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Wang L, Wu Y, Hu J, Yin D, Wei W, Wen J, Chen X, Gao C, Zhou Y, Liu J, Hu G, Li X, Wu J, Zhou Z, Liu L, Song W. Unlocking the function promiscuity of old yellow enzyme to catalyze asymmetric Morita-Baylis-Hillman reaction. Nat Commun 2024; 15:5737. [PMID: 38982157 PMCID: PMC11233575 DOI: 10.1038/s41467-024-50141-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Exploring the promiscuity of native enzymes presents a promising strategy for expanding their synthetic applications, particularly for catalyzing challenging reactions in non-native contexts. In this study, we explore the promiscuous potential of old yellow enzymes (OYEs) to facilitate the Morita-Baylis-Hillman reaction (MBH reaction), leveraging substrate similarities between MBH reaction and reduction reaction. Using mass spectrometry and spectroscopic techniques, we confirm promiscuity of GkOYE in both MBH and reduction reactions. By blocking H- and H+ transfer pathways, we engineer GkOYE.8, which loses its reduction ability but enhances its MBH activity. The structural basis of MBH reaction catalyzed by GkOYE.8 is obtained through mutation studies and kinetic simulations. Furthermore, enantiocomplementary mutants GkOYE.11 and GkOYE.13 are obtained by directed evolution, exhibiting the ability to accept various aromatic aldehydes and alkenes as substrates. This study demonstrates the potential of leveraging substrate similarities to unlock enzyme functionalities, enabling the catalysis of new-to-nature reactions.
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Affiliation(s)
- Lei Wang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yaoyun Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jun Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Dejing Yin
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Wen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yiwen Zhou
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiaomin Li
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Zhi Zhou
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China.
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Zhao Z, Zhang Z, Meng Q, Chen B, Song J, Liu H, Han B. Aerobic Oxidative Cleavage of C(OH)-C Bonds to Produce Aromatic Aldehydes Catalyzed by Cu I -1,10-phenanthroline Complex. CHEMSUSCHEM 2023; 16:e202300373. [PMID: 37258454 DOI: 10.1002/cssc.202300373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/02/2023] [Accepted: 05/31/2023] [Indexed: 06/02/2023]
Abstract
Effective cleavage and functionalization of C(OH)-C bonds is of great importance for the production of value-added chemicals from renewable biomass resources such as carbohydrates, lignin and their derivatives. The efficiency and selectivity of oxidative cleavage of C(OH)-C bonds are hindered by their inert nature and various side reactions associated with the hydroxyl group. The oxidative conversion of secondary alcohols to produce aldehydes is particularly challenging because the generated aldehydes tend to be over-oxidized to acids or the other side products. Noble-metal based catalysts are necessary to get satisfactory aldehyde yields. Herein, for the first time, the efficient aerobic oxidative conversion of secondary aromatic alcohols into aromatic aldehydes is reported using non-noble metal catalysts and environmentally benign oxygen, without any additional base. It was found that CuI -1,10-phenanthroline (Cu-phen) complex showed outstanding performance for the reactions. The C(OH)-C bonds of a diverse array of aromatic secondary alcohols were effectively cleaved and functionalized, selectively affording aldehydes with excellent yields. Detailed mechanism study revealed a radical mediated pathway for the oxidative reaction. We believe that the findings in this work will lead to many explorations in non-noble metal catalyzed oxidative reactions.
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Affiliation(s)
- Ziwei Zhao
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Colloid and Interface and Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhanrong Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Colloid and Interface and Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qinglei Meng
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Colloid and Interface and Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Bingfeng Chen
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Colloid and Interface and Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
| | - Jinliang Song
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510006, P. R. China
| | - Huizhen Liu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Colloid and Interface and Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Colloid and Interface and Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, 100190, Beijing, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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3
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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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Guo W, Han J, Li X, He Z, Zhang Y. Large-scale analysis of protein crotonylation reveals its diverse functions in Pinellia ternata. BMC PLANT BIOLOGY 2022; 22:457. [PMID: 36151520 PMCID: PMC9502611 DOI: 10.1186/s12870-022-03835-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pinellia ternata is an important traditional medicine in China, and its growth is regulated by the transcriptome or proteome. Lysine crotonylation, a newly identified and important type of posttranslational modification, plays a key role in many aspects of cell metabolism. However, little is known about its functions in Pinellia ternata. RESULTS In this study, we generated a global crotonylome analysis of Pinellia ternata and examined its overlap with lysine succinylation. A total of 2106 crotonylated sites matched on 1006 proteins overlapping in three independent tests were identified, and we found three specific amino acids surrounding crotonylation sites in Pinellia ternata: KcrF, K***Y**Kcr and Kcr****R. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that two crucial alkaloid biosynthesis-related enzymes and many stress-related proteins were also highly crotonylated. Furthermore, several enzymes participating in carbohydrate metabolism pathways were found to exhibit both lysine crotonylation and succinylation modifications. CONCLUSIONS These results indicate that lysine crotonylation performs important functions in many biological processes in Pinellia ternata, especially in the biosynthesis of alkaloids, and some metabolic pathways are simultaneously regulated by lysine crotonylation and succinylation.
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Affiliation(s)
- Weiwei Guo
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Jiayi Han
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Ximei Li
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Zihan He
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China
| | - Yumei Zhang
- Shandong Provincial Key Laboratory of Dry Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops/College of Agronomy, Qingdao Agricultural University, Qingdao Shandong, 266109, China.
