1
|
Ghatak A, Shanbhag AP, Datta S. Reducing the vicissitudes of heterologous prochiral substrate catalysis by alcohol dehydrogenases through machine learning algorithms. Biochem Biophys Res Commun 2024; 691:149298. [PMID: 38011820 DOI: 10.1016/j.bbrc.2023.149298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/31/2023] [Accepted: 11/19/2023] [Indexed: 11/29/2023]
Abstract
Alcohol dehydrogenases (ADHs) are popular catalysts for synthesizing chiral synthons a vital step for active pharmaceutical intermediate (API) production. They are grouped into three superfamilies namely, medium-chain (MDRs), short-chain dehydrogenase/reductases (SDRs), and iron-containing alcohol dehydrogenases. The former two are used extensively for producing various chiral synthons. Many studies screen multiple enzymes or engineer a specific enzyme for catalyzing a substrate of interest. These processes are resource-intensive and intricate. The current study attempts to decipher the ability to match different ADHs with their ideal substrates using machine learning algorithms. We explore the catalysis of 284 antibacterial ketone intermediates, against MDRs and SDRs to demonstrate a unique pattern of activity. To facilitate machine learning we curated a dataset comprising 33 features, encompassing 4 descriptors for each compound. Subsequently, an ensemble of machine learning techniques viz. Partial Least Squares (PLS) regression, k-Nearest Neighbors (kNN) regression, and Support Vector Machine (SVM) regression, was harnessed. Moreover, the assimilation of Principal Component Analysis (PCA) augmented precision and accuracy, thereby refining and demarcating diverse compound classes. As such, this classification is useful for discerning substrates amenable to diverse alcohol dehydrogenases, thereby mitigating the reliance on high-throughput screening or engineering in identifying the optimal enzyme for specific substrate.
Collapse
Affiliation(s)
- Arindam Ghatak
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India; Biomoneta Research Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK, Bangalore, 560065, India
| | - Anirudh P Shanbhag
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK, Bangalore, 560065, India.
| | - Santanu Datta
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK, Bangalore, 560065, India
| |
Collapse
|
2
|
Cheng J, Zhang C, Zhang K, Li J, Hou Y, Xin J, Sun Y, Xu C, Xu W. Cyanobacteria-Mediated Light-Driven Biotransformation: The Current Status and Perspectives. ACS OMEGA 2023; 8:42062-42071. [PMID: 38024730 PMCID: PMC10653055 DOI: 10.1021/acsomega.3c05407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/29/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Most chemicals are manufactured by traditional chemical processes but at the expense of toxic catalyst use, high energy consumption, and waste generation. Biotransformation is a green, sustainable, and cost-effective process. As cyanobacteria can use light as the energy source to power the synthesis of NADPH and ATP, using cyanobacteria as the chassis organisms to design and develop light-driven biotransformation platforms for chemical synthesis has been gaining attention, since it can provide a theoretical and practical basis for the sustainable and green production of chemicals. Meanwhile, metabolic engineering and genome editing techniques have tremendous prospects for further engineering and optimizing chassis cells to achieve efficient light-driven systems for synthesizing various chemicals. Here, we display the potential of cyanobacteria as a promising light-driven biotransformation platform for the efficient synthesis of green chemicals and current achievements of light-driven biotransformation processes in wild-type or genetically modified cyanobacteria. Meanwhile, future perspectives of one-pot enzymatic cascade biotransformation from biobased materials in cyanobacteria have been proposed, which could provide additional research insights for green biotransformation and accelerate the advancement of biomanufacturing industries.
