1
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Franceus J, Steynen M, Allaert Y, Bredael K, D'hooghe M, Desmet T. High-yield synthesis of 2-O-α-D-glucosyl-D-glycerate by a bifunctional glycoside phosphorylase. Appl Microbiol Biotechnol 2024; 108:55. [PMID: 38175244 DOI: 10.1007/s00253-023-12970-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/02/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
Osmolytes are produced by various microorganisms as a defense mechanism to protect cells and macromolecules from damage caused by external stresses in harsh environments. Due to their useful stabilizing properties, these molecules are applied as active ingredients in a wide range of cosmetics and healthcare products. The metabolic pathways and biocatalytic syntheses of glycosidic osmolytes such as 2-O-α-D-glucosyl-D-glycerate often involve the action of a glycoside phosphorylase. Here, we report the discovery of a glucosylglycerate phosphorylase from carbohydrate-active enzyme family GH13 that is also active on sucrose, which contrasts the strict specificity of known glucosylglycerate phosphorylases that can only use α-D-glucose 1-phosphate as glycosyl donor in transglycosylation reactions. The novel enzyme can be distinguished from other phosphorylases from the same family by the presence of an atypical conserved sequence motif at specificity-determining positions in the active site. The promiscuity of the sucrose-active glucosylglycerate phosphorylase can be exploited for the high-yielding and rapid synthesis of 2-O-α-D-glucosyl-D-glycerate from sucrose and D-glycerate. KEY POINTS: • A Xylanimonas protaetiae glycoside phosphorylase can use both d-glycerate and fructose as glucosyl acceptor with high catalytic efficiency • Biocatalytic synthesis of the osmolyte 2-O-α-d-glucosyl-d-glycerate • Positions in the active site of GH13 phosphorylases act as convenient specificity fingerprints.
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Affiliation(s)
- Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Manon Steynen
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Yentl Allaert
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Kato Bredael
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Matthias D'hooghe
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
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2
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Liu J, Ren M, Ma H, Zhang H, Cui X, Kang R, Feng X, Meng D. One-pot sustainable synthesis of glucosylglycerate from starch and glycerol through artificial in vitro enzymatic cascade. BIORESOURCE TECHNOLOGY 2024; 399:130611. [PMID: 38508282 DOI: 10.1016/j.biortech.2024.130611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/15/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Glucosylglycerate (R-2-O-α-D-glucopyranosyl-glycerate, GG) is a negatively charged compatible solution with versatile functions. Here, an artificial in vitro enzymatic cascade was designed to feasibly and sustainably produce GG from affordable starch and glycerol. First, Spirochaeta thermophila glucosylglycerate phosphorylase (GGP) was carefully selected because of its excellent heterologous expression, specific activity, and thermostability. The optimized two-enzyme cascade, consisting of alpha-glucan phosphorylase (αGP) and GGP, achieved a remarkable 81 % conversion rate from maltodextrin and D-glycerate. Scaling up this cascade resulted in a practical concentration of 58 g/L GG with a 62 % conversion rate based on the added D-glycerate. Additionally, the production of GG from inexpensive starch and glycerol in one-pot using artificial four-enzyme cascade was successfully implemented, which integrates alditol oxidase and catalase with αGP and GGP. Collectively, this sustainable enzymatic cascade demonstrates the feasibility of the practical synthesis of GG and has the potential to produce other glycosides using the phosphorylase-and-phosphorylase paradigm.
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Affiliation(s)
- Juanjuan Liu
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China
| | - Mengfei Ren
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China
| | - Haoran Ma
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China
| | - Huilin Zhang
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China
| | - Xinyu Cui
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China
| | - Runyuan Kang
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China
| | - Xinming Feng
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China; Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Yantai University, Yantai 264005, Shandong, China
| | - Dongdong Meng
- College of Life Sciences, Yantai University, Yantai 264005, Shandong, China; Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Yantai University, Yantai 264005, Shandong, China.
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3
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Allaert Y, Leyder A, Franceus J, Desmet T. Strategies for the synthesis of the osmolyte glucosylglycerate and its precursor glycerate. Appl Microbiol Biotechnol 2024; 108:297. [PMID: 38607564 PMCID: PMC11009771 DOI: 10.1007/s00253-024-13139-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
Glycosidic osmolytes are widespread natural compounds that protect microorganisms and their macromolecules from the deleterious effects of various environmental stresses. Their protective properties have attracted considerable interest for industrial applications, especially as active ingredients in cosmetics and healthcare products. In that regard, the osmolyte glucosylglycerate is somewhat overlooked. Glucosylglycerate is typically accumulated by certain organisms when they are exposed to high salinity and nitrogen starvation, and its potent stabilizing effects have been demonstrated in vitro. However, the applications of this osmolyte have not been thoroughly explored due to the lack of a cost-efficient production process. Here, we present an overview of the progress that has been made in developing promising strategies for the synthesis of glucosylglycerate and its precursor glycerate, and discuss the remaining challenges. KEY POINTS: • Bacterial milking could be explored for fermentative production of glucosylglycerate • Glycoside phosphorylases of GH13_18 represent attractive alternatives for biocatalytic production • Conversion of glycerol with alditol oxidase is a promising strategy for generating the precursor glycerate.
