|
1
|
Whitehead JN, Leferink NGH, Hay S, Scrutton NS. Determinants of Product Outcome in Two Sesquiterpene Synthases from the Thermotolerant Bacterium Rubrobacter radiotolerans. Chembiochem 2025; 26:e202400672. [PMID: 39400489 DOI: 10.1002/cbic.202400672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 10/09/2024] [Accepted: 10/14/2024] [Indexed: 10/15/2024]
Abstract
Rubrobacter radiotolerans nerolidol synthase (NerS) and trans-α-bergamotene synthase (BerS) are among the first terpene synthases (TPSs) discovered from thermotolerant bacteria, and, despite sharing the same substrate, make terpenoid products with different carbon scaffolds. Here, the potential thermostability of NerS and BerS was investigated, and NerS was found to retain activity up to 55 °C. A library of 22 NerS and BerS variants was designed to probe the differing reaction mechanisms of NerS and BerS, including residues putatively involved in substrate sequestration, cation-π stabilisation of reactive intermediates, and shaping of the active site contour. Two BerS variants showed improved in vivo titres vs the WT enzyme, and also yielded different ratios of the related sesquiterpenoids (E)-β-farnesene and trans-α-bergamotene. BerS-L86F was proposed to encourage substrate isomerisation by cation-π stabilisation of the first cationic intermediate, resulting in a greater proportion of trans-α-bergamotene. By contrast, BerS-S82L significantly preferred (E)-β-farnesene formation, attributed to steric blocking of the isomerisation step, consistent with what has been observed in several plant TPSs. Our work highlights the importance of isomerisation as a key determinant of product outcome in TPSs, and shows how a combined computational and experimental approach can characterise TPSs and variants with improved and altered functionality.
Collapse
Affiliation(s)
- Joshua N Whitehead
- Future, Biomanufacturing Research Hub, Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, University of Manchester, 131 Princess Street, Manchester, M7 7DN, UK
| | - Nicole G H Leferink
- Future, Biomanufacturing Research Hub, Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, University of Manchester, 131 Princess Street, Manchester, M7 7DN, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, University of Manchester, 131 Princess Street, Manchester, M7 7DN, UK
| | - Nigel S Scrutton
- Future, Biomanufacturing Research Hub, Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, University of Manchester, 131 Princess Street, Manchester, M7 7DN, UK
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, University of Manchester, 131 Princess Street, Manchester, M7 7DN, UK
| |
Collapse
|
|
2
|
Messaoudi K, Benmeddour T, Flamini G. First report on the chemical composition and the free radical scavenging and antimicrobial activities of the essential oil of Ononis aurasiaca, an endemic plant of Algeria. Nat Prod Res 2024; 38:4355-4367. [PMID: 37971903 DOI: 10.1080/14786419.2023.2282113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 11/19/2023]
Abstract
This study represents the first investigation of the chemical composition and the antioxidant and antimicrobial activities of Ononis aurasiaca Förther & Podlech, a plant species endemic to the Aures Mountains of Algeria. The essential oil of the plant aerial parts was analysed using GC-MS. The in vitro antioxidant activity was evaluated using three methods. A total of 44 compounds were identified. The major constituents were dodecanal, hexahydrofarnesylacetone, 2-tridecanone, phytol, 1-heneicosene, and n-heneicosane. The oil displayed significant activity in the β-carotene bleaching assay, moderate scavenging activity against DPPH radicals and a low ability to reduce iron ions. Antibacterial tests conducted on four strains revealed effectiveness primarily against Gram-positive strains, specifically Staphylococcus aureus ATCC 25923 and ATCC 43300, while showing limited impact on Gram-negative strains, Pseudomonas aeruginosa ATCC 27853 and Escherichia coli ATCC 25922. Antifungal activity tests involving two moulds revealed a stronger inhibition against Scedosporium apiospermum compared to Aspergillus niger.
Collapse
Affiliation(s)
- Khadidja Messaoudi
- Department of Nature and Life Sciences, University of Biskra, Biskra, Algeria
- Laboratory of Genetics, Biotechnology and Valorization of Bioresources, University of Biskra, Algeria
| | - Tarek Benmeddour
- Department of Nature and Life Sciences, University of Biskra, Biskra, Algeria
- Laboratory of Genetics, Biotechnology and Valorization of Bioresources, University of Biskra, Algeria
| | - Guido Flamini
- Dipartimento di Farmacia, Università di Pisa, Pisa, Italy
| |
Collapse
|
|
3
|
Kang MK, Nguyen MP, Yoon SH, Jayasundera KB, Son JW, Wang C, Kwon M, Kim SW. Reconstitution of the Mevalonate Pathway for Improvement of Isoprenoid Production and Industrial Applicability in Escherichia coli. J Microbiol Biotechnol 2024; 34:2338-2346. [PMID: 39467704 PMCID: PMC11637829 DOI: 10.4014/jmb.2408.08053] [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: 08/29/2024] [Revised: 09/30/2024] [Accepted: 10/01/2024] [Indexed: 10/30/2024]
Abstract
Natural products, especially isoprenoids have many industrial applications, including medicine, fragrances, food additives, personal care and cosmetics, colorants, and even advanced biofuels. Recent advancements in metabolic engineering with synthetic biology and systems biology have drawn increased interest in microbial-based isoprenoid production. In order to engineer microorganisms to produce a large amount of value-added isoprenoids, great efforts have been made by employing various strategies from synthetic biology and systems biology. We also have engineered E. coli to produce various isoprenoids by targeting and engineering the isoprenoid biosynthetic pathways, methylerythritol phosphate (MEP), and mevalonate (MVA) pathways. Here, we introduced new combinations of the MVA pathway in E. coli with genes from biosafety level 1 (BSL 1) organisms. The reconstituted MVA pathway constructs (pSCS) are not only preferred to the living modified organism (LMO) regulation, but they also improved carotenoid production. In addition, the pSCS constructs resulted in enhanced lycopene production and cell-specific productivity compared to the previous MVA pathway combination (pSNA) in fed-batch fermentation. The pSCS constructs would not only bring an increase in isoprenoid production in E. coli, but they could be an efficient system to be applied for the industrial production of isoprenoids with industry-preferred genetic combinations.
Collapse
Affiliation(s)
- Min-Kyoung Kang
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Minh Phuong Nguyen
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Sang-Hwal Yoon
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Keerthi B. Jayasundera
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jong-Wook Son
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Chonglong Wang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, People's Republic of China
| | - Moonhyuk Kwon
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
- Research Institute of Molecular Alchemy (RIMA), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Seon-Won Kim
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
- Plant Molecular Biology & Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| |
Collapse
|
|
4
|
Wenger ES, Schultz K, Marmorstein R, Christianson DW. Engineering substrate channeling in a bifunctional terpene synthase. Proc Natl Acad Sci U S A 2024; 121:e2408064121. [PMID: 39365814 PMCID: PMC11474042 DOI: 10.1073/pnas.2408064121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 08/26/2024] [Indexed: 10/06/2024] Open
Abstract
Fusicoccadiene synthase from Phomopsis amygdala (PaFS) is a bifunctional terpene synthase. It contains a prenyltransferase (PT) domain that generates geranylgeranyl diphosphate (GGPP) from dimethylallyl diphosphate and three equivalents of isopentenyl diphosphate, and a cyclase domain that converts GGPP into fusicoccadiene, a precursor of the diterpene glycoside Fusicoccin A. The two catalytic domains are connected by a flexible 69-residue linker. The PT domain mediates oligomerization to form predominantly octamers, with cyclase domains randomly splayed out around the PT core. Surprisingly, despite the random positioning of cyclase domains, substrate channeling is operative in catalysis since most of the GGPP generated by the PT remains on the enzyme for cyclization. Here, we demonstrate that covalent linkage of the PT and cyclase domains is not required for GGPP channeling, although covalent linkage may improve channeling efficiency. Moreover, GGPP competition experiments with other diterpene cyclases indicate that the PaFS PT and cyclase domains are preferential partners regardless of whether they are covalently linked or not. The cryoelectron microscopy structure of the 600-kD "linkerless" construct, in which the 69-residue linker is spliced out and replaced with the tripeptide PTQ, reveals that cyclase pairs associate with all four sides of the PT octamer and exhibit fascinating quaternary structural flexibility. These results suggest that optimal substrate channeling is achieved when a cyclase domain associates with the side of the PT octamer, regardless of whether the two domains are covalently linked and regardless of whether this interaction is transient or locked in place.
Collapse
Affiliation(s)
- Eliott S. Wenger
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA19104-6323
| | - Kollin Schultz
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ronen Marmorstein
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA19104-6323
| |
Collapse
|
|
5
|
McBee DP, Hulsey ZN, Hedges MR, Baccile JA. Biological Demands and Toxicity of Isoprenoid Precursors in Bacillus Subtilis Through Cell-Permeant Analogs of Isopentenyl Pyrophosphate and Dimethylallyl Pyrophosphate. Chembiochem 2024; 25:e202400064. [PMID: 38568158 DOI: 10.1002/cbic.202400064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/28/2024] [Indexed: 04/25/2024]
Abstract
Bacterial isoprenoids are necessary for many biological processes, including maintaining membrane integrity, facilitating intercellular communication, and preventing oxidative damage. All bacterial isoprenoids are biosynthesized from two five carbon structural isomers, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), which are cell impermeant. Herein, we demonstrate exogenous delivery of IPP and DMAPP into Bacillus subtilis by utilizing a self-immolative ester (SIE)-caging approach. We initially evaluated native B. subtilis esterase activity, which revealed a preference for short straight chain esters. We then examined the viability of the SIE-caging approach in B. subtilis and demonstrate that the released caging groups are well tolerated and the released IPP and DMAPP are bioavailable, such that isoprenoid biosynthesis can be rescued in the presence of pathway inhibitors. We further show that IPP and DMAPP are both toxic and inhibit growth of B. subtilis at the same concentration. Lastly, we establish the optimal ratio of IPP to DMAPP (5 : 1) for B. subtilis growth and find that, surprisingly, DMAPP alone is insufficient to rescue isoprenoid biosynthesis under high concentrations of fosmidomycin. These findings showcase the potential of the SIE-caging approach in B. subtilis and promise to both aid in novel isoprenoid discovery and to inform metabolic engineering efforts in bacteria.
