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Pang B, Li J, Eiben CB, Oksen E, Barcelos C, Chen R, Englund E, Sundstrom E, Keasling JD. Lepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuels. Metab Eng 2021; 68:210-219. [PMID: 34673235 DOI: 10.1016/j.ymben.2021.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/12/2021] [Accepted: 10/16/2021] [Indexed: 12/31/2022]
Abstract
Terpenes constitute the largest class of natural products with over 55,000 compounds with versatile applications including drugs and biofuels. Introducing structural modifications to terpenes through metabolic engineering is an efficient and sustainable way to improve their properties. Here, we report the optimization of the lepidopteran mevalonate (LMVA) pathway towards the efficient production of isopentenyl pyrophosphate (IPP) analogs as terpene precursors. First, we linked the LMVA pathway to NudB, a promiscuous phosphatase, resulting in the production of the six-carbon analog of 3-methyl-3-buten-1-ol (isoprenol), 3-ethyl-3-buten-1-ol (C6-isoprenol). Using C6-isoprenol as the final product, we then engineered the LMVA pathway by redirecting its upstream portion from a thiolase-dependent pathway to a beta-oxidation pathway. The beta-oxidation LMVA pathway transforms valeric acid, a platform chemical that can be produced from biomass, into C6-isoprenol at a titer of 110.3 mg/L, improved from 5.5 mg/L by the thiolase LMVA pathway, which used propionic acid as a feedstock. Knockout of the E. coli endogenous thiolase genes further improved the C6-isoprenol titer to 390 mg/L, implying efficient production of homo isopentenyl pyrophosphate (HIPP). The beta-oxidation LMVA-NudB pathway also converts butanoic acid and hexanoic acid into isoprenol and isoprenol's seven-carbon analog, 3-propyl-3-buten-1-ol (C7-isoprenol), respectively, suggesting the beta-oxidation LMVA pathway produces IPP and C7-IPP from the corresponding fatty acids. Fuel property tests revealed the longer chain isoprenol analogs have lower water solubilities, similar or higher energy densities, and comparable research octane number (RON) boosting effects to isopentenols. This work not only optimizes the LMVA pathway, setting the basis for homoterpene biosynthesis to expand terpene chemical space, but provides an efficient pathway to produce isoprenol analogs as next-generation biofuels from sustainable feedstocks.
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Affiliation(s)
- Bo Pang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, United States
| | - Jia Li
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, PR China; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Christopher B Eiben
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Ethan Oksen
- Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Carolina Barcelos
- Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Rong Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; School of Public Health, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, PR China
| | - Elias Englund
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Eric Sundstrom
- Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, United States; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK 2970 Horsholm, Denmark; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, Guangdong, 518055, PR China.
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2
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Ellis GA, Klein WP, Lasarte-Aragonés G, Thakur M, Walper SA, Medintz IL. Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02413] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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3
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Wu YW, Yang SH, Hwangbo M, Chu KH. Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system. PLoS One 2019; 14:e0222143. [PMID: 31513626 PMCID: PMC6742469 DOI: 10.1371/journal.pone.0222143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/22/2019] [Indexed: 01/25/2023] Open
Abstract
Polyhydroxybutyrate (PHB) is biodegradable and renewable and thus considered as a promising alternative to petroleum-based plastics. However, PHB production is costly due to expensive carbon sources for culturing PHB-accumulating microorganisms under sterile conditions. We discovered a hyper PHB-accumulating denitrifying bacterium, Zobellella denitrificans ZD1 (referred as strain ZD1 hereafter) capable of using non-sterile crude glycerol (a waste from biodiesel production) and nitrate to produce high PHB yield under saline conditions. Nevertheless, the underlying genetic mechanisms of PHB production in strain ZD1 have not been elucidated. In this study, we discovered a complete pathway of glycerol conversion to PHB, a novel PHB synthesis gene cluster, a salt-tolerant gene cluster, denitrifying genes, and an assimilatory nitrate reduction gene cluster in the ZD1 genome. Interestingly, the novel PHB synthesis gene cluster was found to be conserved among marine Gammaproteobacteria. Higher levels of PHB accumulation were linked to higher expression levels of the PHB synthesis gene cluster in ZD1 grown with glycerol and nitrate under saline conditions. Additionally, a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas type-I-E antiviral system was found in the ZD1 genome along with a long spacer list, in which most of the spacers belong to either double-stranded DNA viruses or unknown phages. The results of the genome analysis revealed strain ZD1 used the novel PHB gene cluster to produce PHB from non-sterile crude glycerol under saline conditions.
