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Ashaq B, Rasool K, Habib S, Bashir I, Nisar N, Mustafa S, Ayaz Q, Nayik GA, Uddin J, Ramniwas S, Mugabi R, Wani SM. Insights into chemistry, extraction and industrial application of lemon grass essential oil -A review of recent advances. Food Chem X 2024; 22:101521. [PMID: 38952570 PMCID: PMC11215000 DOI: 10.1016/j.fochx.2024.101521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/16/2024] [Accepted: 05/27/2024] [Indexed: 07/03/2024] Open
Abstract
Lemongrass essential oil (LEO), extracted from high-oil lemongrass, gains prominence as a versatile natural product due to growing demand for safe health solutions. LEO comprises beneficial compounds like citral, isoneral, geraniol, and citronellal, offering diverse pharmacological benefits such as antioxidant, antifungal, antibacterial, antiviral, and anticancer effects. LEO finds applications in food preservation, cosmetics, and pharmaceuticals, enhancing profitability across these sectors. The review focuses on the extraction of LEO, emphasizing the need for cost-effective methods. Ultrasound and supercritical fluid extraction are effective in reducing extraction time, increasing yields, and enhancing oil quality. LEO shows promise as a valuable natural resource across industries, with applications in packaging, coating, and film development. LEO's ability to extend the shelf life of food items and impart natural flavors positions it as a valuable asset. Overall, the review emphasizes LEO's therapeutic, antimicrobial, and antioxidant properties, strengthening its potential in the food, pharmaceutical, and cosmetic sectors.
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Affiliation(s)
- Barjees Ashaq
- Division of Food Science and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, 190025, J&K, India
| | - Khansa Rasool
- Division of Food Science and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, 190025, J&K, India
| | - Samira Habib
- Division of Food Science and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, 190025, J&K, India
| | - Iqra Bashir
- Division of Food Science and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, 190025, J&K, India
| | - Naseh Nisar
- Division of Food Science and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, 190025, J&K, India
| | - Sehrish Mustafa
- Division of Food Science and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, 190025, J&K, India
| | - Qudsiya Ayaz
- Division of Food Science and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, 190025, J&K, India
| | - Gulzar Ahmad Nayik
- Department of Food Science & Technology, Govt. Degree College, Shopian 192303, J&K, India
| | - Jalal Uddin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Asir 61421, Saudi Arabia
| | - Seema Ramniwas
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali 140413, Punjab, India
| | - Robert Mugabi
- Department of Food Technology and Nutrition, Makerere University, Kampala, Uganda
| | - Sajad Mohd Wani
- Division of Food Science and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, 190025, J&K, India
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Dayarathne K, Ishikawa T, Watanabe S, Ishikawa Y, Aikeranmu K, Kitagawaa H, Komatsubara N, Yamaguchi M, Kawai-Yamada M. Heterologous expression of mtf and mtc genes of Pseudanabaena foetida var. intermedia is sufficient to produce 2-methylisoborneol in Escherichia coli. Microbiol Spectr 2023; 11:e0256123. [PMID: 37732762 PMCID: PMC10580876 DOI: 10.1128/spectrum.02561-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/31/2023] [Indexed: 09/22/2023] Open
Abstract
Microbial volatile metabolite 2-methylisoborneol (2-MIB) causes odor and taste issues in drinking water, making it unappealing for human consumption. It has been suggested that 2-MIB biosynthesis consists of two main steps, namely, methylation of geranyl diphosphate into 2-methyl geranyl diphosphate by geranyl diphosphate methyl transferase (GPPMT) and subsequent cyclization into 2-MIB by 2-MIB synthase (MIBS). Pseudanabaena foetida var. intermedia is a 2-MIB-producing cyanobacterium whose GPPMT and MIBS enzymes are encoded by adjacent mtf and mtc genes. The present study identified a 2-MIB-related gene cluster composed of cnbA, mtf, mtc, and cnbB genes in P. foetida var. intermedia. The two homologous cyclic nucleotide-binding protein genes, cnbA and cnbB, were detected adjacent to the mtf and mtc genes, respectively. The nucleotide sequence of the cnbA-mtf-mtc-cnbB gene cluster showed 99.55% identity with 2-MIB synthesis-associated gene cluster of Pseudanabaena sp. dqh15. RT-PCR results revealed that mtf and mtc genes are co-expressed, while cnbA and cnbB genes are expressed independently in P. foetida var. intermedia. To investigate whether only mtf and mtc genes are sufficient for 2-MIB synthesis, the two-gene unit (mtf-mtc) was introduced into Escherichia coli strain JM109 via overexpression vector pYS1C. Gas chromatograph-mass spectrometry results showed that the E. coli strain transformed with mtf-mtc was able to produce 2-MIB. The intracellular 2-MIB level in P. foetida var. intermedia was higher than the extracellular 2-MIB level, while the transformed E. coli strain showed an opposite trend. Growth inhibition was observed in the 2-MIB-producing transformed E. coli strain. IMPORTANCE Contamination of drinking water with odiferous microbial metabolite 2-MIB is a worldwide concern. Removal of 2-MIB from drinking water burdens the water purification process. Therefore, it is important to search for alternative methods, such as suppressing the production of 2-MIB by aquatic microorganisms. For that, it is necessary to expand the current knowledge about the mechanism of 2-MIB synthesis at the genetic level. This study revealed that mtf and mtc genes of the 2-MIB-related gene cluster are transcribed as a single unit in P. foetida var. intermedia, and the expression of both mtf and mtc genes is essential and sufficient for 2-MIB synthesis in E. coli heterologous gene expression system.
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Affiliation(s)
- Kaushalya Dayarathne
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, 1-chōme-1-1 Sakuragaoka, Setagaya-city, Tokyo, Japan
| | - Yuuma Ishikawa
- Institute for Molecular Physiology, Heinrich-Heine-Universität, Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Kadeer Aikeranmu
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Hina Kitagawaa
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Natsumi Komatsubara
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Masatoshi Yamaguchi
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
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Hamid R, Adam S, Lacour A, Monjas L, Köhnke J, Hirsch AKH. 1-deoxy-D-xylulose-5-phosphate synthase from Pseudomonas aeruginosa and Klebsiella pneumoniae reveals conformational changes upon cofactor binding. J Biol Chem 2023; 299:105152. [PMID: 37567475 PMCID: PMC10504544 DOI: 10.1016/j.jbc.2023.105152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
The ESKAPE bacteria are the six highly virulent and antibiotic-resistant pathogens that require the most urgent attention for the development of novel antibiotics. Detailed knowledge of target proteins specific to bacteria is essential to develop novel treatment options. The methylerythritol-phosphate (MEP) pathway, which is absent in humans, represents a potentially valuable target for the development of novel antibiotics. Within the MEP pathway, the enzyme 1-deoxy-D-xylulose-5-phosphate synthase (DXPS) catalyzes a crucial, rate-limiting first step and a branch point in the biosynthesis of the vitamins B1 and B6. We report the high-resolution crystal structures of DXPS from the important ESKAPE pathogens Pseudomonas aeruginosa and Klebsiella pneumoniae in both the co-factor-bound and the apo forms. We demonstrate that the absence of the cofactor thiamine diphosphate results in conformational changes that lead to disordered loops close to the active site that might be important for the design of potent DXPS inhibitors. Collectively, our results provide important structural details that aid in the assessment of DXPS as a potential target in the ongoing efforts to combat antibiotic resistance.
