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Lanza L, Rabe von Pappenheim F, Bjarnesen D, Leogrande C, Paul A, Krug L, Tittmann K, Müller M. Identification and Characterization of Thiamine Diphosphate-Dependent Lyases with an Unusual CDG Motif. Angew Chem Int Ed Engl 2024:e202404045. [PMID: 38874074 DOI: 10.1002/anie.202404045] [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: 02/28/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/15/2024]
Abstract
The thiamine diphosphate (ThDP)-binding motif, characterized by the canonical GDG(X)24-27N sequence, is highly conserved among ThDP-dependent enzymes. We investigated a ThDP-dependent lyase (JanthE from Janthinobacterium sp. HH01) with an unusual cysteine (C458) replacing the first glycine of this motif. JanthE exhibits a high substrate promiscuity and accepts long aliphatic α-keto acids as donors. Sterically hindered aromatic aldehydes or non-activated ketones are acceptor substrates, giving access to a variety of secondary and tertiary alcohols as carboligation products. The crystal structure solved at a resolution of 1.9 Å reveals that C458 is not primarily involved in cofactor binding as previously thought for the canonical glycine. Instead, it coordinates methionine 406, thus ensuring the integrity of the active site and the enzyme activity. In addition, we have determined the long-sought genuine tetrahedral intermediates formed with pyruvate and 2-oxobutyrate in the pre-decarboxylation states and deciphered the atomic details for their stabilization in the active site. Collectively, we unravel an unexpected role for the first residue of the ThDP-binding motif and unlock a family of lyases that can perform valuable carboligation reactions.
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Affiliation(s)
- Lucrezia Lanza
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany
| | - Fabian Rabe von Pappenheim
- Department of Molecular Enzymology, Georg-August Universität Göttingen, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Daniela Bjarnesen
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany
| | - Camilla Leogrande
- Department of Molecular Enzymology, Georg-August Universität Göttingen, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alexandra Paul
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany
| | - Leonhard Krug
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Georg-August Universität Göttingen, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany
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2
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Toci EM, Austin SL, Majumdar A, Woodcock HL, Freel Meyers CL. Disruption of an Active Site Network Leads to Activation of C2α-Lactylthiamin Diphosphate on the Antibacterial Target 1-Deoxy-d-xylulose-5-phosphate Synthase. Biochemistry 2024; 63:671-687. [PMID: 38393327 PMCID: PMC11015862 DOI: 10.1021/acs.biochem.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The bacterial metabolic enzyme 1-deoxy-d-xylulose-5-phosphate synthase (DXPS) catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde-3-phosphate (d-GAP). DXP is an essential bacteria-specific metabolite that feeds into the biosynthesis of isoprenoids, pyridoxal phosphate (PLP), and ThDP. DXPS catalyzes the activation of pyruvate to give the C2α-lactylThDP (LThDP) adduct that is long-lived on DXPS in a closed state in the absence of the cosubstrate. Binding of d-GAP shifts the DXPS-LThDP complex to an open state which coincides with LThDP decarboxylation. This gated mechanism distinguishes DXPS in ThDP enzymology. How LThDP persists on DXPS in the absence of cosubstrate, while other pyruvate decarboxylases readily activate LThDP for decarboxylation, is a long-standing question in the field. We propose that an active site network functions to prevent LThDP activation on DXPS until the cosubstrate binds. Binding of d-GAP coincides with a conformational shift and disrupts the network causing changes in the active site that promote LThDP activation. Here, we show that the substitution of putative network residues, as well as nearby residues believed to contribute to network charge distribution, predictably affects LThDP reactivity. Substitutions predicted to disrupt the network have the effect to activate LThDP for decarboxylation, resulting in CO2 and acetate production. In contrast, a substitution predicted to strengthen the network fails to activate LThDP and has the effect to shift DXPS toward the closed state. Network-disrupting substitutions near the carboxylate of LThDP also have a pronounced effect to shift DXPS to an open state. These results offer initial insights to explain the long-lived LThDP intermediate and its activation through disruption of an active site network, which is unique to DXPS. These findings have important implications for DXPS function in bacteria and its development as an antibacterial target.
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Affiliation(s)
- Eucolona M Toci
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Steven L Austin
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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3
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Li ZM, Hu Z, Wang X, Chen S, Yu W, Liu J, Li Z. Biochemical and Structural Insights into a Thiamine Diphosphate-Dependent α-Ketoglutarate Decarboxylase from Cyanobacterium Microcystis aeruginosa NIES-843. Int J Mol Sci 2023; 24:12198. [PMID: 37569577 PMCID: PMC10418658 DOI: 10.3390/ijms241512198] [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: 06/28/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
α-Ketoglutarate decarboxylase is a crucial enzyme in the tricarboxylic acid cycle of cyanobacteria, catalyzing the non-oxidative decarboxylation of α-ketoglutarate to produce succinate semialdehyde and CO2. The decarboxylation process is reliant on the cofactor of thiamine diphosphate. However, this enzyme's biochemical and structural properties have not been well characterized. In this work, two α-ketoglutarate decarboxylases encoded by MAE_06010 and MiAbw_01735 genes from Microcystis aeruginosa NIES-843 (MaKGD) and NIES-4325 (MiKGD), respectively, were overexpressed and purified by using an Escherichia coli expression system. It was found that MaKGD exhibited 9.2-fold higher catalytic efficiency than MiKGD, which may be attributed to the absence of glutamate decarboxylase in Microcystis aeruginosa NIES-843. Further biochemical investigation of MaKGD demonstrated that it displayed optimum activity at pH 6.5-7.0 and was most activated by Mg2+. Additionally, MaKGD showed substrate specificity towards α-ketoglutarate. Structural modeling and autodocking results revealed that the active site of MaKGD contained a distinct binding pocket where α-ketoglutarate and thiamine diphosphate interacted with specific amino acid residues via hydrophobic interactions, hydrogen bonds and salt bridges. Furthermore, the mutagenesis study provided strong evidence supporting the importance of certain residues in the catalysis of MaKGD. These findings provide new insights into the structure-function relationships of α-ketoglutarate decarboxylases from cyanobacteria.