Collapse
Affiliation(s)
- Jie Cheng
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Chaobo Zhang
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Kaidian Zhang
- State
Key Laboratory of Marine Resource Utilization in the South China Sea,
School of Marine Biology and Aquaculture, Hainan University, Haikou, Hainan 570100, China
- Xiamen
Key Laboratory of Urban Sea Ecological Conservation and Restoration,
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Jiashun Li
- Xiamen
Key Laboratory of Urban Sea Ecological Conservation and Restoration,
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Yuyong Hou
- Key
Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotech-nology, Chinese
Academy of Sciences, Tianjin 300308, China
| | - Jiachao Xin
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Yang Sun
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Chengshuai Xu
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Wei Xu
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| |
Collapse
|
3
|
Assil-Companioni L, Büchsenschütz HC, Solymosi D, Dyczmons-Nowaczyk NG, Bauer KKF, Wallner S, Macheroux P, Allahverdiyeva Y, Nowaczyk MM, Kourist R. Engineering of NADPH Supply Boosts Photosynthesis-Driven Biotransformations. ACS Catal 2020; 10:11864-11877. [PMID: 33101760 PMCID: PMC7574619 DOI: 10.1021/acscatal.0c02601] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/04/2020] [Indexed: 02/08/2023]
Abstract
![]()
Light-driven biocatalysis
in recombinant cyanobacteria provides
highly atom-efficient cofactor regeneration via photosynthesis,
thereby remediating constraints associated with sacrificial cosubstrates.
However, despite the remarkable specific activities of photobiocatalysts,
self-shading at moderate-high cell densities limits efficient space-time-yields
of heterologous enzymatic reactions. Moreover, efficient integration
of an artificial electron sink into the tightly regulated network
of cyanobacterial electron pathways can be highly challenging. Here,
we used C=C bond reduction of 2-methylmaleimide by the NADPH-dependent
ene-reductase YqjM as a model reaction for light-dependent biotransformations.
Time-resolved NADPH fluorescence spectroscopy allowed direct monitoring
of in-cell YqjM activity and revealed differences in NADPH steady-state
levels and oxidation kinetics between different genetic constructs.
This effect correlates with specific activities of whole-cells, which
demonstrated conversions of >99%. Further channelling of electrons
toward heterologous YqjM by inactivation of the flavodiiron proteins
(Flv1/Flv3) led to a 2-fold improvement in specific activity at moderate
cell densities, thereby elucidating the possibility of accelerating
light-driven biotransformations by the removal of natural competing
electron sinks. In the best case, an initial product formation rate
of 18.3 mmol h–1 L–1 was reached,
allowing the complete conversion of a 60 mM substrate solution within
4 h.
Collapse
Affiliation(s)
- Leen Assil-Companioni
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
| | - Hanna C. Büchsenschütz
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Dániel Solymosi
- Molecular Plant Biology unit, Department of Biochemistry, Faculty of Science and Engineering, University of Turku, Turku 20014, Finland
| | - Nina G. Dyczmons-Nowaczyk
- Department of Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Kristin K. F. Bauer
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 10, 8010 Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 10, 8010 Graz, Austria
| | - Yagut Allahverdiyeva
- Molecular Plant Biology unit, Department of Biochemistry, Faculty of Science and Engineering, University of Turku, Turku 20014, Finland
| | - Marc M. Nowaczyk
- Department of Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| |
Collapse
|
4
|
Tanaka S, Kojima H, Takeda S, Yamanaka R, Takemura T. Asymmetric visible-light photobiocatalytic reduction of β-keto esters utilizing the cofactor recycling system in Synechocystis sp. PCC 6803. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
5
|
Shanbhag AP. FabG: from a core to circumstantial catalyst. Biotechnol Lett 2019; 41:675-688. [PMID: 31037463 DOI: 10.1007/s10529-019-02678-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/22/2019] [Indexed: 12/30/2022]
Abstract
Core biochemical pathways such as Fatty-acid synthesis II (FAS II) is ascribed to the synthesis of fatty-acids, biotin and lipoic acid in prokaryotes. It has two dehydrogenases namely, FabG and FabI which interact with the fatty-acid chain bound to Acyl-carrier protein (ACP), a well-studied enzyme which binds to substrates of varying lengths. This protein-protein interaction 'broadens' the active site of these dehydrogenases thus, contributing to their flexible nature. This property is exploited for catalysing numerous chiral synthons, alkanes, long-chain alcohols and secondary metabolites in industries especially with FabG. FASI relegates FASII in eukaryotes making it a 'relic gene pool' and an antibacterial drug target with diverse inhibitor and substrate markush. FabG often substitutes other dehydrogenases for producing secondary metabolites in nature. This redundancy is probably due to gene duplication or addition events possibly making FabG, a progenitor to some of the complex short-chain dehydrogenases used in organisms and industries today.
