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Maheshwari S, Kim YS, Aripirala S, Murphy M, Amzel LM, Gabelli SB. Identifying Structural Determinants of Product Specificity in Leishmania major Farnesyl Diphosphate Synthase. Biochemistry 2020; 59:2751-2759. [PMID: 32584028 PMCID: PMC8049779 DOI: 10.1021/acs.biochem.0c00432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Farnesyl diphosphate synthase (FPPS) is an isoprenoid chain elongation enzyme that catalyzes the sequential condensation of dimethylallyl diphosphate (C5) with isopentenyl diphosphate (IPP; C5) and the resulting geranyl diphosphate (GPP; C10) with another molecule of IPP, eventually producing farnesyl diphosphate (FPP; C15), which is a precursor for the biosynthesis of a vast majority of isoprenoids. Previous studies of FPPS have highlighted the importance of the structure around the hydrophobic chain elongation path in determining product specificity. To investigate what structural features define the final chain length of the product in FPPS from Leishmania major, we designed and expressed six mutants of LmFPPS by replacing small amino acids around the binding pocket with bulky residues. Using enzymatic assays, binding kinetics, and crystallographic studies, we analyzed the effects of these mutations on the activity and product specificity of FPPS. Our results revealed that replacement of Thr-164 with tryptophan and phenylalanine completely abolished the activity of FPPS. Intriguingly, the T164Y substitution displayed dual product specificity and produced a mixture GPP and FPP as final products, with an activity for FPP synthesis that was lower than that of the wild-type enzyme. These data indicate that Thr-164 is a potential regulator of product specificity.
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Affiliation(s)
- Sweta Maheshwari
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yu Seon Kim
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Srinivas Aripirala
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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2
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Nagel R, Thomas JA, Adekunle FA, Mann FM, Peters RJ. Arginine in the FARM and SARM: A Role in Chain-Length Determination for Arginine in the Aspartate-Rich Motifs of Isoprenyl Diphosphate Synthases from Mycobacterium tuberculosis. Molecules 2018; 23:molecules23102546. [PMID: 30301210 PMCID: PMC6214179 DOI: 10.3390/molecules23102546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/02/2018] [Accepted: 10/05/2018] [Indexed: 01/20/2023] Open
Abstract
Isoprenyl chains are found in many important metabolites. These are derived from precursors of the appropriate length produced by isoprenyl diphosphate synthases (IDSs). The human pathogen Mycobacterium tuberculosis makes various isoprenoids/terpenoids, with important roles in their biosynthesis played by two closely related IDSs, encoded by grcC1 (Rv0562) and grcC2 (Rv0989c), with Rv0989c generating the 10-carbon precursor (E)-geranyl diphosphate (GPP), and Rv0562 the 20-carbon precursor (E,E,E)-geranylgeranyl diphosphate (GGPP). Intriguingly, while Rv0562 contains the prototypical trans-IDS first and second aspartate-rich (DDxxD) motifs (FARM and SARM, respectively), Rv0989c uniquely contains arginine in place of the second Asp in the FARM and first Asp in the SARM. Here site-directed mutagenesis of the corresponding residues in both Rv0562 and Rv0989c reveals that these play a role in determination of product chain length. Specifically, substitution of Asp for the Arg in the FARM and SARM of Rv0989c leads to increased production of the longer 15-carbon farnesyl diphosphate (FPP), while substitution of Arg for the corresponding Asp in Rv0562 leads to increased release of shorter products, both FPP and GPP. Accordingly, while the primary role of the FARM and SARM is known to be chelation of the divalent magnesium ion co-factors that assist substrate binding and catalysis, the Arg substitutions found in Rv0989c seem to provide a novel means by which product chain length is moderated, at least in these M. tuberculosis IDSs.
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Affiliation(s)
- Raimund Nagel
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Jill A Thomas
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Faith A Adekunle
- Department of Chemistry, University of Wisconsin-Parkside, Kenosha, WI 53141, USA.
| | - Francis M Mann
- Department of Chemistry, University of Wisconsin-Parkside, Kenosha, WI 53141, USA.
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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3
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Picard MÈ, Nisole A, Béliveau C, Sen S, Barbar A, Shi R, Cusson M. Structural characterization of a lepidopteran type-II farnesyl diphosphate synthase from the spruce budworm, Choristoneura fumiferana: Implications for inhibitor design. Insect Biochem Mol Biol 2018; 92:84-92. [PMID: 29183817 DOI: 10.1016/j.ibmb.2017.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
Farnesyl diphosphate synthase (FPPS) is an enzyme from the class of short chain (E)-prenyltransferases that catalyzes the condensation of two molecules of isopentenyl diphosphate (IPP, C5) with dimethylallyl diphosphate (DMAPP, C5) to generate the C15 product FPP. In insects, FPPS plays a key role in the biosynthesis of the morphogenetic and gonadotropic "juvenile hormone" (JH). Lepidopteran genomes encode two very distinct FPPS paralogs, one of which ("type-II") is expressed almost exclusively in the JH-producing glands, the corpora allata. This paralog has been hypothesized to display structural features that enable the binding of the bulkier precursors required for the biosynthesis of lepidopteran ethyl-branched JHs. Here, we report on the first crystal structures of an insect FPPS solved to date. Apo, ligand-bound, and inhibitor-bound structures of type-II FPPS (FPPS2) from the spruce budworm, Choristoneura fumiferana (Order: Lepidoptera), were obtained. Comparison of apo and inhibitor-bound enzymes revealed differences in both inhibitor binding and structural plasticity of CfFPPS2 compared to other FPPSs. Our data showed that IPP is not essential to the closure of the C-terminal tail. Ortho-substituted pyridinium bisphosphonates, previously shown to inhibit CfFPPS2, bound to the allylic site, as predicted; however, their alkyl groups were oriented towards the homoallylic binding site, with the bulkier propyl-substituted inhibitor penetrating deeply into the IPP binding pocket. The current study sheds light on the structural basis of substrate specificity of type-II FPPS of the spruce budworm. Through a comparison with other inhibitor-bound FPPSs, we propose several approaches to improve inhibitor selectivity and potency.
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Affiliation(s)
- Marie-Ève Picard
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada.
| | - Audrey Nisole
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
| | - Catherine Béliveau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
| | - Stephanie Sen
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ, 08628, USA.
| | - Aline Barbar
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
| | - Rong Shi
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada.