Collapse
Affiliation(s)
- Dillon P McBee
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| | - Zackary N Hulsey
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| | - Makayla R Hedges
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| | - Joshua A Baccile
- Department of Chemistry, University of Tennessee, Knoxville, TN, United States
| |
Collapse
|
|
6
|
Li M, Tao H. Enhancing structural diversity of terpenoids by multisubstrate terpene synthases. Beilstein J Org Chem 2024; 20:959-972. [PMID: 38711588 PMCID: PMC11070974 DOI: 10.3762/bjoc.20.86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Terpenoids are one of the largest class of natural products with diverse structures and activities. This enormous diversity is embedded in enzymes called terpene synthases (TSs), which generate diverse terpene skeletons via sophisticated cyclization cascades. In addition to the many highly selective TSs, there are many promiscuous TSs that accept multiple prenyl substrates, or even noncanonical ones, with 6, 7, 8, 11, and 16 carbon atoms, synthesized via chemical approaches, C-methyltransferases, or engineered lepidopteran mevalonate pathways. The substrate promiscuity of TSs not only expands the structural diversity of terpenes but also highlights their potential for the discovery of novel terpenoids via combinatorial biosynthesis. In this review, we focus on the current knowledge on multisubstrate terpene synthases (MSTSs) and highlight their potential applications.
Collapse
Affiliation(s)
- Min Li
- Department of Otolaryngology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University, Wuhan, Hubei 430071, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
| | - Hui Tao
- Department of Otolaryngology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University, Wuhan, Hubei 430071, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
| |
Collapse
|
|
7
|
Eaton SA, Christianson DW. Structure-Based Engineering of a Sesquiterpene Cyclase to Generate an Alcohol Product: Conversion of epi-Isozizaene Synthase into α-Bisabolol Synthase. Biochemistry 2024; 63:797-805. [PMID: 38420671 PMCID: PMC10961106 DOI: 10.1021/acs.biochem.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The sesquiterpene cyclase epi-isozizaene synthase (EIZS) from Streptomyces coelicolor catalyzes the metal-dependent conversion of farnesyl diphosphate (FPP) into the complex tricyclic product epi-isozizaene. This remarkable transformation is governed by an active site contour that serves as a template for catalysis, directing the conformations of multiple carbocation intermediates leading to the final product. Mutagenesis of residues defining the active site contour remolds its three-dimensional shape and reprograms the cyclization cascade to generate alternative cyclization products. In some cases, mutagenesis enables alternative chemistry to quench carbocation intermediates, e.g., through hydroxylation. Here, we combine structural and biochemical data from previously characterized EIZS mutants to design and prepare F95S-F198S EIZS, which converts EIZS into an α-bisabolol synthase with moderate fidelity (65% at 18 °C, 74% at 4 °C). We report the complete biochemical characterization of this double mutant as well as the 1.47 Å resolution X-ray crystal structure of its complex with three Mg2+ ions, inorganic pyrophosphate, and the benzyltriethylammonium cation, which partially mimics a carbocation intermediate. Most notably, the two mutations together create an active site contour that stabilizes the bisabolyl carbocation intermediate and positions a water molecule for the hydroxylation reaction. Structural comparison with a naturally occurring α-bisabolol synthase reveals common active site features that direct α-bisabolol generation. In showing that EIZS can be redesigned to generate a sesquiterpene alcohol product instead of a sesquiterpene hydrocarbon product, we have expanded the potential of EIZS as a platform for the development of designer cyclases that could be utilized in synthetic biology applications.
Collapse
Affiliation(s)
- Samuel A. Eaton
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| |
Collapse
|
|
8
|
Gaynes MN, Ronnebaum TA, Schultz K, Faylo JL, Marmorstein R, Christianson DW. Structure of the prenyltransferase in bifunctional copalyl diphosphate synthase from Penicillium fellutanum reveals an open hexamer conformation. J Struct Biol 2024; 216:108060. [PMID: 38184156 PMCID: PMC10939776 DOI: 10.1016/j.jsb.2023.108060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
Copalyl diphosphate synthase from Penicillium fellutanum (PfCPS) is an assembly-line terpene synthase that contains both prenyltransferase and class II cyclase activities. The prenyltransferase catalyzes processive chain elongation reactions using dimethylallyl diphosphate and three equivalents of isopentenyl diphosphate to yield geranylgeranyl diphosphate, which is then utilized as a substrate by the class II cyclase domain to generate copalyl diphosphate. Here, we report the 2.81 Å-resolution cryo-EM structure of the hexameric prenyltransferase of full-length PfCPS, which is surrounded by randomly splayed-out class II cyclase domains connected by disordered polypeptide linkers. The hexamer can be described as a trimer of dimers; surprisingly, one of the three dimer-dimer interfaces is separated to yield an open hexamer conformation, thus breaking the D3 symmetry typically observed in crystal structures of other prenyltransferase hexamers such as wild-type human GGPP synthase (hGGPPS). Interestingly, however, an open hexamer conformation was previously observed in the crystal structure of D188Y hGGPPS, apparently facilitated by hexamer-hexamer packing in the crystal lattice. The cryo-EM structure of the PfCPS prenyltransferase hexamer is the first to reveal that an open conformation can be achieved even in the absence of a point mutation or interaction with another hexamer. Even though PfCPS octamers are not detected, we suggest that the open hexamer conformation represents an intermediate in the hexamer-octamer equilibrium for those prenyltransferases that do exhibit oligomeric heterogeneity.
Collapse
Affiliation(s)
- Matthew N Gaynes
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Trey A Ronnebaum
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Kollin Schultz
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jacque L Faylo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Ronen Marmorstein
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.
| |
Collapse
|
|
9
|
Benmeddour T, Messaoudi K, Flamini G. First investigation of the chemical composition, antioxidant, antimicrobial and larvicidal activities of the essential oil of the subspecies Ononis angustissima Lam. subsp. filifolia Murb. Nat Prod Res 2024:1-16. [PMID: 38247329 DOI: 10.1080/14786419.2024.2305211] [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: 11/21/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024]
Abstract
This study is the first to explore the essential oil of Ononis angustissima Lam. subsp. filifolia Murb., a subspecies growing in the Algerian northeastern Sahara. The chemical composition was evaluated by GC/GC-EIMS. Antioxidant activity was evaluated using two methods. Thirty-four (91.6%) individual components were identified. The main constituents were linalool (12.6%), hexahydrofarnesylacetone (8.4%), β-eudesmol (6.6%), α-cadinol (6.4%) and T-cadinol (6.1%). The findings provide a chemical basis for understanding relationships between North African subspecies, supporting botanical and genetic classification. The oil exhibited moderate scavenging activity against DPPH radicals (IC50 = 102.30 µg/ml) and high activity in the β-carotene bleaching assay (91.346%). Antimicrobial tests revealed effectiveness against Gram-positive bacteria (Staphylococcus aureus ATCC 25923 and ATCC 43300), limited impact on Gram-negative bacteria (Pseudomonas aeruginosa ATCC 27853 and Escherichia coli ATCC 25922), and good inhibition against Aspergillus niger and Scedosporium apiospermum. A notable larvicidal activity was observed against Date Moth, particularly on L2 larvae.
Collapse
Affiliation(s)
- Tarek Benmeddour
- Department of Nature and Life Sciences, University of Biskra, Biskra, Algeria
- Laboratory of Genetics, Biotechnology and Valorization of Bioresources, University of Biskra, Algeria
| | - Khadidja Messaoudi
- Department of Nature and Life Sciences, University of Biskra, Biskra, Algeria
- Laboratory of Genetics, Biotechnology and Valorization of Bioresources, University of Biskra, Algeria
| | - Guido Flamini
- Dipartimento di Farmacia, Università di Pisa, Pisa, Italy
| |
Collapse
|
|
10
|
Chen W, Tang L, Li Q, Cai Y, Ahmad S, Wang Y, Tang S, Guo N, Wei X, Tang S, Shao G, Jiao G, Xie L, Hu S, Sheng Z, Hu P. YGL3 Encoding an IPP and DMAPP Synthase Interacts with OsPIL11 to Regulate Chloroplast Development in Rice. RICE (NEW YORK, N.Y.) 2024; 17:8. [PMID: 38228921 DOI: 10.1186/s12284-024-00687-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/10/2024] [Indexed: 01/18/2024]
Abstract
As the source of isoprenoid precursors, the plastidial methylerythritol phosphate (MEP) pathway plays an essential role in plant development. Here, we report a novel rice (Oryza sativa L.) mutant ygl3 (yellow-green leaf3) that exhibits yellow-green leaves and lower photosynthetic efficiency compared to the wild type due to abnormal chloroplast ultrastructure and reduced chlorophyll content. Map-based cloning showed that YGL3, one of the major genes involved in the MEP pathway, encodes 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, which is localized in the thylakoid membrane. A single base substitution in ygl3 plants resulted in lower 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity and lower contents of isopentenyl diphosphate (IPP) compared to the wild type. The transcript levels of genes involved in the syntheses of chlorophyll and thylakoid membrane proteins were significantly reduced in the ygl3 mutant compared to the wild type. The phytochrome interacting factor-like gene OsPIL11 regulated chlorophyll synthesis during the de-etiolation process by directly binding to the promoter of YGL3 to activate its expression. The findings provides a theoretical basis for understanding the molecular mechanisms by which the MEP pathway regulate chloroplast development in rice.
Collapse
Affiliation(s)
- Wei Chen
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, P. R. China
| | - Liqun Tang
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Qianlong Li
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yicong Cai
- Key Labora tory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Ministry of Education/Collaboration Center for Double-season Rice Modernization Production, Jiangxi Agricultural University, Nanchang, Jiangxi Province, 330045, P. R. China
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yakun Wang
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shengjia Tang
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Naihui Guo
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Lihong Xie
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shikai Hu
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China.
| | - Peisong Hu
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China.
| |
Collapse
|
|
11
|
Wenger ES, Christianson DW. Methods for the preparation and analysis of the diterpene cyclase fusicoccadiene synthase. Methods Enzymol 2023; 699:89-119. [PMID: 38942517 PMCID: PMC11213977 DOI: 10.1016/bs.mie.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Prenyltransferases are terpene synthases that combine 5-carbon precursor molecules into linear isoprenoids of varying length that serve as substrates for terpene cyclases, enzymes that catalyze fascinating cyclization reactions to form diverse terpene natural products. Terpenes and their derivatives comprise the largest class of natural products and have myriad functions in nature and diverse commercial uses. An emerging class of bifunctional terpene synthases contains both prenyltransferase and cyclase domains connected by a disordered linker in a single polypeptide chain. Fusicoccadiene synthase from Phomopsis amygdali (PaFS) is one of the most well-characterized members of this subclass and serves as a model system for the exploration of structure-function relationships. PaFS has been structurally characterized using a variety of biophysical techniques. The enzyme oligomerizes to form a stable core of six or eight prenyltransferase domains that produce a 20-carbon linear isoprenoid, geranylgeranyl diphosphate (GGPP), which then transits to the cyclase domains for the generation of fusicoccadiene. Cyclase domains are in dynamic equilibrium between randomly splayed-out and prenyltransferase-associated positions; cluster channeling is implicated for GGPP transit from the prenyltransferase core to the cyclase domains. In this chapter, we outline the methods we are developing to interrogate the nature of cluster channeling in PaFS, including enzyme activity and product analysis assays, approaches for engineering the linker segment connecting the prenyltransferase and cyclase domains, and structural analysis by cryo-EM.
