1
|
Whitehead J, Leferink NGH, Johannissen LO, Hay S, Scrutton NS. Decoding Catalysis by Terpene Synthases. ACS Catal 2023; 13:12774-12802. [PMID: 37822860 PMCID: PMC10563020 DOI: 10.1021/acscatal.3c03047] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/31/2023] [Indexed: 10/13/2023]
Abstract
The review by Christianson, published in 2017 on the twentieth anniversary of the emergence of the field, summarizes the foundational discoveries and key advances in terpene synthase/cyclase (TS) biocatalysis (Christianson, D. W. Chem Rev2017, 117 (17), 11570-11648. DOI: 10.1021/acs.chemrev.7b00287). Here, we review the TS literature published since then, bringing the field up to date and looking forward to what could be the near future of TS rational design. Many revealing discoveries have been made in recent years, building on the knowledge and fundamental principles uncovered during those initial two decades of study. We use these to explore TS reaction chemistry and see how a combined experimental and computational approach helps to decipher the complexities of TS catalysis. Revealed are a suite of catalytic motifs which control product outcome in TSs, some obvious, some more subtle. We examine each in detail, using the most recent papers and insights to illustrate how exactly this fascinating class of enzymes takes a single acyclic substrate and turns it into the many thousands of complex terpenoids found in Nature. We then explore some of the recent strategies for TS engineering, including machine learning and other data-driven approaches. From this, rational and predictive engineering of TSs, "designer terpene synthases", will begin to emerge as a realistic goal.
Collapse
Affiliation(s)
- Joshua
N. Whitehead
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole G. H. Leferink
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
| |
Collapse
|
2
|
de Kok NAW, Driessen AJM. The catalytic and structural basis of archaeal glycerophospholipid biosynthesis. Extremophiles 2022; 26:29. [PMID: 35976526 PMCID: PMC9385802 DOI: 10.1007/s00792-022-01277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the “lipid-divide”. The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.
Collapse
Affiliation(s)
- Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
| |
Collapse
|
3
|
Ronnebaum TA, Eaton SA, Brackhahn EAE, Christianson DW. Engineering the Prenyltransferase Domain of a Bifunctional Assembly-Line Terpene Synthase. Biochemistry 2021; 60:3162-3172. [PMID: 34609847 DOI: 10.1021/acs.biochem.1c00600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Copalyl diphosphate (CPP) synthase from Penicillium verruculosum (PvCPS) is a bifunctional diterpene synthase with both prenyltransferase and class II cyclase activities. The prenyltransferase α domain catalyzes the condensation of C5 dimethylallyl diphosphate with three successively added C5 isopentenyl diphosphates (IPPs) to form C20 geranylgeranyl diphosphate (GGPP), which then undergoes a class II cyclization reaction at the βγ domain interface to generate CPP. The prenyltransferase α domain mediates oligomerization to form a 648-kD (αβγ)6 hexamer. In the current study, we explore prenyltransferase structure-function relationships in this oligomeric assembly-line platform with the goal of generating alternative linear isoprenoid products. Specifically, we report steady-state enzyme kinetics, product analysis, and crystal structures of various site-specific variants of the prenyltransferase α domain. Crystal structures of the H786A, F760A, S723Y, S723F, and S723T variants have been determined at resolutions of 2.80, 3.10, 3.15, 2.65, and 2.00 Å, respectively. The substitution of S723 with bulky aromatic amino acids in the S723Y and S723F variants constricts the active site, thereby directing the formation of the shorter C15 isoprenoid, farnesyl diphosphate. While the S723T substitution only subtly alters enzyme kinetics and does not compromise GGPP biosynthesis, the crystal structure of this variant reveals a nonproductive binding mode for IPP that likely accounts for substrate inhibition at high concentrations. Finally, mutagenesis of the catalytic general acid in the class II cyclase domain, D313A, significantly compromises prenyltransferase activity. This result suggests molecular communication between the prenyltransferase and cyclase domains despite their distant connection by a flexible polypeptide linker.
Collapse
Affiliation(s)
- Trey A Ronnebaum
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Samuel A Eaton
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Emily A E Brackhahn
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| |
Collapse
|
4
|
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] [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.
Collapse
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
| |
Collapse
|
5
|
Kim SH, Liu C, Zhou Y, Zhang YK, McGregor C, Steere L, Frederick BH, Liu CT, Whitesell L, Cowen LE. Inhibiting Protein Prenylation with Benzoxaboroles to Target Fungal Plant Pathogens. ACS Chem Biol 2020; 15:1930-1941. [PMID: 32573189 DOI: 10.1021/acschembio.0c00290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fungal pathogens pose an increasing threat to global food security through devastating effects on staple crops and contamination of food supplies with carcinogenic toxins. Widespread deployment of agricultural fungicides has increased crop yields but is driving increasingly frequent resistance to available agents and creating environmental reservoirs of drug-resistant fungi that can also infect susceptible human populations. To uncover non-cross-resistant modes of antifungal action, we leveraged the unique chemical properties of boron chemistry to synthesize novel 6-thiocarbamate benzoxaboroles with broad spectrum activity against diverse fungal plant pathogens. Through whole genome sequencing of Saccharomyces cerevisiae isolates selected for stable resistance to these compounds, we identified mutations in the protein prenylation-related genes, CDC43 and ERG20. Allele-swapping experiments confirmed that point mutations in CDC43, which encodes an essential catalytic subunit within geranylgeranyl transferase I (GGTase I) complex, were sufficient to confer resistance to the benzoxaboroles. Mutations in ERG20, which encodes an upstream farnesyl pyrophosphate synthase in the geranylgeranylation pathway, also conferred resistance. Consistent with impairment of protein prenylation, the compounds disrupted membrane localization of the classical geranylgeranylation substrate Cdc42. Guided by molecular docking predictions, which favored Cdc43 as the most likely direct target, we overexpressed and purified functional GGTase I complex to demonstrate direct binding of benzoxaboroles to it and concentration-dependent inhibition of its transferase activity. Further development of the boron-containing scaffold described here offers a promising path to the development of GGTase I inhibitors as a mechanistically distinct broad spectrum fungicide class with reduced potential for cross-resistance to antifungals in current use.
Collapse
Affiliation(s)
- Sang Hu Kim
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Chunliang Liu
- Boragen, Inc., 5 Laboratory Drive, Ste. 2150, Durham, North Carolina 27709, United States
| | - Yasheen Zhou
- Boragen, Inc., 5 Laboratory Drive, Ste. 2150, Durham, North Carolina 27709, United States
| | - Yong-Kang Zhang
- Boragen, Inc., 5 Laboratory Drive, Ste. 2150, Durham, North Carolina 27709, United States
| | - Cari McGregor
- Boragen, Inc., 5 Laboratory Drive, Ste. 2150, Durham, North Carolina 27709, United States
| | - Luke Steere
- Boragen, Inc., 5 Laboratory Drive, Ste. 2150, Durham, North Carolina 27709, United States
| | - Brittany H. Frederick
- Boragen, Inc., 5 Laboratory Drive, Ste. 2150, Durham, North Carolina 27709, United States
| | - C. Tony Liu
- Boragen, Inc., 5 Laboratory Drive, Ste. 2150, Durham, North Carolina 27709, United States
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| |
Collapse
|
6
|
Branco Santos JC, de Melo JA, Maheshwari S, de Medeiros WMTQ, de Freitas Oliveira JW, Moreno CJ, Mario Amzel L, Gabelli SB, Sousa Silva M. Bisphosphonate-Based Molecules as Potential New Antiparasitic Drugs. Molecules 2020; 25:E2602. [PMID: 32503272 PMCID: PMC7321420 DOI: 10.3390/molecules25112602] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022] Open
Abstract
Neglected tropical diseases such as Chagas disease and leishmaniasis affect millions of people around the world. Both diseases affect various parts of the globe and drugs traditionally used in therapy against these diseases have limitations, especially with regard to low efficacy and high toxicity. In this context, the class of bisphosphonate-based compounds has made significant advances regarding the chemical synthesis process as well as the pharmacological properties attributed to these compounds. Among this spectrum of pharmacological activity, bisphosphonate compounds with antiparasitic activity stand out, especially in the treatment of Chagas disease and leishmaniasis caused by Trypanosoma cruzi and Leishmania spp., respectively. Some bisphosphonate compounds can inhibit the mevalonate pathway, an essential metabolic pathway, by interfering with the synthesis of ergosterol, a sterol responsible for the growth and viability of these parasites. Therefore, this review aims to present the information about the importance of these compounds as antiparasitic agents and as potential new drugs to treat Chagas disease and leishmaniasis.