| | - Michel Cusson
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
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Park J, Rodionov D, De Schutter JW, Lin YS, Tsantrizos YS, Berghuis AM. Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase. PLoS One 2017; 12:e0186447. [PMID: 29036218 PMCID: PMC5643135 DOI: 10.1371/journal.pone.0186447] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/02/2017] [Indexed: 11/18/2022] Open
Abstract
Human farnesyl pyrophosphate synthase (hFPPS) catalyzes the production of the 15-carbon isoprenoid farnesyl pyrophosphate. The enzyme is a key regulator of the mevalonate pathway and a well-established drug target. Notably, it was elucidated as the molecular target of nitrogen-containing bisphosphonates, a class of drugs that have been widely successful against bone resorption disorders. More recently, research has focused on the anticancer effects of these inhibitors. In order to achieve increased non-skeletal tissue exposure, we created phenylaminopyridine bisphosphonates (PNP-BPs) that have bulky hydrophobic side chains through a structure-based approach. Some of these compounds have proven to be more potent than the current clinical drugs in a number of antiproliferation assays using multiple myeloma cell lines. In the present work, we characterized the binding of our most potent PNP-BPs to the target enzyme, hFPPS. Co-crystal structures demonstrate that the molecular interactions designed to elicit tighter binding are indeed established. We carried out thermodynamic studies as well; the newly introduced protein-ligand interactions are clearly reflected in the enthalpy of binding measured, which is more favorable for the new PNP-BPs than for the lead compound. These studies also indicate that the affinity of the PNP-BPs to hFPPS is comparable to that of the current drug risedronate. Risedronate forms additional polar interactions via its hydroxyl functional group and thus exhibits more favorable binding enthalpy; however, the entropy of binding is more favorable for the PNP-BPs, owing to the greater desolvation effects resulting from their large hydrophobic side chains. These results therefore confirm the overall validity of our drug design strategy. With a distinctly different molecular scaffold, the PNP-BPs described in this report represent an interesting new group of future drug candidates. Further investigation should follow to characterize the tissue distribution profile and assess the potential clinical benefits of these compounds.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Dmitry Rodionov
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | | | - Yih-Shyan Lin
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Youla S. Tsantrizos
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Albert M. Berghuis
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- * E-mail:
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5
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Zhu J, Khalil SM, Mitchell RD, Bissinger BW, Egekwu N, Sonenshine DE, Roe RM. Mevalonate-Farnesal Biosynthesis in Ticks: Comparative Synganglion Transcriptomics and a New Perspective. PLoS One 2016; 11:e0141084. [PMID: 26959814 PMCID: PMC4785029 DOI: 10.1371/journal.pone.0141084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/03/2015] [Indexed: 11/19/2022] Open
Abstract
Juvenile hormone (JH) controls the growth, development, metamorphosis, and reproduction of insects. For many years, the general assumption has been that JH regulates tick and other acarine development and reproduction the same as in insects. Although researchers have not been able to find the common insect JHs in hard and soft tick species and JH applications appear to have no effect on tick development, it is difficult to prove the negative or to determine whether precursors to JH are made in ticks. The tick synganglion contains regions which are homologous to the corpora allata, the biosynthetic source for JH in insects. Next-gen sequencing of the tick synganglion transcriptome was conducted separately in adults of the American dog tick, Dermacentor variabilis, the deer tick, Ixodes scapularis, and the relapsing fever tick, Ornithodoros turicata as a new approach to determine whether ticks can make JH or a JH precursor. All of the enzymes that make up the mevalonate pathway from acetyl-CoA to farnesyl diphosphate (acetoacetyl-CoA thiolase, HMG-S, HMG-R, mevalonate kinase, phosphomevalonate kinase, diphosphomevalonate decarboxylase, and farnesyl diphosphate synthase) were found in at least one of the ticks studied but most were found in all three species. Sequence analysis of the last enzyme in the mevalonate pathway, farnesyl diphosphate synthase, demonstrated conservation of the seven prenyltransferase regions and the aspartate rich motifs within those regions typical of this enzyme. In the JH branch from farnesyl diphosphate to JH III, we found a putative farnesol oxidase used for the conversion of farnesol to farnesal in the synganglion transcriptome of I. scapularis and D. variabilis. Methyltransferases (MTs) that add a methyl group to farnesoic acid to make methyl farnesoate were present in all of the ticks studied with similarities as high as 36% at the amino acid level to insect JH acid methyltransferase (JHAMT). However, when the tick MTs were compared to the known insect JHAMTs from several insect species at the amino acid level, the former lacked the farnesoic acid binding motif typical in insects. The P450s shown in insects to add the C10,11 epoxide to methyl farnesoate, are in the CYP15 family; this family was absent in our tick transcriptomes and in the I. scapularis genome, the only tick genome available. These data suggest that ticks do not synthesize JH III but have the mevalonate pathway and may produce a JH III precursor.
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Affiliation(s)
- Jiwei Zhu
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Sayed M. Khalil
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Robert D. Mitchell
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Brooke W. Bissinger
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Noble Egekwu
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, 23529, United States of America
| | - Daniel E. Sonenshine
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, 23529, United States of America
| | - R. Michael Roe
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
- * E-mail:
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Tsoumpra MK, Muniz JR, Barnett BL, Kwaasi AA, Pilka ES, Kavanagh KL, Evdokimov A, Walter RL, Von Delft F, Ebetino FH, Oppermann U, Russell RGG, Dunford JE. The inhibition of human farnesyl pyrophosphate synthase by nitrogen-containing bisphosphonates. Elucidating the role of active site threonine 201 and tyrosine 204 residues using enzyme mutants. Bone 2015; 81:478-486. [PMID: 26318908 PMCID: PMC4652608 DOI: 10.1016/j.bone.2015.08.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/19/2015] [Accepted: 08/23/2015] [Indexed: 11/22/2022]
Abstract
Farnesyl pyrophosphate synthase (FPPS) is the major molecular target of nitrogen-containing bisphosphonates (N-BPs), used clinically as bone resorption inhibitors. We investigated the role of threonine 201 (Thr201) and tyrosine 204 (Tyr204) residues in substrate binding, catalysis and inhibition by N-BPs, employing kinetic and crystallographic studies of mutated FPPS proteins. Mutants of Thr201 illustrated the importance of the methyl group in aiding the formation of the Isopentenyl pyrophosphate (IPP) binding site, while Tyr204 mutations revealed the unknown role of this residue in both catalysis and IPP binding. The interaction between Thr201 and the side chain nitrogen of N-BP was shown to be important for tight binding inhibition by zoledronate (ZOL) and risedronate (RIS), although RIS was also still capable of interacting with the main-chain carbonyl of Lys200. The interaction of RIS with the phenyl ring of Tyr204 proved essential for the maintenance of the isomerized enzyme-inhibitor complex. Studies with conformationally restricted analogues of RIS reaffirmed the importance of Thr201 in the formation of hydrogen bonds with N-BPs. In conclusion we have identified new features of FPPS inhibition by N-BPs and revealed unknown roles of the active site residues in catalysis and substrate binding.
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Affiliation(s)
- Maria K Tsoumpra
- Botnar Research Centre, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, UK; Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Joao R Muniz
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Bobby L Barnett
- Chemistry Department, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Aaron A Kwaasi
- Botnar Research Centre, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, UK
| | - Ewa S Pilka
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Kathryn L Kavanagh
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | | | | | - Frank Von Delft
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Frank H Ebetino
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
| | - Udo Oppermann
- Botnar Research Centre, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, UK; Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - R Graham G Russell
- Botnar Research Centre, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, UK; Mellanby Centre for Bone Research, University of Sheffield Medical School, Sheffield S10 2RX, UK
| | - James E Dunford
- Botnar Research Centre, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7LD, UK; Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.
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Nagel R, Bernholz C, Vranová E, Košuth J, Bergau N, Ludwig S, Wessjohann L, Gershenzon J, Tissier A, Schmidt A. Arabidopsis thaliana isoprenyl diphosphate synthases produce the C25 intermediate geranylfarnesyl diphosphate. Plant J 2015; 84:847-59. [PMID: 26505977 DOI: 10.1111/tpj.13064] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/11/2015] [Accepted: 10/21/2015] [Indexed: 05/22/2023]
Abstract
Isoprenyl diphosphate synthases (IDSs) catalyze some of the most basic steps in terpene biosynthesis by producing the prenyl diphosphate precursors of each of the various terpenoid classes. Most plants investigated have distinct enzymes that produce the short-chain all-trans (E) prenyl diphosphates geranyl diphosphate (GDP, C10 ), farnesyl diphosphate (FDP, C15 ) or geranylgeranyl diphosphate (GGDP, C20 ). In the genome of Arabidopsis thaliana, 15 trans-product-forming IDSs are present. Ten of these have recently been shown to produce GGDP by genetic complementation of a carotenoid pathway engineered into Escherichia coli. When verifying the product pattern of IDSs producing GGDP by a new LC-MS/MS procedure, we found that five of these IDSs produce geranylfarnesyl diphosphate (GFDP, C25 ) instead of GGDP as their major product in enzyme assays performed in vitro. Over-expression of one of the GFDP synthases in A. thaliana confirmed the production of GFDP in vivo. Enzyme assays with A. thaliana protein extracts from roots but not other organs showed formation of GFDP. Furthermore, GFDP itself was detected in root extracts. Subcellular localization studies in leaves indicated that four of the GFDP synthases were targeted to the plastoglobules of the chloroplast and one was targeted to the mitochondria. Sequence comparison and mutational studies showed that the size of the R group of the 5th amino acid residue N-terminal to the first aspartate-rich motif is responsible for C25 versus C20 product formation, with smaller R groups (Ala and Ser) resulting in GGDP (C20 ) as a product and a larger R group (Met) resulting in GFDP (C25 ).
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Affiliation(s)
- Raimund Nagel
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans Knoell Straße 8, D-07745 Jena, Germany
| | - Carolin Bernholz
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Eva Vranová
- Institute of Biology and Ecology, Pavol Jozef Šafárik University Košice, Mánesova 23, 04154 Košice, Slovakia
| | - Ján Košuth
- Institute of Biology and Ecology, Pavol Jozef Šafárik University Košice, Mánesova 23, 04154 Košice, Slovakia
| | - Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Steve Ludwig
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Ludger Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans Knoell Straße 8, D-07745 Jena, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Axel Schmidt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans Knoell Straße 8, D-07745 Jena, Germany
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8
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Guo D, Li HL, Peng SQ. Structure Conservation and Differential Expression of Farnesyl Diphosphate Synthase Genes in Euphorbiaceous Plants. Int J Mol Sci 2015; 16:22402-14. [PMID: 26389894 PMCID: PMC4613314 DOI: 10.3390/ijms160922402] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/01/2015] [Accepted: 09/06/2015] [Indexed: 02/06/2023] Open
Abstract
Farnesyl diphosphate synthase (FPS) is a key enzyme of isoprenoids biosynthesis. However, knowledge of the FPSs of euphorbiaceous species is limited. In this study, ten FPSs were identified in four euphorbiaceous plants. These FPSs exhibited similar exon/intron structure. The deduced FPS proteins showed close identities and exhibited the typical structure of plant FPS. The members of the FPS family exhibit tissue expression patterns that vary among several euphorbiaceous plant species under normal growth conditions. The expression profiles reveal spatial and temporal variations in the expression of FPSs of different tissues from Euphorbiaceous plants. Our results revealed wide conservation of FPSs and diverse expression in euphorbiaceous plants during growth and development.
