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Zhang K, Foster L, Boothman C, Bassil NM, Pittman JK, Lloyd JR. Control of cyanobacterial growth with potassium; implications for bloom control in nuclear storage ponds. HARMFUL ALGAE 2024; 137:102654. [PMID: 39003020 DOI: 10.1016/j.hal.2024.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/19/2024] [Accepted: 05/21/2024] [Indexed: 07/15/2024]
Abstract
Microbial blooms have been reported in the First Generation Magnox Storage Pond at the Sellafield Nuclear Facility. The pond is kept alkaline with NaOH to minimise fuel rod corrosion, however alkali-tolerant microbial blooms dominated by the cyanobacterium Pseudanabaena catenata are able to thrive in this hostile environment. This study assessed the impact of alternative alkali-dosing regimens (KOH versus NaOH treatment) on biomass accumulation, using a P. catenata dominated mixed culture, which is representative of the pond environment. Optical density was reduced by 40-67 % with KOH treatment over the 3-month chemostat experiment. Microbial community analysis and proteomics demonstrated that the KOH-dependent inhibition of cell growth was mostly specific to P. catenata. The addition of KOH to nuclear storage ponds may therefore help control growth of this pioneer photosynthetic organism due to its sensitivity to potassium, while maintaining the high pH needed to inhibit the corrosion of stored nuclear fuel.
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Affiliation(s)
- Kejing Zhang
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Lynn Foster
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Christopher Boothman
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Naji M Bassil
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Jon K Pittman
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Jonathan R Lloyd
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
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Liu C, Zhao Z, Xu Q, Zhang H, Liu X, Yin C, Yan H, Liu Y. Comparative Genomic Analysis of Sphingomonas morindae sp. NBD5 and Sphingopyxis sp. USTB-05 for Producing Macular Pigment. Microorganisms 2023; 11:microorganisms11020266. [PMID: 36838230 PMCID: PMC9967899 DOI: 10.3390/microorganisms11020266] [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: 12/11/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
Sphingomonas morindae sp. NBD5, which we previously identified and tested, is a new bacterial strain for producing lutein. Here, based on the next-generation sequencing technology, we analyzed high throughput genomic sequences and compared related functional genes of Sphingomonas morindae sp. NBD5 and Sphingopyxis sp. USTB-05. The genome of Sphingomonas morindae sp. NBD5 has two sets of chromosomes, which is 4,239,716 bp and harbors 3882 protein coding genes. There are 59 protein-coding genes related to the macular pigment (MP) biosynthesis, of which four genes (ackA, pgm, gpmI and pckA) are unique. These genes, pckG, porB, meh, and fldA, are unique in Sphingopyxis sp. USTB-05. The analysis of Sphingomonas morindae sp. NBD5 and Sphingopyxis sp. USTB-05 genomes gives an insight into the new pathway for MP production. These genes for the transformation of glucose to MP were also found in Sphingomonas morindae sp. NBD5 and Sphingopyxis sp. USTB-05. This study expands the understanding of the pathway for complete biosynthesis of MP by Sphingomonas morindae sp. NBD5 and Sphingopyxis sp. USTB-05.
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Affiliation(s)
| | | | | | | | | | | | - Hai Yan
- Correspondence: (H.Y.); (Y.L.)
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3
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Davis I, Geng J, Liu A. Metalloenzymes involved in carotenoid biosynthesis in plants. Methods Enzymol 2022; 671:207-222. [PMID: 35878978 PMCID: PMC9315058 DOI: 10.1016/bs.mie.2022.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Carotenoids are a family of pigment compounds, a subset of which are precursors for vitamin A biosynthesis. These pigments are derived from isopentenyl pyrophosphate (IPP), with geranylgeranyl diphosphate being the first metabolite unique to carotenoid biosynthesis in plants, algae, fungi, some bacteria, and arthropods. This chapter highlights the metal-dependent enzymes involved in synthesizing carotenoids in plants and the current state of knowledge of their cofactors and mechanisms. Emphasis is given to spectroscopic methods used to characterize metal centers. The recently discovered heme-dependent isomerase Z-ISO is presented as a case study in how to interrogate a metalloenzyme. Use of UV-vis, electron paramagnetic resonance, and magnetic circular dichroism spectroscopies of a metal center at various oxidation states and with external small molecule probes (CN-, CO, and NO) can provide information about the nature of the metal center, the identity of its ligands, and its mechanism of action. Z-ISO is a histidine/cysteine ligated heme-dependent enzyme that is only active in the ferrous state and possesses redox-linked ligand switching. The choice and design of experiments are discussed as well as the conclusions that can be drawn.
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Affiliation(s)
- Ian Davis
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, United States.
| | - Jiafeng Geng
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, United States.
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Liu X, Cao PH, Huang QQ, Yang YR, Tao DD. Disruption of a Rice Chloroplast-Targeted Gene OsHMBPP Causes a Seedling-Lethal Albino Phenotype. RICE (NEW YORK, N.Y.) 2020; 13:51. [PMID: 32712772 PMCID: PMC7382669 DOI: 10.1186/s12284-020-00408-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/06/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Chloroplast development is coordinately regulated by plastid- and nuclear-encoding genes. Although many regulators have been reported to be involved in chloroplast development, new factors remain to be identified, given the complexity of this process. RESULTS In this study, we characterized a rice mutant lethal albinic seedling 1(las1)form of a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (OsHMBPP) that was targeted to the chloroplasts. The LAS1 mutation caused the albino lethal phenotype in seedlings. Transmission electron microscopy indicated that las1 were defective in early chloroplast development. LAS1 is preferentially expressed in leaves, implying its role in controlling chloroplast development. The expression levels of many chloroplast-encoded genes were altered significantly in las1. The expression levels of nuclear-encoded gene involved in Chl biosynthesis were also decreased in las1. We further investigated plastidic RNA editing in las1 and found that the edit efficiency of four chloroplast genes were markly altered. Compared with WT, las1 exhibited defective in biogenesis of chloroplast ribosomes. CONCLUSIONS Our results show that LAS1/OsHMBPP plays an essential role in the early chloroplast development in rice.
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Affiliation(s)
- X Liu
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China.
| | - P H Cao
- Suzhou Academy of Agricultural Sciences, Suzhou, 215155, China
| | - Q Q Huang
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China
| | - Y R Yang
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China
| | - D D Tao
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China
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Microbiological Advances in Bioactives from High Altitude. MICROBIOLOGICAL ADVANCEMENTS FOR HIGHER ALTITUDE AGRO-ECOSYSTEMS & SUSTAINABILITY 2020. [DOI: 10.1007/978-981-15-1902-4_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Calcagnile M, Tredici SM, Talà A, Alifano P. Bacterial Semiochemicals and Transkingdom Interactions with Insects and Plants. INSECTS 2019; 10:E441. [PMID: 31817999 PMCID: PMC6955855 DOI: 10.3390/insects10120441] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023]
Abstract
A peculiar feature of all living beings is their capability to communicate. With the discovery of the quorum sensing phenomenon in bioluminescent bacteria in the late 1960s, it became clear that intraspecies and interspecies communications and social behaviors also occur in simple microorganisms such as bacteria. However, at that time, it was difficult to imagine how such small organisms-invisible to the naked eye-could influence the behavior and wellbeing of the larger, more complex and visible organisms they colonize. Now that we know this information, the challenge is to identify the myriad of bacterial chemical signals and communication networks that regulate the life of what can be defined, in a whole, as a meta-organism. In this review, we described the transkingdom crosstalk between bacteria, insects, and plants from an ecological perspective, providing some paradigmatic examples. Second, we reviewed what is known about the genetic and biochemical bases of the bacterial chemical communication with other organisms and how explore the semiochemical potential of a bacterium can be explored. Finally, we illustrated how bacterial semiochemicals managing the transkingdom communication may be exploited from a biotechnological point of view.
