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Wan L, Huang Q, Li C, Yu H, Tan G, Wei S, El-Sappah AH, Sooranna S, Zhang K, Pan L, Zhang Z, Lei M. Integrated metabolome and transcriptome analysis identifies candidate genes involved in triterpenoid saponin biosynthesis in leaves of Centella asiatica (L.) Urban. FRONTIERS IN PLANT SCIENCE 2024; 14:1295186. [PMID: 38283979 PMCID: PMC10811118 DOI: 10.3389/fpls.2023.1295186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024]
Abstract
Centella asiatica (L.) Urban is a well-known medicinal plant which has multiple pharmacological properties. Notably, the leaves of C. asiatica contain large amounts of triterpenoid saponins. However, there have only been a few studies systematically elucidating the metabolic dynamics and transcriptional differences regarding triterpenoid saponin biosynthesis during the leaf development stages of C. asiatica. Here, we performed a comprehensive analysis of the metabolome and transcriptome to reveal the dynamic patterns of triterpenoid saponin accumulation and identified the key candidate genes associated with their biosynthesis in C. asiatica leaves. In this study, we found that the key precursors in the synthesis of terpenoids, including DMAPP, IPP and β-amyrin, as well as 22 triterpenes and eight triterpenoid saponins were considered as differentially accumulated metabolites. The concentrations of DMAPP, IPP and β-amyrin showed significant increases during the entire stage of leaf development. The levels of 12 triterpenes decreased only during the later stages of leaf development, but five triterpenoid saponins rapidly accumulated at the early stages, and later decreased to a constant level. Furthermore, 48 genes involved in the MVA, MEP and 2, 3-oxidosqualene biosynthetic pathways were selected following gene annotation. Then, 17 CYP450s and 26 UGTs, which are respectively responsible for backbone modifications, were used for phylogenetic-tree construction and time-specific expression analysis. From these data, by integrating metabolomics and transcriptomics analyses, we identified CaHDR1 and CaIDI2 as the candidate genes associated with DMAPP and IPP synthesis, respectively, and CaβAS1 as the one regulating β-amyrin synthesis. Two genes from the CYP716 family were confirmed as CaCYP716A83 and CaCYP716C11. We also selected two UGT73 families as candidate genes, associated with glycosylation of the terpenoid backbone at C-3 in C. asiatica. These findings will pave the way for further research on the molecular mechanisms associated with triterpenoid saponin biosynthesis in C. asiatica.
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Affiliation(s)
- Lingyun Wan
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Qiulan Huang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Cui Li
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Haixia Yu
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guiyu Tan
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Shugen Wei
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Suren Sooranna
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Kun Zhang
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Limei Pan
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhanjiang Zhang
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ming Lei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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Krause T, Wiesinger P, González-Cabanelas D, Lackus N, Köllner TG, Klüpfel T, Williams J, Rohwer J, Gershenzon J, Schmidt A. HDR, the last enzyme in the MEP pathway, differently regulates isoprenoid biosynthesis in two woody plants. PLANT PHYSIOLOGY 2023; 192:767-788. [PMID: 36848194 DOI: 10.1093/plphys/kiad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 06/01/2023]
Abstract
Dimethylallyl diphosphate (DMADP) and isopentenyl diphosphate (IDP) serves as the universal C5 precursors of isoprenoid biosynthesis in plants. These compounds are formed by the last step of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, catalyzed by (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase (HDR). In this study, we investigated the major HDR isoforms of two woody plant species, Norway spruce (Picea abies) and gray poplar (Populus × canescens), to determine how they regulate isoprenoid formation. Since each of these species has a distinct profile of isoprenoid compounds, they may require different proportions of DMADP and IDP with proportionally more IDP being needed to make larger isoprenoids. Norway spruce contained two major HDR isoforms differing in their occurrence and biochemical characteristics. PaHDR1 produced relatively more IDP than PaHDR2 and it encoding gene was expressed constitutively in leaves, likely serving to form substrate for production of carotenoids, chlorophylls, and other primary isoprenoids derived from a C20 precursor. On the other hand, Norway spruce PaHDR2 produced relatively more DMADP than PaHDR1 and its encoding gene was expressed in leaves, stems, and roots, both constitutively and after induction with the defense hormone methyl jasmonate. This second HDR enzyme likely forms a substrate for the specialized monoterpene (C10), sesquiterpene (C15), and diterpene (C20) metabolites of spruce oleoresin. Gray poplar contained only one dominant isoform (named PcHDR2) that produced relatively more DMADP and the gene of which was expressed in all organs. In leaves, where the requirement for IDP is high to make the major carotenoid and chlorophyll isoprenoids derived from C20 precursors, excess DMADP may accumulate, which could explain the high rate of isoprene (C5) emission. Our results provide new insights into the biosynthesis of isoprenoids in woody plants under conditions of differentially regulated biosynthesis of the precursors IDP and DMADP.
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Affiliation(s)
- Toni Krause
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Piera Wiesinger
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Diego González-Cabanelas
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Nathalie Lackus
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Thomas Klüpfel
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Germany
| | - Jonathan Williams
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Germany
| | - Johann Rohwer
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602 Stellenbosch, South Africa
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Axel Schmidt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
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Rodrigues JS, Kovács L, Lukeš M, Höper R, Steuer R, Červený J, Lindberg P, Zavřel T. Characterizing isoprene production in cyanobacteria - Insights into the effects of light, temperature, and isoprene on Synechocystis sp. PCC 6803. BIORESOURCE TECHNOLOGY 2023; 380:129068. [PMID: 37084984 DOI: 10.1016/j.biortech.2023.129068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/03/2023] [Accepted: 04/16/2023] [Indexed: 05/03/2023]
Abstract
Engineering cyanobacteria for the production of isoprene and other terpenoids has gained increasing attention in the field of biotechnology. Several studies have addressed optimization of isoprene synthesis in cyanobacteria via enzyme and pathway engineering. However, only little attention has been paid to the optimization of cultivation conditions. In this study, an isoprene-producing strain of Synechocystis sp. PCC 6803 and two control strains were grown under a variety of cultivation conditions. Isoprene production, as quantified by modified membrane inlet mass spectrometer (MIMS) and interpreted using Flux Balance Analysis (FBA), increased under violet light and at elevated temperature. Increase of thermotolerance in the isoprene producer was attributed to the physical presence of isoprene, similar to plants. The results demonstrate a beneficial effect of isoprene on cell survival at higher temperatures. This increased thermotolerance opens new possibilities for sustainable bio-production of isoprene and other products.
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Affiliation(s)
| | - László Kovács
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Martin Lukeš
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
| | - Rune Höper
- Institute for Biology, Theoretical Biology (ITB), Humboldt-University of Berlin, Berlin, Germany
| | - Ralf Steuer
- Institute for Biology, Theoretical Biology (ITB), Humboldt-University of Berlin, Berlin, Germany
| | - Jan Červený
- Department of Adaptive Biotechnologies, Global Change Research Institute of the Czech Academy of Sciences, Brno, Czech Republic
| | - Pia Lindberg
- Department of Chemistry - Ångström, Uppsala University, Sweden
| | - Tomáš Zavřel
- Department of Adaptive Biotechnologies, Global Change Research Institute of the Czech Academy of Sciences, Brno, Czech Republic.
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Umeyama Y, Taniguchi H, Gyotoku H, Senju H, Tomono H, Takemoto S, Yamaguchi H, Tagod MSO, Iwasaki M, Tanaka Y, Mukae H. Three distinct mechanisms underlying human γδ T cell-mediated cytotoxicity against malignant pleural mesothelioma. Front Immunol 2023; 14:1058838. [PMID: 37006249 PMCID: PMC10063812 DOI: 10.3389/fimmu.2023.1058838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionMalignant pleural mesothelioma (MPM) is a rare and highly aggressive thoracic tumor with poor prognosis and limited therapeutic options. Although immune checkpoint inhibitors exhibit a promising effect in some patients with unresectable MPM in clinical trials, the majority of MPM patients show only modest response rates to the currently available treatments. It is thus imperative to develop novel and innovative therapeutic modalities for MPM, including immune effector cell-based therapies.Methodsγδ T cells were expanded using tetrakis-pivaloyloxymethyl 2-(thiazole-2-ylamino) ethylidene-1,1-bisphosphonate (PTA) and interleukin-2, and the therapeutic potential of γδ T cells was examined through analyzing cell surface markers and cellular cytotoxicity against MPM in vitro using a europium chelate-based time-resolved fluorescence assay system and a luciferase-based luminescence assay system.Results and discussionWe successfully expanded γδ T cells from peripheral blood mononuclear cells of healthy donors and MPM patients. γδ T cells expressed natural killer receptors such as NKG2D and DNAM-1 and exhibited a moderate level of cytotoxicity to MPM cells in the absence of antigens. The inclusion of PTA, (E)-4-hydroxy-3- methylbut-2-enyl diphosphate (HMBPP) or zoledronic acid (ZOL) induced a TCR-dependent cytotoxicity in γδ T cells and secreted interferon-γ (IFN-γ). In addition, γδ T cells expressing CD16 exhibited a significant level of cytotoxicity against MPM cells in the presence of an anti-epidermal growth factor receptor (EGFR) mAb, at lower concentrations than in clinical settings, whereas a detectable level of IFN-γ was not produced. Taken together, γδ T cells showed cytotoxic activity against MPM in three distinct mechanisms through NK receptors, TCRs and CD16. Since major histocompatibility complex (MHC) molecules are not involved in the recognition, both autologous and allogeneic γδ T cells could be used for the development of γδ T cell-based adoptive immunotherapy for MPM.
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Affiliation(s)
- Yasuhiro Umeyama
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Center for Medical Innovation, Nagasaki University, Nagasaki, Japan
| | - Hirokazu Taniguchi
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- *Correspondence: Hirokazu Taniguchi,
| | - Hiroshi Gyotoku
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Hiroaki Senju
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Respiratory Medicine, Senju Hospital, Sasebo, Japan
| | - Hiromi Tomono
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Center for Medical Innovation, Nagasaki University, Nagasaki, Japan
| | - Shinnosuke Takemoto
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Hiroyuki Yamaguchi
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Clinical Oncology Center, Nagasaki University Hospital, Nagasaki, Japan
| | | | - Masashi Iwasaki
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshimasa Tanaka
- Center for Medical Innovation, Nagasaki University, Nagasaki, Japan
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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Huang S, Xue Y, Ma Y, Zhou C. Microbial (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate reductase (IspH) and its biotechnological potential: A mini review. Front Bioeng Biotechnol 2022; 10:1057938. [DOI: 10.3389/fbioe.2022.1057938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
(E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) reductase (IspH) is a [4Fe-4S] cluster-containing enzyme, involved in isoprenoid biosynthesis as the final enzyme of the methylerythritol phosphate (MEP) pathway found in many bacteria and malaria parasites. In recent years, many studies have revealed that isoprenoid compounds are an alternative to petroleum-derived fuels. Thus, ecofriendly methods harnessing the methylerythritol phosphate pathway in microbes to synthesize isoprenoid compounds and IspH itself have received notable attention from researchers. In addition to its applications in the field of biosynthesis, IspH is considered to be an attractive drug target for infectious diseases such as malaria and tuberculosis due to its survivability in most pathogenic bacterium and its absence in humans. In this mini-review, we summarize previous reports that have systematically illuminated the fundamental and structural properties, substrate binding and catalysis, proposed catalytic mechanism, and novel catalytic activities of IspH. Potential bioengineering and biotechnological applications of IspH are also discussed.
