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Wagschal K, Chan VJ, Pereira JH, Zwart PH, Sankaran B. Chromohalobacter salixigens Uronate Dehydrogenase: Directed Evolution for Improved Thermal Stability and Mutant CsUDH-inc X-ray Crystal Structure. Process Biochem 2022; 114:185-192. [PMID: 35462854 PMCID: PMC9031460 DOI: 10.1016/j.procbio.2020.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Chromohalobacter salixigens contains a uronate dehydrogenase termed CsUDH that can convert uronic acids to their corresponding C1,C6-dicarboxy aldaric acids, an important enzyme reaction applicable for biotechnological use of sugar acids. To increase the thermal stability of this enzyme for biotechnological processes, directed evolution using gene family shuffling was applied, and the hits selected from 2-tier screening of a shuffled gene family library contained in total 16 mutations, only some of which when examined individually appreciably increased thermal stability. Most mutations, while having minimal or no effect on thermal stability when tested in isolation, were found to exhibit synergy when combined; CsUDH-inc containing all 16 mutations had ΔK t 0.5 +18 °C, such that k cat was unaffected by incubation for 1 hr at ~70 °C. X-ray crystal structure of CsUDH-inc showed tight packing of the mutated residue side-chains, and comparison of rescaled B-values showed no obvious differences between wild type and mutant structures. Activity of CsUDH-inc was severely depressed on glucuronic and galacturonic acids. Combining select combinations of only three mutations resulted in good or comparable activity on these uronic acids, while maintaining some improved thermostability with ΔK t 0.5 ~+ 10 °C, indicating potential to further thermally optimize CsUDH for hyperthermophilic reaction environments.
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Affiliation(s)
- Kurt Wagschal
- USDA Agricultural Research Service, Western Regional Research Center, Albany, CA 94710, USA,Corresponding Authors: ,
| | - Victor J. Chan
- USDA Agricultural Research Service, Western Regional Research Center, Albany, CA 94710, USA
| | - Jose H. Pereira
- Molecular Biophysics and Integrated Bioimaging, Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Peter H. Zwart
- Molecular Biophysics and Integrated Bioimaging & Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratories,1 Cyclotron Road, Berkeley, CA, 94703, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA,Corresponding Authors: ,
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Murugan A, Prathiviraj R, Mothay D, Chellapandi P. Substrate-imprinted docking of Agrobacterium tumefaciens uronate dehydrogenase for increased substrate selectivity. Int J Biol Macromol 2019; 140:1214-1225. [PMID: 31472210 DOI: 10.1016/j.ijbiomac.2019.08.194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/15/2019] [Accepted: 08/22/2019] [Indexed: 11/18/2022]
Abstract
Agrobacterium tumefaciens uronate dehydrogenase (AtuUdh) belongs to the short-chain dehydrogenase superfamily, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor. It is apparently required for the production of D-glucaric acid. AtuUdh-catalyzed reaction is reversible with dual substrate-specific activity (D-galacturonic acid and D-glucuronic acid) in nature. In our study, 34 mutants were pre-screened from 155 mutants generated from AtuUdh (wild-type) and selected 10 structurally stable mutants with increased substrate selectivity. The specificity, efficiency, and selectivity of these mutants for different substrates and cofactors were predicted from 121 docked models using a substrate-imprinted docking approach. Q14F, S36L, and S75T mutants have shown a high binding affinity to D-glucuronic acid and its substrate intermediates such as D-glucaro-1,4-lactone and D-glucaro-1,5-lactone. These mutants exhibited a low binding affinity to the substrate and cofactor required for D-galactaric acid. D34S, N112E and S165E mutants found to show a high selectivity of D-galacturonic acid and its substrate intermediates for D-galactaric acid production. Ser75, Ser165, and Arg174 are active residues playing an imperative role in the substrate selectivity and also contributed in the conjecture the mechanism of transition state stabilization catalyzed by AtuUdh mutants. The present approach was used to reveal the substrate binding mechanism of AtuUdh mutants for a better understanding of the structural basis for selectivity and function.
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Affiliation(s)
- A Murugan
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Dipti Mothay
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India.
