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Escayola S, Bahri-Laleh N, Poater A. % VBur index and steric maps: from predictive catalysis to machine learning. Chem Soc Rev 2024; 53:853-882. [PMID: 38113051 DOI: 10.1039/d3cs00725a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Steric indices are parameters used in chemistry to describe the spatial arrangement of atoms or groups of atoms in molecules. They are important in determining the reactivity, stability, and physical properties of chemical compounds. One commonly used steric index is the steric hindrance, which refers to the obstruction or hindrance of movement in a molecule caused by bulky substituents or functional groups. Steric hindrance can affect the reactivity of a molecule by altering the accessibility of its reactive sites and influencing the geometry of its transition states. Notably, the Tolman cone angle and %VBur are prominent among these indices. Actually, steric effects can also be described using the concept of steric bulk, which refers to the space occupied by a molecule or functional group. Steric bulk can affect the solubility, melting point, boiling point, and viscosity of a substance. Even though electronic indices are more widely used, they have certain drawbacks that might shift preferences towards others. They present a higher computational cost, and often, the weight of electronics in correlation with chemical properties, e.g. binding energies, falls short in comparison to %VBur. However, it is worth noting that this may be because the steric index inherently captures part of the electronic content. Overall, steric indices play an important role in understanding the behaviour of chemical compounds and can be used to predict their reactivity, stability, and physical properties. Predictive chemistry is an approach to chemical research that uses computational methods to anticipate the properties and behaviour of these compounds and reactions, facilitating the design of new compounds and reactivities. Within this domain, predictive catalysis specifically targets the prediction of the performance and behaviour of catalysts. Ultimately, the goal is to identify new catalysts with optimal properties, leading to chemical processes that are both more efficient and sustainable. In this framework, %VBur can be a key metric for deepening our understanding of catalysis, emphasizing predictive catalysis and sustainability. Those latter concepts are needed to direct our efforts toward identifying the optimal catalyst for any reaction, minimizing waste, and reducing experimental efforts while maximizing the efficacy of the computational methods.
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Affiliation(s)
- Sílvia Escayola
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Mª Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
| | - Naeimeh Bahri-Laleh
- Iran Polymer and Petrochemical Institute (IPPI), P.O. Box 14965/115, Tehran, Iran
- Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM), Hiroshima University, Hiroshima, 739-8526, Japan
| | - Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Mª Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
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2
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Zhgun AA. Fungal BGCs for Production of Secondary Metabolites: Main Types, Central Roles in Strain Improvement, and Regulation According to the Piano Principle. Int J Mol Sci 2023; 24:11184. [PMID: 37446362 PMCID: PMC10342363 DOI: 10.3390/ijms241311184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Filamentous fungi are one of the most important producers of secondary metabolites. Some of them can have a toxic effect on the human body, leading to diseases. On the other hand, they are widely used as pharmaceutically significant drugs, such as antibiotics, statins, and immunosuppressants. A single fungus species in response to various signals can produce 100 or more secondary metabolites. Such signaling is possible due to the coordinated regulation of several dozen biosynthetic gene clusters (BGCs), which are mosaically localized in different regions of fungal chromosomes. Their regulation includes several levels, from pathway-specific regulators, whose genes are localized inside BGCs, to global regulators of the cell (taking into account changes in pH, carbon consumption, etc.) and global regulators of secondary metabolism (affecting epigenetic changes driven by velvet family proteins, LaeA, etc.). In addition, various low-molecular-weight substances can have a mediating effect on such regulatory processes. This review is devoted to a critical analysis of the available data on the "turning on" and "off" of the biosynthesis of secondary metabolites in response to signals in filamentous fungi. To describe the ongoing processes, the model of "piano regulation" is proposed, whereby pressing a certain key (signal) leads to the extraction of a certain sound from the "musical instrument of the fungus cell", which is expressed in the production of a specific secondary metabolite.
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Affiliation(s)
- Alexander A Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky Prosp. 33-2, 119071 Moscow, Russia
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3
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Goldfinger V, Spohn M, Rodler JP, Sigle M, Kulik A, Cryle MJ, Rapp J, Link H, Wohlleben W, Stegmann E. Metabolic engineering of the shikimate pathway in Amycolatopsis strains for optimized glycopeptide antibiotic production. Metab Eng 2023; 78:84-92. [PMID: 37244369 DOI: 10.1016/j.ymben.2023.05.005] [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: 02/04/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Glycopeptide antibiotics (GPA) consist of a glycosylated heptapeptide backbone enriched in aromatic residues originating from the shikimate pathway. Since the enzymatic reactions within the shikimate pathway are highly feedback-regulated, this raises the question as to how GPA producers control the delivery of precursors for GPA assembly. We chose Amycolatopsis balhimycina, the producer of balhimycin, as a model strain for analyzing the key enzymes of the shikimate pathway. A. balhimycina contains two copies each of the key enzymes of the shikimate pathway, deoxy-d-arabino-heptulosonate-7-phosphate synthase (Dahp) and prephenate dehydrogenase (Pdh), with one pair (Dahpsec and Pdhsec) encoded within the balhimycin biosynthetic gene cluster and one pair (Dahpprim and Pdhprim) in the core genome. While overexpression of the dahpsec gene resulted in a significant (>4-fold) increase in balhimycin yield, no positive effects were observed after overexpression of the pdhprim or pdhsec genes. Investigation of allosteric enzyme inhibition revealed that cross-regulation between the tyrosine and phenylalanine pathways plays an important role. Tyrosine, a key precursor of GPAs, was found to be a putative activator of prephenate dehydratase (Pdt), which catalyzes the first step reaction from prephenate to phenylalanine in the shikimate pathway. Surprisingly, overexpression of pdt in A. balhimycina led to an increase in antibiotic production in this modified strain. In order to demonstrate that this metabolic engineering approach is generally applicable to GPA producers, we subsequently applied this strategy to Amycolatopsis japonicum and improved the production of ristomycin A, which is used in diagnosis of genetic disorders. Comparison of "cluster-specific" enzymes with the isoenzymes from the primary metabolism's pathway provided insights into the adaptive mechanisms used by producers to ensure adequate precursor supply and GPA yields. These insights further demonstrate the importance of a holistic approach in bioengineering efforts that takes into account not only peptide assembly but also adequate precursor supply.
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Affiliation(s)
- Valentina Goldfinger
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Marius Spohn
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Jens-Peter Rodler
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Melanie Sigle
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia; EMBL Australia, Monash University, Clayton, VIC, 3800, Australia; ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC, 3800, Australia
| | - Johanna Rapp
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Bacterial Metabolomics, University of Tübingen, Auf der Morgenstelle 25, 72076, Tübingen, Germany
| | - Hannes Link
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Bacterial Metabolomics, University of Tübingen, Auf der Morgenstelle 25, 72076, Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence CMFI, Bacterial Metabolomics University of Tübingen, Auf der Morgenstelle 25, 72076, Tübingen, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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Tan Y, Gao C, Song W, Wei W, Liu J, Gao C, Guo L, Chen X, Liu L, Wu J. Rational Design of Meso-Diaminopimelate Dehydrogenase with Enhanced Reductive Amination Activity for Efficient Production of d- p-Hydroxyphenylglycine. Appl Environ Microbiol 2023; 89:e0010923. [PMID: 37070978 PMCID: PMC10231207 DOI: 10.1128/aem.00109-23] [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: 02/10/2023] [Accepted: 03/16/2023] [Indexed: 04/19/2023] Open
Abstract
d-p-hydroxyphenylglycine (d-HPG) is an important intermediate in the pharmaceutical industry. In this study, a tri-enzyme cascade for the production of d-HPG from l-HPG was designed. However, the amination activity of Prevotella timonensis meso-diaminopimelate dehydrogenase (PtDAPDH) toward 4-hydroxyphenylglyoxylate (HPGA) was identified as the rate-limiting step. To overcome this issue, the crystal structure of PtDAPDH was solved, and a "binding pocket and conformation remodeling" strategy was developed to improve the catalytic activity toward HPGA. The best variant obtained, PtDAPDHM4, exhibited a catalytic efficiency (kcat/Km) that was 26.75-fold higher than that of the wild type. This improvement was due to the enlarged substrate-binding pocket and enhanced hydrogen bond networks around the active center; meanwhile, the increased number of interdomain residue interactions drove the conformation distribution toward the closed state. Under optimal transformation conditions, PtDAPDHM4 produced 19.8 g/L d-HPG from 40 g/L racemate DL-HPG in a 3 L fermenter within 10 h, with 49.5% conversion and >99% enantiomeric excess. Our study provides an efficient three-enzyme cascade pathway for the industrial production of d-HPG from racemate DL-HPG. IMPORTANCE d-p-hydroxyphenylglycine (d-HPG) is an important intermediate in the synthesis of antimicrobial compounds. d-HPG is mainly produced via chemical and enzymatic approaches, and enzymatic asymmetric amination employing diaminopimelate dehydrogenase (DAPDH) is considered an attractive method. However, the low catalytic activity of DAPDH toward bulky 2-keto acids limits its applications. In this study, we identified a DAPDH from Prevotella timonensis and created a mutant, PtDAPDHM4, which exhibited a catalytic efficiency (kcat/Km) toward 4-hydroxyphenylglyoxylate that was 26.75-fold higher than that of the wild type. The novel strategy developed in this study has practical value for the production of d-HPG from inexpensive racemate DL-HPG.
