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Zhou Q, Wu Y, Deng J, Liu Y, Li J, Du G, Lv X, Liu L. Combinatorial metabolic engineering enables high yield production of α-arbutin from sucrose by biocatalysis. Appl Microbiol Biotechnol 2023; 107:2897-2910. [PMID: 37000229 DOI: 10.1007/s00253-023-12496-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/18/2023] [Accepted: 03/22/2023] [Indexed: 04/01/2023]
Abstract
α-Arbutin has been widely used as a skin-whitening ingredient. Previously, we successfully produced α-arbutin via whole-cell biocatalysis and found that the conversion rate of sucrose to α-arbutin was low (~45%). To overcome this issue, herein, we knocked out the genes of enzymes related to the sucrose hydrolysis, including sacB, sacC, levB, and sacA. The sucrose consumption was reduced by 17.4% in 24 h, and the sucrose conversion rate was increased to 51.5%. Furthermore, we developed an inducible protein degradation system with Lon protease isolated from Mesoplasma florum (MfLon) and proteolytic tag to control the PfkA activity, so that more fructose-6-phosphate (F6P) can be converted into glucose-1-phosphate (Glc1P) for α-arbutin synthesis, which can reduce the addition of sucrose and increase the sucrose conversion efficiency. Finally, the pathway of F6P to Glc1P was enhanced by integrating another copy of glucose 6-phosphate isomerase (Pgi) and phosphoglucomutase (PgcA); a high α-arbutin titer (~120 g/L) was obtained. The sucrose conversion rate was increased to 60.4% (mol/mol). In this study, the substrate utilization rate was boosted due to the attenuation of its hydrolysis and the assistance of the intracellular enzymes that converted the side product back into the substrate for α-arbutin synthesis. This strategy provides a new idea for the whole-cell biocatalytic synthesis of other products using sucrose as substrate, especially valuable glycosides.Key points The genes of sucrose metabolic pathway were knocked out to reduce the sucrose consumption. The by-product fructose was reused to synthesize α-arbutin. The optimized whole-cell system improved sucrose conversion by 15.3%.
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Affiliation(s)
- Qi Zhou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Wuxi Food Safety Inspection and Test Center & Technology Innovation Center of Special Food for State Market Regulation, Wuxi, 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jieying Deng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Food Laboratory of Zhongyuan, Jiangnan University, Wuxi, 214122, China
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2
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Pfeiffer M, Crean RM, Moreira C, Parracino A, Oberdorfer G, Brecker L, Hammerschmidt F, Kamerlin SCL, Nidetzky B. Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase. ACS Catal 2022; 12:3357-3370. [PMID: 35356705 PMCID: PMC8938923 DOI: 10.1021/acscatal.1c05656] [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: 12/08/2021] [Revised: 01/31/2022] [Indexed: 01/15/2023]
Abstract
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The cooperative interplay
between the functional devices of a preorganized
active site is fundamental to enzyme catalysis. An in-depth understanding
of this phenomenon is central to elucidating the remarkable efficiency
of natural enzymes and provides an essential benchmark for enzyme
design and engineering. Here, we study the functional interconnectedness
of the catalytic nucleophile (His18) in an acid phosphatase by analyzing
the consequences of its replacement with aspartate. We present crystallographic,
biochemical, and computational evidence for a conserved mechanistic
pathway via a phospho-enzyme intermediate on Asp18. Linear free-energy
relationships for phosphoryl transfer from phosphomonoester substrates
to His18/Asp18 provide evidence for the cooperative interplay between
the nucleophilic and general-acid catalytic groups in the wild-type
enzyme, and its substantial loss in the H18D variant. As an isolated
factor of phosphatase efficiency, the advantage of a histidine compared
to an aspartate nucleophile is ∼104-fold. Cooperativity
with the catalytic acid adds ≥102-fold to that advantage.
Empirical valence bond simulations of phosphoryl transfer from glucose
1-phosphate to His and Asp in the enzyme explain the loss of activity
of the Asp18 enzyme through a combination of impaired substrate positioning
in the Michaelis complex, as well as a shift from early to late protonation
of the leaving group in the H18D variant. The evidence presented furthermore
suggests that the cooperative nature of catalysis distinguishes the
enzymatic reaction from the corresponding reaction in solution and
is enabled by the electrostatic preorganization of the active site.
Our results reveal sophisticated discrimination in multifunctional
catalysis of a highly proficient phosphatase active site.
