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Ma D, Cheng Z, Han L, Guo J, Peplowski L, Zhou Z. Structure-oriented engineering of nitrile hydratase: Reshaping of substrate access tunnel and binding pocket for efficient synthesis of cinnamamide. Int J Biol Macromol 2024; 254:127800. [PMID: 37918589 DOI: 10.1016/j.ijbiomac.2023.127800] [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: 08/30/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 11/04/2023]
Abstract
Cinnamamide and its derivatives are the most common and important building blocks widely present in natural products. Currently, nitrile hydratase (NHase, EC 4.2.1.84) has been widely used in large-scale industrial production of nicotinamide and acrylamide, while its catalytic activity is extremely low or inactive for bulky nitrile substrates such as cinnamonitrile. Therefore, beneficial variant βF37P/L48P/F51N were obtained from PtNHase of Pseudonocardia thermophila JCM3095 by reshaping of substrate access tunnel and binding pocket, which exhibited 14.88-fold improved catalytic efficiency compared to the wild-type PtNHase. Structure analysis, molecular dynamics simulations and dynamical cross-correlation matrix (DCCM) analysis revealed that the introduced mutations enlarged the substrate access tunnel and binding pocket, enhanced overall anti-correlated movements of enzymes, which would promote product release during the dynamic process of catalysis. In a hydration process, the complete conversion of 5 mM cinnamonitrile was achieved by βF37P/L48P/F51N in a 50 mL reaction, with cinnamamide yield of almost 100 % and productivity of 0.736 g L-1 h-1. The study demonstrates the co-evolution of substrate access tunnel and binding pocket is an effective strategy, and provides a valuable reference for future research. Furthermore, NHases have huge potential for catalyzing bulky nitriles to form corresponding amides in large-scale industrial production.
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Affiliation(s)
- Dong Ma
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Junling Guo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland.
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China; Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao, Jiangsu, China.
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Nasir A, Ashok S, Shim JY, Park S, Yoo TH. Recent Progress in the Understanding and Engineering of Coenzyme B 12-Dependent Glycerol Dehydratase. Front Bioeng Biotechnol 2020; 8:500867. [PMID: 33224925 PMCID: PMC7674605 DOI: 10.3389/fbioe.2020.500867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 09/17/2020] [Indexed: 01/21/2023] Open
Abstract
Coenzyme B12-dependent glycerol dehydratase (GDHt) catalyzes the dehydration reaction of glycerol in the presence of adenosylcobalamin to yield 3-hydroxypropanal (3-HPA), which can be converted biologically to versatile platform chemicals such as 1,3-propanediol and 3-hydroxypropionic acid. Owing to the increased demand for biofuels, developing biological processes based on glycerol, which is a byproduct of biodiesel production, has attracted considerable attention recently. In this review, we will provide updates on the current understanding of the catalytic mechanism and structure of coenzyme B12-dependent GDHt, and then summarize the results of engineering attempts, with perspectives on future directions in its engineering.
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Affiliation(s)
- Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | | | - Jeung Yeop Shim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
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Fu B, Balskus EP. Discovery of CC bond-forming and bond-breaking radical enzymes: enabling transformations for metabolic engineering. Curr Opin Biotechnol 2020; 65:94-101. [PMID: 32171888 PMCID: PMC7670169 DOI: 10.1016/j.copbio.2020.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 11/23/2022]
Abstract
Radical enzymes catalyze difficult C—C bond-forming and bond-breaking transformations. Radical enzymes catalyzing unprecedented reactions continue to be discovered. The products of radical enzymes are often of high value. Understanding mechanisms of radical enzymes will aid metabolic engineering efforts.
Radical enzymes catalyze some of the most chemically challenging C—C bond-forming and bond-breaking reactions. Advances in DNA sequencing have accelerated the discovery of radical enzymes from microbes, including radical S-adenosylmethionine (rSAM) enzymes, glycyl radical enzymes (GREs), and diiron enzymes. These enzymes catalyze various reactions that yield products of industrial relevance (e.g. aromatics, hydrocarbons, and natural product derivatives), making their incorporation into engineered metabolic pathways enticing. Elucidating the mechanisms of radical enzymes that cleave and construct C—C bonds will enable further enzyme discovery and engineering efforts.
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Affiliation(s)
- Beverly Fu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA 02138, United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA 02138, United States.