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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: 1.0] [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.
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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:
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Ball HS, Girma MB, Zainab M, Soojhawon I, Couch RD, Noble SM. Characterization and Inhibition of 1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase: A Promising Drug Target in Acinetobacter baumannii and Klebsiella pneumoniae. ACS Infect Dis 2021; 7:2987-2998. [PMID: 34672535 PMCID: PMC8594541 DOI: 10.1021/acsinfecdis.1c00132] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The ESKAPE pathogens
comprise a group of multidrug-resistant bacteria
that are the leading cause of nosocomial infections worldwide. The
prevalence of antibiotic resistant strains and the relative ease by
which bacteria acquire resistance genes highlight the continual need
for the development of novel antibiotics against new drug targets.
The methylerythritol phosphate (MEP) pathway is an attractive target
for the development of new antibiotics. The MEP pathway governs the
synthesis of isoprenoids, which are key lipid precursors for vital
cell components such as ubiquinone and bacterial hopanoids. Additionally,
the MEP pathway is entirely distinct from the corresponding mammalian
pathway, the mevalonic acid (MVA) pathway, making the first committed
enzyme of the MEP pathway, 1-deoxy-d-xylulose 5-phosphate
reductoisomerase (IspC), an attractive target for antibiotic development.
To facilitate drug development against two of the ESKAPE pathogens, Acinetobacter baumannii and Klebsiella
pneumoniae, we cloned, expressed, purified, and characterized
IspC from these two Gram-negative bacteria. Enzyme inhibition assays
using IspC from these two pathogens, and compounds fosmidomycin and
FR900098, indicate IC50 values ranging from 19.5–45.5
nM. Antimicrobial susceptibility tests with these inhibitors reveal
that A. baumannii is susceptible to
FR900098, whereas K. pneumoniae is
susceptible to both compounds. Finally, to facilitate structure-based
drug design of inhibitors targeting A. baumannii IspC, we determined the 2.5 Å crystal structure of IspC from A. baumannii in complex with inhibitor FR900098,
and cofactors NADPH and magnesium.
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Affiliation(s)
- Haley S. Ball
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20109, United States of America
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Springs, Maryland 20910, United States of America
| | - Misgina B. Girma
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20109, United States of America
| | - Mosufa Zainab
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20109, United States of America
| | - Iswarduth Soojhawon
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Springs, Maryland 20910, United States of America
| | - Robin D. Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20109, United States of America
| | - Schroeder M. Noble
- Wound Infections Department, Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Springs, Maryland 20910, United States of America
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Sasaki S, Ma Y, Ishizuka T, Bao HL, Hirokawa T, Xu Y, Tera M, Nagasawa K. Linear consecutive hexaoxazoles as G4 ligands inducing chair-type anti-parallel topology of a telomeric G-quadruplex. RSC Adv 2020; 10:43319-43323. [PMID: 35519695 PMCID: PMC9058415 DOI: 10.1039/d0ra09413g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
G-quadruplex structures (G4s) in guanine-rich regions of DNA play critical roles in various biological phenomena, including replication, translation, and gene expression. There are three types of G4 topology, i.e., parallel, anti-parallel, and hybrid, and ligands that selectively interact with or stabilize a specific topology have been extensively explored to enable studies of topology-related functions. Here, we describe the synthesis of a new series of G4 ligands based on 6LCOs (6-linear consecutive oxazoles), i.e., L2H2-2M2EA-6LCO (2), L2A2-2M2EAc-6LCO (3), and L2G2-2M2EG-6LCO (4), which bear four aminoalkyl, acetamidealkyl, and guanidinylalkyl side chains, respectively. Among them, ligand 2 stabilized telomeric G4 and induced anti-parallel topology independently of the presence of cations. The anti-parallel topology induced by 2 was identified as chair-type by means of 19F NMR spectroscopy and fluorescence experiments with 2-aminopurine-labeled DNA.
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Affiliation(s)
- Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Division of Biomedical Science, University of Tsukuba 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology 2-4-7 Aomi, Koto-ward Tokyo 135-0064 Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Masayuki Tera
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
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Krause T, Reichelt M, Gershenzon J, Schmidt A. Analysis of the isoprenoid pathway intermediates, dimethylallyl diphosphate and isopentenyl diphosphate, from crude plant extracts by liquid chromatography tandem mass spectrometry. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:770-777. [PMID: 32337807 DOI: 10.1002/pca.2941] [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: 01/16/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE We sought to develop a sensitive and accurate analytical method for the detection and quantification of IDP and DMADP as well as their monophosphate derivatives in crude plant extracts. METHODS A liquid chromatography method coupled to tandem mass spectrometry (LC-MS/MS) with multiple reaction monitoring (MRM) was established to measure the amounts of IDP and DMADP down to low picogram levels, which was linear over at least three orders of magnitude. Extracts were enriched using an anion exchanger, and chromatographic separation was achieved using a β-cyclodextrin column. A S-thiolodiphosphate analog of DMADP was employed as an internal standard. RESULTS Dilution series of authentic compounds were used to determine the limits of detection and quantification for IDP, DMADP and their corresponding monophosphates. A survey of plant species producing varying amounts of isoprenoids showed a corresponding variation in IDP and DMADP with the ratio of DMADP/IDP ranging from 4:1 to 2:1. Trace levels of isopentenyl monophosphate (IP) and dimethylallyl monophosphate (DMAP) were also detected. CONCLUSION The LC-MS/MS method described enables absolute quantification of in planta levels of IDP and DMADP for the first time. The method is also suitable for analysing bacterial and animal samples as well as enzyme assays.
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Affiliation(s)
- Toni Krause
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Axel Schmidt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
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10
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Okuno D, Sugiura Y, Sakamoto N, Tagod MSO, Iwasaki M, Noda S, Tamura A, Senju H, Umeyama Y, Yamaguchi H, Suematsu M, Morita CT, Tanaka Y, Mukae H. Comparison of a Novel Bisphosphonate Prodrug and Zoledronic Acid in the Induction of Cytotoxicity in Human Vγ2Vδ2 T Cells. Front Immunol 2020; 11:1405. [PMID: 32793196 PMCID: PMC7385076 DOI: 10.3389/fimmu.2020.01405] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022] Open
Abstract
Increasing attention has been paid to human γδ T cells expressing Vγ2Vδ2 T cell receptor (also termed Vγ9Vδ2) in the field of cancer immunotherapy. We have previously demonstrated that a novel bisphosphonate prodrug, tetrakis-pivaloyloxymethyl 2-(thiazole-2-ylamino)ethylidene-1,1-bisphosphonate (PTA), efficiently expands peripheral blood Vγ2Vδ2 T cells to purities up to 95–99% in 10–11 days. In the present study, we first examined the effect of PTA on farnesyl diphosphate synthase (FDPS) using liquid chromatography mass spectrometry (LC-MS) to analyze the mechanism underlying the PTA-mediated expansion of Vγ2Vδ2 T cells. We find that the prodrug induced the accumulation of both isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), direct upstream metabolites of FDPS. This indicates that not only IPP but also DMAPP plays an important role in PTA-mediated stimulation of Vγ2Vδ2 T cells. We next analyzed TCR-independent cytotoxicity of Vγ2Vδ2 T cells. When human lung cancer cell lines were challenged by Vγ2Vδ2 T cells, no detectable cytotoxicity was observed in 40 min. The lung cancer cell lines were, however, significantly killed by Vγ2Vδ2 T cells after 4–16 h in an effector-to-target ratio-dependent manner, demonstrating that Vγ2Vδ2 T cell-based cell therapy required a large number of cells and longer time when tumor cells were not sensitized. By contrast, pulsing tumor cell lines with 10–30 nM of PTA induced significant lysis of tumor cells by Vγ2Vδ2 T cells even in 40 min. Similar levels of cytotoxicity were elicited by ZOL at concentrations of 100–300 μM, which were much higher than blood levels of ZOL after infusion (1–2 μM), suggesting that standard 4 mg infusion of ZOL was not enough to sensitize lung cancer cells in clinical settings. In addition, Vγ2Vδ2 T cells secreted interferon-γ (IFN-γ) when challenged by lung cancer cell lines pulsed with PTA in a dose-dependent manner. Taken together, PTA could be utilized for both expansion of Vγ2Vδ2 T cells ex vivo and sensitization of tumor cells in vivo in Vγ2Vδ2 T cell-based cancer immunotherapy. For use in patients, further studies on drug delivery are essential because of the hydrophobic nature of the prodrug.
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Affiliation(s)
- Daisuke Okuno
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Tokyo, Japan
| | - Noriho Sakamoto
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | | | - Masashi Iwasaki
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuto Noda
- Center for Medical Innovation, Nagasaki University, Nagasaki, Japan
| | - Akihiro Tamura
- Center for Medical Innovation, Nagasaki University, Nagasaki, Japan
| | - Hiroaki Senju
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yasuhiro Umeyama
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Hiroyuki Yamaguchi
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Tokyo, Japan
| | - Craig T Morita
- Department of Internal Medicine and the Interdisciplinary Graduate Program in Immunology, University of Iowa Carver College of Medicine, Veterans Affairs Health Care System, Iowa City, IA, United States
| | - Yoshimasa Tanaka
- Center for Medical Innovation, Nagasaki University, Nagasaki, Japan.,Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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11
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Liu X, Cao PH, Huang QQ, Yang YR, Tao DD. Disruption of a Rice Chloroplast-Targeted Gene OsHMBPP Causes a Seedling-Lethal Albino Phenotype. RICE (NEW YORK, N.Y.) 2020; 13:51. [PMID: 32712772 PMCID: PMC7382669 DOI: 10.1186/s12284-020-00408-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/06/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Chloroplast development is coordinately regulated by plastid- and nuclear-encoding genes. Although many regulators have been reported to be involved in chloroplast development, new factors remain to be identified, given the complexity of this process. RESULTS In this study, we characterized a rice mutant lethal albinic seedling 1(las1)form of a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (OsHMBPP) that was targeted to the chloroplasts. The LAS1 mutation caused the albino lethal phenotype in seedlings. Transmission electron microscopy indicated that las1 were defective in early chloroplast development. LAS1 is preferentially expressed in leaves, implying its role in controlling chloroplast development. The expression levels of many chloroplast-encoded genes were altered significantly in las1. The expression levels of nuclear-encoded gene involved in Chl biosynthesis were also decreased in las1. We further investigated plastidic RNA editing in las1 and found that the edit efficiency of four chloroplast genes were markly altered. Compared with WT, las1 exhibited defective in biogenesis of chloroplast ribosomes. CONCLUSIONS Our results show that LAS1/OsHMBPP plays an essential role in the early chloroplast development in rice.