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Su HH, Peng F, Xu P, Wu XL, Zong MH, Yang JG, Lou WY. Enhancing the thermostability and activity of uronate dehydrogenase from Agrobacterium tumefaciens LBA4404 by semi-rational engineering. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0267-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Glucaric acid, one of the aldaric acids, has been declared a “top value-added chemical from biomass”, and is especially important in the food and pharmaceutical industries. Biocatalytic production of glucaric acid from glucuronic acid is more environmentally friendly, efficient and economical than chemical synthesis. Uronate dehydrogenases (UDHs) are the key enzymes for the preparation of glucaric acid in this way, but the poor thermostability and low activity of UDH limit its industrial application. Therefore, improving the thermostability and activity of UDH, for example by semi-rational design, is a major research goal.
Results
In the present work, three UDHs were obtained from different Agrobacterium tumefaciens strains. The three UDHs have an approximate molecular weight of 32 kDa and all contain typically conserved UDH motifs. All three UDHs showed optimal activity within a pH range of 6.0–8.5 and at a temperature of 30 °C, but the UDH from A. tumefaciens (At) LBA4404 had a better catalytic efficiency than the other two UDHs (800 vs 600 and 530 s−1 mM−1). To further boost the catalytic performance of the UDH from AtLBA4404, site-directed mutagenesis based on semi-rational design was carried out. An A39P/H99Y/H234K triple mutant showed a 400-fold improvement in half-life at 59 °C, a 5 °C improvement in $$ {\text{T}}_{ 5 0}^{ 1 0} $$
T
50
10
value and a 2.5-fold improvement in specific activity at 30 °C compared to wild-type UDH.
Conclusions
In this study, we successfully obtained a triple mutant (A39P/H99Y/H234K) with simultaneously enhanced activity and thermostability, which provides a novel alternative for the industrial production of glucaric acid from glucuronic acid.
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Novel Metabolic Pathways and Regulons for Hexuronate Utilization in Proteobacteria. J Bacteriol 2018; 201:JB.00431-18. [PMID: 30249705 DOI: 10.1128/jb.00431-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023] Open
Abstract
We used comparative genomics to reconstruct d-galacturonic and d-glucuronic acid catabolic pathways and associated transcriptional regulons involving the tripartite ATP-independent periplasmic (TRAP) family transporters that bind hexuronates in proteobacteria. The reconstructed catabolic network involves novel transcription factors, catabolic enzymes, and transporters for utilization of both hexuronates and aldarates (d-glucarate and meso-galactarate). The reconstructed regulons for a novel GntR family transcription factor, GguR, include the majority of hexuronate/aldarate utilization genes in 47 species from the Burkholderiaceae, Comamonadaceae, Halomonadaceae, and Pseudomonadaceae families. GudR, GulR, and UdhR are additional local regulators of some hexuronate/aldarate utilization genes in some of the above-mentioned organisms. The predicted DNA binding motifs of GguR and GudR regulators from Ralstonia pickettii and Polaromonas were validated by in vitro binding assays. Genes from the GulR- and GguR-controlled loci were differentially expressed in R. pickettii grown on hexuronates and aldarates. By a combination of bioinformatics and experimental techniques we identified a novel variant of the oxidative pathway for hexuronate utilization, including two previously uncharacterized subfamilies of lactone hydrolases (UxuL and UxuF). The genomic context of respective genes and reconstruction of associated pathways suggest that both enzymes catalyze the conversion of d-galactaro- and d-glucaro-1,5-lactones to the ring-opened aldarates. The activities of the purified recombinant enzymes, UxuL and UxuF, from four proteobacterial species were directly confirmed and kinetically characterized. The inferred novel aldarate-specific transporter from the tripartite tricarboxylate transporter (TTT) family transporter TctC was confirmed to bind d-glucarate in vitro This study expands our knowledge of bacterial carbohydrate catabolic pathways by identifying novel families of catabolic enzymes, transcriptional regulators, and transporters.IMPORTANCE Hexuronate catabolic pathways and their transcriptional networks are highly variable among different bacteria. We identified novel transcriptional regulators that control the hexuronate and aldarate utilization genes in four families of proteobacteria. By regulon reconstruction and genome context analysis we identified several novel components of the common hexuronate/aldarate utilization pathways, including novel uptake transporters and catabolic enzymes. Two novel families of lactonases involved in the oxidative pathway of hexuronate catabolism were characterized. Novel transcriptional regulons were validated via in vitro binding assays and gene expression studies with Polaromonas and Ralstonia species. The reconstructed catabolic pathways are interconnected with each other metabolically and coregulated via the GguR regulons in proteobacteria.