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Affiliation(s)
- Zhi-Min Li
- College of Chemistry and Materials, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Ziwei Hu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoqin Wang
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Suhang Chen
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Weiyan Yu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jianping Liu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
- Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Jiangxi Agricultural University, Nanchang 330045, China
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4
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Xu H, Yu B, Wei W, Chen X, Gao C, Liu J, Guo L, Song W, Liu L, Wu J. Improving tyrosol production efficiency through shortening the allosteric signal transmission distance of pyruvate decarboxylase. Appl Microbiol Biotechnol 2023; 107:3535-3549. [PMID: 37099057 DOI: 10.1007/s00253-023-12540-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/22/2023] [Accepted: 04/14/2023] [Indexed: 04/27/2023]
Abstract
Tyrosol is an important chemical in medicine and chemical industries, which can be synthesized by a four-enzyme cascade pathway constructed in our previous study. However, the low catalytic efficiency of pyruvate decarboxylase from Candida tropicalis (CtPDC) in this cascade is a rate-limiting step. In this study, we resolved the crystal structure of CtPDC and investigated the mechanism of allosteric substrate activation and decarboxylation of this enzyme toward 4-hydroxyphenylpyruvate (4-HPP). In addition, based on the molecular mechanism and structural dynamic changes, we conducted protein engineering of CtPDC to improve decarboxylation efficiency. The conversion of the best mutant, CtPDCQ112G/Q162H/G415S/I417V (CtPDCMu5), had over two-fold improvement compared to the wild-type. Molecular dynamic (MD) simulation revealed that the key catalytic distances and allosteric transmission pathways were shorter in CtPDCMu5 than in the wild type. Furthermore, when CtPDC in the tyrosol production cascade was replaced with CtPDCMu5, the tyrosol yield reached 38 g·L-1 with 99.6% conversion and 1.58 g·L-1·h-1 space-time yield in 24 h through further optimization of the conditions. Our study demonstrates that protein engineering of the rate-limiting enzyme in the tyrosol synthesis cascade provides an industrial-scale platform for the biocatalytic production of tyrosol. KEY POINTS: • Protein engineering of CtPDC based on allosteric regulation improved the catalytic efficiency of decarboxylation. • The application of the optimum mutant of CtPDC removed the rate-limiting bottleneck in the cascade. • The final titer of tyrosol reached 38 g·L-1 in 24 h in 3 L bioreactor.
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Affiliation(s)
- Huanhuan Xu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Bicheng Yu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China.
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5
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Mushtaq Z, Mukhtar H. Process optimization for biosynthesis of pyruvate decarboxylase (PDC) and Neuberg’s ketol (PAC) from a novel Pichia cecembensis through response surface methodology. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01700-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Abstract
Purpose
Phenylacetylcarbinol (PAC) is an intermediate for the synthesis of several active pharmaceutical ingredients (ephedrine, pseudoephedrine, norephedrine, etc.) used for the production of antiasthematics and decongestants. An efficient biosynthesis of PAC through condensation of benzaldehyde and acetaldehyde catalyzed by a solvent tolerant pyruvate decarboxylase (PDC) is being reported. A process for the biosynthesis of PAC was designed and optimized through response surface methodology (RSM) in the present study.
Methods
The effects of incubation time (8–18 h), incubation temperature (30–38 °C), medium pH (4–10), and inoculum size (4–10%) on PAC yield, sugar consumption, and PDC activity were determined through submerged fermentation using a newly isolated potent yeast strain of Pichia cecembensis. PAC was quantified spectrophotometerically and through HPLC. PDC produced was exposed to 40 mM benzaldehyde as whole cells, crude extract, and partialy purified preparation to check its stability against the said solvent.
Results
The highest PDC activity and PAC yield during present study were found to be 56.27 U/ml and 8.44 g/l, respectively. The yield of PAC was increased by 71% (2.22 to 8.44 g/l) after process optimization through RSM with incubation time of 13 h, incubation temperature of 33 °C, and 18% total sugar as significant factors (P-values, 0.902, 0.260, and 0.247, respectively). R-squared value of 0.770 and Adeq Precision value of 4.888 show the goodness of fit of the process design. PDC is used in the form of Pichia cecembensis whole cells revealed higher stability towards benzaldehyde and elevated temperature as compared to partially purified PDC. Whole cells and partially purified PDC showed half-lives of 240 and 72 h at 4 °C, whereas 33 and 28.5 h at 25 °C. PAC was purified though HPLC with a purity level of 76.18%.