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Affiliation(s)
- X Liu
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China.
| | - P H Cao
- Suzhou Academy of Agricultural Sciences, Suzhou, 215155, China
| | - Q Q Huang
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China
| | - Y R Yang
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China
| | - D D Tao
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China
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12
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Comparative transcriptome analysis of a taxol-producing endophytic fungus, Aspergillus aculeatinus Tax-6, and its mutant strain. Sci Rep 2020; 10:10558. [PMID: 32601443 PMCID: PMC7324598 DOI: 10.1038/s41598-020-67614-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 06/11/2020] [Indexed: 12/02/2022] Open
Abstract
Taxol is a rare but extremely effective antitumor agent extracted from Taxus yew barks. Taxus plants are valuable and rare species, and the production of taxol from them is a complex process. Therefore, taxol-producing endophytic fungi seem to be a promising alternative because of their high practical value and convenient progress. In this study, the transcriptome of an endophytic fungus, Aspergillus aculeatinus Tax-6 was analyzed in order to understand the molecular mechanisms of producing fungal taxol. The results showed that genes involved in the mevalonate (MVA) pathway and non-mevalonate (MEP) pathway were expressed, including isopentenyl pyrophosphate transferase, geranyl pyrophosphate transferase, and geranylgeranyl pyrophosphate synthetase. However, those downstream genes involved in the conversion of taxa-4(5)-11(12)-diene from geranylgeranyl pyrophosphate were not expressed except for taxane 10-beta-hydroxylase. Additionally, a mutant strain, A. aculeatinus BT-2 was obtained from the original strain, A. aculeatinus Tax-6, using fungicidin as the mutagenic agent. The taxol yield of BT-2 was 560 µg L−1, which was higher than that of Tax-6. To identify the mechanism of the difference in taxol production, we compared the transcriptomes of the two fungi and explored the changes in the gene expression between them. When compared with the original strain, Tax-6, most genes related to the MVA pathway in the mutant strain BT-2 showed upregulation, including GGPPS. Moreover, most of the downstream genes were not expressed in the mutant fungi as well. Overall, the results revealed the pathway and mechanism of taxol synthesis in endophytic fungi and the potential for the construction of taxol-producing genetic engineering strains.
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13
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Bongers M, Perez-Gil J, Hodson MP, Schrübbers L, Wulff T, Sommer MO, Nielsen LK, Vickers CE. Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production. eLife 2020; 9:48685. [PMID: 32163032 PMCID: PMC7067565 DOI: 10.7554/elife.48685] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 02/16/2020] [Indexed: 12/12/2022] Open
Abstract
Volatile isoprenoids produced by plants are emitted in vast quantities into the atmosphere, with substantial effects on global carbon cycling. Yet, the molecular mechanisms regulating the balance between volatile and non-volatile isoprenoid production remain unknown. Isoprenoids are synthesised via sequential condensation of isopentenyl pyrophosphate (IPP) to dimethylallyl pyrophosphate (DMAPP), with volatile isoprenoids containing fewer isopentenyl subunits. The DMAPP:IPP ratio could affect the balance between volatile and non-volatile isoprenoids, but the plastidic DMAPP:IPP ratio is generally believed to be similar across different species. Here we demonstrate that the ratio of DMAPP:IPP produced by hydroxymethylbutenyl diphosphate reductase (HDR/IspH), the final step of the plastidic isoprenoid production pathway, is not fixed. Instead, this ratio varies greatly across HDRs from phylogenetically distinct plants, correlating with isoprenoid production patterns. Our findings suggest that adaptation of HDR plays a previously unrecognised role in determining in vivo carbon availability for isoprenoid emissions, directly shaping global biosphere-atmosphere interactions.
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Affiliation(s)
- Mareike Bongers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Jordi Perez-Gil
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - Mark P Hodson
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,Metabolomics Australia, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,School of Pharmacy, The University of Queensland, Brisbane, Australia
| | - Lars Schrübbers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Morten Oa Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lars K Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
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14
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The Nonmevalonate Pathway of Isoprenoid Biosynthesis Supports Anaerobic Growth of Listeria monocytogenes. Infect Immun 2020; 88:IAI.00788-19. [PMID: 31792073 DOI: 10.1128/iai.00788-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/21/2019] [Indexed: 11/20/2022] Open
Abstract
Isoprenoids are an essential and diverse class of molecules, present in all forms of life, that are synthesized from an essential common precursor derived from either the mevalonate pathway or the nonmevalonate pathway. Most bacteria have one pathway or the other, but the Gram-positive, facultative intracellular pathogen Listeria monocytogenes is unusual because it carries all the genes for both pathways. While the mevalonate pathway has previously been reported to be essential, here we demonstrate that the nonmevalonate pathway can support growth of strains 10403S and EGD-e, but only anaerobically. L. monocytogenes lacking the gene hmgR, encoding the rate-limiting enzyme of the mevalonate pathway, had a doubling time of 4 h under anaerobic conditions, in contrast to the 45 min doubling time of the wild type. In contrast, deleting hmgR in two clinical isolates resulted in mutants that grew significantly faster, doubling in approximately 2 h anaerobically, although they still failed to grow under aerobic conditions without mevalonate. The difference in anaerobic growth rate was traced to three amino acid changes in the nonmevalonate pathway enzyme GcpE, and these changes were sufficient to increase the growth rate of 10403S to the rate observed in the clinical isolates. Despite an increased growth rate, virulence was still dependent on the mevalonate pathway in 10403S strains expressing the more active GcpE allele.
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15
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Ihmels H, Karbasiyoun M, Löhl K, Stremmel C. Structural flexibility versus rigidity of the aromatic unit of DNA ligands: binding of aza- and azoniastilbene derivatives to duplex and quadruplex DNA. Org Biomol Chem 2019; 17:6404-6413. [PMID: 31225566 DOI: 10.1039/c9ob00809h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The known azastilbene (E)-1,2-di(quinolin-3-yl)ethane (2a) and the novel azoniastilbene derivatives (E)-2-(2-(naphthalen-2-yl)vinyl)quinolizinium (2b) and (E)-3,3'-(ethane-1,2-diyl)bis(1-methylquinolinin-1-ium) (2c) were synthesized. Their interactions with duplex and quadruplex DNA (G4-DNA) were studied by photometric, fluorimetric, polarimetric and flow-LD analysis, and by thermal DNA denaturation studies, as well as by 1H-NMR spectroscopy. The main goal of this study was a comparison of these conformationally flexible compounds with the known G4-DNA-binding diazoniadibenzo[b,k]chrysenes, that have a comparable π-system extent, but a rigid structure. We have observed that the aza- and azoniastilbene derivatives 2a-c, i.e. compounds with almost the same spatial dimensions and steric demand, bind to DNA with an affinity and selectivity that depends significantly on the number of positive charges. Whereas the charge neutral derivative 2a binds unspecifically to the DNA backbone of duplex DNA, the ionic compounds 2b and 2c are typical DNA intercalators. Notably, the bis-quinolinium derivative 2c binds to G4-DNA with moderate affinity (Kb = 4.8 × 105 M-1) and also stabilizes the G4-DNA towards thermal denaturation (ΔTm = 11 °C at ligand-DNA ratio = 5.0). Strikingly, the corresponding rigid counterpart, 4a,12a-diazonia-8,16-dimethyldibenzo[b,k]chrysene, stabilizes the G4-DNA to an even greater extent under identical conditions (ΔTm = 27 °C). These results indicate that the increased flexibility of a G4-DNA ligand does not necessarily lead to stronger interactions with the G4-DNA as compared with rigid ligands that have essentially the same size and π system extent.
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Affiliation(s)
- H Ihmels
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - M Karbasiyoun
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - K Löhl
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - C Stremmel
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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16
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Cao Y, Zhang R, Liu W, Zhao G, Niu W, Guo J, Xian M, Liu H. Manipulation of the precursor supply for high-level production of longifolene by metabolically engineered Escherichia coli. Sci Rep 2019; 9:95. [PMID: 30643175 PMCID: PMC6331559 DOI: 10.1038/s41598-018-36495-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/16/2018] [Indexed: 01/26/2023] Open
Abstract
Longifolene is a naturally occurring tricyclic sesquiterpene widely used in many different fields. Up to now, this valuable terpene was mainly manufactured from the high-boiling fraction of certain pine resins. Microbial production can be a promising alternative to the extraction from natural plant sources. Here, we present the metabolic engineering strategy to assemble biosynthetic pathway for longifolene production in Escherichia coli. E. coli was rendered to produce longifolene by heterologously expressing a codon optimized longifolene synthase from Picea abies. Augmentation of the metabolic flux to farnesyl pyrophosphate (FPP) by different FPP synthases conferred a 1.8-fold increase in longifolene production. An additional enhancement of longifolene production (up to 2.64 mg/L) was achieved by introducing an exogenous mevalonate pathway. Under fed-batch conditions, the best-performing strain was able to produce 382 mg/L of longifolene in a 5 L bioreactor. These results demonstrated the feasibility of producing longifolene by microbial fermentation and could serve as the basis for the construction of more robust strains in the future.