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5
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Functional Versatility of the Human 2-Oxoadipate Dehydrogenase in the L-Lysine Degradation Pathway toward Its Non-Cognate Substrate 2-Oxopimelic Acid. Int J Mol Sci 2022; 23:ijms23158213. [PMID: 35897808 PMCID: PMC9367764 DOI: 10.3390/ijms23158213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/23/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
The human 2-oxoadipate dehydrogenase complex (OADHc) in L-lysine catabolism is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to glutaryl-CoA and NADH (+H+). Genetic findings have linked the DHTKD1 encoding 2-oxoadipate dehydrogenase (E1a), the first component of the OADHc, to pathogenesis of AMOXAD, eosinophilic esophagitis (EoE), and several neurodegenerative diseases. A multipronged approach, including circular dichroism spectroscopy, Fourier Transform Mass Spectrometry, and computational approaches, was applied to provide novel insight into the mechanism and functional versatility of the OADHc. The results demonstrate that E1a oxidizes a non-cognate substrate 2-oxopimelate (OP) as well as OA through the decarboxylation step, but the OADHc was 100-times less effective in reactions producing adipoyl-CoA and NADH from the dihydrolipoamide succinyltransferase (E2o) and dihydrolipoamide dehydrogenase (E3). The results revealed that the E2o is capable of producing succinyl-CoA, glutaryl-CoA, and adipoyl-CoA. The important conclusions are the identification of: (i) the functional promiscuity of E1a and (ii) the ability of the E2o to form acyl-CoA products derived from homologous 2-oxo acids with five, six, and even seven carbon atoms. The findings add to our understanding of both the OADHc function in the L-lysine degradative pathway and of the molecular mechanisms leading to the pathogenesis associated with DHTKD1 variants.
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6
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Ding Y, Perez-Ortiz G, Peate J, Barry SM. Redesigning Enzymes for Biocatalysis: Exploiting Structural Understanding for Improved Selectivity. Front Mol Biosci 2022; 9:908285. [PMID: 35936784 PMCID: PMC9355150 DOI: 10.3389/fmolb.2022.908285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
The discovery of new enzymes, alongside the push to make chemical processes more sustainable, has resulted in increased industrial interest in the use of biocatalytic processes to produce high-value and chiral precursor chemicals. Huge strides in protein engineering methodology and in silico tools have facilitated significant progress in the discovery and production of enzymes for biocatalytic processes. However, there are significant gaps in our knowledge of the relationship between enzyme structure and function. This has demonstrated the need for improved computational methods to model mechanisms and understand structure dynamics. Here, we explore efforts to rationally modify enzymes toward changing aspects of their catalyzed chemistry. We highlight examples of enzymes where links between enzyme function and structure have been made, thus enabling rational changes to the enzyme structure to give predictable chemical outcomes. We look at future directions the field could take and the technologies that will enable it.
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7
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Tan LR, Liu JJ, Deewan A, Lee JW, Xia PF, Rao CV, Jin YS, Wang SG. Genome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxide. FEMS Yeast Res 2022; 22:6595876. [PMID: 35640892 DOI: 10.1093/femsyr/foac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/30/2022] [Accepted: 05/26/2022] [Indexed: 11/12/2022] Open
Abstract
Sugar metabolism by Saccharomyces cerevisiae produces ample amounts of CO2 under both aerobic and anaerobic conditions. High solubility of CO2 in fermentation media, contributing to enjoyable sensory properties of sparkling wine and beers by S. cerevisiae, might affect yeast metabolism. To elucidate the overlooked effects of CO2 on yeast metabolism, we examined glucose fermentation by S. cerevisiae under CO2 as compared to N2 and O2 limited conditions. While both CO2 and N2 conditions are considered anaerobic, less glycerol and acetate but more ethanol were produced under CO2 condition. Transcriptomic analysis revealed that significantly decreased mRNA levels of GPP1 coding for glycerol-3-phosphate phosphatase in glycerol synthesis explained the reduced glycerol production under CO2 condition. Besides, transcriptional regulations in signal transduction, carbohydrate synthesis, heme synthesis, membrane and cell wall metabolism, and respiration were detected in response to CO2. Interestingly, signal transduction was uniquely regulated under CO2 condition, where up-regulated genes (STE3, MSB2, WSC3, STE12 and TEC1) in the signal sensors and transcriptional factors suggested that MAPK signaling pathway plays a critical role in CO2 sensing and CO2-induced metabolisms in yeast. Our study identifies CO2 as an external stimulus for modulating metabolic activities in yeast and a transcriptional effector for diverse applications.
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Affiliation(s)
- Lin-Rui Tan
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, P. R. China.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jing-Jing Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Anshu Deewan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jae Won Lee
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, P. R. China
| | - Christopher V Rao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, P. R. China.,Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao 266237, P. R. China
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8
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Engineering the 2-Oxoglutarate Dehydrogenase Complex to Understand Catalysis and Alter Substrate Recognition. REACTIONS 2022. [DOI: 10.3390/reactions3010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The E. coli 2-oxoglutarate dehydrogenase complex (OGDHc) is a multienzyme complex in the tricarboxylic acid cycle, consisting of multiple copies of three components, 2-oxoglutarate dehydrogenase (E1o), dihydrolipoamide succinyltransferase (E2o) and dihydrolipoamide dehydrogenase (E3), which catalyze the formation of succinyl-CoA and NADH (+H+) from 2-oxoglutarate. This review summarizes applications of the site saturation mutagenesis (SSM) to engineer E. coli OGDHc with mechanistic and chemoenzymatic synthetic goals. First, E1o was engineered by creating SSM libraries at positions His260 and His298.Variants were identified that: (a) lead to acceptance of substrate analogues lacking the 5-carboxyl group and (b) performed carboligation reactions producing acetoin-like compounds with good enantioselectivity. Engineering the E2o catalytic (core) domain enabled (a) assignment of roles for pivotal residues involved in catalysis, (b) re-construction of the substrate-binding pocket to accept substrates other than succinyllysyldihydrolipoamide and (c) elucidation of the mechanism of trans-thioesterification to involve stabilization of a tetrahedral oxyanionic intermediate with hydrogen bonds by His375 and Asp374, rather than general acid–base catalysis which has been misunderstood for decades. The E. coli OGDHc is the first example of a 2-oxo acid dehydrogenase complex which was evolved to a 2-oxo aliphatic acid dehydrogenase complex by engineering two consecutive E1o and E2o components.