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Affiliation(s)
- Rawia Hamid
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Sebastian Adam
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
| | - Antoine Lacour
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
| | - Leticia Monjas
- Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | - Jesko Köhnke
- Institute of Food Chemistry, Leibniz University Hannover, Hannover, Germany; School of Chemistry, University of Glasgow, Glasgow, UK
| | - Anna K H Hirsch
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany.
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Wang P, Wei J, Hua X, Dong G, Dziedzic K, Wahab AT, Efferth T, Sun W, Ma P. Plant anthraquinones: Classification, distribution, biosynthesis, and regulation. J Cell Physiol 2023. [PMID: 37393608 DOI: 10.1002/jcp.31063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/10/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Anthraquinones are polycyclic compounds with an unsaturated diketone structure (quinoid moiety). As important secondary metabolites of plants, anthraquinones play an important role in the response of many biological processes and environmental factors. Anthraquinones are common in the human diet and have a variety of biological activities including anticancer, antibacterial, and antioxidant activities that reduce disease risk. The biological activity of anthraquinones depends on the substitution pattern of their hydroxyl groups on the anthraquinone ring structure. However, there is still a lack of systematic summary on the distribution, classification, and biosynthesis of plant anthraquinones. Therefore, this paper systematically reviews the research progress of the distribution, classification, biosynthesis, and regulation of plant anthraquinones. Additionally, we discuss future opportunities in anthraquinone research, including biotechnology, therapeutic products, and dietary anthraquinones.
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Affiliation(s)
- Peng Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Jia Wei
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xin Hua
- College of Life Sciences, Northeast Forestry University, Harbin, China
| | | | - Krzysztof Dziedzic
- Department of Food Technology of Plant Origin, Poznan' University of Life Sciences, Poznań, Poland
| | - Atia-Tul Wahab
- Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Pengda Ma
- College of Life Sciences, Northwest A&F University, Yangling, China
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Giannotta C, Autino F, Massaia M. Vγ9Vδ2 T-cell immunotherapy in blood cancers: ready for prime time? Front Immunol 2023; 14:1167443. [PMID: 37143664 PMCID: PMC10153673 DOI: 10.3389/fimmu.2023.1167443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
In the last years, the tumor microenvironment (TME) has emerged as a promising target for therapeutic interventions in cancer. Cancer cells are highly dependent on the TME to growth and evade the immune system. Three major cell subpopulations are facing each other in the TME: cancer cells, immune suppressor cells, and immune effector cells. These interactions are influenced by the tumor stroma which is composed of extracellular matrix, bystander cells, cytokines, and soluble factors. The TME can be very different depending on the tissue where cancer arises as in solid tumors vs blood cancers. Several studies have shown correlations between the clinical outcome and specific patterns of TME immune cell infiltration. In the recent years, a growing body of evidence suggests that unconventional T cells like natural killer T (NKT) cells, mucosal-associated invariant T (MAIT) cells, and γδ T cells are key players in the protumor or antitumor TME commitment in solid tumors and blood cancers. In this review, we will focus on γδ T cells, especially Vγ9Vδ2 T cells, to discuss their peculiarities, pros, and cons as potential targets of therapeutic interventions in blood cancers.
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Affiliation(s)
- Claudia Giannotta
- Laboratorio di Immunologia dei Tumori del Sangue (LITS), Centro Interdipartimentale di Biotecnologie Molecolari “Guido Tarone”, Dipartimento di Biotecnologie Molecolari e Scienze per la Salute, Università Degli Studi di Torino, Torino, Italy
| | - Federica Autino
- Laboratorio di Immunologia dei Tumori del Sangue (LITS), Centro Interdipartimentale di Biotecnologie Molecolari “Guido Tarone”, Dipartimento di Biotecnologie Molecolari e Scienze per la Salute, Università Degli Studi di Torino, Torino, Italy
| | - Massimo Massaia
- Laboratorio di Immunologia dei Tumori del Sangue (LITS), Centro Interdipartimentale di Biotecnologie Molecolari “Guido Tarone”, Dipartimento di Biotecnologie Molecolari e Scienze per la Salute, Università Degli Studi di Torino, Torino, Italy
- Struttura Complessa (SC) Ematologia, Azienda Ospedaliera (AO) S. Croce e Carle, Cuneo, Italy
- *Correspondence: Massimo Massaia,
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Guo L, Zhang S, Xu Y, Huang Y, Luo W, Wen Q, Liu G, Huang W, Xu H, Chen B, Nie Q. A missense mutation in ISPD contributes to maintain muscle fiber stability. Poult Sci 2022; 101:102143. [PMID: 36167018 PMCID: PMC9513258 DOI: 10.1016/j.psj.2022.102143] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 06/11/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022] Open
Abstract
Background Results Conclusion
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Wang Z, Sun J, Yang Q, Yang J. Metabolic Engineering Escherichia coli for the Production of Lycopene. Molecules 2020; 25:molecules25143136. [PMID: 32659911 PMCID: PMC7397254 DOI: 10.3390/molecules25143136] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 12/25/2022] Open
Abstract
Lycopene, a potent antioxidant, has been widely used in the fields of pharmaceuticals, nutraceuticals, and cosmetics. However, the production of lycopene extracted from natural sources is far from meeting the demand. Consequently, synthetic biology and metabolic engineering have been employed to develop microbial cell factories for lycopene production. Due to the advantages of rapid growth, complete genetic background, and a reliable genetic operation technique, Escherichia coli has become the preferred host cell for microbial biochemicals production. In this review, the recent advances in biological lycopene production using engineered E. coli strains are summarized: First, modification of the endogenous MEP pathway and introduction of the heterogeneous MVA pathway for lycopene production are outlined. Second, the common challenges and strategies for lycopene biosynthesis are also presented, such as the optimization of other metabolic pathways, modulation of regulatory networks, and optimization of auxiliary carbon sources and the fermentation process. Finally, the future prospects for the improvement of lycopene biosynthesis are also discussed.
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Affiliation(s)
- Zhaobao Wang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China;
| | - JingXin Sun
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China;
| | - Qun Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China;
- Correspondence: (Q.Y.); (J.Y.); Tel.: +86-131-4543-1413 (Q.Y.); +86-135-8938-5827 (J.Y.); Fax: +86-532-589-57640 (J.Y.)
| | - Jianming Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China;
- Correspondence: (Q.Y.); (J.Y.); Tel.: +86-131-4543-1413 (Q.Y.); +86-135-8938-5827 (J.Y.); Fax: +86-532-589-57640 (J.Y.)
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Chaignon P, Petit BE, Vincent B, Allouche L, Seemann M. Methylerythritol Phosphate Pathway: Enzymatic Evidence for a Rotation in the LytB/IspH-Catalyzed Reaction. Chemistry 2020; 26:1032-1036. [PMID: 31756006 DOI: 10.1002/chem.201904676] [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: 10/11/2019] [Indexed: 11/10/2022]
Abstract
IspH/LytB, an oxygen-sensitive [4Fe-4S] enzyme, catalyzes the last step of the methylerythritol phosphate (MEP) pathway, a target for the development of new antimicrobial agents. This metalloenzyme converts (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Here, the synthesis of (S)-[4-2 H1 ]HMBPP and (R)-[4-2 H1 ]HMBPP is reported together with a detailed NMR analysis of the products formed after their respective incubation with E. coli IspH/LytB in the presence of the biological reduction system used by E. coli to reduce the [4Fe-4S] center. (S)-[4-2 H1 ]HMBPP was converted into [4-2 H1 ]DMAPP and (E)-[4-2 H1 ]IPP, whereas (R)-[4-2 H1 ]HMBPP yielded [4-2 H1 ]DMAPP and (Z)-[4-2 H1 ]IPP, hence providing the direct enzymatic evidence that the mechanism catalyzed by IspH/LytB involves a rotation of the CH2 OH group of the substrate to display it away from the [4Fe-4S].