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Affiliation(s)
- Yujin Cao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
| | - Rubing Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Niu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
| | - Huizhou Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
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17
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Haymond A, Dowdy T, Johny C, Johnson C, Ball H, Dailey A, Schweibenz B, Villarroel K, Young R, Mantooth CJ, Patel T, Bases J, Dowd CS, Couch RD. A high-throughput screening campaign to identify inhibitors of DXP reductoisomerase (IspC) and MEP cytidylyltransferase (IspD). Anal Biochem 2018; 542:63-75. [PMID: 29180070 PMCID: PMC5817008 DOI: 10.1016/j.ab.2017.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 11/17/2022]
Abstract
The rise of antibacterial resistance among human pathogens represents a problem that could change the landscape of healthcare unless new antibiotics are developed. The methyl erythritol phosphate (MEP) pathway represents an attractive series of targets for novel antibiotic design, considering each enzyme of the pathway is both essential and has no human homologs. Here we describe a pilot scale high-throughput screening (HTS) campaign against the first and second committed steps in the pathway, catalyzed by DXP reductoisomerase (IspC) and MEP cytidylyltransferase (IspD), using compounds present in the commercially available LOPAC1280 library as well as in an in-house natural product extract library. Hit compounds were characterized to deduce their mechanism of inhibition; most function through aggregation. The HTS workflow outlined here is useful for quickly screening a chemical library, while effectively identifying false positive compounds associated with assay constraints and aggregation.
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Affiliation(s)
- Amanda Haymond
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Tyrone Dowdy
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Chinchu Johny
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Claire Johnson
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Haley Ball
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Allyson Dailey
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Brandon Schweibenz
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Karen Villarroel
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Richard Young
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Clark J Mantooth
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Trishal Patel
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Jessica Bases
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Cynthia S Dowd
- Department of Chemistry, George Washington University, Washington DC 20052, USA.
| | - Robin D Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA.
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18
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Huang R, Wang Y, Wang P, Li C, Xiao F, Chen N, Li N, Li C, Sun C, Li L, Chen R, Xu Z, Zhu J, Deng X. A single nucleotide mutation of IspF gene involved in the MEP pathway for isoprenoid biosynthesis causes yellow-green leaf phenotype in rice. PLANT MOLECULAR BIOLOGY 2018; 96:5-16. [PMID: 29143298 DOI: 10.1007/s11103-017-0668-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 10/09/2017] [Indexed: 05/20/2023]
Abstract
We identified IspF gene through yellow-green leaf mutant 505ys in rice. OsIspF was expressed in all tissues detected, and its encoded protein was targeted to the chloroplast. On expression levels of genes in this mutant, OsIspF itself and the genes encoding other enzymes of the MEP pathway and chlorophyll synthase were all up-regulated, however, among eight genes associated with photosynthesis, only psaA, psaN and psbA genes for three reaction center subunits of photosystem obviously changed. Isoprenoids are the most abundant natural compounds in all organisms, which originate from the basic five-carbon units isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In plants, IPP and DMAPP are synthesized through two independent pathways, the mevalonic acid pathway in cytoplasm and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway in plastids. The MEP pathway comprises seven enzymatic steps, in which IspF is the fifth enzyme. So far, no IspF gene has been identified in monocotyledonous plants. In this study, we isolated a leaf-color mutant, 505ys, in rice (Oryza sativa). The mutant displayed yellow-green leaf phenotype, reduced level of photosynthetic pigments, and arrested development of chloroplasts. By map-based cloning of this mutant, we identified OsIspF gene (LOC_Os02g45660) showing significant similarity to IspF gene of Arabidopsis, in which a missense mutation occurred in the mutant, resulting in an amino acid change in the encoded protein. OsIspF gene was expressed in all tissues detected, and its encoded protein was targeted to the chloroplast. Further, the mutant phenotype of 505ys was complemented by transformation with the wild-type OsIspF gene. Therefore, we successfully identified an IspF gene in monocotyledonous plants. In addition, real-time quantitative RT-PCR implied that a positive regulation could exist between the OsIspF gene and the genes encoding other enzymes of the MEP pathway and chlorophyll synthase. At the same time, it also implied that the individual genes involved in the MEP pathway might differentially regulated expression levels of the genes associated with photosynthesis.
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Affiliation(s)
- Rui Huang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yang Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Pingrong Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Chunmei Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Fuliang Xiao
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Nenggang Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Na Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Caixia Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Changhui Sun
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lihua Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Rongjun Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhengjun Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jianqing Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaojian Deng
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Ma Y, Tsushima Y, Sakuma M, Sasaki S, Iida K, Okabe S, Seimiya H, Hirokawa T, Nagasawa K. Development of G-quadruplex ligands for selective induction of a parallel-type topology. Org Biomol Chem 2018; 16:7375-7382. [DOI: 10.1039/c8ob01702f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Parallel type of topology in G4 is selectively induced by tetra-guanidinylalkyl substituted 6OTD derivative.
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Affiliation(s)
- Yue Ma
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Yamato Tsushima
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Mai Sakuma
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Shogo Sasaki
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Keisuke Iida
- Department of Chemistry
- Faculty of Science
- Chiba University
- Chiba 263-8522
- Japan
| | - Sachiko Okabe
- Division of Molecular Biotherapy
- Cancer Chemotherapy Center
- Japanese Foundation for Cancer Research
- Koto-ward
- Tokyo 135-8550
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy
- Cancer Chemotherapy Center
- Japanese Foundation for Cancer Research
- Koto-ward
- Tokyo 135-8550
| | - Takatsugu Hirokawa
- Transborder Medical Research Center
- University of Tsukuba
- Tsukuba, 305-8575
- Japan
- Division of Biomedical Science
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
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Biosynthesis and production of sabinene: current state and perspectives. Appl Microbiol Biotechnol 2017; 102:1535-1544. [DOI: 10.1007/s00253-017-8695-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 01/10/2023]
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Genomic Analysis of Calderihabitans maritimus KKC1, a Thermophilic, Hydrogenogenic, Carboxydotrophic Bacterium Isolated from Marine Sediment. Appl Environ Microbiol 2017; 83:AEM.00832-17. [PMID: 28526793 DOI: 10.1128/aem.00832-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/13/2017] [Indexed: 11/20/2022] Open
Abstract
Calderihabitans maritimus KKC1 is a thermophilic, hydrogenogenic carboxydotroph isolated from a submerged marine caldera. Here, we describe the de novo sequencing and feature analysis of the C. maritimus KKC1 genome. Genome-based phylogenetic analysis confirmed that C. maritimus KKC1 was most closely related to the genus Moorella, which includes well-studied acetogenic members. Comparative genomic analysis revealed that, like Moorella, C. maritimus KKC1 retained both the CO2-reducing Wood-Ljungdahl pathway and energy-converting hydrogenase-based module activated by reduced ferredoxin, but it lacked the HydABC and NfnAB electron-bifurcating enzymes and pyruvate:ferredoxin oxidoreductase required for ferredoxin reduction for acetogenic growth. Furthermore, C. maritimus KKC1 harbored six genes encoding CooS, a catalytic subunit of the anaerobic CO dehydrogenase that can reduce ferredoxin via CO oxidation, whereas Moorella possessed only two CooS genes. Our analysis revealed that three cooS genes formed known gene clusters in other microorganisms, i.e., cooS-acetyl coenzyme A (acetyl-CoA) synthase (which contained a frameshift mutation), cooS-energy-converting hydrogenase, and cooF-cooS-FAD-NAD oxidoreductase, while the other three had novel genomic contexts. Sequence composition analysis indicated that these cooS genes likely evolved from a common ancestor. Collectively, these data suggest that C. maritimus KKC1 may be highly dependent on CO as a low-potential electron donor to directly reduce ferredoxin and may be more suited to carboxydotrophic growth compared to the acetogenic growth observed in Moorella, which show adaptation at a thermodynamic limit.IMPORTANCECalderihabitans maritimus KKC1 and members of the genus Moorella are phylogenetically related but physiologically distinct. The former is a hydrogenogenic carboxydotroph that can grow on carbon monoxide (CO) with H2 production, whereas the latter include acetogenic bacteria that grow on H2 plus CO2 with acetate production. Both species may require reduced ferredoxin as an actual "energy equivalent," but ferredoxin is a low-potential electron carrier and requires a high-energy substrate as an electron donor for reduction. Comparative genomic analysis revealed that C. maritimus KKC1 lacked specific electron-bifurcating enzymes and possessed six CO dehydrogenases, unlike Moorella species. This suggests that C. maritimus KKC1 may be more dependent on CO, a strong electron donor that can directly reduce ferredoxin via CO dehydrogenase, and may exhibit a survival strategy different from that of acetogenic Moorella, which solves the energetic barrier associated with endergonic reduction of ferredoxin with hydrogen.
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Shin BK, Kim M, Han J. Exceptionally high percentage of IPP synthesis by Ginkgo biloba IspH is mainly due to Phe residue in the active site. PHYTOCHEMISTRY 2017; 136:9-14. [PMID: 28139297 DOI: 10.1016/j.phytochem.2017.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/13/2017] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) reductase (IspH, HDR or LytB) is an Fe/S enzyme catalyzing the reductive dehydroxylation of HMBPP to isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the last step of methylerythritol phosphate (MEP) pathway. The MEP pathway is known to produce 4-6:1 ratio of IPP and DMAPP mixture by the last enzyme, IspH. Plant IspH in plastids follows same catalytic mechanism as others, but GbIspH (Ginkgo biloba IspH) was reported to produce a mixture of IPP and DMAPP in a ratio of 16:1. Present catalytic mechanisms of IspH involve a common allyl anion intermediate, and the intramolecular proton transfer to the allyl moiety is considered as the key reaction step determining the product between IPP and DMAPP. The F212 residue in plant IspH was found as a potential amino acid residue that could mediate the proton transfer to the allyl anion intermediate before the product release. In this report, catalytic function of GbIspH F212 residue (H74 in E. coli), especially during the product formation in the active site, was studied by means of site-directed mutation. The product ratio of IPP/DMAPP was measured as 6.5 ± 0.1 for F212H GbIspH, and the value was close to the reported bacterial IspH having His residue on that specific position. Along with the other F212Y mutant, of which ratio was determined as 10.9 ± 0.1, the results strongly support that the Phe residue in plant IspH is the key amino acid residue that allows exclusive production of IPP in plant chloroplast.
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Affiliation(s)
- Bok-Kyu Shin
- Metalloenzyme Research Group and Department of Integrative Plant Science, Chung-Ang University, Anseong, 456-756, South Korea
| | - Mihyang Kim
- Metalloenzyme Research Group and Department of Integrative Plant Science, Chung-Ang University, Anseong, 456-756, South Korea
| | - Jaehong Han
- Metalloenzyme Research Group and Department of Integrative Plant Science, Chung-Ang University, Anseong, 456-756, South Korea.