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Li Y, Xue Y, Cao Z, Zhou T, Alnadari F. Characterization of a uronate dehydrogenase from Thermobispora bispora for production of glucaric acid from hemicellulose substrate. World J Microbiol Biotechnol 2018; 34:102. [DOI: 10.1007/s11274-018-2486-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 06/18/2018] [Indexed: 10/28/2022]
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Roth T, Beer B, Pick A, Sieber V. Thermostabilization of the uronate dehydrogenase from Agrobacterium tumefaciens by semi-rational design. AMB Express 2017; 7:103. [PMID: 28545260 PMCID: PMC5442039 DOI: 10.1186/s13568-017-0405-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/17/2017] [Indexed: 11/12/2022] Open
Abstract
Aldaric acids represent biobased 'top value-added chemicals' that have the potential to substitute petroleum-derived chemicals. Until today they are mostly produced from corresponding aldoses using strong chemical oxidizing agents. An environmentally friendly and more selective process could be achieved by using natural resources such as seaweed or pectin as raw material. These contain large amounts of uronic acids as major constituents such as glucuronic acid and galacturonic acid which can be converted into the corresponding aldaric acids via an enzyme-based oxidation using uronate dehydrogenase (Udh). The Udh from Agrobacterium tumefaciens (UdhAt) features the highest catalytic efficiency of all characterized Udhs using glucuronic acid as substrate (829 s-1 mM-1). Unfortunately, it suffers from poor thermostability. To overcome this limitation, we created more thermostable variants using semi-rational design. The amino acids for substitution were chosen according to the B factor in combination with four additional knowledge-based criteria. The triple variant A41P/H101Y/H236K showed higher kinetic and thermodynamic stability with a T 5015 value of 62.2 °C (3.2 °C improvement) and a ∆∆GU of 2.3 kJ/mol compared to wild type. Interestingly, it was only obtained when including a neutral mutation in the combination.
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Affiliation(s)
- Teresa Roth
- Chair of Chemistry of Biogenic Resources, Straubing Centre of Science, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
- Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Barbara Beer
- Chair of Chemistry of Biogenic Resources, Straubing Centre of Science, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - André Pick
- Chair of Chemistry of Biogenic Resources, Straubing Centre of Science, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Straubing Centre of Science, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
- TUM Catalysis Research Center, Ernst-Otto-Fischer-Straße 1, 85748 Garching, Germany
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Bio, Electro and Chemocatalysis BioCat, Straubing Branch, Schulgasse 11a, 94315 Straubing, Germany
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Wagschal KC, Rose Stoller J, Chan VJ, Jordan DB. Expression and Characterization of Hyperthermostable Exopolygalacturonase RmGH28 from Rhodothermus marinus. Appl Biochem Biotechnol 2017; 183:1503-1515. [DOI: 10.1007/s12010-017-2518-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/19/2017] [Indexed: 11/28/2022]
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Stoller JR, Wagschal K, Lee CC, Jordan DB. A general correction to catalytic rates determined for nonprocessive exo-depolymerases acting on both substrate and product in the initial-rate measurement. Anal Biochem 2017; 523:46-49. [DOI: 10.1016/j.ab.2017.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/03/2017] [Accepted: 02/09/2017] [Indexed: 11/16/2022]
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Lee CC, Kibblewhite RE, Paavola CD, Orts WJ, Wagschal K. Production of Glucaric Acid from Hemicellulose Substrate by Rosettasome Enzyme Assemblies. Mol Biotechnol 2017; 58:489-96. [PMID: 27198564 DOI: 10.1007/s12033-016-9945-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Hemicellulose biomass is a complex polymer with many different chemical constituents that can be utilized as industrial feedstocks. These molecules can be released from the polymer and transformed into value-added chemicals through multistep enzymatic pathways. Some bacteria produce cellulosomes which are assemblies composed of lignocellulolytic enzymes tethered to a large protein scaffold. Rosettasomes are artificial engineered ring scaffolds designed to mimic the bacterial cellulosome. Both cellulosomes and rosettasomes have been shown to facilitate much higher rates of biomass hydrolysis compared to the same enzymes free in solution. We investigated whether tethering enzymes involved in both biomass hydrolysis and oxidative transformation to glucaric acid onto a rosettasome scaffold would result in an analogous production enhancement in a combined hydrolysis and bioconversion metabolic pathway. Three different enzymes were used to hydrolyze birchwood hemicellulose and convert the substituents to glucaric acid, a top-12 DOE value added chemical feedstock derived from biomass. It was demonstrated that colocalizing the three different enzymes to the synthetic scaffold resulted in up to 40 % higher levels of product compared to uncomplexed enzymes.