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Affiliation(s)
- Philippe Chaignon
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg, CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Benoît Eric Petit
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg, CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Bruno Vincent
- Service de R.M.N., Fédération de Chimie Le Bel FR2010, Université de Strasbourg, CNRS, 1, rue Blaise Pascal, 67008, Strasbourg, France
| | - Lionel Allouche
- Service de R.M.N., Fédération de Chimie Le Bel FR2010, Université de Strasbourg, CNRS, 1, rue Blaise Pascal, 67008, Strasbourg, France
| | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg, CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
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9
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Salwan R, Sharma V. Molecular and biotechnological aspects of secondary metabolites in actinobacteria. Microbiol Res 2020; 231:126374. [DOI: 10.1016/j.micres.2019.126374] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022]
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10
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Athanasakoglou A, Kampranis SC. Diatom isoprenoids: Advances and biotechnological potential. Biotechnol Adv 2019; 37:107417. [PMID: 31326522 DOI: 10.1016/j.biotechadv.2019.107417] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/09/2019] [Accepted: 07/15/2019] [Indexed: 12/31/2022]
Abstract
Diatoms are among the most productive and ecologically important groups of microalgae in contemporary oceans. Due to their distinctive metabolic and physiological features, they offer exciting opportunities for a broad range of commercial and industrial applications. One such feature is their ability to synthesize a wide diversity of isoprenoid compounds. However, limited understanding of how these molecules are synthesized have until recently hindered their exploitation. Following comprehensive genomic and transcriptomic analysis of various diatom species, the biosynthetic mechanisms and regulation of the different branches of the pathway are now beginning to be elucidated. In this review, we provide a summary of the recent advances in understanding diatom isoprenoid synthesis and discuss the exploitation potential of diatoms as chassis for high-value isoprenoid synthesis.
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Affiliation(s)
- Anastasia Athanasakoglou
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Sotirios C Kampranis
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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Chellapandi P, Prathiviraj R, Prisilla A. Deciphering structure, function and mechanism of Plasmodium IspD homologs from their evolutionary imprints. J Comput Aided Mol Des 2019; 33:419-436. [DOI: 10.1007/s10822-019-00191-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 02/12/2019] [Indexed: 12/17/2022]
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12
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Synthesis and Kinetic evaluation of an azido analogue of methylerythritol phosphate: a Novel Inhibitor of E. coli YgbP/IspD. Sci Rep 2018; 8:17892. [PMID: 30559447 PMCID: PMC6297244 DOI: 10.1038/s41598-018-35586-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/05/2018] [Indexed: 12/04/2022] Open
Abstract
As multidrug resistant pathogenic microorganisms are a serious health menace, it is crucial to continuously develop novel medicines in order to overcome the emerging resistance. The methylerythritol phosphate pathway (MEP) is an ideal target for antimicrobial development as it is absent in humans but present in most bacteria and in the parasite Plasmodium falciparum. Here, we report the synthesis and the steady-state kinetics of a novel potent inhibitor (MEPN3) of Escherichia coli YgbP/IspD, the third enzyme of the MEP pathway. MEPN3 inhibits E. coli YgbP/IspD in mixed type mode regarding both substrates. Interestingly, MEPN3 shows the highest inhibitory activity when compared to known inhibitors of E. coli YgbP/IspD. The mechanism of this enzyme was also studied by steady-state kinetic analysis and it was found that the substrates add to the enzyme in sequential manner.
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Chellapandi P, Prathiviraj R, Prisilla A. Molecular evolution and functional divergence of IspD homologs in malarial parasites. INFECTION GENETICS AND EVOLUTION 2018; 65:340-349. [DOI: 10.1016/j.meegid.2018.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 01/19/2023]
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14
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Bhuyan R, Seal A. Exploration and validation of diphosphate-based Plasmodium
LytB inhibitors using computational approaches. J Mol Recognit 2018; 32:e2762. [PMID: 30191613 DOI: 10.1002/jmr.2762] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Rajabrata Bhuyan
- BIF Centre, Department of Biochemistry & Biophysics; University of Kalyani; Kalyani West Bengal India
| | - Alpana Seal
- BIF Centre, Department of Biochemistry & Biophysics; University of Kalyani; Kalyani West Bengal India
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A Defective Undecaprenyl Pyrophosphate Synthase Induces Growth and Morphological Defects That Are Suppressed by Mutations in the Isoprenoid Pathway of Escherichia coli. J Bacteriol 2018; 200:JB.00255-18. [PMID: 29986944 DOI: 10.1128/jb.00255-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/05/2018] [Indexed: 01/10/2023] Open
Abstract
The peptidoglycan exoskeleton shapes bacteria and protects them against osmotic forces, making its synthesis the target of many current antibiotics. Peptidoglycan precursors are attached to a lipid carrier and flipped from the cytoplasm into the periplasm to be incorporated into the cell wall. In Escherichia coli, this carrier is undecaprenyl phosphate (Und-P), which is synthesized as a diphosphate by the enzyme undecaprenyl pyrophosphate synthase (UppS). E. coli MG1655 exhibits wild-type morphology at all temperatures, but one of our laboratory strains (CS109) was highly aberrant when grown at 42°C. This strain contained mutations affecting the Und-P synthetic pathway genes uppS, ispH, and idi Normal morphology was restored by overexpressing uppS or by replacing the mutant (uppS31) with the wild-type allele. Importantly, moving uppS31 into MG1655 was lethal even at 30°C, indicating that the altered enzyme was highly deleterious, but growth was restored by adding the CS109 versions of ispH and idi Purified UppSW31R was enzymatically defective at all temperatures, suggesting that it could not supply enough Und-P during rapid growth unless suppressor mutations were present. We conclude that cell wall synthesis is profoundly sensitive to changes in the pool of polyisoprenoids and that isoprenoid homeostasis exerts a particularly strong evolutionary pressure.IMPORTANCE Bacterial morphology is determined primarily by the overall structure of the semirigid macromolecule peptidoglycan. Not only does peptidoglycan contribute to cell shape, but it also protects cells against lysis caused by excess osmotic pressure. Because it is critical for bacterial survival, it is no surprise that many antibiotics target peptidoglycan biosynthesis. However, important gaps remain in our understanding about how this process is affected by peptidoglycan precursor availability. Here, we report that a mutation altering the enzyme that synthesizes Und-P prevents cells from growing at high temperatures and that compensatory mutations in enzymes functioning upstream of uppS can reverse this phenotype. The results highlight the importance of Und-P metabolism for maintaining normal cell wall synthesis and shape.
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Li M, Nian R, Xian M, Zhang H. Metabolic engineering for the production of isoprene and isopentenol by Escherichia coli. Appl Microbiol Biotechnol 2018; 102:7725-7738. [PMID: 30006784 PMCID: PMC6132537 DOI: 10.1007/s00253-018-9200-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/23/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Abstract
The biotechnological production of isoprene and isopentenol has recently been studied. Isoprene, which is currently made mainly from petroleum, is an important platform chemical for synthesizing pesticides, medicines, oil additives, fragrances, and more and is especially important in the rubber production industry. Isopentenols, which have better combustion properties than well-known biofuels (ethanol), have recently received more attention. Supplies of petroleum, the conventional source of isoprene and isopentenols, are unsustainable, and chemical synthesis processes could cause serious environmental problems. As an alternative, the biosynthesis of isoprene and isopentenols in cell factories is more sustainable and environmentally friendly. With a number of advantages over other microorganisms, Escherichia coli is considered to be a powerful workhorse organism for producing these compounds. This review will highlight the recent advances in metabolic engineering for isoprene and isopentenol production, especially using E. coli cell factories.