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Affiliation(s)
- Dong Guo
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Hui-Liang Li
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Shi-Qing Peng
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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9
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Zhao YJ, Chen X, Zhang M, Su P, Liu YJ, Tong YR, Wang XJ, Huang LQ, Gao W. Molecular Cloning and Characterisation of Farnesyl Pyrophosphate Synthase from Tripterygium wilfordii. PLoS One 2015; 10:e0125415. [PMID: 25938487 PMCID: PMC4418688 DOI: 10.1371/journal.pone.0125415] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/23/2015] [Indexed: 11/23/2022] Open
Abstract
Farnesylpyrophosphate synthase (FPS) catalyzes the biosynthesis of farnesyl pyrophosphate (FPP), which is an important precursor of sesquiterpenoids such as artemisinin and wilfordine. In the present study, we report the molecular cloning and characterization of two full-length cDNAs encoding FPSs from Tripterygium wilfordii (TwFPSs). TwFPSs maintained their capability to synthesise FPP in vitro when purified as recombinant proteins from E. coli. Consistent with the endogenous role of FPS in FPP biosynthesis, TwFPSs were highly expressed in T. wilfordii roots, and were up-regulated upon methyl jasmonate (MeJA) treatment. The global gene expression profiles suggested that the TwFPSs might play an important regulatory role interpenoid biosynthesis in T. wilfordii, laying the groundwork for the future study of the synthetic biology of natural terpene products.
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Affiliation(s)
- Yu-Jun Zhao
- Capital Medical University School of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China
| | - Xin Chen
- Capital Medical University School of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China
- * E-mail: (XC); (LH); (WG)
| | - Meng Zhang
- Capital Medical University School of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China
| | - Ping Su
- Capital Medical University School of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China
| | - Yu-Jia Liu
- Capital Medical University School of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China
| | - Yu-Ru Tong
- Capital Medical University School of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China
| | - Xiu-Juan Wang
- Capital Medical University School of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China
| | - Lu-Qi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
- * E-mail: (XC); (LH); (WG)
| | - Wei Gao
- Capital Medical University School of Traditional Chinese Medicine, Capital Medical University, Beijing, People’s Republic of China
- * E-mail: (XC); (LH); (WG)
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10
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Zhang Y, Li ZX, Yu XD, Fan J, Pickett JA, Jones HD, Zhou JJ, Birkett MA, Caulfield J, Napier JA, Zhao GY, Cheng XG, Shi Y, Bruce TJA, Xia LQ. Molecular characterization of two isoforms of a farnesyl pyrophosphate synthase gene in wheat and their roles in sesquiterpene synthesis and inducible defence against aphid infestation. New Phytol 2015; 206:1101-1115. [PMID: 25644034 DOI: 10.1111/nph.13302] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/16/2014] [Indexed: 05/09/2023]
Abstract
Aphids are important pests of wheat (Triticum aestivum) that affect crop production globally. Herbivore-induced emission of sesquiterpenes can repel pests, and farnesyl pyrophosphate synthase (FPS) is a key enzyme involved in sesquiterpene biosynthesis. However, fps orthologues in wheat and their functional roles in sesquiterpene synthesis and defence against aphid infestation are unknown. Here, two fps isoforms, Tafps1 and Tafps2, were identified in wheat. Quantitative real-time polymerase chain reaction (qRT-PCR) and in vitro catalytic activity analyses were conducted to investigate expression patterns and activity. Heterologous expression of these isoforms in Arabidopsis thaliana, virus-induced gene silencing (VIGS) in wheat and aphid behavioural assays were performed to understand the functional roles of these two isoforms. We demonstrated that Tafps1 and Tafps2 played different roles in induced responses to aphid infestation and in sesquiterpene synthesis. Heterologous expression in A. thaliana resulted in repulsion of the peach aphid (Myzus persicae). Wheat plants with these two isoforms transiently silenced were significantly attractive to grain aphid (Sitobion avenae). Our results provide new insights into induced defence against aphid herbivory in wheat, in particular, the different roles of the two Tafps isoforms in both sesquiterpene biosynthesis and defence against aphid infestation.
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Affiliation(s)
- Yan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS)/Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, 11 Keyuanjing 4 Road, Laoshan District, Qingdao, 266101, China
| | - Zhi-Xia Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xiu-Dao Yu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Jia Fan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - John A Pickett
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Huw D Jones
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | | | | | - John Caulfield
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | | | - Guang-Yao Zhao
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xian-Guo Cheng
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yi Shi
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS)/Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, 11 Keyuanjing 4 Road, Laoshan District, Qingdao, 266101, China
| | - Toby J A Bruce
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Lan-Qin Xia
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
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11
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Schmidberger JW, Schnell R, Schneider G. Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa. Acta Crystallogr D Biol Crystallogr 2015; 71:721-31. [PMID: 25760619 PMCID: PMC4356374 DOI: 10.1107/s1399004715001121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/19/2015] [Indexed: 12/23/2022]
Abstract
Locus PA4043 in the genome of Pseudomonas aeruginosa PAO1 has been annotated as coding for a farnesyl pyrophosphate synthase (FPPS). This open reading frame was cloned and expressed recombinantly in Escherichia coli. The dimeric enzyme shows farnesyl pyrophosphate synthase activity and is strongly inhibited by ibandronate and zoledronate, drugs that are presently in clinical use. The structures of the unliganded enzyme and complexes with the substrate geranyl diphosphate (GPP), the inhibitor ibandronate and two compounds obtained from a differential scanning fluorimetry-based screen of a fragment library were determined by X-ray crystallography to resolutions of better than 2.0 Å. The enzyme shows the typical α-helical fold of farnesyl pyrophosphate synthases. The substrate GPP binds in the S1 substrate site in an open conformation of the enzyme. In the enzyme-ibandronate complex three inhibitor molecules are bound in the active site of the enzyme. One inhibitor molecule occupies the allylic substrate site (S1) of each subunit, as observed in complexes of nitrogen-containing bisphosphonate inhibitors of farnesyl synthases from other species. Two (in subunit A) and one (in subunit B) additional ibandronate molecules are bound in the active site. The structures of the fragment complexes show two molecules bound in a hydrophobic pocket adjacent to the active site. This allosteric pocket, which has previously only been described for FPPS from eukaryotic organisms, is thus also present in enzymes from pathogenic prokaryotes and might be utilized for the design of inhibitors of bacterial FPPS with a different chemical scaffold to the highly charged bisphosphonates, which are less likely to pass bacterial membranes.
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Affiliation(s)
- Jason W. Schmidberger
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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12
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Guo L, Kong JQ. cDNA cloning and expression analysis of farnesyl pyrophosphate synthase from Ornithogalum saundersiae. ACTA ACUST UNITED AC 2014; 69:259-70. [PMID: 25069165 DOI: 10.5560/znc.2013-0130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Farnesyl pyrophosphate synthase (FPPS, EC 2.5.1.10) catalyzes the consecutive head-to-tail condensations of isopentenyl diphosphate (IPP) with dimethylallyl diphosphate (DMAPP) to form farnesyl pyrophosphate (FPP), a key precursor of sesquiterpenoids, triterpenoids, sterols, and farnesylated proteins. Here we report the molecular cloning and functional identification of a new full-length cDNA encoding FPPS from Ornithogalum saundersiae, a potential medicinal plant that produces a promising antitumour sterol glycoside, OSW-1. An 1327 bp long unigene with an open reading frame of 1044 bp was retrieved from the transcriptome sequencing of O. saundersiae. The full-length FPPS cDNA, designated OsaFPPS, was isolated from O. saundersiae with gene-specific primers. The resultant OsaFPPS encodes a 347-amino acids protein with a calculated molecular mass of 40,085.6 Da, and a theoretical isoelectric point of 5.01. Phylogenetic tree analysis indicated that OsaFPPS belongs to the plant FPPS super-family. Expression of soluble OsaFPPS in E. coli was verified by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis. Functional analysis of the purified OsaFPPS protein was carried out using IPP and DMAPP as substrates, and the product was unambiguously determined by gas chromatography-mass spectrometry (GC-MS) analyses.
