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Liu L, Liu S, Hu X, Zhou S, Deng Y. Enhancing the activity and succinyl-CoA specificity of 3-ketoacyl-CoA thiolase Tfu_0875 through rational binding pocket engineering. Synth Syst Biotechnol 2024; 9:558-568. [PMID: 38694995 PMCID: PMC11061225 DOI: 10.1016/j.synbio.2024.04.014] [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: 02/12/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 05/04/2024] Open
Abstract
The 3-ketoacyl-CoA thiolase is the rate-limiting enzyme for linear dicarboxylic acids production. However, the promiscuous substrate specificity and suboptimal catalytic performance have restricted its application. Here we present both biochemical and structural analyses of a high-efficiency 3-ketoacyl-CoA thiolase Tfu_0875. Notably, Tfu_0875 displayed heightened activity and substrate specificity for succinyl-CoA, a key precursor in adipic acid production. To enhance its performance, a deep learning approach (DLKcat) was employed to identify effective mutants, and a computational strategy, known as the greedy accumulated strategy for protein engineering (GRAPE), was used to accumulate these effective mutants. Among the mutants, Tfu_0875N249W/L163H/E217L exhibited the highest specific activity (320% of wild-type Tfu_0875), the greatest catalytic efficiency (kcat/KM = 1.00 min-1mM-1), the highest succinyl-CoA specificity (KM = 0.59 mM, 28.1% of Tfu_0875) and dramatically reduced substrate binding energy (-30.25 kcal mol-1v.s. -15.94 kcal mol-1). A structural comparison between Tfu_0875N249W/L163H/E217L and the wild type Tfu_0875 revealed that the increased interaction between the enzyme and succinyl-CoA was the primary reason for the enhanced enzyme activity. This interaction facilitated rapid substrate anchoring and stabilization. Furthermore, a reduced binding pocket volume improved substrate specificity by enhancing the complementarity between the binding pocket and the substrate in stereo conformation. Finally, our rationally designed mutant, Tfu_0875N249W/L163H/E217L, increased the adipic acid titer by 1.35-fold compared to the wild type Tfu_0875 in shake flask. The demonstrated enzymatic methods provide a promising enzyme variant for the adipic acid production. The above effective substrate binding pocket engineering strategy can be beneficial for the production of other industrially competitive biobased chemicals when be applied to other thiolases.
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Affiliation(s)
- Lixia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, 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
| | - Shuang Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, 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
| | - Xiangyang Hu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, 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
| | - Shenghu Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, 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 Research Center of Cereal Fermentation and Food Biomanufacturing, 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
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2
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Moon J, Hu G, Hayashi T. Application of Machine Learning in the Quantitative Analysis of the Surface Characteristics of Highly Abundant Cytoplasmic Proteins: Toward AI-Based Biomimetics. Biomimetics (Basel) 2024; 9:162. [PMID: 38534847 DOI: 10.3390/biomimetics9030162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
Proteins in the crowded environment of human cells have often been studied regarding nonspecific interactions, misfolding, and aggregation, which may cause cellular malfunction and disease. Specifically, proteins with high abundance are more susceptible to these issues due to the law of mass action. Therefore, the surfaces of highly abundant cytoplasmic (HAC) proteins directly exposed to the environment can exhibit specific physicochemical, structural, and geometrical characteristics that reduce nonspecific interactions and adapt to the environment. However, the quantitative relationships between the overall surface descriptors still need clarification. Here, we used machine learning to identify HAC proteins using hydrophobicity, charge, roughness, secondary structures, and B-factor from the protein surfaces and quantified the contribution of each descriptor. First, several supervised learning algorithms were compared to solve binary classification problems for the surfaces of HAC and extracellular proteins. Then, logistic regression was used for the feature importance analysis of descriptors considering model performance (80.2% accuracy and 87.6% AUC) and interpretability. The HAC proteins showed positive correlations with negatively and positively charged areas but negative correlations with hydrophobicity, the B-factor, the proportion of beta structures, roughness, and the proportion of disordered regions. Finally, the details of each descriptor could be explained concerning adaptative surface strategies of HAC proteins to regulate nonspecific interactions, protein folding, flexibility, stability, and adsorption. This study presented a novel approach using various surface descriptors to identify HAC proteins and provided quantitative design rules for the surfaces well-suited to human cellular crowded environments.