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Mahakuntha C, Reungsang A, Nunta R, Leksawasdi N. Kinetics of Whole Cells and Ethanol Production from Candida tropicalis TISTR 5306 Cultivation in Batch and Fed-batch Modes Using Assorted Grade Fresh Longan Juice. AN ACAD BRAS CIENC 2021; 93:e20200220. [PMID: 34877969 DOI: 10.1590/0001-3765202120200220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/13/2020] [Indexed: 11/22/2022] Open
Abstract
The kinetic profiles of Candida tropicalis TISTR 5306 cultivation based on modified yeast-malt (MYM), assorted grade fresh longan juice (AsgLG) and longan solid waste extract (LSWE) medium were evaluated in 1 l batch mode. The highest ethanol concentration level (25.5 ± 0.8 g/l) and ethanol yield - Yp/s of 0.491 ± 0.017 g ethanol/g consumed substrate, dried biomass concentration level (9.44 ± 0.05 g/l) and dried biomass yield - Yp/s of 0.533 ± 0.170 g dried biomass/g consumed substrate, specific pyruvate decarboxylase (PDC) activity (0.037 ± 0.003 U/mg protein) were achieved (p ≤ 0.05) in AsgLG medium. Scores ranking strategy were employed and AsgLG medium was subsequently selected with in the highest total score (p ≤ 0.05) of 698 ± 7 at 48 h. The cultivation in fed-batch mode with three rounds of pulse feeding (PF) in 1 l AsgLG medium was carried out. The apparent highest ethanol and dried biomass concentration levels with corresponding yields relative to time zero were (28.3 ± 0.5 g/l, 0.482 ± 0.012 g/g) at 120 h of PF2 and (9.39 ± 0.04 g/l, 0.110 ± 0.001 g/g) at 192 h of PF3. The maximum specific PDC activity was 0.057 ± 0.006 U/mg protein during PF1 feeding.
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Affiliation(s)
- Chatchadaporn Mahakuntha
- Division of Biotechnology, Faculty of Graduate School, Chiang Mai University, Chiang Mai, 50100, Thailand.,Cluster of Agro Bio-Circular-Green Industry (Agro BCG) and Bioprocess Research Cluster (BRC), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Alissara Reungsang
- Research Group for Development of Microbial Hydrogen Production Process, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Rojarej Nunta
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG) and Bioprocess Research Cluster (BRC), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, 50100, Thailand.,Division of Food Innovation and Business, Faculty of Agricultural Technology, Lampang Rajabhat University, Lampang, 52100, Thailand
| | - Noppol Leksawasdi
- Cluster of Agro Bio-Circular-Green Industry (Agro BCG) and Bioprocess Research Cluster (BRC), School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, 50100, Thailand.,Division of Food Process Engineering, School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, 50100, Thailand
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10
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Alvarado O, García-Meseguer R, Ruiz-Pernía JJ, Tuñon I, Delgado EJ. Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Arch Biochem Biophys 2021; 707:108849. [PMID: 33832752 DOI: 10.1016/j.abb.2021.108849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the Cβ atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH+) form. The calculated activation free energy for this step is 17.4 kcal mol-1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP intermediate by the Oβ atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH+ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9 kcal mol-1 at 27 °C.
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Affiliation(s)
- Omar Alvarado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile
| | - Rafael García-Meseguer
- School of Mathematics, University of Bristol, Bristol, UK; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | | | - Iñaki Tuñon
- Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | - Eduardo J Delgado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
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11
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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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12
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Alvarado O, García-Meseguer R, Ruiz-Pernía JJ, Tuñon I, Delgado EJ. Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Arch Biochem Biophys 2021; 701:108807. [PMID: 33587902 DOI: 10.1016/j.abb.2021.108807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 11/26/2022]
Abstract
The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the Cβ atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH+) form. The calculated activation free energy for this step is 17.4kcal mol-1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP intermediate by the Oβ atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH+ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9kcal mol-1 at 27 °C.
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Affiliation(s)
- Omar Alvarado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile
| | - Rafael García-Meseguer
- School of Mathematics, University of Bristol, Bristol, United Kingdom; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | | | - Iñaki Tuñon
- Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | - Eduardo J Delgado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
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13
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Liang YF, Yan LT, Yue Q, Zhao JK, Luo CY, Gao F, Li H, Gao WY. Preparation of a whole cell catalyst overexpressing acetohydroxyacid synthase of Thermotoga maritima and its application in the syntheses of α-hydroxyketones. Sci Rep 2020; 10:15404. [PMID: 32958806 PMCID: PMC7505981 DOI: 10.1038/s41598-020-72416-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022] Open
Abstract
The large catalytic subunit of acetohydroxyacid synthase (AHAS, EC 2.2.1.6) of Thermotoga maritima (TmcAHAS) was prepared in this study. It possesses high specific activity and excellent stability. The protein and a whole cell catalyst overexpressing the protein were applied to the preparation of α-hydroxyketones including acetoin (AC), 3-hydroxy-2-pentanone (HP), and (R)-phenylacetylcarbinol (R-PAC). The results show that AC and HP could be produced in high yields (84% and 62%, respectively), while R-PAC could be synthesized in a high yield (about 78%) with an R/S ratio of 9:1. Therefore, TmcAHAS and the whole cell catalyst overexpressing the protein could be practically useful bio-catalysts in the preparation of α-hydroxyketones including AC, HP, and R-PAC. To the best of our knowledge, this is the first time that bacterial AHAS was used as a catalyst to prepare HP with a good yield, and also the first time that TmcAHAS was employed to synthesize AC and R-PAC.
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Affiliation(s)
- Yan-Fei Liang
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Le-Tian Yan
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Qiao Yue
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Ji-Kui Zhao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Cai-Yun Luo
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Feng Gao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Heng Li
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China.
| | - Wen-Yun Gao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China.
