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Jones BS, Ross CM, Foley G, Pozhydaieva N, Sharratt JW, Kress N, Seibt LS, Thomson RES, Gumulya Y, Hayes MA, Gillam EMJ, Flitsch SL. Engineering Biocatalysts for the C-H Activation of Fatty Acids by Ancestral Sequence Reconstruction. Angew Chem Int Ed Engl 2024; 63:e202314869. [PMID: 38163289 DOI: 10.1002/anie.202314869] [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: 10/04/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Selective, one-step C-H activation of fatty acids from biomass is an attractive concept in sustainable chemistry. Biocatalysis has shown promise for generating high-value hydroxy acids, but to date enzyme discovery has relied on laborious screening and produced limited hits, which predominantly oxidise the subterminal positions of fatty acids. Herein we show that ancestral sequence reconstruction (ASR) is an effective tool to explore the sequence-activity landscape of a family of multidomain, self-sufficient P450 monooxygenases. We resurrected 11 catalytically active CYP116B ancestors, each with a unique regioselectivity fingerprint that varied from subterminal in the older ancestors to mid-chain in the lineage leading to the extant, P450-TT. In lineages leading to extant enzymes in thermophiles, thermostability increased from ancestral to extant forms, as expected if thermophily had arisen de novo. Our studies show that ASR can be applied to multidomain enzymes to develop active, self-sufficient monooxygenases as regioselective biocatalysts for fatty acid hydroxylation.
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Affiliation(s)
- Bethan S Jones
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Connie M Ross
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Gabriel Foley
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Nadiia Pozhydaieva
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Joseph W Sharratt
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Nico Kress
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Lisa S Seibt
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Raine E S Thomson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Sabine L Flitsch
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
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Karpov M, Strizhov N, Novikova L, Lobastova T, Khomutov S, Shutov A, Kazantsev A, Donova M. Pregnenolone and progesterone production from natural sterols using recombinant strain of Mycolicibacterium smegmatis mc 2 155 expressing mammalian steroidogenesis system. Microb Cell Fact 2024; 23:105. [PMID: 38594656 PMCID: PMC11005228 DOI: 10.1186/s12934-024-02385-2] [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: 11/01/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Pregnenolone and progesterone are the life-important steroid hormones regulating essential vital functions in mammals, and widely used in different fields of medicine. Microbiological production of these compounds from sterols is based on the use of recombinant strains expressing the enzyme system cholesterol hydroxylase/C20-C22 lyase (CH/L) of mammalian steroidogenesis. However, the efficiency of the known recombinant strains is still low. New recombinant strains and combination approaches are now needed to produce these steroid hormones. RESULTS Based on Mycolicibacterium smegmatis, a recombinant strain was created that expresses the steroidogenesis system (CYP11A1, adrenodoxin reductase, adrenodoxin) of the bovine adrenal cortex. The recombinant strain transformed cholesterol and phytosterol to form progesterone among the metabolites. When 3-methoxymethyl ethers of sterols were applied as bioconversion substrates, the corresponding 3-ethers of pregnenolone and dehydroepiandrosterone (DHEA) were identified as major metabolites. Under optimized conditions, the recombinant strain produced 85.2 ± 4.7 mol % 3-methoxymethyl-pregnenolone within 48 h, while production of 3-substituted DHEA was not detected. After the 3-methoxymethyl function was deprotected by acid hydrolysis, crystalline pregnenolone was isolated in high purity (over 98%, w/w). The structures of steroids were confirmed using TLC, HPLC, MS and 1H- and 13C-NMR analyses. CONCLUSION The use of mycolicybacteria as a microbial platform for the expression of systems at the initial stage of mammalian steroidogenesis ensures the production of valuable steroid hormones-progesterone and pregnenolone from cholesterol. Selective production of pregnenolone from cholesterol is ensured by the use of 3-substituted cholesterol as a substrate and optimization of the conditions for its bioconversion. The results open the prospects for the generation of the new microbial biocatalysts capable of effectively producing value-added steroid hormones.
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Affiliation(s)
- Mikhail Karpov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, 142290, Russia.
| | - Nicolai Strizhov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, 142290, Russia
| | - Ludmila Novikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1/40, Moscow, 119234, Russia
| | - Tatyana Lobastova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, 142290, Russia
| | - Sergey Khomutov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, 142290, Russia
| | - Andrei Shutov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, 142290, Russia
| | - Alexey Kazantsev
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Marina Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, 142290, Russia.