Collapse
Affiliation(s)
- Anirudh P Shanbhag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India. .,Bugworks Research India Pvt. Ltd, C-CAMP, NCBS Campus, UAS-GKVK, Bellary Road, Bangalore, 560065, India.
| |
Collapse
|
6
|
Schmermund L, Jurkaš V, Özgen FF, Barone GD, Büchsenschütz HC, Winkler CK, Schmidt S, Kourist R, Kroutil W. Photo-Biocatalysis: Biotransformations in the Presence of Light. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00656] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Luca Schmermund
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
| | - Valentina Jurkaš
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
| | - F. Feyza Özgen
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Giovanni D. Barone
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Hanna C. Büchsenschütz
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Christoph K. Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
| | - Sandy Schmidt
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
| |
Collapse
|
7
|
Żyszka-Haberecht B, Poliwoda A, Lipok J. 'Structural constraints in cyanobacteria-mediated whole-cell biotransformation of methoxylated and methylated derivatives of 2'-hydroxychalcone. J Biotechnol 2019; 293:36-46. [PMID: 30690100 DOI: 10.1016/j.jbiotec.2019.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/14/2018] [Accepted: 01/03/2019] [Indexed: 11/24/2022]
Abstract
Halophilic and freshwater strains of cyanobacteria representing the Oscillatoriales, Nostocales, Chroococcales, and Synechococcales orders of Cyanophyta were examined to determine (i) the resistance of their cultures when suppressed by the presence of exogenous methoxylated and methylated derivatives of 2'-hydroxychalcone, (ii) morphological changes in cells treated with the tested chalcones and, most importantly, (iii) whether these photoautotrophic microorganisms transform chalcone derivatives in a structure- or strain-dependent manner. The growth of cyanobacterial cultures depended on chalcone derivatives and the strain; nevertheless, trends for correlations between these parameters are difficult to determine. The exposure of cyanobacteria to the tested chalcones revealed severe membrane damage that was consistent with the disruption of membrane integrity. All examined blue-green algae transformed methoxy derivatives of 2'-hydroxychalcone via hydrogenative bio-reduction and formed the corresponding hydroxydihydro derivatives with various efficiencies (≤1 - 70%), depending more on the structure than on the strain. We observed dependency of the routes and efficiency of biohydrogenation of tested chalcones on the location of the methoxyl substituent and, to a lesser extent, on cyanobacterial strains. 2'-hydroxy-4″-methylchalcone was also converted by cyanobacteria to various products, amongst which the most interesting were 2'-ethoxy derivatives. The final products of biocatalytic transformation were extracted from the cyanobacterial media, separated by high performance thin-layer chromatography (HPTLC) and identified by a combination of liquid chromatography-tandem mass spectrometry (LC-MS/MS technique) and one-dimensional (1D 1H and 13C) and two-dimensional (2D HSQC and COSY) nuclear magnetic resonance (NMR) spectroscopy.
Collapse
Affiliation(s)
- Beata Żyszka-Haberecht
- Department of Analytical and Ecological Chemistry, Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland.
| | - Anna Poliwoda
- Department of Analytical and Ecological Chemistry, Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland.
| | - Jacek Lipok
- Department of Analytical and Ecological Chemistry, Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland.
| |
Collapse
|
8
|
Żyszka-Haberecht B, Niemczyk E, Lipok J. Metabolic relation of cyanobacteria to aromatic compounds. Appl Microbiol Biotechnol 2019. [PMID: 30580382 DOI: 10.1007/s0025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Cyanobacteria, also known as blue-green (micro)algae, are able to sustain many types of chemical stress because of metabolic adaptations that allow them to survive and successfully compete in a variety of ecosystems, including polluted ones. As photoautotrophic bacteria, these microorganisms synthesize aromatic amino acids, which are precursors for a large variety of substances that contain aromatic ring(s) and that are naturally formed in the cells of these organisms. Hence, the transformation of aromatic secondary metabolites by cyanobacteria is the result of the possession of a suitable "enzymatic apparatus" to carry out the biosynthesis of these compounds according to cellular requirements. Another crucial aspect that should be evaluated using varied criteria is the response of cyanobacteria to the presence of extracellular aromatic compounds. Some aspects of the relationship between aromatic compounds and cyanobacteria such as the biosynthesis of aromatic compounds, the influence of aromatic compounds on these organisms and the fate of aromatic substances inside microalgal cells are presented in this paper. The search for this information has suggested that there is a lack of knowledge about the regulation of the biosynthesis of aromatic substances and about the transport of these compounds into cyanobacterial cells. These aspects are of pivotal importance with regard to the biotransformation of aromatic compounds and understanding them may be the goals of future research.