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Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Rory M Crean
- Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Catia Moreira
- Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Antonietta Parracino
- Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Gustav Oberdorfer
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Petersgasse 12/II, 8010 Graz, Austria
| | - Lothar Brecker
- Department of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090 Vienna, Austria
| | - Friedrich Hammerschmidt
- Department of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090 Vienna, Austria
| | | | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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3
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Klimacek M, Sigg A, Nidetzky B. On the donor substrate dependence of group-transfer reactions by hydrolytic enzymes: Insight from kinetic analysis of sucrose phosphorylase-catalyzed transglycosylation. Biotechnol Bioeng 2020; 117:2933-2943. [PMID: 32573774 PMCID: PMC7540478 DOI: 10.1002/bit.27471] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/15/2020] [Accepted: 06/21/2020] [Indexed: 12/30/2022]
Abstract
Chemical group-transfer reactions by hydrolytic enzymes have considerable importance in biocatalytic synthesis and are exploited broadly in commercial-scale chemical production. Mechanistically, these reactions have in common the involvement of a covalent enzyme intermediate which is formed upon enzyme reaction with the donor substrate and is subsequently intercepted by a suitable acceptor. Here, we studied the glycosylation of glycerol from sucrose by sucrose phosphorylase (SucP) to clarify a peculiar, yet generally important characteristic of this reaction: partitioning between glycosylation of glycerol and hydrolysis depends on the type and the concentration of the donor substrate used (here: sucrose, α-d-glucose 1-phosphate (G1P)). We develop a kinetic framework to analyze the effect and provide evidence that, when G1P is used as donor substrate, hydrolysis occurs not only from the β-glucosyl-enzyme intermediate (E-Glc), but additionally from a noncovalent complex of E-Glc and substrate which unlike E-Glc is unreactive to glycerol. Depending on the relative rates of hydrolysis of free and substrate-bound E-Glc, inhibition (Leuconostoc mesenteroides SucP) or apparent activation (Bifidobacterium adolescentis SucP) is observed at high donor substrate concentration. At a G1P concentration that excludes the substrate-bound E-Glc, the transfer/hydrolysis ratio changes to a value consistent with reaction exclusively through E-Glc, independent of the donor substrate used. Collectively, these results give explanation for a kinetic behavior of SucP not previously accounted for, provide essential basis for design and optimization of the synthetic reaction, and establish a theoretical framework for the analysis of kinetically analogous group-transfer reactions by hydrolytic enzymes.
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Affiliation(s)
- Mario Klimacek
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Alexander Sigg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria.,Austrian Centre of Industrial Biotechnology (acib), Graz, Austria
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4
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Taguchi Y, Saburi W, Imai R, Mori H. Efficient one-pot enzymatic synthesis of trehalose 6-phosphate using GH65 α-glucoside phosphorylases. Carbohydr Res 2020; 488:107902. [PMID: 31911362 DOI: 10.1016/j.carres.2019.107902] [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: 10/07/2019] [Revised: 12/18/2019] [Accepted: 12/21/2019] [Indexed: 10/25/2022]
Abstract
Trehalose 6-phosphate (Tre6P) is an important intermediate for trehalose biosynthesis. Recent researches have revealed that Tre6P is an endogenous signaling molecule that regulates plant development and stress responses. The necessity of Tre6P in physiological studies is expected to be increasing. To achieve the cost-effective production of Tre6P, a novel approach is required. In this study, we utilized trehalose 6-phosphate phosphorylase (TrePP) from Lactococcus lactis to produce Tre6P. In the reverse phosphorolysis by the TrePP, 91.9 mM Tre6P was produced from 100 mM β-glucose 1-phosphate (β-Glc1P) and 100 mM glucose 6-phosphate (Glc6P). The one-pot reaction of TrePP and maltose phosphorylase (MP) enabled production of 65 mM Tre6P from 100 mM maltose, 100 mM Glc6P, and 20 mM inorganic phosphate. Addition of β-phosphoglucomutase to this reaction produced Glc6P from β-Glc1P and thus reduced requirement of Glc6P as a starting material. Within the range of 20-469 mM inorganic phosphate tested, the 54 mM concentration yielded the highest amount of Tre6P (33 mM). Addition of yeast increased the yield because of its glucose consumption. Finally, from 100 mmol maltose and 60 mmol inorganic phosphate, we successfully achieved production of 37.5 mmol Tre6P in a one-pot reaction (100 mL), and 9.4 g Tre6P dipotassium salt was obtained.
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Affiliation(s)
- Yodai Taguchi
- Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, 060-8589, Japan.
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, 060-8589, Japan.
| | - Ryozo Imai
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan.
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, 060-8589, Japan.