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Affiliation(s)
- Yang Tan
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Changzheng Gao
- Department of Cardiology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
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Awakawa T, Mori T, Ushimaru R, Abe I. Structure-based engineering of α-ketoglutarate dependent oxygenases in fungal meroterpenoid biosynthesis. Nat Prod Rep 2023; 40:46-61. [PMID: 35642933 DOI: 10.1039/d2np00014h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Non-heme iron- and α-ketoglutarate-dependent oxygenases (αKG OXs) are key enzymes that play a major role in diversifying the structure of fungal meroterpenoids. They activate a specific C-H bond of the substrate to first generate radical species, which is usually followed by oxygen rebound to produce cannonical hydroxylated products. However, in some cases remarkable chemistry induces dramatic structural changes in the molecular scaffolds, depending on the stereoelectronic characters of the substrate/intermediates and the resulting conformational changes/movements of the active site of the enzyme. Their molecular bases have been extensively investigated by crystallographic structural analyses and structure-based mutagenesis, which revealed intimate structural details of the enzyme reactions. This information facilitates the manipulation of the enzyme reactions to create unnatural, novel molecules for drug discovery. This review summarizes recent progress in the structure-based engineering of αKG OX enzymes, involved in the biosynthesis of polyketide-derived fungal meroterpenoids. The literature published from 2016 through February 2022 is reviewed.
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Affiliation(s)
- Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,ACT-X, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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6
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Jung DY, Li X, Li Z. Engineering of Hydroxymandelate Oxidase and Cascade Reactions for High-Yielding Conversion of Racemic Mandelic Acids to Phenylglyoxylic Acids and ( R)- and ( S)-Phenylglycines. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Do-Yun Jung
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Xirui Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
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Amino acid (acyl carrier protein) ligase-associated biosynthetic gene clusters reveal unexplored biosynthetic potential. Mol Genet Genomics 2023; 298:49-65. [PMID: 36271918 DOI: 10.1007/s00438-022-01962-7] [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: 05/04/2022] [Accepted: 10/09/2022] [Indexed: 01/10/2023]
Abstract
This study aimed to evaluate the postulated cellular function of a novel family of amino acid (acyl carrier protein) ligases (AALs) in natural product biosynthesis. Here, we analyzed the manually curated, putative, aal-associated natural product biosynthetic gene clusters (NP BGCs) using two computational platforms for NP prediction, antiSMASH-BiG-SCAPE-CORASON and DeepBGC. The detected BGCs included a diversity of type I polyketide/nonribosomal peptide (PKS/NRPS) hybrid BGCs, exemplified by the guadinomine BGC, which suggested a dedicated function of AALs in the biosynthesis of rare (2S)-aminomalonyl-ACP extension units. Besides modular PKS/NRPSs and NRPSs, AAL-associated BGCs were predicted to assemble arylpolyenes, ladderane lipids, phosphonates, aminoglycosides, β-lactones, and thioamides of both nonribosomal and ribosomal origins. Additionally, we revealed a frequent association of AALs with putative, seldom observed transglutaminase-like and BtrH-like transferases of the cysteine protease superfamily, which may form larger families of ACP-dependent amide bond catalysts used in NP synthesis. Our results disclosed an exceptional chemical novelty and biosynthetic potential of the AAL-associated BGCs in NP biosynthesis. The presented in silico evidence supports the initial hypothesis and provides an important foundation for future experimental studies aimed at discovering novel pharmaceutically relevant active compounds.
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8
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Khatua H, Das S, Patra S, Das SK, Roy S, Chattopadhyay B. Iron-Catalyzed Intermolecular Amination of Benzylic C(sp 3)-H Bonds. J Am Chem Soc 2022; 144:21858-21866. [PMID: 36416746 DOI: 10.1021/jacs.2c10719] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A catalytic system for intermolecular benzylic C(sp3)-H amination is developed utilizing 1,2,3,4-tetrazole as a nitrene precursor via iron catalysis. This method enables direct installation of 2-aminopyridine into the benzylic and heterobenzylic position. The method selectively aminates 2° benzylic C(sp3)-H bond over the 3° and 1° benzylic C(sp3)-H bonds. Experimental studies reveal that the C(sp3)-H amination undergoes via the formation of a benzylic radical intermediate. This study reports the discovery of new method for 2-pyridine substituted benzylamine synthesis using inexpensive, biocompatible base metal catalysis that should have wide application in the context of medicinal chemistry and drug discovery.
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Affiliation(s)
- Hillol Khatua
- Department of Biological & Synthetic Chemistry, Center of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Subrata Das
- Department of Biological & Synthetic Chemistry, Center of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Sima Patra
- Department of Biological & Synthetic Chemistry, Center of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Sandip Kumar Das
- Department of Biological & Synthetic Chemistry, Center of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Satyajit Roy
- Department of Biological & Synthetic Chemistry, Center of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Buddhadeb Chattopadhyay
- Department of Biological & Synthetic Chemistry, Center of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
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Mao HF, Xing HM, Jin MM, Liu JB, Yao YL, Zhao Y. An in-depth mechanistic study of the p-hydroxyphenylglycine synthetic process using in situ ATR-IR spectroscopy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2833-2840. [PMID: 35786717 DOI: 10.1039/d2ay00706a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this study, an in situ ATR-IR technique was used as a powerful tool to gain insight into the synthetic process of p-hydroxyphenylglycine (p-HPG) by the sulfamic acid-glyoxylic acid-phenol method. Combined with other chemical and instrumental analysis technologies, the reaction sequence and key intermediates of this one-pot reaction were determined, and two concomitant reaction paths have been put forward for the first time. The possible reaction mechanism has been suggested, and the reaction efficiency of each path is discussed in detail. Through the optimization of the experimental parameters, an approximately 40% increase in the final product yield was achieved compared with previous reports. We believe that this study will without a doubt trigger research interest in understanding the industrial production process of important chemicals and pharmaceuticals and as a result will promote the sustainable development and application of novel, efficient chemical reaction routes.
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Affiliation(s)
- Hai-Fang Mao
- Shanghai Institute of Technology, No. 100 Haiquan Road, Shanghai, 201418, China.
| | - Hui-Min Xing
- Shanghai Institute of Technology, No. 100 Haiquan Road, Shanghai, 201418, China.
| | - Miao-Miao Jin
- Shanghai Institute of Technology, No. 100 Haiquan Road, Shanghai, 201418, China.
| | - Ji-Bo Liu
- Shanghai Institute of Technology, No. 100 Haiquan Road, Shanghai, 201418, China.
| | - Yue-Liang Yao
- Shanghai Institute of Technology, No. 100 Haiquan Road, Shanghai, 201418, China.
| | - Yun Zhao
- Shanghai Institute of Technology, No. 100 Haiquan Road, Shanghai, 201418, China.
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Kang S, Han J, Jang SC, An JS, Kang I, Kwon Y, Nam SJ, Shim SH, Cho JC, Lee SK, Oh DC. Epoxinnamide: An Epoxy Cinnamoyl-Containing Nonribosomal Peptide from an Intertidal Mudflat-Derived Streptomyces sp. Mar Drugs 2022; 20:md20070455. [PMID: 35877748 PMCID: PMC9321520 DOI: 10.3390/md20070455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/09/2022] [Accepted: 07/09/2022] [Indexed: 12/03/2022] Open
Abstract
Cinnamoyl-containing nonribosomal peptides (CCNPs) form a unique family of actinobacterial secondary metabolites and display various biological activities. A new CCNP named epoxinnamide (1) was discovered from intertidal mudflat-derived Streptomyces sp. OID44. The structure of 1 was determined by the analysis of one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance (NMR) data along with a mass spectrum. The absolute configuration of 1 was assigned by the combination of advanced Marfey’s method, 3JHH and rotating-frame overhauser effect spectroscopy (ROESY) analysis, DP4 calculation, and genomic analysis. The putative biosynthetic pathway of epoxinnamide (1) was identified through the whole-genome sequencing of Streptomyces sp. OID44. In particular, the thioesterase domain in the nonribosomal peptide synthetase (NRPS) biosynthetic gene cluster was proposed as a bifunctional enzyme, which catalyzes both epimerization and macrocyclization. Epoxinnamide (1) induced quinone reductase (QR) activity in murine Hepa-1c1c7 cells by 1.6-fold at 5 μM. It also exhibited effective antiangiogenesis activity in human umbilical vein endothelial cells (IC50 = 13.4 μM).
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Affiliation(s)
- Sangwook Kang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Jaeho Han
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (J.-C.C.)
| | - Yun Kwon
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea;
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea;
| | - Sang Hee Shim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (J.-C.C.)