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Affiliation(s)
- Yentl Allaert
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Arthur Leyder
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
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4
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Cheng L, Zhang Z, Zhu D, Luo Q, Lu X. Glucosylglycerol phosphorylase, a potential novel pathway of microbial glucosylglycerol catabolism. Appl Microbiol Biotechnol 2024; 108:214. [PMID: 38363425 PMCID: PMC10873239 DOI: 10.1007/s00253-024-13035-3] [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: 11/08/2023] [Revised: 01/11/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Glucosylglycerol (GG) is a natural compatible solute that can be synthesized by many cyanobacteria and a few heterotrophic bacteria under high salinity conditions. In cyanobacteria, GG is synthesized by GG-phosphate synthase and GG-phosphate phosphatase, and a hydrolase GGHA catalyzes its degradation. In heterotrophic bacteria (such as some Marinobacter species), a fused form of GG-phosphate phosphatase and GG-phosphate synthase is present, but the cyanobacteria-like degradation pathway is not available. Instead, a phosphorylase GGP, of which the coding gene is located adjacent to the gene that encodes the GG-synthesizing enzyme, is supposed to perform the GG degradation function. In the present study, a GGP homolog from the salt-tolerant M. salinexigens ZYF650T was characterized. The recombinant GGP catalyzed GG decomposition via a two-step process of phosphorolysis and hydrolysis in vitro and exhibited high substrate specificity toward GG. The activity of GGP was enhanced by inorganic salts at low concentrations but significantly inhibited by increasing salt concentrations. While the investigation on the physiological role of GGP in M. salinexigens ZYF650T was limited due to the failed induction of GG production, the heterologous expression of ggp in the living cells of the GG-producing cyanobacterium Synechocystis sp. PCC 6803 significantly reduced the salt-induced GG accumulation. Together, these data suggested that GGP may represent a novel pathway of microbial GG catabolism. KEY POINTS: • GGP catalyzes GG degradation by a process of phosphorolysis and hydrolysis • GGP-catalyzed GG degradation is different from GGHA-based GG degradation • GGP represents a potential novel pathway of microbial GG catabolism.
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Affiliation(s)
- Lin Cheng
- College of Chemical Engineering and Materials Sciences, Tianjin University of Science & Technology, Tianjin, 300457, China
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao, 266101, China
| | - Zhichao Zhang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao, 266101, China
- Shandong Energy Institute, Songling Rd 189, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Songling Rd 189, Qingdao, 266101, China
| | - Daling Zhu
- College of Chemical Engineering and Materials Sciences, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Quan Luo
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao, 266101, China.
- Shandong Energy Institute, Songling Rd 189, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Songling Rd 189, Qingdao, 266101, China.
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao, 266101, China
- Shandong Energy Institute, Songling Rd 189, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Songling Rd 189, Qingdao, 266101, China
- Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Wenhai Rd 168, Qingdao, 266237, China
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5
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Nedashkovskaya O, Otstavnykh N, Balabanova L, Bystritskaya E, Kim SG, Zhukova N, Tekutyeva L, Isaeva M. Rhodoalgimonas zhirmunskyi gen. nov., sp. nov., a Marine Alphaproteobacterium Isolated from the Pacific Red Alga Ahnfeltia tobuchiensis: Phenotypic Characterization and Pan-Genome Analysis. Microorganisms 2023; 11:2463. [PMID: 37894121 PMCID: PMC10608839 DOI: 10.3390/microorganisms11102463] [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] [Received: 08/17/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
A novel Gram-staining negative, strictly aerobic, rod-shaped, and non-motile bacterium, designated strain 10Alg 79T, was isolated from the red alga Ahnfeltia tobuchiensis. A phylogenetic analysis based on 16S rRNA gene sequences placed the novel strain within the family Roseobacteraceae, class Alphaproteobacteria, phylum Pseudomonadota, where the nearest neighbor was Shimia sediminis ZQ172T (97.33% of identity). However, a phylogenomic study clearly showed that strain 10Alg 79T forms a distinct evolutionary lineage at the genus level within the family Roseobacteraceae combining with strains Aquicoccus porphyridii L1 8-17T, Marimonas arenosa KCTC 52189T, and Lentibacter algarum DSM 24677T. The ANI, AAI, and dDDH values between them were 75.63-78.15%, 67.41-73.08%, and 18.8-19.8%, respectively. The genome comprises 3,754,741 bp with a DNA GC content of 62.1 mol%. The prevalent fatty acids of strain 10Alg 79T were C18:1 ω7c and C16:0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. A pan-genome analysis showed that the unique part of the 10Alg 79T genome consists of 13 genus-specific clusters and 413 singletons. The annotated singletons were more often related to transport protein systems, transcriptional regulators, and enzymes. A functional annotation of the draft genome sequence revealed that this bacterium could be a source of a new phosphorylase, which may be used for phosphoglycoside synthesis. A combination of the genotypic and phenotypic data showed that the bacterial isolate represents a novel species and a novel genus, for which the name Rhodoalgimonas zhirmunskyi gen. nov., sp. nov. is proposed. The type strain is 10Alg 79T (=KCTC 72611T = KMM 6723T).