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Affiliation(s)
- Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
| | - Shih-Hung Yang
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
| | - Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
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4
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Sagong HY, Son HF, Choi SY, Lee SY, Kim KJ. Structural Insights into Polyhydroxyalkanoates Biosynthesis. Trends Biochem Sci 2018; 43:790-805. [PMID: 30139647 DOI: 10.1016/j.tibs.2018.08.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/27/2018] [Accepted: 08/04/2018] [Indexed: 12/25/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are diverse biopolyesters produced by numerous microorganisms and have attracted much attention as a substitute for petroleum-based polymers. Despite several decades of study, the detailed molecular mechanisms of PHA biosynthesis have remained unknown due to the lack of structural information on the key PHA biosynthetic enzyme PHA synthase. The recently determined crystal structure of PHA synthase, together with the structures of acetyl-coenzyme A (CoA) acetyltransferase and reductase, have changed this situation. Structural and biochemical studies provided important clues for the molecular mechanisms of each enzyme as well as the overall mechanism of PHA biosynthesis from acetyl-CoA. This new information and knowledge is expected to facilitate production of designed novel PHAs and also enhanced production of PHAs.
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Affiliation(s)
- Hye-Young Sagong
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyeoncheol Francis Son
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.
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5
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Torres-Salas P, Bernal V, López-Gallego F, Martínez-Crespo J, Sánchez-Murcia PA, Barrera V, Morales-Jiménez R, García-Sánchez A, Mañas-Fernández A, Seoane JM, Sagrera Polo M, Miranda JD, Calvo J, Huertas S, Torres JL, Alcalde-Bascones A, González-Barrera S, Gago F, Morreale A, González-Barroso MDM. Engineering Erg10 Thiolase from Saccharomyces cerevisiae as a Synthetic Toolkit for the Production of Branched-Chain Alcohols. Biochemistry 2018; 57:1338-1348. [PMID: 29360348 DOI: 10.1021/acs.biochem.7b01186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thiolases catalyze the condensation of acyl-CoA thioesters through the Claisen condensation reaction. The best described enzymes usually yield linear condensation products. Using a combined computational/experimental approach, and guided by structural information, we have studied the potential of thiolases to synthesize branched compounds. We have identified a bulky residue located at the active site that blocks proper accommodation of substrates longer than acetyl-CoA. Amino acid replacements at such a position exert effects on the activity and product selectivity of the enzymes that are highly dependent on a protein scaffold. Among the set of five thiolases studied, Erg10 thiolase from Saccharomyces cerevisiae showed no acetyl-CoA/butyryl-CoA branched condensation activity, but variants at position F293 resulted the most active and selective biocatalysts for this reaction. This is the first time that a thiolase has been engineered to synthesize branched compounds. These novel enzymes enrich the toolbox of combinatorial (bio)chemistry, paving the way for manufacturing a variety of α-substituted synthons. As a proof of concept, we have engineered Clostridium's 1-butanol pathway to obtain 2-ethyl-1-butanol, an alcohol that is interesting as a branched model compound.