Conclusion
Incubation time, temperature, and sugar concentration were found to be significant factors for the biosynthesis of PAC. A newly isolated Pichia cecembensis produced a highly active, solvent, and temperature-tolerant pyruvate decarboxylase (PDC) which is superior to its counterpart being presently used in the industry. Hence, this novel yeast species is a promising candidate for commercial production of PAC and other related APIs owing to its highly stable PDC.
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6
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Prajapati S, Rabe von Pappenheim F, Tittmann K. Frontiers in the enzymology of thiamin diphosphate-dependent enzymes. Curr Opin Struct Biol 2022; 76:102441. [PMID: 35988322 DOI: 10.1016/j.sbi.2022.102441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022]
Abstract
Enzymes that use thiamin diphosphate (ThDP), the biologically active derivative of vitamin B1, as a cofactor play important roles in cellular metabolism in all domains of life. The analysis of ThDP enzymes in the past decades have provided a general framework for our understanding of enzyme catalysis of this protein family. In this review, we will discuss recent advances in the field that include the observation of "unusual" reactions and reaction intermediates that highlight the chemical versatility of the thiamin cofactor. Further topics cover the structural basis of cooperativity of ThDP enzymes, novel insights into the mechanism and structure of selected enzymes, and the discovery of "superassemblies" as reported, for example, acetohydroxy acid synthase. Finally, we summarize recent findings in the structural organisation and mode of action of 2-keto acid dehydrogenase multienzyme complexes and discuss future directions of this exciting research field.
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Affiliation(s)
- Sabin Prajapati
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany; Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany.
| | - Fabian Rabe von Pappenheim
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany; Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany.
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany; Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany.
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7
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Rindfleisch S, Krull M, Uranga J, Schmidt T, Rabe von Pappenheim F, Kirck LL, Balouri A, Schneider T, Chari A, Kluger R, Bourenkov G, Diederichsen U, Mata RA, Tittmann K. Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5′-monophosphate decarboxylase catalysis. Nat Catal 2022. [DOI: 10.1038/s41929-022-00771-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Wang L, Song W, Wang B, Zhang Y, Xu X, Wu J, Gao C, Liu J, Chen X, Chen J, Liu L. One-Pot Enzymatic–Chemical Cascade Route for Synthesizing Aromatic α-Hydroxy Ketones. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04961] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Lei Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Wei Song
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 360015, P. R. China
| | - Yan Zhang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, P. R. China
| | - Xin Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Jing Wu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, P. R. China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Jinghua Chen
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
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9
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Qin M, Song H, Dai X, Chan C, Chan W, Guo Z. Single‐Turnover Kinetics Reveal a Distinct Mode of Thiamine Diphosphate‐Dependent Catalysis in Vitamin K Biosynthesis. Chembiochem 2018; 19:1514-1522. [DOI: 10.1002/cbic.201800143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Mingming Qin
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Haigang Song
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Present address: Division of Structural BiologyWellcome Trust Centre of Human GenomicsUniversity of Oxford Roosevelt Drive Oxford OX3 7BN UK
| | - Xin Dai
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Chi‐Kong Chan
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Environmental Science ProgramThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Wan Chan
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Environmental Science ProgramThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Zhihong Guo
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
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10
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Buddrus L, Andrews ESV, Leak DJ, Danson MJ, Arcus VL, Crennell SJ. Crystal structure of an inferred ancestral bacterial pyruvate decarboxylase. Acta Crystallogr F Struct Biol Commun 2018; 74:179-186. [PMID: 29497023 PMCID: PMC5947705 DOI: 10.1107/s2053230x18002819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/16/2018] [Indexed: 12/30/2022] Open
Abstract
Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophosphate- and Mg2+ ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. As this enzyme class is rare in bacteria, current knowledge of bacterial PDCs is extremely limited. One approach to further the understanding of bacterial PDCs is to exploit the diversity provided by evolution. Ancestral sequence reconstruction (ASR) is a method of computational molecular evolution to infer extinct ancestral protein sequences, which can then be synthesized and experimentally characterized. Through ASR a novel PDC was generated, designated ANC27, that shares only 78% amino-acid sequence identity with its closest extant homologue (Komagataeibacter medellinensis PDC, GenBank accession No. WP_014105323.1), yet is fully functional. Crystals of this PDC diffracted to 3.5 Å resolution. The data were merged in space group P3221, with unit-cell parameters a = b = 108.33, c = 322.65 Å, and contained two dimers (two tetramer halves) in the asymmetric unit. The structure was solved by molecular replacement using PDB entry 2wvg as a model, and the final R values were Rwork = 0.246 (0.3671 in the highest resolution bin) and Rfree = 0.319 (0.4482 in the highest resolution bin). Comparison with extant bacterial PDCs supports the previously observed correlation between decreased tetramer interface area (and number of interactions) and decreased thermostability.