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Affiliation(s)
| | | | | | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Prov.le Lecce-Monteroni, 73100 Lecce, Italy; (M.C.); (S.M.T.); (A.T.)
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Cattaneo F, De Marino S, Parisi M, Festa C, Castaldo M, Finamore C, Duraturo F, Zollo C, Ammendola R, Zollo F, Iorizzi M. Wound healing activity and phytochemical screening of purified fractions of Sempervivum tectorum L. leaves on HCT 116. PHYTOCHEMICAL ANALYSIS : PCA 2019; 30:524-534. [PMID: 31168900 DOI: 10.1002/pca.2844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/12/2019] [Accepted: 04/17/2019] [Indexed: 06/09/2023]
Abstract
INTRODUCTION Sempervivum tectorum L. (Crassulaceae), is a succulent perennial plant widespread in Mediterranean countries and commonly used in traditional medicine for ear inflammation, ulcers and skin rashes as a refrigerant and astringent. OBJECTIVE To demonstrate the therapeutic effects of the plant, various fractions were purified and characterised. The potential wound healing activity, proliferation rate and intracellular signalling cascades were investigated by using human epithelial colorectal carcinoma (HCT 116) cells. METHODOLOGY An extraction method without organic solvents was applied for the first time. The purification was carried out by droplet counter current chromatography (DCCC) coupled with high-performance liquid chromatography (HPLC) and electrospray ionisation mass spectrometry (ESI-MS) data. By nuclear magnetic resonance (NMR) [1 H, 13 C and two-dimensional (2D) experiments] pure components were identified. Wound healing and cell proliferation assays were utilised to determine the role of the isolated S. tectorum (SVT) fraction on cellular migration and proliferation. The signalling pathways elicited from the SVT fractions, were analysed by Western blot analysis. RESULTS In this study two rare natural components were identified, namely monosaccharide sedoheptulose and polyalcohol 2-C-methyl-D-erythritol, along with known organic acids and flavonoids. The fractions with high level of sedoheptulose enhance the proliferation and the cellular migration of epithelial HCT 116 cells. The intracellular signalling cascades elicited from the purified fractions induce the c-Src-mediated transactivation of EGFR and the activation of the STAT3 pathway which, in turn, are crucially involved in the cellular proliferation and migration. CONCLUSIONS Our study demonstrates the efficacy of purified fractions of S. tectorum L. in enhancing cellular proliferation and migration, suggesting their potential role as topical therapeutic treatments for wound healing.
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Affiliation(s)
- Fabio Cattaneo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Simona De Marino
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Melania Parisi
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Carmen Festa
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Martina Castaldo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Claudia Finamore
- Dipartimento di Bioscienze e Territorio, Università degli Studi del Molise, Pesche, (Isernia), Italy
| | - Francesca Duraturo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Cristiana Zollo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Rosario Ammendola
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Franco Zollo
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Maria Iorizzi
- Dipartimento di Bioscienze e Territorio, Università degli Studi del Molise, Pesche, (Isernia), Italy
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Validation of suitable reference genes for quantitative gene expression analysis in Tripterygium wilfordii. Mol Biol Rep 2019; 46:4161-4174. [PMID: 31111371 DOI: 10.1007/s11033-019-04867-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/09/2019] [Indexed: 12/21/2022]
Abstract
Validation of suitable reference genes is critical in quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Suitable and reliable reference genes for the normalization of gene expression data are characterized by high gene expression stability across tissues and different experimental conditions. This study evaluated the gene expression stability of ten reference genes commonly used in Arabidopsis thaliana for their suitability in qRT-PCR analysis in Tripterygium wilfordii Hook.f. The orthologous sequences of these ten candidate genes were identified from T. wilfordii transcriptomic data (Project No. SRX472292). Five algorithms including GeNorm, NormFinder, BestKeeper, ΔCt, and RefFinder were used to assess the gene expression stability of these putative reference genes in different plant tissues and different stress conditions. The results identified ACTINT7 and TBP as the most suitable reference genes across all samples. The gene expressions of TwHMGR (3-hydroxy-3-methylglutaryl coenzyme A reductase, KU246037.1) and of TwDXR (1-deoxy-D-xylulose-5-phosphate reductoisomerase, KJ174341.1) were investigated to validate the suitability of the reference genes. The validation analysis confirmed the suitability of ACTINT7 and TBP as the best reference genes for elucidating secondary metabolite biosynthesis pathway in T. wilfordii. In summary, this study identified the most suitable and reliable reference genes for future qRT-PCR- based studies in T. wilfordii.
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10
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Root K, Barylyuk K, Schwab A, Thelemann J, Illarionov B, Geist JG, Gräwert T, Bacher A, Fischer M, Diederich F, Zenobi R. Aryl bis-sulfonamides bind to the active site of a homotrimeric isoprenoid biosynthesis enzyme IspF and extract the essential divalent metal cation cofactor. Chem Sci 2018; 9:5976-5986. [PMID: 30079212 PMCID: PMC6050538 DOI: 10.1039/c8sc00814k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/17/2018] [Indexed: 12/22/2022] Open
Abstract
Characterizing the mode of action of non-covalent inhibitors in multisubunit enzymes often presents a great challenge. Most of the conventionally used methods are based on ensemble measurements of protein-ligand binding in bulk solution. They often fail to accurately describe multiple binding processes occurring in such systems. Native electrospray ionization mass spectrometry (ESI-MS) of intact protein complexes is a direct, label-free approach that can render the entire distribution of ligand-bound states in multimeric protein complexes. Here we apply native ESI-MS to comprehensively characterize the isoprenoid biosynthesis enzyme IspF from Arabidopsis thaliana, an example of a homomeric protein complex with multiple binding sites for several types of ligands, including a metal cofactor and a synthetic inhibitor. While standard biophysical techniques failed to reveal the mode of action of recently discovered aryl-sulfonamide-based inhibitors of AtIspF, direct native ESI-MS titrations of the protein with the ligands and ligand competition assays allowed us to accurately capture the solution-phase protein-ligand binding equilibria in full complexity and detail. Based on these combined with computational modeling, we propose a mechanism of AtIspF inhibition by aryl bis-sulfonamides that involves both the competition with the substrate for the ligand-binding pocket and the extraction of Zn2+ from the enzyme active site. This inhibition mode is therefore mixed competitive and non-competitive, the latter exerting a key inhibitory effect on the enzyme activity. The results of our study deliver a profound insight into the mechanisms of AtIspF action and inhibition, open new perspectives for designing inhibitors of this important drug target, and demonstrate the applicability and value of the native ESI-MS approach for deep analysis of complex biomolecular binding equilibria.
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Affiliation(s)
- Katharina Root
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Anatol Schwab
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Jonas Thelemann
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Boris Illarionov
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - Julie G Geist
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Tobias Gräwert
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - Adelbert Bacher
- Department of Chemistry , Technical University of Munich , Garching , Germany
| | - Markus Fischer
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - François Diederich
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
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Sandhu D, Coleman Z, Atkinson T, Rai KM, Mendu V. Genetics and Physiology of the Nuclearly Inherited Yellow Foliar Mutants in Soybean. FRONTIERS IN PLANT SCIENCE 2018; 9:471. [PMID: 29696030 PMCID: PMC5904354 DOI: 10.3389/fpls.2018.00471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/26/2018] [Indexed: 05/27/2023]
Abstract
Plant photosynthetic pigments are important in harvesting the light energy and transfer of energy during photosynthesis. There are several yellow foliar mutants discovered in soybean and chromosomal locations for about half of them have been deduced. Viable-yellow mutants are capable of surviving with decreased photosynthesis, while lethal-yellow mutants die shortly after germination. In addition to the decreased chlorophyll content, other features associated with yellow mutants include altered Chl a and Chl b ratio, reduction in chloroplast size and number, lower levels of other photosynthetic pigments, inability of thylakoids to stack into granum, lack of lamellae to interconnect granum and reduced size of the light harvesting complex. For some yellow mutants, temperature and/or light play a critical role in the manifestation of phenotype. Although yellow foliar mutants are viewed as undesirable for crop production, there is the possibility of these mutants to create a positive impact by reducing the total amount of chlorophyll and diverting resources toward increased biochemical photosynthetic capacity leading to increased yield. Recent advances in model plants led to the isolation and characterization of various genes associated with yellow foliar phenotype. Knowledge gained from the model plants can be applied using homology based cloning approach to isolate genes in soybean and understanding the modes of actions of the involved proteins. Identifying and characterizing yellow foliar mutants will not only aid in understanding the biosynthetic pathways involved in the photosynthetic machinery, but may also provide ways to increase soybean productivity.