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Zhang Z, Huang L, Zhang ZJ, Xu JH, Yu HL. Rational Design of Taxadiene Hydroxylase by Ancestral Enzyme Construction and the Elucidation of Key Amino Acids. Biochemistry 2023; 62:3214-3221. [PMID: 37902563 DOI: 10.1021/acs.biochem.3c00411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Cytochrome P450 monooxygenases (CYP450s) play an important role in the biosynthesis of natural products by activating inert C-H bonds and inserting hydroxyl groups. However, the activities of most plant-derived CYP450s are extremely low, limiting the heterologous biosynthesis of natural products. Traditional enzyme engineering methods, either rational or screening-based, are not suitable for CYP450s because of the lack of crystal structures and high-throughput screening methods for this class of enzymes. CYP725A4 is the first hydroxylase involved in the biosynthesis pathway of Taxol. Its low activity, promiscuity, and multispecificity make it a bottleneck in Taxol biosynthesis. Here, we identified key amino acids that affect the in vivo activity of CYP725A4 by constructing the ancestral enzymes of CYP725A4. We obtained positive mutants that showed an improved yield of hydroxylated products based on the key amino acids identified, providing guidance for the modification of other CYP450s involved in the biosynthesis of natural products.
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Affiliation(s)
- Zihan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Longhao Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Zhi-Jun Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
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4
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Jóźwik IK, Bombino E, Abdulmughni A, Hartz P, Rozeboom HJ, Wijma HJ, Kappl R, Janssen DB, Bernhardt R, Thunnissen AMWH. Regio- and stereoselective steroid hydroxylation by CYP109A2 from Bacillus megaterium explored by X-ray crystallography and computational modeling. FEBS J 2023; 290:5016-5035. [PMID: 37453052 DOI: 10.1111/febs.16906] [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: 12/12/2022] [Revised: 05/31/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
The P450 monooxygenase CYP109A2 from Bacillus megaterium DSM319 was previously found to convert vitamin D3 (VD3) to 25-hydroxyvitamin D3. Here, we show that this enzyme is also able to convert testosterone in a highly regio- and stereoselective manner to 16β-hydroxytestosterone. To reveal the structural determinants governing the regio- and stereoselective steroid hydroxylation reactions catalyzed by CYP109A2, two crystal structures of CYP109A2 were solved in similar closed conformations, one revealing a bound testosterone in the active site pocket, albeit at a nonproductive site away from the heme-iron. To examine whether the closed crystal structures nevertheless correspond to a reactive conformation of CYP109A2, docking and molecular dynamics (MD) simulations were performed with testosterone and vitamin D3 (VD3) present in the active site. These MD simulations were analyzed for catalytically productive conformations, the relative occurrences of which were in agreement with the experimentally determined stereoselectivities if the predicted stability of each carbon-hydrogen bond was taken into account. Overall, the first-time determination and analysis of the catalytically relevant 3D conformation of CYP109A2 will allow for future small molecule ligand screening in silico, as well as enabling site-directed mutagenesis toward improved enzymatic properties of this enzyme.
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Affiliation(s)
- Ilona K Jóźwik
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Elvira Bombino
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Ammar Abdulmughni
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Philip Hartz
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Henriette J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Reinhard Kappl
- Department of Biophysics, CIPMM, School of Medicine, Saarland University, Saarbrücken, Germany
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Andy-Mark W H Thunnissen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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5
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Shiko G, Paulmann MJ, Feistel F, Ntefidou M, Hermann-Ene V, Vetter W, Kost B, Kunert G, Zedler JAZ, Reichelt M, Oelmüller R, Klein J. Occurrence and conversion of progestogens and androgens are conserved in land plants. THE NEW PHYTOLOGIST 2023; 240:318-337. [PMID: 37559351 DOI: 10.1111/nph.19163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/28/2023] [Indexed: 08/11/2023]
Abstract
Progestogens and androgens have been found in many plants, but little is known about their biosynthesis and the evolution of steroidogenesis in these organisms. Here, we show that the occurrence and biosynthesis of progestogens and androgens are conserved across the viridiplantae lineage. An UHPLC-ESI-MS/MS method allowed high-throughput analysis of the occurrence and chemical conversion of progestogens and androgens in 41 species across the green plant lineage. Dehydroepiandrosterone, testosterone, and 5α-dihydrotestosterone are plants' most abundant mammalian-like steroids. Progestogens are converted into 17α-hydroxyprogesterone and 5α-pregnane-3,20-dione. Androgens are converted into testosterone and 5α-dihydrotestosterone. 17,20-Lyases, essential for converting progestogens to androgens, seem to be most effective in monocot species. Our data suggest that the occurrence of progestogens and androgens is highly conserved in plants, and their biosynthesis might favor a route using the Δ4 pathway.