Collapse
Affiliation(s)
- Eliott S Wenger
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States.
| |
Collapse
|
|
12
|
Liu J, Liang P. Complexation and evolution of cis-prenyltransferase homologues in Cinnamomum kanehirae deduced from kinetic and functional characterizations. Protein Sci 2023; 32:e4828. [PMID: 37916302 PMCID: PMC10661081 DOI: 10.1002/pro.4828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Eukaryotic dehydrodolichyl diphosphate synthases (DHDDSs), cis-prenyltransferases (cis-PTs) synthesizing precursors of dolichols to mediate glycoprotein biosynthesis require partners, for eample Nus1 in yeast and NgBR in animals, which are cis-PTs homologues without activity but to boost the DHDDSs activity. Unlike animals, plants have multiple cis-PT homologues to pair or stand alone to produce various chain-length products with less known physiological roles. We chose Cinnamomum kanehirae, a tree that contains two DHDDS-like and three NgBR-like proteins from genome analysis, and found that one DHDDS-like protein acted as a homodimeric cis-PT to make a medium-chain C55 product, while the other formed heterodimeric complexes with either one of two NgBR homologues to produce longer-chain products. Both complexes were functional to complement the growth defect of the yeast rer2 deficient strain at a higher temperature. From the roles for the polyprenol and dolichol biosynthesis and sequence motifs, their homologues in various species were compared to reveal their possible evolutionary paths.
Collapse
Affiliation(s)
- Jia‐Jin Liu
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
| | - Po‐Huang Liang
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
| |
Collapse
|
|
13
|
Zhang WS, Ji DW, Yang Y, Song TT, Zhang G, Wang XY, Chen QA. Nucleophilic aromatization of monoterpenes from isoprene under nickel/iodine cascade catalysis. Nat Commun 2023; 14:7087. [PMID: 37925506 PMCID: PMC10625535 DOI: 10.1038/s41467-023-42847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023] Open
Abstract
As a large number of organic compounds possessing two isoprene units, monoterpenes and monoterpenoids play important roles in pharmaceutical, cosmetic, agricultural, and food industries. In nature, monoterpenes are constructed from geranyl pyrophosphate (C10) via various transformations. Herein, the bulk C5 chemical-isoprene, is used for the creation of various monoterpenoids via a nucleophilic aromatization of monoterpenes under cascade catalysis of nickel and iodine. Drugs and oil mixtures from conifer and lemon can be convergently transformed to the desired monoterpenoid. Preliminary mechanistic studies are conducted to get insights about reaction pathway. Two types of cyclic monoterpenes can be respectively introduced onto two similar heterocycles via orthogonal C-H functionalization. And various hybrid terpenyl indoles are programmatically assembled from abundant C5 or C10 blocks. This work not only contributes a high chemo-, regio-, and redox-selective transformation of isoprene, but also provides a complementary approach for the creation of unnatural monoterpenoids.
Collapse
Affiliation(s)
- Wei-Song Zhang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Ding-Wei Ji
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
| | - Yang Yang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
| | - Ting-Ting Song
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
| | - Gong Zhang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiao-Yu Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qing-An Chen
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| |
Collapse
|
|
14
|
Whitehead J, Leferink NGH, Johannissen LO, Hay S, Scrutton NS. Decoding Catalysis by Terpene Synthases. ACS Catal 2023; 13:12774-12802. [PMID: 37822860 PMCID: PMC10563020 DOI: 10.1021/acscatal.3c03047] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/31/2023] [Indexed: 10/13/2023]
Abstract
The review by Christianson, published in 2017 on the twentieth anniversary of the emergence of the field, summarizes the foundational discoveries and key advances in terpene synthase/cyclase (TS) biocatalysis (Christianson, D. W. Chem Rev2017, 117 (17), 11570-11648. DOI: 10.1021/acs.chemrev.7b00287). Here, we review the TS literature published since then, bringing the field up to date and looking forward to what could be the near future of TS rational design. Many revealing discoveries have been made in recent years, building on the knowledge and fundamental principles uncovered during those initial two decades of study. We use these to explore TS reaction chemistry and see how a combined experimental and computational approach helps to decipher the complexities of TS catalysis. Revealed are a suite of catalytic motifs which control product outcome in TSs, some obvious, some more subtle. We examine each in detail, using the most recent papers and insights to illustrate how exactly this fascinating class of enzymes takes a single acyclic substrate and turns it into the many thousands of complex terpenoids found in Nature. We then explore some of the recent strategies for TS engineering, including machine learning and other data-driven approaches. From this, rational and predictive engineering of TSs, "designer terpene synthases", will begin to emerge as a realistic goal.
Collapse
Affiliation(s)
- Joshua
N. Whitehead
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole G. H. Leferink
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
| |
Collapse
|
|
15
|
Eaton SA, Christianson DW. Reprogramming the Cyclization Cascade of epi-Isozizaene Synthase to Generate Alternative Terpene Products. Biochemistry 2023; 62:2301-2313. [PMID: 37449555 PMCID: PMC10527993 DOI: 10.1021/acs.biochem.3c00247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
The class I sesquiterpene cyclase epi-isozizaene synthase from Streptomyces coelicolor (EIZS) catalyzes the transformation of linear farnesyl diphosphate (FPP) into the tricyclic hydrocarbon epi-isozizaene in the biosynthesis of albaflavenone antibiotics. The active site cavity of EIZS is largely framed by four aromatic residues - F95, F96, F198, and W203 - that form a product-shaped contour, serving as a template to chaperone conformations of the flexible substrate and multiple carbocation intermediates leading to epi-isozizaene. Remolding the active site contour by mutagenesis can redirect the cyclization cascade away from epi-isozizaene biosynthesis to generate alternative sesquiterpene products. Here, we present the biochemical and structural characterization of four EIZS mutants in which aromatic residues have been substituted with polar residues (F95S, F96H, F198S, and F198T) to generate alternative cyclization products. Most notably, F95S EIZS generates a mixture of monocyclic sesquiterpene precursors of bisabolane, a D2 diesel fuel substitute. X-ray crystal structures of the characterized mutants reveal subtle changes in the active site contour showing how each aromatic residue influences the chemistry of a different carbocation intermediate in the cyclization cascade. We advance that EIZS may serve as a robust platform for the development of designer cyclases for the generation of high-value sesquiterpene products ranging from pharmaceuticals to biofuels in synthetic biology approaches.
Collapse
Affiliation(s)
- Samuel A. Eaton
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| |
Collapse
|
|
16
|
Brescia FF, Koch M, Wende RC, Schreiner PR, Zorn H, Fraatz MA. Structure Elucidation of Aroma-Active Bicyclic Benzofuran Derivatives Formed by Cystostereum murrayi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7744-7751. [PMID: 37172111 DOI: 10.1021/acs.jafc.3c01807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Among the monoterpenoid aroma compounds formed by the basidiomycete Cystostereum murrayi are highly potent bicyclic benzofuran derivatives. In addition to the dill ethers previously described in a few fungi, two stereoisomers of the rare 3,6-dimethyl-3a,4,5,6,7,7a-hexahydro-3H-1-benzofuran-2-one (1a and 2c), also known as dihydromenthofurolactones, and a C3-unsaturated analogue (3a) are formed by C. murrayi. The analysis of synthesized reference standards of the lactones allowed an unambiguous assignment of the stereoisomers formed by the fungus. Despite a similar structure, two key differences in the stereochemistry of the lactones and dill ethers emerged. The analysis of submerged cultures further revealed the formation of additional, so far unknown, fungal terpenoids, including limonen-10-ol (7) and the corresponding aldehyde limonen-10-al (8). Analysis of chiral terpenoids as well as supplementation studies, including stable isotope-labeled compounds, indicated independent biogenesis pathways for dill ethers and lactones.
Collapse
Affiliation(s)
- Fabio F Brescia
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Maximilian Koch
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Raffael C Wende
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Marco A Fraatz
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| |
Collapse
|
|
17
|
Wei Q, Zhang YH. Composition and Antioxidative and Antibacterial Activities of the Essential Oil from Farfugium japonicum. Molecules 2023; 28:molecules28062774. [PMID: 36985745 PMCID: PMC10054140 DOI: 10.3390/molecules28062774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
The composition of volatile oils of the leaf and stem of Farfugium japonicum (L.) Kitamura were prepared by supercritical fluid extraction (SFE)-CO2. A total 47 and 40 compounds were identified by GC/MS analysis, respectively, and only 13 compounds coexisted. The main constituent types in the leaf oil included alcohols (34.1%), hydrocarbons (24.1%), terpenoids (16.2%), benzenes (7.5%), and fatty acids (4.9%). In the stem oil, the constituent types chiefly included benzenes (18.8%), ketones (13.9%), terpenoids (17.0%), fatty acids (8.8%), phenolics (8.7%), steroids (8.6%), hydrocarbons (8.0%), and esters (5.7%). The predominant volatile compounds in the stem were 2-(1-cyclopent-1-enyl-1-methylethyl) cyclopentanone (11.7%), 1,2,3,4,5,6,7,8-octahydro- 9,10-dimethyl-anthracene (8.4%), 5-heptylresorcinol (6.5%), and α-sitosterol (5.2%). Those in the leaf mainly included (E)-3-hexen-1-ol (13.7%) and (Z)-3-hexen-1-ol (14.0%). This demonstrated a significant difference in the composition of both oils. Further study showed that stem oils demonstrated the highest DPPH (1,1-diphenyl-2-pinylhydrazyl) and ·OH free radical scavenging capacities at IC50 values of 9.22 and 0.90 mg/mL, respectively. In addition, they demonstrated the strongest antibacterial capacity against the Gram-positive bacteria methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) at a minimum inhibitory concentration (MIC) of 0.16 mg/mL. This could be due to the SFE-CO2 extraction and the high accumulation of benzenes, terpenoids, and phenolics in the stem. In particular, the monoterpenes presented in terpenoids could play a special role in these findings.