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Mar MJ, Andersen JM, Kandasamy V, Liu J, Solem C, Jensen PR. Synergy at work: linking the metabolism of two lactic acid bacteria to achieve superior production of 2-butanol. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:45. [PMID: 32180827 PMCID: PMC7065357 DOI: 10.1186/s13068-020-01689-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND The secondary alcohol 2-butanol has many important applications, e.g., as a solvent. Industrially, it is usually made by sulfuric acid-catalyzed hydration of butenes. Microbial production of 2-butanol has also been attempted, however, with little success as witnessed by the low titers and yields reported. Two important reasons for this, are the growth-hampering effect of 2-butanol on microorganisms, and challenges associated with one of the key enzymes involved in its production, namely diol dehydratase. RESULTS We attempt to link the metabolism of an engineered Lactococcus lactis strain, which possesses all enzyme activities required for fermentative production of 2-butanol from glucose, except for diol dehydratase, which acts on meso-2,3-butanediol (mBDO), with that of a Lactobacillus brevis strain which expresses a functional dehydratase natively. We demonstrate growth-coupled production of 2-butanol by the engineered L. lactis strain, when co-cultured with L. brevis. After fine-tuning the co-culture setup, a titer of 80 mM (5.9 g/L) 2-butanol, with a high yield of 0.58 mol/mol is achieved. CONCLUSIONS Here, we demonstrate that it is possible to link the metabolism of two bacteria to achieve redox-balanced production of 2-butanol. Using a simple co-cultivation setup, we achieved the highest titer and yield from glucose in a single fermentation step ever reported. The data highlight the potential that lies in harnessing microbial synergies for producing valuable compounds.
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Affiliation(s)
- Mette J. Mar
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Joakim M. Andersen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Vijayalakshmi Kandasamy
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Jianming Liu
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Peter R. Jensen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
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Unbiased libraries in protein directed evolution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140321. [DOI: 10.1016/j.bbapap.2019.140321] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/03/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022]
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Costa Brandão Cruz D, Lima Santana L, Siqueira Guedes A, Teodoro de Souza J, Arthur Santos Marbach P. Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes. Genome Biol Evol 2019; 11:1235-1249. [PMID: 30785193 PMCID: PMC6486802 DOI: 10.1093/gbe/evz035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2019] [Indexed: 01/27/2023] Open
Abstract
The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs. Based on the results, we propose that the gene purO was present in the common ancestor of all living beings, whereas the gene encoding PurP emerged after the divergence of Archaea and Bacteria and their isoforms originated in duplication events in the common ancestor of phyla Crenarchaeota and Euryarchaeota. The results reported here expand our understanding of the diversity and evolution of the last two steps of the purine biosynthetic pathway in prokaryotes.
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Affiliation(s)
| | - Lenon Lima Santana
- CCAAB, Biological Sciences, Recôncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil
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Murugayah SA, Warring SL, Gerth ML. Optimisation of a high-throughput fluorescamine assay for detection of N-acyl-l-homoserine lactone acylase activity. Anal Biochem 2018; 566:10-12. [PMID: 30391461 DOI: 10.1016/j.ab.2018.10.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 10/17/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022]
Abstract
N-acyl-l-homoserine lactone (AHL) acylases are a well-known group of enzymes that disrupt quorum sensing in Gram-negative bacteria by degrading AHL signalling molecules. This degradation of signalling molecules (termed 'quorum quenching') has potential uses in the prevention or reduction of biofilm formation and/or bacterial infections. Therefore, there is a great deal of interest in the identification and characterisation of quorum quenching enzymes. Here, we present an optimised fluorescamine-based assay for the detection of AHL acylase activity and demonstrate it can be used in a high-throughput screening format.
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Affiliation(s)
- Shereen A Murugayah
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand
| | - Suzanne L Warring
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Monica L Gerth
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand.
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Liang B, Huang X, Teng Y, Liang Y, Yang Y, Zheng L, Lu X. Enhanced Single-Step Bioproduction of the Simvastatin Precursor Monacolin J in an Industrial Strain ofAspergillus terreusby Employing the Evolved Lovastatin Hydrolase. Biotechnol J 2018; 13:e1800094. [DOI: 10.1002/biot.201800094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/03/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Bo Liang
- Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266101 China
| | - Yun Teng
- Zhejiang Key Laboratory of Antifungal Drugs; Zhejiang Hisun Pharmaceutical Co., Ltd.; Taizhou 318000 China
| | - Yajing Liang
- Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266101 China
- Key Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266101 China
| | - Yong Yang
- Zhejiang Key Laboratory of Antifungal Drugs; Zhejiang Hisun Pharmaceutical Co., Ltd.; Taizhou 318000 China
| | - Linghui Zheng
- Zhejiang Key Laboratory of Antifungal Drugs; Zhejiang Hisun Pharmaceutical Co., Ltd.; Taizhou 318000 China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266101 China
- Key Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266101 China
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