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Affiliation(s)
- Olga Nedashkovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (L.B.); (E.B.)
| | - Nadezhda Otstavnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (L.B.); (E.B.)
| | - Larissa Balabanova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (L.B.); (E.B.)
| | - Evgenia Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (L.B.); (E.B.)
| | - Song-Gun Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si 56212, Republic of Korea;
| | - Natalia Zhukova
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia;
| | - Liudmila Tekutyeva
- Innovative Technology Center, Far Eastern Federal University, 8 Suhanova St., Vladivostok 690950, Russia;
- ARNIKA, Territory of PDA Nadezhdinskaya, Centralnaya St. 42, Volno-Nadezhdinskoye, Vladivostok 692481, Russia
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (L.B.); (E.B.)
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6
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Mogul R, Miller DR, Ramos B, Lalla SJ. Metabolomic and cultivation insights into the tolerance of the spacecraft-associated Acinetobacter toward Kleenol 30, a cleanroom floor detergent. Front Microbiol 2023; 14:1090740. [PMID: 36950167 PMCID: PMC10025500 DOI: 10.3389/fmicb.2023.1090740] [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: 11/05/2022] [Accepted: 01/20/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Stringent cleaning procedures during spacecraft assembly are critical to maintaining the integrity of life-detection missions. To ensure cleanliness, NASA spacecraft are assembled in cleanroom facilities, where floors are routinely cleansed with Kleenol 30 (K30), an alkaline detergent. Methods Through metabolomic and cultivation approaches, we show that cultures of spacecraft-associated Acinetobacter tolerate up to 1% v/v K30 and are fully inhibited at ≥2%; in comparison, NASA cleanrooms are cleansed with ~0.8-1.6% K30. Results For A. johnsonii 2P08AA (isolated from a cleanroom floor), cultivations with 0.1% v/v K30 yield (1) no changes in cell density at late-log phase, (2) modest decreases in growth rate (~17%), (3) negligible lag phase times, (4) limited changes in the intracellular metabolome, and (5) increases in extracellular sugar acids, monosaccharides, organic acids, and fatty acids. For A. radioresistens 50v1 (isolated from a spacecraft surface), cultivations yield (1) ~50% survivals, (2) no changes in growth rate, (3) ~70% decreases in the lag phase time, (4) differential changes in intracellular amino acids, compatible solutes, nucleotide-related metabolites, dicarboxylic acids, and saturated fatty acids, and (5) substantial yet differential impacts to extracellular sugar acids, monosaccharides, and organic acids. Discussion These combined results suggest that (1) K30 manifests strain-dependent impacts on the intracellular metabolomes, cultivation kinetics, and survivals, (2) K30 influences extracellular trace element acquisition in both strains, and (3) K30 is better tolerated by the floor-associated strain. Hence, this work lends support towards the hypothesis that repeated cleansing during spacecraft assembly serve as selective pressures that promote tolerances towards the cleaning conditions.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
- Blue Marble Institute of Science, Seattle, WA, United States
| | - Daniel R. Miller
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
| | - Brian Ramos
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
| | - Sidharth J. Lalla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
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Dolan JP, Cosgrove SC, Miller GJ. Biocatalytic Approaches to Building Blocks for Enzymatic and Chemical Glycan Synthesis. JACS AU 2023; 3:47-61. [PMID: 36711082 PMCID: PMC9875253 DOI: 10.1021/jacsau.2c00529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
While the field of biocatalysis has bloomed over the past 20-30 years, advances in the understanding and improvement of carbohydrate-active enzymes, in particular, the sugar nucleotides involved in glycan building block biosynthesis, have progressed relatively more slowly. This perspective highlights the need for further insight into substrate promiscuity and the use of biocatalysis fundamentals (rational design, directed evolution, immobilization) to expand substrate scopes toward such carbohydrate building block syntheses and/or to improve enzyme stability, kinetics, or turnover. Further, it explores the growing premise of using biocatalysis to provide simple, cost-effective access to stereochemically defined carbohydrate materials, which can undergo late-stage chemical functionalization or automated glycan synthesis/polymerization.