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13
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Alcaíno J, Romero I, Niklitschek M, Sepúlveda D, Rojas MC, Baeza M, Cifuentes V. Functional characterization of the Xanthophyllomyces dendrorhous farnesyl pyrophosphate synthase and geranylgeranyl pyrophosphate synthase encoding genes that are involved in the synthesis of isoprenoid precursors. PLoS One 2014; 9:e96626. [PMID: 24796858 PMCID: PMC4010515 DOI: 10.1371/journal.pone.0096626] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/09/2014] [Indexed: 12/21/2022] Open
Abstract
The yeast Xanthophyllomyces dendrorhous synthesizes the carotenoid astaxanthin, which has applications in biotechnology because of its antioxidant and pigmentation properties. However, wild-type strains produce too low amounts of carotenoids to be industrially competitive. Considering this background, it is indispensable to understand how the synthesis of astaxanthin is controlled and regulated in this yeast. In this work, the steps leading to the synthesis of the carotenoid precursor geranylgeranyl pyrophosphate (GGPP, C20) in X. dendrorhous from isopentenyl pyrophosphate (IPP, C5) and dimethylallyl pyrophosphate (DMAPP, C5) was characterized. Two prenyl transferase encoding genes, FPS and crtE, were expressed in E. coli. The enzymatic assays using recombinant E. coli protein extracts demonstrated that FPS and crtE encode a farnesyl pyrophosphate (FPP, C15) synthase and a GGPP-synthase, respectively. X. dendrorhous FPP-synthase produces geranyl pyrophosphate (GPP, C10) from IPP and DMAPP and FPP from IPP and GPP, while the X. dendrorhous GGPP-synthase utilizes only FPP and IPP as substrates to produce GGPP. Additionally, the FPS and crtE genes were over-expressed in X. dendrorhous, resulting in an increase of the total carotenoid production. Because the parental strain is diploid, the deletion of one of the alleles of these genes did not affect the total carotenoid production, but the composition was significantly altered. These results suggest that the over-expression of these genes might provoke a higher carbon flux towards carotenogenesis, most likely involving an earlier formation of a carotenogenic enzyme complex. Conversely, the lower carbon flux towards carotenogenesis in the deletion mutants might delay or lead to a partial formation of a carotenogenic enzyme complex, which could explain the accumulation of astaxanthin carotenoid precursors in these mutants. In conclusion, the FPS and the crtE genes represent good candidates to manipulate to favor carotenoid biosynthesis in X. dendrorhous.
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Affiliation(s)
- Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ignacio Romero
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio Niklitschek
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dionisia Sepúlveda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - María Cecilia Rojas
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Park J, Lin YS, Tsantrizos YS, Berghuis AM. Structure of human farnesyl pyrophosphate synthase in complex with an aminopyridine bisphosphonate and two molecules of inorganic phosphate. Acta Crystallogr F Struct Biol Commun 2014; 70:299-304. [PMID: 24598914 PMCID: PMC3944689 DOI: 10.1107/s2053230x14002106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/29/2014] [Indexed: 12/12/2022] Open
Abstract
Human farnesyl pyrophosphate synthase (hFPPS) produces farnesyl pyrophosphate, an isoprenoid essential for a variety of cellular processes. The enzyme has been well established as the molecular target of the nitrogen-containing bisphosphonates (N-BPs), which are best known for their antiresorptive effects in bone but are also known for their anticancer properties. Crystal structures of hFPPS in ternary complexes with a novel bisphosphonate, YS0470, and the secondary ligands inorganic phosphate (Pi), inorganic pyrophosphate (PPi) and isopentenyl pyrophosphate (IPP) have recently been reported. Only the co-binding of the bisphosphonate with either PPi or IPP resulted in the full closure of the C-terminal tail of the enzyme, a conformational change that is required for catalysis and that is also responsible for the potent in vivo efficacy of N-BPs. In the present communication, a co-crystal structure of hFPPS in complex with YS0470 and two molecules of Pi is reported. The unusually close proximity between these ligands, which was confirmed by anomalous diffraction data, suggests that they interact with one another, with their anionic charges neutralized in their bound state. The structure also showed the tail of the enzyme to be fully disordered, indicating that simultaneous binding of two Pi molecules with a bisphosphonate cannot induce the tail-closing conformational change in hFPPS. Examination of homologous FPPSs suggested that this ligand-dependent tail closure is only conserved in the mammalian proteins. The prevalence of Pi-bound hFPPS structures in the PDB raises a question regarding the in vivo relevance of Pi binding to the function of the enzyme.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Yih-Shyan Lin
- Department of Chemistry, McGill University, 801 Rue Sherbrooke Ouest, Montreal, QC H3A 0B8, Canada
| | - Youla S. Tsantrizos
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Department of Chemistry, McGill University, 801 Rue Sherbrooke Ouest, Montreal, QC H3A 0B8, Canada
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
| | - Albert M. Berghuis
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
- Department of Microbiology and Immunology, McGill University, 3775 Rue University, Montreal, QC H3A 2B4, Canada
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15
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Kang JH, Gonzales-Vigil E, Matsuba Y, Pichersky E, Barry CS. Determination of residues responsible for substrate and product specificity of Solanum habrochaites short-chain cis-prenyltransferases. Plant Physiol 2014; 164:80-91. [PMID: 24254315 PMCID: PMC3875827 DOI: 10.1104/pp.113.230466] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Isoprenoids are diverse compounds that have their biosynthetic origin in the initial condensation of isopentenyl diphosphate and dimethylallyl diphosphate to form C10 prenyl diphosphates that can be elongated by the addition of subsequent isopentenyl diphosphate units. These reactions are catalyzed by either cis-prenyltransferases (CPTs) or trans-prenyltransferases. The synthesis of volatile terpenes in plants typically proceeds through either geranyl diphosphate (C10) or trans-farnesyl diphosphate (C15), to yield monoterpenes and sesquiterpenes, respectively. However, terpene biosynthesis in glandular trichomes of tomato (Solanum lycopersicum) and related wild relatives also occurs via the cis-substrates neryl diphosphate (NPP) and 2Z,6Z-farnesyl diphosphate (Z,Z-FPP). NPP and Z,Z-FPP are synthesized by neryl diphosphate synthase1 (NDPS1) and Z,Z-farnesyl diphosphate synthase (zFPS), which are encoded by the orthologous CPT1 locus in tomato and Solanum habrochaites, respectively. In this study, comparative sequence analysis of NDPS1 and zFPS enzymes from S. habrochaites accessions that synthesize either monoterpenes or sesquiterpenes was performed to identify amino acid residues that correlate with the ability to synthesize NPP or Z,Z-FPP. Subsequent structural modeling, coupled with site-directed mutagenesis, highlighted the importance of four amino acids located within conserved domain II of CPT enzymes that form part of the second α-helix, for determining substrate and product specificity of these enzymes. In particular, the relative positioning of aromatic amino acid residues at positions 100 and 107 determines the ability of these enzymes to synthesize NPP or Z,Z-FPP. This study provides insight into the biochemical evolution of terpene biosynthesis in the glandular trichomes of Solanum species.
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16
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Sun Y, Long R, Kang J, Zhang T, Zhang Z, Zhou H, Yang Q. Molecular cloning and characterization of three isoprenyl diphosphate synthase genes from alfalfa. Mol Biol Rep 2013; 40:2035-44. [PMID: 23238915 DOI: 10.1007/s11033-012-2262-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 11/19/2012] [Indexed: 10/27/2022]
Abstract
Isoprenoid is the precursor for the biosynthesis of saponins, abscisic acid, gibberellins, chlorophylls and many other products in plants. Saponins are an important group of bioactive plant natural products. The alfalfa (Medicago sativa L.) saponins are glycosides of different triterpene aglycones and possess many biological activities. We isolated three genes (MsFPPS, MsGPPS and MsGGPPS) encoding isoprenyl diphosphate synthases (IDS) from alfalfa via a homology-based PCR approach. The enzyme activity assay of purified recombined MsFPPS and MsGGPPS expressed in Escherichia coli indicated that they all had IDS activity. Expression analysis of the three genes in different alfalfa tissues using real time PCR displayed that they were expressed in all tissues although they had a different expression patterns. MsFPPS and MsGPS displayed a significant increase in transcript level in response to methyl jasmonate, but the transcript level of MsGGPPS decreased obviously. To elucidate the functions of the three IDSs, their overexpression driven by a constitutive cauliflower mosaic virus-35S promoter in tobacco plants was applied and analyzed. The T(0) transgenic plants of MsFPPS showed high levels of squalene content when compared with control. However, no differences were detected in T(0) transgenic plants of MsGPPS and MsGGPPS. In addition, the overexpression of MsFPPS induced senescence response in transgenic plant leaves. This result may indicate that MsFPPS performs a role not only in phytosterol and triterpene biosynthesis, but also in growth regulation.