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14
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Horvat M, Winkler M. In Vivo
Reduction of Medium‐ to Long‐Chain Fatty Acids by Carboxylic Acid Reductase (CAR) Enzymes: Limitations and Solutions. ChemCatChem 2020. [DOI: 10.1002/cctc.202000895] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Melissa Horvat
- acib –Austrian Center of Industrial Biotechnology Krenngasse 37 8010 Graz Austria
| | - Margit Winkler
- acib –Austrian Center of Industrial Biotechnology Krenngasse 37 8010 Graz Austria
- Institute of Molecular Biotechnology Graz University of Technology Petersgasse 14 8010 Graz Austria
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15
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Oxalyl‐CoA Decarboxylase katalysiert die nukleophile ein‐Kohlenstoff‐Verlängerung von Aldehyden zu chiralen α‐Hydroxysäuren. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Burgener S, Cortina NS, Erb TJ. Oxalyl-CoA Decarboxylase Enables Nucleophilic One-Carbon Extension of Aldehydes to Chiral α-Hydroxy Acids. Angew Chem Int Ed Engl 2020; 59:5526-5530. [PMID: 31894608 PMCID: PMC7154664 DOI: 10.1002/anie.201915155] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 11/11/2022]
Abstract
The synthesis of complex molecules from simple, renewable carbon units is the goal of a sustainable economy. Here we explored the biocatalytic potential of the thiamine-diphosphate-dependent (ThDP) oxalyl-CoA decarboxylase (OXC)/2-hydroxyacyl-CoA lyase (HACL) superfamily that naturally catalyzes the shortening of acyl-CoA thioester substrates through the release of the C1 -unit formyl-CoA. We show that the OXC/HACL superfamily contains promiscuous members that can be reversed to perform nucleophilic C1 -extensions of various aldehydes to yield the corresponding 2-hydroxyacyl-CoA thioesters. We improved the catalytic properties of Methylorubrum extorquens OXC by rational enzyme engineering and combined it with two newly described enzymes-a specific oxalyl-CoA synthetase and a 2-hydroxyacyl-CoA thioesterase. This enzymatic cascade enabled continuous conversion of oxalate and aromatic aldehydes into valuable (S)-α-hydroxy acids with enantiomeric excess up to 99 %.
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Affiliation(s)
- Simon Burgener
- Department of Biochemistry & Synthetic MetabolismMax-Planck-Institute for terrestrial MicrobiologyKarl-von-Frisch-Str. 1035043MarburgGermany
| | - Niña Socorro Cortina
- Department of Biochemistry & Synthetic MetabolismMax-Planck-Institute for terrestrial MicrobiologyKarl-von-Frisch-Str. 1035043MarburgGermany
| | - Tobias J. Erb
- Department of Biochemistry & Synthetic MetabolismMax-Planck-Institute for terrestrial MicrobiologyKarl-von-Frisch-Str. 1035043MarburgGermany
- LOEWE-Center for Synthetic MicrobiologyPhilipps-University MarburgKarl-von-Frisch-Str. 835043MarburgGermany
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17
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Carboxylic acid reductases in metabolic engineering. J Biotechnol 2020; 307:1-14. [DOI: 10.1016/j.jbiotec.2019.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 01/29/2023]
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18
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Yu H, Hernández López RI, Steadman D, Méndez‐Sánchez D, Higson S, Cázares‐Körner A, Sheppard TD, Ward JM, Hailes HC, Dalby PA. Engineering transketolase to accept both unnatural donor and acceptor substrates and produce α‐hydroxyketones. FEBS J 2019; 287:1758-1776. [DOI: 10.1111/febs.15108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/26/2019] [Accepted: 10/23/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering University College London UK
| | | | | | | | - Sally Higson
- Department of Chemistry University College London UK
| | | | | | - John M. Ward
- Department of Biochemical Engineering University College London UK
| | | | - Paul A. Dalby
- Department of Biochemical Engineering University College London UK
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19
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Buchholz PCF, Ferrario V, Pohl M, Gardossi L, Pleiss J. Navigating within thiamine diphosphate-dependent decarboxylases: Sequences, structures, functional positions, and binding sites. Proteins 2019; 87:774-785. [PMID: 31070804 DOI: 10.1002/prot.25706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/23/2019] [Accepted: 05/05/2019] [Indexed: 11/10/2022]
Abstract
Thiamine diphosphate-dependent decarboxylases catalyze both cleavage and formation of CC bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP-dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (principle component analysis and principal coordinate analysis) enabling complexity reduction. The different results obtained both locally and globally, that is, individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP-dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, to facilitate family assignments for homologous protein sequences.
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Affiliation(s)
- Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.,Laboratory of Applied and Computational Biocatalysis, Department of Chemical and Pharmaceutical Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Martina Pohl
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany
| | - Lucia Gardossi
- Laboratory of Applied and Computational Biocatalysis, Department of Chemical and Pharmaceutical Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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20
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Hsu N, Wang Y, Lin K, Chang C, Ke S, Lyu S, Hsu L, Li Y, Chen S, Wang K, Li T. Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions. Chembiochem 2018; 19:2395-2402. [PMID: 30155962 PMCID: PMC6282555 DOI: 10.1002/cbic.201800378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Indexed: 11/12/2022]
Abstract
Transketolase (TK) catalyzes a reversible transfer of a two-carbon (C2 ) unit between phosphoketose donors and phosphoaldose acceptors, for which the group-transfer reaction that follows a one- or two-electron mechanism and the force that breaks the C2"-C3" bond of the ketose donors remain unresolved. Herein, we report ultrahigh-resolution crystal structures of a TK (TKps) from Pichia stipitis in previously undiscovered intermediate states and support a diradical mechanism for a reversible group-transfer reaction. In conjunction with MS, NMR spectroscopy, EPR and computational analyses, it is concluded that the enzyme-catalyzed non-Kekulé diradical cofactor brings about the C2"-C3" bond cleavage/formation for the C2 -unit transfer reaction, for which suppression of activation energy and activation and destabilization of enzymatic intermediates are facilitated.
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Affiliation(s)
- Ning‐Shian Hsu
- Genomics Research CenterAcademia SinicaTaipei115Taiwan
- Institute of Biochemistry and Molecular BiologyNational Yang-Ming UniversityTaipei112Taiwan
| | - Yung‐Lin Wang
- Genomics Research CenterAcademia SinicaTaipei115Taiwan
| | - Kuan‐Hung Lin
- Genomics Research CenterAcademia SinicaTaipei115Taiwan
- Institute of Biochemistry and Molecular BiologyNational Yang-Ming UniversityTaipei112Taiwan
| | - Chi‐Fon Chang
- Genomics Research CenterAcademia SinicaTaipei115Taiwan
| | - Shyue‐Chu Ke
- Department of PhysicsNational Dong Hwa UniversityHualien974Taiwan
| | - Syue‐Yi Lyu
- Genomics Research CenterAcademia SinicaTaipei115Taiwan
| | - Li‐Jen Hsu
- Genomics Research CenterAcademia SinicaTaipei115Taiwan
| | - Yi‐Shan Li
- Genomics Research CenterAcademia SinicaTaipei115Taiwan
| | | | | | - Tsung‐Lin Li
- Genomics Research CenterAcademia SinicaTaipei115Taiwan
- Biotechnology CenterNational Chung Hsing UniversityTaichung City402Taiwan
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21
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Lee YC, Chen YY, Lin JS, Chen YW, Li CC, Liang KX, Chan HH, Lin WD, Kao CH. Stereoselective synthesis of (1R, 2S)-norephedrine by recombinant whole-cell biocatalysts coupling acetohydroxyacid synthase I and ω-transaminase. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Wang ZX, Xiang JC, Cheng Y, Ma JT, Wu YD, Wu AX. Direct Biomimetic Synthesis of β-Carboline Alkaloids from Two Amino Acids. J Org Chem 2018; 83:12247-12254. [PMID: 30134110 DOI: 10.1021/acs.joc.8b01668] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The increasing importance of enzyme mimics in organic synthesis inspired us to design a novel biomimetic synthesis of β-carboline alkaloids directly from tryptophan and a second amino acid. This novel one-pot protocol utilizes abundant and readily available starting materials and thus presents a green and user-friendly alternative to conventional methods that rely on stepwise synthesis. Driven by molecular iodine and TFA, decarboxylation, deamination, Pictet-Spengler reaction, and oxidation reactions proceeded sequentially, transforming biomass amino acids into value-added alkaloid motifs.