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Affiliation(s)
- Jooa Moon
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Guanghao Hu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Tomohiro Hayashi
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-0882, Japan
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3
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He S, Bai X, Xu Y. Structural insight into the role of thiolase from Fusobacterium nucleatum. Biochem Biophys Res Commun 2023; 688:149151. [PMID: 37951156 DOI: 10.1016/j.bbrc.2023.149151] [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: 10/12/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/13/2023]
Abstract
Fusobacterium nucleatum (F. nucleatum) is an anaerobic gram-negative bacterium that was previously thought to be related to the progression of colorectal cancer. In F. nucleatum, thiolase participates in fatty acid metabolism, and it can catalyse the transfer of an acetyl group from acetyl-CoA to another molecule, typically a fatty acid or another molecule in the synthesis of lipids. To gain deeper insight into the molecular mechanism governing the function of thiolase in F. nucleatum (Fn0495), we herein report the structure of Fn0495. The monomer of Fn0495 consists of three subdomains, namely, the N-terminal domain (residues 1-117 and 252-270), the C-terminal domain (residues 273-393), and the loop domain (residues 118-251). Fn0495 shows a unique difference in the charge and structure of the substrate binding pocket compared with homologous proteins. This research found three conserved residues (Cys88, His357, and Cys387) in Fn0495 arranged near a potential substrate binding pocket. In this study, the conformational changes between the covering loop, catalytic cysteine loop, regulatory determinant region, and homologous protein were compared. These results will enhance our understanding of the molecular characteristics and roles of the thiolase family.
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Affiliation(s)
- Shanru He
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
| | - Xue Bai
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China.
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4
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Singh R, Kundu P, Mishra VK, Singh BK, Bhattacharyya S, Das AK. Crystal structure of FadA2 thiolase from Mycobacterium tuberculosis and prediction of its substrate specificity and membrane-anchoring properties. FEBS J 2023; 290:3997-4022. [PMID: 37026388 DOI: 10.1111/febs.16792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/17/2023] [Accepted: 04/05/2023] [Indexed: 04/08/2023]
Abstract
Tuberculosis (TB) is one of the leading causes of human death caused by Mycobacterium tuberculosis (Mtb). Mtb can enter into a long-lasting persistence where it can utilize fatty acids as the carbon source. Hence, fatty acid metabolism pathway enzymes are considered promising and pertinent mycobacterial drug targets. FadA2 (thiolase) is one of the enzymes involved in Mtb's fatty acid metabolism pathway. FadA2 deletion construct (ΔL136-S150) was designed to produce soluble protein. The crystal structure of FadA2 (ΔL136-S150) at 2.9 Å resolution was solved and analysed for membrane-anchoring region. The four catalytic residues of FadA2 are Cys99, His341, His390 and Cys427, and they belong to four loops with characteristic sequence motifs, i.e., CxT, HEAF, GHP and CxA. FadA2 is the only thiolase of Mtb which belongs to the CHH category containing the HEAF motif. Analysing the substrate-binding channel, it has been suggested that FadA2 is involved in the β-oxidation pathway, i.e., the degradative pathway, as the long-chain fatty acid can be accommodated in the channel. The catalysed reaction is favoured by the presence of two oxyanion holes, i.e., OAH1 and OAH2. OAH1 formation is unique in FadA2, formed by the NE2 of His390 present in the GHP motif and NE2 of His341 present in the HEAF motif, whereas OAH2 formation is similar to CNH category thiolase. Sequence and structural comparison with the human trifunctional enzyme (HsTFE-β) suggests the membrane-anchoring region in FadA2. Molecular dynamics simulations of FadA2 with a membrane containing POPE lipid were conducted to understand the role of a long insertion sequence of FadA2 in membrane anchoring.
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Affiliation(s)
- Rashika Singh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Prasun Kundu
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | | | - Bina Kumari Singh
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Sudipta Bhattacharyya
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
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5
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Tarasava K, Lee SH, Chen J, Köpke M, Jewett MC, Gonzalez R. Reverse β-oxidation pathways for efficient chemical production. J Ind Microbiol Biotechnol 2022; 49:6537408. [PMID: 35218187 PMCID: PMC9118988 DOI: 10.1093/jimb/kuac003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022]
Abstract
Microbial production of fuels, chemicals, and materials has the potential to reduce greenhouse gas emissions and contribute to a sustainable bioeconomy. While synthetic biology allows readjusting of native metabolic pathways for the synthesis of desired products, often these native pathways do not support maximum efficiency and are affected by complex regulatory mechanisms. A synthetic or engineered pathway that allows modular synthesis of versatile bioproducts with minimal enzyme requirement and regulation while achieving high carbon and energy efficiency could be an alternative solution to address these issues. The reverse β-oxidation (rBOX) pathways enable iterative non-decarboxylative elongation of carbon molecules of varying chain lengths and functional groups with only four core enzymes and no ATP requirement. Here, we describe recent developments in rBOX pathway engineering to produce alcohols and carboxylic acids with diverse functional groups, along with other commercially important molecules such as polyketides. We discuss the application of rBOX beyond the pathway itself by its interfacing with various carbon-utilization pathways and deployment in different organisms, which allows feedstock diversification from sugars to glycerol, carbon dioxide, methane, and other substrates.