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Affiliation(s)
| | - Zachary Coleman
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI, United States
| | - Taylor Atkinson
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI, United States
| | - Krishan M. Rai
- Fiber and Biopolymer Research Institute, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Venugopal Mendu
- Fiber and Biopolymer Research Institute, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
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Haymond A, Dowdy T, Johny C, Johnson C, Ball H, Dailey A, Schweibenz B, Villarroel K, Young R, Mantooth CJ, Patel T, Bases J, Dowd CS, Couch RD. A high-throughput screening campaign to identify inhibitors of DXP reductoisomerase (IspC) and MEP cytidylyltransferase (IspD). Anal Biochem 2018; 542:63-75. [PMID: 29180070 PMCID: PMC5817008 DOI: 10.1016/j.ab.2017.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 11/17/2022]
Abstract
The rise of antibacterial resistance among human pathogens represents a problem that could change the landscape of healthcare unless new antibiotics are developed. The methyl erythritol phosphate (MEP) pathway represents an attractive series of targets for novel antibiotic design, considering each enzyme of the pathway is both essential and has no human homologs. Here we describe a pilot scale high-throughput screening (HTS) campaign against the first and second committed steps in the pathway, catalyzed by DXP reductoisomerase (IspC) and MEP cytidylyltransferase (IspD), using compounds present in the commercially available LOPAC1280 library as well as in an in-house natural product extract library. Hit compounds were characterized to deduce their mechanism of inhibition; most function through aggregation. The HTS workflow outlined here is useful for quickly screening a chemical library, while effectively identifying false positive compounds associated with assay constraints and aggregation.
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Affiliation(s)
- Amanda Haymond
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Tyrone Dowdy
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Chinchu Johny
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Claire Johnson
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Haley Ball
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Allyson Dailey
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Brandon Schweibenz
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Karen Villarroel
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Richard Young
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Clark J Mantooth
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Trishal Patel
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Jessica Bases
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA
| | - Cynthia S Dowd
- Department of Chemistry, George Washington University, Washington DC 20052, USA.
| | - Robin D Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA.
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Huang R, Wang Y, Wang P, Li C, Xiao F, Chen N, Li N, Li C, Sun C, Li L, Chen R, Xu Z, Zhu J, Deng X. A single nucleotide mutation of IspF gene involved in the MEP pathway for isoprenoid biosynthesis causes yellow-green leaf phenotype in rice. PLANT MOLECULAR BIOLOGY 2018; 96:5-16. [PMID: 29143298 DOI: 10.1007/s11103-017-0668-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 10/09/2017] [Indexed: 05/20/2023]
Abstract
We identified IspF gene through yellow-green leaf mutant 505ys in rice. OsIspF was expressed in all tissues detected, and its encoded protein was targeted to the chloroplast. On expression levels of genes in this mutant, OsIspF itself and the genes encoding other enzymes of the MEP pathway and chlorophyll synthase were all up-regulated, however, among eight genes associated with photosynthesis, only psaA, psaN and psbA genes for three reaction center subunits of photosystem obviously changed. Isoprenoids are the most abundant natural compounds in all organisms, which originate from the basic five-carbon units isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In plants, IPP and DMAPP are synthesized through two independent pathways, the mevalonic acid pathway in cytoplasm and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway in plastids. The MEP pathway comprises seven enzymatic steps, in which IspF is the fifth enzyme. So far, no IspF gene has been identified in monocotyledonous plants. In this study, we isolated a leaf-color mutant, 505ys, in rice (Oryza sativa). The mutant displayed yellow-green leaf phenotype, reduced level of photosynthetic pigments, and arrested development of chloroplasts. By map-based cloning of this mutant, we identified OsIspF gene (LOC_Os02g45660) showing significant similarity to IspF gene of Arabidopsis, in which a missense mutation occurred in the mutant, resulting in an amino acid change in the encoded protein. OsIspF gene was expressed in all tissues detected, and its encoded protein was targeted to the chloroplast. Further, the mutant phenotype of 505ys was complemented by transformation with the wild-type OsIspF gene. Therefore, we successfully identified an IspF gene in monocotyledonous plants. In addition, real-time quantitative RT-PCR implied that a positive regulation could exist between the OsIspF gene and the genes encoding other enzymes of the MEP pathway and chlorophyll synthase. At the same time, it also implied that the individual genes involved in the MEP pathway might differentially regulated expression levels of the genes associated with photosynthesis.
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Affiliation(s)
- Rui Huang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yang Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Pingrong Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Chunmei Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Fuliang Xiao
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Nenggang Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Na Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Caixia Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Changhui Sun
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lihua Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Rongjun Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhengjun Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jianqing Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaojian Deng
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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14
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Zheng X, Zhang X, Zhao L, Apaliya MT, Yang Q, Sun W, Zhang X, Zhang H. Screening of Deoxynivalenol Producing Strains and Elucidation of Possible Toxigenic Molecular Mechanism. Toxins (Basel) 2017; 9:toxins9060184. [PMID: 28587179 PMCID: PMC5488034 DOI: 10.3390/toxins9060184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/24/2017] [Accepted: 05/27/2017] [Indexed: 12/13/2022] Open
Abstract
In this study, seven strains of Fusarium graminearum were isolated from wheat, of which six were identified to produce deoxynivalenol and the production of deoxynivalenol was assessed. F. graminearum strain Fg1 was noted to produce 1.0 μg/g deoxynivalenol during the incubation period in the Czapek yeast broth, while none was detected in F. graminearum strain Fg2. Hence, the differences in proteomes and transcriptomes of Fg1 and Fg2 were compared to analyze the mechanism underlying deoxynivalenol production. Among the 66 significantly differentially expressed proteins in Fg1, 39 and 27 were more or less abundant expressed. Functional analysis suggested that the enzymes involved in the methylerythritol 4-phosphate and mevalonate pathways, which provide a substrate for biosynthesis of farnesyl pyrophosphate, a precursor of DON, were activated in Fg1. The transcriptomics data demonstrated that the expression level of a majority of genes, including trichothecene biosynthetic genes, protein kinases, and transcription factors, involved in trichothecene biosynthesis was higher in Fg1 than in Fg2. The results also revealed differential expression profiles of deoxynivalenol biosynthesis genes in strains Fg1 and Fg2, which emphasized their deoxynivalenol producing ability and the underlying mechanism.
