1
|
Ducrot L, López IL, Orrego AH, López-Gallego F. Coenzyme A Thioester Intermediates as Platform Molecules in Cell-Free Chemical Biomanufacturing. Chembiochem 2024; 25:e202300673. [PMID: 37994376 DOI: 10.1002/cbic.202300673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/06/2023] [Indexed: 11/24/2023]
Abstract
The in vitro synthesis of Coenzyme A (CoA)-thioester intermediates opens new avenues to transform simple molecules into more complex and multifunctional ones by assembling cell-free biosynthetic cascades. In this review, we have systematically cataloged known CoA-dependent enzyme reactions that have been successfully implemented in vitro. To faciliate their identification, we provide their UniProt ID when available. Based on this catalog, we have organized enzymes into three modules: activation, modification, and removal. i) The activation module includes enzymes capable of fusing CoA with organic molecules. ii) The modification module includes enzymes capable of catalyzing chemical modifications in the structure of acyl-CoA intermediates. And iii) the removal module includes enzymes able to remove the CoA and release an organic molecule different from the one activated in the upstream. Based on these reactions, we constructed a reaction network that summarizes the most relevant CoA-dependent biosynthetic pathways reported until today. From the information available in the articles, we have plotted the total turnover number of CoA as a function of the product titer, observing a positive correlation between both parameters. Therefore, the success of a CoA-dependent in vitro pathway depends on its ability to regenerate CoA, but also to regenerate other cofactors such as NAD(P)H and ATP.
Collapse
Affiliation(s)
- Laurine Ducrot
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Idania L López
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Alejandro H Orrego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
| |
Collapse
|
2
|
Platero-Rochart D, Krivobokova T, Gastegger M, Reibnegger G, Sánchez-Murcia PA. Prediction of Enzyme Catalysis by Computing Reaction Energy Barriers via Steered QM/MM Molecular Dynamics Simulations and Machine Learning. J Chem Inf Model 2023; 63:4623-4632. [PMID: 37479222 PMCID: PMC10430765 DOI: 10.1021/acs.jcim.3c00772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Indexed: 07/23/2023]
Abstract
The prediction of enzyme activity is one of the main challenges in catalysis. With computer-aided methods, it is possible to simulate the reaction mechanism at the atomic level. However, these methods are usually expensive if they are to be used on a large scale, as they are needed for protein engineering campaigns. To alleviate this situation, machine learning methods can help in the generation of predictive-decision models. Herein, we test different regression algorithms for the prediction of the reaction energy barrier of the rate-limiting step of the hydrolysis of mono-(2-hydroxyethyl)terephthalic acid by the MHETase ofIdeonella sakaiensis. As a training data set, we use steered quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation snapshots and their corresponding pulling work values. We have explored three algorithms together with three chemical representations. As an outcome, our trained models are able to predict pulling works along the steered QM/MM MD simulations with a mean absolute error below 3 kcal mol-1 and a score value above 0.90. More challenging is the prediction of the energy maximum with a single geometry. Whereas the use of the initial snapshot of the QM/MM MD trajectory as input geometry yields a very poor prediction of the reaction energy barrier, the use of an intermediate snapshot of the former trajectory brings the score value above 0.40 with a low mean absolute error (ca. 3 kcal mol-1). Altogether, we have faced in this work some initial challenges of the final goal of getting an efficient workflow for the semiautomatic prediction of enzyme-catalyzed energy barriers and catalytic efficiencies.