Collapse
Affiliation(s)
- Qiang Wei
- School of Medicine, Anhui Xinhua University, Hefei 230088, China
| | - Yi-Han Zhang
- School of Medicine, Anhui Xinhua University, Hefei 230088, China
| |
Collapse
|
|
18
|
Chen J, Tan J, Duan X, Wang Y, Wen J, Li W, Li Z, Wang G, Xu H. Plastidial engineering with coupled farnesyl diphosphate pool reconstitution and enhancement for sesquiterpene biosynthesis in tomato fruit. Metab Eng 2023; 77:41-52. [PMID: 36893914 DOI: 10.1016/j.ymben.2023.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/20/2023] [Accepted: 03/05/2023] [Indexed: 03/09/2023]
Abstract
Sesquiterpenes represent a large class of terpene compounds found in plants with broad applications such as pharmaceuticals and biofuels. The plastidial MEP pathway in ripening tomato fruit is naturally optimized to provide the 5-carbon isoprene building blocks of all terpenes for production of the tetraterpene pigment lycopene and other carotenoids, making it an excellent plant system to be engineered for production of high-value terpenoids. We reconstituted and enhanced the pool of sesquiterpene precursor farnesyl diphosphate (FPP) in plastids of tomato fruit by overexpressing the fusion gene DXS-FPPS encoding a fusion protein of 1-deoxy-D-xylulose 5-phosphate synthase (DXS) linked with farnesyl diphosphate synthase (originally called farnesyl pyrophosphate synthase, and abbreviated as FPPS) under the control of fruit-ripening specific polygalacturonase (PG) promoter concomitant with substantial reduction in lycopene content and large production of FPP-derived squalene. The supply of precursors achieved by the fusion gene expression can be harnessed by an engineered sesquiterpene synthase that is retargeted to plastid to engineer high-yield sesquiterpene production in tomato fruit, offering an effective production system for high-value sesquiterpene ingredients.
Collapse
Affiliation(s)
- Jing Chen
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| | - Jing Tan
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| | - Xinyu Duan
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| | - Ying Wang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| | - Jing Wen
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| | - Wei Li
- Shenzhen Key Laboratory of Agricultural Synthetic Biology, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China; Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, China.
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Haiyang Xu
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| |
Collapse
|
|
19
|
Chakraborty P, Pradhan S, Richard Premkumar J, Sundararaju B. Valorization of Terpenols Under Iron Catalysis. J Catal 2023. [DOI: 10.1016/j.jcat.2023.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
|
|
20
|
Rossi FM, McBee DP, Trybala TN, Hulsey ZN, Gonzalez Curbelo C, Mazur W, Baccile JA. Membrane Permeant Analogs for Independent Cellular Introduction of the Terpene Precursors Isopentenyl- and Dimethylallyl-Pyrophosphate. Chembiochem 2023; 24:e202200512. [PMID: 36354788 DOI: 10.1002/cbic.202200512] [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: 09/05/2022] [Revised: 11/09/2022] [Indexed: 11/12/2022]
Abstract
Isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) are the central five-carbon precursors to all terpenes. Despite their significance, exogenous, independent delivery of IPP and DMAPP to cells is impossible as the negatively charged pyrophosphate makes these molecules membrane impermeant. Herein, we demonstrate a facile method to circumvent this challenge through esterification of the β-phosphate with two self-immolative esters (SIEs) that neutralize the negatively charged pyrophosphate to yield membrane-permeant analogs of IPP and DMAPP. Following cellular incorporation, general esterase activity initiates cleavage of the SIEs, resulting in traceless release of IPP and DMAPP for metabolic utilization. Addition of the synthesized IPP and DMAPP precursor analogs rescued cell growth of glioblastoma (U-87MG) cancer cells concurrently treated with the HMG-CoA reductase inhibitor pitavastatin, which otherwise abrogates cell growth via blocking production of IPP and DMAPP. This work demonstrates a new application of a prodrug strategy to incorporate a metabolic intermediate and promises to enable future interrogation of the distinct biological roles of IPP and DMAPP.
Collapse
Affiliation(s)
- Francis M Rossi
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA.,Department of Chemistry SUNY Cortland, Cortland, NY, USA
| | - Dillon P McBee
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Thomas N Trybala
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Zackary N Hulsey
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | | | - William Mazur
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Joshua A Baccile
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| |
Collapse
|
|
21
|
Sharma D, Pareek A, Arya H, Soni R, Rai P, Agrawal A, Nimesh S, Kumar D, Yaragorla S, Bhatt TK. Synthesis and inhibition studies towards the discovery of benzodiazepines as potential antimalarial compounds. Exp Parasitol 2022; 243:108411. [DOI: 10.1016/j.exppara.2022.108411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/04/2022] [Accepted: 10/18/2022] [Indexed: 11/25/2022]
|
|
22
|
Whitehead JN, Leferink NGH, Komati Reddy G, Levy CW, Hay S, Takano E, Scrutton NS. How a 10- epi-Cubebol Synthase Avoids Premature Reaction Quenching to Form a Tricyclic Product at High Purity. ACS Catal 2022; 12:12123-12131. [PMID: 36249875 PMCID: PMC9552170 DOI: 10.1021/acscatal.2c03155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/02/2022] [Indexed: 11/29/2022]
Abstract
![]()
Terpenes are the largest class of natural products and
are attractive
targets in the fuel, fragrance, pharmaceutical, and flavor industries.
Harvesting terpenes from natural sources is environmentally intensive
and often gives low yields and purities, requiring further downstream
processing. Engineered terpene synthases (TSs) offer a solution to
these problems, but the low sequence identity and high promiscuity
among TSs are major challenges for targeted engineering. Rational
design of TSs requires identification of key structural and chemical
motifs that steer product outcomes. Producing the sesquiterpenoid
10-epi-cubebol from farnesyl pyrophosphate (FPP)
requires many steps and some of Nature’s most difficult chemistry.
10-epi-Cubebol synthase from Sorangium
cellulosum (ScCubS) guides a highly reactive carbocationic
substrate through this pathway, preventing early quenching and ensuring
correct stereochemistry at every stage. The cyclizations carried out
by ScCubS potentially represent significant evolutionary expansions
in the chemical space accessible by TSs. Here, we present the high-resolution
crystal structure of ScCubS in complex with both a trinuclear magnesium
cluster and pyrophosphate. Computational modeling, experiment, and
bioinformatic analysis identified residues important in steering the
reaction chemistry. We show that S206 is crucial in 10-epi-cubebol synthesis by enlisting the nearby F211 to shape the active
site contour and prevent the formation of early escape cadalane products.
We also show that N327 and F104 control the distribution between several
early-stage cations and whether the final product is derived from
the germacrane, cadalane, or cubebane hydrocarbon scaffold. Using
these insights, we reengineered ScCubS so that its main product was
germacradien-4-ol, which derives from the germacrane, rather than
the cubebane, scaffold. Our work emphasizes that mechanistic understanding
of cation stabilization in TSs can be used to guide catalytic outcomes.
Collapse
Affiliation(s)
- Joshua N. Whitehead
- Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Nicole G. H. Leferink
- Future Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Gajendar Komati Reddy
- Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Colin W. Levy
- Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
- Future Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
- Future Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| |
Collapse
|
|
23
|
|
|
24
|
Herrscher V, Witjaksono C, Buchotte M, Ferret C, Massicot F, Vasse J, Borel F, Behr J, Seemann M. Irreversible Inhibition of IspG, a Target for the Development of New Antimicrobials, by a 2‐Vinyl Analogue of its MEcPP Substrate. Chemistry 2022; 28:e202200241. [DOI: 10.1002/chem.202200241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Vivien Herrscher
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Clea Witjaksono
- Equipe Chimie Biologique et Applications Thérapeutiques Institut de Chimie de Strasbourg UMR 7177 Université de Strasbourg/CNRS 4, rue Blaise Pascal 67070 Strasbourg France
| | - Marie Buchotte
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Claire Ferret
- Equipe Chimie Biologique et Applications Thérapeutiques Institut de Chimie de Strasbourg UMR 7177 Université de Strasbourg/CNRS 4, rue Blaise Pascal 67070 Strasbourg France
| | - Fabien Massicot
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Jean‐Luc Vasse
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Franck Borel
- Univ. Grenoble Alpes, CEA, CNRS, IBS 38000 Grenoble France
| | - Jean‐Bernard Behr
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques Institut de Chimie de Strasbourg UMR 7177 Université de Strasbourg/CNRS 4, rue Blaise Pascal 67070 Strasbourg France
| |
Collapse
|
|
25
|
Giladi M, Lisnyansky Bar-El M, Vaňková P, Ferofontov A, Melvin E, Alkaderi S, Kavan D, Redko B, Haimov E, Wiener R, Man P, Haitin Y. Structural basis for long-chain isoprenoid synthesis by cis-prenyltransferases. SCIENCE ADVANCES 2022; 8:eabn1171. [PMID: 35584224 PMCID: PMC9116609 DOI: 10.1126/sciadv.abn1171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Isoprenoids are synthesized by the prenyltransferase superfamily, which is subdivided according to the product stereoisomerism and length. In short- and medium-chain isoprenoids, product length correlates with active site volume. However, enzymes synthesizing long-chain products and rubber synthases fail to conform to this paradigm, because of an unexpectedly small active site. Here, we focused on the human cis-prenyltransferase complex (hcis-PT), residing at the endoplasmic reticulum membrane and playing a crucial role in protein glycosylation. Crystallographic investigation of hcis-PT along the reaction cycle revealed an outlet for the elongating product. Hydrogen-deuterium exchange mass spectrometry analysis showed that the hydrophobic active site core is flanked by dynamic regions consistent with separate inlet and outlet orifices. Last, using a fluorescence substrate analog, we show that product elongation and membrane association are closely correlated. Together, our results support direct membrane insertion of the elongating isoprenoid during catalysis, uncoupling active site volume from product length.