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Bufadienolides from amphibians: A promising source of anticancer prototypes for radical innovation, apoptosis triggering and Na +/K +-ATPase inhibition. Toxicon 2017; 127:63-76. [PMID: 28069354 DOI: 10.1016/j.toxicon.2017.01.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/27/2016] [Accepted: 01/05/2017] [Indexed: 12/22/2022]
Abstract
Amphibians present pharmacologically active aliphatic, aromatic and heterocyclic molecules in their skin as defense against microorganisms, predators and infections, such as steroids, alkaloids, biogenic amines, guanidine derivatives, proteins and peptides. Based on the discovered bioactive potential of bufadienolides, this work reviewed the contribution of amphibians, especially from members of Bufonidae family, as source of new cytotoxic and antitumor molecules, highlighting the mechanisms responsible for such amazing biological potentialities. Bufonidae species produce bufadienolides related to cholesterol through the mevalonate-independent and acidic bile acid pathways as polyhydroxy steroids with 24 carbons. In vitro antitumor studies performed with skin secretions and its isolated components (specially marinobufagin, telocinobufagin, bufalin and cinobufagin) from Rhinella, Bufo and Rhaebo species have shown remarkable biological action on hematological, solid, sensitive and/or resistant human tumor cell lines. Some compounds revealed higher selectivity against neoplastic lines when compared to dividing normal cells and some molecules may biochemically associate with Na+/K+-ATPase and there is structural similarity to the digoxin- and ouabain-Na+/K+-ATPase complexs, implying a similar mechanism of the Na+/K+-ATPase inhibition by cardenolides and bufadienolides. Some bufadienolides also reduce levels of antiapoptotic proteins and DNA synthesis, cause morphological changes (chromatin condensation, nuclear fragmentation, cytoplasm shrinkage, cytoplasmic vacuoles, stickiness reduction and apoptotic bodies), cell cycle arrest in G2/M or S phases, mitochondrial depolarization, PARP [poly (ADPribose) polymerase] and Bid cleavages, cytochrome c release, activation of Bax and caspases (-3, -9, -8 and -10), increased expression of the Fas-Associated protein with Death Domain (FADD), induce topoisomerase II inhibition, DNA fragmentation, cell differentiation, angiogenesis inhibition, multidrug resistance reversion, and also regulate immune responses. Then, bufadienolides isolated from amphibians, some of them at risk of extinction, emerge as a natural class of incredible chemical biodiversity, has moderate selectivity against human tumor cells and weak activity on murine cells, probably due to structural differences between subunits of human and mice Na+/K+-ATPases.
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Affiliation(s)
- Annika Frank
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Michael Groll
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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Chaves JE, Romero PR, Kirst H, Melis A. Role of isopentenyl-diphosphate isomerase in heterologous cyanobacterial (Synechocystis) isoprene production. PHOTOSYNTHESIS RESEARCH 2016; 130:517-527. [PMID: 27412351 DOI: 10.1007/s11120-016-0293-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
Heterologous production of isoprene (C5H8) hydrocarbons in cyanobacteria, emanating from sunlight, CO2, and water, is now attracting increasing attention. The concept entails application of an isoprene synthase transgene from terrestrial plants, heterologously expressed in cyanobacteria, aiming to reprogram carbon flux in the terpenoid biosynthetic pathway toward formation and spontaneous release of this volatile chemical from the cell and liquid culture. However, flux manipulations and carbon-partitioning reactions between isoprene (the product) and native terpenoid biosynthesis for cellular needs are not yet optimized for isoprene yield. The primary reactant for isoprene biosynthesis is dimethylallyl diphosphate (DMAPP), whereas both DMAPP and its isopentenyl diphosphate (IPP) isomer are needed for cellular terpenoid biosynthesis. The present work addressed the function of an isopentenyl diphosphate (IPP) isomerase in cyanobacteria and its role in carbon partitioning between IPP and DMAPP, both of which serve, in variable ratios, as reactants for the synthesis of different cellular terpenoids. The work was approached upon the heterologous expression in Synechocystis of the "isopentenyl diphosphate isomerase" gene (FNI) from Streptococcus pneumoniae, using isoprene production as a "reporter process" for substrate partitioning between DMAPP and IPP. It is shown that transgenic expression of the FNI gene in Synechocystis resulted in a 250 % increase in the "reporter isoprene" rate and yield, suggesting that the FNI isomerase shifted the endogenous DMAPP-IPP steady-state pool size toward DMAPP, thereby enhancing rates and yield of isoprene production. The work provides insight into the significance and functional role of the IPP isomerase in these photosynthetic microorganisms.
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Affiliation(s)
- Julie E Chaves
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720-3102, USA
| | - Paloma Rueda Romero
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720-3102, USA
| | - Henning Kirst
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720-3102, USA
| | - Anastasios Melis
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720-3102, USA.
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Zheng W, Komatsu S, Zhu W, Zhang L, Li X, Cui L, Tian J. Response and Defense Mechanisms of Taxus chinensis Leaves Under UV-A Radiation are Revealed Using Comparative Proteomics and Metabolomics Analyses. PLANT & CELL PHYSIOLOGY 2016; 57:1839-1853. [PMID: 27318281 DOI: 10.1093/pcp/pcw106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 05/22/2016] [Indexed: 06/06/2023]
Abstract
Taxus chinensis var. mairei is a species endemic to south-eastern China and one of the natural sources for the anticancer medicine paclitaxel. To investigate the molecular response and defense mechanisms of T. chinensis leaves to enhanced ultraviolet-A (UV-A) radiation, gel-free/label-free and gel-based proteomics and gas chromatography-mass spectrometry (GC-MS) analyses were performed. The transmission electron microscopy results indicated damage to the chloroplast under UV-A radiation. Proteomics analyses in leaves and chloroplasts showed that photosynthesis-, glycolysis-, secondary metabolism-, stress-, and protein synthesis-, degradation- and activation-related systems were mainly changed under UV-A radiation. Forty-seven PSII proteins and six PSI proteins were identified as being changed in leaves and chloroplasts under UV-A treatment. This indicated that PSII was more sensitive to UV-A than PSI as the target of UV-A light. Enhanced glycolysis, with four glycolysis-related key enzymes increased, provided precursors for secondary metabolism. The 1-deoxy-d-xylulose-5-phosphate reductoisomerase and 4-hydroxy-3-methylbut-2-enyl diphosphate reductase were identified as being significantly increased during UV-A radiation, which resulted in paclitaxel enhancement. Additionally, mRNA expression levels of genes involved in the paclitaxel biosynthetic pathway indicated a down-regulation under UV-A irradiation and up-regulation in dark incubation. These results reveal that a short-term high dose of UV-A radiation could stimulate the plant stress defense system and paclitaxel production.
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Affiliation(s)
- Wen Zheng
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518 Japan
| | - Wei Zhu
- Education Ministry Key Laboratory for Biomedical Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Lin Zhang
- Education Ministry Key Laboratory for Biomedical Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Ximin Li
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Lei Cui
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Jingkui Tian
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China Education Ministry Key Laboratory for Biomedical Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
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Wang R, Yang X, Wang N, Liu X, Nelson RS, Li W, Fan Z, Zhou T. An efficient virus-induced gene silencing vector for maize functional genomics research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:102-15. [PMID: 26921244 DOI: 10.1111/tpj.13142] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/01/2016] [Accepted: 02/08/2016] [Indexed: 05/02/2023]
Abstract
Maize is a major crop whose rich genetic diversity provides an advanced resource for genetic research. However, a tool for rapid transient gene function analysis in maize that may be utilized in most maize cultivars has been lacking, resulting in reliance on time-consuming stable transformation and mutation studies to obtain answers. We developed an efficient virus-induced gene silencing (VIGS) vector for maize based on a naturally maize-infecting cucumber mosaic virus (CMV) strain, ZMBJ-CMV. An infectious clone of ZMBJ-CMV was constructed, and a vascular puncture inoculation method utilizing Agrobacterium was optimized to improve its utility for CMV infection of maize. ZMBJ-CMV was then modified to function as a VIGS vector. The ZMBJ-CMV vector induced mild to moderate symptoms in many maize lines, making it useful for gene function studies in critically important maize cultivars, such as the sequenced reference inbred line B73. Using this CMV VIGS system, expression of two endogenous genes, ZmPDS and ZmIspH, was found to be decreased by 75% and 78%, respectively, compared with non-silenced tissue. Inserts with lengths of 100-300 bp produced the most complete transcriptional and visual silencing phenotypes. Moreover, genes related to autophagy, ZmATG3 and ZmATG8a, were also silenced, and it was found that they function in leaf starch degradation. These results indicate that our ZMBJ-CMV VIGS vector provides a tool for rapid and efficient gene function studies in maize.
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Affiliation(s)
- Rong Wang
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xinxin Yang
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Nian Wang
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xuedong Liu
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Richard S Nelson
- Plant Biology Division, The Samuel Roberts Noble Foundation Inc., 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
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Kim MJ, Jin J, Zheng J, Wong L, Chua NH, Jang IC. Comparative Transcriptomics Unravel Biochemical Specialization of Leaf Tissues of Stevia for Diterpenoid Production. PLANT PHYSIOLOGY 2015; 169:2462-2480. [PMID: 26438788 PMCID: PMC4677913 DOI: 10.1104/pp.15.01353] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/02/2015] [Indexed: 05/29/2023]
Abstract
Stevia (Stevia rebaudiana) produces not only a group of diterpenoid glycosides known as steviol glycosides (SGs), but also other labdane-type diterpenoids that may be spatially separated from SGs. However, their biosynthetic routes and spatial distribution in leaf tissues have not yet been elucidated. Here, we integrate metabolome and transcriptome analyses of Stevia to explore the biosynthetic capacity of leaf tissues for diterpenoid metabolism. Tissue-specific chemical analyses confirmed that SGs were accumulated in leaf cells but not in trichomes. On the other hand, Stevia leaf trichomes stored other labdane-type diterpenoids such as oxomanoyl oxide and agatholic acid. RNA sequencing analyses from two different tissues of Stevia provided a comprehensive overview of dynamic metabolic activities in trichomes and leaf without trichomes. These metabolite-guided transcriptomics and phylogenetic and gene expression analyses clearly identified specific gene members encoding enzymes involved in the 2-C-methyl-d-erythritol 4-phosphate pathway and the biosynthesis of steviol or other labdane-type diterpenoids. Additionally, our RNA sequencing analysis uncovered copalyl diphosphate synthase (SrCPS) and kaurene synthase1 (SrKS1) homologs, SrCPS2 and KS-like (SrKSL), which were specifically expressed in trichomes. In vitro and in planta assays showed that unlike SrCPS and SrKS1, SrCPS2 synthesized labda-13-en-8-ol diphosphate and successively catalyzed the formation of manoyl oxide and epi-manoyl oxide in combination with SrKSL. Our findings suggest that Stevia may have evolved to use distinct metabolic pathways to avoid metabolic interferences in leaf tissues for efficient production of diverse secondary metabolites.