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Domingo G, Villa F, Vannini C, Garuglieri E, Onelli E, Bracale M, Cappitelli F. Label-Free Proteomic Approach to Study the Non-lethal Effects of Silver Nanoparticles on a Gut Bacterium. Front Microbiol 2019; 10:2709. [PMID: 31866956 PMCID: PMC6906586 DOI: 10.3389/fmicb.2019.02709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/08/2019] [Indexed: 01/14/2023] Open
Abstract
Among all the food-related nanoparticles consumed every day, silver nanoparticles (AgNPs) have become one of the most commonly utilized because of their antimicrobial properties. Despite their common use, the effects of sublethal concentrations of AgNPs, especially on gut biofilms, have been poorly investigated. To address this issue, we investigated in vitro the proteomic response of a monospecies Escherichia coli gut biofilm to chronic and acute exposures in sublethal concentrations of AgNPs. We used a new gel- and label-free proteomic approach based on shotgun nanoflow liquid chromatography-tandem mass spectrometry. This approach allows a quantification of the whole proteome at a dynamic range that is higher than the traditional proteomic investigation. To assess all different possible exposure scenarios, we compared the biofilm proteome of four treatments: (i) untreated cells for the control treatment, (ii) cells treated with 1 μg/ml AgNPs for 24 h for the acute treatment, (iii) cells grown with 1 μg/ml AgNPs for 96 h for the chronic treatment, and (iv) cells grown in the presence of 1 μg/ml AgNPs for 72 h and then further treated for 24 h with 10 μg/ml AgNPs for the chronic + acute treatment. Among the 1,917 proteins identified, 212 were significantly differentially expressed proteins. Several pathways were altered including biofilm formation, bacterial adhesion, stress response to reactive oxygen species, and glucose utilization.
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Affiliation(s)
- Guido Domingo
- Department of Biotechnology and Life Sciences, Università degli Studi dell'Insubria, Varese, Italy
| | - Federica Villa
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Candida Vannini
- Department of Biotechnology and Life Sciences, Università degli Studi dell'Insubria, Varese, Italy
| | - Elisa Garuglieri
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Onelli
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Marcella Bracale
- Department of Biotechnology and Life Sciences, Università degli Studi dell'Insubria, Varese, Italy
| | - Francesca Cappitelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
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6
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Pfeiffer M, Bulfon D, Weber H, Nidetzky B. A Kinase-Independent One-Pot Multienzyme Cascade for an Expedient Synthesis of Guanosine 5′-Diphospho-d-mannose. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600761] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12/I A-8010 Graz Austria
| | - Dominik Bulfon
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12/I A-8010 Graz Austria
| | - Hansjoerg Weber
- Institute of Organic Chemistry; Graz University of Technology, NAWI Graz; Stremayrgasse 9/4 A-8010 Graz Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12/I A-8010 Graz Austria
- Austrian Center of Industrial Biotechnology; Petersgasse 14 A-8010 Graz Austria
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7
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Wildberger P, Pfeiffer M, Brecker L, Nidetzky B. Diastereoselektive Synthese von Glykosylphosphaten mit einem Phosphorylase‐Phosphatase‐Kombikatalysator. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Patricia Wildberger
- Institut für Biotechnologie und Bioprozesstechnik, Technische Universität Graz, Petersgasse 12, 8010 Graz (Österreich)
| | - Martin Pfeiffer
- Institut für Biotechnologie und Bioprozesstechnik, Technische Universität Graz, Petersgasse 12, 8010 Graz (Österreich)
| | - Lothar Brecker
- Institut für Organische Chemie, Universität Wien, Währingerstraße 38, 1090 Wien (Österreich)
| | - Bernd Nidetzky
- Institut für Biotechnologie und Bioprozesstechnik, Technische Universität Graz, Petersgasse 12, 8010 Graz (Österreich)
- acib – Austrian Centre of Industrial Biotechnology (Österreich)
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8
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Wildberger P, Pfeiffer M, Brecker L, Nidetzky B. Diastereoselective Synthesis of Glycosyl Phosphates by Using a Phosphorylase-Phosphatase Combination Catalyst. Angew Chem Int Ed Engl 2015; 54:15867-71. [PMID: 26565075 PMCID: PMC4737314 DOI: 10.1002/anie.201507710] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 11/10/2022]
Abstract
Sugar phosphates play an important role in metabolism and signaling, but also as constituents of macromolecular structures. Selective phosphorylation of sugars is chemically difficult, particularly at the anomeric center. We report phosphatase-catalyzed diastereoselective "anomeric" phosphorylation of various aldose substrates with α-D-glucose 1-phosphate, derived from phosphorylase-catalyzed conversion of sucrose and inorganic phosphate, as the phosphoryl donor. Simultaneous and sequential two-step transformations by the phosphorylase-phosphatase combination catalyst yielded glycosyl phosphates of defined anomeric configuration in yields of up to 70 % based on the phosphate applied to the reaction. An efficient enzyme-assisted purification of the glycosyl phosphate products from reaction mixtures was established.
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Affiliation(s)
- Patricia Wildberger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, 8010 Graz (Austria)
| | - Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, 8010 Graz (Austria)
| | - Lothar Brecker
- Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090 Vienna (Austria)
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, 8010 Graz (Austria). .,acib - Austrian Centre of Industrial Biotechnology (Austria).
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