Collapse
Affiliation(s)
- Beata Żyszka-Haberecht
- Department of Analytical and Ecological Chemistry, Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Emilia Niemczyk
- Department of Analytical and Ecological Chemistry, Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Jacek Lipok
- Department of Analytical and Ecological Chemistry, Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland.
| |
Collapse
|
9
|
Żyszka-Haberecht B, Niemczyk E, Lipok J. Metabolic relation of cyanobacteria to aromatic compounds. Appl Microbiol Biotechnol 2018; 103:1167-1178. [PMID: 30580382 PMCID: PMC6394484 DOI: 10.1007/s00253-018-9568-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022]
Abstract
Cyanobacteria, also known as blue-green (micro)algae, are able to sustain many types of chemical stress because of metabolic adaptations that allow them to survive and successfully compete in a variety of ecosystems, including polluted ones. As photoautotrophic bacteria, these microorganisms synthesize aromatic amino acids, which are precursors for a large variety of substances that contain aromatic ring(s) and that are naturally formed in the cells of these organisms. Hence, the transformation of aromatic secondary metabolites by cyanobacteria is the result of the possession of a suitable "enzymatic apparatus" to carry out the biosynthesis of these compounds according to cellular requirements. Another crucial aspect that should be evaluated using varied criteria is the response of cyanobacteria to the presence of extracellular aromatic compounds. Some aspects of the relationship between aromatic compounds and cyanobacteria such as the biosynthesis of aromatic compounds, the influence of aromatic compounds on these organisms and the fate of aromatic substances inside microalgal cells are presented in this paper. The search for this information has suggested that there is a lack of knowledge about the regulation of the biosynthesis of aromatic substances and about the transport of these compounds into cyanobacterial cells. These aspects are of pivotal importance with regard to the biotransformation of aromatic compounds and understanding them may be the goals of future research.
Collapse
Affiliation(s)
- Beata Żyszka-Haberecht
- Department of Analytical and Ecological Chemistry, Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Emilia Niemczyk
- Department of Analytical and Ecological Chemistry, Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Jacek Lipok
- Department of Analytical and Ecological Chemistry, Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland.
| |
Collapse
|
10
|
Haq SF, Shanbhag AP, Karthikeyan S, Hassan I, Thanukrishnan K, Ashok A, Sukumaran S, Ramaswamy S, Bharatham N, Datta S, Samant S, Katagihallimath N. A strategy to identify a ketoreductase that preferentially synthesizes pharmaceutically relevant (S)-alcohols using whole-cell biotransformation. Microb Cell Fact 2018; 17:192. [PMID: 30509260 PMCID: PMC6276252 DOI: 10.1186/s12934-018-1036-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/21/2018] [Indexed: 01/10/2023] Open
Abstract
Introduction Chemical industries are constantly in search of an expeditious and environmentally benign method for producing chiral synthons. Ketoreductases have been used as catalysts for enantioselective conversion of desired prochiral ketones to their corresponding alcohol. We chose reported promiscuous ketoreductases belonging to different protein families and expressed them in E. coli to evaluate their ability as whole-cell catalysts for obtaining chiral alcohol intermediates of pharmaceutical importance. Apart from establishing a method to produce high value (S)-specific alcohols that have not been evaluated before, we propose an in silico analysis procedure to predict product chirality. Results Six enzymes originating from Sulfolobus sulfotaricus, Zygosaccharomyces rouxii, Hansenula polymorpha, Corynebacterium sp. ST-10, Synechococcus sp. PCC 7942 and Bacillus sp. ECU0013 with reported efficient activity for dissimilar substrates are compared here to arrive at an optimal enzyme for the method. Whole–cell catalysis of ketone intermediates for drugs like