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (S.K.); (J.H.); (S.C.J.); (J.S.A.); (S.H.S.); (S.K.L.)
- Correspondence: ; Tel.: +82-880-2491; Fax: +82-762-8322
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11
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Ouchene R, Stien D, Segret J, Kecha M, Rodrigues AMS, Veckerlé C, Suzuki MT. Integrated Metabolomic, Molecular Networking, and Genome Mining Analyses Uncover Novel Angucyclines From Streptomyces sp. RO-S4 Strain Isolated From Bejaia Bay, Algeria. Front Microbiol 2022; 13:906161. [PMID: 35814649 PMCID: PMC9260717 DOI: 10.3389/fmicb.2022.906161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Multi-omic approaches have recently made big strides toward the effective exploration of microorganisms, accelerating the discovery of new bioactive compounds. We combined metabolomic, molecular networking, and genomic-based approaches to investigate the metabolic potential of the Streptomyces sp. RO-S4 strain isolated from the polluted waters of Bejaia Bay in Algeria. Antagonistic assays against methicillin-resistant Staphylococcus aureus with RO-S4 organic extracts showed an inhibition zone of 20 mm by using the agar diffusion method, and its minimum inhibitory concentration was 16 μg/ml. A molecular network was created using GNPS and annotated through the comparison of MS/MS spectra against several databases. The predominant compounds in the RO-S4 extract belonged to the angucycline family. Three compounds were annotated as known metabolites, while all the others were putatively new to Science. Notably, all compounds had fridamycin-like aglycones, and several of them had a lactonized D ring analogous to that of urdamycin L. The whole genome of Streptomyces RO-S4 was sequenced to identify the biosynthetic gene cluster (BGC) linked to these angucyclines, which yielded a draft genome of 7,497,846 bp with 72.4% G+C content. Subsequently, a genome mining analysis revealed 19 putative biosynthetic gene clusters, including a grincamycin-like BGC with high similarity to that of Streptomyces sp. CZN-748, that was previously reported to also produce mostly open fridamycin-like aglycones. As the ring-opening process leading to these compounds is still not defined, we performed a comparative analysis with other angucycline BGCs and advanced some hypotheses to explain the ring-opening and lactonization, possibly linked to the uncoupling between the activity of GcnE and GcnM homologs in the RO-S4 strain. The combination of metabolomic and genomic approaches greatly improved the interpretation of the metabolic potential of the RO-S4 strain.
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Affiliation(s)
- Rima Ouchene
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650, Banyuls-sur-mer, France
| | - Didier Stien
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650, Banyuls-sur-mer, France
- *Correspondence: Didier Stien
| | - Juliette Segret
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650, Banyuls-sur-mer, France
| | - Mouloud Kecha
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
| | - Alice M. S. Rodrigues
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650, Banyuls-sur-mer, France
| | - Carole Veckerlé
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650, Banyuls-sur-mer, France
| | - Marcelino T. Suzuki
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650, Banyuls-sur-mer, France
- Marcelino T. Suzuki
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12
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Liang Y, Luo J, Yang C, Guo S, Zhang B, Chen F, Su K, Zhang Y, Dong Y, Wang Z, Fu H, Sui G, Wang P. Directed evolution of the PobR allosteric transcription factor to generate a biosensor for 4-hydroxymandelic acid. World J Microbiol Biotechnol 2022; 38:104. [PMID: 35501522 DOI: 10.1007/s11274-022-03286-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
Abstract
Hydroxy-mandelic acid (HMA) is widely applied in pharmaceuticals, food and cosmetics. In this study, we aimed to develop an allosteric transcription factors (aTFs) based biosensor for HMA. PobR, an aTF for HMA analog 4-hydroxybenzoic acid, was used to alter its selectivity and create novel aTFs responsive to HMA by directed evolution. We established a PobR mutant library with a capacity of 550,000 mutants using error-prone PCR and Megawhop PCR. Through our screening, two mutants were obtained with responsiveness to HMA. Analysis of each missense mutation indicating residues 122-126 were involved in its PobR ligand specificity. These results showed the effectiveness of directed evolution in switching the ligand specificity of a biosensor and improving HMA production.
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Affiliation(s)
- YaoYao Liang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Juan Luo
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Chenhao Yang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Shuning Guo
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Bowen Zhang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Fengqianrui Chen
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Kairui Su
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Yulong Zhang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Yi Dong
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Zhihao Wang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Hongda Fu
- NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Guangchao Sui
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Northeast Forestry University, No. 26 Hexing Road, Harbin, 150000, People's Republic of China.
| | - Pengchao Wang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, Heilongjiang, 150040, People's Republic of China. .,Northeast Forestry University, No. 26 Hexing Road, Harbin, 150000, People's Republic of China.
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13
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An JS, Kim MS, Han J, Jang SC, Im JH, Cui J, Lee Y, Nam SJ, Shin J, Lee SK, Yoon YJ, Oh DC. Nyuzenamide C, an Antiangiogenic Epoxy Cinnamic Acid-Containing Bicyclic Peptide from a Riverine Streptomyces sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:804-814. [PMID: 35294831 DOI: 10.1021/acs.jnatprod.1c00837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A new nonribosomal peptide, nyuzenamide C (1), was discovered from riverine sediment-derived Streptomyces sp. DM14. Comprehensive analysis of the spectroscopic data of nyuzenamide C (1) revealed that 1 has a bicyclic backbone composed of six common amino acid residues (Asn, Leu, Pro, Gly, Val, and Thr) and four nonproteinogenic amino acid units, including hydroxyglycine, β-hydroxyphenylalanine, p-hydroxyphenylglycine, and 3,β-dihydroxytyrosine, along with 1,2-epoxypropyl cinnamic acid. The absolute configuration of 1 was proposed by J-based configuration analysis, the advanced Marfey's method, quantum mechanics-based DP4 calculations, and bioinformatic analysis of its nonribosomal peptide synthetase biosynthetic gene cluster. Nyuzenamide C (1) displayed antiangiogenic activity in human umbilical vein endothelial cells and induced quinone reductase in murine Hepa-1c1c7 cells.
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Myoun-Su Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaeho Han
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonjin Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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14
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Wojdyla Z, Borowski T. Properties of the Reactants and Their Interactions within and with the Enzyme Binding Cavity Determine Reaction Selectivities. The Case of Fe(II)/2-Oxoglutarate Dependent Enzymes. Chemistry 2022; 28:e202104106. [PMID: 34986268 DOI: 10.1002/chem.202104106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate dependent dioxygenases (ODDs) share a double stranded beta helix (DSBH) fold and utilise a common reactive intermediate, ferryl species, to catalyse oxidative transformations of substrates. Despite the structural similarities, ODDs accept a variety of substrates and facilitate a wide range of reactions, that is hydroxylations, desaturations, (oxa)cyclisations and ring rearrangements. In this review we present and discuss the factors contributing to the observed (regio)selectivities of ODDs. They span from inherent properties of the reactants, that is, substrate molecule and iron cofactor, to the interactions between the substrate and the enzyme's binding cavity; the latter can counterbalance the effect of the former. Based on results of both experimental and computational studies dedicated to ODDs, we also line out the properties of the reactants which promote reaction outcomes other than the "default" hydroxylation. It turns out that the reaction selectivity depends on a delicate balance of interactions between the components of the investigated system.
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Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
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15
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Liu Y, Xie N, Yu B. De Novo Biosynthesis of D- p-Hydroxyphenylglycine by a Designed Cofactor Self-Sufficient Route and Co-culture Strategy. ACS Synth Biol 2022; 11:1361-1372. [PMID: 35244401 DOI: 10.1021/acssynbio.2c00007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
d-p-Hydroxyphenylglycine (D-HPG) is an important intermediate for the synthesis of β-lactam antibiotics with an annual market demand of thousands of tons. Currently, the main production processes are via chemical approaches. Although enzymatic conversion has been investigated for D-HPG production, synthesis of the substrate DL-hydroxyphenylhydantoin is still chemically based, which suffers from high pollution and harsh reaction conditions. In this study, one cofactor self-sufficient route for D-HPG production from l-phenylalanine was newly designed and the artificial pathway was functionalized by selecting suitable enzymes and adjusting their expressions in strain Pseudomonas putida KT2440. Notably, a new R-mandelate dehydrogenase from Lactococcus lactis with relatively high activity under pH neutral conditions was successfully mined to demonstrate the biosynthetic pathway in vivo. The performance of the engineered P. putida strain was further increased by enhancing cellular NAD availability and blocking l-phenylalanine consumption. Coupled with the l-phenylalanine producer, Escherichia coli strain ATCC 31884, a stable and interactive co-culture process was also developed by engineering a "cross-link auxotrophic" system to produce D-HPG directly from glucose. Thus, this study is the first approach for the de novo biosynthesis of D-HPG by engineering a non-natural pathway and lays the foundation for further improving the efficiency of D-HPG production via a green and sustainable route.