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Affiliation(s)
- Mi Jung Kim
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604 (M.J.K., J.J., J.Z., I.-C.J.);School of Computing, National University of Singapore, Singapore 117417 (J.J., L.W.);Department of Biological Sciences, National University of Singapore, Singapore 117543 (J.Z., I.-C.J.); andLaboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065 (N.-H.C.)
| | - Jingjing Jin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604 (M.J.K., J.J., J.Z., I.-C.J.);School of Computing, National University of Singapore, Singapore 117417 (J.J., L.W.);Department of Biological Sciences, National University of Singapore, Singapore 117543 (J.Z., I.-C.J.); andLaboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065 (N.-H.C.)
| | - Junshi Zheng
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604 (M.J.K., J.J., J.Z., I.-C.J.);School of Computing, National University of Singapore, Singapore 117417 (J.J., L.W.);Department of Biological Sciences, National University of Singapore, Singapore 117543 (J.Z., I.-C.J.); andLaboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065 (N.-H.C.)
| | - Limsoon Wong
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604 (M.J.K., J.J., J.Z., I.-C.J.);School of Computing, National University of Singapore, Singapore 117417 (J.J., L.W.);Department of Biological Sciences, National University of Singapore, Singapore 117543 (J.Z., I.-C.J.); andLaboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065 (N.-H.C.)
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604 (M.J.K., J.J., J.Z., I.-C.J.);School of Computing, National University of Singapore, Singapore 117417 (J.J., L.W.);Department of Biological Sciences, National University of Singapore, Singapore 117543 (J.Z., I.-C.J.); andLaboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065 (N.-H.C.)
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604 (M.J.K., J.J., J.Z., I.-C.J.);School of Computing, National University of Singapore, Singapore 117417 (J.J., L.W.);Department of Biological Sciences, National University of Singapore, Singapore 117543 (J.Z., I.-C.J.); andLaboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065 (N.-H.C.)
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29
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Tera M, Hirokawa T, Okabe S, Sugahara K, Seimiya H, Shimamoto K. Design and synthesis of a berberine dimer: a fluorescent ligand with high affinity towards G-quadruplexes. Chemistry 2015; 21:14519-28. [PMID: 26272465 DOI: 10.1002/chem.201501693] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 12/20/2022]
Abstract
G-quadruplexes (G4) are thought to be important factors for telomerase inhibition and transcriptional/translational modulations. Bioinformatic analyses imply that the human genome and mRNA contain a multitude of G4-forming sequences; however, their analysis requires selective and detectable ligands. Given that two molecules of fluorescent berberine (BBR) coordinate to telomeric G4 in their co-crystals, we designed hydrocarbon-linked BBR-analogue dimers because we expected the alignment of two BBR chromophores would avoid Watson-Crick base pair intercalation, which should result in high selectivity towards G4. An alkene-cis-C2 BBR dimer showed the highest affinity (Kd ≤2.6 nM) and selectivity (ca. 900-fold vs. duplex) towards G4. The intrinsic "light-up" fluorescence properties of this BBR dimer, derived from its conformational switching by G4, allowed a selective visualization of various G4 in the gel without using additional bulky fluorescence dyes, which, combined with the observed lack of conformational change of the ligand, suggested future applications in in vitro detection systems.
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Affiliation(s)
- Masayuki Tera
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan).
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ward, Tokyo, 135-0064 (Japan)
| | - Sachiko Okabe
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550 (Japan)
| | - Kohtaro Sugahara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan)
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550 (Japan)
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan)
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N-Terminal Region of GbIspH1, Ginkgo biloba IspH Type 1, May Be Involved in the pH-Dependent Regulation of Enzyme Activity. Bioinorg Chem Appl 2015; 2015:241479. [PMID: 25892986 PMCID: PMC4393896 DOI: 10.1155/2015/241479] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 02/28/2015] [Indexed: 11/18/2022] Open
Abstract
GbIspH1, IspH type 1 in Ginkgo biloba chloroplast, is the Fe/S enzyme catalyzing the reductive dehydroxylation of HMBPP to isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) at the final step of methylerythritol phosphate pathway in chloroplast. Compared to the bacterial IspH, plant IspH, including GbIspH1, has an additional polypeptide chain at the N-terminus. Here, biochemical function of the N-terminal region of GbIspH1 was investigated with the N-terminal truncated GbIspH1 (GbIspH1-truncated). Both wild type GbIspH1 (GbIspH1-full) and GbIspH1-truncated were catalytically active and produced IPP and DMAPP in a ratio of 15 : 1. Kinetic parameters of KM (17.3 ± 1.9 and 14.9 ± 2.3 µM) and kcat (369 ± 10 and 347 ± 12 min−1) at pH 8.0 were obtained for GbIspH1-full and GbIspH1-truncated, respectively. Interestingly, GbIspH1-full and GbIspH1-truncated showed significantly different pH-dependent activities, and the maximum enzyme activities were obtained at pH 8.0 and 7.5, respectively. However, catalytic activation energies (Ea) of GbIspH1-full and GbIspH1-truncated were almost the same with 36.5 ± 1.6 and 35.0 ± 1.9 kJ/mol, respectively. It was suggested that the N-terminal region of GbIspH1 is involved in the pH-dependent regulation of enzyme activity during photosynthesis.
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Production of squalene by squalene synthases and their truncated mutants in Escherichia coli. J Biosci Bioeng 2015; 119:165-71. [DOI: 10.1016/j.jbiosc.2014.07.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/31/2014] [Accepted: 07/31/2014] [Indexed: 02/08/2023]
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32
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Hsieh WY, Hsieh MH. The amino-terminal conserved domain of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase is critical for its function in oxygen-evolving photosynthetic organisms. PLANT SIGNALING & BEHAVIOR 2015; 10:e988072. [PMID: 25723575 PMCID: PMC4622703 DOI: 10.4161/15592324.2014.988072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 05/22/2023]
Abstract
4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), also known as isoprenoid synthesis H (IspH) or lysis-tolerant B (LytB), catalyzes the last step of the methylerythritol phosphate pathway to synthesize isopentenyl diphosphate and dimethylallyl diphosphate. The structure and reaction mechanism of IspH have been actively investigated in Escherichia coli but little is known in plants. Compared with the bacterial IspH, cyanobacterial and plant HDRs all contain an extra N-terminal conserved domain (NCD) that is essential for their function. Tyr72 in the NCD and several plant-specific residues around the central active site are critical for Arabidopsis HDR function. These results suggest that the structure and reaction mechanism of HDR/IspH may be different between plants and bacteria. The E. coli IspH is an iron-sulfur protein that is sensitive to oxygen. It is possible that the cyanobacterial HDR may independently evolve from the common ancestor of prokaryotes to obtain the NCD, which may protect the enzyme from high concentration of oxygen during photosynthesis.
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Affiliation(s)
- Wei-Yu Hsieh
- Institute of Plant and Microbial Biology; Academia Sinica; Taipei, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology; Academia Sinica; Taipei, Taiwan
- Correspondence to: Ming-Hsiun Hsieh;
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Hsieh WY, Sung TY, Wang HT, Hsieh MH. Functional evidence for the critical amino-terminal conserved domain and key amino acids of Arabidopsis 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE. PLANT PHYSIOLOGY 2014; 166:57-69. [PMID: 25037211 PMCID: PMC4149731 DOI: 10.1104/pp.114.243642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The plant 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE (HDR) catalyzes the last step of the methylerythritol phosphate pathway to synthesize isopentenyl diphosphate and its allyl isomer dimethylallyl diphosphate, which are common precursors for the synthesis of plastid isoprenoids. The Arabidopsis (Arabidopsis thaliana) genomic HDR transgene-induced gene-silencing lines are albino, variegated, or pale green, confirming that HDR is essential for plants. We used Escherichia coli isoprenoid synthesis H (Protein Data Bank code 3F7T) as a template for homology modeling to identify key amino acids of Arabidopsis HDR. The predicted model reveals that cysteine (Cys)-122, Cys-213, and Cys-350 are involved in iron-sulfur cluster formation and that histidine (His)-152, His-241, glutamate (Glu)-242, Glu-243, threonine (Thr)-244, Thr-312, serine-379, and asparagine-381 are related to substrate binding or catalysis. Glu-242 and Thr-244 are conserved only in cyanobacteria, green algae, and land plants, whereas the other key amino acids are absolutely conserved from bacteria to plants. We used site-directed mutagenesis and complementation assay to confirm that these amino acids, except His-152 and His-241, were critical for Arabidopsis HDR function. Furthermore, the Arabidopsis HDR contains an extra amino-terminal domain following the transit peptide that is highly conserved from cyanobacteria, and green algae to land plants but not existing in the other bacteria. We demonstrated that the amino-terminal conserved domain was essential for Arabidopsis and cyanobacterial HDR function. Further analysis of conserved amino acids in the amino-terminal conserved domain revealed that the tyrosine-72 residue was critical for Arabidopsis HDR. These results suggest that the structure and reaction mechanism of HDR evolution have become specific for oxygen-evolving photosynthesis organisms and that HDR probably evolved independently in cyanobacteria versus other prokaryotes.
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Affiliation(s)
- Wei-Yu Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Tzu-Ying Sung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-Tzu Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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Haymond A, Johny C, Dowdy T, Schweibenz B, Villarroel K, Young R, Mantooth CJ, Patel T, Bases J, Jose GS, Jackson ER, Dowd CS, Couch RD. Kinetic characterization and allosteric inhibition of the Yersinia pestis 1-deoxy-D-xylulose 5-phosphate reductoisomerase (MEP synthase). PLoS One 2014; 9:e106243. [PMID: 25171339 PMCID: PMC4149570 DOI: 10.1371/journal.pone.0106243] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/29/2014] [Indexed: 11/19/2022] Open
Abstract
The methylerythritol phosphate (MEP) pathway found in many bacteria governs the synthesis of isoprenoids, which are crucial lipid precursors for vital cell components such as ubiquinone. Because mammals synthesize isoprenoids via an alternate pathway, the bacterial MEP pathway is an attractive target for novel antibiotic development, necessitated by emerging antibiotic resistance as well as biodefense concerns. The first committed step in the MEP pathway is the reduction and isomerization of 1-deoxy-D-xylulose-5-phosphate (DXP) to methylerythritol phosphate (MEP), catalyzed by MEP synthase. To facilitate drug development, we cloned, expressed, purified, and characterized MEP synthase from Yersinia pestis. Enzyme assays indicate apparent kinetic constants of KMDXP = 252 µM and KMNADPH = 13 µM, IC50 values for fosmidomycin and FR900098 of 710 nM and 231 nM respectively, and Ki values for fosmidomycin and FR900098 of 251 nM and 101 nM respectively. To ascertain if the Y. pestis MEP synthase was amenable to a high-throughput screening campaign, the Z-factor was determined (0.9) then the purified enzyme was screened against a pilot scale library containing rationally designed fosmidomycin analogs and natural product extracts. Several hit molecules were obtained, most notably a natural product allosteric affector of MEP synthase and a rationally designed bisubstrate derivative of FR900098 (able to associate with both the NADPH and DXP binding sites in MEP synthase). It is particularly noteworthy that allosteric regulation of MEP synthase has not been described previously. Thus, our discovery implicates an alternative site (and new chemical space) for rational drug development.