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Affiliation(s)
- Pamela Torres-Salas
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Vicente Bernal
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Fernando López-Gallego
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain.,CIC biomaGUNE , Paseo de Miramón 182, 20014 San Sebastián, Spain.,ARAID Foundation , Zaragoza, Spain
| | - Javier Martínez-Crespo
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Pedro A Sánchez-Murcia
- Departamento de Ciencias Biomédicas and "Unidad Asociada IQM-CSIC", Universidad de Alcalá , E-28805 Alcalá de Henares, Madrid, Spain
| | - Victor Barrera
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Rocío Morales-Jiménez
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Ana García-Sánchez
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Aurora Mañas-Fernández
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - José M Seoane
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Marta Sagrera Polo
- Centro de Investigaciones Biológicas (CSIC) , Calle Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Juande D Miranda
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Javier Calvo
- CIC biomaGUNE , Paseo de Miramón 182, 20014 San Sebastián, Spain
| | - Sonia Huertas
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - José L Torres
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Ana Alcalde-Bascones
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Sergio González-Barrera
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas and "Unidad Asociada IQM-CSIC", Universidad de Alcalá , E-28805 Alcalá de Henares, Madrid, Spain
| | - Antonio Morreale
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
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6
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Blaisse MR, Fu B, Chang MCY. Structural and Biochemical Studies of Substrate Selectivity in Ascaris suum Thiolases. Biochemistry 2018; 57:3155-3166. [PMID: 29381332 DOI: 10.1021/acs.biochem.7b01123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thiolases are a class of carbon-carbon bond forming enzymes with important applications in biotechnology and metabolic engineering as they provide a general method for the condensation of two acyl coenzyme A (CoA) substrates. As such, developing a greater understanding of their substrate selectivity would expand our ability to engineer the enzymatic or microbial production of a broad range of small-molecule targets. Here, we report the crystal structures and biochemical characterization of Acat2 and Acat5, two biosynthetic thiolases from Ascaris suum with varying selectivity toward branched compared to linear compounds. The structure of the Acat2-C91S mutant bound to propionyl-CoA shows that the terminal methyl group of the substrate, representing the α-branch point, is directed toward the conserved Phe 288 and Met 158 residues. In Acat5, the Phe ring is rotated to accommodate a hydroxyl-π interaction with an adjacent Thr side chain, decreasing space in the binding pocket and possibly accounting for its strong preference for linear substrates compared to Acat2. Comparison of the different Acat thiolase structures shows that Met 158 is flexible, adopting alternate conformations with the side chain rotated toward or away from a covering loop at the back of the active site. Mutagenesis of residues in the covering loop in Acat5 with the corresponding residues from Acat2 allows for highly increased accommodation of branched substrates, whereas the converse mutations do not significantly affect Acat2 substrate selectivity. Our results suggest an important contribution of second-shell residues to thiolase substrate selectivity and offer insights into engineering this enzyme class.
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7
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Zhou P, Zhu Z, Hidayatullah Khan M, Zheng P, Teng M, Niu L. Crystal structure of cytoplasmic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2018; 74:6-13. [PMID: 29372902 PMCID: PMC5947687 DOI: 10.1107/s2053230x17016971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/25/2017] [Indexed: 11/10/2022] Open
Abstract
Thiolases are vital enzymes which participate in both degradative and biosynthetic pathways. Biosynthetic thiolases catalyze carbon-carbon bond formation by a Claisen condensation reaction. The cytoplasmic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae, ERG10, catalyses carbon-carbon bond formation in the mevalonate pathway. The structure of a S. cerevisiae biosynthetic thiolase has not previously been reported. Here, crystal structures of apo ERG10 and its Cys91Ala variant were solved at resolutions of 2.2 and 1.95 Å, respectively. The structure determined shows that ERG10 shares the characteristic thiolase superfamily fold, with a similar active-site architecture to those of type II thiolases and a similar binding pocket, apart from Ala159 at the entrance to the pantetheine-binding cavity, which appears to be a determinant of the poor binding ability of the substrate. Moreover, comparative binding-pocket analysis of molecule B in the asymmetric unit of the apo structure with that of the CoA-bound complex of human mitochondrial acetoacetyl-CoA thiolase indicates the canonical binding mode of CoA. Furthermore, the steric hindrance revealed in a structural comparison of molecule A with the CoA-bound form raise the possibility of conformational changes that are associated with substrate binding.