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Affiliation(s)
- Yang Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nengzhong Xie
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, Nanning 530007, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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16
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Wang P, Zhang X, Tao Y, Lv X, Cheng S, Liu C. Improved l-phenylglycine synthesis by introducing an engineered cofactor self-sufficient system. Synth Syst Biotechnol 2022; 7:513-521. [PMID: 35024478 PMCID: PMC8715069 DOI: 10.1016/j.synbio.2021.12.008] [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: 08/16/2021] [Revised: 11/18/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022] Open
Abstract
l-phenylglycine (L-phg) is a valuable non-proteinogenic amino acid used as a precursor to β-lactam antibiotics, antitumor agent taxol and many other pharmaceuticals. L-phg synthesis through microbial bioconversion allows for high enantioselectivity and sustainable production, which will be of great commercial and environmental value compared with organic synthesis methods. In this work, an L-phg synthesis pathway was built in Escherichia coli resulting in 0.23 mM L-phg production from 10 mM l-phenylalanine. Then, new hydroxymandelate synthases and hydroxymandelate oxidases were applied in the L-phg synthesis leading to a 5-fold increase in L-phg production. To address 2-oxoglutarate, NH4 +, and NADH shortage, a cofactor self-sufficient system was introduced, which converted by-product l-glutamate and NAD+ to these three cofactors simultaneously. In this way, L-phg increased 2.5-fold to 2.82 mM. Additionally, in order to reduce the loss of these three cofactors, a protein scaffold between synthesis pathway and cofactor regeneration modular was built, which further improved the L-phg production to 3.72 mM with a yield of 0.34 g/g L-phe. This work illustrated a strategy applying for whole-cell biocatalyst converting amino acid to its value-added chiral amine in a cofactor self-sufficient manner.
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Affiliation(s)
- Pengchao Wang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
- Key Laboratory for Enzymes and Enzyme-like Material Engineering of Heilongjiang, PR China
| | - Xiwen Zhang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
| | - Yucheng Tao
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
| | - Xubing Lv
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
| | - Shengjie Cheng
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
| | - Chengwei Liu
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, PR China
- Key Laboratory for Enzymes and Enzyme-like Material Engineering of Heilongjiang, PR China
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17
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Martín JF, Liras P. Comparative Molecular Mechanisms of Biosynthesis of Naringenin and Related Chalcones in Actinobacteria and Plants: Relevance for the Obtention of Potent Bioactive Metabolites. Antibiotics (Basel) 2022; 11:antibiotics11010082. [PMID: 35052959 PMCID: PMC8773403 DOI: 10.3390/antibiotics11010082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/01/2022] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
Naringenin and its glycosylated derivative naringin are flavonoids that are synthesized by the phenylpropanoid pathway in plants. We found that naringenin is also formed by the actinobacterium Streptomyces clavuligerus, a well-known microorganism used to industrially produce clavulanic acid. The production of naringenin in S. clavuligerus involves a chalcone synthase that uses p-coumaric as a starter unit and a P450 monoxygenase, encoded by two adjacent genes (ncs-ncyP). The p-coumaric acid starter unit is formed by a tyrosine ammonia lyase encoded by an unlinked, tal, gene. Deletion and complementation studies demonstrate that these three genes are required for biosynthesis of naringenin in S. clavuligerus. Other actinobacteria chalcone synthases use caffeic acid, ferulic acid, sinapic acid or benzoic acid as starter units in the formation of different antibiotics and antitumor agents. The biosynthesis of naringenin is restricted to a few Streptomycess species and the encoding gene cluster is present also in some Saccharotrix and Kitasatospora species. Phylogenetic comparison of S. clavuligerus naringenin chalcone synthase with homologous proteins of other actinobacteria reveal that this protein is closely related to chalcone synthases that use malonyl-CoA as a starter unit for the formation of red-brown pigment. The function of the core enzymes in the pathway, such as the chalcone synthase and the tyrosine ammonia lyase, is conserved in plants and actinobacteria. However, S. clavuligerus use a P450 monooxygenase proposed to complete the cyclization step of the naringenin chalcone, whereas this reaction in plants is performed by a chalcone isomerase. Comparison of the plant and S. clavuligerus chalcone synthases indicates that they have not been transmitted between these organisms by a recent horizontal gene transfer phenomenon. We provide a comprehensive view of the molecular genetics and biochemistry of chalcone synthases and their impact on the development of antibacterial and antitumor compounds. These advances allow new bioactive compounds to be obtained using combinatorial strategies. In addition, processes of heterologous expression and bioconversion for the production of naringenin and naringenin-derived compounds in yeasts are described.
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18
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Li X, Awakawa T, Mori T, Ling M, Hu D, Wu B, Abe I. Heterodimeric Non-heme Iron Enzymes in Fungal Meroterpenoid Biosynthesis. J Am Chem Soc 2021; 143:21425-21432. [PMID: 34881885 DOI: 10.1021/jacs.1c11548] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Talaromyolides (1-6) are a group of unusual 6/6/6/6/6/6 hexacyclic meroterpenoids with (3R)-6-hydroxymellein and 4,5-seco-drimane substructures, isolated from the marine fungus Talaromyces purpureogenus. We have identified the biosynthetic gene cluster tlxA-J by heterologous expression in Aspergillus, in vitro enzyme assays, and CRISPR-Cas9-based gene inactivation. Remarkably, the heterodimer of non-heme iron (NHI) enzymes, TlxJ-TlxI, catalyzes three steps of oxidation including a key reaction, hydroxylation at C-5 and C-9 of 12, the intermediate with 3-ketohydroxydrimane scaffold, to facilitate a retro-aldol reaction, leading to the construction of the 4,5-secodrimane skeleton and characteristic ketal scaffold of 1-6. The products of TlxJ-TlxI, 1 and 4, were further hydroxylated at C-4'β by another NHI heterodimer, TlxA-TlxC, and acetylated by TlxB to yield the final products, 3 and 6. The X-ray structural analysis coupled with site-directed mutagenesis provided insights into the heterodimer TlxJ-TlxI formation and its catalysis. This is the first report to show that two NHI proteins form a heterodimer for catalysis and utilizes a novel methodology to create functional oxygenase structures in secondary metabolite biosynthesis.
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Affiliation(s)
- Xinyang Li
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Meiqi Ling
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Bin Wu
- Ocean College, Zhejiang University, Hangzhou 310058, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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19
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Wu Z, Li Y, Zhang L, Ding Z, Shi G. Microbial production of small peptide: pathway engineering and synthetic biology. Microb Biotechnol 2021; 14:2257-2278. [PMID: 33459516 PMCID: PMC8601181 DOI: 10.1111/1751-7915.13743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 01/14/2023] Open
Abstract
Small peptides are a group of natural products with low molecular weights and complex structures. The diverse structures of small peptides endow them with broad bioactivities and suggest their potential therapeutic use in the medical field. The remaining challenge is methods to address the main limitations, namely (i) the low amount of available small peptides from natural sources, and (ii) complex processes required for traditional chemical synthesis. Therefore, harnessing microbial cells as workhorse appears to be a promising approach to synthesize these bioactive peptides. As an emerging engineering technology, synthetic biology aims to create standard, well-characterized and controllable synthetic systems for the biosynthesis of natural products. In this review, we describe the recent developments in the microbial production of small peptides. More importantly, synthetic biology approaches are considered for the production of small peptides, with an emphasis on chassis cells, the evolution of biosynthetic pathways, strain improvements and fermentation.
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Affiliation(s)
- Zhiyong Wu
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Youran Li
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Liang Zhang
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Zhongyang Ding
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Guiyang Shi
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
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20
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Rembeza E, Boverio A, Fraaije MW, Engqvist MKM. Discovery of Two Novel Oxidases Using a High-Throughput Activity Screen. Chembiochem 2021; 23:e202100510. [PMID: 34709726 PMCID: PMC9299179 DOI: 10.1002/cbic.202100510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/27/2021] [Indexed: 12/17/2022]
Abstract
Discovery of novel enzymes is a challenging task, yet a crucial one, due to their increasing relevance as chemical catalysts and biotechnological tools. In our work we present a high-throughput screening approach to discovering novel activities. A screen of 96 putative oxidases with 23 substrates led to the discovery of two new enzymes. The first enzyme, N-acetyl-D-hexosamine oxidase (EC 1.1.3.29) from Ralstonia solanacearum, is a vanillyl alcohol oxidase-like flavoprotein displaying the highest activity with N-acetylglucosamine and N-acetylgalactosamine. Before our discovery of the enzyme, its activity was an orphan one - experimentally characterized but lacking the link to amino acid sequence. The second enzyme, from an uncultured marine euryarchaeota, is a long-chain alcohol oxidase (LCAO, EC 1.1.3.20) active with a range of fatty alcohols, with 1-dodecanol being the preferred substrate. The enzyme displays no sequence similarity to previously characterised LCAOs, and thus is a completely novel representative of a protein with such activity.