Aprepitant, Sitagliptin and Dolastatin using E. coli over-expressing these enzymes yielded (S)-specific chiral alcohols. We explain this chiral specificity for the best-performing enzyme, i.e., Z. rouxii ketoreductase using in silico modelling and MD simulations. This rationale was applied to five additional ketones that are used in the synthesis of Crizotinib, MA-20565 (an antifungal agent), Sulopenem, Rivastigmine, Talampanel and Barnidipine and predicted the yield of (S) enantiomers. Experimental evaluation matched the in silico analysis wherein ~ 95% (S)-specific alcohol with a chemical yield of 23–79% was obtained through biotransformation. Further, the cofactor re-cycling was optimized by switching the carbon source from glucose to sorbitol that improved the chemical yield to 85–99%. Conclusions Here, we present a strategy to synthesize pharmaceutically relevant chiral alcohols by ketoreductases using a cofactor balanced whole-cell catalysis scheme that is useful for the industry. Based on the results obtained in these trials, Zygosaccharomyces rouxii ketoreductase was identified as a proficient enzyme to obtain (S)-specific alcohols from their respective ketones. The whole–cell catalyst when combined with nutrient modulation of using sorbitol as a carbon source helped obtain high enantiomeric and chemical yield. Electronic supplementary material The online version of this article (10.1186/s12934-018-1036-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Anirudh P Shanbhag
- Bugworks Research India, Pvt. Ltd, Bengaluru, India.,Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Subbulakshmi Karthikeyan
- Anthem Biosciences Pvt. Ltd, Bengaluru, India.,Centre for Pharmaceutical Biotechnology, University of Illinois Chicago, Chicago, USA
| | - Imran Hassan
- Anthem Biosciences Pvt. Ltd, Bengaluru, India.,PerkinElmer, Bengaluru, India
| | - Kannan Thanukrishnan
- Anthem Biosciences Pvt. Ltd, Bengaluru, India.,Shasun Research Center, Chennai, India
| | | | | | - S Ramaswamy
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru, India
| | | | | | | | | |
Collapse
|
11
|
Enzymatic Oxyfunctionalization Driven by Photosynthetic Water-Splitting in the Cyanobacterium Synechocystis sp. PCC 6803. Catalysts 2017. [DOI: 10.3390/catal7080240] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
|
12
|
Schmideder A, Schottroff F, Klermund L, Castiglione K, Weuster-Botz D. Studies on the enzymatic synthesis of N-acetylneuraminic acid with continuously operated enzyme membrane reactors on a milliliter scale. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
13
|
Delineating Substrate Diversity of Disparate Short-Chain Dehydrogenase Reductase from Debaryomyces hansenii. PLoS One 2017; 12:e0170202. [PMID: 28107498 PMCID: PMC5249140 DOI: 10.1371/journal.pone.0170202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 12/30/2016] [Indexed: 11/19/2022] Open
Abstract
Short-chain dehydrogenase reductases (SDRs) have been utilized for catalyzing the reduction of many aromatic/aliphatic prochiral ketones to their respective alcohols. However, there is a paucity of data that elucidates their innate biological role and diverse substrate space. In this study, we executed an in-depth biochemical characterization and substrate space mapping (with 278 prochiral ketones) of an unannotated SDR (DHK) from Debaryomyces hansenii and compared it with structurally and functionally characterized SDR Synechococcus elongatus. PCC 7942 FabG to delineate its industrial significance. It was observed that DHK was significantly more efficient than FabG, reducing a diverse set of ketones albeit at higher conversion rates. Comparison of the FabG structure with a homology model of DHK and a docking of substrate to both structures revealed the presence of additional flexible loops near the substrate binding site of DHK. The comparative elasticity of the cofactor and substrate binding site of FabG and DHK was experimentally substantiated using differential scanning fluorimetry. It is postulated that the loop flexibility may account for the superior catalytic efficiency of DHK although the positioning of the catalytic triad is conserved.