Collapse
Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Michal Lisnyansky Bar-El
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Pavla Vaňková
- Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Alisa Ferofontov
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Emelia Melvin
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Suha Alkaderi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Daniel Kavan
- Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Boris Redko
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Elvira Haimov
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, IMRIC, Hadassah Medical School, The Hebrew University, Jerusalem 9112001, Israel
| | - Petr Man
- Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| |
Collapse
|
|
26
|
Gong K, Yong D, Fu J, Li A, Zhang Y, Li R. Diterpenoids from Streptomyces: Structures, Biosyntheses and Bioactivities. Chembiochem 2022; 23:e202200231. [PMID: 35585772 DOI: 10.1002/cbic.202200231] [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: 04/22/2022] [Revised: 05/16/2022] [Indexed: 11/09/2022]
Abstract
Bacteria, especially Streptomyces spp., have been emerging as rich sources of natural diterpenoids with diverse structures and broad bioactivities. Here, we review diterpenoids biosynthesized by Streptomyces , with an emphasis on their structures, biosyntheses, and bioactivities. Although diterpenoids from Streptomyces are relatively rare compared to those from plants and fungi, their novel skeletons, biosyntheses and bioactivities present opportunities for discovering new drugs, enzyme mechanisms, and applications in bio-catalysis and metabolic pathway engineering.
Collapse
Affiliation(s)
- Kai Gong
- Shandong University, State Key Laboratory of Microbial Technology, CHINA
| | - Daojing Yong
- Shandong University, State Key Laboratory of Microbial Technology, CHINA
| | - Jun Fu
- Shandong University, State Key Laboratory of Microbial Technology, CHINA
| | - Aiying Li
- Shandong University, State Key Laboratory of Microbial Technology, CHINA
| | - Youming Zhang
- Shandong University, State Key Laboratory of Microbial Technology, CHINA
| | - Ruijuan Li
- Shandong University, State Key Laboratory of Microbial Technology, Binhai Road 72, 266237, Qingdao, CHINA
| |
Collapse
|
|
27
|
Peters VCT, Dunkel A, Frank O, Rajmohan N, McCormack B, Dowd E, Didzbalis J, Gianfagna TJ, Dawid C, Hofmann T. High-Throughput Flavor Analysis and Mapping of Flavor Alterations Induced by Different Genotypes of Mentha by Means of UHPLC-MS/MS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5668-5679. [PMID: 35475602 DOI: 10.1021/acs.jafc.2c01689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The demand for mint is increasing from year to year, and it is more important than ever to secure a sustainable and robust supply of such an important plant. The USDA mint core collection provides the basis for many researches worldwide regarding, e.g., sequencing, cytology, and disease resistances. A recently developed toolbox enables here for the first time the analysis of such a complex collection in terms of the aroma compound composition and the mapping of flavor alterations depending on taxonomy, environmental conditions, and growing stages by means of comprehensive liquid chromatography tandem mass spectrometry. Therefore, in this study, not only the aroma compound composition of 153 genotypes was characterized but it was also demonstrated that the composition varies depending on taxonomy and changes during the growth of the plant. Furthermore, it could be shown that greenhouse conditions have an enormous influence on the concentrations of aroma compounds.
Collapse
Affiliation(s)
- Verena Christina Tabea Peters
- Chair of Food Chemistry and Molecular and Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, D-85354 Freising, Germany
| | - Andreas Dunkel
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, D-85354 Freising, Germany
| | - Oliver Frank
- Chair of Food Chemistry and Molecular and Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, D-85354 Freising, Germany
| | - Nimmi Rajmohan
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Brian McCormack
- Flavor/Mint Science, Mars Wrigley, 1132 W. Blackhawk Street, Chicago, Illinois 60642, United States
| | - Eric Dowd
- Flavor/Mint Science, Mars Wrigley, 1132 W. Blackhawk Street, Chicago, Illinois 60642, United States
| | - John Didzbalis
- Mars, Incorporated, Mars Advanced Research Institute, McLean, Virginia 22101, United States
| | - Thomas J Gianfagna
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Corinna Dawid
- Chair of Food Chemistry and Molecular and Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, D-85354 Freising, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular and Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, D-85354 Freising, Germany
| |
Collapse
|
|
28
|
Hoti G, Matencio A, Rubin Pedrazzo A, Cecone C, Appleton SL, Khazaei Monfared Y, Caldera F, Trotta F. Nutraceutical Concepts and Dextrin-Based Delivery Systems. Int J Mol Sci 2022; 23:4102. [PMID: 35456919 PMCID: PMC9031143 DOI: 10.3390/ijms23084102] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/26/2022] [Accepted: 04/02/2022] [Indexed: 12/12/2022] Open
Abstract
Nutraceuticals are bioactive or chemical compounds acclaimed for their valuable biological activities and health-promoting effects. The global community is faced with many health concerns such as cancers, cardiovascular and neurodegenerative diseases, diabetes, arthritis, osteoporosis, etc. The effect of nutraceuticals is similar to pharmaceuticals, even though the term nutraceutical has no regulatory definition. The usage of nutraceuticals, to prevent and treat the aforementioned diseases, is limited by several features such as poor water solubility, low bioavailability, low stability, low permeability, low efficacy, etc. These downsides can be overcome by the application of the field of nanotechnology manipulating the properties and structures of materials at the nanometer scale. In this review, the linear and cyclic dextrin, formed during the enzymatic degradation of starch, are highlighted as highly promising nanomaterials- based drug delivery systems. The modified cyclic dextrin, cyclodextrin (CD)-based nanosponges (NSs), are well-known delivery systems of several nutraceuticals such as quercetin, curcumin, resveratrol, thyme essential oil, melatonin, and appear as a more advanced drug delivery system than modified linear dextrin. CD-based NSs prolong and control the nutraceuticals release, and display higher biocompatibility, stability, and solubility of poorly water-soluble nutraceuticals than the CD-inclusion complexes, or uncomplexed nutraceuticals. In addition, the well-explored CD-based NSs pathways, as drug delivery systems, are described. Although important progress is made in drug delivery, all the findings will serve as a source for the use of CD-based nanosystems for nutraceutical delivery. To sum up, our review introduces the extensive literature about the nutraceutical concepts, synthesis, characterization, and applications of the CD-based nano delivery systems that will further contribute to the nutraceutical delivery with more potent nanosystems based on linear dextrins.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Francesco Trotta
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy; (G.H.); (A.M.); (A.R.P.); (C.C.); (S.L.A.); (Y.K.M.); (F.C.)
| |
Collapse
|
|
29
|
Dai A, Zheng Z, Yu L, Huang Y, Wu J. 1,3,4-Oxadiazole Contained Sesquiterpene Derivatives: Synthesis and Microbiocidal Activity for Plant Disease. Front Chem 2022; 10:854274. [PMID: 35273952 PMCID: PMC8902154 DOI: 10.3389/fchem.2022.854274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 11/16/2022] Open
Abstract
A series of 1,3,4-oxadiazole contained sesquiterpene derivatives were synthesized, and the activity of the target compounds against Xanthomonas oryzae pv. oryzae (Xoo), Xanthomonas axonopodis pv. citri (Xac), and tobacco mosaic virus (TMV) were evaluated. The biological activity results showed that the EC50 values of compounds H4, H8, H11, H12, H14, H16, and H19 for Xac inhibitory activity were 33.3, 42.7, 56.1, 74.5, 37.8, 43.8, and 38.4 μg/ml, respectively. Compounds H4, H8, H15, H19, H22, and H23 had inhibitory effects on Xoo, with EC50 values of 51.0, 43.3, 43.4, 50.5, 74.6, and 51.4 μg/ml, respectively. In particular, the curative and protective activities of compound H8 against Xoo in vivo were 51.9 and 49.3%, respectively. In addition, the EC50 values of the inactivation activity of compounds H4, H5, H9, H10, and H16 against TMV were 69.6, 58.9, 69.4, 43.9, and 60.5 μg/ml, respectively. The results of molecular docking indicated that compound H10 exhibited a strong affinity for TMV-coat protein, with a binding energy of −8.88 kcal/mol. It may inhibit the self-assembly and replication of TMV particles and have an anti-TMV effect, which supports its potential usefulness as an antiviral agent.
Collapse
|
|
30
|
Jobelius H, Bianchino GI, Borel F, Chaignon P, Seemann M. The Reductive Dehydroxylation Catalyzed by IspH, a Source of Inspiration for the Development of Novel Anti-Infectives. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030708. [PMID: 35163971 PMCID: PMC8837944 DOI: 10.3390/molecules27030708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
Abstract
The non-mevalonate or also called MEP pathway is an essential route for the biosynthesis of isoprenoid precursors in most bacteria and in microorganisms belonging to the Apicomplexa phylum, such as the parasite responsible for malaria. The absence of this pathway in mammalians makes it an interesting target for the discovery of novel anti-infectives. As last enzyme of this pathway, IspH is an oxygen sensitive [4Fe-4S] metalloenzyme that catalyzes 2H+/2e− reductions and a water elimination by involving non-conventional bioinorganic and bioorganometallic intermediates. After a detailed description of the discovery of the [4Fe-4S] cluster of IspH, this review focuses on the IspH mechanism discussing the results that have been obtained in the last decades using an approach combining chemistry, enzymology, crystallography, spectroscopies, and docking calculations. Considering the interesting druggability of this enzyme, a section about the inhibitors of IspH discovered up to now is reported as well. The presented results constitute a useful and rational help to inaugurate the design and development of new potential chemotherapeutics against pathogenic organisms.