Collapse
Affiliation(s)
- Joice Castelo Branco Santos
- Immunoparasitology Laboratory, Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil; (J.C.B.S.); (J.A.d.M.); (W.M.T.Q.d.M.); (J.W.d.F.O.); (C.J.M.)
- Postgraduate Program in Pharmaceutical Sciences, Health Sciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil
| | - Jonathas Alves de Melo
- Immunoparasitology Laboratory, Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil; (J.C.B.S.); (J.A.d.M.); (W.M.T.Q.d.M.); (J.W.d.F.O.); (C.J.M.)
- Postgraduate Program in Biochemistry, Biosciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil
| | - Sweta Maheshwari
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (S.M.); (L.M.A.)
| | - Wendy Marina Toscano Queiroz de Medeiros
- Immunoparasitology Laboratory, Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil; (J.C.B.S.); (J.A.d.M.); (W.M.T.Q.d.M.); (J.W.d.F.O.); (C.J.M.)
- Postgraduate Program in Pharmaceutical Sciences, Health Sciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil
| | - Johny Wysllas de Freitas Oliveira
- Immunoparasitology Laboratory, Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil; (J.C.B.S.); (J.A.d.M.); (W.M.T.Q.d.M.); (J.W.d.F.O.); (C.J.M.)
- Postgraduate Program in Biochemistry, Biosciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil
| | - Cláudia Jassica Moreno
- Immunoparasitology Laboratory, Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil; (J.C.B.S.); (J.A.d.M.); (W.M.T.Q.d.M.); (J.W.d.F.O.); (C.J.M.)
- Postgraduate Program in Pharmaceutical Sciences, Health Sciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil
- Postgraduate Program in Biochemistry, Biosciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (S.M.); (L.M.A.)
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (S.M.); (L.M.A.)
- Department of Medicine and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marcelo Sousa Silva
- Immunoparasitology Laboratory, Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil; (J.C.B.S.); (J.A.d.M.); (W.M.T.Q.d.M.); (J.W.d.F.O.); (C.J.M.)
- Postgraduate Program in Pharmaceutical Sciences, Health Sciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil
- Postgraduate Program in Biochemistry, Biosciences Center, Federal University of Rio Grande do Norte, 59012-570 Natal, Brazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, 1800-166 Lisbon, Portugal
| |
Collapse
|
7
|
Zhu QL, Zheng JL, Liu J. Transcription activation of β-carotene biosynthetic genes at the initial stage of stresses as an indicator of the increased β-carotene accumulation in isolated Dunaliella salina strain GY-H13. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 222:105472. [PMID: 32203794 DOI: 10.1016/j.aquatox.2020.105472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 06/10/2023]
Abstract
β-carotene is an efficient antioxidant and its accumulation is an oxidative response to stressors. Dunaliella salina strain GY-H13 is rich in β-carotene under environmental stresses, which was selected as material to understand the molecular mechanism underlying β-carotene biosynthesis. Seven full length cDNA sequences in β-carotene biosynthesis pathway were cloned, including geranylgeranyl pyrophosphate synthase (GGPS), phytoene synthase (PSY), phytoene desaturase (PDS), 15-cis-zeta-carotene isomerase (ZISO), zeta-carotene desaturase (ZDS), prolycopene isomerase (CRTISO), lycopene beta-cyclase (LCYb). The seven protein sequences from the strain GY-H13 showed the highest similarity with other D. salina strains. Especially, PSY, PDS and LCYb protein sequences shared 100 % identity. Phylogenetic analysis indicated all proteins from GY-H13 firstly clustered with those from other D. salina strains with a bootstrap of 100 %. Multiple alignment indicated several distinct conserved motifs such as aspartate-rich domain (ARD), dinucleotide binding domain (DBD), and carotene binding domain (CBD). These motifs are located near ligand-binding pocket, which may be required for the activity of enzyme. Expression levels of these genes and β-carotene content were measured over 24-h cycle, showing clear daily dynamics. All genes were dramatically up-regulated in the morning but the highest accumulation of β-carotene was observed at noon, suggesting a lag-effect between gene transcription and biological response. Furthermore, the accumulation of β-carotene increased under nitrogen deficiency, Cd exposure and high light and decreased under high salinity in a time-dependent manner. No gene of β-carotene biosynthesis was up-regulated by high salinity while most genes were activated by the other stresses at the beginning stage of exposure. Growth inhibition and oxidative damage were also observed under high salinity. Overall, transcription activation of β-carotene biosynthetic genes at the initial stage of stress exposure is a determinant of the increased accumulation of β-carotene in microalgae, which help their survive under harsh environments. The newly isolated D. salina strain GY-H13 would be a promising microalgae model for investigating the molecular mechanism of stress-induced β-carotene biosynthesis.
Collapse
Affiliation(s)
- Qing-Ling Zhu
- Institute of Marine Biology & Pharmacology, Ocean College, Zhejiang University, 1 Zheda Road, Dinghai District, Zhoushan, 316000, Zhejiang, PR China; College of Marine Ocean Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, PR China
| | - Jia-Lang Zheng
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, PR China.
| | - Jianhua Liu
- Institute of Marine Biology & Pharmacology, Ocean College, Zhejiang University, 1 Zheda Road, Dinghai District, Zhoushan, 316000, Zhejiang, PR China; College of Marine Ocean Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, PR China.
| |
Collapse
|
8
|
A Genetic Screen for the Isolation of Mutants with Increased Flux in the Isoprenoid Pathway of Yeast. Methods Mol Biol 2019; 1927:231-246. [PMID: 30788796 DOI: 10.1007/978-1-4939-9142-6_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The yeast Saccharomyces cerevisiae is one of the preferred hosts for the production of terpenoids through metabolic engineering. A genetic screen to identify novel mutants that can increase the flux in the isoprenoid pathway has been lacking. We present here the method that has led to the development of a carotenoid based visual screen by exploiting the carotenogenic genes from the red yeast Rhodosporidium toruloides, an organism known to have high levels of carotenoids. We also discuss the methods to use this screen for the identification of mutants that can lead to higher isoprenoid flux. The carotenoid based screen was developed in S. cerevisiae using phytoene synthase RtPSY1 and a hyperactive mutant of the enzyme phytoene dehydrogenase, RtCRTI(A393T) from Rhodosporidium toruloides. As validation of the genetic screen is critical at all stages, we describe the method to validate the screen using a known flux increasing gene, a truncated HMG1 (tHMG1). To demonstrate how this screen can be exploited to isolate mutants, we described how targeted mutagenesis of candidate gene, SPT15 a TATA binding protein involved in the global transcription machinery can be carried out to yield novel mutants with increased metabolic flux. Since it is also important to ensure that the isolated mutants are enhancing general isoprenoid flux, we describe how this can be established using an alternate isoprenoid, α-farnesene.
Collapse
|
9
|
Lao YM, Jin H, Zhou J, Zhang HJ, Zhu XS, Cai ZH. A Novel Hydrolytic Activity of Tri-Functional Geranylgeranyl Pyrophosphate Synthase in Haematococcus pluvialis. PLANT & CELL PHYSIOLOGY 2018; 59:2536-2548. [PMID: 30137453 DOI: 10.1093/pcp/pcy173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Under environmental stresses, Haematococcus pluvialis accumulates large amounts of carotenoids. Scale of carotenoid biosynthesis depends on availability of geranylgeranyl pyrophosphate (GGPP) precursor, which is supplied by GGPP synthase (GGPPS) through sequential 1'-4 condensation of three isopentenyl pyrophosphates (IPPs) into dimethylallyl pyrophosphate (DMAPP). Using IPP and DMAPP as substrates, a tri-functional HpGGPPS was identified in this study to promiscuously synthesize allylic prenyl pyrophosphates (PPPs), e.g. C10 geranyl pyrophosphate (GPP), C15 farnesyl pyrophosphate (FPP), and C20 GGPP. Intriguingly, HpGGPPS can utilize GPP or FPP as a single substrate to synthesize GGPP by hydrolyzing the allylic PPP substrate into C5 IPP. Transcription of HpGGPPS and key carotenogenesis genes, morphological transformation, and carotenoid biosynthesis were differentially induced by environmental stresses, while HpGGPPS's products were low in vivo, implying that most of PPP flux had been shunted into carotenoid biosynthesis. Hydrolyzing allylic PPP intermediates into C5 building blocks by promiscuous HpGGPPS may be a fail safe for carotenoid accumulation against environmental stress.