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Affiliation(s)
- Meijie Li
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Rui Nian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China
| | - Mo Xian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.
| | - Haibo Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.
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Wang X, Dowd CS. The Methylerythritol Phosphate Pathway: Promising Drug Targets in the Fight against Tuberculosis. ACS Infect Dis 2018; 4:278-290. [PMID: 29390176 DOI: 10.1021/acsinfecdis.7b00176] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a severe infectious disease in need of new chemotherapies especially for drug-resistant cases. To meet the urgent requirement of new TB drugs with novel modes of action, the TB research community has been validating numerous targets from several biosynthetic pathways. The methylerythritol phosphate (MEP) pathway is utilized by Mtb for the biosynthesis of isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl pyrophosphate (DMAPP), the universal five-carbon building blocks of isoprenoids. While being a common biosynthetic pathway in pathogens, the MEP pathway is completely absent in humans. Due to its unique presence in pathogens as well as the essentiality of the MEP pathway in Mtb, the enzymes in this pathway are promising targets for the development of new drugs against tuberculosis. In this Review, we discuss three enzymes in the MEP pathway: 1-deoxy-d-xylulose-5-phosphate synthase (DXS), 1-deoxy-d-xylulose-5-phosphate reductoisomerase (IspC/DXR), and 2 C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF), which appear to be the most promising antitubercular drug targets. Structural and mechanistic features of these enzymes are reviewed, as well as selected inhibitors that show promise as antitubercular agents.
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Affiliation(s)
- Xu Wang
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington, D.C. 20052, United States
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington, D.C. 20052, United States
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18
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Handa S, Dempsey DR, Ramamoorthy D, Cook N, Guida WC, Spradling TJ, White JK, Woodcock HL, Merkler DJ. Mechanistic Studies of 1-Deoxy-D-Xylulose-5-Phosphate Synthase from Deinococcus radiodurans. ACTA ACUST UNITED AC 2018; 4. [PMID: 29552677 PMCID: PMC5851014 DOI: 10.21767/2471-8084.100051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The non-mevalonate dependent (NMVA) pathway for the biosynthesis of isopentenyl pyrophosphate and dimethylallyl pyrophosphate is the sole source of these terpenoids for the production of isoprenoids in the apicomplexan parasites, in many eubacteria, and in plants. The absence of this pathway in higher organisms has opened a new platform for the development of novel antibiotics and anti-malarials. The enzyme catalyzing the first step of the NMVA pathway is 1-deoxy-D-xylulose-5-phosphate synthase (DXPS). DXPS catalyzes the thiamine pyrophosphate- and Mg (II)-dependent conjugation of pyruvate and D-glyceraldehyde-3-phosphate to form 1-deoxy-D-xylulose-5-phosphate and CO2. The kinetic mechanism of DXPS from Deinococcus radiodurans most consistent with our data is random sequential as shown using a combination of kinetic analysis and product and dead-end inhibition studies. The role of active site amino acids, identified by sequence alignment to other DXPS proteins, was probed by constructing and analyzing the catalytic efficacy of a set of targeted site-directed mutants.
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Affiliation(s)
- Sumit Handa
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel R Dempsey
- Departments of Medicine, Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, UK
| | | | - Nanci Cook
- Department of Chemistry, University of South Florida, USA
| | - Wayne C Guida
- Department of Chemistry, University of South Florida, USA
| | | | - Justin K White
- Department of Chemistry, University of South Florida, USA
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, USA
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Borel F, Barbier E, Krasutsky S, Janthawornpong K, Chaignon P, Poulter CD, Ferrer JL, Seemann M. Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials. Chembiochem 2017; 18:2137-2144. [PMID: 28862365 DOI: 10.1002/cbic.201700363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Indexed: 01/12/2023]
Abstract
IspH, also called LytB, a protein involved in the biosynthesis of isoprenoids through the methylerythritol phosphate pathway, is an attractive target for the development of new antimicrobial drugs. Here, we report crystal structures of Escherichia coli IspH in complex with the two most potent inhibitors: (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate (TMBPP) and (E)-4-amino-3-methylbut-2-en-1-yl diphosphate (AMBPP) at 1.95 and 1.7 Å resolution, respectively. The structure of the E. coli IspH:TMBPP complex exhibited two conformers of the inhibitor. This unexpected feature was exploited to design and evolve new antimicrobial candidates in silico.
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Affiliation(s)
- Franck Borel
- Institut de Biologie Structurale IBS, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Elodie Barbier
- Institut de Biologie Structurale IBS, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Sergiy Krasutsky
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT, 84112, USA
| | - Karnjapan Janthawornpong
- Université de Strasbourg, CNRS, Institut de Chimie UMR 7177, Chim Biol&Appl Therap, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Philippe Chaignon
- Université de Strasbourg, CNRS, Institut de Chimie UMR 7177, Chim Biol&Appl Therap, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - C Dale Poulter
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT, 84112, USA
| | - Jean-Luc Ferrer
- Institut de Biologie Structurale IBS, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Myriam Seemann
- Université de Strasbourg, CNRS, Institut de Chimie UMR 7177, Chim Biol&Appl Therap, 4, rue Blaise Pascal, 67070, Strasbourg, France
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20
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Jadaun JS, Sangwan NS, Narnoliya LK, Singh N, Bansal S, Mishra B, Sangwan RS. Over-expression of DXS gene enhances terpenoidal secondary metabolite accumulation in rose-scented geranium and Withania somnifera: active involvement of plastid isoprenogenic pathway in their biosynthesis. PHYSIOLOGIA PLANTARUM 2017; 159:381-400. [PMID: 27580641 DOI: 10.1111/ppl.12507] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/18/2016] [Accepted: 08/05/2016] [Indexed: 05/08/2023]
Abstract
Rose-scented geranium (Pelargonium spp.) is one of the most important aromatic plants and is well known for its diverse perfumery uses. Its economic importance is due to presence of fragrance rich essential oil in its foliage. The essential oil is a mixture of various volatile phytochemicals which are mainly terpenes (isoprenoids) in nature. In this study, on the geranium foliage genes related to isoprenoid biosynthesis (DXS, DXR and HMGR) were isolated, cloned and confirmed by sequencing. Further, the first gene of 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway, 1-deoxy-d-xylulose-5-phosphate synthase (GrDXS), was made full length by using rapid amplification of cDNA ends strategy. GrDXS contained a 2157 bp open reading frame that encoded a polypeptide of 792 amino acids having calculated molecular weight 77.5 kDa. This study is first report on heterologous expression and kinetic characterization of any gene from this economically important plant. Expression analysis of these genes was performed in different tissues as well as at different developmental stages of leaves. In response to external elicitors, such as methyl jasmonate, salicylic acid, light and wounding, all the three genes showed differential expression profiles. Further GrDXS was over expressed in the homologous (rose-scented geranium) as well as in heterologous (Withania somnifera) plant systems through genetic transformation approach. The over-expression of GrDXS led to enhanced secondary metabolites production (i.e. essential oil in rose-scented geranium and withanolides in W. somnifera). To the best of our knowledge, this is the first report showing the expression profile of the three genes related to isoprenoid biosynthesis pathways operated in rose-scented geranium as well as functional characterization study of any gene from rose-scented geranium through a genetic transformation system.