Collapse
Affiliation(s)
- Hannah Jobelius
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Gabriella Ines Bianchino
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Franck Borel
- Institut de Biologie Structurale, Université Grenoble Alpes/CEA/CNRS, 38000 Grenoble, France;
| | - Philippe Chaignon
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
- Correspondence:
| |
Collapse
|
|
31
|
Yang J, Chen Y, Gao M, Wu L, Xiong S, Wang S, Gao J, Zhao Y, Wang Y. Comprehensive identification of bHLH transcription factors in Litsea cubeba reveals candidate gene involved in the monoterpene biosynthesis pathway. FRONTIERS IN PLANT SCIENCE 2022; 13:1081335. [PMID: 36618662 PMCID: PMC9811127 DOI: 10.3389/fpls.2022.1081335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 05/13/2023]
Abstract
Litsea cubeba (Lour.) Person, an economically important aromatic plant producing essential oils, has lemon-like fragrance and 96.44-98.44% monoterpene contents. bHLH transcription factor plays an important role in plant secondary metabolism and terpene biosynthesis. In this study, we used bioinformatics to identify bHLH transcription factors in L. cubeba, 173 bHLH genes were identified from L. cubeba and divided these into 26 subfamilies based on phylogenetic analysis. The majority of bHLHs in each subfamily shared comparable structures and motifs. While LcbHLHs were unevenly distributed across 12 chromosomes, 10 tandem repeats were discovered. Expression profiles of bHLH genes in different tissues demonstrated that LcbHLH78 is a potential candidate gene for regulating monoterpene biosynthesis. LcbHLH78 and the terpene synthase LcTPS42 showed comparable expression patterns in various tissues and fruit development stages of L. cubeba. Subcellular localization analysis revealed that LcbHLH78 protein localizes to the nucleus, consistent with a transcription factor function. Importantly, transient overexpression of LcbHLH78 increased geraniol and linalol contents. Our research demonstrates that LcbHLH78 enhances terpenoid biosynthesis. This finding will be beneficial for improving the quality of L. cubeba and provides helpful insights for further research into the control mechanism of LcbHLH genes over terpenoid biosynthesis.
Collapse
Affiliation(s)
- Jiahui Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Liwen Wu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Shifa Xiong
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Siqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Jing Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
| | - Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
- *Correspondence: Yunxiao Zhao, ; Yangdong Wang,
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, HangZhou, Zhejiang, China
- *Correspondence: Yunxiao Zhao, ; Yangdong Wang,
| |
Collapse
|
|
32
|
Jiang J, Liu Y, Yang S, Peng H, Liu J, Cheng YX, Li N. Photoaffinity-Based Chemical Proteomics Reveals 7-Oxocallitrisic Acid Targets CPT1A to Trigger Lipogenesis Inhibition. ACS Med Chem Lett 2021; 12:1905-1911. [PMID: 34917253 DOI: 10.1021/acsmedchemlett.1c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/28/2021] [Indexed: 11/29/2022] Open
Abstract
One of the natural terpenoids isolated from Resina Commiphora, 7-oxocallitrisic acid (7-OCA), has lipid metabolism regulatory activity. To uncover its lipogenesis inhibition mechanism, we developed a photoaffinity and clickable probe based on the 7-OCA scaffold and performed chemical proteomics to profile its potential cellular targets. It was found that 7-OCA could directly interact with carnitine palmitoyl transferase 1A (CPT1A) to promote its activity to reduce lipid accumulation. The present work reveals our understanding of the mode of lipid mebabolism regulation by abietic acids and provides new clues for antiobesity drug development with CPT1A as a main target.
Collapse
Affiliation(s)
- Jianbing Jiang
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Ying Liu
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Shuxin Yang
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Huipai Peng
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiawang Liu
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yong-Xian Cheng
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Nan Li
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
|
33
|
Ma S, Mandalapu D, Wang S, Zhang Q. Biosynthesis of cyclopropane in natural products. Nat Prod Rep 2021; 39:926-945. [PMID: 34860231 DOI: 10.1039/d1np00065a] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: 2012 to 2021Cyclopropane attracts wide interests in the fields of synthetic and pharmaceutical chemistry, and chemical biology because of its unique structural and chemical properties. This structural motif is widespread in natural products, and is usually essential for biological activities. Nature has evolved diverse strategies to access this structural motif, and increasing knowledge of the enzymes forming cyclopropane (i.e., cyclopropanases) has been revealed over the last two decades. Here, the scientific literature from the last two decades relating to cyclopropane biosynthesis is summarized, and the enzymatic cyclopropanations, according to reaction mechanism, which can be grouped into two major pathways according to whether the reaction involves an exogenous C1 unit from S-adenosylmethionine (SAM) or not, is discussed. The reactions can further be classified based on the key intermediates required prior to cyclopropane formation, which can be carbocations, carbanions, or carbon radicals. Besides the general biosynthetic pathways of the cyclopropane-containing natural products, particular emphasis is placed on the mechanism and engineering of the enzymes required for forming this unique structure motif.
Collapse
Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | | | - Shu Wang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| |
Collapse
|
|
34
|
Towards an Improvement of Anticancer Activity of Benzyl Adenosine Analogs. Molecules 2021; 26:molecules26237146. [PMID: 34885721 PMCID: PMC8658949 DOI: 10.3390/molecules26237146] [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: 10/28/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/17/2022] Open
Abstract
N6-Isopentenyladenosine (i6A) is a naturally occurring modified nucleoside displaying in vitro and in vivo antiproliferative and pro-apoptotic properties. In our previous studies, including an in silico inverse virtual screening, NMR experiments and in vitro enzymatic assays, we demonstrated that i6A targeted farnesyl pyrophosphate synthase (FPPS), a key enzyme involved in the mevalonate (MVA) pathway and prenylation of downstream proteins, which are aberrant in several cancers. Following our interest in the anticancer effects of FPPS inhibition, we developed a panel of i6A derivatives bearing bulky aromatic moieties in the N6 position of adenosine. With the aim of clarifying molecular action of N6-benzyladenosine analogs on the FPPS enzyme inhibition and cellular toxicity and proliferation, herein we report the evaluation of the N6-benzyladenosine derivatives’ (compounds 2a–m) effects on cell viability and proliferation on HCT116, DLD-1 (human) and MC38 (murine) colorectal cancer cells (CRC). We found that compounds 2, 2a and 2c showed a persistent antiproliferative effect on human CRC lines and compound 2f exerted a significant effect in impairing the prenylation of RAS and Rap-1A proteins, confirming that the antitumor activity of 2f was related to the ability to inhibit FPPS activity.
Collapse
|
|
35
|
Maiti B, Bhattacharya S. Liposomal nanoparticles based on steroids and isoprenoids for nonviral gene delivery. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 14:e1759. [PMID: 34729941 DOI: 10.1002/wnan.1759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/24/2021] [Accepted: 08/10/2021] [Indexed: 11/11/2022]
Abstract
Natural lipid molecules are an essential part of life as they constitute the membrane of cells and organelle. In most of these cases, the hydrophobicity of natural lipids is contributed by alkyl chains. Although natural lipids with a nonfatty acid hydrophobic backbone are quite rare, steroids and isoprenoids have been strong candidates as part of a lipid. Over the years, these natural molecules (steroid and isoprenoids) have been used to make either lipid-based nanoparticle or functionalize in such a way that it could form nano assembly alone for therapeutic delivery. Here we mainly focus on the synthetic functionalized version of these natural molecules which forms cationic liposomal nanoparticles (LipoNPs). These cationic LipoNPs were further used to deliver various negatively charged genetic materials in the form of pDNA, siRNA, mRNA (nucleic acids), and so on. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures.
Collapse
Affiliation(s)
- Bappa Maiti
- Technical Research Centre, Indian Association for the Cultivation of Science, Kolkata, India
| | - Santanu Bhattacharya
- Technical Research Centre, Indian Association for the Cultivation of Science, Kolkata, India.,School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India.,Department of Organic Chemistry, Indian Institute of Science, Bangalore, India
| |
Collapse
|
|
36
|
Ronnebaum TA, Eaton SA, Brackhahn EAE, Christianson DW. Engineering the Prenyltransferase Domain of a Bifunctional Assembly-Line Terpene Synthase. Biochemistry 2021; 60:3162-3172. [PMID: 34609847 DOI: 10.1021/acs.biochem.1c00600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Copalyl diphosphate (CPP) synthase from Penicillium verruculosum (PvCPS) is a bifunctional diterpene synthase with both prenyltransferase and class II cyclase activities. The prenyltransferase α domain catalyzes the condensation of C5 dimethylallyl diphosphate with three successively added C5 isopentenyl diphosphates (IPPs) to form C20 geranylgeranyl diphosphate (GGPP), which then undergoes a class II cyclization reaction at the βγ domain interface to generate CPP. The prenyltransferase α domain mediates oligomerization to form a 648-kD (αβγ)6 hexamer. In the current study, we explore prenyltransferase structure-function relationships in this oligomeric assembly-line platform with the goal of generating alternative linear isoprenoid products. Specifically, we report steady-state enzyme kinetics, product analysis, and crystal structures of various site-specific variants of the prenyltransferase α domain. Crystal structures of the H786A, F760A, S723Y, S723F, and S723T variants have been determined at resolutions of 2.80, 3.10, 3.15, 2.65, and 2.00 Å, respectively. The substitution of S723 with bulky aromatic amino acids in the S723Y and S723F variants constricts the active site, thereby directing the formation of the shorter C15 isoprenoid, farnesyl diphosphate. While the S723T substitution only subtly alters enzyme kinetics and does not compromise GGPP biosynthesis, the crystal structure of this variant reveals a nonproductive binding mode for IPP that likely accounts for substrate inhibition at high concentrations. Finally, mutagenesis of the catalytic general acid in the class II cyclase domain, D313A, significantly compromises prenyltransferase activity. This result suggests molecular communication between the prenyltransferase and cyclase domains despite their distant connection by a flexible polypeptide linker.