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Affiliation(s)
- Pengfei Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Muhammad Hidayatullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Peiyi Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
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8
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Blaisse MR, Dong H, Fu B, Chang MCY. Discovery and Engineering of Pathways for Production of α-Branched Organic Acids. J Am Chem Soc 2017; 139:14526-14532. [PMID: 28990776 DOI: 10.1021/jacs.7b07400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cell-based synthesis offers many opportunities for preparing small molecules from simple renewable carbon sources by telescoping multiple reactions into a single fermentation step. One challenge in this area is the development of enzymatic carbon-carbon bond forming cycles that enable a modular disconnection of a target structure into cellular building blocks. In this regard, synthetic pathways based on thiolase enzymes to catalyze the initial carbon-carbon bond forming step between acyl coenzyme A (CoA) substrates offer a versatile route for biological synthesis, but the substrate diversity of such pathways is currently limited. In this report, we describe the identification and biochemical characterization of a thiolase-ketoreductase pair involved in production of branched acids in the roundworm, Ascaris suum, that demonstrates selectivity for forming products with an α-methyl branch using a propionyl-CoA extender unit. Engineering synthetic pathways for production of α-methyl acids in Escherichia coli using these enzymes allows the construction of microbial strains that produce either chiral 2-methyl-3-hydroxy acids (1.1 ± 0.2 g L-1) or branched enoic acids (1.12 ± 0.06 g L-1) in the presence of a dehydratase at 44% and 87% yield of fed propionate, respectively. In vitro characterization along with in vivo analysis indicates that the ketoreductase is the key driver for selectivity, forming predominantly α-branched products even when paired with a thiolase that highly prefers unbranched linear products. Our results expand the utility of thiolase-based pathways and provide biosynthetic access to α-branched compounds as precursors for polymers and other chemicals.
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Affiliation(s)
- Michael R Blaisse
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720-1460, United States
| | - Hongjun Dong
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720-1460, United States
| | - Beverly Fu
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720-1460, United States
| | - Michelle C Y Chang
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720-1460, United States.,Department of Molecular and Cell Biology, University of California, Berkeley , Berkeley, California 94720-1460, United States
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9
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Harijan RK, Kiema TR, Syed SM, Qadir I, Mazet M, Bringaud F, Michels PAM, Wierenga RK. Crystallographic substrate binding studies of Leishmania mexicana SCP2-thiolase (type-2): unique features of oxyanion hole-1. Protein Eng Des Sel 2017; 30:225-233. [PMID: 28062645 DOI: 10.1093/protein/gzw080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/15/2016] [Indexed: 12/26/2022] Open
Abstract
C Structures of the C123A variant of the dimeric Leishmania mexicana SCP2-thiolase (type-2) (Lm-thiolase), complexed with acetyl-CoA and acetoacetyl-CoA, respectively, are reported. The catalytic site of thiolase contains two oxyanion holes, OAH1 and OAH2, which are important for catalysis. The two structures reveal for the first time the hydrogen bond interactions of the CoA-thioester oxygen atom of the substrate with the hydrogen bond donors of OAH1 of a CHH-thiolase. The amino acid sequence fingerprints ( xS, EAF, G P) of three catalytic loops identify the active site geometry of the well-studied CNH-thiolases, whereas SCP2-thiolases (type-1, type-2) are classified as CHH-thiolases, having as corresponding fingerprints xS, DCF and G P. In all thiolases, OAH2 is formed by the main chain NH groups of two catalytic loops. In the well-studied CNH-thiolases, OAH1 is formed by a water (of the Wat-Asn(NEAF) dyad) and NE2 (of the GHP-histidine). In the two described liganded Lm-thiolase structures, it is seen that in this CHH-thiolase, OAH1 is formed by NE2 of His338 (HDCF) and His388 (GHP). Analysis of the OAH1 hydrogen bond networks suggests that the GHP-histidine is doubly protonated and positively charged in these complexes, whereas the HDCF histidine is neutral and singly protonated.