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Affiliation(s)
- Jyoti Singh Jadaun
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Neelam S Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Lokesh K Narnoliya
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Neha Singh
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Shilpi Bansal
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Bhawana Mishra
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Rajender Singh Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
- Center of Innovative and Applied Bioprocessing (A National Institute under Department of Biotechnology, Govt. of India), C-127, Phase-8, Industrial Area, S.A.S. Nagar, Mohali - 160071, Punjab, India
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Improving the Concentrations of the Active Components in the Herbal Tea Ingredient, Uraria crinita: The Effect of Post-harvest Oven-drying Processing. Sci Rep 2017; 7:38763. [PMID: 28079108 PMCID: PMC5227699 DOI: 10.1038/srep38763] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/11/2016] [Indexed: 01/01/2023] Open
Abstract
Uraria crinita is widely used as a popular folk drink; however, little is known about how the post-harvest operations affect the chemical composition and bioactivity of UC. We assessed three drying methods (Oven-drying, Air-drying, Sun-drying), as well as the Oven-drying temperature using metabolomics approaches and bioactivity assays. The samples processed at 40 degree show a greater effect on the levels of estrogen receptor-alpha activity and nuclear factor erythroid 2-related factor 2 activity, anti-oxidative activity, and cyclooxygenase-2 inhibition compared with the other samples. A multivariate analysis showed a clear separation between the 40 degree Oven-dried samples and the other samples, which is consistent with the results of bioactivity assay. These results are ascribed to at least two-fold increase in the concentrations of flavonoids, spatholosineside A and triterpenoids in the oven-dried samples compared with the other groups. The proposed Oven-drying method at 40 degree results in an improved quality of UC.
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22
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Antimicrobial mechanism of the major active essential oil compounds and their structure–activity relationship. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1762-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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23
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Goswami AM. Computational analysis, structural modeling and ligand binding site prediction of Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate synthase. Comput Biol Chem 2016; 66:1-10. [PMID: 27842226 DOI: 10.1016/j.compbiolchem.2016.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 11/27/2022]
Abstract
Malaria remains one of the most serious infectious diseases in the world. There are five human species of the Plasmodium genus, of which Plasmodium falciparum is the most virulent and responsible for the vast majority of malaria related deaths. The unique biochemical processes that exist in Plasmodium falciparum provide a useful way to develop novel inhibitors. One such biochemical pathway is the methyl erythritol phosphate pathway (MEP), required to synthesize isoprenoid precursors. In the present study, a detailed computational analysis has been performed for 1-deoxy-d-xylulose-5-phosphate synthase, a key enzyme in MEP. The protein is found to be stable and residues from 825 to 971 are highly conserved across species. The homology model of the enzyme is developed using three web-based servers and Modeller software. It has twelve disordered regions indicating its druggability. Virtual screening of ZINC database identifies ten potential compounds in thiamine diphosphate binding region of the enzyme.
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Affiliation(s)
- Achintya Mohan Goswami
- Department of Physiology, Krishnagar Govt. College, Krishnagar, Nadia, West Bengal, India.
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24
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Gerin I, Ury B, Breloy I, Bouchet-Seraphin C, Bolsée J, Halbout M, Graff J, Vertommen D, Muccioli GG, Seta N, Cuisset JM, Dabaj I, Quijano-Roy S, Grahn A, Van Schaftingen E, Bommer GT. ISPD produces CDP-ribitol used by FKTN and FKRP to transfer ribitol phosphate onto α-dystroglycan. Nat Commun 2016; 7:11534. [PMID: 27194101 PMCID: PMC4873967 DOI: 10.1038/ncomms11534] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/06/2016] [Indexed: 01/27/2023] Open
Abstract
Mutations in genes required for the glycosylation of α-dystroglycan lead to muscle and brain diseases known as dystroglycanopathies. However, the precise structure and biogenesis of the assembled glycan are not completely understood. Here we report that three enzymes mutated in dystroglycanopathies can collaborate to attach ribitol phosphate onto α-dystroglycan. Specifically, we demonstrate that isoprenoid synthase domain-containing protein (ISPD) synthesizes CDP-ribitol, present in muscle, and that both recombinant fukutin (FKTN) and fukutin-related protein (FKRP) can transfer a ribitol phosphate group from CDP-ribitol to α-dystroglycan. We also show that ISPD and FKTN are essential for the incorporation of ribitol into α-dystroglycan in HEK293 cells. Glycosylation of α-dystroglycan in fibroblasts from patients with hypomorphic ISPD mutations is reduced. We observe that in some cases glycosylation can be partially restored by addition of ribitol to the culture medium, suggesting that dietary supplementation with ribitol should be evaluated as a therapy for patients with ISPD mutations.
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Affiliation(s)
- Isabelle Gerin
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Benoît Ury
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Isabelle Breloy
- Institute for Biochemistry II, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Céline Bouchet-Seraphin
- AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Biochimie Métabolique et Cellulaire, F-75018 Paris, France
| | - Jennifer Bolsée
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Mathias Halbout
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Julie Graff
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Didier Vertommen
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Giulio G Muccioli
- Louvain Drug Research Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Nathalie Seta
- AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Biochimie Métabolique et Cellulaire, F-75018 Paris, France
| | - Jean-Marie Cuisset
- Hôpital Roger-Salengro, Service de neuropédiatrie, Centre de Référence des Maladies Neuromusculaires, CHRU, F-59000 Lille, France
| | - Ivana Dabaj
- AP-HP, Hôpital R Poincaré, Service de pédiatrie, F-92380 Garches, France
| | - Susana Quijano-Roy
- AP-HP, Hôpital R Poincaré, Service de pédiatrie, F-92380 Garches, France.,Centre de Référence des Maladies Neuromusculaires, F-92380 Garches, France.,Université de Versailles-St Quentin, U1179 UVSQ - INSERM, F-78180 Montigny, France
| | - Ammi Grahn
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Emile Van Schaftingen
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Guido T Bommer
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
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Harder M, Schäfer E, Kümin T, Illarionov B, Bacher A, Fischer M, Diederich F, Bernet B. 8-Substituted, syn-Configured Adenosine Derivatives as Potential Inhibitors of the Enzyme IspE from the Non-Mevalonate Pathway of Isoprenoid Biosynthesis. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Rekittke I, Warkentin E, Jomaa H, Ermler U. Structure of the GcpE-HMBPP complex from Thermus thermophilius. Biochem Biophys Res Commun 2015; 458:246-50. [DOI: 10.1016/j.bbrc.2015.01.088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 01/19/2015] [Indexed: 11/28/2022]
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27
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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28
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 419] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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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: 14] [Impact Index Per Article: 1.4] [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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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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31
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Kholodar SA, Tombline G, Liu J, Tan Z, Allen CL, Gulick AM, Murkin AS. Alteration of the flexible loop in 1-deoxy-D-xylulose-5-phosphate reductoisomerase boosts enthalpy-driven inhibition by fosmidomycin. Biochemistry 2014; 53:3423-31. [PMID: 24825256 PMCID: PMC4045324 DOI: 10.1021/bi5004074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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1-Deoxy-d-xylulose-5-phosphate reductoisomerase (DXR),
which catalyzes the first committed step in the 2-C-methyl-d-erythritol 4-phosphate pathway of isoprenoid biosynthesis
used by Mycobacterium tuberculosis and other infectious
microorganisms, is absent in humans and therefore an attractive drug
target. Fosmidomycin is a nanomolar inhibitor of DXR, but despite
great efforts, few analogues with comparable potency have been developed.