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Affiliation(s)
- Xiangfeng Zheng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Xiaoli Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Lina Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Maurice T Apaliya
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Wei Sun
- Zhen Jiang Grain and Oil Quality Testing Center, Zhenjiang 212013, Jiangsu, China.
| | - Xiaoyun Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
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15
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Hampel T, Brückner R. Towards a Total Synthesis of Phenalinolactone Core Diterpenoid 6: Synthesis of a Racemic Decahydrobenzocyclobutaisobenzofuran with a trans-anti-cis
Junction of the Isocyclic Rings. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Thomas Hampel
- Institut für Organische Chemie; Albert-Ludwigs-Universität; Albertstraße 21 79104 Freiburg Germany
| | - Reinhard Brückner
- Institut für Organische Chemie; Albert-Ludwigs-Universität; Albertstraße 21 79104 Freiburg Germany
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16
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Shukla V, Asthana S, Gupta P, Dwivedi PD, Tripathi A, Das M. Toxicity of Naturally Occurring Anthraquinones. ADVANCES IN MOLECULAR TOXICOLOGY 2017. [DOI: 10.1016/b978-0-12-812522-9.00001-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Affiliation(s)
- Annika Frank
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Michael Groll
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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18
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Abstract
This article summarizes what is currently known of the structures, physiological roles, involvement in pathogenicity, and biogenesis of a variety of noncovalently bound cell envelope lipids and glycoconjugates of Mycobacterium tuberculosis and other Mycobacterium species. Topics addressed in this article include phospholipids; phosphatidylinositol mannosides; triglycerides; isoprenoids and related compounds (polyprenyl phosphate, menaquinones, carotenoids, noncarotenoid cyclic isoprenoids); acyltrehaloses (lipooligosaccharides, trehalose mono- and di-mycolates, sulfolipids, di- and poly-acyltrehaloses); mannosyl-beta-1-phosphomycoketides; glycopeptidolipids; phthiocerol dimycocerosates, para-hydroxybenzoic acids, and phenolic glycolipids; mycobactins; mycolactones; and capsular polysaccharides.
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19
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In silico approaches for the identification of virulence candidates amongst hypothetical proteins of Mycoplasma pneumoniae 309. Comput Biol Chem 2015; 59 Pt A:67-80. [DOI: 10.1016/j.compbiolchem.2015.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 09/08/2015] [Accepted: 09/14/2015] [Indexed: 01/25/2023]
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20
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Guan Z, Xue D, Abdallah II, Dijkshoorn L, Setroikromo R, Lv G, Quax WJ. Metabolic engineering of Bacillus subtilis for terpenoid production. Appl Microbiol Biotechnol 2015; 99:9395-406. [PMID: 26373726 PMCID: PMC4628092 DOI: 10.1007/s00253-015-6950-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/17/2015] [Accepted: 08/20/2015] [Indexed: 11/04/2022]
Abstract
Terpenoids are the largest group of small-molecule natural products, with more than 60,000 compounds made from isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). As the most diverse group of small-molecule natural products, terpenoids play an important role in the pharmaceutical, food, and cosmetic industries. For decades, Escherichia coli (E. coli) and Saccharomyces cerevisiae (S. cerevisiae) were extensively studied to biosynthesize terpenoids, because they are both fully amenable to genetic modifications and have vast molecular resources. On the other hand, our literature survey (20 years) revealed that terpenoids are naturally more widespread in Bacillales. In the mid-1990s, an inherent methylerythritol phosphate (MEP) pathway was discovered in Bacillus subtilis (B. subtilis). Since B. subtilis is a generally recognized as safe (GRAS) organism and has long been used for the industrial production of proteins, attempts to biosynthesize terpenoids in this bacterium have aroused much interest in the scientific community. This review discusses metabolic engineering of B. subtilis for terpenoid production, and encountered challenges will be discussed. We will summarize some major advances and outline future directions for exploiting the potential of B. subtilis as a desired "cell factory" to produce terpenoids.
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Affiliation(s)
- Zheng Guan
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands
- Institute of Materia Medica, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Dan Xue
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands
| | - Ingy I Abdallah
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands
| | - Linda Dijkshoorn
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands
| | - Rita Setroikromo
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands
| | - Guiyuan Lv
- Institute of Materia Medica, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Wim J Quax
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands.
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21
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RNA-Seq mediated root transcriptome analysis of Chlorophytum borivilianum for identification of genes involved in saponin biosynthesis. Funct Integr Genomics 2015; 16:37-55. [DOI: 10.1007/s10142-015-0465-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 08/26/2015] [Accepted: 09/22/2015] [Indexed: 10/23/2022]
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22
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Gupta P, Phulara SC. Metabolic engineering for isoprenoid-based biofuel production. J Appl Microbiol 2015; 119:605-19. [PMID: 26095690 DOI: 10.1111/jam.12871] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 05/31/2015] [Accepted: 06/01/2015] [Indexed: 01/14/2023]
Abstract
Sustainable economic and industrial growth is the need of the hour and it requires renewable energy resources having better performance and compatibility with existing fuel infrastructure from biological routes. Isoprenoids (C ≥ 5) can be a potential alternative due to their diverse nature and physiochemical properties similar to that of petroleum based fuels. In the past decade, extensive research has been done to utilize metabolic engineering strategies in micro-organisms primarily, (i) to overcome the limitations associated with their natural and non-natural production and (ii) to develop commercially competent microbial strain for isoprenoid-based biofuel production. This review briefly describes the engineered isoprenoid biosynthetic pathways in well-characterized microbial systems for the production of several isoprenoid-based biofuels and fuel precursors.
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Affiliation(s)
- P Gupta
- National Institute of Technology, Raipur, Chhattisgarh, India
| | - S C Phulara
- National Institute of Technology, Raipur, Chhattisgarh, India
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23
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Singh B, Sharma RA. Plant terpenes: defense responses, phylogenetic analysis, regulation and clinical applications. 3 Biotech 2015; 5:129-151. [PMID: 28324581 PMCID: PMC4362742 DOI: 10.1007/s13205-014-0220-2] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/10/2014] [Indexed: 12/11/2022] Open
Abstract
The terpenoids constitute the largest class of natural products and many interesting products are extensively applied in the industrial sector as flavors, fragrances, spices and are also used in perfumery and cosmetics. Many terpenoids have biological activities and also used for medical purposes. In higher plants, the conventional acetate-mevalonic acid pathway operates mainly in the cytosol and mitochondria and synthesizes sterols, sesquiterpenes and ubiquinones mainly. In the plastid, the non-mevalonic acid pathway takes place and synthesizes hemi-, mono-, sesqui-, and diterpenes along with carotenoids and phytol tail of chlorophyll. In this review paper, recent developments in the biosynthesis of terpenoids, indepth description of terpene synthases and their phylogenetic analysis, regulation of terpene biosynthesis as well as updates of terpenes which have entered in the clinical studies are reviewed thoroughly.
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Affiliation(s)
- Bharat Singh
- AIB, Amity University Rajasthan, NH-11C, Kant Kalwar, Jaipur, 303 002, India.
| | - Ram A Sharma
- Department of Botany, University of Rajasthan, Jaipur, 302 055, India
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24
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Involvement of the gut chemosensory system in the regulation of colonic anion secretion. BIOMED RESEARCH INTERNATIONAL 2015; 2015:403919. [PMID: 25866781 PMCID: PMC4383346 DOI: 10.1155/2015/403919] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/09/2014] [Indexed: 12/26/2022]
Abstract
The primary function of the gastrointestinal (GI) tract is the extraction of nutrients from the diet. Therefore, the GI tract must possess an efficient surveillance system that continuously monitors the luminal content for beneficial or harmful compounds. Recent studies have shown that specialized cells in the intestinal lining can sense changes in this content. These changes directly influence fundamental GI processes such as secretion, motility, and local blood flow via hormonal and/or neuronal pathways. Until recently, most studies examining the control of ion transport in the colon have focused on neural and hormonal regulation. However, study of the regulation of gut function by the gut chemosensory system has become increasingly important, as failure of this system causes dysfunctions in host homeostasis, as well as functional GI disorders. Furthermore, regulation of ion transport in the colon is critical for host defense and for electrolytes balance. This review discusses the role of the gut chemosensory system in epithelial transport, with a particular emphasis on the colon.