Collapse
Affiliation(s)
- Trey A Ronnebaum
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Samuel A Eaton
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Emily A E Brackhahn
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| |
Collapse
|
|
37
|
Faylo JL, Ronnebaum TA, Christianson DW. Assembly-Line Catalysis in Bifunctional Terpene Synthases. Acc Chem Res 2021; 54:3780-3791. [PMID: 34254507 DOI: 10.1021/acs.accounts.1c00296] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The magnificent chemodiversity of more than 95 000 terpenoid natural products identified to date largely originates from catalysis by two types of terpene synthases, prenyltransferases and cyclases. Prenyltransferases utilize 5-carbon building blocks in processive chain elongation reactions to generate linear C5n isoprenoid diphosphates (n ≥ 2), which in turn serve as substrates for terpene cyclases that convert these linear precursors into structurally complex hydrocarbon products containing multiple rings and stereocenters. Terpene cyclization reactions are the most complex organic transformations found in nature in that more than half of the substrate carbon atoms undergo changes in chemical bonding during a multistep reaction sequence proceeding through several carbocation intermediates. Two general classes of cyclases are established on the basis of the chemistry of initial carbocation formation, and structural studies from our laboratory and others show that three fundamental protein folds designated α, β, and γ govern this chemistry. Catalysis by a class I cyclase occurs in an α domain, where a trinuclear metal cluster activates the substrate diphosphate leaving group to generate an allylic cation. Catalysis by a class II cyclase occurs in a β domain or at the interface of β and γ domains, where an aspartic acid protonates the terminal π bond of the substrate to yield a tertiary carbocation. Crystal structures reveal domain architectures of α, αβ, αβγ, βγ, and β.In some terpene synthases, these domains are combined to yield bifunctional enzymes that catalyze successive biosynthetic steps in assembly line fashion. Structurally characterized examples include bacterial geosmin synthase, an αα domain enzyme that catalyzes a class I cyclization reaction of C15 farnesyl diphosphate in one active site and a transannulation-fragmentation reaction in the other to yield C12 geosmin and C3 acetone products. In comparison, plant abietadiene synthase is an αβγ domain enzyme in which C20 geranylgeranyl diphosphate undergoes tandem class II-class I cyclization reactions to yield the tricyclic product. Recent structural studies from our laboratory show that bifunctional fungal cyclases form oligomeric complexes for assembly line catalysis. Bifunctional (+)-copalyl diphosphate synthase adopts (αβγ)6 architecture in which the α domain generates geranylgeranyl diphosphate, which then undergoes class II cyclization in the βγ domains to yield the bicyclic product. Bifunctional fusicoccadiene synthase adopts (αα)6 or (αα)8 architecture in which one α domain generates geranylgeranyl diphosphate, which then undergoes class I cyclization in the other α domain to yield the tricyclic product. The prenyltransferase α domain mediates oligomerization in these systems. Attached by flexible polypeptide linkers, cyclase domains splay out from oligomeric prenyltransferase cores.In this Account, we review structure-function relationships for these bifunctional terpene synthases, with a focus on the oligomeric systems studied in our laboratory. The observation of substrate channeling for fusicoccadiene synthase suggests a model for dynamic cluster channeling in catalysis by oligomeric assembly line terpenoid synthases. Resulting efficiencies in carbon management suggest that such systems could be particularly attractive for use in synthetic biology approaches to generate high-value terpenoid natural products.
Collapse
Affiliation(s)
- Jacque L. Faylo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Trey A. Ronnebaum
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| |
Collapse
|
|
38
|
Morack T, Onneken C, Nakakohara H, Mück-Lichtenfeld C, Gilmour R. Enantiodivergent Prenylation via Deconjugative Isomerization. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tobias Morack
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Carina Onneken
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Hiroshi Nakakohara
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Christian Mück-Lichtenfeld
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Ryan Gilmour
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| |
Collapse
|
|
39
|
de Luna-Valdez L, Chenge-Espinosa M, Hernández-Muñoz A, Cordoba E, López-Leal G, Castillo-Ramírez S, León P. Reassessing the evolution of the 1-deoxy-D-xylulose 5-phosphate synthase family suggests a possible novel function for the DXS class 3 proteins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110960. [PMID: 34315585 DOI: 10.1016/j.plantsci.2021.110960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/06/2021] [Accepted: 05/26/2021] [Indexed: 06/13/2023]
Abstract
The methylerythritol 4-phosphate (MEP) pathway is of paramount importance for generating plastidial isoprenoids. The first enzyme of the MEP pathway, 1-deoxy-D-xylulose-5-phosphate synthase (DXS), catalyzes a flux-controlling step. In plants the DXS gene family is composed of three distinct classes with non-redundant functions. Although the DXS1 and DXS2 subfamilies have been well characterized, the DXS3 subfamily has been considerably understudied. Here, we carried out in silico and functional analyses to better understand the DXS3 class. Our phylogenetic analysis showed high variation in copy number among the different DXS classes, with the apparent absence of DXS1 class in some species. We found that DXS3 subfamily emerged later than DXS1 and DXS2 and it is under less intense purifying selection. Furthermore, in the DXS3 subfamily critical amino acids positions in the thiamine pyrophosphate binding pocket are not conserved. We demonstrated that the DXS3 proteins from Arabidopsis, Maize, and Rice lack functional DXS activity. Moreover, the Arabidopsis DXS3 protein displayed distinctive sub-organellar chloroplast localization not observed in any DXS1 or DXS2 proteins. Co-expression analysis of the DXS3 from Arabidopsis showed that, unlike DXS1 and DXS2 proteins, it co-expresses with genes related to post-embryonic development and reproduction and not with primary metabolism and isoprenoid synthesis.
Collapse
Affiliation(s)
- Luis de Luna-Valdez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico
| | - Marel Chenge-Espinosa
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico
| | - Arihel Hernández-Muñoz
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico
| | - Elizabeth Cordoba
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico
| | - Gamaliel López-Leal
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Patricia León
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico.
| |
Collapse
|
|
40
|
Liu CL, Xue K, Yang Y, Liu X, Li Y, Lee TS, Bai Z, Tan T. Metabolic engineering strategies for sesquiterpene production in microorganism. Crit Rev Biotechnol 2021; 42:73-92. [PMID: 34256675 DOI: 10.1080/07388551.2021.1924112] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Sesquiterpenes are a large variety of terpene natural products, widely existing in plants, fungi, marine organisms, insects, and microbes. Value-added sesquiterpenes are extensively used in industries such as: food, drugs, fragrances, and fuels. With an increase in market demands and the price of sesquiterpenes, the biosynthesis of sesquiterpenes by microbial fermentation methods from renewable feedstocks is acquiring increasing attention. Synthetic biology provides robust tools of sesquiterpene production in microorganisms. This review presents a summary of metabolic engineering strategies on the hosts and pathway engineering for sesquiterpene production. Advances in synthetic biology provide new strategies on the creation of desired hosts for sesquiterpene production. Especially, metabolic engineering strategies for the production of sesquiterpenes such as: amorphadiene, farnesene, bisabolene, and caryophyllene are emphasized in: Escherichia coli, Saccharomyces cerevisiae, and other microorganisms. Challenges and future perspectives of the bioprocess for translating sesquiterpene production into practical industrial work are also discussed.
Collapse
Affiliation(s)
- Chun-Li Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Kai Xue
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Ye Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Tianwei Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| |
Collapse
|
|
41
|
Zhang J, Li Y, Wang S, Wang R. Labeling of prenylated nucleic acid by Ene-type fluorination under physiological condition. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
|
42
|
Abstract
Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.
Collapse
Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| |
Collapse
|
|
43
|
Zeng L, Dehesh K. The eukaryotic MEP-pathway genes are evolutionarily conserved and originated from Chlaymidia and cyanobacteria. BMC Genomics 2021; 22:137. [PMID: 33637041 PMCID: PMC7912892 DOI: 10.1186/s12864-021-07448-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
Background Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes. Results Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development. Conclusion Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07448-x.
Collapse
Affiliation(s)
- Liping Zeng
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Katayoon Dehesh
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
| |
Collapse
|
|
44
|
Oliveira JR, Ribeiro GHM, Rezende LF, Fraga-Silva RA. Plant terpenes on treating cardiovascular and metabolic disease: a review. Protein Pept Lett 2021; 28:750-760. [PMID: 33511924 DOI: 10.2174/0929866528999210128210145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/03/2020] [Accepted: 12/09/2020] [Indexed: 11/22/2022]
Abstract
The use of medicinal plants as a therapy alternative is old as human existence itself. Nowadays, the search for effective molecules for chronic diseases treatments has increased. The cardiometabolic disorders still the main cause of death worldwide and plants may offer potential pharmacological innovative approaches to treat and prevent diseases. In the range of plant molecules are inserted the terpenes, which constituent essential elements with several pharmacological characteristics and applications, including cardiovascular and metabolic properties. Thus, the aim of the present review is to update the terpenes use on chronic disorders such as obesity, diabetes, hypertension and vascular conditions. The review includes a brief terpenes description based on the scientific literature in addition to data collected from secondary sources such as books and conference proceedings. We concluded that terpenes could act as adjuvant or main alternative treatment (when started earlier) to improve cardiometabolic diseases, contributing to reduce side effects of conventional drugs, in addition to preserving ethnopharmacological knowledge.
Collapse
Affiliation(s)
- Janaína Ribeiro Oliveira
- Laboratory of Health Science, Postgraduate Program in Health Science, Universidade Estadual de Montes Claros (Unimontes), Montes Claros, Minas Gerais,. Brazil
| | - Guilherme Henrique Mendes Ribeiro
- Instituto de Ciências Agrárias (ICA), Food Engineering Department, Universidade Federal de Minas Gerais (UFMG), Montes Claros, Minas Gerais,. Brazil
| | - Luiz Fernando Rezende
- Laboratory of Health Science, Postgraduate Program in Health Science, Universidade Estadual de Montes Claros (Unimontes), Montes Claros, Minas Gerais,. Brazil
| | | |
Collapse
|
|
45
|
Yan X, Li W, Liang D, Caiyin Q, Zhao G, Zhang Z, Wenzhang M, Qiao J. De novo assembly of the Mylia taylorii transcriptome and identification of sesquiterpene synthases. Arch Biochem Biophys 2020; 698:108742. [PMID: 33359564 DOI: 10.1016/j.abb.2020.108742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 12/15/2020] [Accepted: 12/20/2020] [Indexed: 11/25/2022]
Abstract
Mylia taylorii is an ancient nonseed land plant that accumulates various sesquiterpenes with insecticidal and antibacterial activities. Recently, microbial-type sesquiterpene synthases (STSs) with atypical aspartate-rich metal ion binding motifs have been identified in some liverworts. Here, transcriptome analysis of M. taylorii was performed to identify M. taylorii sesquiterpene synthases (MtSTSs) that are potentially involved in sesquiterpene biosynthesis and diversity. A total of 255,669 unigenes were obtained with an average length of 963 bp in the transcriptome data of M. taylorii, among which 148,093 (57.92%) unigenes had BLAST results. Forty-eight unigenes were related to the sesquiterpene backbone biosynthesis according to KEGG annotation. In addition, MtSTS1, MtSTS2 and MtSTS3 identified from putative MtSTSs display sesquiterpene catalytic activities on the basis of functional characterizations in yeast. Interestingly, MtSTSs exhibit a noncanonical metal ion binding motif and the structural composition of a single α-domain, which are features of microbial STSs instead of archetypical plant STSs. This study revealed new microbial-type STS members of nonseed plants, and functionally identified that MtSTSs may contribute to the investigation of the biosynthesis and biological role of sesquiterpenes in M. taylorii.