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Affiliation(s)
- Elzbieta Rembeza
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Alessandro Boverio
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Martin K M Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
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21
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Pandey RP, Casini A, Voigt CA, Gordon DB. Four-Step Pathway from Phenylpyruvate to Benzylamine, an Intermediate to the High-Energy Propellant CL-20. ACS Synth Biol 2021; 10:2187-2196. [PMID: 34491727 DOI: 10.1021/acssynbio.1c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benzylamine is a commodity chemical used in the synthesis of motion-sickness treatments and anticonvulsants, in dyeing textiles, and as a precursor to the high-energy propellant CL-20. Because chemical production generates toxic waste streams, biosynthetic alternatives have been explored, recently resulting in a functional nine-step pathway from central metabolism (phenylalanine) in E. coli. We report a novel four-step pathway for benzylamine production, which generates the product from cellular phenylpyruvate using enzymes from different sources: a mandelate synthase (Amycolatopsis orientalis), a mandelate oxidase (Streptomyces coelicolor), a benzoylformate decarboxylase (Pseudomonas putida), and an aminotransferase (Salicibacter pomeroyi). This pathway produces benzylamine at 24 mg/L in 15 h (4.5% yield) in cultures of unoptimized cells supplemented with phenylpyruvate. Because the yield is low, supplementation with pathway intermediates is used to troubleshoot the design. This identifies conversion inefficiencies in the mandelate synthase-mediated synthesis of (S)-mandelic acid, and subsequent genome mining identifies a new mandelate synthase (Streptomyces sp. 1114.5) with improved yield. Supplementation experiments also reveal native redirection of ambient phenylpyruvate away from the pathway to phenylalanine. Overall, this work illustrates how retrosynthetic design can dramatically reduce the number of enzymes in a pathway, potentially reducing its draw on cellular resources. However, it also shows that such benefits can be abrogated by inefficiencies of individual conversions. Addressing these barriers can provide an alternative approach to green production of benzylamine, eliminating upstream dependence on chlorination chemistry.
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Affiliation(s)
- Ramesh Prasad Pandey
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Arturo Casini
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Christopher A. Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - D. Benjamin Gordon
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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22
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Banh RS, Kim ES, Spillier Q, Biancur DE, Yamamoto K, Sohn ASW, Shi G, Jones DR, Kimmelman AC, Pacold ME. The polar oxy-metabolome reveals the 4-hydroxymandelate CoQ10 synthesis pathway. Nature 2021; 597:420-425. [PMID: 34471290 PMCID: PMC8538427 DOI: 10.1038/s41586-021-03865-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/29/2021] [Indexed: 12/17/2022]
Abstract
Oxygen is critical for a multitude of metabolic processes that are essential for human life. Biological processes can be identified by treating cells with 18O2 or other isotopically labelled gases and systematically identifying biomolecules incorporating labeled atoms. Here we labelled cell lines of distinct tissue origins with 18O2 to identify the polar oxy-metabolome, defined as polar metabolites labelled with 18O under different physiological O2 tensions. The most highly 18O-labelled feature was 4-hydroxymandelate (4-HMA). We demonstrate that 4-HMA is produced by hydroxyphenylpyruvate dioxygenase-like (HPDL), a protein of previously unknown function in human cells. We identify 4-HMA as an intermediate involved in the biosynthesis of the coenzyme Q10 (CoQ10) headgroup in human cells. The connection of HPDL to CoQ10 biosynthesis provides crucial insights into the mechanisms underlying recently described neurological diseases related to HPDL deficiencies1-4 and cancers with HPDL overexpression5.
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Affiliation(s)
- Robert S Banh
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Esther S Kim
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Quentin Spillier
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Douglas E Biancur
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Keisuke Yamamoto
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Albert S W Sohn
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Guangbin Shi
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Drew R Jones
- Metabolomics Core Resource Laboratory, New York University Langone Health, New York, NY, USA
| | - Alec C Kimmelman
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Michael E Pacold
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA.
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA.
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23
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Walker AS, Clardy J. A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters. J Chem Inf Model 2021; 61:2560-2571. [PMID: 34042443 PMCID: PMC8243324 DOI: 10.1021/acs.jcim.0c01304] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Research in natural products, the genetically encoded small molecules produced by organisms in an idiosyncratic fashion, deals with molecular structure, biosynthesis, and biological activity. Bioinformatics analyses of microbial genomes can successfully reveal the genetic instructions, biosynthetic gene clusters, that produce many natural products. Genes to molecule predictions made on biosynthetic gene clusters have revealed many important new structures. There is no comparable method for genes to biological activity predictions. To address this missing pathway, we developed a machine learning bioinformatics method for predicting a natural product's antibiotic activity directly from the sequence of its biosynthetic gene cluster. We trained commonly used machine learning classifiers to predict antibacterial or antifungal activity based on features of known natural product biosynthetic gene clusters. We have identified classifiers that can attain accuracies as high as 80% and that have enabled the identification of biosynthetic enzymes and their corresponding molecular features that are associated with antibiotic activity.
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Affiliation(s)
- Allison S Walker
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
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24
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Tan X, Zhang S, Song W, Liu J, Gao C, Chen X, Liu L, Wu J. A multi-enzyme cascade for efficient production of D-p-hydroxyphenylglycine from L-tyrosine. BIORESOUR BIOPROCESS 2021; 8:41. [PMID: 38650231 PMCID: PMC10991500 DOI: 10.1186/s40643-021-00394-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/10/2021] [Indexed: 11/10/2022] Open
Abstract
In this study, a four-enzyme cascade pathway was developed and reconstructed in vivo for the production of D-p-hydroxyphenylglycine (D-HPG), a valuable intermediate used to produce β-lactam antibiotics and in fine-chemical synthesis, from L-tyrosine. In this pathway, catalytic conversion of the intermediate 4-hydroxyphenylglyoxalate by meso-diaminopimelate dehydrogenase from Corynebacterium glutamicum (CgDAPDH) was identified as the rate-limiting step, followed by application of a mechanism-guided "conformation rotation" strategy to decrease the hydride-transfer distance d(C6HDAP-C4NNADP) and increase CgDAPDH activity. Introduction of the best variant generated by protein engineering (CgDAPDHBC621/D120S/W144S/I169P with 5.32 ± 0.85 U·mg-1 specific activity) into the designed pathway resulted in a D-HPG titer of 42.69 g/L from 50-g/L L-tyrosine in 24 h, with 92.5% conversion, 71.5% isolated yield, and > 99% enantiomeric excess in a 3-L fermenter. This four-enzyme cascade provides an efficient enzymatic approach for the industrial production of D-HPG from cheap amino acids.
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Affiliation(s)
- Xu Tan
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Sheng Zhang
- Zhejiang Tianrui Chemical Co., Ltd, Quzhou, 324400, China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
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25
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Upert G, Luther A, Obrecht D, Ermert P. Emerging peptide antibiotics with therapeutic potential. MEDICINE IN DRUG DISCOVERY 2021; 9:100078. [PMID: 33398258 PMCID: PMC7773004 DOI: 10.1016/j.medidd.2020.100078] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/15/2020] [Accepted: 12/27/2020] [Indexed: 02/09/2023] Open
Abstract
This review covers some of the recent progress in the field of peptide antibiotics with a focus on compounds with novel or established mode of action and with demonstrated efficacy in animal infection models. Novel drug discovery approaches, linear and macrocyclic peptide antibiotics, lipopeptides like the polymyxins as well as peptides addressing targets located in the plasma membrane or in the outer membrane of bacterial cells are discussed.