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25
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Hsieh WY, Hsieh MH. The amino-terminal conserved domain of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase is critical for its function in oxygen-evolving photosynthetic organisms. PLANT SIGNALING & BEHAVIOR 2015; 10:e988072. [PMID: 25723575 PMCID: PMC4622703 DOI: 10.4161/15592324.2014.988072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 05/22/2023]
Abstract
4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), also known as isoprenoid synthesis H (IspH) or lysis-tolerant B (LytB), catalyzes the last step of the methylerythritol phosphate pathway to synthesize isopentenyl diphosphate and dimethylallyl diphosphate. The structure and reaction mechanism of IspH have been actively investigated in Escherichia coli but little is known in plants. Compared with the bacterial IspH, cyanobacterial and plant HDRs all contain an extra N-terminal conserved domain (NCD) that is essential for their function. Tyr72 in the NCD and several plant-specific residues around the central active site are critical for Arabidopsis HDR function. These results suggest that the structure and reaction mechanism of HDR/IspH may be different between plants and bacteria. The E. coli IspH is an iron-sulfur protein that is sensitive to oxygen. It is possible that the cyanobacterial HDR may independently evolve from the common ancestor of prokaryotes to obtain the NCD, which may protect the enzyme from high concentration of oxygen during photosynthesis.
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Affiliation(s)
- Wei-Yu Hsieh
- Institute of Plant and Microbial Biology; Academia Sinica; Taipei, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology; Academia Sinica; Taipei, Taiwan
- Correspondence to: Ming-Hsiun Hsieh;
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26
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Masini T, Hirsch AKH. Development of Inhibitors of the 2C-Methyl-d-erythritol 4-Phosphate (MEP) Pathway Enzymes as Potential Anti-Infective Agents. J Med Chem 2014; 57:9740-63. [DOI: 10.1021/jm5010978] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tiziana Masini
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
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27
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Haymond A, Johny C, Dowdy T, Schweibenz B, Villarroel K, Young R, Mantooth CJ, Patel T, Bases J, Jose GS, Jackson ER, Dowd CS, Couch RD. Kinetic characterization and allosteric inhibition of the Yersinia pestis 1-deoxy-D-xylulose 5-phosphate reductoisomerase (MEP synthase). PLoS One 2014; 9:e106243. [PMID: 25171339 PMCID: PMC4149570 DOI: 10.1371/journal.pone.0106243] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/29/2014] [Indexed: 11/19/2022] Open
Abstract
The methylerythritol phosphate (MEP) pathway found in many bacteria governs the synthesis of isoprenoids, which are crucial lipid precursors for vital cell components such as ubiquinone. Because mammals synthesize isoprenoids via an alternate pathway, the bacterial MEP pathway is an attractive target for novel antibiotic development, necessitated by emerging antibiotic resistance as well as biodefense concerns. The first committed step in the MEP pathway is the reduction and isomerization of 1-deoxy-D-xylulose-5-phosphate (DXP) to methylerythritol phosphate (MEP), catalyzed by MEP synthase. To facilitate drug development, we cloned, expressed, purified, and characterized MEP synthase from Yersinia pestis. Enzyme assays indicate apparent kinetic constants of KMDXP = 252 µM and KMNADPH = 13 µM, IC50 values for fosmidomycin and FR900098 of 710 nM and 231 nM respectively, and Ki values for fosmidomycin and FR900098 of 251 nM and 101 nM respectively. To ascertain if the Y. pestis MEP synthase was amenable to a high-throughput screening campaign, the Z-factor was determined (0.9) then the purified enzyme was screened against a pilot scale library containing rationally designed fosmidomycin analogs and natural product extracts. Several hit molecules were obtained, most notably a natural product allosteric affector of MEP synthase and a rationally designed bisubstrate derivative of FR900098 (able to associate with both the NADPH and DXP binding sites in MEP synthase). It is particularly noteworthy that allosteric regulation of MEP synthase has not been described previously. Thus, our discovery implicates an alternative site (and new chemical space) for rational drug development.
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Affiliation(s)
- Amanda Haymond
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Chinchu Johny
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Tyrone Dowdy
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Brandon Schweibenz
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Karen Villarroel
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Richard Young
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Clark J. Mantooth
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Trishal Patel
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Jessica Bases
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Geraldine San Jose
- Department of Chemistry, George Washington University, Washington DC, United States of America
| | - Emily R. Jackson
- Department of Chemistry, George Washington University, Washington DC, United States of America
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington DC, United States of America
| | - Robin D. Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
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28
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Jarchow-Choy SK, Koppisch AT, Fox DT. Synthetic Routes to Methylerythritol Phosphate Pathway Intermediates and Downstream Isoprenoids. CURR ORG CHEM 2014; 18:1050-1072. [PMID: 25009443 PMCID: PMC4082188 DOI: 10.2174/1385272819666140501001101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/22/2014] [Accepted: 04/26/2014] [Indexed: 11/22/2022]
Abstract
Isoprenoids constitute the largest class of natural products with greater than 55,000 identified members. They play essential roles in maintaining proper cellular function leading to maintenance of human health, plant defense mechanisms against predators, and are often exploited for their beneficial properties in the pharmaceutical and nutraceutical industries. Most impressively, all known isoprenoids are derived from one of two C5-precursors, isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). In order to study the enzyme transformations leading to the extensive structural diversity found within this class of compounds there must be access to the substrates. Sometimes, intermediates within a biological pathway can be isolated and used directly to study enzyme/pathway function. However, the primary route to most of the isoprenoid intermediates is through chemical catalysis. As such, this review provides the first exhaustive examination of synthetic routes to isoprenoid and isoprenoid precursors with particular emphasis on the syntheses of intermediates found as part of the 2C-methylerythritol 4-phosphate (MEP) pathway. In addition, representative syntheses are presented for the monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), triterpenes (C30) and tetraterpenes (C40). Finally, in some instances, the synthetic routes to substrate analogs found both within the MEP pathway and downstream isoprenoids are examined.
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29
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Affiliation(s)
| | - Salim Al-Babili
- BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Eleanore T. Wurtzel
- The Graduate School and University Center, The City University of New York, New York, New York, USA
- Department of Biological Sciences, Lehman College, The City University of New York, Bronx, New York, USA
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30
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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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31
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Yang L, Peng K, Zhao S, Zhao F, Chen L, Qiu F. 2-Methyl-l-erythritol glycosides from Gardenia jasminoides. Fitoterapia 2013; 89:126-30. [DOI: 10.1016/j.fitote.2013.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 05/22/2013] [Accepted: 05/23/2013] [Indexed: 11/27/2022]
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32
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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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33
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Carlsen S, Ajikumar PK, Formenti LR, Zhou K, Phon TH, Nielsen ML, Lantz AE, Kielland-Brandt MC, Stephanopoulos G. Heterologous expression and characterization of bacterial 2-C-methyl-D-erythritol-4-phosphate pathway in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2013; 97:5753-69. [PMID: 23636690 DOI: 10.1007/s00253-013-4877-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/21/2013] [Accepted: 03/22/2013] [Indexed: 10/26/2022]
Abstract
Transfer of a biosynthetic pathway between evolutionary distant organisms can create a metabolic shunt capable of bypassing the native regulation of the host organism, hereby improving the production of secondary metabolite precursor molecules for important natural products. Here, we report the engineering of Escherichia coli genes encoding the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway into the genome of Saccharomyces cerevisiae and the characterization of intermediate metabolites synthesized by the MEP pathway in yeast. Our UPLC-MS analysis of the MEP pathway metabolites from engineered yeast showed that the pathway is active until the synthesis of 2-C-methyl-D-erythritol-2,4-cyclodiphosphate, but appears to lack functionality of the last two steps of the MEP pathway, catalyzed by the [4Fe-4S] iron sulfur cluster proteins encoded by ispG and ispH. In order to functionalize the last two steps of the MEP pathway, we co-expressed the genes for the E. coli iron sulfur cluster (ISC) assembly machinery. By deleting ERG13, thereby incapacitating the mevalonate pathway, in conjunction with labeling experiments with U-¹³C₆ glucose and growth experiments, we found that the ISC assembly machinery was unable to functionalize ispG and ispH. However, we have found that leuC and leuD, encoding the heterodimeric iron-sulfur cluster protein, isopropylmalate isomerase, can complement the S. cerevisiae leu1 auxotrophy. To our knowledge, this is the first time a bacterial iron-sulfur cluster protein has been functionally expressed in the cytosol of S. cerevisiae under aerobic conditions and shows that S. cerevisiae has the capability to functionally express at least some bacterial iron-sulfur cluster proteins in its cytosol.