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Affiliation(s)
- Lisa Buddrus
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, England
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Emma S. V. Andrews
- School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - David J. Leak
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Michael J. Danson
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Vickery L. Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Susan J. Crennell
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
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11
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Paulikat M, Wechsler C, Tittmann K, Mata RA. Theoretical Studies of the Electronic Absorption Spectra of Thiamin Diphosphate in Pyruvate Decarboxylase. Biochemistry 2017; 56:1854-1864. [PMID: 28296385 DOI: 10.1021/acs.biochem.6b00984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electronic absorption spectra are oftentimes used to identify reaction intermediates or substrates/products in enzymatic systems, as long as absorption bands can be unequivocally assigned to the species being studied. The latter task is far from trivial given the transient nature of some states and the complexity of the surrounding environment around the active site. To identify unique spectral fingerprints, controlled experiments with model compounds have been used in the past, but even these can sometimes be unreliable. Circular dichroism (CD) and ultraviolet-visible spectra have been tools of choice in the study of the rich chemistry of thiamin diphosphate-dependent enzymes. In this study, we focus on the Zymomonas mobilis pyruvate decarboxylase, and mutant analogues thereof, as a prototypical representative of the thiamin diphosphate (ThDP) enzyme superfamily. Through the use of electronic structure methods, we analyze the nature of electronic excitations in the cofactor. We find that all the determining CD bands around the 280-340 nm spectral range correspond to charge-transfer excitations between the pyrimidine and thiazolium rings of ThDP, which, most likely, is a general property of related ThDP-dependent enzymes. While we can confirm the assignments of previously proposed bands to chemical states, our calculations further suggest that a hitherto unassigned band of enzyme-bound ThDP reports on the ionization state of the canonical glutamate that is required for cofactor activation. This finding expands the spectroscopic "library" of chemical states of ThDP enzymes, permitting a simultaneous assignment of both the cofactor ThDP and the activating glutamate. We anticipate this finding to be helpful for mechanistic analyses of related ThDP enzymes.
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Affiliation(s)
- Mirko Paulikat
- Institute of Physical Chemistry, University of Goettingen , Tammannstraße 6, D-37077 Göttingen, Germany
| | - Cindy Wechsler
- Department of Molecular Enzymology, Albrecht-von-Haller-Institute for Plant Sciences, and Göttingen Center for Molecular Biosciences, University of Goettingen , Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Albrecht-von-Haller-Institute for Plant Sciences, and Göttingen Center for Molecular Biosciences, University of Goettingen , Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, University of Goettingen , Tammannstraße 6, D-37077 Göttingen, Germany
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12
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Mechanistic and Structural Insight to an Evolved Benzoylformate Decarboxylase with Enhanced Pyruvate Decarboxylase Activity. Catalysts 2016. [DOI: 10.3390/catal6120190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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13
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Buddrus L, Andrews ESV, Leak DJ, Danson MJ, Arcus VL, Crennell SJ. Crystal structure of pyruvate decarboxylase from Zymobacter palmae. Acta Crystallogr F Struct Biol Commun 2016; 72:700-6. [PMID: 27599861 PMCID: PMC5012210 DOI: 10.1107/s2053230x16012012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/23/2016] [Indexed: 11/10/2022] Open
Abstract
Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate- and Mg(2+) ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. It is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. Here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from Zymobacter palmae is presented. The crystals were shown to diffract to 2.15 Å resolution. They belonged to space group P21, with unit-cell parameters a = 204.56, b = 177.39, c = 244.55 Å and Rr.i.m. = 0.175 (0.714 in the highest resolution bin). The structure was solved by molecular replacement using PDB entry 2vbi as a model and the final R values were Rwork = 0.186 (0.271 in the highest resolution bin) and Rfree = 0.220 (0.300 in the highest resolution bin). Each of the six tetramers is a dimer of dimers, with each monomer sharing its thiamine pyrophosphate across the dimer interface, and some contain ethylene glycol mimicking the substrate pyruvate in the active site. Comparison with other bacterial PDCs shows a correlation of higher thermostability with greater tetramer interface area and number of interactions.
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Affiliation(s)
- Lisa Buddrus
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Emma S. V. Andrews
- School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - David J. Leak
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Michael J. Danson
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Vickery L. Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Susan J. Crennell
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
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Cheng M, Yoshiyasu H, Okano K, Ohtake H, Honda K. Redirection of the Reaction Specificity of a Thermophilic Acetolactate Synthase toward Acetaldehyde Formation. PLoS One 2016; 11:e0146146. [PMID: 26731734 PMCID: PMC4701669 DOI: 10.1371/journal.pone.0146146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/13/2015] [Indexed: 11/18/2022] Open
Abstract
Acetolactate synthase and pyruvate decarboxylase are thiamine pyrophosphate-dependent enzymes that convert pyruvate into acetolactate and acetaldehyde, respectively. Although the former are encoded in the genomes of many thermophiles and hyperthermophiles, the latter has been found only in mesophilic organisms. In this study, the reaction specificity of acetolactate synthase from Thermus thermophilus was redirected to catalyze acetaldehyde formation to develop a thermophilic pyruvate decarboxylase. Error-prone PCR and mutant library screening led to the identification of a quadruple mutant with 3.1-fold higher acetaldehyde-forming activity than the wild-type. Site-directed mutagenesis experiments revealed that the increased activity of the mutant was due to H474R amino acid substitution, which likely generated two new hydrogen bonds near the thiamine pyrophosphate-binding site. These hydrogen bonds might result in the better accessibility of H+ to the substrate-cofactor-enzyme intermediate and a shift in the reaction specificity of the enzyme.