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Affiliation(s)
- Yan Sun
- College of Animal Science and Technology, China Agriculture University, Beijing, 100193, China
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17
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Xing Z, Long Y, He S, Liang N, Li B. [Molecular cloning of farnesyl diphosphate synthase from Eleutherococcus senticosus and its bioinformatics and expression analysis]. Zhongguo Zhong Yao Za Zhi 2012; 37:1725-1730. [PMID: 22997812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
OBJECTIVE To clone farnesyl diphosphate synthase (FPS) gene from Eleutherococcus senticosus and analyze the bioinformatics and expression of the gene. METHOD The FPS full length cDNA was cloned by rapid amplification of cDNA ends (RACE). The data was analyzed by bioinformatics method, the structure and function of FPS was deduced. The expression of FPS in different organ of E. senticosus was detected by RT-PCR. RESULT The full length of FPS cDNA was 1 499 bp containing a 1 029 bp ORF that encoded 342 amino acids. The deduced protein sequence exhibited two Asp riches conserved motifs (DDXXD). Without transmembrane domain, FPS was located in cytoplasm. RT-PCR result showed that FPS gene expressed in different organs of E. senticosus. The expression amounts of FPS in different organs were different significantly (P < 0.05). CONCLUSION The FPS gene of E. senticosus was successfully cloned for the first time, and provided a stable foundation for studying on its effect and expression control on E. senticosus saponins biosynthesis.
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Affiliation(s)
- Zhaobin Xing
- College of Life Science, Hebei United University, Tangshan 063000, China.
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18
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Hariharan S. Pharmacophoric studies of in vitro inhibition of Plasmodium falciparum growth. Indian J Biochem Biophys 2012; 49:101-108. [PMID: 22650007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Malaria continues to be a scourge in India and the situation has been compounded by the emergence of resistant strains of Plasmodium falciparum which is the primary cause of fatality in this disease. Therefore, there is an urgent need to develop newer drugs. Molecular modeling and pharmacophoric determination have become predominant methods today in the design and synthesis of newer and more effective drugs. Many Plasmodium specific enzymes and proteins involved in crucial biochemical pathways have been identified and their structures have been determined by X-ray crystallography. These enzymes and proteins are excellent targets for newer antimalarial agents. Bisphosphonates have shown potent inhibitory activity against Plasmodium farneysl diphosphate synthase (FPPS) enzyme, which is vital to the protein prenylation pathway of the organism. In this study, a set of 26 bisphosphonate inhibitors, synthesized by Oldfield et al [J Med Chem (2008) 51, 7827-7833] were subjected to rigorous 3D-QSAR studies using the PHASE computational package. In vitro Plasmodium growth inhibition rather than direct enzyme inhibition was considered in the study for a more realistic approach. Good statistical correlations were obtained for the pharmacophoric model as revealed by the regression values, indicating good stability of the model. Three hydrogen bond acceptors and a hydrogen bond donor defined the pharmacophore from the present study. This pharmacophore, AAAD (A = Hydrogen bond acceptor and D = Hydrogen bond donor) was put through a search-run for matching structures from the SPECS database yielding four matching structures, which could function as starting points for more novel and potent antimalarials.
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Affiliation(s)
- Sivaram Hariharan
- Department of Chemistry, PSG College of Pharmacy, Peelamedu, Coimbatore 641004, India.
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19
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Thabet I, Guirimand G, Courdavault V, Papon N, Godet S, Dutilleul C, Bouzid S, Giglioli-Guivarc'h N, Clastre M, Simkin AJ. The subcellular localization of periwinkle farnesyl diphosphate synthase provides insight into the role of peroxisome in isoprenoid biosynthesis. J Plant Physiol 2011; 168:2110-6. [PMID: 21872968 DOI: 10.1016/j.jplph.2011.06.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/06/2011] [Accepted: 06/27/2011] [Indexed: 05/24/2023]
Abstract
Farnesyl diphosphate (FPP) synthase (FPS: EC.2.5.1.1, EC.2.5.1.10) catalyzes the formation of FPP from isopentenyl diphosphate and dimethylallyl diphosphate via two successive condensation reactions. A cDNA designated CrFPS, encoding a protein showing high similarities with trans-type short FPS isoforms, was isolated from the Madagascar periwinkle (Catharanthus roseus). This cDNA was shown to functionally complement the lethal FPS deletion mutant in the yeast Saccharomyces cerevisiae. At the subcellular level, while short FPS isoforms are usually described as cytosolic proteins, we showed, using transient transformations of C. roseus cells with yellow fluorescent protein-fused constructs, that CrFPS is targeted to peroxisomes. This finding is discussed in relation to the subcellular distribution of FPS isoforms in plants and animals and opens new perspectives towards the understanding of isoprenoid biosynthesis.
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Affiliation(s)
- Insaf Thabet
- Université François-Rabelais de Tours, EA2106, Biomolécules et Biotechnologies Végétales, 37200 Tours, France
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20
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Trost BM, Malhotra S, Chan WH. Exercising regiocontrol in palladium-catalyzed asymmetric prenylations and geranylation: unifying strategy toward flustramines A and B. J Am Chem Soc 2011; 133:7328-31. [PMID: 21520958 PMCID: PMC3144703 DOI: 10.1021/ja2020873] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pd-catalyzed asymmetric prenylation of oxindoles to afford selectively either the prenyl or reverse-prenyl product has been demonstrated. Control of the regioselectivity in this transformation is governed by the choice of ligand, solvent, and halide additive. The resulting prenylated and reverse-prenylated products were transformed into ent-flustramides and ent-flustramines A and B. Additionally, control of the regio- and diastereoselectivity was obtained using π-geranylpalladium complexes.
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Affiliation(s)
- Barry M Trost
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.
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21
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Vandermoten S, Santini S, Haubruge E, Heuze F, Francis F, Brasseur R, Cusson M, Charloteaux B. Structural features conferring dual geranyl/farnesyl diphosphate synthase activity to an aphid prenyltransferase. Insect Biochem Mol Biol 2009; 39:707-716. [PMID: 19720147 DOI: 10.1016/j.ibmb.2009.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 08/14/2009] [Accepted: 08/17/2009] [Indexed: 05/28/2023]
Abstract
In addition to providing lipid chains for protein prenylation, short-chain isoprenyl diphosphate synthases (scIPPSs) play a pivotal role in the biosynthesis of numerous mevalonate pathway end-products, including insect juvenile hormone and terpenoid pheromones. For this reason, they are being considered as targets for pesticide development. Recently, we characterized an aphid scIPPS displaying dual geranyl diphosphate (GPP; C(10))/farnesyl diphosphate (FPP; C(15)) synthase activity in vitro. To identify the mechanism(s) responsible for this dual activity, we assessed the product selectivity of aphid scIPPSs bearing mutations at Gln107 and/or Leu110, the fourth and first residue upstream from the "first aspartate-rich motif" (FARM), respectively. All but one resulted in significant changes in product chain-length selectivity, effectively increasing the production of either GPP (Q107E, L110W) or FPP (Q107F, Q107F-L110A); the other mutation (L110A) abolished activity. Although some of these effects could be attributed to changes in steric hindrance within the catalytic cavity, molecular dynamics simulations identified other contributing factors, including residue-ligand Van der Waals interactions and the formation of hydrogen bonds or salt bridges between Gln107 and other residues across the catalytic cavity, which constitutes a novel product chain-length determination mechanism for scIPPSs. Thus the aphid enzyme apparently evolved to maintain the capacity to produce both GPP and FPP through a balance between these mechanisms.
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Affiliation(s)
- Sophie Vandermoten
- Gembloux Agricultural University, Department of Functional and Evolutionary Entomology, Passage des Déportés 2, Gembloux, Belgium.