Collapse
|
14
|
Wang D, Yang Z, Zhang J, Han Y, Hao J, He L. The Asymmetric Reduction of Acetophenone and Its Derivatives to (S)-Aromatic Secondary Alcohols by Rhodotorula mucilaginosa CCTCC M2014255 Resting Cells. Catal Letters 2016. [DOI: 10.1007/s10562-016-1730-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
15
|
Asymmetric synthesis of lipitor chiral intermediate using a robust carbonyl reductase at high substrate to catalyst ratio. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
16
|
Klermund L, Riederer A, Groher A, Castiglione K. High-level soluble expression of a bacterial N-acyl-d-glucosamine 2-epimerase in recombinant Escherichia coli. Protein Expr Purif 2015; 111:36-41. [PMID: 25804337 DOI: 10.1016/j.pep.2015.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 01/13/2023]
Abstract
N-Acyl-d-glucosamine 2-epimerase (AGE) is an important enzyme for the biocatalytic synthesis of N-acetylneuraminic acid (Neu5Ac). Due to the wide range of biological applications of Neu5Ac and its derivatives, there has been great interest in its large-scale synthesis. Thus, suitable strategies for achieving high-level production of soluble AGE are needed. Several AGEs from various organisms have been recombinantly expressed in Escherichia coli. However, the soluble expression level was consistently low with an excessive formation of inclusion bodies. In this study, the effects of different solubility-enhancement tags, expression temperatures, chaperones and host strains on the soluble expression of the AGE from the freshwater cyanobacterium Anabaena variabilis ATCC 29413 (AvaAGE) were examined. The optimum combination of tag, expression temperature, co-expression of chaperones and host strain (His6-tag, 37°C, GroEL/GroES, E. coli BL21(DE3)) led to a 264-fold improvement of the volumetric epimerase activity, a measure of the soluble expression, compared to the starting conditions (His6-maltose-binding protein-tag, 20°C, without chaperones, E. coli BL21(DE3)). A maximum yield of 22.5mg isolated AvaAGE per liter shake flask culture was obtained.
Collapse
Affiliation(s)
- Ludwig Klermund
- Institute of Biochemical Engineering, Technische Universität München, Boltzmannstr. 15, 85748 Garching, Germany.
| | - Amelie Riederer
- Institute of Biochemical Engineering, Technische Universität München, Boltzmannstr. 15, 85748 Garching, Germany.
| | - Anna Groher
- Institute of Biochemical Engineering, Technische Universität München, Boltzmannstr. 15, 85748 Garching, Germany.
| | - Kathrin Castiglione
- Institute of Biochemical Engineering, Technische Universität München, Boltzmannstr. 15, 85748 Garching, Germany.
| |
Collapse
|
17
|
Yamanaka R, Nakamura K, Murakami M, Murakami A. Selective synthesis of cinnamyl alcohol by cyanobacterial photobiocatalysts. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.01.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
18
|
Chen R, Liu X, Wang J, Lin J, Wei D. Cloning, expression, and characterization of an anti-Prelog stereospecific carbonyl reductase from Gluconobacter oxydans DSM2343. Enzyme Microb Technol 2014; 70:18-27. [PMID: 25659628 DOI: 10.1016/j.enzmictec.2014.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
A new anti-Prelog stereospecific carbonyl reductase (GoKR) from Gluconobacter oxydans DSM2343 was cloned and identified in Escherichia coli. This GoKR formed a homo-tetramer with a subunit size of approximately 27.0kDa. GoKR exhibited full activity with NADPH but not with NADH as a cofactor. The optimal pH and temperature were 9.0 and 30°C, respectively. GoKR reduced various ketones, including aliphatic and aromatic ketones, α- and β-keto esters. Aromatic ketones were reduced to (R)-enantiomers, whereas keto esters were reduced to (S)-hydroxy esters with different enantioselectivities. The data indicate that GoKR does not obey Prelog's rule and exhibits anti-Prelog enantiopreference. Enzyme-substrate-cofactor docking analysis showed that hydride transfer occurred at the si faces of carbonyl group for ethyl 4-chloro-3-oxobutanoate (COBE), which was then selectively reduced to the chiral (S)-alcohol. Excellent enantioselectivities were obtained for reducing COBE and ethyl 2-oxo-4-phenylbutyrate into the corresponding (S)-type products. These products are important for synthesizing HMG-CoA reductase (statins) and angiotensin-converting enzyme inhibitors, respectively.