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Affiliation(s)
- Jonathan P. Dolan
- School of Chemical and Physical
Sciences & Centre for Glycosciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Sebastian C. Cosgrove
- School of Chemical and Physical
Sciences & Centre for Glycosciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Gavin J. Miller
- School of Chemical and Physical
Sciences & Centre for Glycosciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
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The Power of Biocatalysts for Highly Selective and Efficient Phosphorylation Reactions. Catalysts 2022. [DOI: 10.3390/catal12111436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Reactions involving the transfer of phosphorus-containing groups are of key importance for maintaining life, from biological cells, tissues and organs to plants, animals, humans, ecosystems and the whole planet earth. The sustainable utilization of the nonrenewable element phosphorus is of key importance for a balanced phosphorus cycle. Significant advances have been achieved in highly selective and efficient biocatalytic phosphorylation reactions, fundamental and applied aspects of phosphorylation biocatalysts, novel phosphorylation biocatalysts, discovery methodologies and tools, analytical and synthetic applications, useful phosphoryl donors and systems for their regeneration, reaction engineering, product recovery and purification. Biocatalytic phosphorylation reactions with complete conversion therefore provide an excellent reaction platform for valuable analytical and synthetic applications.
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9
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Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases. Int J Mol Sci 2022; 23:ijms23063043. [PMID: 35328479 PMCID: PMC8950772 DOI: 10.3390/ijms23063043] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Among carbohydrate active enzymes, glycoside phosphorylases (GPs) are valuable catalysts for white biotechnologies, due to their exquisite capacity to efficiently re-modulate oligo- and poly-saccharides, without the need for costly activated sugars as substrates. The reversibility of the phosphorolysis reaction, indeed, makes them attractive tools for glycodiversification. However, discovery of new GP functions is hindered by the difficulty in identifying them in sequence databases, and, rather, relies on extensive and tedious biochemical characterization studies. Nevertheless, recent advances in automated tools have led to major improvements in GP mining, activity predictions, and functional screening. Implementation of GPs into innovative in vitro and in cellulo bioproduction strategies has also made substantial advances. Herein, we propose to discuss the latest developments in the strategies employed to efficiently discover GPs and make the best use of their exceptional catalytic properties for glycoside bioproduction.
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10
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Saburi W, Nihira T, Nakai H, Kitaoka M, Mori H. Discovery of solabiose phosphorylase and its application for enzymatic synthesis of solabiose from sucrose and lactose. Sci Rep 2022; 12:259. [PMID: 34997180 PMCID: PMC8741936 DOI: 10.1038/s41598-021-04421-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/22/2021] [Indexed: 11/09/2022] Open
Abstract
Glycoside phosphorylases (GPs), which catalyze the reversible phosphorolysis of glycosides, are promising enzymes for the efficient production of glycosides. Various GPs with new catalytic activities are discovered from uncharacterized proteins phylogenetically distant from known enzymes in the past decade. In this study, we characterized Paenibacillus borealis PBOR_28850 protein, belonging to glycoside hydrolase family 94. Screening of acceptor substrates for reverse phosphorolysis, in which α-D-glucose 1-phosphate was used as the donor substrate, revealed that the recombinant PBOR_28850 produced in Escherichia coli specifically utilized D-galactose as an acceptor and produced solabiose (β-D-Glcp-(1 → 3)-D-Gal). This indicates that PBOR_28850 is a new GP, solabiose phosphorylase. PBOR_28850 catalyzed the phosphorolysis and synthesis of solabiose through a sequential bi-bi mechanism involving the formation of a ternary complex. The production of solabiose from lactose and sucrose has been established. Lactose was hydrolyzed to D-galactose and D-glucose by β-galactosidase. Phosphorolysis of sucrose and synthesis of solabiose were then coupled by adding sucrose, sucrose phosphorylase, and PBOR_28850 to the reaction mixture. Using 210 mmol lactose and 280 mmol sucrose, 207 mmol of solabiose was produced. Yeast treatment degraded the remaining monosaccharides and sucrose without reducing solabiose. Solabiose with a purity of 93.7% was obtained without any chromatographic procedures.
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Affiliation(s)
- Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Sapporo, 060-8589, Japan.