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Affiliation(s)
- Katia Tarasava
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Seung Hwan Lee
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Jing Chen
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | | | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
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6
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Truong DP, Rousseau S, Machala BW, Huddleston JP, Zhu M, Hull KG, Romo D, Raushel FM, Sacchettini JC, Glasner ME. Second-Shell Amino Acid R266 Helps Determine N-Succinylamino Acid Racemase Reaction Specificity in Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Enzymes. Biochemistry 2021; 60:3829-3840. [PMID: 34845903 DOI: 10.1021/acs.biochem.1c00627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Catalytic promiscuity is the coincidental ability to catalyze nonbiological reactions in the same active site as the native biological reaction. Several lines of evidence show that catalytic promiscuity plays a role in the evolution of new enzyme functions. Thus, studying catalytic promiscuity can help identify structural features that predispose an enzyme to evolve new functions. This study identifies a potentially preadaptive residue in a promiscuous N-succinylamino acid racemase/o-succinylbenzoate synthase (NSAR/OSBS) enzyme from Amycolatopsis sp. T-1-60. This enzyme belongs to a branch of the OSBS family which includes many catalytically promiscuous NSAR/OSBS enzymes. R266 is conserved in all members of the NSAR/OSBS subfamily. However, the homologous position is usually hydrophobic in other OSBS subfamilies, whose enzymes lack NSAR activity. The second-shell amino acid R266 is close to the catalytic acid/base K263, but it does not contact the substrate, suggesting that R266 could affect the catalytic mechanism. Mutating R266 to glutamine in Amycolatopsis NSAR/OSBS profoundly reduces NSAR activity but moderately reduces OSBS activity. This is due to a 1000-fold decrease in the rate of proton exchange between the substrate and the general acid/base catalyst K263. This mutation is less deleterious for the OSBS reaction because K263 forms a cation-π interaction with the OSBS substrate and/or the intermediate, rather than acting as a general acid/base catalyst. Together, the data explain how R266 contributes to NSAR reaction specificity and was likely an essential preadaptation for the evolution of NSAR activity.
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Affiliation(s)
- Dat P Truong
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - Simon Rousseau
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - Benjamin W Machala
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - Jamison P Huddleston
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843-3255, United States
| | - Mingzhao Zhu
- Baylor Synthesis and Drug-Lead Discovery Laboratory, Department of Chemistry and Biochemistry, Baylor University, One Bear Place, Waco, Texas 76798-7348, United States
| | - Kenneth G Hull
- Baylor Synthesis and Drug-Lead Discovery Laboratory, Department of Chemistry and Biochemistry, Baylor University, One Bear Place, Waco, Texas 76798-7348, United States
| | - Daniel Romo
- Baylor Synthesis and Drug-Lead Discovery Laboratory, Department of Chemistry and Biochemistry, Baylor University, One Bear Place, Waco, Texas 76798-7348, United States
| | - Frank M Raushel
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States.,Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843-3255, United States
| | - James C Sacchettini
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843-3255, United States
| | - Margaret E Glasner
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
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7
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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: 11] [Impact Index Per Article: 2.8] [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.
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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.
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8
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9
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Tan Z, Clomburg JM, Cheong S, Qian S, Gonzalez R. A polyketoacyl-CoA thiolase-dependent pathway for the synthesis of polyketide backbones. Nat Catal 2020. [DOI: 10.1038/s41929-020-0471-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Dong H, Liffland S, Hillmyer MA, Chang MCY. Engineering in Vivo Production of α-Branched Polyesters. J Am Chem Soc 2019; 141:16877-16883. [DOI: 10.1021/jacs.9b08585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Stephanie Liffland
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Marc A. Hillmyer
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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11
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 280] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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12
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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.
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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
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