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Affiliation(s)
- Simon Carlsen
- Department of Systems Biology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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Bitok JK, Meyers CF. Synthesis and evaluation of stable substrate analogs as potential modulators of cyclodiphosphate synthase IspF. MEDCHEMCOMM 2013; 4:130-134. [PMID: 23509611 DOI: 10.1039/c2md20175e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Stable IspF substrate analogs were synthesized. In the presence of substrate analogs, the E. coli IspF-MEP complex shows activities distinct from IspF, and bisphosphonates (BP) behave differently than their diphosphate (DP) counterparts. Bisphosphonate analogs activate and/or stabilize IspF, and only the closest structural substrate analog weakly inhibits the IspF-MEP complex.
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Affiliation(s)
- J Kipchirchir Bitok
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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Partow S, Siewers V, Daviet L, Schalk M, Nielsen J. Reconstruction and evaluation of the synthetic bacterial MEP pathway in Saccharomyces cerevisiae. PLoS One 2012; 7:e52498. [PMID: 23285068 PMCID: PMC3532213 DOI: 10.1371/journal.pone.0052498] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 11/19/2012] [Indexed: 12/03/2022] Open
Abstract
Isoprenoids, which are a large group of natural and chemical compounds with a variety of applications as e.g. fragrances, pharmaceuticals and potential biofuels, are produced via two different metabolic pathways, the mevalonate (MVA) pathway and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Here, we attempted to replace the endogenous MVA pathway in Saccharomyces cerevisiae by a synthetic bacterial MEP pathway integrated into the genome to benefit from its superior properties in terms of energy consumption and productivity at defined growth conditions. It was shown that the growth of a MVA pathway deficient S. cerevisiae strain could not be restored by the heterologous MEP pathway even when accompanied by the co-expression of genes erpA, hISCA1 and CpIscA involved in the Fe-S trafficking routes leading to maturation of IspG and IspH and E. coli genes fldA and fpr encoding flavodoxin and flavodoxin reductase believed to be responsible for electron transfer to IspG and IspH.
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Affiliation(s)
- Siavash Partow
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Verena Siewers
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Laurent Daviet
- Firmenich SA, Corporate R&D Division, Geneva, Switzerland
| | - Michel Schalk
- Firmenich SA, Corporate R&D Division, Geneva, Switzerland
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- * E-mail:
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Bitok JK, Meyers CF. 2C-Methyl-d-erythritol 4-phosphate enhances and sustains cyclodiphosphate synthase IspF activity. ACS Chem Biol 2012; 7:1702-10. [PMID: 22839733 DOI: 10.1021/cb300243w] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
There is significant progress toward understanding catalysis throughout the essential MEP pathway to isoprenoids in human pathogens; however, little is known about pathway regulation. The present study begins by testing the hypothesis that isoprenoid biosynthesis is regulated via feedback inhibition of the fifth enzyme cyclodiphosphate synthase IspF by downstream isoprenoid diphosphates. Here, we demonstrate recombinant E. coli IspF is not inhibited by downstream metabolites isopentenyl diphosphate (IDP), dimethylallyl diphosphate (DMADP), geranyl diphosphate (GDP), and farnesyl diphosphate (FDP) under standard assay conditions. However, 2C-methyl-d-erythritol 4-phosphate (MEP), the product of reductoisomerase IspC and first committed MEP pathway intermediate, activates and sustains this enhanced IspF activity, and the IspF-MEP complex is inhibited by FDP. We further show that the methylerythritol scaffold itself, which is unique to this pathway, drives the activation and stabilization of active IspF. Our results suggest a novel feed-forward regulatory mechanism for 2C-methyl-d-erythritol 2,4-cyclodiphosphate (MEcDP) production and support an isoprenoid biosynthesis regulatory mechanism via feedback inhibition of the IspF-MEP complex by FDP. The results have important implications for development of inhibitors against the IspF-MEP complex, which may be the physiologically relevant form of the enzyme.
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Affiliation(s)
- J. Kipchirchir Bitok
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore,
Maryland 21205, United States
| | - Caren Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore,
Maryland 21205, United States
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Lu XM, Hu XJ, Zhao YZ, Song WB, Zhang M, Chen ZL, Chen W, Dong YB, Wang ZH, Lai JS. Map-based cloning of zb7 encoding an IPP and DMAPP synthase in the MEP pathway of maize. MOLECULAR PLANT 2012; 5:1100-12. [PMID: 22498772 DOI: 10.1093/mp/sss038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
IspH is a key enzyme in the last step of the methyl-D-erythritol-4-phosphate (MEP) pathway. Loss of function of IspH can often result in complete yellow or albino phenotype in many plants. Here, we report the characterization of a recessive mutant of maize, zebra7 (zb7), showing transverse green/yellow striped leaves in young plants. The yellow bands of the mutant have decreased levels of chlorophylls and carotenoids with delayed chloroplast development. Low temperature suppressed mutant phenotype, while alternate light/dark cycle or high temperature enlarged the yellow section. Map-based cloning demonstrated that zb7 encodes the IspH protein with a mis-sense mutation in a conserved region. Transgenic silencing of Zb7 in maize resulted in complete albino plantlets that are aborted in a few weeks, confirming that Zb7 is important in the early stages of maize chloroplast development. Zb7 is constitutively expressed and its expression subject to a 16-h light/8-h dark cycle regulation. Our results suggest that the less effective or unstable IspH in zb7 mutant, together with its diurnal expression, are mechanistically accounted for the zebra phenotype. The increased IspH mRNA in the leaves of zb7 at the late development stage may explain the restoration of mutant phenotype in mature stages.
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Affiliation(s)
- Xiao-Min Lu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
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A whole-cell phenotypic screening platform for identifying methylerythritol phosphate pathway-selective inhibitors as novel antibacterial agents. Antimicrob Agents Chemother 2012; 56:4906-13. [PMID: 22777049 DOI: 10.1128/aac.00987-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Isoprenoid biosynthesis is essential for survival of all living organisms. More than 50,000 unique isoprenoids occur naturally, with each constructed from two simple five-carbon precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Two pathways for the biosynthesis of IPP and DMAPP are found in nature. Humans exclusively use the mevalonate (MVA) pathway, while most bacteria, including all Gram-negative and many Gram-positive species, use the unrelated methylerythritol phosphate (MEP) pathway. Here we report the development of a novel, whole-cell phenotypic screening platform to identify compounds that selectively inhibit the MEP pathway. Strains of Salmonella enterica serovar Typhimurium were engineered to have separately inducible MEP (native) and MVA (nonnative) pathways. These strains, RMC26 and CT31-7d, were then used to differentiate MVA pathway- and MEP pathway-specific perturbation. Compounds that inhibit MEP pathway-dependent bacterial growth but leave MVA-dependent growth unaffected represent MEP pathway-selective antibacterials. This screening platform offers three significant results. First, the compound is antibacterial and is therefore cell permeant, enabling access to the intracellular target. Second, the compound inhibits one or more MEP pathway enzymes. Third, the MVA pathway is unaffected, suggesting selectivity for targeting the bacterial versus host pathway. The cell lines also display increased sensitivity to two reported MEP pathway-specific inhibitors, further biasing the platform toward inhibitors selective for the MEP pathway. We demonstrate development of a robust, high-throughput screening platform that combines phenotypic and target-based screening that can identify MEP pathway-selective antibacterials simply by monitoring optical density as the readout for cell growth/inhibition.