DXR contains a strictly conserved residue, Trp203, within a flexible
loop that closes over and interacts with the bound inhibitor. We report
that while mutation to Ala or Gly abolishes activity, mutation to
Phe and Tyr only modestly impacts kcat and Km. Moreover, pre-steady-state kinetics
and primary deuterium kinetic isotope effects indicate that while
turnover is largely limited by product release for the wild-type enzyme,
chemistry is significantly more rate-limiting for W203F and W203Y.
Surprisingly, these mutants are more sensitive to inhibition by fosmidomycin,
resulting in Km/Ki ratios up to 19-fold higher than that of wild-type DXR. In
agreement, isothermal titration calorimetry revealed that fosmidomycin
binds up to 11-fold more tightly to these mutants. Most strikingly,
mutation strongly tips the entropy–enthalpy balance of total
binding energy from 50% to 75% and 91% enthalpy in W203F and W203Y,
respectively. X-ray crystal structures suggest that these enthalpy
differences may be linked to differences in hydrogen bond interactions
involving a water network connecting fosmidomycin’s phosphonate
group to the protein. These results confirm the importance of the
flexible loop, in particular Trp203, in ligand binding and suggest
that improved inhibitor affinity may be obtained against the wild-type
protein by introducing interactions with this loop and/or the surrounding
structured water network.
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Affiliation(s)
- Svetlana A Kholodar
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260-3000, United States
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32
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Gile GH, Slamovits CH. Transcriptomic analysis reveals evidence for a cryptic plastid in the colpodellid Voromonas pontica, a close relative of chromerids and apicomplexan parasites. PLoS One 2014; 9:e96258. [PMID: 24797661 PMCID: PMC4010437 DOI: 10.1371/journal.pone.0096258] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 04/06/2014] [Indexed: 12/20/2022] Open
Abstract
Colpodellids are free-living, predatory flagellates, but their close relationship to photosynthetic chromerids and plastid-bearing apicomplexan parasites suggests they were ancestrally photosynthetic. Colpodellids may therefore retain a cryptic plastid, or they may have lost their plastids entirely, like the apicomplexan Cryptosporidium. To find out, we generated transcriptomic data from Voromonas pontica ATCC 50640 and searched for homologs of genes encoding proteins known to function in the apicoplast, the non-photosynthetic plastid of apicomplexans. We found candidate genes from multiple plastid-associated pathways including iron-sulfur cluster assembly, isoprenoid biosynthesis, and tetrapyrrole biosynthesis, along with a plastid-type phosphate transporter gene. Four of these sequences include the 5' end of the coding region and are predicted to encode a signal peptide and a transit peptide-like region. This is highly suggestive of targeting to a cryptic plastid. We also performed a taxon-rich phylogenetic analysis of small subunit ribosomal RNA sequences from colpodellids and their relatives, which suggests that photosynthesis was lost more than once in colpodellids, and independently in V. pontica and apicomplexans. Colpodellids therefore represent a valuable source of comparative data for understanding the process of plastid reduction in humanity's most deadly parasite.
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Affiliation(s)
- Gillian H. Gile
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Claudio H. Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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33
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Peña-Rodríguez LM, Yam-Puc A, Knispel N, Schramek N, Huber C, Graßberger C, Ramírez-Torres FG, Escalante-Erosa F, García-Sosa K, Hiebert-Giesbrecht MR, Chan-Bacab MJ, Godoy-Hernández G, Bacher A, Eisenreich W. Isotopologue Profiling of Triterpene Formation under Physiological Conditions. Biosynthesis of Lupeol-3-(3′-R-hydroxy)-stearate in Pentalinon andrieuxii. J Org Chem 2014; 79:2864-73. [DOI: 10.1021/jo402677w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Luis M. Peña-Rodríguez
- Lehrstuhl
für Biochemie, Technische Universität München, Lichtenbergstr.
4, D-85747 Garching, Germany
| | | | - Nihat Knispel
- Lehrstuhl
für Biochemie, Technische Universität München, Lichtenbergstr.
4, D-85747 Garching, Germany
| | - Nicholas Schramek
- Lehrstuhl
für Biochemie, Technische Universität München, Lichtenbergstr.
4, D-85747 Garching, Germany
| | - Claudia Huber
- Lehrstuhl
für Biochemie, Technische Universität München, Lichtenbergstr.
4, D-85747 Garching, Germany
| | - Christoph Graßberger
- Lehrstuhl
für Biochemie, Technische Universität München, Lichtenbergstr.
4, D-85747 Garching, Germany
| | | | | | | | | | - Manuel J. Chan-Bacab
- Departamento
de Microbiología Ambiental y Biotecnología, Universidad Autónoma de Campeche, Av. Agustín Melgar s/n, Campeche, México
| | - Gregorio Godoy-Hernández
- Laboratorio
de Química Orgánica, ‡Unidad de Biotecnología and §Unidad de Bioquímica
y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, C.43 No. 130, Col. Chuburná
de Hidalgo, Mérida, Yucatán, México
| | - Adelbert Bacher
- Lehrstuhl
für Biochemie, Technische Universität München, Lichtenbergstr.
4, D-85747 Garching, Germany
| | - Wolfgang Eisenreich
- Lehrstuhl
für Biochemie, Technische Universität München, Lichtenbergstr.
4, D-85747 Garching, Germany
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Affiliation(s)
| | | | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case
Western Reserve University, 2109 Adelbert Road, Cleveland, Ohio 44106-4965,
United States
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35
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Guerra F, Wang K, Li J, Wang W, Liu YL, Amin S, Oldfield E. Inhibition of the 4Fe-4S Proteins IspG and IspH: an EPR, ENDOR and HYSCORE Investigation. Chem Sci 2014; 5:1642-1649. [PMID: 24999381 DOI: 10.1039/c3sc53301h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
IspG and IspH are proteins that are involved in isoprenoid biosynthesis in most bacteria as well as in malaria parasites and are important drug targets. They contain cubane-type 4Fe-4S clusters that are involved in unusual 2H+/2e- reductions. Here, we report the results of electron paramagnetic resonance spectroscopic investigations of the binding of amino- and thiolo-HMBPP (HMBPP=E-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate) IspH substrate-analog inhibitors to both proteins, as well as the binding of HMBPP and an acetylene diphosphate inhibitor, to IspG. The results show that amino-HMBPP binds to reduced IspH by Fe-C π-bonding with the olefinic carbons interacting with the unique 4th Fe in the 4Fe-4S cluster, quite different to the direct Fe-N ligation seen with the oxidized protein. No such π-complex is observed when amino-HMBPP binds to reduced IspG. No EPR signal is observed with IspH in the presence of dithionite and thiolo-HMBPP, suggesting that the 4Fe-4S cluster is not reduced, consistent with the presence of a 420 nm feature in the absorption spectrum (characteristic of an oxidized cluster). However, with IspG, the EPR spectrum in the presence of dithionite and thiolo-HMBPP is very similar to that seen with HMBPP. The binding of HMBPP to IspG was studied using hyperfine sublevel correlation spectroscopy with 17O and 13C labeled samples: the results rule out direct Fe-O bonding and indicate π-bonding. Finally, the binding to IspG of a potent acetylene diphosphate inhibitor was studied by using electron-nuclear double resonance spectroscopy with 13C labeled ligands: the large hyperfine couplings indicate strong Fe-C π-bonding with the acetylenic group. These results illustrate a remarkable diversity in binding behavior for HMBPP-analog inhibitors, opening up new routes to inhibitor design of interest in the context of anti-bacterial and anti-malarial drug discovery, as well as "cubane-type" metallo-biochemistry, in general.