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Affiliation(s)
- Maria Cheng
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Hayato Yoshiyasu
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Kenji Okano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Hisao Ohtake
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Kohsuke Honda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102–0076, Japan
- * E-mail:
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15
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Wechsler C, Meyer D, Loschonsky S, Funk LM, Neumann P, Ficner R, Brodhun F, Müller M, Tittmann K. Tuning and Switching Enantioselectivity of Asymmetric Carboligation in an Enzyme through Mutational Analysis of a Single Hot Spot. Chembiochem 2015; 16:2580-4. [DOI: 10.1002/cbic.201500529] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Cindy Wechsler
- Abt. Molekulare Enzymologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Danilo Meyer
- Abt. Molekulare Enzymologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Sabrina Loschonsky
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg im Breisgau Germany
| | - Lisa-Marie Funk
- Abt. Molekulare Enzymologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Piotr Neumann
- Abt. Molekulare Strukturbiologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Ralf Ficner
- Abt. Molekulare Strukturbiologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Florian Brodhun
- Abt. Molekulare Enzymologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg im Breisgau Germany
| | - Kai Tittmann
- Abt. Molekulare Enzymologie; Georg-August-Universität Göttingen; Justus-von-Liebig-Weg 11 37077 Göttingen Germany
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16
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Angermayr SA, Gorchs Rovira A, Hellingwerf KJ. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends Biotechnol 2015; 33:352-61. [DOI: 10.1016/j.tibtech.2015.03.009] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 11/24/2022]
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Neumann P, Tittmann K. Marvels of enzyme catalysis at true atomic resolution: distortions, bond elongations, hidden flips, protonation states and atom identities. Curr Opin Struct Biol 2014; 29:122-33. [PMID: 25460275 DOI: 10.1016/j.sbi.2014.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022]
Abstract
Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing.
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Affiliation(s)
- Piotr Neumann
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Justus-von-Liebig-Weg 11, Georg-August-Universität Göttingen, Göttingen D-37077, Germany.
| | - Kai Tittmann
- Abteilung Molekulare Enzymologie, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Justus-von-Liebig-Weg 11, Georg-August-Universität Göttingen, Göttingen D-37077, Germany.
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18
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Sommer B, von Moeller H, Haack M, Qoura F, Langner C, Bourenkov G, Garbe D, Loll B, Brück T. Detailed structure-function correlations of Bacillus subtilis acetolactate synthase. Chembiochem 2014; 16:110-8. [PMID: 25393087 DOI: 10.1002/cbic.201402541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Indexed: 02/04/2023]
Abstract
Isobutanol is deemed to be a next-generation biofuel and a renewable platform chemical.1 Non-natural biosynthetic pathways for isobutanol production have been implemented in cell-based and in vitro systems with Bacillus subtilis acetolactate synthase (AlsS) as key biocatalyst.2-6 AlsS catalyzes the condensation of two pyruvate molecules to acetolactate with thiamine diphosphate and Mg(2+) as cofactors. AlsS also catalyzes the conversion of 2-ketoisovalerate into isobutyraldehyde, the immediate precursor of isobutanol. Our phylogenetic analysis suggests that the ALS enzyme family forms a distinct subgroup of ThDP-dependent enzymes. To unravel catalytically relevant structure-function relationships, we solved the AlsS crystal structure at 2.3 Å in the presence of ThDP, Mg(2+) and in a transition state with a 2-lactyl moiety bound to ThDP. We supplemented our structural data by point mutations in the active site to identify catalytically important residues.
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Affiliation(s)
- Bettina Sommer
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching (Germany)
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van Zyl LJ, Schubert WD, Tuffin MI, Cowan DA. Structure and functional characterization of pyruvate decarboxylase from Gluconacetobacter diazotrophicus. BMC STRUCTURAL BIOLOGY 2014; 14:21. [PMID: 25369873 PMCID: PMC4428508 DOI: 10.1186/s12900-014-0021-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 09/25/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Bacterial pyruvate decarboxylases (PDC) are rare. Their role in ethanol production and in bacterially mediated ethanologenic processes has, however, ensured a continued and growing interest. PDCs from Zymomonas mobilis (ZmPDC), Zymobacter palmae (ZpPDC) and Sarcina ventriculi (SvPDC) have been characterized and ZmPDC has been produced successfully in a range of heterologous hosts. PDCs from the Acetobacteraceae and their role in metabolism have not been characterized to the same extent. Examples include Gluconobacter oxydans (GoPDC), G. diazotrophicus (GdPDC) and Acetobacter pasteutrianus (ApPDC). All of these organisms are of commercial importance. RESULTS This study reports the kinetic characterization and the crystal structure of a PDC from Gluconacetobacter diazotrophicus (GdPDC). Enzyme kinetic analysis indicates a high affinity for pyruvate (K M 0.06 mM at pH 5), high catalytic efficiencies (1.3 • 10(6) M(-1) • s(-1) at pH 5), pHopt of 5.5 and Topt at 45°C. The enzyme is not thermostable (T½ of 18 minutes at 60°C) and the calculated number of bonds between monomers and dimers do not give clear indications for the relatively lower thermostability compared to other PDCs. The structure is highly similar to those described for Z. mobilis (ZmPDC) and A. pasteurianus PDC (ApPDC) with a rmsd value of 0.57 Å for Cα when comparing GdPDC to that of ApPDC. Indole-3-pyruvate does not serve as a substrate for the enzyme. Structural differences occur in two loci, involving the regions Thr341 to Thr352 and Asn499 to Asp503. CONCLUSIONS This is the first study of the PDC from G. diazotrophicus (PAL5) and lays the groundwork for future research into its role in this endosymbiont. The crystal structure of GdPDC indicates the enzyme to be evolutionarily closely related to homologues from Z. mobilis and A. pasteurianus and suggests strong selective pressure to keep the enzyme characteristics in a narrow range. The pH optimum together with reduced thermostability likely reflect the host organisms niche and conditions under which these properties have been naturally selected for. The lack of activity on indole-3-pyruvate excludes this decarboxylase as the enzyme responsible for indole acetic acid production in G. diazotrophicus.