Collapse
Affiliation(s)
- Yong Min Lao
- Shenzhen Public Platform of Screening & Application of Marine Microbial Resources, Graduate School at Shenzhen Tsinghua University, Shenzhen, China
- The Division of Ocean Science and Technology, Graduate School at Shenzhen Tsinghua University, Shenzhen, China
| | - Hui Jin
- Shenzhen Public Platform of Screening & Application of Marine Microbial Resources, Graduate School at Shenzhen Tsinghua University, Shenzhen, China
- The Division of Ocean Science and Technology, Graduate School at Shenzhen Tsinghua University, Shenzhen, China
| | - Jin Zhou
- Shenzhen Public Platform of Screening & Application of Marine Microbial Resources, Graduate School at Shenzhen Tsinghua University, Shenzhen, China
- The Division of Ocean Science and Technology, Graduate School at Shenzhen Tsinghua University, Shenzhen, China
| | - Huai Jin Zhang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiao Shan Zhu
- The Division of Ocean Science and Technology, Graduate School at Shenzhen Tsinghua University, Shenzhen, China
| | - Zhong Hua Cai
- Shenzhen Public Platform of Screening & Application of Marine Microbial Resources, Graduate School at Shenzhen Tsinghua University, Shenzhen, China
- The Division of Ocean Science and Technology, Graduate School at Shenzhen Tsinghua University, Shenzhen, China
| |
Collapse
|
10
|
Hendrikse NM, Charpentier G, Nordling E, Syrén PO. Ancestral diterpene cyclases show increased thermostability and substrate acceptance. FEBS J 2018; 285:4660-4673. [PMID: 30369053 DOI: 10.1111/febs.14686] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/07/2018] [Accepted: 10/25/2018] [Indexed: 11/26/2022]
Abstract
Bacterial diterpene cyclases are receiving increasing attention in biocatalysis and synthetic biology for the sustainable generation of complex multicyclic building blocks. Herein, we explore the potential of ancestral sequence reconstruction (ASR) to generate remodeled cyclases with enhanced stability, activity, and promiscuity. Putative ancestors of spiroviolene synthase, a bacterial class I diterpene cyclase, display an increased yield of soluble protein of up to fourfold upon expression in the model organism Escherichia coli. Two of the resurrected enzymes, with an estimated age of approximately 1.7 million years, display an upward shift in thermostability of 7-13 °C. Ancestral spiroviolene synthases catalyze cyclization of the natural C20 -substrate geranylgeranyl diphosphate (GGPP) and also accept C15 farnesyl diphosphate (FPP), which is not converted by the extant enzyme. In contrast, the consensus sequence generated from the corresponding multiple sequence alignment was found to be inactive toward both substrates. Mutation of a nonconserved position within the aspartate-rich motif of the reconstructed ancestral cyclases was associated with modest effects on activity and relative substrate specificity (i.e., kcat /KM for GGPP over kcat /KM for FPP). Kinetic analyses performed at different temperatures reveal a loss of substrate saturation, when going from the ancestor with highest thermostability to the modern enzyme. The kinetics data also illustrate how an increase in temperature optimum of biocatalysis is reflected in altered entropy and enthalpy of activation. Our findings further highlight the potential and limitations of applying ASR to biosynthetic machineries in secondary metabolism.
Collapse
Affiliation(s)
- Natalie M Hendrikse
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,Swedish Orphan Biovitrum AB, Stockholm, Sweden
| | - Gwenaëlle Charpentier
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,Swedish Orphan Biovitrum AB, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Division of Protein Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
11
|
Petrova TE, Boyko KM, Nikolaeva AY, Stekhanova TN, Gruzdev EV, Mardanov AV, Stroilov VS, Littlechild JA, Popov VO, Bezsudnova EY. Structural characterization of geranylgeranyl pyrophosphate synthase GACE1337 from the hyperthermophilic archaeon Geoglobus acetivorans. Extremophiles 2018; 22:877-888. [PMID: 30062607 DOI: 10.1007/s00792-018-1044-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 07/20/2018] [Indexed: 01/23/2023]
Abstract
A novel type 1 geranylgeranyl pyrophosphate synthase GACE1337 has been identified within the genome of a newly identified hyperthermophilic archaeon Geoglobus acetivorans. The enzyme has been cloned and over-expressed in Escherichia coli. The recombinant enzyme has been biochemically and structurally characterized. It is able to catalyze the synthesis of geranylgeranyl pyrophosphate as a major product and of farnesyl pyrophosphate in smaller amounts, as measured by gas chromatography-mass spectrometry at an elevated temperature of 60 °C. Its ability to produce two products is consistent with the fact that GACE1337 is the only short-chain isoprenyl diphosphate synthase in G. acetivorans. Attempts to crystallize the enzyme were successful only at 37 °C. The three-dimensional structure of GACE1337 was determined by X-ray diffraction to 2.5 Å resolution. A comparison of its structure with those of related enzymes revealed that the Geoglobus enzyme has the features of both type I and type III geranylgeranyl pyrophosphate synthases, which allow it to regulate the product length. The active enzyme is a dimer and has three aromatic amino acids, two Phe, and a Tyr, located in the hydrophobic cleft between the two subunits. It is proposed that these bulky residues play a major role in the synthetic reaction by controlling the product elongation.
Collapse
Affiliation(s)
- Tatiana E Petrova
- Institute of Mathematical Problems of Biology, RAS, Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, Professor Vitkevich St., Pushchino, 142290, Russian Federation.
| | - Konstantin M Boyko
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation.,NBICS Center, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr, 1, Moscow, 123182, Russian Federation
| | - Alena Yu Nikolaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation
| | - Tatiana N Stekhanova
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation
| | - Eugeny V Gruzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation
| | - Andrey V Mardanov
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation
| | - Viktor S Stroilov
- N. D. Zelinsky Institute of Organic Chemistry (ZIOC RAS), Leninsky Prospekt, 47, Moscow, 119991, Russian Federation
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Vladimir O Popov
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation.,NBICS Center, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr, 1, Moscow, 123182, Russian Federation
| | - Ekaterina Yu Bezsudnova
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation
| |
Collapse
|
12
|
Minami A, Ozaki T, Liu C, Oikawa H. Cyclopentane-forming di/sesterterpene synthases: widely distributed enzymes in bacteria, fungi, and plants. Nat Prod Rep 2018; 35:1330-1346. [DOI: 10.1039/c8np00026c] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cyclization mechanisms and structural diversification strategies of novel cyclopentane-forming terpene synthases from various organisms are reviewed.
Collapse
Affiliation(s)
- Atsushi Minami
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
| | - Taro Ozaki
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
| | - Chengwei Liu
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
| | - Hideaki Oikawa
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
| |
Collapse
|
13
|
Hayashi Y, Ito T, Yoshimura T, Hemmi H. Utilization of an intermediate of the methylerythritol phosphate pathway, (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate, as the prenyl donor substrate for various prenyltransferases. Biosci Biotechnol Biochem 2017; 82:993-1002. [PMID: 29191109 DOI: 10.1080/09168451.2017.1398064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) is an intermediate of the methylerythritol phosphate pathway. Utilization of HMBPP by lycopene elongase from Corynebacterium glutamicum, which is a UbiA-family prenyltransferase responsible for C50 carotenoid biosynthesis, was investigated using an Escherichia coli strain that contained the exogenous mevalonate pathway as well as the carotenoid biosynthetic pathway. Inhibition of the endogenous methylerythritol phosphate pathway resulted in loss of the production of C50 carotenoid flavuxanthin, while C40 lycopene formation was retained. Overexpression of E. coli ispH gene, which encodes HMBPP reductase, also decreased the production of flavuxanthin in E. coli cells. These results indicate the preference of lycopene elongase for HMBPP instead of the previously proposed substrate, dimethylallyl diphosphate. Furthermore, several (all-E)-prenyl diphosphate synthases, which are classified in a distinct family of prenyltransferase, were demonstrated to accept HMBPP, which implies that the compound is more widely used as a prenyl donor substrate than was previously expected.