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Affiliation(s)
- Glendis Shiko
- Department of Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Max-Jonas Paulmann
- Department of Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Felix Feistel
- Department for Biochemistry, Max Planck Institute for Chemical Ecology, 07743, Jena, Germany
| | - Maria Ntefidou
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Vanessa Hermann-Ene
- Institute of Food Chemistry, University of Hohenheim, 70599, Stuttgart, Germany
| | - Walter Vetter
- Institute of Food Chemistry, University of Hohenheim, 70599, Stuttgart, Germany
| | - Benedikt Kost
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Grit Kunert
- Department for Biochemistry, Max Planck Institute for Chemical Ecology, 07743, Jena, Germany
| | - Julie A Z Zedler
- Synthetic Biology of Photosynthetic Organisms, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Michael Reichelt
- Department for Biochemistry, Max Planck Institute for Chemical Ecology, 07743, Jena, Germany
| | - Ralf Oelmüller
- Department of Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Jan Klein
- Department of Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
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6
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Liu R, Pan Y, Wang N, Tang D, Urlacher VB, Li S. Comparative biochemical characterization of mammalian-derived CYP11A1s with cholesterol side-chain cleavage activities. J Steroid Biochem Mol Biol 2023; 229:106268. [PMID: 36764495 DOI: 10.1016/j.jsbmb.2023.106268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Steroid drugs, the second largest class of pharmaceuticals after antibiotics, have shown significant anti-inflammatory, anti-allergic, and endocrine-regulating effects. A group of cytochrome P450 enzymes, namely, CYP11A1 isoenzymes from different organisms are capable of converting cholesterol into pregnenolone, which is a pivotal reaction in both steroid metabolism and (bio)synthetic network of steroid products. However, the low activity of CYP11A1s greatly restricts the industrial application of these cholesterol side-chain cleavage enzymes. Herein, we investigate ten CYP11A1 enzymes of different origins and in vitro characterize two CYP11A1s with a relatively higher expression level from Capra hircus and Sus scrofa, together with the CYP11A1s from Homo sapiens and Bos taurus as references. Towards five selected sterol substrates with different side chain structures, S. scrofa CYP11A1 displays relatively higher activities. Through redox partners combination screening, we reveal the optimal redox partner pair of S. scrofa adrenodoxin and C. hircus adrenodoxin reductase. Moreover, the semi-rational mutagenesis for the active sites and substrate entrance channels of human and bovine CYP11A1s is performed based on comparative analysis of their crystal structures. The mutant mBtCYP11A1-Q377A derived from mature B. taurus CYP11A1 shows a 1.46 times higher activity than the wild type enzyme. These results not only demonstrate the tunability of the highly conserved CYP11A1 isoenzymes, but also lay a foundation for the following engineering efforts on these industrially relevant P450 enzymes.
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Affiliation(s)
- Ruxin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yunjun Pan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Dandan Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China.
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7
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Livada J, Vargas AM, Martinez CA, Lewis RD. Ancestral Sequence Reconstruction Enhances Gene Mining Efforts for Industrial Ene Reductases by Expanding Enzyme Panels with Thermostable Catalysts. ACS Catal 2023. [DOI: 10.1021/acscatal.2c03859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Jovan Livada
- Pfizer Global Research and Development, Chemical Research Development, MS 4073 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ariana M. Vargas
- Pfizer Global Research and Development, Chemical Research Development, MS 4073 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Carlos A. Martinez
- Pfizer Global Research and Development, Chemical Research Development, MS 4073 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Russell D. Lewis
- Pfizer Global Research and Development, Chemical Research Development, MS 4073 Eastern Point Road, Groton, Connecticut 06340, United States
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8
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Spotlight on CYP4B1. Int J Mol Sci 2023; 24:ijms24032038. [PMID: 36768362 PMCID: PMC9916508 DOI: 10.3390/ijms24032038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The mammalian cytochrome P450 monooxygenase CYP4B1 can bioactivate a wide range of xenobiotics, such as its defining/hallmark substrate 4-ipomeanol leading to tissue-specific toxicities. Similar to other members of the CYP4 family, CYP4B1 has the ability to hydroxylate fatty acids and fatty alcohols. Structural insights into the enigmatic role of CYP4B1 with functions in both, xenobiotic and endobiotic metabolism, as well as its unusual heme-binding characteristics are now possible by the recently solved crystal structures of native rabbit CYP4B1 and the p.E310A variant. Importantly, CYP4B1 does not play a major role in hepatic P450-catalyzed phase I drug metabolism due to its predominant extra-hepatic expression, mainly in the lung. In addition, no catalytic activity of human CYP4B1 has been observed owing to a unique substitution of an evolutionary strongly conserved proline 427 to serine. Nevertheless, association of CYP4B1 expression patterns with various cancers and potential roles in cancer development have been reported for the human enzyme. This review will summarize the current status of CYP4B1 research with a spotlight on its roles in the metabolism of endogenous and exogenous compounds, structural properties, and cancer association, as well as its potential application in suicide gene approaches for targeted cancer therapy.