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Sen SE, Trobaugh C, Béliveau C, Richard T, Cusson M. Cloning, expression and characterization of a dipteran farnesyl diphosphate synthase. Insect Biochem Mol Biol 2007; 37:1198-1206. [PMID: 17916506 DOI: 10.1016/j.ibmb.2007.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 07/10/2007] [Accepted: 07/13/2007] [Indexed: 05/25/2023]
Abstract
Farnesyl diphosphate synthase (FPPS) of the dipteran Drosophila melanogaster has been cloned and its catalytic properties have been assessed. Analysis of the D. melanogaster genome and of ESTs indicates that FPPS is a single copy gene that produces two transcripts, which differ only by 5' extension. The cDNA of shorter and longer D. melanogaster FPPSs (DmFPPS-1a and DmFPPS-1b, respectively) were each subcloned into pET28a and expressed as an N-His6 fusion protein in BL21 E. coli cells. The DmFPPSs similarly catalyzed the coupling of the allylic substrates, GPP and DMAPP, with IPP, producing FPP as product. The longer protein was further characterized. The enzyme required divalent metal for activity, and was activated by 0.1% Triton X-100. Higher detergent concentration and the addition of glycerol, conditions that activate certain insect FPPSs, inhibited prenyl coupling by DmFPPS-1b. Although DmFPPS-1b does not efficiently couple homologous GPP compounds, homodimethylallyl diphosphate (HDMAPP), which is precursor to all homologous JH structures, was a reactive substrate.
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Affiliation(s)
- Stephanie E Sen
- Department of Chemistry, Indiana U.-Purdue U. Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, USA.
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23
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Mao J, Mukherjee S, Zhang Y, Cao R, Sanders JM, Song Y, Zhang Y, Meints GA, Gao YG, Mukkamala D, Hudock MP, Oldfield E. Solid-state NMR, crystallographic, and computational investigation of bisphosphonates and farnesyl diphosphate synthase-bisphosphonate complexes. J Am Chem Soc 2007; 128:14485-97. [PMID: 17090032 DOI: 10.1021/ja061737c] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bisphosphonates are a class of molecules in widespread use in treating bone resorption diseases and are also of interest as immunomodulators and anti-infectives. They function by inhibiting the enzyme farnesyl diphosphate synthase (FPPS), but the details of how these molecules bind are not fully understood. Here, we report the results of a solid-state (13)C, (15)N, and (31)P magic-angle sample spinning (MAS) NMR and quantum chemical investigation of several bisphosphonates, both as pure compounds and when bound to FPPS, to provide information about side-chain and phosphonate backbone protonation states when bound to the enzyme. We then used computational docking methods (with the charges assigned by NMR) to predict how several bisphosphonates bind to FPPS. Finally, we used X-ray crystallography to determine the structures of two potent bisphosphonate inhibitors, finding good agreement with the computational results, opening up the possibility of using the combination of NMR, quantum chemistry and molecular docking to facilitate the design of other, novel prenytransferase inhibitors.
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Affiliation(s)
- Junhong Mao
- Department of Chemistry and Biophysics, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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24
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Sen SE, Cusson M, Trobaugh C, Béliveau C, Richard T, Graham W, Mimms A, Roberts G. Purification, properties and heteromeric association of type-1 and type-2 lepidopteran farnesyl diphosphate synthases. Insect Biochem Mol Biol 2007; 37:819-28. [PMID: 17628280 DOI: 10.1016/j.ibmb.2007.05.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2007] [Revised: 05/11/2007] [Accepted: 05/15/2007] [Indexed: 05/16/2023]
Abstract
Two forms of farnesyl diphosphate synthase (FPPS) from the spruce budworm, Choristoneura fumiferana, and one from the armyworm Pseudaletia unipuncta, have been cloned and their catalytic properties assessed. The type-2 FPPS of C. fumiferana (CfFPPS2) was efficient in the prenyl coupling of DMAPP or GPP with [(14)C]IPP, producing FPP as its final product; however, type-1 FPPSs (CfFPPS1, PuFPPS1, as well as Agrotis ipsilon FPPS1) were essentially inactive. A variety of purification methods was employed to purify the type-1 enzymes. Under mild chromatographic conditions, the isolated type-1 enzyme showed modest activity, but was apparently contaminated with endogenous prenyltransferase derived from the Escherichia coli host cells. Similarly, unpurified extracts of PuFPPS1 expressed in an E. coli FPPS-null mutant, had low FPPS activity. When equimolar amounts of homogenous CfFPPS1 and CfFPP2 were combined, a sharp synergistic enhancement of activity was observed, and the coupling of several homologous substrates, which are precursors to ethyl-branched JHs, was enhanced. Association between CfFPPS1 and CfFPPS2 was confirmed by both protein interaction chromatography and competitive ELISA. These data suggest that type-1 and type-2 FPPSs can form a heteromer, which may play a role in sesquiterpene biosynthesis, such as JH homologue formation, in moths.
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Affiliation(s)
- Stephanie E Sen
- Department of Chemistry, Indiana U.-Purdue U. Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, USA.
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25
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Ye Y, Fujii M, Hirata A, Kawamukai M, Shimoda C, Nakamura T. Geranylgeranyl diphosphate synthase in fission yeast is a heteromer of farnesyl diphosphate synthase (FPS), Fps1, and an FPS-like protein, Spo9, essential for sporulation. Mol Biol Cell 2007; 18:3568-81. [PMID: 17596513 PMCID: PMC1951748 DOI: 10.1091/mbc.e07-02-0112] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Both farnesyl diphosphate synthase (FPS) and geranylgeranyl diphosphate synthase (GGPS) are key enzymes in the synthesis of various isoprenoid-containing compounds and proteins. Here, we describe two novel Schizosaccharomyces pombe genes, fps1(+) and spo9(+), whose products are similar to FPS in primary structure, but whose functions differ from one another. Fps1 is essential for vegetative growth, whereas, a spo9 null mutant exhibits temperature-sensitive growth. Expression of fps1(+), but not spo9(+), suppresses the lethality of a Saccharomyces cerevisiae FPS-deficient mutant and also restores ubiquinone synthesis in an Escherichia coli ispA mutant, which lacks FPS activity, indicating that S. pombe Fps1 in fact functions as an FPS. In contrast to a typical FPS gene, no apparent GGPS homologues have been found in the S. pombe genome. Interestingly, although neither fps1(+) nor spo9(+) expression alone in E. coli confers clear GGPS activity, coexpression of both genes induces such activity. Moreover, the GGPS activity is significantly reduced in the spo9 mutant. In addition, the spo9 mutation perturbs the membrane association of a geranylgeranylated protein, but not that of a farnesylated protein. Yeast two-hybrid and coimmunoprecipitation analyses indicate that Fps1 and Spo9 physically interact. Thus, neither Fps1 nor Spo9 alone functions as a GGPS, but the two proteins together form a complex with GGPS activity. Because spo9 was originally identified as a sporulation-deficient mutant, we show here that expansion of the forespore membrane is severely inhibited in spo9Delta cells. Electron microscopy revealed significant accumulation membrane vesicles in spo9Delta cells. We suggest that lack of GGPS activity in a spo9 mutant results in impaired protein prenylation in certain proteins responsible for secretory function, thereby inhibiting forespore membrane formation.
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Affiliation(s)
- Yanfang Ye
- *Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Makoto Fujii
- Department of Applied Bioscience and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue 690-8504, Japan
| | - Aiko Hirata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan; and
| | - Makoto Kawamukai
- Department of Applied Bioscience and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue 690-8504, Japan
| | - Chikashi Shimoda
- *Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Taro Nakamura
- *Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
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Abstract
Diversity of scaffold structure and function is a hallmark of the >50,000 isoprenoid natural products such as taxol. Whereas most members of this class are assembled by iterative head-to-tail enzymatic joining reactions between delta2- and delta3-isopentenyl diphosphate (IPP) monomers, dimerization of two delta2-IPP molecules has now been shown to account for three additional modes of "irregular" coupling patterns at the level of C10 monoterpene scaffolds.
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Affiliation(s)
- Christopher T Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
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Abstract
The carbon skeletons of over 55,000 naturally occurring isoprenoid compounds are constructed from four fundamental coupling reactions: chain elongation, cyclopropanation, branching, and cyclobutanation. Enzymes that catalyze chain elongation and cyclopropanation are well studied, whereas those that catalyze branching and cyclobutanation are unknown. We have catalyzed the four reactions with chimeric proteins generated by replacing segments of a chain-elongation enzyme with corresponding sequences from a cyclopropanation enzyme. Stereochemical and mechanistic considerations suggest that the four coupling enzymes could have evolved from a common ancestor through relatively small changes in the catalytic site.