Collapse
Affiliation(s)
- Yoshifumi Hayashi
- a Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Tomokazu Ito
- a Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Tohru Yoshimura
- a Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| | - Hisashi Hemmi
- a Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences , Nagoya University , Nagoya , Japan
| |
Collapse
|
14
|
Molecular Cloning and Characterization of Carotenoid Pathway Genes and Carotenoid Content in Ixeris dentata var. albiflora. Molecules 2017; 22:molecules22091449. [PMID: 28858245 PMCID: PMC6151524 DOI: 10.3390/molecules22091449] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 08/26/2017] [Accepted: 08/30/2017] [Indexed: 11/22/2022] Open
Abstract
Ixeris dentata var. albiflora is considered as a potential therapeutic agent against mithridatism, calculous, indigestion, pneumonia, hepatitis, and tumors as well as good seasoned vegetable in Far East countries. Phytoene synthase (PSY), phytoene desaturase (PDS) ξ-carotene desaturase (ZDS), lycopene β-cyclase (LCYB), lycopene ε-cyclase (LCYE), ε-ring carotene hydroxylase (CHXB), and zeaxanthin epoxidase (ZDS) are vital enzymes in the carotenoid biosynthesis pathway. We have examined these seven genes from I. dentata that are participated in carotenoid biosynthesis utilizing an Illumina/Solexa HiSeq 2000 platform. In silico analysis of the seven deduced amino acid sequences were revealed its closest homology with other Asteracea plants. Further, we explored transcript levels and carotenoid accumulation in various organs of I. dentata using quantitative real time PCR and high-performance liquid chromatography, respectively. The highest transcript levels were noticed in the leaf for all the genes while minimal levels were noticed in the root. The maximal carotenoid accumulation was also detected in the leaf. We proposed that these genes expressions are associated with the accumulation of carotenoids. Our findings may suggest the fundamental clues to unravel the molecular insights of carotenoid biosynthesis in various organs of I. dentata.
Collapse
|
15
|
Abstract
![]()
The
year 2017 marks the twentieth anniversary of terpenoid cyclase
structural biology: a trio of terpenoid cyclase structures reported
together in 1997 were the first to set the foundation for understanding
the enzymes largely responsible for the exquisite chemodiversity of
more than 80000 terpenoid natural products. Terpenoid cyclases catalyze
the most complex chemical reactions in biology, in that more than
half of the substrate carbon atoms undergo changes in bonding and
hybridization during a single enzyme-catalyzed cyclization reaction.
The past two decades have witnessed structural, functional, and computational
studies illuminating the modes of substrate activation that initiate
the cyclization cascade, the management and manipulation of high-energy
carbocation intermediates that propagate the cyclization cascade,
and the chemical strategies that terminate the cyclization cascade.
The role of the terpenoid cyclase as a template for catalysis is paramount
to its function, and protein engineering can be used to reprogram
the cyclization cascade to generate alternative and commercially important
products. Here, I review key advances in terpenoid cyclase structural
and chemical biology, focusing mainly on terpenoid cyclases and related
prenyltransferases for which X-ray crystal structures have informed
and advanced our understanding of enzyme structure and function.
Collapse
Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| |
Collapse
|
16
|
Kajiura H, Suzuki N, Tokumoto Y, Yoshizawa T, Takeno S, Fujiyama K, Kaneko Y, Matsumura H, Nakazawa Y. Two Eucommia farnesyl diphosphate synthases exhibit distinct enzymatic properties leading to end product preferences. Biochimie 2017; 139:95-106. [PMID: 28478108 DOI: 10.1016/j.biochi.2017.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 04/22/2017] [Accepted: 05/01/2017] [Indexed: 01/06/2023]
Abstract
Farnesyl diphosphate synthase (FPS) is an essential enzyme in the biosynthesis of prenyl precursors for the production of primary and secondary metabolites, including sterols, dolichols, carotenoids and ubiquinones, and for the modification of proteins. Here we identified and characterized two FPSs (EuFPS1 and EuFPS2) from the plant Eucommia ulmoides. The EuFPSs had seven highly conserved prenyltransferase-specific domains that are critical for activity. Complementation and biochemical analyses using bacterially produced recombinant EuFPS isoforms showed that the EuFPSs had FPP synthesis activities both in vivo and in vitro. In addition to the typical reaction mechanisms of FPS, EuFPSs utilized farnesyl diphosphate (FPP) as an allylic substrate and participated in further elongation of the isoprenyl chain, resulting in the synthesis of geranylgeranyl diphosphate. However, despite the high amino acid similarities between the two EuFPS isozymes, their specific activities, substrate preferences, and final reaction products were different. The use of dimethylallyl diphosphate (DMAPP) as an allylic substrate highlighted the differences between the two enzymes: depending on the pH, the metal ion cofactor, and the cofactor concentration, EuFPS2 accumulated geranyl diphosphate as an intermediate product at a constant rate, whereas EuFPS1 synthesized little geranyl diphosphate. The reaction kinetics of the EuFPSs demonstrated that isopentenyl diphosphate and DMAPP were used both as substrates and as inhibitors of EuFPS activity. Taken together, the results indicate that the biosynthesis of FPP is highly regulated by various factors indispensable for EuFPS reactions in plants.
Collapse
Affiliation(s)
- Hiroyuki Kajiura
- Technical Research Institute, Hitachi Zosen Corporation, 2-2-11 Funamachi, Taisyo, Osaka, 551-0022, Japan
| | - Nobuaki Suzuki
- Technical Research Institute, Hitachi Zosen Corporation, 2-2-11 Funamachi, Taisyo, Osaka, 551-0022, Japan
| | - Yuji Tokumoto
- Technical Research Institute, Hitachi Zosen Corporation, 2-2-11 Funamachi, Taisyo, Osaka, 551-0022, Japan; Laboratory of Forest Ecology & Physiology, Graduate School of Bioagricultural Science, Nagoya University, E1-1 (300), Furo, Chikusa, Nagoya, Aichi, 464-8601, Japan
| | - Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Shinya Takeno
- Technical Research Institute, Hitachi Zosen Corporation, 2-2-11 Funamachi, Taisyo, Osaka, 551-0022, Japan
| | - Kazuhito Fujiyama
- International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Yoshinobu Kaneko
- Yeast Genetic Resources Lab, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Hiroyoshi Matsumura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Yoshihisa Nakazawa
- Technical Research Institute, Hitachi Zosen Corporation, 2-2-11 Funamachi, Taisyo, Osaka, 551-0022, Japan.
| |
Collapse
|
17
|
Emmerstorfer-Augustin A, Moser S, Pichler H. Screening for improved isoprenoid biosynthesis in microorganisms. J Biotechnol 2016; 235:112-20. [DOI: 10.1016/j.jbiotec.2016.03.051] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 11/26/2022]
|
18
|
Molecular cloning and characterization of an intronless farnesyl diphosphate synthase (FDP) gene from Indian rubber clone (Hevea brasiliensis Muell. Arg. RRII105): A gene involved in isoprenoid biosynthesis. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
19
|
Rodriguez JB, Falcone BN, Szajnman SH. Approaches for Designing new Potent Inhibitors of Farnesyl Pyrophosphate Synthase. Expert Opin Drug Discov 2016; 11:307-20. [DOI: 10.1517/17460441.2016.1143814] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
20
|
Richter A, Seidl-Adams I, Köllner TG, Schaff C, Tumlinson JH, Degenhardt J. A small, differentially regulated family of farnesyl diphosphate synthases in maize (Zea mays) provides farnesyl diphosphate for the biosynthesis of herbivore-induced sesquiterpenes. PLANTA 2015; 241:1351-61. [PMID: 25680349 DOI: 10.1007/s00425-015-2254-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 01/26/2015] [Indexed: 05/26/2023]
Abstract
Of the three functional FPPS identified in maize, fpps3 is induced by herbivory to produce FDP important for the formation of the volatile sesquiterpenes of plant defense. Sesquiterpenes are not only crucial for the growth and development of a plant but also for its interaction with the environment. The biosynthesis of sesquiterpenes proceeds over farnesyl diphosphate (FDP), which is either used as a substrate for protein prenylation, converted to squalene, or to volatile sesquiterpenes. To elucidate the regulation of sesquiterpene biosynthesis in maize, we identified and characterized the farnesyl diphosphate synthase (FPPS) gene family which consists of three genes. Synteny analysis indicates that fpps2 and fpps3 originate from a genome duplication in an ancient tetraploid ancestor. The three FPPSs encode active enzymes that produce predominantly FDP from the isopentenyl diphosphate and dimethylallyl diphosphate substrates. Only fpps1 and fpps3 are induced by elicitor treatment, but induced fpps1 levels are much lower and only increased to the amounts of fpps3 levels in intact leaves. Elicitor-induced fpps3 levels in leaves increase to more than 15-fold of background levels. In undamaged roots, transcript levels of fpps1 are higher than those of fpps3, but only fpps3 transcripts are induced in response to herbivory by Diabrotica virgifera virgifera. A kinetic of transcript abundance in response to herbivory in leaves provided further evidence that the regulation of fpps3 corresponds to that of tps23, a terpene synthase, that converts FDP to the volatile (E)-ß-caryophyllene. Our study indicates that the differential expression of fpps1 and fpps3 provides maize with FDP for both primary metabolism and terpene-based defenses. The expression of fpps3 seems to coincide with the herbivore-induced emission of volatile sesquiterpenes that were demonstrated to be important defense signals.