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9
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Engineering functional thermostable proteins using ancestral sequence reconstruction. J Biol Chem 2022; 298:102435. [PMID: 36041629 PMCID: PMC9525910 DOI: 10.1016/j.jbc.2022.102435] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
Natural proteins are often only slightly more stable in the native state than the denatured state, and an increase in environmental temperature can easily shift the balance towards unfolding. Therefore, the engineering of proteins to improve protein stability is an area of intensive research. Thermostable proteins are required to withstand industrial process conditions, for increased shelf-life of protein therapeutics, for developing robust 'biobricks' for synthetic biology applications, and for research purposes (e.g. structure determination). In addition, thermostability buffers the often destabilizing effects of mutations introduced to improve other properties. Rational design approaches to engineering thermostability require structural information, but even with advanced computational methods, it is challenging to predict or parameterize all the relevant structural factors with sufficient precision to anticipate the results of a given mutation. Directed evolution is an alternative when structures are unavailable but requires extensive screening of mutant libraries. Recently however, bioinspired approaches based on phylogenetic analyses have shown great promise. Leveraging the rapid expansion in sequence data and bioinformatic tools, ancestral sequence reconstruction (ASR) can generate highly stable folds for novel applications in industrial chemistry, medicine, and synthetic biology. This review provides an overview of the factors important for successful inference of thermostable proteins by ASR and what it can reveal about the determinants of stability in proteins.
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10
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Miller JC, Schuler MA. Single mutations toggle the substrate selectivity of multifunctional Camptotheca secologanic acid synthases (CYP72As). J Biol Chem 2022; 298:102237. [PMID: 35809640 PMCID: PMC9424959 DOI: 10.1016/j.jbc.2022.102237] [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: 01/24/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
Terpene indole alkaloids (TIAs) are plant-derived specialized metabolites with widespread use in medicine. Species-specific pathways derive various TIAs from common intermediates, strictosidine or strictosidinic acid, produced by coupling tryptamine with secologanin or secologanic acid. The penultimate reaction in this pathway is catalyzed by either secologanin synthase (SLS) or secologanic acid synthase (SLAS) according to whether plants produce secologanin from loganin or secologanic acid from loganic acid. Previous work has identified SLSs and SLASs from different species, but the determinants of selectivity remain unclear. Here, combining molecular modeling, ancestral sequence reconstruction, and biochemical methodologies, we identified key residues that toggle SLS and SLAS selectivity in two CYP72A (cytochrome P450) subfamily enzymes from Camptotheca acuminata. We found that the positions of foremost importance are in substrate recognition sequence 1 (SRS1), where mutations to either of two adjacent histidine residues switched selectivity; His131Phe selects for and increases secologanin production whereas His132Asp selects for secologanic acid production. Furthermore, a change in SRS3 in the predicted substrate entry channel (Arg/Lys270Thr) and another in SRS4 at the start of the I-helix (Ser324Glu) decreased enzyme activity toward either substrate. We propose that the Camptotheca SLASs have maintained the broadened activities found in a common asterid ancestor, even as the Camptotheca lineage lost its ability to produce loganin while the campanulid and lamiid lineages specialized to produce secologanin by acquiring mutations in SRS1. The identification here of the residues essential for the broad substrate scope of SLASs presents opportunities for more tailored heterologous production of TIAs.
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Affiliation(s)
- Justin C Miller
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA 61801
| | - Mary A Schuler
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA 61801; Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA 61801; Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA 61801.
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