| | - Takanori Nihira
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Motomitsu Kitaoka
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Sapporo, 060-8589, Japan
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De Doncker M, De Graeve C, Franceus J, Beerens K, Křen V, Pelantová H, Vercauteren R, Desmet T. Exploration of GH94 Sequence Space for Enzyme Discovery Reveals a Novel Glucosylgalactose Phosphorylase Specificity. Chembiochem 2021; 22:3319-3325. [PMID: 34541742 DOI: 10.1002/cbic.202100401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/15/2021] [Indexed: 11/05/2022]
Abstract
The substantial increase in DNA sequencing efforts has led to a rapid expansion of available sequences in glycoside hydrolase families. The ever-increasing sequence space presents considerable opportunities for the search for enzymes with novel functionalities. In this work, the sequence-function space of glycoside hydrolase family 94 (GH94) was explored in detail, using a combined approach of phylogenetic analysis and sequence similarity networks. The identification and experimental screening of unknown clusters led to the discovery of an enzyme from the soil bacterium Paenibacillus polymyxa that acts as a 4-O-β-d-glucosyl-d-galactose phosphorylase (GGalP), a specificity that has not been reported to date. Detailed characterization of GGalP revealed that its kinetic parameters were consistent with those of other known phosphorylases. Furthermore, the enzyme could be used for production of the rare disaccharides 4-O-β-d-glucosyl-d-galactose and 4-O-β-d-glucosyl-l-arabinose. Our current work highlights the power of rational sequence space exploration in the search for novel enzyme specificities, as well as the potential of phosphorylases for rare disaccharide synthesis.
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Affiliation(s)
- Marc De Doncker
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links Ghent, 653, 9000, Gent, Belgium
| | - Chloé De Graeve
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links Ghent, 653, 9000, Gent, Belgium
| | - Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links Ghent, 653, 9000, Gent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links Ghent, 653, 9000, Gent, Belgium
| | - Vladimír Křen
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Helena Pelantová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Ronny Vercauteren
- Cargill R&D Centre Europe BVBA, Havenstraat 84, 1800, Vilvoorde, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links Ghent, 653, 9000, Gent, Belgium
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12
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Discovery of a Kojibiose Hydrolase by Analysis of Specificity-Determining Correlated Positions in Glycoside Hydrolase Family 65. Molecules 2021; 26:molecules26206321. [PMID: 34684901 PMCID: PMC8537180 DOI: 10.3390/molecules26206321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/25/2022] Open
Abstract
The Glycoside Hydrolase Family 65 (GH65) is an enzyme family of inverting α-glucoside phosphorylases and hydrolases that currently contains 10 characterized enzyme specificities. However, its sequence diversity has never been studied in detail. Here, an in-silico analysis of correlated mutations was performed, revealing specificity-determining positions that facilitate annotation of the family’s phylogenetic tree. By searching these positions for amino acid motifs that do not match those found in previously characterized enzymes from GH65, several clades that may harbor new functions could be identified. Three enzymes from across these regions were expressed in E. coli and their substrate profile was mapped. One of those enzymes, originating from the bacterium Mucilaginibacter mallensis, was found to hydrolyze kojibiose and α-1,2-oligoglucans with high specificity. We propose kojibiose glucohydrolase as the systematic name and kojibiose hydrolase or kojibiase as the short name for this new enzyme. This work illustrates a convenient strategy for mapping the natural diversity of enzyme families and smartly mining the ever-growing number of available sequences in the quest for novel specificities.
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13
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Zhang C, Chen Q, Fan F, Tang J, Zhan T, Wang H, Zhang X. Directed evolution of alditol oxidase for the production of optically pure D-glycerate from glycerol in the engineered Escherichia coli. J Ind Microbiol Biotechnol 2021; 48:6312499. [PMID: 34196357 PMCID: PMC8788829 DOI: 10.1093/jimb/kuab041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/26/2021] [Indexed: 11/16/2022]
Abstract
D-glycerate is an attractive chemical for a wide variety of pharmaceutical, cosmetic, biodegradable polymers, and other applications. Now several studies have been reported about the synthesis of glycerate by different biotechnological and chemical routes from glycerol or other feedstock. Here, we present the construction of an Escherichia coli engineered strain to produce optically pure D-glycerate by oxidizing glycerol with an evolved variant of alditol oxidase (AldO) from Streptomyces coelicolor. This is achieved by starting from a previously reported variant mAldO and employing three rounds of directed evolution, as well as the combination of growth-coupled high throughput selection with colorimetric screening. The variant eAldO3-24 displays a higher substrate affinity toward glycerol with 5.23-fold than the wild-type AldO, and a 1.85-fold increase of catalytic efficiency (kcat/KM). Then we introduced an isopropyl-β-D-thiogalactopyranoside (IPTG)-inducible T7 expression system in E. coli to overexpress the variant eAldO3-24, and deleted glucosylglycerate phosphorylase encoding gene ycjM to block the consumption of D-glycerate. Finally, the resulting strain TZ-170 produced 30.1 g/l D-glycerate at 70 h with a yield of 0.376 mol/mol in 5-l fed-batch fermentation.