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Affiliation(s)
- Zi-Xuan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , P. R. China
| | - Jia-Chen Xiang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , P. R. China
| | - Yan Cheng
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , P. R. China
| | - Jin-Tian Ma
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , P. R. China
| | - Yan-Dong Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , P. R. China
| | - An-Xin Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , P. R. China
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23
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Morris JS, Groves RA, Hagel JM, Facchini PJ. An N-methyltransferase from Ephedra sinica catalyzing the formation of ephedrine and pseudoephedrine enables microbial phenylalkylamine production. J Biol Chem 2018; 293:13364-13376. [PMID: 29929980 DOI: 10.1074/jbc.ra118.004067] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/19/2018] [Indexed: 01/24/2023] Open
Abstract
Phenylalkylamines, such as the plant compounds ephedrine and pseudoephedrine and the animal neurotransmitters dopamine and adrenaline, compose a large class of natural and synthetic molecules with important physiological functions and pharmaceutically valuable bioactivities. The final steps of ephedrine and pseudoephedrine biosynthesis in members of the plant genus Ephedra involve N-methylation of norephedrine and norpseudoephedrine, respectively. Here, using a plant transcriptome screen, we report the isolation and characterization of an N-methyltransferase (NMT) from Ephedra sinica able to catalyze the formation of (pseudo)ephedrine and other naturally occurring phenylalkylamines, including N-methylcathinone and N-methyl(pseudo)ephedrine. Phenylalkylamine N-methyltransferase (PaNMT) shares substantial amino acid sequence identity with enzymes of the NMT family involved in benzylisoquinoline alkaloid (BIA) metabolism in members of the higher plant order Ranunculales, which includes opium poppy (Papaver somniferum). PaNMT accepted a broad range of substrates with phenylalkylamine, tryptamine, β-carboline, tetrahydroisoquinoline, and BIA structural scaffolds, which is in contrast to the specificity for BIA substrates of NMT enzymes within the Ranunculales. PaNMT transcript levels were highest in young shoots of E. sinica, which corresponded to the location of NMT activity yielding (pseudo)ephedrine, N-methylcathinone, and N-methyl(pseudo)ephedrine, and with in planta accumulation of phenylalkylamines. Co-expression of recombinant genes encoding PaNMT and an ω-transaminase (PP2799) from Pseudomonas putida in Escherichia coli enabled the conversion of exogenous (R)-phenylacetylcarbinol (PAC) and (S)-PAC to ephedrine and pseudoephedrine, respectively. Our work further demonstrates the utility of plant biochemical genomics for the isolation of key enzymes that facilitate microbial engineering for the production of medicinally important metabolites.
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Affiliation(s)
- Jeremy S Morris
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ryan A Groves
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Jillian M Hagel
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Peter J Facchini
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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24
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Bilal M, Iqbal HMN, Guo S, Hu H, Wang W, Zhang X. State-of-the-art protein engineering approaches using biological macromolecules: A review from immobilization to implementation view point. Int J Biol Macromol 2018; 108:893-901. [PMID: 29102791 DOI: 10.1016/j.ijbiomac.2017.10.182] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/18/2017] [Accepted: 10/31/2017] [Indexed: 02/05/2023]
Abstract
Over the past years, technological and scientific advances have proven biocatalysis as a sustainable alternative than traditional chemical catalysis including organo- or metallocatalysis. In this context, immobilization based approaches represent simple but effective routes for engineering enzyme catalysts with higher activities than wild-type derivatives. Many enzymes including oxidoreductases have been engineered by rational and directed evolution, to realize the catalytic activity, enantioselectivity, and stability attributes which are essential for their biotechnological exploitation. Induce yet stable activity in enzyme catalysis offer new insights and motivation to engineer efficient catalysts for practical and commercial purposes. It has now become possible to envisage substrate accessibility to the catalytic site of the enzyme by current computational capabilities that reduce the experimental work related to the enzyme selection, screening, and engineering. Herein, state-of-the-art protein engineering approaches for improving enzymatic activities including chemical modification, directed evolution, and rational design or their combination methods are discussed. The emphasis is also given to the applications of the resulting tailored catalysts ranging from fine chemicals to novel pharmaceutical compounds that use biocatalysts as a vital step.
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Affiliation(s)
- Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., CP 64849, Mexico
| | - Shuqi Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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25
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Li H, Liu N, Hui X, Gao WY. An improved enzymatic method for the preparation of (R)-phenylacetyl carbinol. RSC Adv 2017. [DOI: 10.1039/c7ra04641c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
(R)-Phenylacetyl carbinol (R-PAC) is one of the key chiral α-hydroxyketones utilized as a synthon in the synthesis of a number of pharmaceuticals having α- and β-adrenergic properties.