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Key Words
- ADMET, absorption, distribution, metabolism and excretion – toxicity in pharmacokinetics
- AMP, antimicrobial peptide
- AMR, antimicrobial resistance
- ATCC, ATCC cell collection
- Antibiotic
- BAM, β-barrel assembly machinery
- CC50, cytotoxic concentration to kill 50% of cells
- CD, circular dichroism
- CFU, colony forming unit
- CLSI, clinical and laboratory standards institute
- CMS, colistin methane sulfonate
- DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphocholine
- ESKAPE, acronym encompassing six bacterial pathogens (often carrying antibiotic resistance): Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp
- FDA, U. S. Food and Drug Administration
- HABP, hospital acquired bacterial pneumonia
- HDP, host-defense peptide
- HEK293, human embryonic kidney 293 cells
- HK-2, human kidney 2 cells (proximal tubular cell line)
- HepG2, human hepatocellular carcinoma cell line
- Hpg, 4-hydroxy-phenyl glycine
- ITC, isothermal titration calorimetry
- KPC, Klebsiella pneumoniae metallo-β-lactamase C resistant
- LPS, lipopolysaccharide
- LptA, lipopolysaccharide transport protein A
- LptC, lipopolysaccharide transport protein C
- LptD, lipopolysaccharide transport protein D
- MDR, multidrug-resistant
- MH-I, Müller-Hinton broth I
- MH-II, Müller-Hinton broth II (cation adjusted)
- MIC, minimal inhibitory concentration
- MRSA, methicilline-resistant S. aureus
- MSSA, methicilline-sensitive S. aureus
- MoA, mechanism (mode) of action
- NDM-1, New Delhi metallo-β-lactamase resistant
- NOAEL, no adverse effect level
- ODL, odilorhabdin
- OMPTA (outer membrane targeting antibiotic)
- OMPTA, outer membrane targeting antibiotic
- Omp, outer membrane protein
- PBMC, peripheral mononuclear blood cell
- PBP, penicillin-binding protein
- PBS, phosphate-buffered saline
- PK, pharmacokinetics
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
- POPG, 2-oleoyl-1-palmitoyl-sn-glycero-3-phospho-(1-glycerol)
- PrAMPs, polyproline antimicrobial peptides
- RBC, red blood cell
- SAR, structure-activity relationship
- SPR, surface plasmon resonance
- SPase I, signal peptidase I
- VABP, ventilator associated bacterial pneumonia
- VIM-1, beta-lactamase 2 (K. pneumoniae)
- VISA, vancomycin-intermediate S. aureus
- VRE, vancomycin-resistant enterococcus
- WHO, World Health Organization
- WT, wild type
- WTA, wall teichoic acid
- XDR, extremely drug-resistant
- antimicrobial peptide
- antimicrobial resistance
- bid, bis in die (two times a day)
- i.p., intraperitoneal
- i.v., intravenous
- lipopeptide
- mITT population, minimal intend-to-treat population
- peptide antibiotic
- s.c., subcutaneous
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Affiliation(s)
- Gregory Upert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Anatol Luther
- Bachem AG, Hauptstrasse 114, 4416 Bubendorf, Switzerland
| | - Daniel Obrecht
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Philipp Ermert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
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C-Methylation of S-adenosyl-L-Methionine Occurs Prior to Cyclopropanation in the Biosynthesis of 1-Amino-2-Methylcyclopropanecarboxylic Acid (Norcoronamic Acid) in a Bacterium. Biomolecules 2020; 10:biom10050775. [PMID: 32429436 PMCID: PMC7277169 DOI: 10.3390/biom10050775] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
Many pharmacologically important peptides are bacterial or fungal in origin and contain nonproteinogenic amino acid (NPA) building blocks. Recently, it was reported that, in bacteria, a cyclopropane-containing NPA 1-aminocyclopropanecarboxylic acid (ACC) is produced from the L-methionine moiety of S-adenosyl-L-methionine (SAM) by non-canonical ACC-forming enzymes. On the other hand, it has been suggested that a monomethylated ACC analogue, 2-methyl-ACC (MeACC), is derived from L-valine. Therefore, we have investigated the MeACC biosynthesis by identifying a gene cluster containing bacterial MeACC synthase genes. In this gene cluster, we identified two genes, orf29 and orf30, which encode a cobalamin (B12)-dependent radical SAM methyltransferase and a bacterial ACC synthase, respectively, and were found to be involved in the MeACC biosynthesis. In vitro analysis using their recombinant enzymes (rOrf29 and rOrf30) further revealed that the ACC structure of MeACC was derived from the L-methionine moiety of SAM, rather than L-valine. In addition, rOrf29 was found to catalyze the C-methylation of the L-methionine moiety of SAM. The resulting methylated derivative of SAM was then converted into MeACC by rOrf30. Thus, we demonstrate that C-methylation of SAM occurs prior to cyclopropanation in the biosynthesis of a bacterial MeACC (norcoronamic acid).
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Tan B, Zhang Q, Zhu Y, Jin H, Zhang L, Chen S, Zhang C. Deciphering Biosynthetic Enzymes Leading to 4-Chloro-6-Methyl-5,7-Dihydroxyphenylglycine, a Non-Proteinogenic Amino Acid in Totopotensamides. ACS Chem Biol 2020; 15:766-773. [PMID: 32118401 DOI: 10.1021/acschembio.9b00997] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Totopotensamide A (TPM A, 1) is a polyketide-peptide glycoside featuring a nonproteinogenic amino acid 4-chloro-6-methyl-5,7-dihydroxyphenylglycine (ClMeDPG). The biosynthetic gene cluster (BGC) of totopotensamides (tot) was previously activated by manipulating transcription regulators in marine-derived Streptomyces pactum SCSIO 02999. Herein, we report the heterologous expression of the tot BGC in Streptomyces lividans TK64, and the production improvement of TPM A via in-frame deletion of two negative regulators totR5 and totR3. The formation of ClMeDPG was proposed to require six enzymes, including four enzymes TotC1C2C3C4 for 3,5-dihydroxyphenylglycine (DPG) biosynthesis and two modifying enzymes TotH (halogenase) and TotM (methyltransferase). Heterologous expression of the four-gene cassette totC1C2C3C4 led to production of 3,5-dihydroxyphenylglyoxylate (DPGX). The aminotransferase TotC4 was biochemically characterized to convert DPGX to S-DPG. Inactivation of totH led to a mutant accumulated a deschloro derivative TPM H1, and the ΔtotHi/ΔtotMi double mutant afforded two deschloro-desmethyl products TPMs HM1 and HM2. A hydrolysis experiment demonstrated that the DPG moiety in TPM HM2 was S-DPG, consistent with that of the TotC4 enzymatic product. These results confirmed that TotH and TotM were responsible for ClMeDPG biosynthesis. Bioinformatics analysis indicated that both TotH and TotM might act on thiolation domain-tethered substrates. This study provided evidence for deciphering enzymes leading to ClMeDPG in TPM A, and unambiguously determined its absolute configuration as S.
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Affiliation(s)
- Bin Tan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Qingbo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Hongbo Jin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Siqiang Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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28
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In vivo cascade catalysis of aromatic amino acids to the respective mandelic acids using recombinant E. coli cells expressing hydroxymandelate synthase (HMS) from Amycolatopsis mediterranei. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2019.110713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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29
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Teicoplanin biosynthesis: unraveling the interplay of structural, regulatory, and resistance genes. Appl Microbiol Biotechnol 2020; 104:3279-3291. [PMID: 32076781 DOI: 10.1007/s00253-020-10436-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/26/2020] [Accepted: 02/04/2020] [Indexed: 01/10/2023]
Abstract
Teicoplanin (Tcp) is a clinically relevant glycopeptide antibiotic (GPA) that is produced by the actinobacterium Actinoplanes teichomyceticus. Tcp is a front-line therapy for treating severe infections caused by multidrug-resistant Gram-positive pathogens in adults and infants. In this review, we provide a detailed overview of how Tcp is produced by A. teichomyceticus by describing Tcp biosynthesis, regulation, and resistance. We summarize the knowledge gained from in vivo and in vitro studies to provide an integrated model of teicoplanin biosynthesis. Then, we discuss genetic and nutritional factors that contribute to the regulation of teicoplanin biosynthesis, focusing on those that have been successfully applied for improving teicoplanin production. A current view on teicoplanin self-resistance mechanisms in A. teichomyceticus is given, and we compare the Tcp biosynthetic gene cluster with other glycopeptide gene clusters from actinoplanetes and from unidentified isolates/metagenomics samples. Finally, we provide an outlook for further directions in studying Tcp biosynthesis and regulation.
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30
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Visser SP. Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes. Chemistry 2020; 26:5308-5327. [DOI: 10.1002/chem.201905119] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/04/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Sam P. Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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31
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d-Phenylglycine aminotransferase ( d-PhgAT) – substrate scope and structural insights of a stereo-inverting biocatalyst used in the preparation of aromatic amino acids. Catal Sci Technol 2020. [DOI: 10.1039/d0cy01391a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the crystal structure and substrate scope of a versatile aminotransferase biocatalyst.
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32
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Pecnikaj I, Foschi F, Bucci R, Gelmi ML, Castellano C, Meneghetti F, Penso M. Stereoselective Synthesis of α,α′-Dihydroxy-β,β′-diaryl-β-amino Acids by Mannich-Like Condensation of Hydroarylamides. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ilir Pecnikaj
- Department of Chemistry; University of Milan; Via Golgi 19 20133 Milano Italy
| | - Francesca Foschi
- Department of Chemistry; University of Milan; Via Golgi 19 20133 Milano Italy
| | - Raffaella Bucci
- Department of Pharmaceutical Sciences (DISFARM); University of Milan; Via Venezian 21 20133 Milano Italy
| | - Maria Luisa Gelmi
- Department of Pharmaceutical Sciences (DISFARM); University of Milan; Via Venezian 21 20133 Milano Italy
| | - Carlo Castellano
- Department of Chemistry; University of Milan; Via Golgi 19 20133 Milano Italy
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences (DISFARM); University of Milan; Via Venezian 21 20133 Milano Italy
| | - Michele Penso
- CNR-Institute of Molecular Science and Technologies (ISTM); Via Golgi 19 20133 Milano Italy
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33
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Towards the online computer-aided design of catalytic pockets. Nat Chem 2019; 11:872-879. [DOI: 10.1038/s41557-019-0319-5] [Citation(s) in RCA: 436] [Impact Index Per Article: 87.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 07/25/2019] [Indexed: 12/18/2022]
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34
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Yeh HW, Lin KH, Lyu SY, Li YS, Huang CM, Wang YL, Shih HW, Hsu NS, Wu CJ, Li TL. Biochemical and structural explorations of α-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:733-742. [PMID: 31373572 PMCID: PMC6677016 DOI: 10.1107/s2059798319009574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/03/2019] [Indexed: 11/05/2022]
Abstract
Structural and enzymological explorations of α-hydroxyacid oxidases uncover new flavin mononucleotide-mediated reactions and intermediates. p-Hydroxymandelate oxidase (Hmo) is a flavin mononucleotide (FMN)-dependent enzyme that oxidizes mandelate to benzoylformate. How the FMN-dependent oxidation is executed by Hmo remains unclear at the molecular level. A continuum of snapshots from crystal structures of Hmo and its mutants in complex with physiological/nonphysiological substrates, products and inhibitors provides a rationale for its substrate enantioselectivity/promiscuity, its active-site geometry/reactivity and its direct hydride-transfer mechanism. A single mutant, Y128F, that extends the two-electron oxidation reaction to a four-electron oxidative decarboxylation reaction was unexpectedly observed. Biochemical and structural approaches, including biochemistry, kinetics, stable isotope labeling and X-ray crystallography, were exploited to reach these conclusions and provide additional insights.