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Affiliation(s)
- Charles C Lee
- Bioproducts Research Unit, USDA-ARS-WRRC, 800 Buchanan St., Albany, CA, 94710, USA.
| | - Rena E Kibblewhite
- Bioproducts Research Unit, USDA-ARS-WRRC, 800 Buchanan St., Albany, CA, 94710, USA
| | - Chad D Paavola
- NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - William J Orts
- Bioproducts Research Unit, USDA-ARS-WRRC, 800 Buchanan St., Albany, CA, 94710, USA
| | - Kurt Wagschal
- Bioproducts Research Unit, USDA-ARS-WRRC, 800 Buchanan St., Albany, CA, 94710, USA
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Pick A, Beer B, Hemmi R, Momma R, Schmid J, Miyamoto K, Sieber V. Identification and characterization of two new 5-keto-4-deoxy-D-Glucarate Dehydratases/Decarboxylases. BMC Biotechnol 2016; 16:80. [PMID: 27855668 PMCID: PMC5114784 DOI: 10.1186/s12896-016-0308-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 10/21/2016] [Indexed: 11/11/2022] Open
Abstract
Background Hexuronic acids such as D-galacturonic acid and D-glucuronic acid can be utilized via different pathways within the metabolism of microorganisms. One representative, the oxidative pathway, generates α-keto-glutarate as the direct link entering towards the citric acid cycle. The penultimate enzyme, keto-deoxy glucarate dehydratase/decarboxylase, catalyses the dehydration and decarboxylation of keto-deoxy glucarate to α-keto-glutarate semialdehyde. This enzymatic reaction can be tracked continuously by applying a pH-shift assay. Results Two new keto-deoxy glucarate dehydratases/decarboxylases (EC 4.2.1.41) from Comamonas testosteroni KF-1 and Polaromonas naphthalenivorans CJ2 were identified and expressed in an active form using Escherichia coli ArcticExpress(DE3). Subsequent characterization concerning Km, kcat and thermal stability was conducted in comparison with the known keto-deoxy glucarate dehydratase/decarboxylase from Acinetobacter baylyi ADP1. The kinetic constants determined for A. baylyi were Km 1.0 mM, kcat 4.5 s−1, for C. testosteroni Km 1.1 mM, kcat 3.1 s−1, and for P. naphthalenivorans Km 1.1 mM, kcat 1.7 s−1. The two new enzymes had a slightly lower catalytic activity (increased Km and a decreased kcat) but showed a higher thermal stability than that of A. baylyi. The developed pH-shift assay, using potassium phosphate and bromothymol blue as the pH indicator, enables a direct measurement. The use of crude extracts did not interfere with the assay and was tested for wild-type landscapes for all three enzymes. Conclusions By establishing a pH-shift assay, an easy measurement method for keto-deoxy glucarate dehydratase/decarboxylase could be developed. It can be used for measurements of the purified enzymes or using crude extracts. Therefore, it is especially suitable as the method of choice within an engineering approach for further optimization of these enzymes. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0308-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- André Pick
- Technical University of Munich, Straubing Center of Science, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany
| | - Barbara Beer
- Technical University of Munich, Straubing Center of Science, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany
| | - Risa Hemmi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, 2238522, Yokohama, Japan
| | - Rena Momma
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, 2238522, Yokohama, Japan
| | - Jochen Schmid
- Technical University of Munich, Straubing Center of Science, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, 2238522, Yokohama, Japan
| | - Volker Sieber
- Technical University of Munich, Straubing Center of Science, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany.
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Sakuta R, Takeda K, Igarashi K, Ohno H, Nakamura N. Pyrroloquinoline quinone-dependent glucose dehydrogenase anode: d-Galacturonic acid oxidation and galactaric acid production. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Production of glucaric acid from myo-inositol in engineered Pichia pastoris. Enzyme Microb Technol 2016; 91:8-16. [DOI: 10.1016/j.enzmictec.2016.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/11/2016] [Accepted: 05/22/2016] [Indexed: 02/02/2023]
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Expression and Characterization of Hyperthermostable Exo-polygalacturonase TtGH28 from Thermotoga thermophilus. Mol Biotechnol 2016; 58:509-19. [DOI: 10.1007/s12033-016-9948-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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