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Affiliation(s)
- Francisco Guerra
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Ke Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
| | - Jikun Li
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Weixue Wang
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Yi-Liang Liu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801
| | - Shivani Amin
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
| | - Eric Oldfield
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801 ; Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
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36
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Masini T, Pilger J, Kroezen BS, Illarionov B, Lottmann P, Fischer M, Griesinger C, Hirsch AKH. De novo fragment-based design of inhibitors of DXS guided by spin-diffusion-based NMR spectroscopy. Chem Sci 2014. [DOI: 10.1039/c4sc00588k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A ligand-based NMR methodology (STI) enabled de novo fragment-based design of inhibitors of the enzyme DXS present in the non-mevalonate pathway in the absence of X-ray co-crystal structures.
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Affiliation(s)
- T. Masini
- Stratingh Institute for Chemistry
- University of Groningen
- NL-9747 AG Groningen, The Netherlands
| | - J. Pilger
- Max-Planck-Institute for Biophysical Chemisty
- 37077 Göttingen, Germany
| | - B. S. Kroezen
- Stratingh Institute for Chemistry
- University of Groningen
- NL-9747 AG Groningen, The Netherlands
| | - B. Illarionov
- Hamburg School of Food Science
- Institute of Food Chemistry
- Hamburg, Germany
| | - P. Lottmann
- Max-Planck-Institute for Biophysical Chemisty
- 37077 Göttingen, Germany
| | - M. Fischer
- Hamburg School of Food Science
- Institute of Food Chemistry
- Hamburg, Germany
| | - C. Griesinger
- Max-Planck-Institute for Biophysical Chemisty
- 37077 Göttingen, Germany
| | - A. K. H. Hirsch
- Stratingh Institute for Chemistry
- University of Groningen
- NL-9747 AG Groningen, The Netherlands
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37
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The effect of chain length and unsaturation on Mtb Dxr inhibition and antitubercular killing activity of FR900098 analogs. Bioorg Med Chem Lett 2013; 24:649-53. [PMID: 24360562 DOI: 10.1016/j.bmcl.2013.11.067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 11/20/2022]
Abstract
Inhibition of the nonmevalonate pathway (NMP) of isoprene biosynthesis has been examined as a source of new antibiotics with novel mechanisms of action. Dxr is the best studied of the NMP enzymes and several reports have described potent Dxr inhibitors. Many of these compounds are structurally related to natural products fosmidomycin and FR900098, each bearing retrohydroxamate and phosphonate groups. We synthesized a series of compounds with two to five methylene units separating these groups to examine what linker length was optimal and tested for inhibition against Mtb Dxr. We synthesized ethyl and pivaloyl esters of these compounds to increase lipophilicity and improve inhibition of Mtb growth. Our results show that propyl or propenyl linker chains are optimal. Propenyl analog 22 has an IC50 of 1.07 μM against Mtb Dxr. The pivaloyl ester of 22, compound 26, has an MIC of 9.4 μg/mL, representing a significant improvement in antitubercular potency in this class of compounds.
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38
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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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39
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Rekittke I, Olkhova E, Wiesner J, Demmer U, Warkentin E, Jomaa H, Ermler U. Structure of the (E)-4-hydroxy-3-methyl-but-2-enyl-diphosphate reductase from Plasmodium falciparum. FEBS Lett 2013; 587:3968-72. [PMID: 24188825 DOI: 10.1016/j.febslet.2013.10.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/15/2013] [Accepted: 10/20/2013] [Indexed: 11/28/2022]
Abstract
Terpenoid precursor biosynthesis occurs in human and many pathogenic organisms via the mevalonate and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways, respectively. We determined the X-ray structure of the Fe/S containing (E)-4-hydroxy-3-methyl-but-2-enyl-diphosphate reductase (LytB) of the pathogenic protozoa Plasmodium falciparum which catalyzes the terminal step of the MEP pathway. The cloverleaf fold and the active site of P. falciparum LytB corresponds to those of the Aquifex aeolicus and Escherichia coli enzymes. Its distinct electron donor [2Fe-2S] ferredoxin was modeled to its binding site by docking calculations. The presented structural data provide a platform for a rational search of anti-malarian drugs.
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Affiliation(s)
- Ingo Rekittke
- Medizinische Klinik IV (Hämatologie), Justus-Liebig-Universität Giessen, Klinikstrasse 33, D-35392 Giessen, Germany
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40
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Targeting lipid biosynthesis and salvage in apicomplexan parasites for improved chemotherapies. Nat Rev Microbiol 2013; 11:823-35. [DOI: 10.1038/nrmicro3139] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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41
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Chang WC, Song H, Liu HW, Liu P. Current development in isoprenoid precursor biosynthesis and regulation. Curr Opin Chem Biol 2013; 17:571-9. [PMID: 23891475 PMCID: PMC4068245 DOI: 10.1016/j.cbpa.2013.06.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/12/2013] [Accepted: 06/17/2013] [Indexed: 11/20/2022]
Abstract
Isoprenoids are one of the largest classes of natural products and all of them are constructed from two precursors, isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). For decades, the mevalonic acid (MVA) pathway was proposed to be the only IPP and DMAPP biosynthetic pathway. This review summarizes the newly discovered IPP and DMAPP production pathways since late 1990s, their distribution among different kingdoms, and their roles in secondary metabolite production. These new IPP and DMAPP production pathways include the methylerythritol phosphate (MEP) pathway, a modified MVA pathway, and the 5-methylthioadenosine shunt pathway. Relative to the studies on the MVA pathway, information on the MEP pathway regulation is limited and the mechanistic details of several of its novel transformations remain to be addressed. Current status on both MEP pathway regulation and mechanistic issues is also presented.
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Affiliation(s)
- Wei-chen Chang
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Heng Song
- Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts 02215
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42
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Domonkos I, Kis M, Gombos Z, Ughy B. Carotenoids, versatile components of oxygenic photosynthesis. Prog Lipid Res 2013; 52:539-61. [PMID: 23896007 DOI: 10.1016/j.plipres.2013.07.001] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 07/19/2013] [Accepted: 07/19/2013] [Indexed: 12/13/2022]
Abstract
Carotenoids (CARs) are a group of pigments that perform several important physiological functions in all kingdoms of living organisms. CARs serve as protective agents, which are essential structural components of photosynthetic complexes and membranes, and they play an important role in the light harvesting mechanism of photosynthesizing plants and cyanobacteria. The protection against reactive oxygen species, realized by quenching of singlet oxygen and the excited states of photosensitizing molecules, as well as by the scavenging of free radicals, is one of the main biological functions of CARs. X-ray crystallographic localization of CARs revealed that they are present at functionally and structurally important sites of both the PSI and PSII reaction centers. Characterization of a CAR-less cyanobacterial mutant revealed that while the absence of CARs prevents the formation of PSII complexes, it does not abolish the assembly and function of PSI. CAR molecules assist in the formation of protein subunits of the photosynthetic complexes by gluing together their protein components. In addition to their aforementioned indispensable functions, CARs have a substantial role in the formation and maintenance of proper cellular architecture, and potentially also in the protection of the translational machinery under stress conditions.