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Affiliation(s)
- Chao Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China.,College of Chemistry and Life Science, Changchun University of Technology, Jilin, Changchun 130012, China
| | - Qian Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China
| | - Feiyu Fan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China
| | - Jinlei Tang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China
| | - Tao Zhan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China
| | - Honglei Wang
- College of Chemistry and Life Science, Changchun University of Technology, Jilin, Changchun 130012, China
| | - Xueli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqidao, Tianjin Airport Economic Park, Tianjin 300308, China
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14
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Franceus J, Lormans J, Cools L, D’hooghe M, Desmet T. Evolution of Phosphorylases from N-Acetylglucosaminide Hydrolases in Family GH3. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jolien Lormans
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Lore Cools
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Matthias D’hooghe
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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15
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Yogiara, Mordukhova EA, Kim D, Kim WG, Hwang JK, Pan JG. The food-grade antimicrobial xanthorrhizol targets the enoyl-ACP reductase (FabI) in Escherichia coli. Bioorg Med Chem Lett 2020; 30:127651. [PMID: 33130290 DOI: 10.1016/j.bmcl.2020.127651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 10/14/2020] [Accepted: 10/24/2020] [Indexed: 11/28/2022]
Abstract
Xanthorrhizol, isolated from the Indonesian Java turmeric Curcuma xanthorrhiza, displays broad-spectrum antibacterial activity. We report herein the evidence that mechanism of action of xanthorrhizol may involve FabI, an enoyl-(ACP) reductase, inhibition. The predicted Y156V substitution in the FabI enzyme promoted xanthorrhizol resistance, while the G93V mutation originally known for triclosan resistance was not effective against xanthorrhizol. Two other mutations, F203L and F203V, conferred FabI enzyme resistance to both xanthorrhizol and triclosan. These results showed that xanthorrhizol is a food-grade antimicrobial compound targeting FabI but with a different mode of binding from triclosan.
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Affiliation(s)
- Yogiara
- Department of Biotechnology, Yonsei University, 50-Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jalan Jenderal Sudirman 51, Jakarta 12930, Indonesia.
| | - Elena A Mordukhova
- GenoFocus Inc., 65 Techno 1-ro, Gwanpyeong-dong, Yuseong-gu, Daejeon 34014, Republic of Korea.
| | - Dooil Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 34141, Republic of Korea.
| | - Won-Gon Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 34141, Republic of Korea.
| | - Jae-Kwan Hwang
- Department of Biotechnology, Yonsei University, 50-Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Jae-Gu Pan
- GenoFocus Inc., 65 Techno 1-ro, Gwanpyeong-dong, Yuseong-gu, Daejeon 34014, Republic of Korea; Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 34141, Republic of Korea.
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16
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Tanaka M, Kumakura D, Mino S, Doi H, Ogura Y, Hayashi T, Yumoto I, Cai M, Zhou YG, Gomez-Gil B, Araki T, Sawabe T. Genomic characterization of closely related species in the Rumoiensis clade infers ecogenomic signatures to non-marine environments. Environ Microbiol 2020; 22:3205-3217. [PMID: 32383332 DOI: 10.1111/1462-2920.15062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/21/2020] [Accepted: 05/03/2020] [Indexed: 11/28/2022]
Abstract
Members of the family Vibrionaceae are generally found in marine and brackish environments, playing important roles in nutrient cycling. The Rumoiensis clade is an unconventional group in the genus Vibrio, currently comprising six species from different origins including two species isolated from non-marine environments. In this study, we performed comparative genome analysis of all six species in the clade using their complete genome sequences. We found that two non-marine species, Vibrio casei and Vibrio gangliei, lacked the genes responsible for algal polysaccharide degradation, while a number of glycoside hydrolase genes were enriched in these two species. Expansion of insertion sequences was observed in V. casei and Vibrio rumoiensis, which suggests ongoing genomic changes associated with niche adaptations. The genes responsible for the metabolism of glucosylglycerate, a compound known to play a role as compatible solutes under nitrogen limitation, were conserved across the clade. These characteristics, along with genes encoding species-specific functions, may reflect the habit expansion which has led to the current distribution of Rumoiensis clade species. Genome analysis of all species in a single clade give us valuable insights into the genomic background of the Rumoiensis clade species and emphasize the genomic diversity and versatility of Vibrionaceae.
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Affiliation(s)
- Mami Tanaka
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
| | - Daiki Kumakura
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
| | - Hidetaka Doi
- R&D Strategic Group, R&D Planning Department, Ajinomoto Co., Inc., Tokyo, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
| | - Man Cai
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bruno Gomez-Gil
- CIAD, AC Mazatlan Unit for Aquaculture and Environmental Management, Mazatlán, Sinaloa, AP 711, Mexico
| | - Toshiyoshi Araki
- Iga Community-based Research Institute, Mie University, Iga, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
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17
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Franceus J, Desmet T. Sucrose Phosphorylase and Related Enzymes in Glycoside Hydrolase Family 13: Discovery, Application and Engineering. Int J Mol Sci 2020; 21:E2526. [PMID: 32260541 PMCID: PMC7178133 DOI: 10.3390/ijms21072526] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
Sucrose phosphorylases are carbohydrate-active enzymes with outstanding potential for the biocatalytic conversion of common table sugar into products with attractive properties. They belong to the glycoside hydrolase family GH13, where they are found in subfamily 18. In bacteria, these enzymes catalyse the phosphorolysis of sucrose to yield α-glucose 1-phosphate and fructose. However, sucrose phosphorylases can also be applied as versatile transglucosylases for the synthesis of valuable glycosides and sugars because their broad promiscuity allows them to transfer the glucosyl group of sucrose to a diverse collection of compounds other than phosphate. Numerous process and enzyme engineering studies have expanded the range of possible applications of sucrose phosphorylases ever further. Moreover, it has recently been discovered that family GH13 also contains a few novel phosphorylases that are specialised in the phosphorolysis of sucrose 6F-phosphate, glucosylglycerol or glucosylglycerate. In this review, we provide an overview of the progress that has been made in our understanding and exploitation of sucrose phosphorylases and related enzymes over the past ten years.