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Affiliation(s)
- Amanda Haymond
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Chinchu Johny
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Tyrone Dowdy
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Brandon Schweibenz
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Karen Villarroel
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Richard Young
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Clark J. Mantooth
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Trishal Patel
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Jessica Bases
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Geraldine San Jose
- Department of Chemistry, George Washington University, Washington DC, United States of America
| | - Emily R. Jackson
- Department of Chemistry, George Washington University, Washington DC, United States of America
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington DC, United States of America
| | - Robin D. Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
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35
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Heider SAE, Wolf N, Hofemeier A, Peters-Wendisch P, Wendisch VF. Optimization of the IPP Precursor Supply for the Production of Lycopene, Decaprenoxanthin and Astaxanthin by Corynebacterium glutamicum. Front Bioeng Biotechnol 2014; 2:28. [PMID: 25191655 PMCID: PMC4138558 DOI: 10.3389/fbioe.2014.00028] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/31/2014] [Indexed: 01/21/2023] Open
Abstract
The biotechnologically relevant bacterium Corynebacterium glutamicum, currently used for the million ton-scale production of amino acids for the food and feed industries, is pigmented due to synthesis of the rare cyclic C50 carotenoid decaprenoxanthin and its glucosides. The precursors of carotenoid biosynthesis, isopenthenyl pyrophosphate (IPP) and its isomer dimethylallyl pyrophosphate, are synthesized in this organism via the methylerythritol phosphate (MEP) or non-mevalonate pathway. Terminal pathway engineering in recombinant C. glutamicum permitted the production of various non-native C50 and C40 carotenoids. Here, the role of engineering isoprenoid precursor supply for lycopene production by C. glutamicum was characterized. Overexpression of dxs encoding the enzyme that catalyzes the first committed step of the MEP-pathway by chromosomal promoter exchange in a prophage-cured, genome-reduced C. glutamicum strain improved lycopene formation. Similarly, an increased IPP supply was achieved by chromosomal integration of two artificial operons comprising MEP pathway genes under the control of a constitutive promoter. Combined overexpression of dxs and the other six MEP pathways genes in C. glutamicum strain LYC3-MEP was not synergistic with respect to improving lycopene accumulation. Based on C. glutamicum strain LYC3-MEP, astaxanthin could be produced in the milligrams per gram cell dry weight range when the endogenous genes crtE, crtB, and crtI for conversion of geranylgeranyl pyrophosphate to lycopene were coexpressed with the genes for lycopene cyclase and β-carotene hydroxylase from Pantoea ananatis and carotene C(4) oxygenase from Brevundimonas aurantiaca.
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Affiliation(s)
- Sabine A E Heider
- Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld , Germany
| | - Natalie Wolf
- Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld , Germany
| | - Arne Hofemeier
- Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld , Germany
| | - Petra Peters-Wendisch
- Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld , Germany
| | - Volker F Wendisch
- Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld , Germany
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36
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Span I, Wang K, Eisenreich W, Bacher A, Zhang Y, Oldfield E, Groll M. Insights into the binding of pyridines to the iron-sulfur enzyme IspH. J Am Chem Soc 2014; 136:7926-32. [PMID: 24813236 PMCID: PMC4063180 DOI: 10.1021/ja501127j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Indexed: 11/29/2022]
Abstract
(E)-1-Hydroxy-2-methylbut-2-enyl 4-diphosphate reductase (IspH) is a [Fe4S4] cluster-containing enzyme involved in isoprenoid biosynthesis in many bacteria as well as in malaria parasites and is an important drug target. Several inhibitors including amino and thiol substrate analogues, as well as acetylene and pyridine diphosphates, have been reported. Here, we investigate the mode of binding of four pyridine diphosphates to Escherichia coli IspH by using X-ray crystallography. In three cases, one of the iron atoms in the cluster is absent, but in the structure with (pyridin-3-yl)methyl diphosphate, the most potent pyridine-analogue inhibitor reported previously, the fourth iron of the [Fe4S4] cluster is present and interacts with the pyridine ring of the ligand. Based on the results of quantum chemical calculations together with the crystallographic results we propose a side-on η(2) coordination of the nitrogen and the carbon in the 2-position of the pyridine ring to the unique fourth iron in the cluster, which is in the reduced state. The X-ray structure enables excellent predictions using density functional theory of the (14)N hyperfine coupling and quadrupole coupling constants reported previously using HYSCORE spectroscopy, as well as providing a further example of the ability of such [Fe4S4]-containing proteins to form organometallic complexes.
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Affiliation(s)
- Ingrid Span
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Ke Wang
- Department
of Chemistry, 600 South
Mathews Avenue, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wolfgang Eisenreich
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Adelbert Bacher
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Yong Zhang
- Department
of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken, New Jersey 07030, United States
| | - Eric Oldfield
- Department
of Chemistry, 600 South
Mathews Avenue, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Michael Groll
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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37
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Wang W, Oldfield E. Biometallorganische Chemie mit IspG und IspH: Struktur, Funktion und Hemmung der an der Isoprenoid-Biosynthese beteiligten [Fe 4S 4]-Proteine. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201306712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Wang W, Oldfield E. Bioorganometallic chemistry with IspG and IspH: structure, function, and inhibition of the [Fe(4)S(4)] proteins involved in isoprenoid biosynthesis. Angew Chem Int Ed Engl 2014; 53:4294-310. [PMID: 24481599 DOI: 10.1002/anie.201306712] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Indexed: 11/12/2022]
Abstract
Enzymes of the methylerythritol phosphate pathway of isoprenoid biosynthesis are attractive anti-infective drug targets. The last two enzymes of this pathway, IspG and IspH, are [Fe4 S4 ] proteins that are not produced by humans and catalyze 2 H(+) / 2 e(-) reductions with novel mechanisms. In this Review, we summarize recent advances in structural, mechanistic, and inhibitory studies of these two enzymes. In particular, mechanistic proposals involving bioorganometallic intermediates are presented, and compared with other mechanistic possibilities. In addition, inhibitors based on substrate analogues as well as developed by rational design and compound-library screening, are discussed. The results presented support bioorganometallic catalytic mechanisms for IspG and IspH, and open up new routes to anti-infective drug design targeting [Fe4 S4 ] clusters in proteins.
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Affiliation(s)
- Weixue Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
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39
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Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem 2013; 82:497-530. [PMID: 23746261 DOI: 10.1146/annurev-biochem-052010-100934] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isoprenoids are a class of natural products with more than 55,000 members. All isoprenoids are constructed from two precursors, isopentenyl diphosphate and its isomer dimethylallyl diphosphate. Two of the most important discoveries in isoprenoid biosynthetic studies in recent years are the elucidation of a second isoprenoid biosynthetic pathway [the methylerythritol phosphate (MEP) pathway] and a modified mevalonic acid (MVA) pathway. In this review, we summarize mechanistic insights on the MEP pathway enzymes. Because many isoprenoids have important biological activities, the need to produce them in sufficient quantities for downstream research efforts or commercial application is apparent. Recent advances in both MVA and MEP pathway-based synthetic biology are also illustrated by reviewing the landmark work of artemisinic acid and taxadien-5α-ol production through microbial fermentations.
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Affiliation(s)
- Lishan Zhao
- Amyris, Inc., Emeryville, California 94608, USA.
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40
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Kumar H, Kumar S. A functional (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase exhibits diurnal regulation of expression in Stevia rebaudiana (Bertoni). Gene X 2013; 527:332-8. [PMID: 23800667 DOI: 10.1016/j.gene.2013.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 06/06/2013] [Accepted: 06/07/2013] [Indexed: 11/18/2022] Open
Abstract
The leaves of stevia [Stevia rebaudiana (Bertoni)] are a rich source of steviol glycosides that are used as non-calorific sweetener in many countries around the world. Steviol moiety of steviol glycosides is synthesized via plastidial 2C-methyl-D-erythritol 4-phosphate pathway, where (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR) is the key enzyme. HDR catalyzes the simultaneous conversion of (E)-4-hydroxy-3-methylbut-2-enyl diphosphate into five carbon isoprenoid units, isopentenyl diphosphate and dimethylallyl diphosphate. Stevia HDR (SrHDR) successfully rescued HDR lethal mutant strain MG1655 ara<>ispH upon genetic complementation, suggesting SrHDR to encode a functional protein. The gene exhibited diurnal variation in expression. To identify the possible regulatory elements, upstream region of the gene was cloned and putative cis-acting elements were detected by in silico analysis. Electrophoretic mobility shift assay, using a putative light responsive element GATA showed the binding of nuclear proteins (NP) isolated from leaves during light period of the day, but not with the NP from leaves during the dark period. Data suggested the involvement of GATA box in light mediated gene regulation of SrHDR in stevia.
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Affiliation(s)
- Hitesh Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India.
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41
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Zhou C, Li Z, Wiberley-Bradford AE, Weise SE, Sharkey TD. Isopentenyl diphosphate and dimethylallyl diphosphate/isopentenyl diphosphate ratio measured with recombinant isopentenyl diphosphate isomerase and isoprene synthase. Anal Biochem 2013; 440:130-6. [DOI: 10.1016/j.ab.2013.05.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 05/24/2013] [Accepted: 05/25/2013] [Indexed: 10/26/2022]
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42
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Banerjee A, Wu Y, Banerjee R, Li Y, Yan H, Sharkey TD. Feedback inhibition of deoxy-D-xylulose-5-phosphate synthase regulates the methylerythritol 4-phosphate pathway. J Biol Chem 2013; 288:16926-16936. [PMID: 23612965 DOI: 10.1074/jbc.m113.464636] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway leads to the biosynthesis of isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), the precursors for isoprene and higher isoprenoids. Isoprene has significant effects on atmospheric chemistry, whereas other isoprenoids have diverse roles ranging from various biological processes to applications in commercial uses. Understanding the metabolic regulation of the MEP pathway is important considering the numerous applications of this pathway. The 1-deoxy-D-xylulose-5-phosphate synthase (DXS) enzyme was cloned from Populus trichocarpa, and the recombinant protein (PtDXS) was purified from Escherichia coli. The steady-state kinetic parameters were measured by a coupled enzyme assay. An LC-MS/MS-based assay involving the direct quantification of the end product of the enzymatic reaction, 1-deoxy-D-xylulose 5-phosphate (DXP), was developed. The effect of different metabolites of the MEP pathway on PtDXS activity was tested. PtDXS was inhibited by IDP and DMADP. Both of these metabolites compete with thiamine pyrophosphate for binding with the enzyme. An atomic structural model of PtDXS in complex with thiamine pyrophosphate and Mg(2+) was built by homology modeling and refined by molecular dynamics simulations. The refined structure was used to model the binding of IDP and DMADP and indicated that IDP and DMADP might bind with the enzyme in a manner very similar to the binding of thiamine pyrophosphate. The feedback inhibition of PtDXS by IDP and DMADP constitutes an important mechanism of metabolic regulation of the MEP pathway and indicates that thiamine pyrophosphate-dependent enzymes may often be affected by IDP and DMADP.