Collapse
Affiliation(s)
- Rong Chen
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China; Center for Biomedicine and Health, Division of Basical Medicine, Hangzhou Normal University, Hangzhou 310012, China
| | - Xu Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jiale Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jinping Lin
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| |
Collapse
|
19
|
Sührer I, Haslbeck M, Castiglione K. Asymmetric synthesis of a fluoxetine precursor with an artificial fusion protein of a ketoreductase and a formate dehydrogenase. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
20
|
Chen R, Liu X, Lin J, Wei D. A genomic search approach to identify carbonyl reductases in Gluconobacter oxydans for enantioselective reduction of ketones. Biosci Biotechnol Biochem 2014; 78:1350-6. [DOI: 10.1080/09168451.2014.925775] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
The versatile carbonyl reductases from Gluconobacter oxydans in the enantioselective reduction of ketones to the corresponding alcohols were exploited by genome search approach. All purified enzymes showed activities toward the tested ketoesters with different activities. In the reduction of 4-phenyl-2-butanone with in situ NAD(P)H regeneration system, (S)-alcohol was obtained with an e.e. of up to 100% catalyzed by Gox0644. Under the same experimental condition, all enzymes catalyzed ethyl 4-chloroacetoacetate to give chiral products with an excellent e.e. of up to 99%, except Gox0644. Gox2036 had a strict requirement for NADH as the cofactor and showed excellent enantiospecificity in the synthesis of ethyl (R)-4-chloro-3-hydroxybutanoate. For the reduction of ethyl 2-oxo-4-phenylbutyrate, excellent e.e. (>99%) and high conversion (93.1%) were obtained by Gox0525, whereas the other enzymes showed relatively lower e.e. and conversions. Among them, Gox2036 and Gox0525 showed potentials in the synthesis of chiral alcohols as useful biocatalysts.
Collapse
Affiliation(s)
- Rong Chen
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
- Center for Biomedicine and Health, Division of Basical Medicine, Hangzhou Normal University; Hangzhou, China
| | - Xu Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jinping Lin
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, China
| |
Collapse
|
21
|
|
22
|
Yamanaka R, Nakamura K, Murakami A. Reduction of exogenous ketones depends upon NADPH generated photosynthetically in cells of the cyanobacterium Synechococcus PCC 7942. AMB Express 2011; 1:24. [PMID: 21906270 PMCID: PMC3222321 DOI: 10.1186/2191-0855-1-24] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 09/01/2011] [Indexed: 11/10/2022] Open
Abstract
Effective utilization of photosynthetic microorganisms as potential biocatalysts is favorable for the production of useful biomaterials and the reduction of atmospheric CO2. For example, biocatalytic transformations are used in the synthesis of optically active alcohols. We previously found that ketone reduction in cells of the cyanobacterium Synechococcus PCC 7942 is highly enantioselective and remarkably enhanced under light illumination. In this study, the mechanism of light-enhanced ketone reduction was investigated in detail using several inhibitors of photosynthetic electron transport and of enzymes of the Calvin cycle. It is demonstrated that light intensity and photosynthesis inhibitors significantly affect the ketone reduction activity in Synechococcus. This indicates that the reduction correlates well with photosynthetic activity. Moreover, ketone reduction in Synechococcus specifically depends upon NADPH and not NADH. These results also suggest that cyanobacteria have the potential to be utilized as biocatalytic systems for direct usage of light energy in various applications such as syntheses of useful compounds and remediation of environmental pollutants.
Collapse
|
23
|
Wang LJ, Li CX, Ni Y, Zhang J, Liu X, Xu JH. Highly efficient synthesis of chiral alcohols with a novel NADH-dependent reductase from Streptomyces coelicolor. BIORESOURCE TECHNOLOGY 2011; 102:7023-7028. [PMID: 21570826 DOI: 10.1016/j.biortech.2011.04.046] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/10/2011] [Accepted: 04/15/2011] [Indexed: 05/30/2023]
Abstract
An NADH-dependent reductase (ScCR) from Streptomyces coelicolor was discovered by genome mining for carbonyl reductases. ScCR was overexpressed in Escherichia coli BL21, purified to homogeneity and its catalytic properties were studied. This enzyme catalyzed the asymmetric reduction of a broad range of prochiral ketones including aryl ketones, α- and β-ketoesters, with high activity and excellent enantioselectivity (>99% ee) towards β-ketoesters. Among them, ethyl 4-chloro-3-oxobutanoate (COBE) was efficiently converted to ethyl (S)-4-chloro-3-hydroxybutanoate ((S)-CHBE), an important pharmaceutical intermediate, in water/toluene biphasic system. As much as 600 g/L (3.6M) of COBE was asymmetrically reduced within 22 h using 2-propanol as a co-substrate for NADH regeneration, resulting in a yield of 93%, an enantioselectivity of >99% ee, and a total turnover number (TTN) of 12,100. These results indicate the potential of ScCR for the industrial production of valuable chiral alcohols.