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Affiliation(s)
- Heng Li
- National Engineering Research Center for Miniaturized Detection Systems
- College of Life Sciences
- Northwest University
- Xi'an
- China
| | - Nan Liu
- Department of Experimental Surgery
- Tangdu Hospital
- Fourth Military Medical University
- Xi'an
- China
| | - Xian Hui
- National Engineering Research Center for Miniaturized Detection Systems
- College of Life Sciences
- Northwest University
- Xi'an
- China
| | - Wen-Yun Gao
- National Engineering Research Center for Miniaturized Detection Systems
- College of Life Sciences
- Northwest University
- Xi'an
- China
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26
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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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27
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Regio- and Stereoselective Aliphatic-Aromatic Cross-Benzoin Reaction: Enzymatic Divergent Catalysis. Chemistry 2016; 22:13999-14005. [DOI: 10.1002/chem.201602084] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 11/07/2022]
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28
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Giovannini PP, Bortolini O, Massi A. Thiamine-Diphosphate-Dependent Enzymes as Catalytic Tools for the Asymmetric Benzoin-Type Reaction. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600228] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pier Paolo Giovannini
- Department of Chemical and Pharmaceutical Sciences; University of Ferrara; 17, Via Fossato di Mortara 44121 Ferrara Italy
| | - Olga Bortolini
- Department of Chemical and Pharmaceutical Sciences; University of Ferrara; 17, Via Fossato di Mortara 44121 Ferrara Italy
| | - Alessandro Massi
- Department of Chemical and Pharmaceutical Sciences; University of Ferrara; 17, Via Fossato di Mortara 44121 Ferrara Italy
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29
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Dembska A. The analytical and biomedical potential of cytosine-rich oligonucleotides: A review. Anal Chim Acta 2016; 930:1-12. [PMID: 27265899 DOI: 10.1016/j.aca.2016.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 04/30/2016] [Accepted: 05/04/2016] [Indexed: 02/04/2023]
Abstract
Polycytosine DNA strands are often found among natural sequences, including the ends of telomeres, centromeres, and introns or in the regulatory regions of genes. A characteristic feature of oligonucleotides that are rich in cytosine (C-rich) is their ability to associate under acidic conditions to form a tetraplex i-motif consisting of two parallel stranded cytosine-hemiprotonated cytosine (C·C+) base-paired duplexes that are mutually intercalated in an antiparallel orientation. Nanotechnology has been exploiting the advantages of i-motif pH-dependent formation to fabricate nanomachines, nanoswitches, electrodes and intelligent nanosurfaces or nanomaterials. Although a few reviews regarding the structure, properties and applications of i-motifs have been published, this review focuses on recently developed biosensors (e.g., to detect pH, glucose or silver ions) and drug-delivery biomaterials. Furthermore, we have included examples of sensors based on parallel C-rich triplexes and silver nanoclusters (AgNCs) fabricated on cytosine-rich DNA strands. The potential diagnostic and therapeutic applications of this type of material are discussed.
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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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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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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Mahajabeen P, Chadha A. Regio- and enantioselective reduction of diketones: preparation of enantiomerically pure hydroxy ketones catalysed by Candida parapsilosis ATCC 7330. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.tetasy.2015.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Sukovich DJ, Modavi C, de Raad M, Prince RN, Anderson JC. DNA-Linked Enzyme-Coupled Assay for Probing Glucosyltransferase Specificity. ACS Synth Biol 2015; 4:833-41. [PMID: 25621860 DOI: 10.1021/sb500341a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Traditional enzyme characterization methods are low-throughput and therefore limit engineering efforts in synthetic biology and biotechnology. Here, we propose a DNA-linked enzyme-coupled assay (DLEnCA) to monitor enzyme reactions in a high-throughput manner. Throughput is improved by removing the need for protein purification and by limiting the need for liquid chromatography mass spectrometry (LCMS) product detection by linking enzymatic function to DNA modification. We demonstrate the DLEnCA methodology using glucosyltransferases as an illustration. The assay utilizes cell free transcription/translation systems to produce enzymes of interest, while UDP-glucose and T4-β-glucosyltransferase are used to modify DNA, which is detected postreaction using qPCR or a similar means of DNA analysis. OleD and two glucosyltransferases from Arabidopsis were used to verify the assay's generality toward glucosyltransferases. We further show DLEnCA's utility by mapping out the substrate specificity for these enzymes.
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Affiliation(s)
- David J. Sukovich
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Cyrus Modavi
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Markus de Raad
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Robin N. Prince
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - J. Christopher Anderson
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
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Transcriptome profiling of khat (Catha edulis) and Ephedra sinica reveals gene candidates potentially involved in amphetamine-type alkaloid biosynthesis. PLoS One 2015; 10:e0119701. [PMID: 25806807 PMCID: PMC4373857 DOI: 10.1371/journal.pone.0119701] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/15/2015] [Indexed: 12/25/2022] Open
Abstract
Amphetamine analogues are produced by plants in the genus Ephedra and by khat (Catha edulis), and include the widely used decongestants and appetite suppressants (1S,2S)-pseudoephedrine and (1R,2S)-ephedrine. The production of these metabolites, which derive from L-phenylalanine, involves a multi-step pathway partially mapped out at the biochemical level using knowledge of benzoic acid metabolism established in other plants, and direct evidence using khat and Ephedra species as model systems. Despite the commercial importance of amphetamine-type alkaloids, only a single step in their biosynthesis has been elucidated at the molecular level. We have employed Illumina next-generation sequencing technology, paired with Trinity and Velvet-Oases assembly platforms, to establish data-mining frameworks for Ephedra sinica and khat plants. Sequence libraries representing a combined 200,000 unigenes were subjected to an annotation pipeline involving direct searches against public databases. Annotations included the assignment of Gene Ontology (GO) terms used to allocate unigenes to functional categories. As part of our functional genomics program aimed at novel gene discovery, the databases were mined for enzyme candidates putatively involved in alkaloid biosynthesis. Queries used for mining included enzymes with established roles in benzoic acid metabolism, as well as enzymes catalyzing reactions similar to those predicted for amphetamine alkaloid metabolism. Gene candidates were evaluated based on phylogenetic relationships, FPKM-based expression data, and mechanistic considerations. Establishment of expansive sequence resources is a critical step toward pathway characterization, a goal with both academic and industrial implications.