Collapse
Affiliation(s)
- Annett Richter
- Institute of Pharmacy, Martin Luther University Halle, Hoher Weg 8, 06120, Halle, Germany
| | | | | | | | | | | |
Collapse
|
21
|
Ignea C, Trikka FA, Nikolaidis AK, Georgantea P, Ioannou E, Loupassaki S, Kefalas P, Kanellis AK, Roussis V, Makris AM, Kampranis SC. Efficient diterpene production in yeast by engineering Erg20p into a geranylgeranyl diphosphate synthase. Metab Eng 2015; 27:65-75. [DOI: 10.1016/j.ymben.2014.10.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 08/01/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
|
22
|
Tholl D. Biosynthesis and biological functions of terpenoids in plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:63-106. [PMID: 25583224 DOI: 10.1007/10_2014_295] [Citation(s) in RCA: 249] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Terpenoids (isoprenoids) represent the largest and most diverse class of chemicals among the myriad compounds produced by plants. Plants employ terpenoid metabolites for a variety of basic functions in growth and development but use the majority of terpenoids for more specialized chemical interactions and protection in the abiotic and biotic environment. Traditionally, plant-based terpenoids have been used by humans in the food, pharmaceutical, and chemical industries, and more recently have been exploited in the development of biofuel products. Genomic resources and emerging tools in synthetic biology facilitate the metabolic engineering of high-value terpenoid products in plants and microbes. Moreover, the ecological importance of terpenoids has gained increased attention to develop strategies for sustainable pest control and abiotic stress protection. Together, these efforts require a continuous growth in knowledge of the complex metabolic and molecular regulatory networks in terpenoid biosynthesis. This chapter gives an overview and highlights recent advances in our understanding of the organization, regulation, and diversification of core and specialized terpenoid metabolic pathways, and addresses the most important functions of volatile and nonvolatile terpenoid specialized metabolites in plants.
Collapse
Affiliation(s)
- Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, 409 Latham Hall, 24061, Blacksburg, VA, USA,
| |
Collapse
|
23
|
Tuan PA, Kim YB, Kim JK, Arasu MV, Al-Dhabi NA, Park SU. Molecular characterization of carotenoid biosynthetic genes and carotenoid accumulation in Scutellaria baicalensis Georgi. EXCLI JOURNAL 2014; 14:146-57. [PMID: 26417348 PMCID: PMC4556017 DOI: 10.17179/excli2014-547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/26/2015] [Indexed: 02/03/2023]
Abstract
Scutellaria baicalensis has a wide range of biological activities and has been considered as an important traditional drug in Asia and North America for centuries. A partial-length cDNA clone encoding phytoene synthase (SbPSY) and full-length cDNA clonesencoding phytoene desaturase (SbPDS), ξ-carotene desaturase (SbZDS), β-ring carotene hydroxylase (SbCHXB), and zeaxanthin epoxidase (SbZEP)were identifiedin S. baicalensis. Sequence analyses revealed that these proteins share high identity and conserved domains with their orthologous genes. SbPSY, SbPDS, SbZDS, SbCHXB, and SbZEP were constitutively expressed in the roots, stems, leaves, and flowers of S.baicalensis. SbPSY, SbPDS, and SbZDS were highly expressed in the stems, leaves, and flowers and showed low expression in the roots, where only trace amounts of carotenoids were detected. SbCHXB and SbZEP transcripts were expressed at relatively high levels in the roots, stems, and flowers and were expressed at low levels in the leaves, where carotenoids were mostly distributed. The predominant carotenoids in S.baicalensiswere lutein and β-carotene, with abundant amounts found in the leaves (517.19 and 228.37 μg g-1 dry weight, respectively). Our study on the biosynthesis of carotenoids in S. baicalensis will provide basic data for elucidating the contribution of carotenoids to the considerable medicinal properties of S. baicalensis.
Collapse
Affiliation(s)
- Pham Anh Tuan
- Department of Crop Science, Chungnam National University, 99 Daehak-Ro, Yuseong-gu, Daejeon 305-764, Korea
| | - Yeon Bok Kim
- Herbal Crop Research Division, Department of Herbal Crop Research, Bisanro 92, Eumseong, Chungbuk, 369-873, Korea
| | - Jae Kwang Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 406-772, Korea
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, 99 Daehak-Ro, Yuseong-gu, Daejeon 305-764, Korea ; Visiting Professor Program (VPP), King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| |
Collapse
|
24
|
Prenyl Alcohol Production by Expression of Exogenous Isopentenyl Diphosphate Isomerase and Farnesyl Diphosphate Synthase Genes inEscherichia coli. Biosci Biotechnol Biochem 2014; 73:186-8. [DOI: 10.1271/bbb.80446] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
25
|
Farnesyl pyrophosphate synthase: a key enzyme in isoprenoid biosynthetic pathway and potential molecular target for drug development. N Biotechnol 2013; 30:114-23. [DOI: 10.1016/j.nbt.2012.07.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 07/05/2012] [Accepted: 07/05/2012] [Indexed: 11/19/2022]
|
26
|
Vishwakarma RK, Patel KA, Sonawane P, Singh S, Ruby, Kumari U, Agrawal DC, Khan BM. Molecular characterization of farnesyl pyrophosphate synthase from Bacopa monniera by comparative modeling and docking studies. Bioinformation 2012; 8:1075-81. [PMID: 23251041 PMCID: PMC3523221 DOI: 10.6026/97320630081075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 10/26/2012] [Indexed: 11/29/2022] Open
Abstract
UNLABELLED Farnesyl pyrophosphate synthase (FPS; EC 2.5.1.10) is a key enzyme in isoprenoid biosynthetic pathway and provides precursors for the biosynthesis of various pharmaceutically important metabolites. It catalyzes head to tail condensation of two isopentenyl pyrophosphate molecules with dimethylallyl pyrophosphate to form C15 compound farnesyl pyrophosphate. Recent studies have confirmed FPS as a molecular target of bisphosphonates for drug development against bone diseases as well as pathogens. Although large numbers of FPSs from different sources are known, very few protein structures have been reported till date. In the present study, FPS gene from medicinal plant Bacopa monniera (BmFPS) was characterized by comparative modeling and docking. Multiple sequence alignment showed two highly conserved aspartate rich motifs FARM and SARM (DDXXD). The 3-D model of BmFPS was generated based on structurally resolved FPS crystal information of Gallus gallus. The generated models were validated by various bioinformatics tools and the final model contained only α-helices and coils. Further, docking studies of modeled BmFPS with substrates and inhibitors were performed to understand the protein ligand interactions. The two Asp residues from FARM (Asp100 and Asp104) as well as Asp171, Lys197 and Lys262 were found to be important for catalytic activity. Interaction of nitrogen containing bisphosphonates (risedronate, alendronate, zoledronate and pamidronate) with modeled BmFPS showed competitive inhibition; where, apart from Asp (100, 104 and 171), Thr175 played an important role. The results presented here could be useful for designing of mutants for isoprenoid biosynthetic pathway engineering well as more effective drugs against osteoporosis and human pathogens. ABBREVIATIONS IPP - Isopentenyl Pyrophosphate, DMAPP - Dimethylallyl Pyrophosphate, GPP - Geranyl Pyrophosphate, FPP - FPPFarnesyl Pyrophosphate, DOPE - Discrete Optimized Protein Energy, BmFPS - Bacopa monniera Farnesyl Pyrophosphate Synthase, RMSD - Root Mean square Deviation, OPLS-AA - Optimized Potentials for Liquid Simulations- All Atom, FARM - First Aspartate Rich Motif, SARM - Second Aspartate Rich Motif.