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Affiliation(s)
- Hsien Wei Yeh
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Syue Yi Lyu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yi Shan Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chun Man Huang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yung Lin Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hao Wei Shih
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Tsung Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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35
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Monteiro LS, Paiva-Martins F, Oliveira S, Machado I, Costa M. An efficient one-pot synthesis of polyphenolic amino acids and evaluation of their radical-scavenging activity. Bioorg Chem 2019; 89:102983. [PMID: 31102692 DOI: 10.1016/j.bioorg.2019.102983] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/11/2019] [Accepted: 05/10/2019] [Indexed: 12/24/2022]
Abstract
A simple and efficient procedure for the synthesis of N-acyl 4-hydroxy, 4-hydroxy-3-methoxy and 3,4-dihydroxy phenylglycine amides by a strategy based on the multicomponent Ugi reaction is proposed. Hydroxybenzaldehyde derivatives were reacted with 4-methoxybenzylamine, cyclohexyl isocyanide and benzoic acid or 2-naphthylacetic acid to give Ugi adducts that were treated with trifluoroacetic acid yielding N-acyl hydroxyphenylglycine amides in good yields. The same procedure using as acid component protocatechuic acid or hydrocaffeic acid gave N-catechoyl 3,4-dihydroxyphenylglycine amides. The use of N-benzyloxycarbonylglycine as acid component allowed the preparation of a 3,4-dihydroxyphenylglycyl dipeptide derivative. Radical-scavenging activity studies of the polyphenolic amino acid derivatives showed a sharp increase in activity with the increase in number of hydroxyl or catechol groups present. Cyclic voltammetry experiments established a correlation between oxidation peak potentials and the radical-scavenging activity.
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Affiliation(s)
- Luís S Monteiro
- Chemistry Centre, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Fátima Paiva-Martins
- REQUIMTE/LAQV, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre 687, Porto, Portugal
| | - Sandra Oliveira
- Chemistry Centre, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; REQUIMTE/LAQV, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre 687, Porto, Portugal
| | - Inês Machado
- Chemistry Centre, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Marlene Costa
- REQUIMTE/LAQV, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre 687, Porto, Portugal
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36
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Du YL, Ryan KS. Pyridoxal phosphate-dependent reactions in the biosynthesis of natural products. Nat Prod Rep 2019; 36:430-457. [DOI: 10.1039/c8np00049b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review reactions catalyzed by pyridoxal phosphate-dependent enzymes, highlighting enzymes reported in the recent natural product biosynthetic literature.
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Affiliation(s)
- Yi-Ling Du
- Institute of Pharmaceutical Biotechnology
- Zhejiang University School of Medicine
- Hangzhou
- China
| | - Katherine S. Ryan
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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37
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Gao SS, Naowarojna N, Cheng R, Liu X, Liu P. Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses. Nat Prod Rep 2018; 35:792-837. [PMID: 29932179 PMCID: PMC6093783 DOI: 10.1039/c7np00067g] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to 2018 α-Ketoglutarate (αKG, also known as 2-oxoglutarate)-dependent mononuclear non-haem iron (αKG-NHFe) enzymes catalyze a wide range of biochemical reactions, including hydroxylation, ring fragmentation, C-C bond cleavage, epimerization, desaturation, endoperoxidation and heterocycle formation. These enzymes utilize iron(ii) as the metallo-cofactor and αKG as the co-substrate. Herein, we summarize several novel αKG-NHFe enzymes involved in natural product biosyntheses discovered in recent years, including halogenation reactions, amino acid modifications and tailoring reactions in the biosynthesis of terpenes, lipids, fatty acids and phosphonates. We also conducted a survey of the currently available structures of αKG-NHFe enzymes, in which αKG binds to the metallo-centre bidentately through either a proximal- or distal-type binding mode. Future structure-function and structure-reactivity relationship investigations will provide crucial information regarding how activities in this large class of enzymes have been fine-tuned in nature.
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Affiliation(s)
- Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Xueting Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
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38
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Zou H, Li L, Zhang T, Shi M, Zhang N, Huang J, Xian M. Biosynthesis and biotechnological application of non-canonical amino acids: Complex and unclear. Biotechnol Adv 2018; 36:1917-1927. [PMID: 30063950 DOI: 10.1016/j.biotechadv.2018.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/22/2018] [Accepted: 07/27/2018] [Indexed: 01/05/2023]
Abstract
Compared with the better-studied canonical amino acids, the distribution, metabolism and functions of natural non-canonical amino acids remain relatively obscure. Natural non-canonical amino acids have been mainly discovered in plants as secondary metabolites that perform diversified physiological functions. Due to their specific characteristics, a broader range of natural and artificial non-canonical amino acids have recently been applied in the development of functional materials and pharmaceutical products. With the rapid development of advanced methods in biotechnology, non-canonical amino acids can be incorporated into peptides, proteins and enzymes to improve the function and performance relative to their natural counterparts. Therefore, biotechnological application of non-canonical amino acids in artificial bio-macromolecules follows the central goal of synthetic biology to: create novel life forms and functions. However, many of the non-canonical amino acids are synthesized via chemo- or semi-synthetic methods, and few non-canonical amino acids can be synthesized using natural in vivo pathways. Therefore, further research is needed to clarify the metabolic pathways and key enzymes of the non-canonical amino acids. This will lead to the discovery of more candidate non-canonical amino acids, especially for those that are derived from microorganisms and are naturally bio-compatible with chassis strains for in vivo biosynthesis. In this review, we summarize representative natural and artificial non-canonical amino acids, their known information regarding associated metabolic pathways, their characteristics and their practical applications. Moreover, this review summarizes current barriers in developing in vivo pathways for the synthesis of non-canonical amino acids, as well as other considerations, future trends and potential applications of non-canonical amino acids in advanced biotechnology.
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Affiliation(s)
- Huibin Zou
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China; CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| | - Lei Li
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Tongtong Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Mengxun Shi
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Nan Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jingling Huang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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39
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Characterization of the phenylglycine aminotransferase PglE from Streptomyces pristinaespiralis. J Biotechnol 2018; 278:34-38. [DOI: 10.1016/j.jbiotec.2018.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 01/16/2023]
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40
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de Visser SP. Mechanistic Insight on the Activity and Substrate Selectivity of Nonheme Iron Dioxygenases. CHEM REC 2018; 18:1501-1516. [PMID: 29878456 DOI: 10.1002/tcr.201800033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/05/2023]
Abstract
Nonheme iron dioxygenases catalyze vital reactions for human health particularly related to aging processes. They are involved in the biosynthesis of amino acids, but also the biodegradation of toxic compounds. Typically they react with their substrate(s) through oxygen atom transfer, although often with the assistance of a co-substrate like α-ketoglutarate that is converted to succinate and CO2 . Many reaction processes catalyzed by the nonheme iron dioxygenases are stereoselective or regiospecific and hence understanding the mechanism and protein involvement in the selectivity is important for the design of biotechnological applications of these enzymes. To this end, I will review recent work of our group on nonheme iron dioxygenases and include background information on their general structure and catalytic cycle. Examples of stereoselective and regiospecific reaction mechanisms we elucidated are for the AlkB repair enzyme, prolyl-4-hydroxylase and the ergothioneine biosynthesis enzyme. Finally, I cover an example where we bioengineered S-p-hydroxymandelate synthase into the R-p-hydroxymandelate synthase.