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Heuston S, Begley M, Gahan CGM, Hill C. Isoprenoid biosynthesis in bacterial pathogens. Microbiology (Reading) 2012; 158:1389-1401. [DOI: 10.1099/mic.0.051599-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sinéad Heuston
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Máire Begley
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Cormac G. M. Gahan
- School of Pharmacy, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Department of Microbiology, University College Cork, Cork, Ireland
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Li H, Dai SB, Gao WY. Preparation of Isotope Labeled/Unlabeled Key Intermediates in 2-Methyl-D-erythritol 4-Phosphate Terpenoid Biosynthetic Pathway. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201100396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kuzuyama T, Seto H. Two distinct pathways for essential metabolic precursors for isoprenoid biosynthesis. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2012; 88:41-52. [PMID: 22450534 PMCID: PMC3365244 DOI: 10.2183/pjab.88.41] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Isoprenoids are a diverse group of molecules found in all organisms, where they perform such important biological functions as hormone signaling (e.g., steroids) in mammals, antioxidation (e.g., carotenoids) in plants, electron transport (e.g., ubiquinone), and cell wall biosynthesis intermediates in bacteria. All isoprenoids are synthesized by the consecutive condensation of the five-carbon monomer isopentenyl diphosphate (IPP) to its isomer, dimethylallyl diphosphate (DMAPP). The biosynthetic pathway for the formation of IPP from acetyl-CoA (i.e., the mevalonate pathway) had been established mainly in mice and the budding yeast Saccharomyces cerevisiae. Curiously, most prokaryotic microorganisms lack homologs of the genes in the mevalonate pathway, even though IPP and DMAPP are essential for isoprenoid biosynthesis in bacteria. This observation provided an impetus to search for an alternative pathway to synthesize IPP and DMAPP, ultimately leading to the discovery of the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate pathway. This review article focuses on our significant contributions to a comprehensive understanding of the biosynthesis of IPP and DMAPP.
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Affiliation(s)
- Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.
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Gräwert T, Groll M, Rohdich F, Bacher A, Eisenreich W. Biochemistry of the non-mevalonate isoprenoid pathway. Cell Mol Life Sci 2011; 68:3797-814. [PMID: 21744068 PMCID: PMC11114746 DOI: 10.1007/s00018-011-0753-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/26/2011] [Accepted: 06/14/2011] [Indexed: 02/08/2023]
Abstract
The non-mevalonate pathway of isoprenoid (terpenoid) biosynthesis is essential in many eubacteria including the major human pathogen, Mycobacterium tuberculosis, in apicomplexan protozoa including the Plasmodium spp. causing malaria, and in the plastids of plants. The metabolic route is absent in humans and is therefore qualified as a promising target for new anti-infective drugs and herbicides. Biochemical and structural knowledge about all enzymes involved in the pathway established the basis for discovery and development of inhibitors by high-throughput screening of compound libraries and/or structure-based rational design.
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Affiliation(s)
- Tobias Gräwert
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Michael Groll
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | | | - Adelbert Bacher
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Wolfgang Eisenreich
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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de Ruyck J, Wouters J, Poulter CD. Inhibition Studies on Enzymes Involved in Isoprenoid Biosynthesis: Focus on Two Potential Drug Targets: DXR and IDI-2 Enzymes. ACTA ACUST UNITED AC 2011; 7. [PMID: 24339799 DOI: 10.2174/157340811796575317] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isoprenoid compounds constitute an immensely diverse group of acyclic, monocyclic and polycyclic compounds that play important roles in all living organisms. Despite the diversity of their structures, this plethora of natural products arises from only two 5-carbon precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This review will discuss the enzymes in the mevalonate (MVA) and methylerythritol phosphate (MEP) biosynthetic pathways leading to IPP and DMAPP with a particular focus on MEP synthase (DXR) and IPP isomerase (IDI), which are potential targets for the development of antibiotic compounds. DXR is the second enzyme in the MEP pathway and the only one for which inhibitors with antimicrobial activity at pharmaceutically relevant concentrations are known. All of the published DXR inhibitors are fosmidomycin analogues, except for a few bisphosphonates with moderate inhibitory activity. These far, there are no other candidates that target DXR. IDI was first identified and characterised over 40 years ago (IDI-1) and a second convergently evolved isoform (IDI-2) was discovered in 2001. IDI-1 is a metalloprotein found in Eukarya and many species of Bacteria. Its mechanism has been extensively studied. In contrast, IDI-2 requires reduced flavin mononucleotide as a cofactor. The mechanism of action for IDI-2 is less well defined. This review will describe how lead inhibitors are being improved by structure-based drug design and enzymatic assays against DXR to lead to new drug families and how mechanistic probes are being used to address questions about the mechanisms of the isomerases.
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Affiliation(s)
- Jérôme de Ruyck
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112, USA
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Tsang A, Seidle H, Jawaid S, Zhou W, Smith C, Couch RD. Francisella tularensis 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: kinetic characterization and phosphoregulation. PLoS One 2011; 6:e20884. [PMID: 21694781 PMCID: PMC3111433 DOI: 10.1371/journal.pone.0020884] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/11/2011] [Indexed: 11/29/2022] Open
Abstract
Deliberate and natural outbreaks of infectious disease, the prevalence of antibiotic resistant strains, and the ease by which antibiotic resistant bacteria can be intentionally engineered all underscore the necessity of effective vaccines and continued development of novel antimicrobial/antiviral therapeutics. Isoprenes, a group of molecules fundamentally involved in a variety of crucial biological functions, are derived from either the mevalonic acid (MVA) or methylerythritol phosphate (MEP) pathway. While mammals utilize the MVA pathway, many bacteria utilize the MEP pathway, highlighting the latter as an attractive target for antibiotic development. In this report we describe the cloning and characterization of Francisella tularensis MEP cytidylyltransferase, a MEP pathway enzyme and potential target for antibiotic development. Size exclusion chromatography indicates the protein exists as a dimer in solution. Enzyme assays produced an apparentK(MEP)(M) = 178 μM, K(CTP)(M) = 73 μM , k(MEP)(cat) = 1(s-1), k(CTP)(cat) = 0.8( s-1), and a k(MEP)(cat)/ K(MEP)(M) = 3.4 x 10(5) M(-1) min(-1). The enzyme exhibits a strict preference for Mg(+2) as a divalent cation and CTP as the nucleotide. Titanium dioxide chromatography-tandem mass spectrometry identified Thr141 as a site of phosphorylation. T141D and T141E site-directed mutants are catalytically inactive, suggesting a mechanism for post-translational control of metabolic flux through the F. tularensis MEP pathway. Overall, our study suggests that MEP cytidylyltransferase is an excellent target for the development of novel antibiotics against F. tularensis.