Collapse
Affiliation(s)
| | | | - Prashant Sonawane
- Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
- Authors equally contributed
| | - Somesh Singh
- Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
- Authors equally contributed
| | - Ruby
- Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
- Authors equally contributed
| | - Uma Kumari
- Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
- Authors equally contributed
| | - Dinesh Chandra Agrawal
- Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
- Authors equally contributed
| | | |
Collapse
|
27
|
Li ZH, Cintrón R, Koon NA, Moreno SNJ. The N-terminus and the chain-length determination domain play a role in the length of the isoprenoid product of the bifunctional Toxoplasma gondii farnesyl diphosphate synthase. Biochemistry 2012; 51:7533-40. [PMID: 22931372 DOI: 10.1021/bi3005335] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Toxoplasma gondii possesses a bifunctional farnesyl diphosphate (FPP)/geranylgeranyl diphosphate (GGPP) synthase (TgFPPS) that synthesizes C(15) and C(20) isoprenoid diphosphates from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This enzyme has a unique arrangement of the fourth and fifth amino acid upstream from the first aspartic rich motif (FARM) where the fourth amino acid is aromatic and the fifth is a cysteine. We mutated these amino acids, converting the enzyme to an absolute FPPS by changing the cysteine to a tyrosine. The enzyme could be converted to an absolute GGPPS by changing both the fourth and fifth amino acids to alanines. We also constructed four mutated TgFPPSs whose regions around the first aspartate rich motif were replaced with the corresponding regions of FPP synthases from Arabidopsis thaliana or Saccharomyces cerevisiae or with the corresponding regions of GGPP synthases from Homo sapiens or S. cerevisiae. We determined that the presence of a cysteine at the fifth position is essential for the TgFPPS bifunctionality. We also found that the length of the N-terminal domain plays a role in determining the specificity and the length of the isoprenoid product. Phylogenetic analysis supports the grouping of this enzyme with other type I FPPSs, but the biochemical data indicate that TgFPPS has unique characteristics that differentiate it from mammalian FPPSs and GGPPSs and is therefore an important drug target.
Collapse
Affiliation(s)
- Zhu-Hong Li
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | | | | | | |
Collapse
|
28
|
Substrate specificities of E- and Z-farnesyl diphosphate synthases with substrate analogs. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
29
|
Aripirala S, Szajnman SH, Jakoncic J, Rodriguez JB, Docampo R, Gabelli SB, Amzel LM. Design, synthesis, calorimetry, and crystallographic analysis of 2-alkylaminoethyl-1,1-bisphosphonates as inhibitors of Trypanosoma cruzi farnesyl diphosphate synthase. J Med Chem 2012; 55:6445-54. [PMID: 22715997 DOI: 10.1021/jm300425y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Linear 2-alkylaminoethyl-1,1-bisphosphonates are effective agents against proliferation of Trypanosoma cruzi , the etiologic agent of American trypanosomiasis (Chagas disease), exhibiting IC(50) values in the nanomolar range against the parasites. This activity is associated with inhibition at the low nanomolar level of the T. cruzi farnesyl diphosphate synthase (TcFPPS). X-ray structures and thermodynamic data of the complexes TcFPPS with five compounds of this family show that the inhibitors bind to the allylic site of the enzyme, with their alkyl chain occupying the cavity that binds the isoprenoid chain of the substrate. The compounds bind to TcFPPS with unfavorable enthalpy compensated by a favorable entropy that results from a delicate balance between two opposing effects: the loss of conformational entropy due to freezing of single bond rotations and the favorable burial of the hydrophobic alkyl chains. The data suggest that introduction of strategically placed double bonds and methyl branches should increase affinity substantially.
Collapse
Affiliation(s)
- Srinivas Aripirala
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Furubayashi M, Umeno D. Directed evolution of carotenoid synthases for the production of unnatural carotenoids. Methods Mol Biol 2012; 892:245-253. [PMID: 22623307 DOI: 10.1007/978-1-61779-879-5_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Directed evolution is a well-established strategy to confer novel catalytic functions to the enzymes. Thanks to the relative ease of establishing color screening, carotenogenic enzymes can be rapidly evolved in the laboratory for novel functions. The combinatorial usages of the evolvants result in the creation of diverse set of novel, sometimes unnatural carotenoids. This chapter describes the directed evolution of diapophytoene (C(30) carotenoid) synthase CrtM to function in the foreign C(40) pathway, and the use of the CrtM variants thus obtained for the production of novel backbone structures.
Collapse
Affiliation(s)
- Maiko Furubayashi
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | | |
Collapse
|
31
|
Identification of a lysine residue important for the catalytic activity of yeast farnesyl diphosphate synthase. Protein J 2011; 30:334-9. [PMID: 21643844 DOI: 10.1007/s10930-011-9336-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Saccharomyces cerevisiae ERG20 gene (encoding farnesyl diphosphate synthase) has been subjected to a set of mutations at the catalytic site, at position K254 to determine the in vivo impact. The mutated strains have been shown to exhibit various growth rates, sterol profiles and monoterpenol producing capacities. The results obtained suggest that K at position 254 helps to stabilize one of the three Mg(2+) forming a bridge between the enzyme and DMAPP, and demonstrate that destabilizing two of the three Mg(2+) ions, by introducing a double mutation at positions K197 and K254, results in a loss of FPPS activity and a lethal phenotype.
Collapse
|
32
|
Ogawa T, Yoshimura T, Hemmi H. Connected cavity structure enables prenyl elongation across the dimer interface in mutated geranylfarnesyl diphosphate synthase from Methanosarcina mazei. Biochem Biophys Res Commun 2011; 409:333-7. [DOI: 10.1016/j.bbrc.2011.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 05/03/2011] [Indexed: 10/18/2022]
|
33
|
Tuan PA, Kim JK, Kim HH, Lee SY, Park NI, Park SU. Carotenoid accumulation and characterization of cDNAs encoding phytoene synthase and phytoene desaturase in garlic (Allium sativum). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:5412-5417. [PMID: 21495726 DOI: 10.1021/jf2009827] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Phytoene synthase (PSY) and phytoene desaturase (PDS), which catalyze the first and second steps of the carotenoid biosynthetic pathway, respectively, are key enzymes for the accumulation of carotenoids in many plants. We isolated 2 partial cDNAs encoding PSY (AsPSY-1 and AsPSY-2) and a partial cDNA encoding PDS (AsPDS) from Allium sativum. They shared high sequence identity and conserved motifs with other orthologous genes. Quantitative real-time PCR analysis was used to determine the expression levels of AsPSY1, AsPSY2, and AsPDS in the bulbils, scapes, leaves, stems, bulbs, and roots of garlic. High-performance liquid chromatography demonstrated that carotenoids were not biosynthesized in the underground organs (roots and bulbs), but were very abundant in the photosynthetic organs (leaves) of A. sativum. A significantly higher amount of β-carotene (73.44 μg·g(-1)) was detected in the leaves of A. sativum than in the other organs.
Collapse
Affiliation(s)
- Pham Anh Tuan
- Department of Crop Science, Chungnam National University, Yuseong-gu, Daejeon, Korea
| | | | | | | | | | | |
Collapse
|
34
|
Tholl D, Lee S. Terpene Specialized Metabolism in Arabidopsis thaliana. THE ARABIDOPSIS BOOK 2011; 9:e0143. [PMID: 22303268 PMCID: PMC3268506 DOI: 10.1199/tab.0143] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Terpenes constitute the largest class of plant secondary (or specialized) metabolites, which are compounds of ecological function in plant defense or the attraction of beneficial organisms. Using biochemical and genetic approaches, nearly all Arabidopsis thaliana (Arabidopsis) enzymes of the core biosynthetic pathways producing the 5-carbon building blocks of terpenes have been characterized and closer insight has been gained into the transcriptional and posttranscriptional/translational mechanisms regulating these pathways. The biochemical function of most prenyltransferases, the downstream enzymes that condense the C(5)-precursors into central 10-, 15-, and 20-carbon prenyldiphosphate intermediates, has been described, although the function of several isoforms of C(20)-prenyltranferases is not well understood. Prenyl diphosphates are converted to a variety of C(10)-, C(15)-, and C(20)-terpene products by enzymes of the terpene synthase (TPS) family. Genomic organization of the 32 Arabidopsis TPS genes indicates a species-specific divergence of terpene synthases with tissue- and cell-type specific expression profiles that may have emerged under selection pressures by different organisms. Pseudogenization, differential expression, and subcellular segregation of TPS genes and enzymes contribute to the natural variation of terpene biosynthesis among Arabidopsis accessions (ecotypes) and species. Arabidopsis will remain an important model to investigate the metabolic organization and molecular regulatory networks of terpene specialized metabolism in relation to the biological activities of terpenes.