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Affiliation(s)
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium;
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18
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Multi-enzyme systems and recombinant cells for synthesis of valuable saccharides: Advances and perspectives. Biotechnol Adv 2019; 37:107406. [DOI: 10.1016/j.biotechadv.2019.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/30/2019] [Accepted: 06/08/2019] [Indexed: 02/07/2023]
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19
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Structural Comparison of a Promiscuous and a Highly Specific Sucrose 6 F-Phosphate Phosphorylase. Int J Mol Sci 2019; 20:ijms20163906. [PMID: 31405215 PMCID: PMC6720575 DOI: 10.3390/ijms20163906] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/17/2022] Open
Abstract
In family GH13 of the carbohydrate-active enzyme database, subfamily 18 contains glycoside phosphorylases that act on α-sugars and glucosides. Because their phosphorolysis reactions are effectively reversible, these enzymes are of interest for the biocatalytic synthesis of various glycosidic compounds. Sucrose 6F-phosphate phosphorylases (SPPs) constitute one of the known substrate specificities. Here, we report the characterization of an SPP from Ilumatobacter coccineus with a far stricter specificity than the previously described promiscuous SPP from Thermoanaerobacterium thermosaccharolyticum. Crystal structures of both SPPs were determined to provide insight into their similarities and differences. The residues responsible for binding the fructose 6-phosphate group in subsite +1 were found to differ considerably between the two enzymes. Furthermore, several variants that introduce a higher degree of substrate promiscuity in the strict SPP from I. coccineus were designed. These results contribute to an expanded structural knowledge of enzymes in subfamily GH13_18 and facilitate their rational engineering.
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20
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Transcription factor YcjW controls the emergency H 2S production in E. coli. Nat Commun 2019; 10:2868. [PMID: 31253770 PMCID: PMC6599011 DOI: 10.1038/s41467-019-10785-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 06/03/2019] [Indexed: 12/18/2022] Open
Abstract
Prokaryotes and eukaryotes alike endogenously generate the gaseous molecule hydrogen sulfide (H2S). Bacterial H2S acts as a cytoprotectant against antibiotics-induced stress and promotes redox homeostasis. In E. coli, endogenous H2S production is primarily dependent on 3-mercaptopyruvate sulfurtransferase (3MST), encoded by mstA. Here, we show that cells lacking 3MST acquire a phenotypic suppressor mutation resulting in compensatory H2S production and tolerance to antibiotics and oxidative stress. Using whole genome sequencing, we identified a non-synonymous mutation within an uncharacterized LacI-type transcription factor, ycjW. We then mapped regulatory targets of YcjW and discovered it controls the expression of carbohydrate metabolic genes and thiosulfate sulfurtransferase PspE. Induction of pspE expression in the suppressor strain provides an alternative mechanism for H2S biosynthesis. Our results reveal a complex interaction between carbohydrate metabolism and H2S production in bacteria and the role, a hitherto uncharacterized transcription factor, YcjW, plays in linking the two. Hydrogen sulfide (H2S) production in Escherichia coli is controlled by the sulfurtransferase 3MST. Here, the authors describe an alternative mechanism for H2S biosynthesis via activation of the thiosulfate sulfurtransferase PspE, a process mediated by the transcription factor YcjW.