Collapse
Affiliation(s)
- Daniel Platero-Rochart
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
| | - Tatyana Krivobokova
- Department
of Statistics and Operations Research, University
of Vienna, Oskar-Morgenstern-Platz 1, A-1090 Vienna, Austria
| | - Michael Gastegger
- Institute
of Software Engineering and Theoretical Computer Science, Machine
Learning Group, Technische Universität, 10587 Berlin, Germany
| | - Gilbert Reibnegger
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
| | - Pedro A. Sánchez-Murcia
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
| |
Collapse
|
3
|
Orrego AH, Rubanu MG, López IL, Andrés-Sanz D, García-Marquina G, Pieslinger GE, Salassa L, López-Gallego F. ATP-Independent and Cell-Free Biosynthesis of β-Hydroxy Acids Using Vinyl Esters as Smart Substrates. Angew Chem Int Ed Engl 2023; 62:e202218312. [PMID: 36718873 DOI: 10.1002/anie.202218312] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/01/2023]
Abstract
In vitro biosynthetic pathways that condense and reduce molecules through coenzyme A (CoASH) activation demand energy and redox power in the form of ATP and NAD(P)H, respectively. These coenzymes must be orthogonally recycled by ancillary reactions that consume chemicals, electricity, or light, impacting the atom economy and/or the energy consumption of the biosystem. In this work, we have exploited vinyl esters as dual acyl and electron donor substrates to synthesize β-hydroxy acids through a non-decarboxylating Claisen condensation, reduction and hydrolysis stepwise cascade, including a NADH recycling step, catalyzed by a total of 4 enzymes. Herein, the chemical energy to activate the acyl group with CoASH and the redox power for the reduction are embedded into the vinyl esters. Upon optimization, this self-sustaining cascade reached a titer of (S)-3-hydroxy butyrate of 24 mM without requiring ATP and simultaneously recycling CoASH and NADH. This work illustrates the potential of in vitro biocatalysis to transform simple molecules into multi-functional ones.
Collapse
Affiliation(s)
- Alejandro H Orrego
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain
| | - Maria Grazia Rubanu
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain
| | - Idania L López
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain
| | - Daniel Andrés-Sanz
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain
| | - Guillermo García-Marquina
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain
| | - German E Pieslinger
- CONICET-Universidad de Buenos Aires. Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Buenos Aires, Argentina.,Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018, Donostia, Spain
| | - Luca Salassa
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018, Donostia, Spain.,Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Paseo Manuel de Lardizabal 3, 20018, Donostia, Spain.,Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 5., 48009, . Bilbao, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 5., 48009, . Bilbao, Spain
| |
Collapse
|
4
|
Bannister KR, Prather KL. Engineering polyester monomer diversity through novel pathway design. Curr Opin Biotechnol 2023; 79:102852. [PMID: 36481340 DOI: 10.1016/j.copbio.2022.102852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022]
Abstract
Polyesters composed of hydroxy acids (HAs) and diols serve many material niches and are invaluable to our daily lives. However, their traditional synthesis from petrochemicals creates many environmental concerns. Metabolically engineered microorganisms have been leveraged for the industrially competitive production of a few polyesters with properties that limit their application. Designing new metabolic pathways to polyester building blocks is essential to broadening material property diversity and improving carbon and energy usage of current bioproduction schemes. This review focuses on recently developed pathways to HAs and diols. Specifically, new pathways to 2,3- and ω-Hydroxy acids, as well as C3-C4 and medium-chain-length diols, are discussed. Pathways to the same compound are compared on the basis of criteria such as energy usage, number of pathway steps, and titer. Finally, suggestions for improvements and next steps for each pathway are also discussed.
Collapse
Affiliation(s)
- K'yal R Bannister
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kristala Lj Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
5
|
Liu L, Zhou S, Deng Y. The 3-ketoacyl-CoA thiolase: an engineered enzyme for carbon chain elongation of chemical compounds. Appl Microbiol Biotechnol 2020; 104:8117-8129. [PMID: 32830293 DOI: 10.1007/s00253-020-10848-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 01/03/2023]
Abstract
Because of their function of catalyzing the rearrangement of the carbon chains, thiolases have attracted increasing attentions over the past decades. The 3-ketoacyl-CoA thiolase (KAT) is a member of the thiolase, which is capable of catalyzing the Claisen condensation reaction between the two acyl-CoAs, thereby achieving carbon chain elongation. In this way, diverse value-added compounds might be synthesized starting from simple small CoA thioesters. However, most KATs are hampered by low stability and poor substrate specificity, which has hindered the development of large-scale biosynthesis. In this review, the common characteristics in the three-dimensional structure of KATs from different sources are summarized. Moreover, structure-guided rational engineering is discussed as a strategy for enhancing the performance of KATs. Finally, we reviewed the metabolic engineering applications of KATs for producing various energy-storage molecules, such as n-butanol, fatty acids, dicarboxylic acids, and polyhydroxyalkanoates. KEY POINTS: • Summarize the structural characteristics and catalyzation mechanisms of KATs. • Review on the rational engineering to enhance the performance of KATs. • Discuss the applications of KATs for producing energy-storage molecules.