Collapse
Affiliation(s)
- Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Sungbeom Lee
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| |
Collapse
|
35
|
Geranylfarnesyl diphosphate synthase from Methanosarcina mazei: Different role, different evolution. Biochem Biophys Res Commun 2010; 393:16-20. [DOI: 10.1016/j.bbrc.2010.01.063] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 01/16/2010] [Indexed: 11/21/2022]
|
36
|
Vandermoten S, Haubruge E, Cusson M. New insights into short-chain prenyltransferases: structural features, evolutionary history and potential for selective inhibition. Cell Mol Life Sci 2009; 66:3685-95. [PMID: 19633972 PMCID: PMC11115643 DOI: 10.1007/s00018-009-0100-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 06/28/2009] [Accepted: 07/07/2009] [Indexed: 10/20/2022]
Abstract
Isoprenoids form an extensive group of natural products involved in a number of important biological processes. Their biosynthesis proceeds through sequential 1'-4 condensations of isopentenyl diphosphate (C5) with an allylic acceptor, the first of which is dimethylallyl diphosphate (C5). The reactions leading to the production of geranyl diphosphate (C10), farnesyl diphosphate (C15) and geranylgeranyl diphosphate (C20), which are the precursors of mono-, sesqui- and diterpenes, respectively, are catalyzed by a group of highly conserved enzymes known as short-chain isoprenyl diphosphate synthases, or prenyltransferases. In recent years, the sequences of many new prenyltransferases have become available, including those of several plant and animal geranyl diphosphate synthases, revealing novel mechanisms of product chain-length selectivity and an intricate evolutionary path from a putative common ancestor. Finally, there is considerable interest in designing inhibitors specific to short-chain prenyltransferases, for the purpose of developing new drugs or pesticides that target the isoprenoid biosynthetic pathway.
Collapse
Affiliation(s)
- Sophie Vandermoten
- Department of Functional and Evolutionary Entomology, Gembloux Agricultural University, Passage des Déportés 2, 5030 Gembloux, Belgium.
| | | | | |
Collapse
|
37
|
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 BIOCHEMISTRY AND MOLECULAR BIOLOGY 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] [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.
Collapse
Affiliation(s)
- Sophie Vandermoten
- Gembloux Agricultural University, Department of Functional and Evolutionary Entomology, Passage des Déportés 2, Gembloux, Belgium.
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Brandt W, Bräuer L, Günnewich N, Kufka J, Rausch F, Schulze D, Schulze E, Weber R, Zakharova S, Wessjohann L. Molecular and structural basis of metabolic diversity mediated by prenyldiphosphate converting enzymes. PHYTOCHEMISTRY 2009; 70:1758-1775. [PMID: 19878958 DOI: 10.1016/j.phytochem.2009.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 05/28/2023]
Abstract
General thermodynamic calculations using the semiempiric PM3 method have led to the conclusion that prenyldiphosphate converting enzymes require at least one divalent metal cation for the activation and cleavage of the diphosphate-prenyl ester bond, or they must provide structural elements for the efficient stabilization of the intermediate prenyl cation. The most important common structural features, which guide the product specificity in both terpene synthases and aromatic prenyl transferases are aromatic amino acid side chains, which stabilize prenyl cations by cation-pi interactions. In the case of aromatic prenyl transferases, a proton abstraction from the phenolic hydroxyl group of the second substrate will enhance the electron density in the phenolic ortho-position at which initial prenylation of the aromatic compound usually occurs. A model of the structure of the integral transmembrane-bound aromatic prenyl transferase UbiA was developed, which currently represents the first structural insight into this group of prenylating enzymes with a fold different from most other aromatic prenyl transferases. Based on this model, the structure-activity relationships and mechanistic aspects of related proteins, for example those of Lithospermum erythrorhizon or the enzyme AuaA from Stigmatella aurantiaca involved in the aurachin biosynthesis, were elucidated. The high similarity of this group of aromatic prenyltransferases to 5-epi-aristolochene synthase is an indication of an evolutionary relationship with terpene synthases (cyclases). This is further supported by the conserved DxxxD motif found in both protein families. In contrast, there is no such relationship to the aromatic prenyl transferases with an ABBA-fold, such as NphB, or to any other known family of prenyl converting enzymes. Therefore, it is possible that these two groups might have different evolutionary ancestors.
Collapse
Affiliation(s)
- Wolfgang Brandt
- Leibniz Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Halle (Saale), Germany.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Taban AH, Tittiger C, Blomquist GJ, Welch WH. Isolation and characterization of farnesyl diphosphate synthase from the cotton boll weevil, Anthonomus grandis. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2009; 71:88-104. [PMID: 19309001 DOI: 10.1002/arch.20302] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Farnesyl diphosphate synthase (FPPS) catalyzes the consecutive condensation of two molecules of isopentenyl diphosphate with dimethylallyl diphosphate to form farnesyl diphosphate (FPP). In insects, FPP is used for the synthesis of ubiquinones, dolicols, protein prenyl groups, and juvenile hormone. A full-length cDNA of FPPS was cloned from the cotton boll weevil, Anthonomus grandis (AgFPPS). AgFPPS cDNA consists of 1,835 nucleotides and encodes a protein of 438 amino acids. The deduced amino acid sequence has high similarity to previously isolated insect FPPSs and other known FPPSs. Recombinant AgFPPS expressed in E. coli converted labeled isopentenyl diphosphate in the presence of dimethylallyl diphosphate to FPP. Southern blot analysis indicated the presence of a single copy gene. Using molecular modeling, the three-dimensional structure of coleopteran FPPS was determined and compared to the X-ray crystal structure of avian FPPS. The alpha-helical fold is conserved in AgFPPS and the size of the active site cavity is consistent with the enzyme being a FPPS.
Collapse
Affiliation(s)
- A Huma Taban
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557-0014, USA
| | | | | | | |
Collapse
|
40
|
Noike M, Katagiri T, Nakayama T, Nishino T, Hemmi H. Effect of mutagenesis at the region upstream from the G(Q/E) motif of three types of geranylgeranyl diphosphate synthase on product chain-length. J Biosci Bioeng 2009; 107:235-9. [DOI: 10.1016/j.jbiosc.2008.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2008] [Revised: 10/21/2008] [Accepted: 11/06/2008] [Indexed: 11/28/2022]
|
41
|
Targeting a Uniquely Nonspecific Prenyl Synthase with Bisphosphonates to Combat Cryptosporidiosis. ACTA ACUST UNITED AC 2008; 15:1296-306. [DOI: 10.1016/j.chembiol.2008.10.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 09/30/2008] [Accepted: 10/06/2008] [Indexed: 11/19/2022]
|
42
|
Mohan U, Banerjee UC. Molecular Evolution of a Defined DNA Sequence with Accumulation of Mutations in a Single Round by a Dual Approach to Random Chemical Mutagenesis (DuARCheM). Chembiochem 2008; 9:2238-43. [PMID: 18756549 DOI: 10.1002/cbic.200800259] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Utpal Mohan
- Biocatalysis and Protein Engineering Group, Department of Pharmaceutical Technology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar-160062, Punjab, India
| | | |
Collapse
|
43
|
Hsiao YY, Jeng MF, Tsai WC, Chuang YC, Li CY, Wu TS, Kuoh CS, Chen WH, Chen HH. A novel homodimeric geranyl diphosphate synthase from the orchid Phalaenopsis bellina lacking a DD(X)2-4D motif. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 55:719-33. [PMID: 18466308 DOI: 10.1111/j.1365-313x.2008.03547.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Geranyl diphosphate (GDP) is the precursor of monoterpenes, which are the major floral scent compounds in Phalaenopsis bellina. The cDNA of P. bellina GDP synthase (PbGDPS) was cloned, and its sequence corresponds to the second Asp-rich motif (SARM), but not to any aspartate-rich (Asp-rich) motif. The recombinant PbGDPS enzyme exhibits dual prenyltransferase activity, producing both GDP and farnesyl diphosphate (FDP), and a yeast two-hybrid assay and gel filtration revealed that PbGDPS was able to form a homodimer. Spatial and temporal expression analyses showed that the expression of PbGDPS was flower specific, and that maximal PbGDPS expression was concomitant with maximal emission of monoterpenes on day 5 post-anthesis. Homology modelling of PbGDPS indicated that the Glu-rich motif might provide a binding site for Mg(2+) and catalyze the formation of prenyl products in a similar way to SARM. Replacement of the key Glu residues with alanine totally abolished enzyme activity, whereas their mutation to Asp resulted in a mutant with two-thirds of the activity of the wild-type protein. Phylogenetic analysis indicated that plant GDPS proteins formed four clades: members of both GDPS-a and GDPS-b clades contain Asp-rich motifs, and function as homodimers. In contrast, proteins in the GDPS-c and GDPS-d clades do not contain Asp-rich motifs, but although members of the GDPS-c clade function as heterodimers, PbGDPS, which is more closely related to the GDPS-c clade proteins than to GDPS-a and GDPS-b proteins, and is currently the sole member of the GDPS-d clade, functions as a homodimer.
