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Noda S, Mori Y, Ogawa Y, Fujiwara R, Dainin M, Shirai T, Kondo A. Metabolic and enzymatic engineering approach for the production of 2-phenylethanol in engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2024; 406:130927. [PMID: 38830477 DOI: 10.1016/j.biortech.2024.130927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/05/2024]
Abstract
2-Phenylethanol, known for its rose-like odor and antibacterial activity, is synthesized via exogenous phenylpyruvate by the sequential reaction of phenylpyruvate decarboxylase (PDC) and aldehyde reductase. We first targeted ARO10, a phenylpyruvate decarboxylase gene from Saccharomyces cerevisiae, and identified a suitable aldehyde reductase gene. Co-expression of ARO10 and yahK in E. coli transformants yielded 1.1 g/L of 2-phenylethanol in batch culture. We hypothesized that there might be a bottleneck in PDC activity. The computer-based enzyme evolution was utilized to enhance production. The introduction of an amino acid substitution in ARO10 (ARO10 I544W) stabilized the aromatic ring of the phenylpyruvate substrate, increasing 2-phenylethanol yield 4.1-fold compared to wild-type ARO10. Cultivation of ARO10 I544W-expressing E. coli produced 2.5 g/L of 2-phenylethanol with a yield from glucose of 0.16 g/g after 72 h. This approach represents a significant advancement, achieving the highest yield of 2-phenylethanol from glucose using microbes to date.
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Affiliation(s)
- Shuhei Noda
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; PRESTO, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
| | - Yutaro Mori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Yuki Ogawa
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ryosuke Fujiwara
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mayumi Dainin
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Lemieux P, Bradley D, Dubé AK, Dionne U, Landry CR. Dissection of the role of a Src homology 3 domain in the evolution of binding preference of paralogous proteins. Genetics 2024; 226:iyad175. [PMID: 37793087 PMCID: PMC10763533 DOI: 10.1093/genetics/iyad175] [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: 07/07/2023] [Revised: 07/07/2023] [Accepted: 08/07/2023] [Indexed: 10/06/2023] Open
Abstract
Protein-protein interactions (PPIs) drive many cellular processes. Some interactions are directed by Src homology 3 (SH3) domains that bind proline-rich motifs on other proteins. The evolution of the binding specificity of SH3 domains is not completely understood, particularly following gene duplication. Paralogous genes accumulate mutations that can modify protein functions and, for SH3 domains, their binding preferences. Here, we examined how the binding of the SH3 domains of 2 paralogous yeast type I myosins, Myo3 and Myo5, evolved following duplication. We found that the paralogs have subtly different SH3-dependent interaction profiles. However, by swapping SH3 domains between the paralogs and characterizing the SH3 domains freed from their protein context, we find that very few of the differences in interactions, if any, depend on the SH3 domains themselves. We used ancestral sequence reconstruction to resurrect the preduplication SH3 domains and examined, moving back in time, how the binding preference changed. Although the most recent ancestor of the 2 domains had a very similar binding preference as the extant ones, older ancestral domains displayed a gradual loss of interaction with the modern interaction partners when inserted in the extant paralogs. Molecular docking and experimental characterization of the free ancestral domains showed that their affinity with the proline motifs is likely not the cause for this loss of binding. Taken together, our results suggest that a SH3 and its host protein could create intramolecular or allosteric interactions essential for the SH3-dependent PPIs, making domains not functionally equivalent even when they have the same binding specificity.
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Affiliation(s)
- Pascale Lemieux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec, Université Laval, Québec, QC, Canada G1R 2J6
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada M5G 1X5
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
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Callahan BP, Xu Z. There's more to enzyme antagonism than inhibition. Bioorg Med Chem 2023; 82:117231. [PMID: 36893527 PMCID: PMC10228466 DOI: 10.1016/j.bmc.2023.117231] [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: 12/19/2022] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
A native enzyme's usual assurance in recognizing their physiological substrate(s) at the ground state and on going to the transition state can be undermined by interactions with selected small molecule antagonists, leading to the generation of abnormal products. We classify this mode of enzyme antagonism resulting in the gain-of-nonnative-function as paracatalytic induction. Enzymes bound by paracatalytic inducers exhibit new or enhanced activity toward transformations that appear aberrant or erroneous. The enzyme/ paracatalytic inducer complex may take up native substrate but then bring about a transformation that is chemically distinct from the normal reaction. Alternatively, the enzyme / paracatalytic inducer complex may exhibit abnormal ground state selectivity, preferentially interacting with and transforming a molecule outside the physiological substrate scope. Paracatalytic inducers can be cytotoxic, while in other cases they divert enzyme activity toward transformations that appear adaptive and even therapeutically useful. In this perspective, we highlight two noteworthy examples from recent literature.
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Affiliation(s)
- Brian P Callahan
- Chemistry Department, Binghamton University, Binghamton, NY 13902, United States.
| | - Zihan Xu
- Chemistry Department, Binghamton University, Binghamton, NY 13902, United States
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