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Abstract
Aldehydes are a class of chemicals with many industrial uses. Several aldehydes are responsible for flavors and fragrances present in plants, but aldehydes are not known to accumulate in most natural microorganisms. In many cases, microbial production of aldehydes presents an attractive alternative to extraction from plants or chemical synthesis. During the past 2 decades, a variety of aldehyde biosynthetic enzymes have undergone detailed characterization. Although metabolic pathways that result in alcohol synthesis via aldehyde intermediates were long known, only recent investigations in model microbes such as Escherichia coli have succeeded in minimizing the rapid endogenous conversion of aldehydes into their corresponding alcohols. Such efforts have provided a foundation for microbial aldehyde synthesis and broader utilization of aldehydes as intermediates for other synthetically challenging biochemical classes. However, aldehyde toxicity imposes a practical limit on achievable aldehyde titers and remains an issue of academic and commercial interest. In this minireview, we summarize published efforts of microbial engineering for aldehyde synthesis, with an emphasis on de novo synthesis, engineered aldehyde accumulation in E. coli, and the challenge of aldehyde toxicity.
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Loschonsky S, Wacker T, Waltzer S, Giovannini PP, McLeish MJ, Andrade SLA, Müller M. Extended Reaction Scope of Thiamine Diphosphate Dependent Cyclohexane-1,2-dione Hydrolase: From CC Bond Cleavage to CC Bond Ligation. Angew Chem Int Ed Engl 2014; 53:14402-6. [DOI: 10.1002/anie.201408287] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Indexed: 11/06/2022]
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Loschonsky S, Wacker T, Waltzer S, Giovannini PP, McLeish MJ, Andrade SLA, Müller M. Extended Reaction Scope of Thiamine Diphosphate Dependent Cyclohexane-1,2-dione Hydrolase: From CC Bond Cleavage to CC Bond Ligation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Kunjapur AM, Tarasova Y, Prather KLJ. Synthesis and accumulation of aromatic aldehydes in an engineered strain of Escherichia coli. J Am Chem Soc 2014; 136:11644-54. [PMID: 25076127 DOI: 10.1021/ja506664a] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aromatic aldehydes are useful in numerous applications, especially as flavors, fragrances, and pharmaceutical precursors. However, microbial synthesis of aldehydes is hindered by rapid, endogenous, and redundant conversion of aldehydes to their corresponding alcohols. We report the construction of an Escherichia coli K-12 MG1655 strain with reduced aromatic aldehyde reduction (RARE) that serves as a platform for aromatic aldehyde biosynthesis. Six genes with reported activity on the model substrate benzaldehyde were rationally targeted for deletion: three genes that encode aldo-keto reductases and three genes that encode alcohol dehydrogenases. Upon expression of a recombinant carboxylic acid reductase in the RARE strain and addition of benzoate during growth, benzaldehyde remained in the culture after 24 h, with less than 12% conversion of benzaldehyde to benzyl alcohol. Although individual overexpression results demonstrated that all six genes could contribute to benzaldehyde reduction in vivo, additional experiments featuring subset deletion strains revealed that two of the gene deletions were dispensable under the conditions tested. The engineered strain was next investigated for the production of vanillin from vanillate and succeeded in preventing formation of the byproduct vanillyl alcohol. A pathway for the biosynthesis of vanillin directly from glucose was introduced and resulted in a 55-fold improvement in vanillin titer when using the RARE strain versus the wild-type strain. Finally, synthesis of the chiral pharmaceutical intermediate L-phenylacetylcarbinol (L-PAC) was demonstrated from benzaldehyde and glucose upon expression of a recombinant mutant pyruvate decarboxylase in the RARE strain. Beyond allowing accumulation of aromatic aldehydes as end products in E. coli, the RARE strain expands the classes of chemicals that can be produced microbially via aldehyde intermediates.
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Affiliation(s)
- Aditya M Kunjapur
- Department of Chemical Engineering, ‡Synthetic Biology Engineering Research Center (SynBERC), §Microbiology Graduate Program, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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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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40
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Loschonsky S, Waltzer S, Brecht V, Müller M. Elucidation of the Enantioselective Cyclohexane-1,2-dione Hydrolase Catalyzed Formation of (S
)-Acetoin. ChemCatChem 2014. [DOI: 10.1002/cctc.201300904] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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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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Jiang X, Zhang H, Yang J, Zheng Y, Feng D, Liu W, Xu X, Cao Y, Zou H, Zhang R, Cheng T, Jiao F, Xian M. Biodegradation-inspired bioproduction of methylacetoin and 2-methyl-2,3-butanediol. Sci Rep 2013; 3:2445. [PMID: 23945710 PMCID: PMC3744081 DOI: 10.1038/srep02445] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/25/2013] [Indexed: 11/09/2022] Open
Abstract
Methylacetoin (3-hydroxy-3-methylbutan-2-one) and 2-methyl-2,3-butanediol are currently obtained exclusively via chemical synthesis. Here, we report, to the best of our knowledge, the first alternative route, using engineered Escherichia coli. The biological synthesis of methylacetoin was first accomplished by reversing its biodegradation, which involved modifying the enzyme complex involved, switching the reaction substrate, and coupling the process to an exothermic reaction. 2-Methyl-2,3-butanediol was then obtained by reducing methylacetoin by exploiting the substrate promiscuity of acetoin reductase. A complete biosynthetic pathway from renewable glucose and acetone was then established and optimized via in vivo enzyme screening and host metabolic engineering, which led to titers of 3.4 and 3.2 g l−1 for methylacetoin and 2-methyl-2,3-butanediol, respectively. This work presents a biodegradation-inspired approach to creating new biosynthetic pathways for small molecules with no available natural biosynthetic pathway.