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Affiliation(s)
- Rajesh K Harijan
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014, Finland.,Present address: Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Tiila-Riikka Kiema
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014, Finland
| | - Shahan M Syed
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014, Finland
| | - Imran Qadir
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014, Finland
| | - Muriel Mazet
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR5536, Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076 Bordeaux, France.,Present address: Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), UMR5234, Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Frédéric Bringaud
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR5536, Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076 Bordeaux, France.,Present address: Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), UMR5234, Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Paul A M Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The King's Buildings, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014, Finland
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Tippmann S, Anfelt J, David F, Rand JM, Siewers V, Uhlén M, Nielsen J, Hudson EP. Affibody Scaffolds Improve Sesquiterpene Production in Saccharomyces cerevisiae. ACS Synth Biol 2017; 6:19-28. [PMID: 27560952 DOI: 10.1021/acssynbio.6b00109] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Enzyme fusions have been widely used as a tool in metabolic engineering to increase pathway efficiency by reducing substrate loss and accumulation of toxic intermediates. Alternatively, enzymes can be colocalized through attachment to a synthetic scaffold via noncovalent interactions. Here we describe the use of affibodies for enzyme tagging and scaffolding. The scaffolding is based on the recognition of affibodies to their anti-idiotypic partners in vivo, and was first employed for colocalization of farnesyl diphosphate synthase and farnesene synthase in S. cerevisiae. Different parameters were modulated to improve the system, and the enzyme:scaffold ratio was most critical for its functionality. Ultimately, the yield of farnesene on glucose YSFar could be improved by 135% in fed-batch cultivations using a 2-site affibody scaffold. The scaffolding strategy was then extended to a three-enzyme polyhydroxybutyrate (PHB) pathway, heterologously expressed in E. coli. Within a narrow range of enzyme and scaffold induction, the affibody tagging and scaffolding increased PHB production 7-fold. This work demonstrates how the versatile affibody can be used for metabolic engineering purposes.
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Affiliation(s)
- Stefan Tippmann
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Josefine Anfelt
- Division
of Proteomics and Nanobiotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Science for Life Laboratory, SE171 21 Stockholm, Sweden
| | - Florian David
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jacqueline M. Rand
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Verena Siewers
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Mathias Uhlén
- Division
of Proteomics and Nanobiotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Science for Life Laboratory, SE171 21 Stockholm, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark
| | - Elton P. Hudson
- Division
of Proteomics and Nanobiotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Science for Life Laboratory, SE171 21 Stockholm, Sweden
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Janardan N, Harijan RK, Kiema TR, Wierenga RK, Murthy MRN. Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase fromMycobacterium smegmatis. ACTA ACUST UNITED AC 2015; 71:2479-93. [DOI: 10.1107/s1399004715019331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/12/2015] [Indexed: 11/10/2022]
Abstract
Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) fromMycobacterium smegmatisin apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domainviaflexible hinge regions, generating an asymmetric tetramer. In the liganded structure, CoA is bound to those subunits that are rotated towards the tip of the tetramerization loop of the opposing dimer, suggesting that this loop is important for substrate binding. The hinge regions responsible for this rotation occur near Val123 and Arg149. The Lα1–covering loop–Lα2 region, together with the Nβ2–Nα2 loop of the adjacent subunit, defines a specificity pocket that is larger and more polar than those of other tetrameric thiolases, suggesting that MSM-13 thiolase has a distinct substrate specificity. Consistent with this finding, only residual activity was detected with acetoacetyl-CoA as the substrate in the degradative direction. No activity was observed with acetyl-CoA in the synthetic direction. Structural comparisons with other well characterized thiolases suggest that MSM-13 thiolase is probably a degradative thiolase that is specific for 3-ketoacyl-CoA molecules with polar, bulky acyl chains.