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21
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Tauzin AS, Bruel L, Laville E, Nicoletti C, Navarro D, Henrissat B, Perrier J, Potocki-Veronese G, Giardina T, Lafond M. Sucrose 6 F-phosphate phosphorylase: a novel insight in the human gut microbiome. Microb Genom 2019; 5. [PMID: 30913025 PMCID: PMC6521584 DOI: 10.1099/mgen.0.000253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The human gut microbiome plays an essential role in maintaining human health including in degradation of dietary fibres and carbohydrates further used as nutrients by both the host and the gut bacteria. Previously, we identified a polysaccharide utilization loci (PUL) involved in sucrose and raffinose family oligosaccharide (RFO) metabolism from one of the most common Firmicutes present in individuals, Ruminococcus gnavus E1. One of the enzymes encoded by this PUL was annotated as a putative sucrose phosphate phosphorylase (RgSPP). In the present study, we have in-depth characterized the heterologously expressed RgSPP as sucrose 6F-phosphate phosphorylase (SPP), expanding our knowledge of the glycoside hydrolase GH13_18 subfamily. Specifically, the enzymatic characterization showed a selective activity on sucrose 6F-phosphate (S6FP) acting both in phosphorolysis releasing alpha-d-glucose-1-phosphate (G1P) and alpha-d-fructose-6-phosphate (F6P), and in reverse phosphorolysis from G1P and F6P to S6FP. Interestingly, such a SPP activity had never been observed in gut bacteria before. In addition, a phylogenetic and synteny analysis showed a clustering and a strictly conserved PUL organization specific to gut bacteria. However, a wide prevalence and abundance study with a human metagenomic library showed a correlation between SPP activity and the geographical origin of the individuals and, thus, most likely linked to diet. Rgspp gene overexpression has been observed in mice fed with a high-fat diet suggesting, as observed for humans, that intestine lipid and carbohydrate microbial metabolisms are intertwined. Finally, based on the genomic environment analysis, in vitro and in vivo studies, results provide new insights into the gut microbiota catabolism of sucrose, RFOs and S6FP.
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Affiliation(s)
- Alexandra S Tauzin
- 1Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.,2LISBP, CNRS, INRA, INSAT, Université de Toulouse, F-31400 Toulouse, France.,‡Present address: LISBP, CNRS, INRA, INSAT, Université de Toulouse, F-31400 Toulouse, France
| | - Laetitia Bruel
- 1Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Elisabeth Laville
- 2LISBP, CNRS, INRA, INSAT, Université de Toulouse, F-31400 Toulouse, France
| | | | - David Navarro
- 3INRA, Aix-Marseille Université, UMR1163, Biodiversité et Biotechnologie Fongiques, PolyTech, F-13009, Marseille, France
| | - Bernard Henrissat
- 4Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,5Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia
| | - Josette Perrier
- 1Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | - Thierry Giardina
- 1Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Mickael Lafond
- 1Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
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22
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Mukherjee K, Narindoshvili T, Raushel FM. Discovery of a Kojibiose Phosphorylase in Escherichia coli K-12. Biochemistry 2018; 57:2857-2867. [PMID: 29684280 DOI: 10.1021/acs.biochem.8b00392] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The substrate profiles for three uncharacterized enzymes (YcjM, YcjT, and YcjU) that are expressed from a cluster of 12 genes ( ycjM-W and ompG) of unknown function in Escherichia coli K-12 were determined. Through a comprehensive bioinformatic and steady-state kinetic analysis, the catalytic function of YcjT was determined to be kojibiose phosphorylase. In the presence of saturating phosphate and kojibiose (α-(1,2)-d-glucose-d-glucose), this enzyme catalyzes the formation of d-glucose and β-d-glucose-1-phosphate ( kcat = 1.1 s-1, Km = 1.05 mM, and kcat/ Km = 1.12 × 103 M-1 s-1). Additionally, it was also shown that in the presence of β-d-glucose-1-phosphate, YcjT can catalyze the formation of other disaccharides using 1,5-anhydro-d-glucitol, l-sorbose, d-sorbitol, or l-iditol as a substitute for d-glucose. Kojibiose is a component of cell wall lipoteichoic acids in Gram-positive bacteria and is of interest as a potential low-calorie sweetener and prebiotic. YcjU was determined to be a β-phosphoglucomutase that catalyzes the isomerization of β-d-glucose-1-phosphate ( kcat = 21 s-1, Km = 18 μM, and kcat/ Km = 1.1 × 106 M-1 s-1) to d-glucose-6-phosphate. YcjU was also shown to exhibit catalytic activity with β-d-allose-1-phosphate, β-d-mannose-1-phosphate, and β-d-galactose-1-phosphate. YcjM catalyzes the phosphorolysis of α-(1,2)-d-glucose-d-glycerate with a kcat = 2.1 s-1, Km = 69 μM, and kcat/ Km = 3.1 × 104 M-1 s-1.
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Affiliation(s)
- Keya Mukherjee
- Department of Biochemistry & Biophysics , Texas A&M University , College Station , Texas 77844 , United States
| | - Tamari Narindoshvili
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Biochemistry & Biophysics , Texas A&M University , College Station , Texas 77844 , United States.,Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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23
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Exploring the sequence diversity in glycoside hydrolase family 13_18 reveals a novel glucosylglycerol phosphorylase. Appl Microbiol Biotechnol 2018; 102:3183-3191. [DOI: 10.1007/s00253-018-8856-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/01/2018] [Accepted: 02/06/2018] [Indexed: 12/29/2022]
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