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Affiliation(s)
- Aparajita Banerjee
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Yan Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Rahul Banerjee
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Yue Li
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
| | - Thomas D Sharkey
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
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43
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Partow S, Siewers V, Daviet L, Schalk M, Nielsen J. Reconstruction and evaluation of the synthetic bacterial MEP pathway in Saccharomyces cerevisiae. PLoS One 2012; 7:e52498. [PMID: 23285068 PMCID: PMC3532213 DOI: 10.1371/journal.pone.0052498] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 11/19/2012] [Indexed: 12/03/2022] Open
Abstract
Isoprenoids, which are a large group of natural and chemical compounds with a variety of applications as e.g. fragrances, pharmaceuticals and potential biofuels, are produced via two different metabolic pathways, the mevalonate (MVA) pathway and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Here, we attempted to replace the endogenous MVA pathway in Saccharomyces cerevisiae by a synthetic bacterial MEP pathway integrated into the genome to benefit from its superior properties in terms of energy consumption and productivity at defined growth conditions. It was shown that the growth of a MVA pathway deficient S. cerevisiae strain could not be restored by the heterologous MEP pathway even when accompanied by the co-expression of genes erpA, hISCA1 and CpIscA involved in the Fe-S trafficking routes leading to maturation of IspG and IspH and E. coli genes fldA and fpr encoding flavodoxin and flavodoxin reductase believed to be responsible for electron transfer to IspG and IspH.
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Affiliation(s)
- Siavash Partow
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Verena Siewers
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Laurent Daviet
- Firmenich SA, Corporate R&D Division, Geneva, Switzerland
| | - Michel Schalk
- Firmenich SA, Corporate R&D Division, Geneva, Switzerland
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- * E-mail:
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44
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Lu XM, Hu XJ, Zhao YZ, Song WB, Zhang M, Chen ZL, Chen W, Dong YB, Wang ZH, Lai JS. Map-based cloning of zb7 encoding an IPP and DMAPP synthase in the MEP pathway of maize. MOLECULAR PLANT 2012; 5:1100-12. [PMID: 22498772 DOI: 10.1093/mp/sss038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
IspH is a key enzyme in the last step of the methyl-D-erythritol-4-phosphate (MEP) pathway. Loss of function of IspH can often result in complete yellow or albino phenotype in many plants. Here, we report the characterization of a recessive mutant of maize, zebra7 (zb7), showing transverse green/yellow striped leaves in young plants. The yellow bands of the mutant have decreased levels of chlorophylls and carotenoids with delayed chloroplast development. Low temperature suppressed mutant phenotype, while alternate light/dark cycle or high temperature enlarged the yellow section. Map-based cloning demonstrated that zb7 encodes the IspH protein with a mis-sense mutation in a conserved region. Transgenic silencing of Zb7 in maize resulted in complete albino plantlets that are aborted in a few weeks, confirming that Zb7 is important in the early stages of maize chloroplast development. Zb7 is constitutively expressed and its expression subject to a 16-h light/8-h dark cycle regulation. Our results suggest that the less effective or unstable IspH in zb7 mutant, together with its diurnal expression, are mechanistically accounted for the zebra phenotype. The increased IspH mRNA in the leaves of zb7 at the late development stage may explain the restoration of mutant phenotype in mature stages.
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Affiliation(s)
- Xiao-Min Lu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
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45
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Xu W, Lees NS, Hall D, Welideniya D, Hoffman BM, Duin EC. A closer look at the spectroscopic properties of possible reaction intermediates in wild-type and mutant (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase. Biochemistry 2012; 51:4835-49. [PMID: 22646150 DOI: 10.1021/bi3001215] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase (IspH or LytB) catalyzes the terminal step of the MEP/DOXP pathway where it converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) into the two products, isopentenyl diphosphate and dimethylallyl diphosphate. The reaction involves the reductive elimination of the C4 hydroxyl group, using a total of two electrons. Here we show that the active form of IspH contains a [4Fe-4S] cluster and not the [3Fe-4S] form. Our studies show that the cluster is the direct electron source for the reaction and that a reaction intermediate is bound directly to the cluster. This active form has been trapped in a state, dubbed FeS(A), that was detected by electron paramagnetic resonance (EPR) spectroscopy when one-electron-reduced IspH was incubated with HMBPP. In addition, three mutants of IspH have been prepared and studied, His42, His124, and Glu126 (Aquifex aeolicus numbering), with particular attention paid to the effects on the cluster properties and possible reaction intermediates. None of the mutants significantly affected the properties of the [4Fe-4S](+) cluster, but different effects were observed when one-electron-reduced forms were incubated with HMBPP. Replacing His42 led to an increased K(M) value and a much lower catalytic efficiency, confirming the role of this residue in substrate binding. Replacing the His124 also resulted in a lower catalytic efficiency. In this case, however, the enzyme showed the loss of the [4Fe-4S](+) EPR signal upon addition of HMBPP without the subsequent formation of the FeS(A) signal. Instead, a radical-type signal was observed in some of the samples, indicating that this residue plays a role in the correct positioning of the substrate. The incorrect orientation in the mutant leads to the formation of substrate-based radicals instead of the cluster-bound intermediate complex FeS(A). Replacing the Glu126 also resulted in a lower catalytic efficiency, with yet a third type of EPR signal being detected upon incubation with HMBPP. (31)P and (2)H ENDOR measurements of the FeS(A) species incubated with regular and (2)H-C4-labeled HMBPP reveal that the substrate binds to the enzyme in the proximity of the active-site cluster with C4 adjacent to the site of linkage between the FeS cluster and HMBPP. Comparison of the spectroscopic properties of this intermediate to those of intermediates detected in (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase and ferredoxin:thioredoxin reductase suggests that HMBPP binds to the FeS cluster via its hydroxyl group instead of a side-on binding as previously proposed for the species detected in the inactive Glu126 variant. Consequences for the IspH reaction mechanism are discussed.
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Affiliation(s)
- Weiya Xu
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
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Span I, Gräwert T, Bacher A, Eisenreich W, Groll M. Crystal Structures of Mutant IspH Proteins Reveal a Rotation of the Substrate's Hydroxymethyl Group during Catalysis. J Mol Biol 2012; 416:1-9. [DOI: 10.1016/j.jmb.2011.11.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 11/11/2011] [Accepted: 11/16/2011] [Indexed: 10/15/2022]
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Oldfield E, Lin FY. Terpene biosynthesis: modularity rules. Angew Chem Int Ed Engl 2011; 51:1124-37. [PMID: 22105807 DOI: 10.1002/anie.201103110] [Citation(s) in RCA: 240] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Indexed: 01/10/2023]
Abstract
Terpenes are the largest class of small-molecule natural products on earth, and the most abundant by mass. Here, we summarize recent developments in elucidating the structure and function of the proteins involved in their biosynthesis. There are six main building blocks or modules (α, β, γ, δ, ε, and ζ) that make up the structures of these enzymes: the αα and αδ head-to-tail trans-prenyl transferases that produce trans-isoprenoid diphosphates from C(5) precursors; the ε head-to-head prenyl transferases that convert these diphosphates into the tri- and tetraterpene precursors of sterols, hopanoids, and carotenoids; the βγ di- and triterpene synthases; the ζ head-to-tail cis-prenyl transferases that produce the cis-isoprenoid diphosphates involved in bacterial cell wall biosynthesis; and finally the α, αβ, and αβγ terpene synthases that produce plant terpenes, with many of these modular enzymes having originated from ancestral α and β domain proteins. We also review progress in determining the structure and function of the two 4Fe-4S reductases involved in formation of the C(5) diphosphates in many bacteria, where again, highly modular structures are found.
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Affiliation(s)
- Eric Oldfield
- Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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Lin X, Zhang J, Li Y, Luo H, Wu Q, Sun C, Song J, Li X, Wei J, Lu A, Qian Z, Khan IA, Chen S. Functional genomics of a living fossil tree, Ginkgo, based on next-generation sequencing technology. PHYSIOLOGIA PLANTARUM 2011; 143:207-18. [PMID: 21834857 DOI: 10.1111/j.1399-3054.2011.01500.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Ginkgo biloba is monotypic species native to China and has old, dioecious, medicinally important characteristics. The functional genes related to these characteristics have not been effectively explored due to a limited number of expressed sequence tags (ESTs) from Ginkgo. To discover novel functional genes efficiently and to understand the development of a living fossil tree, Ginkgo, we used massive parallel pyrosequencing on the Roche 454 GS FLX Titanium platform to generate 64 057 ESTs. The ESTs combined with the 21 590 Ginkgo ESTs in genbank were assembled into 22 304 unique putative transcripts, in which 13 922 novel unique putative transcripts were identified by 454 sequencing. After being assigned to putative functions with Gene Ontology terms, a detailed view of the Ginkgo biological systems was displayed, including characterization of unique putative transcripts with homology to known key enzymes and transcription factors involved in ginkgolide/bilobalide and flavonoid biosynthetic pathways, as well as unique putative transcripts related to development, response to disease and defence. The fact that three full-length Ginkgo genes encoding key enzymes were found and cloned, suggests that high-throughput sequencing technology is superior to traditional gene-by-gene approach in discovery of genes. Additionally, a total of 204 simple sequence repeat motifs were detected. Our study not only lays the foundations for transcriptome-led studies in biosynthetic mechanisms, but also contributes significantly to the understanding of functional genomics and development in non-model plants.
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Affiliation(s)
- Xiaohan Lin
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Wang C, Yoon SH, Jang HJ, Chung YR, Kim JY, Choi ES, Kim SW. Metabolic engineering of Escherichia coli for α-farnesene production. Metab Eng 2011; 13:648-55. [DOI: 10.1016/j.ymben.2011.08.001] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 07/02/2011] [Accepted: 08/15/2011] [Indexed: 11/25/2022]
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