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Fage CD, Meinke JL, Keatinge-Clay AT. Coenzyme A-free activity, crystal structure, and rational engineering of a promiscuous β-ketoacyl thiolase from Ralstonia eutropha. ACTA ACUST UNITED AC 2015; 121:113-121. [PMID: 26494979 DOI: 10.1016/j.molcatb.2015.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Thiolases catalyze the formation of carbon-carbon bonds in diverse biosynthetic pathways. The promiscuous β-ketoacyl thiolase B of Ralstonia eutropha (ReBktB) has been utilized in the in vivo conversion of Coenzyme A (CoA)-linked precursors such as acetyl-CoA and glycolyl-CoA into β-hydroxy acids, including the pharmaceutically-important 3,4-dihydroxybutyric acid. Such thiolases could serve as powerful carbon-carbon bond-forming biocatalysts in vitro if handles less costly than CoA were employable. Here, thiolase activity is demonstrated toward substrates linked to the readily-available CoA mimic, N-acetylcysteamine (NAC). ReBktB was observed to catalyze the retro-Claisen condensation of several β-ketoacyl-S-NAC substrates, with a preference for 3-oxopentanoyl-S-NAC over 3-oxobutanoyl-, 3-oxohexanoyl-, and 3-oxoheptanoyl-S-NAC. A 2.0 Å-resolution crystal structure, in which the asymmetric unit consists of four ReBktB tetramers, provides insight into acyl group specificity and how it may be engineered. By replacing an active site methionine with an alanine, a mutant possessing significant activity towards α-methyl substituted, NAC-linked substrates was engineered. The ability of ReBktB and its engineered mutants to utilize NAC-linked substrates will facilitate the in vitro biocatalytic synthesis of diketide chiral building blocks from feedstock molecules such as acetate and propionate.
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Affiliation(s)
- Christopher D Fage
- Department of Molecular Biosciences, The University of Texas, Austin, TX 78712, USA
| | - Jessica L Meinke
- Department of Molecular Biosciences, The University of Texas, Austin, TX 78712, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas, Austin, TX 78712, USA. ; Department of Chemistry, The University of Texas, Austin, TX 78712, USA
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Kim J, Kim KJ. Purification, crystallization and preliminary X-ray diffraction analysis of 3-ketoacyl-CoA thiolase A1887 from Ralstonia eutropha H16. Acta Crystallogr F Struct Biol Commun 2015; 71:758-62. [PMID: 26057808 PMCID: PMC4461343 DOI: 10.1107/s2053230x15007888] [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: 02/16/2015] [Accepted: 04/21/2015] [Indexed: 11/10/2022] Open
Abstract
The gene product of A1887 from Ralstonia eutropha (ReH16_A1887) has been annotated as a 3-ketoacyl-CoA thiolase, an enzyme that catalyzes the fourth step of β-oxidation degradative pathways by converting 3-ketoacyl-CoA to acyl-CoA. ReH16_A1887 was overexpressed and purified to homogeneity by affinity and size-exclusion chromatography. The degradative thiolase activity of the purified ReH16_A1887 was measured and enzyme-kinetic parameters for the protein were obtained, with Km, Vmax and kcat values of 158 µM, 32 mM min(-1) and 5 × 10(6) s(-1), respectively. The ReH16_A1887 protein was crystallized in 17% PEG 8K, 0.1 M HEPES pH 7.0 at 293 K and a complete data set was collected to 1.4 Å resolution. The crystal belonged to space group P4(3)2(1)2, with unit-cell parameters a = b = 129.52, c = 114.13 Å, α = β = γ = 90°. The asymmetric unit contained two molecules, with a solvent content of 58.9%.
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Affiliation(s)
- Jieun Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
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