Collapse
Affiliation(s)
- Xiaoguang Yan
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, PR China.
| | - Weiguo Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, PR China.
| | - Dongmei Liang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, PR China.
| | - Qinggele Caiyin
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, PR China.
| | - Guangrong Zhao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, PR China.
| | - Zhijun Zhang
- Tianjin Research Institute of Forestry and Pomology, Tianjin, 300384, PR China; National Engineering Technology Research Center for Preservation of Agricultural Products, Tianjin, 300384, PR China; Key Laboratory of Storage of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin, 300384, PR China; Tianjin Key Laboratory of Postharvest Physiology and Storage of Agricultural Products, Tianjin, 300384, PR China.
| | - Ma Wenzhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, 650201, PR China.
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, PR China.
| |
Collapse
|
|
46
|
Wang Z, Zhang R, Yang Q, Zhang J, Zhao Y, Zheng Y, Yang J. Recent advances in the biosynthesis of isoprenoids in engineered Saccharomyces cerevisiae. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:1-35. [PMID: 33934850 DOI: 10.1016/bs.aambs.2020.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Isoprenoids, as the largest group of chemicals in the domains of life, constitute more than 50,000 members. These compounds consist of different numbers of isoprene units (C5H8), by which they are typically classified into hemiterpenoids (C5), monoterpenoids (C10), sesquiterpenoids (C15), diterpenoids (C20), triterpenoids (C30), and tetraterpenoids (C40). In recent years, isoprenoids have been employed as food additives, in the pharmaceutical industry, as advanced biofuels, and so on. To realize the sufficient and efficient production of valuable isoprenoids on an industrial scale, fermentation using engineered microorganisms is a promising strategy compared to traditional plant extraction and chemical synthesis. Due to the advantages of mature genetic manipulation, robustness and applicability to industrial bioprocesses, Saccharomyces cerevisiae has become an attractive microbial host for biochemical production, including that of various isoprenoids. In this review, we summarized the advances in the biosynthesis of isoprenoids in engineered S. cerevisiae over several decades, including synthetic pathway engineering, microbial host engineering, and central carbon pathway engineering. Furthermore, the challenges and corresponding strategies towards improving isoprenoid production in engineered S. cerevisiae were also summarized. Finally, suggestions and directions for isoprenoid production in engineered S. cerevisiae in the future are discussed.
Collapse
Affiliation(s)
- Zhaobao Wang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Rubing Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Qun Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jintian Zhang
- College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Youxi Zhao
- College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianming Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
| |
Collapse
|
|
47
|
Zhang Y, Prach LM, O'Brien TE, DiMaio F, Prigozhin DM, Corn JE, Alber T, Siegel JB, Tantillo DJ. Crystal Structure and Mechanistic Molecular Modeling Studies of Mycobacterium tuberculosis Diterpene Cyclase Rv3377c. Biochemistry 2020; 59:4507-4515. [PMID: 33182997 DOI: 10.1021/acs.biochem.0c00762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Terpenes make up the largest class of natural products, with extensive chemical and structural diversity. Diterpenes, mostly isolated from plants and rarely prokaryotes, exhibit a variety of important biological activities and valuable applications, including providing antitumor and antibiotic pharmaceuticals. These natural products are constructed by terpene synthases, a class of enzymes that catalyze one of the most complex chemical reactions in biology: converting simple acyclic oligo-isoprenyl diphosphate substrates to complex polycyclic products via carbocation intermediates. Here we obtained the second ever crystal structure of a class II diterpene synthase from bacteria, tuberculosinol pyrophosphate synthase (i.e., Halimadienyl diphosphate synthase, MtHPS, or Rv3377c) from Mycobacterium tuberculosis (Mtb). This enzyme transforms (E,E,E)-geranylgeranyl diphosphate into tuberculosinol pyrophosphate (Halimadienyl diphosphate). Rv3377c is part of the Mtb diterpene pathway along with Rv3378c, which converts tuberculosinol pyrophosphate to 1-tuberculosinyl adenosine (1-TbAd). This pathway was shown to exist only in virulent Mycobacterium species, but not in closely related avirulent species, and was proposed to be involved in phagolysosome maturation arrest. To gain further insight into the reaction pathway and the mechanistically relevant enzyme substrate binding orientation, electronic structure calculation and docking studies of reaction intermediates were carried out. Results reveal a plausible binding mode of the substrate that can provide the information to guide future drug design and anti-infective therapies of this biosynthetic pathway.
Collapse
Affiliation(s)
- Yue Zhang
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Lisa M Prach
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Terrence E O'Brien
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob E Corn
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tom Alber
- Department of Molecular & Cell Biology and QB3 Institute, University of California, Berkeley, California 94720, United States
| | - Justin B Siegel
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States.,Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, California 95616, United States.,Genome Center, University of California-Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| |
Collapse
|
|
48
|
Hou J, Zhang J, Zhang B, Jin X, Zhang H, Jin Z. Transcriptional Analysis of Metabolic Pathways and Regulatory Mechanisms of Essential Oil Biosynthesis in the Leaves of Cinnamomum camphora (L.) Presl. Front Genet 2020; 11:598714. [PMID: 33281883 PMCID: PMC7689033 DOI: 10.3389/fgene.2020.598714] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/14/2020] [Indexed: 01/01/2023] Open
Abstract
The roots, bark, and leaves of Cinnamomum camphora are rich in essential oils, which mainly comprised monoterpenes and sesquiterpenes. Although the essential oils obtained from C. camphora have been widely used in pharmaceutical, medicinal, perfume, and food industries, the molecular mechanisms underlying terpenoid biosynthesis are poorly understood. To address this lack of knowledge, we performed transcriptome analysis to investigate the key regulatory genes involved in terpenoid biosynthesis in C. camphora. High-oil-yield trees of linalool type and low-oil-yield trees were used to assemble a de novo transcriptome of C. camphora. A total of 121,285 unigenes were assembled, and the total length, average length, N50, and GC content of unigenes were 87,869,987, 724, 1,063, and 41.1%, respectively. Comparison of the transcriptome profiles of linalool-type C. camphora with trees of low oil yield resulted in a total of 3,689 differentially expressed unigenes, among them 31 candidate genes had annotations associated with metabolism of terpenoids and polyketides, including four in the monoterpenoid biosynthesis pathway and three in the terpenoid backbone biosynthesis pathway. Collectively, this genome-wide transcriptome provides a valuable tool for future identification of genes related to essential oil biosynthesis. Additionally, the identification of a cohort of genes in the biosynthetic pathways of terpenoids provides a theoretical basis for metabolic engineering of essential oils in C. camphora.
Collapse
Affiliation(s)
- Jiexi Hou
- Jiangxi Provincial Engineering Research Center for Seed-Breeding and Utilization of Camphor Trees, The School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China
| | - Jie Zhang
- Jiangxi Provincial Engineering Research Center for Seed-Breeding and Utilization of Camphor Trees, The School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China
| | - Beihong Zhang
- Jiangxi Provincial Engineering Research Center for Seed-Breeding and Utilization of Camphor Trees, The School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China.,Key Laboratory of Silviculture, Co-Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Xiaofang Jin
- Jiangxi Provincial Engineering Research Center for Seed-Breeding and Utilization of Camphor Trees, The School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China
| | - Haiyan Zhang
- Jiangxi Provincial Engineering Research Center for Seed-Breeding and Utilization of Camphor Trees, The School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China
| | - Zhinong Jin
- Jiangxi Provincial Engineering Research Center for Seed-Breeding and Utilization of Camphor Trees, The School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China
| |
Collapse
|
|
49
|
Tang X, Zhang F, Zeng T, Li W, Yin S, Wu R. Enzymatic Plasticity Inspired by the Diterpene Cyclase CotB2. ACS Chem Biol 2020; 15:2820-2832. [PMID: 32986400 DOI: 10.1021/acschembio.0c00645] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymatic plasticity, as a modern term referring to the functional conversion of an enzyme, is significant for enzymatic activity redesign. The bacterial diterpene cyclase CotB2 is a typical plastic enzyme by which its native form precisely conducts a chemical reaction while its mutants diversify the catalytic functions drastically. Many efforts have been made to disclose the mysteries of CotB2 enzyme catalysis. However, the catalytic details and regulatory mechanism toward the precise chemo- and stereoselectivity are still elusive. In this work, multiscale simulations are employed to illuminate the biocyclization mechanisms of the linear substrate into the final product cyclooctat-9-en-7-ol with a 5-8-5 fused ring scaffold, and the derailment products arising from the premature quenching of reactive carbocation intermediates are also discussed. The two major regulatory factors, local electrostatic stabilization effects from aromatic residues or polar residue in pocket and global features of active site including pocket-contour and pocket-hydrophobicity, are responsible for the enzymatic plasticity of CotB2. Further comparative studies of representative Euphorbiaceae and fungal diterpene cyclase (RcCS and PaFS) show a correlation between pocket plasticity and product diversity, which inspires a tentative enzyme product prediction and the rational diterpene cyclases' reengineering in the future.
Collapse
Affiliation(s)
- Xiaowen Tang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China
| | - Fan Zhang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Tao Zeng
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wei Li
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Sheng Yin
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ruibo Wu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| |
Collapse
|
|
50
|
Bhaskar P, Sareen D. Bioinformatics approach to understand nature's unified mechanism of stereo-divergent synthesis of isoprenoid skeletons. World J Microbiol Biotechnol 2020; 36:142. [PMID: 32851438 DOI: 10.1007/s11274-020-02918-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/13/2020] [Indexed: 11/27/2022]
Abstract
In isoprenoid metabolism, cyclisation is the important gateway to chemical diversity. Terpene synthase is responsible for the cyclisation of a few universal substrates forming hundreds of often stereo-chemically complex mono- and poly-cyclic terpene hydrocarbons with a broad spectrum of functions in pharmaceuticals, flavours and fragrance industry. Although they are discovered and characterised mainly from plants and fungi, yet only a small share of bacterial terpenes has been investigated so far owing to their low level of expression in wild-type microorganisms. Extensive bacterial genome mining has revealed a treasure trove of terpene synthase genes and their regulated heterologous overexpression has pitched-in to describe the biochemical function of putative genes and sequester new terpene metabolites. This review deals with the modern genome mining techniques and molecular methods, providing more experimental tools for studying the structure and functions of terpenoid metabolites and strongly supports the idea that genome mining is a utile approach in deciphering the terpenoid diversity in bacteria.
Collapse
Affiliation(s)
- Pranav Bhaskar
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Dipti Sareen
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India.
| |
Collapse
|