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Affiliation(s)
- Leonardo J van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa.
| | - Wolf-Dieter Schubert
- Department of Biochemistry, University of Pretoria, 2 Lynnwood Road, Pretoria, 0002, South Africa.
| | - Marla I Tuffin
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa.
| | - Don A Cowan
- Department of Genetics, University of Pretoria, Pretoria, 0002, South Africa.
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Tittmann K. Sweet siblings with different faces: the mechanisms of FBP and F6P aldolase, transaldolase, transketolase and phosphoketolase revisited in light of recent structural data. Bioorg Chem 2014; 57:263-280. [PMID: 25267444 DOI: 10.1016/j.bioorg.2014.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/25/2014] [Accepted: 09/01/2014] [Indexed: 10/24/2022]
Abstract
Nature has evolved different strategies for the reversible cleavage of ketose phosphosugars as essential metabolic reactions in all domains of life. Prominent examples are the Schiff-base forming class I FBP and F6P aldolase as well as transaldolase, which all exploit an active center lysine to reversibly cleave the C3-C4 bond of fructose-1,6-bisphosphate or fructose-6-phosphate to give two 3-carbon products (aldolase), or to shuttle 3-carbon units between various phosphosugars (transaldolase). In contrast, transketolase and phosphoketolase make use of the bioorganic cofactor thiamin diphosphate to cleave the preceding C2-C3 bond of ketose phosphates. While transketolase catalyzes the reversible transfer of 2-carbon ketol fragments in a reaction analogous to that of transaldolase, phosphoketolase forms acetyl phosphate as final product in a reaction that comprises ketol cleavage, dehydration and phosphorolysis. In this review, common and divergent catalytic principles of these enzymes will be discussed, mostly, but not exclusively, on the basis of crystallographic snapshots of catalysis. These studies in combination with mutagenesis and kinetic analysis not only delineated the stereochemical course of substrate binding and processing, but also identified key catalytic players acting at the various stages of the reaction. The structural basis for the different chemical fates and lifetimes of the central enamine intermediates in all five enzymes will be particularly discussed, in addition to the mechanisms of substrate cleavage, dehydration and ring-opening reactions of cyclic substrates. The observation of covalent enzymatic intermediates in hyperreactive conformations such as Schiff-bases with twisted double-bond linkages in transaldolase and physically distorted substrate-thiamin conjugates with elongated substrate bonds to be cleaved in transketolase, which probably epitomize a canonical feature of enzyme catalysis, will be also highlighted.
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Affiliation(s)
- Kai Tittmann
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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21
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Basta LAB, Patel H, Kakalis L, Jordan F, Meyers CLF. Defining critical residues for substrate binding to 1-deoxy-D-xylulose 5-phosphate synthase--active site substitutions stabilize the predecarboxylation intermediate C2α-lactylthiamin diphosphate. FEBS J 2014; 281:2820-2837. [PMID: 24767541 PMCID: PMC4065394 DOI: 10.1111/febs.12823] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/06/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
Abstract
1-Deoxy-D-xylulose 5-phosphate (DXP) synthase catalyzes the formation of DXP from pyruvate and D-glyceraldehyde 3-phosphate (GraP) in a thiamin diphosphate-dependent manner, and is the first step in the essential pathway to isoprenoids in human pathogens. Understanding the mechanism of this unique enzyme is critical for developing new anti-infective agents that selectively target isoprenoid biosynthesis. The present study used mutagenesis and a combination of protein fluorescence, CD and kinetics experiments to investigate the roles of Arg420, Arg478 and Tyr392 in substrate binding and catalysis. The results support a random sequential, preferred order mechanism, and predict that Arg420 and Arg478 are involved in binding of the acceptor substrate, GraP. D-Glyceraldehyde, an alternative acceptor substrate lacking the phosphoryl group predicted to interact with Arg420 and Arg478, also accelerates decarboxylation of the predecarboxylation intermediate C2α-lactylthiamin diphosphate (LThDP) on DXP synthase, indicating that this binding interaction is not absolutely required, and that the hydroxyaldehyde sufficiently triggers decarboxylation. Unexpectedly, Tyr392 contributes to GraP affinity, and is not required for LThDP formation or its GraP-promoted decarboxylation. Time-resolved CD spectroscopy and NMR experiments indicate that LThDP is significantly stabilized on R420A and Y392F variants as compared with wild-type DXP synthase in the absence of acceptor substrate, but these substitutions do not appear to affect the rate of GraP-promoted LThDP decarboxylation in the presence of high levels of GraP, and LThDP formation remains the rate-limiting step. These results suggest a role of these residues in promoting GraP binding, which in turn facilitates decarboxylation, and also highlight interesting differences between DXP synthase and other thiamin diphosphate-dependent enzymes.
