404, Las Condes, Santiago 7550000, Chile
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Nakamichi Y, Mikami B, Murata K, Hashimoto W. Crystal structure of a bacterial unsaturated glucuronyl hydrolase with specificity for heparin. J Biol Chem 2014; 289:4787-97. [PMID: 24403065 DOI: 10.1074/jbc.m113.522573] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Extracellular matrix molecules such as glycosaminoglycans (GAGs) are typical targets for some pathogenic bacteria, which allow adherence to host cells. Bacterial polysaccharide lyases depolymerize GAGs in β-elimination reactions, and the resulting unsaturated disaccharides are subsequently degraded to constituent monosaccharides by unsaturated glucuronyl hydrolases (UGLs). UGL substrates are classified as 1,3- and 1,4-types based on the glycoside bonds. Unsaturated chondroitin and heparin disaccharides are typical members of 1,3- and 1,4-types, respectively. Here we show the reaction modes of bacterial UGLs with unsaturated heparin disaccharides by x-ray crystallography, docking simulation, and site-directed mutagenesis. Although streptococcal and Bacillus UGLs were active on unsaturated heparin disaccharides, those preferred 1,3- rather than 1,4-type substrates. The genome of GAG-degrading Pedobacter heparinus encodes 13 UGLs. Of these, Phep_2830 is known to be specific for unsaturated heparin disaccharides. The crystal structure of Phep_2830 was determined at 1.35-Å resolution. In comparison with structures of streptococcal and Bacillus UGLs, a pocket-like structure and lid loop at subsite +1 are characteristic of Phep_2830. Docking simulations of Phep_2830 with unsaturated heparin disaccharides demonstrated that the direction of substrate pyranose rings differs from that in unsaturated chondroitin disaccharides. Acetyl groups of unsaturated heparin disaccharides are well accommodated in the pocket at subsite +1, and aromatic residues of the lid loop are required for stacking interactions with substrates. Thus, site-directed mutations of the pocket and lid loop led to significantly reduced enzyme activity, suggesting that the pocket-like structure and lid loop are involved in the recognition of 1,4-type substrates by UGLs.
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Affiliation(s)
- Yusuke Nakamichi
- From the Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, and
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Jongkees SAK, Yoo H, Withers SG. Mechanistic Insights from Substrate Preference in Unsaturated Glucuronyl Hydrolase. Chembiochem 2013; 15:124-34. [PMID: 24227702 DOI: 10.1002/cbic.201300547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Seino A K Jongkees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1 (Canada)
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Mann AJ, Hahnke RL, Huang S, Werner J, Xing P, Barbeyron T, Huettel B, Stüber K, Reinhardt R, Harder J, Glöckner FO, Amann RI, Teeling H. The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides. Appl Environ Microbiol 2013; 79:6813-22. [PMID: 23995932 PMCID: PMC3811500 DOI: 10.1128/aem.01937-13] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/26/2013] [Indexed: 11/20/2022] Open
Abstract
In recent years, representatives of the Bacteroidetes have been increasingly recognized as specialists for the degradation of macromolecules. Formosa constitutes a Bacteroidetes genus within the class Flavobacteria, and the members of this genus have been found in marine habitats with high levels of organic matter, such as in association with algae, invertebrates, and fecal pellets. Here we report on the generation and analysis of the genome of the type strain of Formosa agariphila (KMM 3901(T)), an isolate from the green alga Acrosiphonia sonderi. F. agariphila is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification. Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced specialization for the degradation of proteins, polysaccharides, and glycoproteins. Sixty-five of the glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci, where they are clustered with TonB-dependent receptors, SusD-like proteins, sensors/transcription factors, transporters, and often sulfatases. These loci play a pivotal role in bacteroidetal polysaccharide biodegradation and in the case of F. agariphila revealed the capacity to degrade a wide range of algal polysaccharides from green, red, and brown algae and thus a strong specialization of toward an alga-associated lifestyle. This was corroborated by growth experiments, which confirmed usage particularly of those monosaccharides that constitute the building blocks of abundant algal polysaccharides, as well as distinct algal polysaccharides, such as laminarins, xylans, and κ-carrageenans.
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Affiliation(s)
- Alexander J. Mann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen gGmbH, Bremen, Germany
| | | | - Sixing Huang
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Johannes Werner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen gGmbH, Bremen, Germany
| | - Peng Xing
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tristan Barbeyron
- National Center of Scientific Research/Pierre and Marie Curie University Paris 6, UMR 7139 Marine Plants and Biomolecules, Roscoff, Bretagne, France
| | | | - Kurt Stüber
- Max Planck Genome Centre Cologne, Cologne, Germany
| | | | - Jens Harder
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Jacobs University Bremen gGmbH, Bremen, Germany
| | - Rudolf I. Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Kinetic isotope effects for studying post-translational modifying enzymes. Curr Opin Chem Biol 2012; 16:472-8. [PMID: 23146439 DOI: 10.1016/j.cbpa.2012.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 11/20/2022]
Abstract
The ongoing development of new experimental approaches for the measurement of isotope effects is improving our understanding of the physical and chemical changes that occur during biological catalysis. Biological catalysis involves numerous steps that include binding, conformational changes, chemical catalysis and product release. The critical points on the free energy surface for biologically catalyzed reactions include all bound intermediates and the intervening transition states. Isotope effects can be used to investigate both intermediate (equilibrium isotope effects) and transition state (kinetic isotope effects) structures along the reaction coordinate. This review details new techniques for measuring isotope effects and provides several examples of their use in solving transition state structures for post-translational modifying enzymes.
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