Collapse
Affiliation(s)
- Li-Juan Wang
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | | | | | | | | | | |
Collapse
|
24
|
Kinetic mechanism of 3-ketoacyl-(acyl-carrier-protein) reductase from Synechococcus sp. strain PCC 7942: A useful enzyme for the production of chiral alcohols. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2010.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
25
|
A novel L-isoleucine metabolism in Bacillus thuringiensis generating (2S,3R,4S)-4-hydroxyisoleucine, a potential insulinotropic and anti-obesity amino acid. Appl Microbiol Biotechnol 2010; 89:1929-38. [PMID: 21069315 DOI: 10.1007/s00253-010-2983-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 10/19/2010] [Accepted: 10/24/2010] [Indexed: 12/12/2022]
Abstract
4-Hydroxyisoleucine (HIL) found in fenugreek seeds has insulinotropic and anti-obesity effects and is expected to be a novel orally active drug for insulin-independent diabetes. Here, we show that the newly isolated strain Bacillus thuringiensis 2e2 and the closely related strain B. thuringiensis ATCC 35646 operate a novel metabolic pathway for L-isoleucine (L-Ile) via HIL and 2-amino-3-methyl-4-ketopentanoic acid (AMKP). The HIL synthesis was catalyzed stereoselectively by an α-ketoglutaric acid-dependent dioxygenase and to be useful for efficient production of a naturally occurring HIL isomer, (2S,3R,4S)-HIL. The (2S,3R,4S)-HIL was oxidized to (2S,3R)-AMKP by a NAD(+)-dependent dehydrogenase. The metabolic pathway functions as an effective bypass pathway that compensates for the incomplete tricarboxylic acid (TCA) cycle in Bacillus species and also explains how AMKP, a vitamin B(12) antimetabolite with antibiotic activity, is synthesized. These novel findings pave a new way for the commercial production of HIL and also for AMKP.
Collapse
|
26
|
|
27
|
Enantioselective reduction of prochiral ketones by engineered bifunctional fusion proteins. Biotechnol Appl Biochem 2010; 56:131-40. [PMID: 20590527 DOI: 10.1042/ba20100143] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
NADPH-dependent oxidoreductases are useful catalysts for the production of chiral synthons. However, preparative applications of oxidoreductases require efficient methods for in situ regeneration of the expensive nicotinamide cofactors. An advantageous method for cofactor regeneration is the construction of bifunctional fusion proteins composed of two enzymes, one catalysing the reduction reaction and the other one mediating the recycling of cofactors. Herein, we describe the in-frame fusion between an NADP+-accepting mutant of FDH (formate dehydrogenase) from Mycobacterium vaccae N10 and KR [3-ketoacyl-(acyl-carrier-protein) reductase] from Synechococcus sp. strain PCC 7942. The generation of linker insertion mutants led to a fusion protein exhibiting 100 and 80% of the enzymatic activities of native KR and FDH respectively. Escherichia coli cells expressing the fusion protein showed an approx. 2-fold higher initial reaction rate in the production of chiral alcohols than cells expressing the enzymes separately. The application of the engineered fusion protein in whole-cell bioreduction of pentafluoroacetophenone resulted in a substrate conversion of 99.97% with an excellent enantiomeric excess of 99.9% (S)-1-(pentafluorophenyl)ethanol.
Collapse
|
28
|
Bräutigam S, Dennewald D, Schürmann M, Lutje-Spelberg J, Pitner WR, Weuster-Botz D. Whole-cell biocatalysis: Evaluation of new hydrophobic ionic liquids for efficient asymmetric reduction of prochiral ketones. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2009.06.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
29
|
Gadler P, Reiter TC, Hoelsch K, Weuster-Botz D, Faber K. Enantiocomplementary inverting sec-alkylsulfatase activity in cyano- and thio-bacteria Synechococcus and Paracoccus spp.: selectivity enhancement by medium engineering. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|