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Affiliation(s)
- Arthur Tsang
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
| | - Heather Seidle
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
| | - Safdar Jawaid
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
| | - Weidong Zhou
- Department of Molecular and Microbiology, George Mason University, Manassas, Virginia, United States of America
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, United States of America
| | - Clint Smith
- Geospatial Research and Engineering Division, U.S. Army Engineer Research and Development Center, Alexandria, Virginia, United States of America
| | - Robin D. Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
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Kaji I, Karaki SI, Kuwahara A. Effects of luminal thymol on epithelial transport in human and rat colon. Am J Physiol Gastrointest Liver Physiol 2011; 300:G1132-43. [PMID: 21372164 DOI: 10.1152/ajpgi.00503.2010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Gut lumen is continually exposed to a great variety of agents, including noxious compounds. Chemical receptors that detect the luminal environment are thought to play an important role as sensors and to modulate gastrointestinal functions. Recently, it has been reported that odorant receptors (ORs) are expressed in the small intestinal mucosa and that odorants stimulate serotonin secretion. However, ion transport in the responses to odorants has rarely been discussed, particularly in relation to the large intestine. In the present study, we examined the effects of the OR ligand thymol on ion transport in human and rat colonic epithelia using an Ussing chamber. In the mucosal-submucosal preparations, the mucosal addition of thymol evoked anion secretion concentration dependently. In addition, dextran (4 kDa) permeability was enhanced by the mucosal treatment with thymol. The response to thymol was not affected by tetrodotoxin (TTX) or piroxicam treatments in human or rat colon. Thymol-evoked electrogenic anion secretion was abolished under Ca(2+)-free conditions or mucosal treatment with transient receptor potential (TRP) A1 blocker (HC-030031). Pretreatment of thymol did not affect electrical field stimulation-evoked anion secretion but significantly attenuated short-chain fatty acid-evoked secretion in a concentration-dependent manner. OR1G1 and TRPA1 expression was investigated in isolated colonic mucosa by RT-PCR. The present results provide evidence that the OR ligand thymol modulates epithelial permeability and electrogenic anion secretion in human and rat colon. The anion secretion by luminal thymol is most likely mediated by direct activation of TRPA1 channel. We suggest that the sensing and responding to odorants in the colon also plays a role in maintaining intestinal homeostasis.
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Affiliation(s)
- Izumi Kaji
- Laboratory of Physiology, Graduate School of Nutritional and Environmental Sciences, Institute of Environmental Sciences, University of Shizuoka, Japan
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Dairi T, Kuzuyama T, Nishiyama M, Fujii I. Convergent strategies in biosynthesis. Nat Prod Rep 2011; 28:1054-86. [PMID: 21547300 DOI: 10.1039/c0np00047g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This review article focuses on how nature sometimes solves the same problem in the biosynthesis of small molecules but using very different approaches. Four examples, involving isopentenyl diphosphate, menaquinone, lysine, and aromatic polyketides, are highlighted that represent different strategies in convergent metabolism.
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Affiliation(s)
- Tohru Dairi
- Faculty of Engineering and Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
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Tholl D, Lee S. Terpene Specialized Metabolism in Arabidopsis thaliana. THE ARABIDOPSIS BOOK 2011; 9:e0143. [PMID: 22303268 PMCID: PMC3268506 DOI: 10.1199/tab.0143] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Terpenes constitute the largest class of plant secondary (or specialized) metabolites, which are compounds of ecological function in plant defense or the attraction of beneficial organisms. Using biochemical and genetic approaches, nearly all Arabidopsis thaliana (Arabidopsis) enzymes of the core biosynthetic pathways producing the 5-carbon building blocks of terpenes have been characterized and closer insight has been gained into the transcriptional and posttranscriptional/translational mechanisms regulating these pathways. The biochemical function of most prenyltransferases, the downstream enzymes that condense the C(5)-precursors into central 10-, 15-, and 20-carbon prenyldiphosphate intermediates, has been described, although the function of several isoforms of C(20)-prenyltranferases is not well understood. Prenyl diphosphates are converted to a variety of C(10)-, C(15)-, and C(20)-terpene products by enzymes of the terpene synthase (TPS) family. Genomic organization of the 32 Arabidopsis TPS genes indicates a species-specific divergence of terpene synthases with tissue- and cell-type specific expression profiles that may have emerged under selection pressures by different organisms. Pseudogenization, differential expression, and subcellular segregation of TPS genes and enzymes contribute to the natural variation of terpene biosynthesis among Arabidopsis accessions (ecotypes) and species. Arabidopsis will remain an important model to investigate the metabolic organization and molecular regulatory networks of terpene specialized metabolism in relation to the biological activities of terpenes.
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Affiliation(s)
- Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Sungbeom Lee
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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Tholl D, Lee S. Terpene Specialized Metabolism in Arabidopsis thaliana. THE ARABIDOPSIS BOOK 2011; 9:e0143. [PMID: 22303268 DOI: 10.1043/tab.0143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Terpenes constitute the largest class of plant secondary (or specialized) metabolites, which are compounds of ecological function in plant defense or the attraction of beneficial organisms. Using biochemical and genetic approaches, nearly all Arabidopsis thaliana (Arabidopsis) enzymes of the core biosynthetic pathways producing the 5-carbon building blocks of terpenes have been characterized and closer insight has been gained into the transcriptional and posttranscriptional/translational mechanisms regulating these pathways. The biochemical function of most prenyltransferases, the downstream enzymes that condense the C(5)-precursors into central 10-, 15-, and 20-carbon prenyldiphosphate intermediates, has been described, although the function of several isoforms of C(20)-prenyltranferases is not well understood. Prenyl diphosphates are converted to a variety of C(10)-, C(15)-, and C(20)-terpene products by enzymes of the terpene synthase (TPS) family. Genomic organization of the 32 Arabidopsis TPS genes indicates a species-specific divergence of terpene synthases with tissue- and cell-type specific expression profiles that may have emerged under selection pressures by different organisms. Pseudogenization, differential expression, and subcellular segregation of TPS genes and enzymes contribute to the natural variation of terpene biosynthesis among Arabidopsis accessions (ecotypes) and species. Arabidopsis will remain an important model to investigate the metabolic organization and molecular regulatory networks of terpene specialized metabolism in relation to the biological activities of terpenes.
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Affiliation(s)
- Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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Lee M, Gräwert T, Quitterer F, Rohdich F, Eppinger J, Eisenreich W, Bacher A, Groll M. Biosynthesis of isoprenoids: crystal structure of the [4Fe-4S] cluster protein IspG. J Mol Biol 2010; 404:600-10. [PMID: 20932974 DOI: 10.1016/j.jmb.2010.09.050] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Revised: 09/17/2010] [Accepted: 09/21/2010] [Indexed: 11/24/2022]
Abstract
IspG protein serves as the penultimate enzyme of the recently discovered non-mevalonate pathway for the biosynthesis of the universal isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. The enzyme catalyzes the reductive ring opening of 2C-methyl-D-erythritol 2,4-cyclodiphosphate, which affords 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. The protein was crystallized under anaerobic conditions, and its three-dimensional structure was determined to a resolution of 2.7 Å. Each subunit of the c(2) symmetric homodimer folds into two domains connected by a short linker sequence. The N-terminal domain (N domain) is an eight-stranded β barrel that belongs to the large TIM-barrel superfamily. The C-terminal domain (C domain) consists of a β sheet that is flanked on both sides by helices. One glutamate and three cysteine residues of the C domain coordinate a [4Fe-4S] cluster. Homodimer formation involves an extended contact area (about 1100 Å(2)) between helices 8 and 9 of each respective β barrel. Moreover, each C domain contacts the N domain of the partner subunit, but the interface regions are small (about 430 Å(2)). We propose that the enzyme substrate binds to the positively charged surface area at the C-terminal pole of the β barrel. The C domain carrying the iron-sulfur cluster could then move over to form a closed conformation where the substrate is sandwiched between the N domain and the C domain. This article completes the set of three-dimensional structures of the non-mevalonate pathway enzymes, which are of specific interest as potential targets for tuberculostatic and antimalarial drugs.
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Affiliation(s)
- Matthias Lee
- Lehrstuhl für Biochemie, Center for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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