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Affiliation(s)
- Leighanne A. Brammer Basta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hetalben Patel
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Lazaros Kakalis
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Frank Jordan
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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22
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Kourist R, Guterl JK, Miyamoto K, Sieber V. Enzymatic Decarboxylation-An Emerging Reaction for Chemicals Production from Renewable Resources. ChemCatChem 2014. [DOI: 10.1002/cctc.201300881] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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23
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Angermayr SA, van der Woude AD, Correddu D, Vreugdenhil A, Verrone V, Hellingwerf KJ. Exploring metabolic engineering design principles for the photosynthetic production of lactic acid by Synechocystis sp. PCC6803. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:99. [PMID: 24991233 PMCID: PMC4078008 DOI: 10.1186/1754-6834-7-99] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/30/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Molecular engineering of the intermediary physiology of cyanobacteria has become important for the sustainable production of biofuels and commodity compounds from CO2 and sunlight by "designer microbes." The chemical commodity product L-lactic acid can be synthesized in one step from a key intermediary metabolite of these organisms, pyruvate, catalyzed by a lactate dehydrogenase. Synthetic biology engineering to make "designer microbes" includes the introduction and overexpression of the product-forming biochemical pathway. For further optimization of product formation, modifications in the surrounding biochemical network of intermediary metabolism have to be made. RESULTS To improve light-driven L-lactic acid production from CO2, we explored several metabolic engineering design principles, using a previously engineered L-lactic acid producing mutant strain of Synechocystis sp. PCC6803 as the benchmark. These strategies included: (i) increasing the expression level of the relevant product-forming enzyme, lactate dehydrogenase (LDH), for example, via expression from a replicative plasmid; (ii) co-expression of a heterologous pyruvate kinase to increase the flux towards pyruvate; and (iii) knockdown of phosphoenolpyruvate carboxylase to decrease the flux through a competing pathway (from phosphoenolpyruvate to oxaloacetate). In addition, we tested selected lactate dehydrogenases, some of which were further optimized through site-directed mutagenesis to improve the enzyme's affinity for the co-factor nicotinamide adenine dinucleotide phosphate (NADPH). The carbon partitioning between biomass and lactic acid was increased from about 5% to over 50% by strain optimization. CONCLUSION An efficient photosynthetic microbial cell factory will display a high rate and extent of conversion of substrate (CO2) into product (here: L-lactic acid). In the existing CO2-based cyanobacterial cell factories that have been described in the literature, by far most of the control over product formation resides in the genetically introduced fermentative pathway. Here we show that a strong promoter, in combination with increased gene expression, can take away a significant part of the control of this step in lactic acid production from CO2. Under these premises, modulation of the intracellular precursor, pyruvate, can significantly increase productivity. Additionally, production enhancement is achieved by protein engineering to increase co-factor specificity of the heterologously expressed LDH.
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Affiliation(s)
- S Andreas Angermayr
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam and Netherlands Institute of Systems Biology, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | | | - Danilo Correddu
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam and Netherlands Institute of Systems Biology, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Photanol BV, Science Park 408, Amsterdam, The Netherlands
| | | | - Valeria Verrone
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam and Netherlands Institute of Systems Biology, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam and Netherlands Institute of Systems Biology, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Photanol BV, Science Park 408, Amsterdam, The Netherlands
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25
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Van Zyl LJ, Taylor MP, Eley K, Tuffin M, Cowan DA. Engineering pyruvate decarboxylase-mediated ethanol production in the thermophilic host Geobacillus thermoglucosidasius. Appl Microbiol Biotechnol 2013; 98:1247-59. [DOI: 10.1007/s00253-013-5380-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/30/2013] [Accepted: 11/02/2013] [Indexed: 11/25/2022]
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26
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Hailes HC, Rother D, Müller M, Westphal R, Ward JM, Pleiss J, Vogel C, Pohl M. Engineering stereoselectivity of ThDP-dependent enzymes. FEBS J 2013; 280:6374-94. [DOI: 10.1111/febs.12496] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/16/2013] [Accepted: 08/21/2013] [Indexed: 01/12/2023]
Affiliation(s)
- Helen C. Hailes
- Department of Chemistry; Christopher Ingold Laboratories; University College London; UK
| | - Dörte Rother
- IBG-1: Biotechnology; Forschungszentrum Jülich Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences; University of Freiburg; Germany
| | | | - John M. Ward
- Department of Biochemical Engineering; University College London; UK
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| | - Constantin Vogel
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| | - Martina Pohl
- IBG-1: Biotechnology; Forschungszentrum Jülich Germany
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27
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Schröder-Tittmann K, Meyer D, Arens J, Wechsler C, Tietzel M, Golbik R, Tittmann K. Alternating Sites Reactivity Is a Common Feature of Thiamin Diphosphate-Dependent Enzymes As Evidenced by Isothermal Titration Calorimetry Studies of Substrate Binding. Biochemistry 2013; 52:2505-7. [DOI: 10.1021/bi301591e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kathrin Schröder-Tittmann
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
| | - Danilo Meyer
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
| | - Johannes Arens
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
| | - Cindy Wechsler
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
| | - Michael Tietzel
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
| | - Ralph Golbik
- Martin-Luther University Halle-Wittenberg, 06120 Halle/Salle, Germany
| | - Kai Tittmann
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
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28
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Xiang Z. DFT study on the reaction of the α-amino acid anion catalyzed by the aldehyde: Decarboxylation vs. intramolecular CO2 transfer. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.11.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Avoiding CO2 in Catalysis of Decarboxylation. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2013. [DOI: 10.1016/b978-0-12-407754-6.00002-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Baker P, Seah SYK. Rational approaches for engineering novel functionalities in carbon-carbon bond forming enzymes. Comput Struct Biotechnol J 2012; 2:e201209003. [PMID: 24688644 PMCID: PMC3962088 DOI: 10.5936/csbj.201209003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/13/2012] [Accepted: 09/15/2012] [Indexed: 01/17/2023] Open
Abstract
Enzymes that catalyze carbon-carbon bond formation can be exploited as biocatalyst for synthetic organic chemistry. However, natural enzymes frequently do not possess the required properties or specificities to catalyze industrially useful transformations. This mini-review describes recent work using knowledge-guided site-specific mutagenesis of key active site residues to alter substrate specificity, stereospecificity and reaction specificity of these enzymes. In addition, examples of de novo designed enzymes that catalyze C-C bond reactions not found in nature will be discussed.