Collapse
Affiliation(s)
- Yu-Yun Hsiao
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Noike M, Katagiri T, Nakayama T, Koyama T, Nishino T, Hemmi H. The product chain length determination mechanism of type II geranylgeranyl diphosphate synthase requires subunit interaction. FEBS J 2008; 275:3921-33. [PMID: 18616462 DOI: 10.1111/j.1742-4658.2008.06538.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The product chain length determination mechanism of type II geranylgeranyl diphosphate synthase from the bacterium, Pantoea ananatis, was studied. In most types of short-chain (all-E) prenyl diphosphate synthases, bulky amino acids at the fourth and/or fifth positions upstream from the first aspartate-rich motif play a primary role in the product determination mechanism. However, type II geranylgeranyl diphosphate synthase lacks such bulky amino acids at these positions. The second position upstream from the G(Q/E) motif has recently been shown to participate in the mechanism of chain length determination in type III geranylgeranyl diphosphate synthase. Amino acid substitutions adjacent to the residues upstream from the first aspartate-rich motif and from the G(Q/E) motif did not affect the chain length of the final product. Two amino acid insertion in the first aspartate-rich motif, which is typically found in bacterial enzymes, is thought to be involved in the product determination mechanism. However, deletion mutation of the insertion had no effect on product chain length. Thus, based on the structures of homologous enzymes, a new line of mutants was constructed in which bulky amino acids in the alpha-helix located at the expected subunit interface were replaced with alanine. Two mutants gave products with longer chain lengths, suggesting that type II geranylgeranyl diphosphate synthase utilizes an unexpected mechanism of chain length determination, which requires subunit interaction in the homooligomeric enzyme. This possibility is strongly supported by the recently determined crystal structure of plant type II geranylgeranyl diphosphate synthase.
Collapse
Affiliation(s)
- Motoyoshi Noike
- Department of Biochemistry and Engineering, Graduate School of Engineering, Tohoku University, Miyagi, Japan
| | | | | | | | | | | |
Collapse
|
45
|
Unearthing the roots of the terpenome. Curr Opin Chem Biol 2008; 12:141-50. [PMID: 18249199 DOI: 10.1016/j.cbpa.2007.12.008] [Citation(s) in RCA: 229] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 12/27/2007] [Indexed: 11/22/2022]
Abstract
Although terpenoid synthases catalyze the most complex reactions in biology, these enzymes appear to play little role in the chemistry of catalysis other than to trigger the ionization and chaperone the conformation of flexible isoprenoid substrates and carbocation intermediates through multistep reaction cascades. Fidelity and promiscuity in this chemistry (whether a terpenoid synthase generates one or several products), depends on the permissiveness of the active site template in chaperoning each step of an isoprenoid coupling or cyclization reaction. Structure-guided mutagenesis studies of terpenoid synthases such as farnesyl diphosphate synthase, 5-epi-aristolochene synthase, and gamma-humulene synthase suggest that the vast diversity of terpenoid natural products is rooted in the facile evolution of alpha-helical folds shared by terpenoid synthases in all forms of life.
Collapse
|
46
|
Saikia S, Nicholson MJ, Young C, Parker EJ, Scott B. The genetic basis for indole-diterpene chemical diversity in filamentous fungi. ACTA ACUST UNITED AC 2008; 112:184-99. [DOI: 10.1016/j.mycres.2007.06.015] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 05/24/2007] [Accepted: 06/19/2007] [Indexed: 10/23/2022]
|
47
|
Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
| |
Collapse
|
48
|
Cunningham FX, Gantt E. A portfolio of plasmids for identification and analysis of carotenoid pathway enzymes: Adonis aestivalis as a case study. PHOTOSYNTHESIS RESEARCH 2007; 92:245-59. [PMID: 17634749 DOI: 10.1007/s11120-007-9210-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 05/25/2007] [Indexed: 05/16/2023]
Abstract
Carotenoids are indispensable pigments of the photosynthetic apparatus in plants, algae, and cyanobacteria and are produced, as well, by many bacteria and fungi. Elucidation of biochemical pathways leading to the carotenoids that function in the photosynthetic membranes of land plants has been greatly aided by the use of carotenoid-accumulating strains of Escherichia coli as heterologous hosts for functional assays, in vivo, of the otherwise difficult to study membrane-associated pathway enzymes. This same experimental approach is uniquely well-suited to the discovery and characterization of yet-to-be identified enzymes that lead to carotenoids of the photosynthetic membranes in algal cells, to the multitude of carotenoids found in nongreen plant tissues, and to the myriad flavor and aroma compounds that are derived from carotenoids in plant tissues. A portfolio of plasmids suitable for the production in E. coli of a variety of carotenoids is presented herein. The use of these carotenoid-producing E. coli for the identification of cDNAs encoding enzymes of carotenoid and isoprenoid biosynthesis, for characterization of the enzymes these cDNAs encode, and for the production of specific carotenoids for use as enzyme substrates and reference standards, is described using the flowering plant Adonis aestivalis to provide examples. cDNAs encoding nine different A. aestivalis enzymes of carotenoid and isoprenoid synthesis were identified and the enzymatic activity of their products verified. Those cDNAs newly described include ones that encode phytoene synthase, beta-carotene hydroxylase, deoxyxylulose-5-phosphate synthase, isopentenyl diphosphate isomerase, and geranylgeranyl diphosphate synthase.
Collapse
Affiliation(s)
- Francis X Cunningham
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
| | | |
Collapse
|
49
|
Withers ST, Keasling JD. Biosynthesis and engineering of isoprenoid small molecules. Appl Microbiol Biotechnol 2006; 73:980-90. [PMID: 17115212 DOI: 10.1007/s00253-006-0593-1] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Revised: 07/25/2006] [Accepted: 08/07/2006] [Indexed: 12/22/2022]
Abstract
Isoprenoid secondary metabolites are a rich source of commercial products that have not been fully explored. At present, there are isoprenoid products used in cancer therapy, the treatment of infectious diseases, and crop protection. All isoprenoids share universal prenyl diphosphate precursors synthesized via two distinct pathways. From these universal precursors, the biosynthetic pathways to specific isoprenoids diverge resulting in a staggering array of products. Taking advantage of this diversity has been the focus of much effort in metabolic engineering heterologous hosts. In addition, the engineering of the mevalonate pathway has increased levels of the universal precursors available for heterologous production. Finally, we will describe the efforts to produce to commercial terpenoids, paclitaxel and artemisinin.
Collapse
Affiliation(s)
- Sydnor T Withers
- Department of Chemical Engineering, University of California, Berkeley, CA, USA
| | | |
Collapse
|
50
|
Chang TH, Guo RT, Ko TP, Wang AHJ, Liang PH. Crystal Structure of Type-III Geranylgeranyl Pyrophosphate Synthase from Saccharomyces cerevisiae and the Mechanism of Product Chain Length Determination. J Biol Chem 2006; 281:14991-5000. [PMID: 16554305 DOI: 10.1074/jbc.m512886200] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Geranylgeranyl pyrophosphate synthase (GGPPs) catalyzes a condensation reaction of farnesyl pyrophosphate with isopentenyl pyrophosphate to generate C(20) geranylgeranyl pyrophosphate, which is a precursor for carotenoids, chlorophylls, geranylgeranylated proteins, and archaeal ether-linked lipid. For short-chain trans-prenyltransferases that synthesize C(10)-C(25) products, bulky amino acid residues generally occupy the fourth or fifth position upstream from the first DDXXD motif to block further elongation of the final products. However, the short-chain type-III GGPPs in eukaryotes lack any large amino acid at these positions. In this study, the first structure of type-III GGPPs from Saccharomyces cerevisiae has been determined to 1.98 A resolution. The structure is composed entirely of 15 alpha-helices joined by connecting loops and is arranged with alpha-helices around a large central cavity. Distinct from other known structures of trans-prenyltransferases, the N-terminal 17 amino acids (9-amino acid helix A and the following loop) of this GGPPs protrude from the helix core into the other subunit and contribute to the tight dimer formation. Deletion of the first 9 or 17 amino acids caused the dissociation of dimer into monomer, and the Delta(1-17) mutant showed abolished enzyme activity. In each subunit, an elongated hydrophobic crevice surrounded by D, F, G, H, and I alpha-helices contains two DDXXD motifs at the top for substrate binding with one Mg(2+) coordinated by Asp(75), Asp(79), and four water molecules. It is sealed at the bottom with three large residues of Tyr(107), Phe(108), and His(139). Compared with the major product C(30) synthesized by mutant H139A, the products generated by mutant Y107A and F108A are predominantly C(40) and C(30), respectively, suggesting the most important role of Tyr(107) in determining the product chain length.
Collapse
Affiliation(s)
- Tao-Hsin Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | | | | | | | | |
Collapse
|