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Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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29
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Abstract
Farnesyl diphosphate (FPP) synthase catalyzes the consecutive head-to-tail condensations of isopentenyl diphosphate (IPP, C5) with dimethylallyl diphosphate (DMAPP, C5) and geranyl diphosphate (GPP, C10) to give (E,E)-FPP (C15). The enzyme belongs to a genetically distinct family of chain elongation enzymes that install E-double bonds during each addition of a five-carbon isoprene unit. Analysis of the C10 and C15 products from incubations with avian FPP synthase reveals that small amounts of neryl diphosphate (Z-C10) and (Z,E)-FPP are formed along with the E-isomers during the C5 --> C10 and C10 --> C15 reactions. Similar results were obtained for FPP synthase from Escherichia coli, Artemisia tridentata (sage brush), Pyrococcus furiosus, and Methanobacter thermautotrophicus and for GPP and FPP synthesized in vivo by E. coli FPP synthase. When (R)-[2-2H]IPP was a substrate for chain elongation, no deuterium was found in the chain elongation products. In contrast, the deuterium in (S)-[2-2H]IPP was incorporated into all of the products. Thus, the pro-R hydrogen at C2 of IPP is lost when the E- and Z-double bond isomers are formed. The synthesis of Z-double bond isomers by FPP synthase during chain elongation is unexpected for a highly evolved enzyme and probably reflects a compromise between optimizing double bond stereoselectivity and the need to exclude DMAPP from the IPP binding site.
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Affiliation(s)
| | - C. Dale Poulter
- Corresponding author: Phone: 801-581-6685; Fax: 801-581-4391; e-mail:
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30
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Leon A, Liu L, Yang Y, Hudock MP, Hall P, Yin F, Studer D, Puan KJ, Morita CT, Oldfield E. Isoprenoid biosynthesis as a drug target: bisphosphonate inhibition of Escherichia coli K12 growth and synergistic effects of fosmidomycin. J Med Chem 2007; 49:7331-41. [PMID: 17149863 DOI: 10.1021/jm060492b] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We screened a library of 117 bisphosphonates for antibacterial activity against Escherichia coli. The most potent growth inhibitors where N-[methyl(4-phenylalkyl)]-3-aminopropyl-1-hydroxy-1,1-bisphosphonates, known potent bone resorption inhibitors, and there was a generally good correlation between cell growth inhibition and E. coli farnesyl diphosphate synthase (FPPS) inhibition. However, some potent FPPS inhibitors had no activity in cell growth inhibition, and based on the result of Catalyst pharmacophore modeling, this could be attributed to the requirement of a large hydrophobic feature for cellular activity (due most likely to transport). The activity of the most potent compound, N-[methyl(4-phenylbutyl)]-3-aminopropyl-1-hydroxy-1,1-bisphosphonate (13), was strongly potentiated by the drug fosmidomycin. The transcription profiles for 13 or fosmidomycin alone were different from those found with carbenicillin or ciprofloxacin alone, but there were many similarities between the combination (13-fosmidomycin) and carbenicillin or ciprofloxacin, reflecting the more potent bactericidal activity of the drug combination on bacterial growth.
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Affiliation(s)
- Annette Leon
- Center for Biophysics and Computational Biology, University of Illinois at Urbana - Champaign, 607 South Mathews Avenue, Urbana, Illinois 61801, USA
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31
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Cusson M, Béliveau C, Sen SE, Vandermoten S, Rutledge RG, Stewart D, Francis F, Haubruge E, Rehse P, Huggins DJ, Dowling APG, Grant GH. Characterization and tissue-specific expression of two lepidopteran farnesyl diphosphate synthase homologs: Implications for the biosynthesis of ethyl-substituted juvenile hormones. Proteins 2006; 65:742-58. [PMID: 16972283 DOI: 10.1002/prot.21057] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The sesquiterpenoid juvenile hormone (JH) regulates insect development and reproduction. Most insects produce only one chemical form of JH, but the Lepidoptera produce four derivatives featuring ethyl branches. The biogenesis of these JHs requires the synthesis of ethyl-substituted farnesyl diphosphate (FPP) by FPP synthase (FPPS). To determine if there exist more than one lepidopteran FPPS, and whether one FPPS homolog is better adapted for binding the bulkier ethyl-branched substrates/products, we cloned three lepidopteran FPPS cDNAs, two from Choristoneura fumiferana and one from Pseudaletia unipuncta. Amino acid sequence comparisons among these and other eukaryotic FPPSs led to the recognition of two lepidopteran FPPS types. Type-I FPPSs display unique active site substitutions, including several in and near the first aspartate-rich motif, whereas type-II proteins have a more "conventional" catalytic cavity. In a yeast assay, a Drosophila FPPS clone provided full complementation of an FPPS mutation, but lepidopteran FPPS clones of either type yielded only partial complementation, suggesting unusual catalytic features and/or requirements of these enzymes. Although a structural analysis of lepidopteran FPPS active sites suggested that type-I enzymes are better suited than type-II for generating ethyl-substituted products, a quantitative real-time PCR assessment of their relative abundance in insect tissues indicated that type-I expression is ubiquitous whereas that of type-II is essentially confined to the JH-producing glands, where its transcripts are approximately 20 times more abundant than those of type-I. These results suggest that type-II FPPS plays a leading role in lepidopteran JH biosynthesis in spite of its apparently more conventional catalytic cavity.
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Affiliation(s)
- Michel Cusson
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, Québec G1V 4C7, Canada.
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Kavanagh KL, Guo K, Dunford JE, Wu X, Knapp S, Ebetino FH, Rogers MJ, Russell RGG, Oppermann U. The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs. Proc Natl Acad Sci U S A 2006; 103:7829-34. [PMID: 16684881 PMCID: PMC1472530 DOI: 10.1073/pnas.0601643103] [Citation(s) in RCA: 402] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Indexed: 01/05/2023] Open
Abstract
Osteoporosis and low bone mass are currently estimated to be a major public health risk affecting >50% of the female population over the age of 50. Because of their bone-selective pharmacokinetics, nitrogen-containing bisphosphonates (N-BPs), currently used as clinical inhibitors of bone-resorption diseases, target osteoclast farnesyl pyrophosphate synthase (FPPS) and inhibit protein prenylation. FPPS, a key branchpoint of the mevalonate pathway, catalyzes the successive condensation of isopentenyl pyrophosphate with dimethylallyl pyrophosphate and geranyl pyrophosphate. To understand the molecular events involved in inhibition of FPPS by N-BPs, we used protein crystallography, enzyme kinetics, and isothermal titration calorimetry. We report here high-resolution x-ray structures of the human enzyme in complexes with risedronate and zoledronate, two of the leading N-BPs in clinical use. These agents bind to the dimethylallyl/geranyl pyrophosphate ligand pocket and induce a conformational change. The interactions of the N-BP cyclic nitrogen with Thr-201 and Lys-200 suggest that these inhibitors achieve potency by positioning their nitrogen in the proposed carbocation-binding site. Kinetic analyses reveal that inhibition is competitive with geranyl pyrophosphate and is of a slow, tight binding character, indicating that isomerization of an initial enzyme-inhibitor complex occurs with inhibitor binding. Isothermal titration calorimetry indicates that binding of N-BPs to the apoenzyme is entropy-driven, presumably through desolvation entropy effects. These experiments reveal the molecular binding characteristics of an important pharmacological target and provide a route for further optimization of these important drugs.
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Affiliation(s)
- Kathryn L. Kavanagh
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Kunde Guo
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - James E. Dunford
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7LD, United Kingdom
- Bone Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom; and
- Nuffield Department of Orthopaedic Surgery, Oxford University, Institute of Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, United Kingdom
| | - Xiaoqiu Wu
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7LD, United Kingdom
| | | | - Michael J. Rogers
- Bone Research Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom; and
| | - R. Graham G. Russell
- Nuffield Department of Orthopaedic Surgery, Oxford University, Institute of Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, United Kingdom
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7LD, United Kingdom
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Manzano D, Busquets A, Closa M, Hoyerová K, Schaller H, Kamínek M, Arró M, Ferrer A. Overexpression of farnesyl diphosphate synthase in Arabidopsis mitochondria triggers light-dependent lesion formation and alters cytokinin homeostasis. Plant Mol Biol 2006; 61:195-213. [PMID: 16786301 DOI: 10.1007/s11103-006-6263-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Accepted: 12/31/2005] [Indexed: 05/10/2023]
Abstract
To investigate the role of mitochondrial farnesyl diphosphate synthase (FPS) in plant isoprenoid biosynthesis we characterized transgenic Arabidopsis thaliana plants overexpressing FPS1L isoform. This overexpressed protein was properly targeted to mitochondria yielding a mature and active form of the enzyme of 40 kDa. Leaves from transgenic plants grown under continuous light exhibited symptoms of chlorosis and cell death correlating to H(2)O(2) accumulation, and leaves detached from the same plants displayed accelerated senescence. Overexpression of FPS in mitochondria also led to altered leaf cytokinin profile, with a reduction in the contents of physiologically active trans-zeatin- and isopentenyladenine-type cytokinins and their corresponding riboside monophosphates as well as enhanced levels of cis-zeatin 7-glucoside and storage cytokinin O-glucosides. Overexpression of 3-hydroxy-3-methylglutaryl coenzyme A reductase did not prevent chlorosis in plants overexpressing FPS1L, but did rescue accelerated senescence of detached leaves and restored wild-type levels of cytokinins. We propose that the overexpression of FPS1L leads to an enhanced uptake and metabolism of mevalonic acid-derived isopentenyl diphosphate and/or dimethylallyl diphosphate by mitochondria, thereby altering cytokinin homeostasis and causing a mitochondrial dysfunction that renders plants more sensitive to the oxidative stress induced by continuous light.