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Affiliation(s)
- Perrin Baker
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario Canada, N1G 2W1
| | - Stephen Y K Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario Canada, N1G 2W1
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Balakrishnan A, Gao Y, Moorjani P, Nemeria NS, Tittmann K, Jordan F. Bifunctionality of the thiamin diphosphate cofactor: assignment of tautomeric/ionization states of the 4'-aminopyrimidine ring when various intermediates occupy the active sites during the catalysis of yeast pyruvate decarboxylase. J Am Chem Soc 2012; 134:3873-85. [PMID: 22300533 PMCID: PMC3295232 DOI: 10.1021/ja211139c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiamin diphosphate (ThDP) dependent enzymes perform crucial C-C bond forming and breaking reactions in sugar and amino acid metabolism and in biosynthetic pathways via a sequence of ThDP-bound covalent intermediates. A member of this superfamily, yeast pyruvate decarboxylase (YPDC) carries out the nonoxidative decarboxylation of pyruvate and is mechanistically a simpler ThDP enzyme. YPDC variants created by substitution at the active center (D28A, E51X, and E477Q) and on the substrate activation pathway (E91D and C221E) display varying activity, suggesting that they stabilize different covalent intermediates. To test the role of both rings of ThDP in YPDC catalysis (the 4'-aminopyrimidine as acid-base, and thiazolium as electrophilic covalent catalyst), we applied a combination of steady state and time-resolved circular dichroism experiments (assessing the state of ionization and tautomerization of enzyme-bound ThDP-related intermediates), and chemical quench of enzymatic reaction mixtures followed by NMR characterization of the ThDP-bound intermediates released from YPDC (assessing occupancy of active centers by these intermediates and rate-limiting steps). Results suggest the following: (1) Pyruvate and analogs induce active site asymmetry in YPDC and variants. (2) The rare 1',4'-iminopyrimidine ThDP tautomer participates in formation of ThDP-bound intermediates. (3) Propionylphosphinate also binds at the regulatory site and its binding is reflected by catalytic events at the active site 20 Å away. (4) YPDC stabilizes an electrostatic model for the 4'-aminopyrimidinium ionization state, an important contribution of the protein to catalysis. The combination of tools used provides time-resolved details about individual events during ThDP catalysis; the methods are transferable to other ThDP superfamily members.
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Affiliation(s)
| | - Yuhong Gao
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Prerna Moorjani
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | | | - Kai Tittmann
- Albrecht-von-Haller Institute & Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, D-37077 Göttingen, Germany
| | - Frank Jordan
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
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Substrate specificity in thiamin diphosphate-dependent decarboxylases. Bioorg Chem 2011; 43:26-36. [PMID: 22245019 DOI: 10.1016/j.bioorg.2011.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 11/20/2022]
Abstract
Thiamin diphosphate (ThDP) is the biologically active form of vitamin B(1), and ThDP-dependent enzymes are found in all forms of life. The catalytic mechanism of this family requires the formation of a common intermediate, the 2α-carbanion-enamine, regardless of whether the enzyme is involved in C-C bond formation or breakdown, or even formation of C-N, C-O and C-S bonds. This demands that the enzymes must screen substrates prior to, and/or after, formation of the common intermediate. This review is focused on the group for which the second step is the protonation of the 2α-carbanion, i.e., the ThDP-dependent decarboxylases. Based on kinetic data, sequence/structure alignments and mutagenesis studies the factors involved in substrate specificity have been identified.
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Kneen MM, Stan R, Yep A, Tyler RP, Saehuan C, McLeish MJ. Characterization of a thiamin diphosphate-dependent phenylpyruvate decarboxylase from Saccharomyces cerevisiae. FEBS J 2011; 278:1842-53. [DOI: 10.1111/j.1742-4658.2011.08103.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Meyer D, Walter L, Kolter G, Pohl M, Müller M, Tittmann K. Conversion of Pyruvate Decarboxylase into an Enantioselective Carboligase with Biosynthetic Potential. J Am Chem Soc 2011; 133:3609-16. [PMID: 21341803 DOI: 10.1021/ja110236w] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Danilo Meyer
- Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Lydia Walter
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Geraldine Kolter
- Institute of Biotechnology 2, Research Centre Jülich, 52425 Jülich, Germany
| | - Martina Pohl
- Institute of Biotechnology 2, Research Centre Jülich, 52425 Jülich, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Kai Tittmann
- Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
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