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Affiliation(s)
- Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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41
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Clark JR, Feng K, Sookezian A, White MC. Manganese-catalysed benzylic C(sp 3)-H amination for late-stage functionalization. Nat Chem 2018; 10:583-591. [PMID: 29713037 PMCID: PMC6217814 DOI: 10.1038/s41557-018-0020-0] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/29/2018] [Indexed: 11/09/2022]
Abstract
Reactions that directly install nitrogen into C-H bonds of complex molecules are significant because of their potential to change the chemical and biological properties of a given compound. Although selective intramolecular C-H amination reactions are known, achieving high levels of reactivity while maintaining excellent site selectivity and functional-group tolerance remains a challenge for intermolecular C-H amination. Here, we report a manganese perchlorophthalocyanine catalyst [MnIII(ClPc)] for intermolecular benzylic C-H amination of bioactive molecules and natural products that proceeds with unprecedented levels of reactivity and site selectivity. In the presence of a Brønsted or Lewis acid, the [MnIII(ClPc)]-catalysed C-H amination demonstrates unique tolerance for tertiary amine, pyridine and benzimidazole functionalities. Mechanistic studies suggest that C-H amination likely proceeds through an electrophilic metallonitrene intermediate via a stepwise pathway where C-H cleavage is the rate-determining step of the reaction. Collectively, these mechanistic features contrast with previous base-metal-catalysed C-H aminations and provide new opportunities for tunable selectivities.
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Affiliation(s)
- Joseph R Clark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Kaibo Feng
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Anasheh Sookezian
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - M Christina White
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL, USA.
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42
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Parthasarathy A, Cross PJ, Dobson RCJ, Adams LE, Savka MA, Hudson AO. A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals. Front Mol Biosci 2018; 5:29. [PMID: 29682508 PMCID: PMC5897657 DOI: 10.3389/fmolb.2018.00029] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed.
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Affiliation(s)
- Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Penelope J. Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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43
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Old and new glycopeptide antibiotics: From product to gene and back in the post-genomic era. Biotechnol Adv 2018; 36:534-554. [PMID: 29454983 DOI: 10.1016/j.biotechadv.2018.02.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/22/2018] [Accepted: 02/14/2018] [Indexed: 02/05/2023]
Abstract
Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by multi-drug resistant Gram-positive pathogens. First-generation glycopeptides (vancomycin and teicoplanin) are produced by soil-dwelling actinomycetes. Second-generation glycopeptides (dalbavancin, oritavancin, and telavancin) are semi-synthetic derivatives of the progenitor natural products. Herein, we cover past and present biotechnological approaches for searching for and producing old and new glycopeptide antibiotics. We review the strategies adopted to increase microbial production (from classical strain improvement to rational genetic engineering), and the recent progress in genome mining, chemoenzymatic derivatization, and combinatorial biosynthesis for expanding glycopeptide chemical diversity and tackling the never-ceasing evolution of antibiotic resistance.
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44
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Reifenrath M, Boles E. Engineering of hydroxymandelate synthases and the aromatic amino acid pathway enables de novo biosynthesis of mandelic and 4-hydroxymandelic acid with Saccharomyces cerevisiae. Metab Eng 2018; 45:246-254. [DOI: 10.1016/j.ymben.2018.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/12/2017] [Accepted: 01/07/2018] [Indexed: 10/18/2022]
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45
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Aleku GA, Nowicka B, Turner NJ. Biocatalytic Potential of Enzymes Involved in the Biosynthesis of Isoprenoid Quinones. ChemCatChem 2017. [DOI: 10.1002/cctc.201700685] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Godwin A. Aleku
- School of Chemistry and Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Beatrycze Nowicka
- Department of Plant Physiology and Biochemistry; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gronostajowa 7 30-387 Krakow Poland
| | - Nicholas J. Turner
- School of Chemistry and Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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46
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Süssmuth RD, Mainz A. Nonribosomal Peptide Synthesis-Principles and Prospects. Angew Chem Int Ed Engl 2017; 56:3770-3821. [PMID: 28323366 DOI: 10.1002/anie.201609079] [Citation(s) in RCA: 518] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 01/05/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multienzyme machineries that assemble numerous peptides with large structural and functional diversity. These peptides include more than 20 marketed drugs, such as antibacterials (penicillin, vancomycin), antitumor compounds (bleomycin), and immunosuppressants (cyclosporine). Over the past few decades biochemical and structural biology studies have gained mechanistic insights into the highly complex assembly line of nonribosomal peptides. This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis. Such a reprogramming of NRPSs would immediately spur chances to generate analogues of existing drugs or new compound libraries of otherwise nearly inaccessible compound structures.
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Affiliation(s)
- Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
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47
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Süssmuth RD, Mainz A. Nicht-ribosomale Peptidsynthese - Prinzipien und Perspektiven. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609079] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Roderich D. Süssmuth
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Andi Mainz
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
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48
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Falivene L, Credendino R, Poater A, Petta A, Serra L, Oliva R, Scarano V, Cavallo L. SambVca 2. A Web Tool for Analyzing Catalytic Pockets with Topographic Steric Maps. Organometallics 2016. [DOI: 10.1021/acs.organomet.6b00371] [Citation(s) in RCA: 500] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Laura Falivene
- Physical Sciences & Engineering Division (PSE), KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Raffaele Credendino
- Physical Sciences & Engineering Division (PSE), KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Albert Poater
- Physical Sciences & Engineering Division (PSE), KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Institut
de Química Computacional i Catàlisi and Departament
de Química, Universitat de Girona, Girona 17003, Spain
| | - Andrea Petta
- Dipartimento
di Informatica ed Applicazioni, University of Salerno, Fisciano (SA), Italy
| | - Luigi Serra
- Dipartimento
di Informatica ed Applicazioni, University of Salerno, Fisciano (SA), Italy
| | - Romina Oliva
- Department
of Sciences and Technologies, University “Parthenope” of Naples, Centro Direzionale Isola C4, Naples 80143, Italy
| | - Vittorio Scarano
- Dipartimento
di Informatica ed Applicazioni, University of Salerno, Fisciano (SA), Italy
| | - Luigi Cavallo
- Physical Sciences & Engineering Division (PSE), KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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49
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Li FF, Zhao Y, Li BZ, Qiao JJ, Zhao GR. Engineering Escherichia coli for production of 4-hydroxymandelic acid using glucose-xylose mixture. Microb Cell Fact 2016; 15:90. [PMID: 27234226 PMCID: PMC4884394 DOI: 10.1186/s12934-016-0489-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 4-Hydroxymandelic acid (4-HMA) is a valuable aromatic fine chemical and widely used for production of pharmaceuticals and food additives. 4-HMA is conventionally synthesized by chemical condensation of glyoxylic acid with excessive phenol, and the process is environmentally unfriendly. Microbial cell factory would be an attractive approach for 4-HMA production from renewable and sustainable resources. RESULTS In this study, a biosynthetic pathway for 4-HMA production was constructed by heterologously expressing the fully synthetic 4-hydroxymandelic acid synthase (shmaS) in our L-tyrosine-overproducing Escherichia coli BKT5. The expression level of shmaS was optimized to improve 4-HMA production by fine tuning of four promoters of different strength combined with three plasmids of different copy number. Furthermore, two genes aspC and tyrB in the competitive pathway were deleted to block the formation of byproduct to enhance 4-HMA biosynthesis. The final engineered E. coli strain HMA15 utilized glucose and xylose simultaneously and produced 15.8 g/L of 4-HMA by fed-batch fermentation in 60 h. CONCLUSIONS Metabolically engineered E. coli strain for 4-HMA production was designed and constructed, and efficiently co-fermented glucose and xylose, the major components in the hydrolysate mixture of agricultural biomass. Our research provided a promising biomanufacturing route to produce 4-HMA from lignocellulosic biomass.
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Affiliation(s)
- Fei-Fei Li
- />Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- />Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- />SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Ying Zhao
- />Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- />Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- />SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Bing-Zhi Li
- />Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- />Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- />SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Jian-Jun Qiao
- />Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- />Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- />SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Guang-Rong Zhao
- />Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- />Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- />SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
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Ray L, Yamanaka K, Moore BS. A Peptidyl-Transesterifying Type I Thioesterase in Salinamide Biosynthesis. Angew Chem Int Ed Engl 2016; 55:364-7. [PMID: 26553755 PMCID: PMC4715598 DOI: 10.1002/anie.201508576] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Indexed: 11/10/2022]
Abstract
Salinamide A belongs to a rare class of bicyclic depsipeptide antibiotics in which the installation of a (4-methylhexa-2,4-dienoyl)glycine handle across a hexadepsipeptide core contributes to its chemical complexity and biological properties. Herein, we report the genetic and biochemical basis for salinamide construction in the marine bacterium Streptomyces sp. CNB-091, which involves a novel intermolecular transesterification reaction catalyzed by a type I thioesterase. Heterologous expression studies revealed the central role of the nonribosomal peptide synthetase Sln9 in constructing and installing the distinctive acylglycine "basket handle" of salinamide. Biochemical characterization of the Sln9 thioesterase domain established that transesterification of the serine residue of desmethylsalinamide E with acylated glycyl thioesters yields desmethylsalinamide C.
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Affiliation(s)
- Lauren Ray
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037 (USA) http://scrippsscholars.ucsd.edu/bsmoore
| | - Kazuya Yamanaka
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037 (USA) http://scrippsscholars.ucsd.edu/bsmoore
- Yokohama Research Center, JNC Corporation, Yokohama 236-8605 (Japan)
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037 (USA) http://scrippsscholars.ucsd.edu/bsmoore.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92037 (USA).
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