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Affiliation(s)
- David Manzano
- Departament de Bioquímica i Biologia Molecular, Facultat de Farmàcia, Universitat de Barcelona, Spain
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Cervantes-Cervantes M, Gallagher CE, Zhu C, Wurtzel ET. Maize cDNAs expressed in endosperm encode functional farnesyl diphosphate synthase with geranylgeranyl diphosphate synthase activity. Plant Physiol 2006; 141:220-31. [PMID: 16581875 PMCID: PMC1459322 DOI: 10.1104/pp.106.077008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Isoprenoids are the most diverse and abundant group of natural products. In plants, farnesyl diphosphate (FPP) and geranylgeranyl diphosphate (GGPP) are precursors to many isoprenoids having essential functions. Terpenoids and sterols are derived from FPP, whereas gibberellins, carotenoids, casbenes, taxenes, and others originate from GGPP. The corresponding synthases (FPP synthase [FPPS] and GGPP synthase [GGPPS]) catalyze, respectively, the addition of two and three isopentenyl diphosphate molecules to dimethylallyl diphosphate. Maize (Zea mays L. cv B73) endosperm cDNAs encoding isoprenoid synthases were isolated by functional complementation of Escherichia coli cells carrying a bacterial gene cluster encoding all pathway enzymes needed for carotenoid biosynthesis, except for GGPPS. This approach indicated that the maize gene products were functional GGPPS enzymes. Yet, the predicted enzyme sequences revealed FPPS motifs and homology with FPPS enzymes. In vitro assays demonstrated that indeed these maize enzymes produced both FPP and GGPP and that the N-terminal sequence affected the ratio of FPP to GGPP. Their functionality in E. coli demonstrated that these maize enzymes can be coupled with a metabolon to provide isoprenoid substrates for pathway use, and suggests that enzyme bifunctionality can be harnessed. The maize cDNAs are encoded by a small gene family whose transcripts are prevalent in endosperm beginning mid development. These maize cDNAs will be valuable tools for assessing the critical structural properties determining prenyl transferase specificity and in metabolic engineering of isoprenoid pathways, especially in cereal crops.
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Affiliation(s)
- Miguel Cervantes-Cervantes
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York 10468, USA
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35
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Gabelli SB, McLellan JS, Montalvetti A, Oldfield E, Docampo R, Amzel LM. Structure and mechanism of the farnesyl diphosphate synthase from Trypanosoma cruzi: implications for drug design. Proteins 2006; 62:80-8. [PMID: 16288456 DOI: 10.1002/prot.20754] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Typanosoma cruzi, the causative agent of Chagas disease, has recently been shown to be sensitive to the action of the bisphosphonates currently used in bone resorption therapy. These compounds target the mevalonate pathway by inhibiting farnesyl diphosphate synthase (farnesyl pyrophosphate synthase, FPPS), the enzyme that condenses the diphosphates of C5 alcohols (isopentenyl and dimethylallyl) to form C10 and C15 diphosphates (geranyl and farnesyl). The structures of the T. cruzi FPPS (TcFPPS) alone and in two complexes with substrates and inhibitors reveal that following binding of the two substrates and three Mg2+ ions, the enzyme undergoes a conformational change consisting of a hinge-like closure of the binding site. In this conformation, it would be possible for the enzyme to bind a bisphosphonate inhibitor that spans the sites usually occupied by dimethylallyl diphosphate (DMAPP) and the homoallyl moiety of isopentenyl diphosphate. This observation may lead to the design of new, more potent anti-trypanosomal bisphosphonates, because existing FPPS inhibitors occupy only the DMAPP site. In addition, the structures provide an important mechanistic insight: after its formation, geranyl diphosphate can swing without leaving the enzyme, from the product site to the substrate site to participate in the synthesis of farnesyl diphosphate.
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Affiliation(s)
- Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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Sigman L, Sánchez VM, Turjanski AG. Characterization of the farnesyl pyrophosphate synthase of Trypanosoma cruzi by homology modeling and molecular dynamics. J Mol Graph Model 2006; 25:345-52. [PMID: 16540358 DOI: 10.1016/j.jmgm.2006.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2005] [Revised: 02/02/2006] [Accepted: 02/06/2006] [Indexed: 11/23/2022]
Abstract
Chagas' disease, caused by the Trypanosoma cruzi parasite, is one of the largest public health problems in the Western hemisphere, with 16-18 million people infected, and approximately 100 million people at risk. Many efforts towards the development of targeted antiparasitic agents have recently been described. Of interest, bisphosphonates, pyrophosphate analogs in which the oxygen bridge between the two phosphorus atoms has been replaced by a carbon substituted with different side chains, are able to inhibit the growth of T. cruzi. The enzyme T. cruzi farnesyl pyrophosphate synthase (TcFPPS) involved in the mevalonate pathway, has been recently identified as the target of bisphosphonates. The protein has 362 amino acids and a molecular mass of 41.2 kDa. Several sequence motifs found in other FPPSs are present in TcFPPS. In this study we have modeled the structure of TcFPPS based on the structure of the avian FPPS. We have characterized the interaction with its substrates, isopentyl pyrophosphate and dimethylallyl pyrophosphate, and the mechanism of inhibition by the potent bisphosphonate risedronate (K(i) of 0.032+/-0.002 microM) by means of molecular dynamics techniques. We propose that homorisedronate, which has an extra methylene and a K(i) of 8.17+/-1.36 microM, does not form strong hydrogen bonds with TYR 211 and THR 208, which may be responsible for its lower activity as compared to risedronate. Moreover, we were able to reproduce the structural changes that occur upon the binding of the third Mg2+ to the active site of the protein. Taken together, our results provide a structural model for the design of novel inhibitors that may prove useful for the treatment of Chagas' disease.
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Affiliation(s)
- Lucas Sigman
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires/CONICET, Ciudad Universitaria, Pab. II, P. 3, C1428EHA Buenos Aires, Argentina
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Abstract
We report the results of an ITC (isothermal titration calorimetry) investigation of the binding of six bisphosphonates to the enzyme farnesyl diphosphate synthase (FPPS; EC 2.5.1.10) from Trypanosoma brucei. The bisphosphonates investigated were zoledronate, risedronate, ibandronate, pamidronate, 2-phenyl-1-hydroxyethane-1,1-bisphosphonate, and 1-(2,2-bisphosphonoethyl)-3-iodo pyridinium. At pH = 7.4, both risedronate and the phenylethane bisphosphonate bind in an enthalpy-driven manner (DeltaH approximately -9 to 10 kcal mol-1), but the other four bisphosphonates bind in an entropy-driven manner (DeltaS varying from 31.2 to 55.1 cal K-1 mol-1). However, at pH = 8.5, zoledronate binding switches from entropy to enthalpy-driven. The DeltaG results are highly correlated with FPPS inhibition results obtained using a radiochemical assay (R2 = 0.85, N = 11, P < 0.001). The DeltaH and DeltaS results are interpreted in terms of a model in which bisphosphonates with charged side chains have positive DeltaH values, due to the enthalpic cost of desolvation (due to strong ion-dipole interactions) and, likewise, a positive DeltaS, due to an increase in water entropy (both ligand and protein associated) on ligand binding to FPPS: the hydrophobic effect. For the neutral side chains (risedronate at pH 7.4, 8.5 and zoledronate at pH 8.5, as well as the phenylethane bisphosphonate), binding is overwhelmingly enthalpy-driven, with the enhanced activity of the basic side chain containing species being attributable to their becoming protonated in the active site. Given the large size of the bisphosphonate market and the potential importance of the development of these compounds for cancer immunotherapy and anti-parasitic chemotherapy, these results are of broad general interest in the context of the development of new, potent, and selective FPPS inhibitors.
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Affiliation(s)
- Fenglin Yin
- Department of Biophysics, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, Illinois 61801, USA
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