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Affiliation(s)
- Ildikó Domonkos
- Institute of Plant Biology, Biological Research Centre of Hungarian Academy of Sciences, P.O. Box 521, H-6701 Szeged, Hungary
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43
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Witschel M, Röhl F, Niggeweg R, Newton T. In search of new herbicidal inhibitors of the non-mevalonate pathway. PEST MANAGEMENT SCIENCE 2013; 69:559-563. [PMID: 23471898 DOI: 10.1002/ps.3479] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 12/04/2012] [Accepted: 01/03/2013] [Indexed: 06/01/2023]
Abstract
The first five steps of the non-mevalonate pathway have been tested in high-throughput screening (HTS) campaigns, using enzymes of plant origin. Hit rates were in general relatively low, which could be attributed to the high polarity and charged nature of substrates and active sites of these enzymes. Still, for all the enzymes, apart from IspF (2-methylerythritol 2,4-cyclodiphosphate synthase), inhibitors could be identified with activities below 100 μM, and these were followed up to identify structure-activity relationships (SARs). For the enzyme IspD (2C-methyl-D-erythritol 4-phosphate cytidyltransferase), inhibitors with IC50 down to 35 nM were identified that also showed herbicidal activity.
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Affiliation(s)
- Matthias Witschel
- BASF-SE, GVA/HC-B009, Global Research Herbicides, Ludwigshafen, Germany.
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44
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Kholodar SA, Murkin AS. DXP reductoisomerase: reaction of the substrate in pieces reveals a catalytic role for the nonreacting phosphodianion group. Biochemistry 2013; 52:2302-8. [PMID: 23473304 DOI: 10.1021/bi400092n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of the nonreacting phosphodianion group of 1-deoxy-d-xylulose-5-phosphate (DXP) in catalysis by DXP reductoisomerase (DXR) was investigated for the reaction of the "substrate in pieces". The truncated substrate 1-deoxy-l-erythrulose is converted by DXR to 2-C-methylglycerol with a kcat/Km that is 10(6)-fold lower than that for DXP. Phosphite dianion was found to be a nonessential activator, providing 3.2 kcal/mol of transition state stabilization for the truncated substrate. These results implicate a phosphate-driven conformational change involving loop closure over the DXR active site to generate an environment poised for catalysis.
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Affiliation(s)
- Svetlana A Kholodar
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
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45
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Characterization of Burkholderia glumae BGR1 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), the terminal enzyme in 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s13765-012-2231-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Handa S, Ramamoorthy D, Spradling TJ, Guida WC, Adams JH, Bendinskas KG, Merkler DJ. Production of recombinant 1-deoxy-d-xylulose-5-phosphate synthase from Plasmodium vivax in Escherichia coli. FEBS Open Bio 2013; 3:124-9. [PMID: 23772383 PMCID: PMC3668541 DOI: 10.1016/j.fob.2013.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/18/2013] [Accepted: 01/21/2013] [Indexed: 10/27/2022] Open
Abstract
Humanity is burdened by malaria as millions are infected with this disease. Although advancements have been made in the treatment of malaria, optimism regarding our fight against malaria must be tempered against the problem of drug resistance in the Plasmodium parasites causing malaria. New targets are required to overcome the resistance problem. The enzymes of the mevalonate-independent pathway of isoprenoid biosynthesis are targets for the development of novel antimalarial drugs. One enzyme in this pathway, 1-deoxy-d-xylulose-5-phosphate synthase (DXS), catalyzes the conversion of 1-deoxy-d-xylulose-5-phosphate to isopentenylpyrophosphate and dimethylallyl phosphate. We demonstrate the use of a step deletion method to identify and eliminate the putative nuclear-encoded and transit peptides from full length DXS to yield a truncated, active, and soluble form of Plasmodium vivax DXS, the DXS catalytic core (DXScc).
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Affiliation(s)
- Sumit Handa
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
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Mombelli P, Le Chapelain C, Munzinger N, Joliat E, Illarionov B, Schweizer WB, Hirsch AKH, Fischer M, Bacher A, Diederich F. Imidazole- and Benzimidazole-Based Inhibitors of the Kinase IspE: Targeting the Substrate-Binding Site and the Triphosphate-Binding Loop of the ATP Site. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201467] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Hansson D, Menkis A, Olson K, Stenlid J, Broberg A, Karlsson M. Biosynthesis of fomannoxin in the root rotting pathogen Heterobasidion occidentale. PHYTOCHEMISTRY 2012; 84:31-39. [PMID: 22981000 DOI: 10.1016/j.phytochem.2012.08.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/08/2012] [Accepted: 08/13/2012] [Indexed: 06/01/2023]
Abstract
Fomannoxin is a biologically active benzohydrofuran, which has been suggested to be involved in the pathogenicity of the root rotting fungus Heterobasidion annosum sensu lato. The biosynthesis of fomannoxin was investigated through an isotopic enrichment study utilizing [1-¹³C]glucose as metabolic tracer. ¹³C NMR spectroscopic analysis revealed the labeling pattern and showed that the isoprene building block originates from the mevalonic acid pathway, whereas the aromatic motif is formed via the shikimic acid route by elimination of pyruvate from chorismic acid. A natural product, 4-hydroxy-3-(3-methylbut-2-enyl)benzaldehyde, was isolated and characterized, and was suggested to be a key intermediate in the biosynthesis of fomannoxin and related secondary metabolites previously identified from the H. annosum fungal species complex.
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Affiliation(s)
- David Hansson
- Department of Chemistry, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-75007 Uppsala, Sweden
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Jozwiak A, Ples M, Skorupinska-Tudek K, Kania M, Dydak M, Danikiewicz W, Swiezewska E. Sugar availability modulates polyisoprenoid and phytosterol profiles in Arabidopsis thaliana hairy root culture. Biochim Biophys Acta Mol Cell Biol Lipids 2012. [PMID: 23178167 DOI: 10.1016/j.bbalip.2012.11.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sugars are recognized as signaling molecules regulating the biosynthesis of secondary metabolites in plants. Here, a modulatory effect of sugars on dolichol and phytosterol profiles was noted in the hairy roots of Arabidopsis thaliana. Arabidopsis roots contain a complex dolichol mixture comprising three groups ('families') of dolichols differing in the chain-length. These dolichols, especially the longest ones are accompanied by considerable amounts of polyprenols of the same length. The spectrum of polyisoprenoid alcohols, i.e. dolichols and polyprenols, was dependent on sugar type (glucose or sucrose) and its concentration in the medium. Among the long-chain dolichols Dol/Pren-20 (dolichol or prenol molecule composed of 20 isoprene residues) and Dol/Pren-23 were the main components at 0.5% and 2% glucose, respectively. Moreover, the ratio of polyprenols versus respective dolichols was also modulated by sugar in this group of polyisoprenoids, with polyprenols dominating at 3% sucrose and dolichols at 2% glucose. Glucose concentration affected the expression level of genes encoding cis-prenyltransferases, enzymes responsible for elongation of the polyisoprenoid chain. The most abundant phytosterols of the A. thaliana roots, β-sitosterol, stigmasterol and campesterol, were accompanied by corresponding stanols and traces of brassicasterol, stigmast-4,22-dien-3-one and stigmast-4-en-3-one. Similar to the polyisoprenoids, sterol profile responded to the sugar present in the medium, β-sitosterol dominating in roots grown on 3% or lower glucose concentrations and stigmasterol in 3% sucrose. These results indicate an involvement of sugar signaling in the regulation of cis-prenyltransferases and phytosterol pathway enzymes.
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Affiliation(s)
- Adam Jozwiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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Structure of the GcpE (IspG)-MEcPP complex from Thermus thermophilus. FEBS Lett 2012; 586:3452-7. [DOI: 10.1016/j.febslet.2012.07.070] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/22/2022]
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