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Affiliation(s)
- Xinglin Jiang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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Balakrishnan A, Jordan F, Nathan CF. Influence of allosteric regulators on individual steps in the reaction catalyzed by Mycobacterium tuberculosis 2-hydroxy-3-oxoadipate synthase. J Biol Chem 2013; 288:21688-702. [PMID: 23760263 DOI: 10.1074/jbc.m113.465419] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Allosteric regulation often controls key branch points in metabolic processes. Mycobacterium tuberculosis 2-hydroxy-3-oxoadipate synthase (HOAS), a thiamin diphosphate (ThDP)-dependent enzyme, produces 2-hydroxy-3-oxoadipate using 2-ketoglutarate and glyoxylate. The proposed chemical mechanism in analogy with other ThDP-dependent carboligases involves multiple ThDP-bound covalent intermediates. Acetyl coenzyme A is an activator, and GarA, a forkhead association domain-containing protein known to regulate glutamate metabolism, is an allosteric inhibitor of HOAS. Steady state kinetics using assays to study the first half and the full catalytic cycle suggested that the regulators act at different steps in the overall mechanism. To explore the modes of regulation and to test the effects on individual catalytic steps, we performed circular dichroism (CD) studies using a non-decarboxylatable 2-ketoglutarate analog and determined the distribution of ThDP-bound covalent intermediates during the steady state of the HOAS reaction using one-dimensional (1)H gradient carbon heteronuclear single quantum coherence NMR. The results suggest that acetyl coenzyme A acts as a mixed V and K type activator and predominantly affects the predecarboxylation steps. GarA does not inhibit the formation of the predecarboxylation analog and does not affect the accumulation of the postdecarboxylation covalent intermediate derived from 2-ketoglutarate; however, it decreases the abundance of the product ThDP adduct in the HOAS pathway. Thus, the two regulators act on different halves of the catalytic cycle in an unusual regulatory regime.
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Affiliation(s)
- Anand Balakrishnan
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
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45
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Müller M, Sprenger GA, Pohl M. CC bond formation using ThDP-dependent lyases. Curr Opin Chem Biol 2013; 17:261-70. [PMID: 23523314 DOI: 10.1016/j.cbpa.2013.02.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/02/2013] [Accepted: 02/14/2013] [Indexed: 01/17/2023]
Abstract
The present review summarizes recent achievements in enzymatic thiamine catalysis during the past three years. With well-established enzymes such as BAL, PDC and TK new reactions have been identified and respective variants were prepared, which enable access to stereoisomeric products. Further we highlight recent progress with 'new' ThDP-dependent enzymes like MenD and PigD, which catalyze the Stetter-like 1,4 addition of aldehydes and YerE, which is the first known ThDP-dependent enzyme accepting ketones as acceptors.
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Affiliation(s)
- Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104 Freiburg, Germany.
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46
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Beigi M, Waltzer S, Fries A, Eggeling L, Sprenger GA, Müller M. TCA Cycle Involved Enzymes SucA and Kgd, as well as MenD: Efficient Biocatalysts for Asymmetric C–C Bond Formation. Org Lett 2013; 15:452-5. [DOI: 10.1021/ol3031186] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maryam Beigi
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Simon Waltzer
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Alexander Fries
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Lothar Eggeling
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Georg A. Sprenger
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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48
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Steiner K, Schwab H. Recent advances in rational approaches for enzyme engineering. Comput Struct Biotechnol J 2012; 2:e201209010. [PMID: 24688651 PMCID: PMC3962183 DOI: 10.5936/csbj.201209010] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/16/2012] [Accepted: 10/18/2012] [Indexed: 11/29/2022] Open
Abstract
Enzymes are an attractive alternative in the asymmetric syntheses of chiral building blocks. To meet the requirements of industrial biotechnology and to introduce new functionalities, the enzymes need to be optimized by protein engineering. This article specifically reviews rational approaches for enzyme engineering and de novo enzyme design involving structure-based approaches developed in recent years for improvement of the enzymes’ performance, broadened substrate range, and creation of novel functionalities to obtain products with high added value for industrial applications.
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Affiliation(s)
- Kerstin Steiner
- ACIB GmbH, (Austrian Centre of Industrial Biotechnology), c/o TU Graz, 8010 Graz, Austria
| | - Helmut Schwab
- ACIB GmbH, (Austrian Centre of Industrial Biotechnology), c/o TU Graz, 8010 Graz, Austria ; Institute of Molecular Biotechnology, TU Graz, 8010 Graz, Austria
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49
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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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50
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Krizevski R, Bar E, Shalit OR, Levy A, Hagel JM, Kilpatrick K, Marsolais F, Facchini PJ, Ben-Shabat S, Sitrit Y, Lewinsohn E. Benzaldehyde is a precursor of phenylpropylamino alkaloids as revealed by targeted metabolic profiling and comparative biochemical analyses in Ephedra spp. PHYTOCHEMISTRY 2012; 81:71-9. [PMID: 22727117 DOI: 10.1016/j.phytochem.2012.05.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 05/13/2012] [Accepted: 05/14/2012] [Indexed: 05/13/2023]
Abstract
Ephedrine and pseudoephedrine are phenylpropylamino alkaloids widely used in modern medicine. Some Ephedra species such as E. sinica Stapf (Ephedraceae), a widely used Chinese medicinal plant (Chinese name: Ma Huang), accumulate ephedrine alkaloids as active constituents. Other Ephedra species, such as E. foeminea Forssk. (syn. E. campylopoda C.A. Mey) lack ephedrine alkaloids and their postulated metabolic precursors 1-phenylpropane-1,2-dione and (S)-cathinone. Solid-phase microextraction analysis of freshly picked young E. sinica and E. foeminea stems revealed the presence of increased benzaldehyde levels in E. foeminea, whereas 1-phenylpropane-1,2-dione was detected only in E. sinica. Soluble protein preparations from E. sinica and E. foeminea stems catalyzed the conversion of benzaldehyde and pyruvate to (R)-phenylacetylcarbinol, (S)-phenylacetylcarbinol, (R)-2-hydroxypropiophenone (S)-2-hydroxypropiophenone and 1-phenylpropane-1,2-dione. The activity, termed benzaldehyde carboxyligase (BCL) required the presence of magnesium and thiamine pyrophosphate and was 40 times higher in E. sinica as compared to E. foeminea. The distribution patterns of BCL activity in E. sinica tissues correlates well with the distribution pattern of the ephedrine alkaloids. (S)-Cathinone reductase enzymatic activities generating (1R,2S)-norephedrine and (1S,1R)-norephedrine were significantly higher in E. sinica relative to the levels displayed by E. foeminea. Surprisingly, (1R,2S)-norephedrine N-methyltransferase activity which is a downstream enzyme in ephedrine biosynthesis was significantly higher in E. foeminea than in E. sinica. Our studies further support that benzaldehyde is the metabolic precursor to phenylpropylamino alkaloids in E. sinica.
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Affiliation(s)
- Raz Krizevski
- Department of Aromatic, Medicinal and Spice Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay 30095, Israel
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