Collapse
Affiliation(s)
- Lixia Liu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.
| |
Collapse
|
6
|
Zhou S, Hao T, Xu S, Deng Y. Coenzyme A thioester-mediated carbon chain elongation as a paintbrush to draw colorful chemical compounds. Biotechnol Adv 2020; 43:107575. [PMID: 32512221 DOI: 10.1016/j.biotechadv.2020.107575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
The biosynthesis of various useful chemicals from simple substrates using industrial microorganisms is becoming increasingly crucial to address the challenge of dwindling non-renewable resources. As the most common intermediate substrates in organisms, Coenzyme A (CoA) thioesters play a central role in the carbon chain elongation process of their products. As a result, numerous of chemicals can be synthesized by the iterative addition of various CoA thioester extender units at a given CoA thioester primer backbone. However, these elongation reactions and the product yields are still restricted due to the low enzymatic performance and supply of CoA thioesters. This review highlights the current protein and metabolic engineering strategies used to enhance the diversity and product yield by coupling different primers, extender units, enzymes, and termination pathways, in an attempt to provide a road map for producing a more diverse range of industrial chemicals.
Collapse
Affiliation(s)
- Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Tingting Hao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shumin Xu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
7
|
Valencia LE, Zhang Z, Cepeda AJ, Keatinge-Clay AT. Seven-enzyme in vitro cascade to (3R)-3-hydroxybutyryl-CoA. Org Biomol Chem 2019; 17:1375-1378. [PMID: 30652175 DOI: 10.1039/c8ob02858c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Economical and environmentally-friendly routes to convert feedstock chemicals like acetate into valuable chiral products such as (R)-3-hydroxybutyrate are in demand. Here, seven enzymes (CoaA, CoaD, CoaE, ACS, BktB, PhaB, and GDH) are employed in a one-pot, in vitro, biocatalytic synthesis of (3R)-3-hydroxybutyryl-CoA, which was readily isolated. This platform generates not only chiral diketide building blocks but also desirable CoA derivatives.
Collapse
Affiliation(s)
- Luis E Valencia
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | | | | | | |
Collapse
|
8
|
Bonk BM, Tarasova Y, Hicks MA, Tidor B, Prather KL. Rational design of thiolase substrate specificity for metabolic engineering applications. Biotechnol Bioeng 2018; 115:2167-2182. [PMID: 29877597 PMCID: PMC6131064 DOI: 10.1002/bit.26737] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/14/2018] [Accepted: 05/31/2018] [Indexed: 12/29/2022]
Abstract
Metabolic engineering efforts require enzymes that are both highly active and specific toward the synthesis of a desired output product to be commercially feasible. The 3-hydroxyacid (3HA) pathway, also known as the reverse β-oxidation or coenzyme-A-dependent chain-elongation pathway, can allow for the synthesis of dozens of useful compounds of various chain lengths and functionalities. However, this pathway suffers from byproduct formation, which lowers the yields of the desired longer chain products, as well as increases downstream separation costs. The thiolase enzyme catalyzes the first reaction in this pathway, and its substrate specificity at each of its two catalytic steps sets the chain length and composition of the chemical scaffold upon which the other downstream enzymes act. However, there have been few attempts reported in the literature to rationally engineer thiolase substrate specificity. In this study, we present a model-guided, rational design study of ordered substrate binding applied to two biosynthetic thiolases, with the goal of increasing the ratio of C6/C4 products formed by the 3HA pathway, 3-hydroxy-hexanoic acid and 3-hydroxybutyric acid. We identify thiolase mutants that result in nearly 10-fold increases in C6/C4 selectivity. Our findings can extend to other pathways that employ the thiolase for chain elongation, as well as expand our knowledge of sequence-structure-function relationship for this important class of enzymes.
Collapse
Affiliation(s)
- Brian M. Bonk
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, MA
| | - Yekaterina Tarasova
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA
| | - Michael A. Hicks
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - Bruce Tidor
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, MA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA
| | - Kristala L.J. Prather
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA
| |
Collapse
|